@article {pmid30771209, year = {2019}, author = {Shin, MK and Cheong, JH}, title = {Mitochondria-centric bioenergetic characteristics in cancer stem-like cells.}, journal = {Archives of pharmacal research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12272-019-01127-y}, pmid = {30771209}, issn = {0253-6269}, support = {1020390//Ministry of Health and Welfare/ ; 1320360//Ministry of Health and Welfare/ ; NRF-2017R1D1A1B03032553//National Research Fund, Republic of Korea/ ; 6-2007-0095//Yonsei University College of Medicine/ ; 6-2008-0193//Yonsei University College of Medicine/ ; }, abstract = {Metabolic and genotoxic stresses that arise during tumor progression and anti-cancer treatment, respectively, can impose a selective pressure to promote cancer evolution in the tumor microenvironment. This process ultimately selects for the most "fit" clones, which generally have a cancer stem cell like phenotype with features of drug resistance, epithelial-mesenchymal transition, invasiveness, and high metastatic potential. From a bioenergetics perspective, these cancer stem-like cells (CSCs) exhibit mitochondria-centric energy metabolism and are capable of opportunistically utilizing available nutrients such as fatty acids to generate ATP and other metabolic substances, providing a selective advantage for their survival in an impermissible environment and metabolic context. Thus, diverse therapeutic strategies are needed to efficiently tackle these CSCs and eliminate their advantage. Here, we review the metabolic and bioenergetic characteristics and vulnerabilities specific to CSCs, which can provide an unprecedented opportunity to curb CSC-driven cancer mortality rates. We particularly focus on the potential of a CSC bioenergetics-targeted strategy as a versatile therapeutic component of treatment modalities applicable to most cancer types. A cancer bioenergetics-targeted strategy can expand the inventory of combinatorial regimens in the current anti-cancer armamentarium.}, }
@article {pmid28717207, year = {2017}, author = {Brennan, IG and Bauer, AM and Van Tri, N and Wang, YY and Wang, WZ and Zhang, YP and Murphy, RW}, title = {Barcoding utility in a mega-diverse, cross-continental genus: keeping pace with Cyrtodactylus geckos.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5592}, pmid = {28717207}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Evolution, Molecular ; Geography ; Lizards/*classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.}, }
@article {pmid30760198, year = {2019}, author = {Pinard, D and Myburg, AA and Mizrachi, E}, title = {The plastid and mitochondrial genomes of Eucalyptus grandis.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {132}, doi = {10.1186/s12864-019-5444-4}, pmid = {30760198}, issn = {1471-2164}, support = {97911//National Research Foundation/ ; 86936//Department of Science and Technology, Republic of South Africa/ ; }, abstract = {BACKGROUND: Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes.<br><br>RESULTS: In order to facilitate further studies of cytonuclear interactions in Eucalyptus, we report an updated annotation of the E. grandis plastid genome, and the second sequenced and annotated mitochondrial genome of the Myrtales, that of E. grandis. The 478,813 bp mitochondrial genome shows the conserved protein coding regions and gene order rearrangements typical of land plants. There have been widespread insertions of organellar DNA into the E. grandis nuclear genome, which span 141 annotated nuclear genes. Further, we identify predicted editing sites to allow for the discrimination of RNA-sequencing reads between nuclear and organellar gene copies, finding that nuclear copies of organellar genes are not expressed in E. grandis.<br><br>CONCLUSIONS: The implications of organellar DNA transfer to the nucleus are often ignored, despite the insight they can give into the ongoing evolution of plant genomes, and the problems they can cause in many applications of genomics. Future comparisons of the transcription and regulation of organellar genes between Eucalyptus genotypes may provide insight to the cytonuclear interactions that impact economically important traits in this widely grown lignocellulosic crop species.}, }
@article {pmid30759299, year = {2019}, author = {Kaila, T and Saxena, S and Ramakrishna, G and Tyagi, A and Tribhuvan, KU and Srivastava, H and Sandhya,  and Chaudhury, A and Singh, NK and Gaikwad, K}, title = {Comparative RNA editing profile of mitochondrial transcripts in cytoplasmic male sterile and fertile pigeonpea reveal significant changes at the protein level.}, journal = {Molecular biology reports}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11033-019-04657-2}, pmid = {30759299}, issn = {1573-4978}, abstract = {RNA editing is a process which leads to post-transcriptional alteration of the nucleotide sequence of the corresponding mRNA molecule which may or may not lead to changes at the protein level. Apart from its role in providing variability at the transcript and protein levels, sometimes, such changes may lead to abnormal expression of the mitochondrial gene leading to a cytoplasmic male sterile phenotype. Here we report the editing status of 20 major mitochondrial transcripts in both male sterile (AKCMS11) and male fertile (AKPR303) pigeonpea genotypes. The validation of the predicted editing sites was done by mapping RNA-seq reads onto the amplified mitochondrial genes, and 165 and 159 editing sites were observed in bud tissues of the male sterile and fertile plant respectively. Among the resulting amino acid alterations, the most frequent one was the conversion of hydrophilic amino acids to hydrophobic. The alterations thus detected in our study indicates differential editing, but no major change in terms of the abnormal protein structure was detected. However, the above investigation provides an insight into the behaviour of pigeonpea mitochondrial genome in native and alloplasmic state and could hold clues in identification of editing factors and their role in adaptive evolution in pigeonpea.}, }
@article {pmid30555069, year = {2018}, author = {Idnurm, A}, title = {Mystique of Phycomyces blakesleeanus is a peculiar mitochondrial genetic element that is highly variable in DNA sequence while subjected to strong negative selection.}, journal = {Journal of genetics}, volume = {97}, number = {5}, pages = {1195-1204}, pmid = {30555069}, issn = {0973-7731}, mesh = {Biological Evolution ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; *Genome, Mitochondrial ; *Interspersed Repetitive Sequences ; Mitochondria/*genetics ; Phycomyces/*genetics ; Phylogeny ; *Selection, Genetic ; Sequence Homology ; }, abstract = {A DNA region in the mitochondrial genome of the fungus Phycomyces blakesleeanus (Mucorales, Mucoromycota) was characterized in a population of wild-type strains. The region encodes a predicted protein similar to the reverse transcriptases encoded by mitochondrial retroplasmids of Neurospora species and other Sordariomycetes (Ascomycota), but is uncommon in other fungi. DNA sequences of this element, named mystique, are highly variable between the strains, having greater than 2.5% divergence, yet most of the nucleotide differences fall in codon positions that do not change the amino acid sequence. The high proportion of polymorphisms coupled to the rarity of nonsynonymous changes suggests that mystique is subject to counteracting forces of hypermutation and purifying selection. However, while evidence for negative selection may infer that the element provides a fitness benefit, some strains of P. blakesleeanus do not have the element and grow equivalently well as those strains with it. A mechanism to explain the variability between the mystique alleles is proposed, of error-prone replication through an RNA intermediate, reverse transcription and reintegration of the element into the mitochondrial genome.}, }
@article {pmid30356218, year = {2018}, author = {Katsyuba, E and Mottis, A and Zietak, M and De Franco, F and van der Velpen, V and Gariani, K and Ryu, D and Cialabrini, L and Matilainen, O and Liscio, P and Giacchè, N and Stokar-Regenscheit, N and Legouis, D and de Seigneux, S and Ivanisevic, J and Raffaelli, N and Schoonjans, K and Pellicciari, R and Auwerx, J}, title = {De novo NAD+ synthesis enhances mitochondrial function and improves health.}, journal = {Nature}, volume = {563}, number = {7731}, pages = {354-359}, doi = {10.1038/s41586-018-0645-6}, pmid = {30356218}, issn = {1476-4687}, mesh = {Animals ; Caenorhabditis elegans/cytology/enzymology/metabolism ; Carboxy-Lyases/antagonists &amp; inhibitors/chemistry/deficiency/*metabolism ; Cell Line ; Choline ; *Conserved Sequence ; Disease Models, Animal ; *Evolution, Molecular ; Female ; Gene Knockdown Techniques ; *Health ; Hepatocytes/cytology/drug effects ; Homeostasis/drug effects ; Humans ; Kidney/cytology/drug effects ; Liver/cytology/drug effects ; Longevity/drug effects ; Male ; Methionine/deficiency ; Mice ; Mice, Inbred C57BL ; Mitochondria/*physiology ; NAD/*biosynthesis ; Non-alcoholic Fatty Liver Disease/physiopathology/prevention &amp; control ; Rats ; Sirtuins/metabolism ; }, abstract = {Nicotinamide adenine dinucleotide (NAD+) is a co-substrate for several enzymes, including the sirtuin family of NAD+-dependent protein deacylases. Beneficial effects of increased NAD+ levels and sirtuin activation on mitochondrial homeostasis, organismal metabolism and lifespan have been established across species. Here we show that α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD), the enzyme that limits spontaneous cyclization of α-amino-β-carboxymuconate-ε-semialdehyde in the de novo NAD+ synthesis pathway, controls cellular NAD+ levels via an evolutionarily conserved mechanism in Caenorhabditis elegans and mouse. Genetic and pharmacological inhibition of ACMSD boosts de novo NAD+ synthesis and sirtuin 1 activity, ultimately enhancing mitochondrial function. We also characterize two potent and selective inhibitors of ACMSD. Because expression of ACMSD is largely restricted to kidney and liver, these inhibitors may have therapeutic potential for protection of these tissues from injury. In summary, we identify ACMSD as a key modulator of cellular NAD+ levels, sirtuin activity and mitochondrial homeostasis in kidney and liver.}, }
@article {pmid29909242, year = {2018}, author = {Pinheiro, GMS and Ramos, CHI}, title = {Initial characterization of newly identified mitochondrial and chloroplast small HSPs from sugarcane shows that these chaperones have different oligomerization states and substrate specificities.}, journal = {Plant physiology and biochemistry : PPB}, volume = {129}, number = {}, pages = {285-294}, doi = {10.1016/j.plaphy.2018.06.002}, pmid = {29909242}, issn = {1873-2690}, mesh = {Chloroplasts/*metabolism ; Chromatography, Gel ; Cloning, Molecular ; Heat-Shock Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Mitochondria/*metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Saccharum/genetics/*metabolism ; Sequence Alignment ; Spectrometry, Fluorescence ; Substrate Specificity ; }, abstract = {Chaperones belonging to the small heat shock protein (sHSP) family are ubiquitous and exhibit elevated expression under stresses conditions to protect proteins against aggregation, thereby contributing to the stress tolerance of the organism. Tropical plants are constantly exposed to high temperatures, and the mechanisms by which these plants tolerate heat stress are of foremost importance to basic science as well as applied agrobiotechnology. Therefore, this study aims to characterize sHSPs from different organelles from sugarcane, an important crop that is associated with sugar and bioenergy production. An expression sequence tag database of sugarcane was searched, and sHsp genes of mitochondrial and chloroplast organelles were selected and cloned. The proteins were expressed in Escherichia coli and isolated and purified by two chromatographic steps with high purity as single species. Circular dichroism and fluorescence spectroscopy showed that both proteins were purified in their folded states with a predominant β-sheet secondary structure. Determination of the molecular weight, diffusion coefficient and Stokes radius parameters showed that both chaperones form large spherical-like oligomers in solution. The two sHSPs had different oligomeric states and substrate specificities. The mitochondrial sHSP was a 20-mer with ability to protect model substrates that differ from that of the 16-meric sHSP from chloroplasts. These results indicate that both sHSPs are key agents to protect against stress confirming the importance of the great diversity of sHSP chaperones in plants for homeostasis maintenance. Moreover, to our knowledge, this is the first report about small HSPs from sugarcane organelles.}, }
@article {pmid30742851, year = {2019}, author = {Teng, H and Wang, D and Lu, J and Zhou, Y and Pang, Y and Li, Q}, title = {Novel insights into the evolution of the caveolin superfamily and mechanisms of antiapoptotic effects and cell proliferation in lamprey.}, journal = {Developmental and comparative immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.dci.2019.01.005}, pmid = {30742851}, issn = {1879-0089}, abstract = {Caveolin-1 is the main structural and functional component of caveolin, and it is involved in the regulation of cholesterol transport, endocytosis, and signal transduction. Moreover, changes in caveolin-1 play an important role in tumorigenesis and inflammatory processes. Previous studies have demonstrated that human caveolin-1 is mainly located in the cell membrane and exhibits cell type- and stage-dependent functional differences during cancer development and inflammatory responses. However, the role of Lamprey-caveolin-like (L-caveolin-like) in lamprey remained unknown. Here, we demonstrated that L-caveolin-like performs anti-inflammation and oncogenic functions and the function of caveolin-1 diverged during vertebrate evolution. Moreover, the results reveal the mechanism underlying the antiapoptotic effects of L-caveolin-like. An L-caveolin-like gene from Lampetra japonica (L. japonica) was identified and characterized. L-Caveolin-like was primarily distributed in the leukocytes, intestines and supraneural bodies (Sp-bodies) immune organs as indicated by QPCR and immunohistochemistry assays. The mRNA and protein expression levels of L-caveolin exhibited consistent increases in expression at 2 and 72 h in adult tissues after exposure to lipopolysaccharide (LPS) and in leukocytes stimulated by Vibrio anguillarum (V. anguillarum), Staphylococcus aureus (S. aureus), and Poly I:C. Furthermore, the overexpression of pEGFP-N1-L-caveolin-like was associated with a distinct localization in mitochondria, with decreased cytochrome C (Cyt C) and mitochondrial Cyt C oxidase subunit I (CO I) expression. In addition, increased cellular ATP levels suggested that this protein prevented mitochondrial damage. The overexpression of pEGFP-N1-L-caveolin-like led to the altered expression of factors related to apoptosis, such as decreased Caspase-9, Caspase-3, p53, and Bax expression and increased Bcl-2 expression. In addition, the overexpression of pEGFP-N1-L-caveolin-like promoted cell proliferation associated with upregulated EGF, bFGF, and PDGFB expression. Together, these findings indicated that the L-caveolin-like protein from L. japonica induced the activation of antiapoptotic effects via the mitochondrial Cyt C-mediated Caspase-3 signaling pathway. Our analysis further suggests that L-caveolin-like is an oncogene protein product and anti-inflammatory molecule from lamprey that evolved early in vertebrate evolution.}, }
@article {pmid30740458, year = {2019}, author = {Oborník, M}, title = {In the beginning was the word: How terminology drives our understanding of endosymbiotic organelles.}, journal = {Microbial cell (Graz, Austria)}, volume = {6}, number = {2}, pages = {134-141}, doi = {10.15698/mic2019.02.669}, pmid = {30740458}, issn = {2311-2638}, abstract = {The names we give objects of research, to some extent, predispose our ways of thinking about them. Misclassifications of Oomycota, Microsporidia, Myxosporidia, and Helicosporidia have obviously affected not only their formal taxonomic names, but also the methods and approaches with which they have been investigated. Therefore, it is important to name biological entities with accurate terms in order to avoid discrepancies in researching them. The endosymbiotic origin of mitochondria and plastids is now the most accepted scenario for their evolution. Since it is apparent that there is no natural definitive border between bacteria and semiautonomous organelles, I propose that mitochondria and plastids should be called bacteria and classified accordingly, in the bacterial classification system. I discuss some consequences of this approach, including: i) the resulting &quot;changes&quot; in the abundances of bacteria, ii) the definitions of terms like microbiome or multicellularity, and iii) the concept of endosymbiotic domestication.}, }
@article {pmid30740457, year = {2019}, author = {Gruber, A}, title = {What's in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts.}, journal = {Microbial cell (Graz, Austria)}, volume = {6}, number = {2}, pages = {123-133}, doi = {10.15698/mic2019.02.668}, pmid = {30740457}, issn = {2311-2638}, abstract = {Mitochondria and plastids evolved from free-living bacteria, but are now considered integral parts of the eukaryotic species in which they live. Therefore, they are implicitly called by the same eukaryotic species name. Historically, mitochondria and plastids were known as &quot;organelles&quot;, even before their bacterial origin became fully established. However, since organelle evolution by endosymbiosis has become an established theory in biology, more and more endosymbiotic systems have been discovered that show various levels of host/symbiont integration. In this context, the distinction between &quot;host/symbiont&quot; and &quot;eukaryote/organelle&quot; systems is currently unclear. The criteria that are commonly considered are genetic integration (via gene transfer from the endosymbiont to the nucleus), cellular integration (synchronization of the cell cycles), and metabolic integration (the mutual dependency of the metabolisms). Here, I suggest that these criteria should be evaluated according to the resulting coupling of genetic recombination between individuals and congruence of effective population sizes, which determines if independent speciation is possible for either of the partners. I would like to call this aspect of integration &quot;sexual symbiont integration&quot;. If the partners lose their independence in speciation, I think that they should be considered one species. The partner who maintains its genetic recombination mechanisms and life cycle should then be the name giving &quot;host&quot;; the other one would be the organelle. Distinguishing between organelles and symbionts according to their sexual symbiont integration is independent of any particular mechanism or structural property of the endosymbiont/host system under investigation.}, }
@article {pmid30114217, year = {2018}, author = {Shi, Y and Liu, Y and Zhang, S and Zou, R and Tang, J and Mu, W and Peng, Y and Dong, S}, title = {Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica 'JinhuaiJ2'.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202485}, pmid = {30114217}, issn = {1932-6203}, mesh = {Base Composition ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Genes, Plant ; *Genome, Mitochondrial ; Homologous Recombination ; Introns ; Mitochondria/genetics ; Phylogeny ; Plant Proteins/genetics ; RNA, Plant/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Sophora/*genetics ; Whole Genome Sequencing ; }, abstract = {Sophora japonica L. (Faboideae, Leguminosae) is an important traditional Chinese herb with a long history of cultivation. Its flower buds and fruits contain abundant flavonoids, and therefore, the plants are cultivated for the industrial extraction of rutin. Here, we determined the complete nucleotide sequence of the mitochondrial genome of S. japonica 'JinhuaiJ2', the most widely planted variety in Guangxi region of China. The total length of the mtDNA sequence is 484,916 bp, with a GC content of 45.4%. Sophora japonica mtDNA harbors 32 known protein-coding genes, 17 tRNA genes, and three rRNA genes with 17 cis-spliced and five trans-spliced introns disrupting eight protein-coding genes. The gene coding and intron regions, and intergenic spacers account for 7.5%, 5.8% and 86.7% of the genome, respectively. The gene profile of S. japonica mitogenome differs from that of the other Faboideae species by only one or two gene gains or losses. Four of the 17 cis-spliced introns showed distinct length variations in the Faboideae, which could be attributed to the homologous recombination of the short repeats measuring a few bases located precisely at the edges of the putative deletions. This reflects the importance of small repeats in the sequence evolution in Faboideae mitogenomes. Repeated sequences of S. japonica mitogenome are mainly composed of small repeats, with only 20 medium-sized repeats, and one large repeat, adding up to 4% of its mitogenome length. Among the 25 pseudogene fragments detected in the intergenic spacer regions, the two largest ones and their corresponding functional gene copies located in two different sets of medium-sized repeats, point to their origins from homologous recombinations. As we further observed the recombined reads associated with the longest repeats of 2,160 bp with the PacBio long read data set of just 15 × in depth, repeat mediated homologous recombinations may play important role in the mitogenomic evolution of S. japonica. Our study provides insightful knowledge to the genetic background of this important herb species and the mitogenomic evolution in the Faboideae species.}, }
@article {pmid30729162, year = {2019}, author = {Li, XC and Peris, D and Hittinger, CT and Sia, EA and Fay, JC}, title = {Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast.}, journal = {Science advances}, volume = {5}, number = {1}, pages = {eaav1848}, doi = {10.1126/sciadv.aav1848}, pmid = {30729162}, issn = {2375-2548}, abstract = {Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum. The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence in COX1 affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence.}, }
@article {pmid30728898, year = {2019}, author = {Speirs, MMP and Swensen, AC and Chan, TY and Jones, PM and Holman, JC and Harris, MB and Maschek, JA and Cox, JE and Carson, RH and Hill, JT and Andersen, JL and Prince, JT and Price, JC}, title = {Imbalanced sphingolipid signaling is maintained as a core proponent of a cancerous phenotype in spite of metabolic pressure and epigenetic drift.}, journal = {Oncotarget}, volume = {10}, number = {4}, pages = {449-479}, doi = {10.18632/oncotarget.26533}, pmid = {30728898}, issn = {1949-2553}, abstract = {Tumor heterogeneity may arise through genetic drift and environmentally driven clonal selection for metabolic fitness. This would promote subpopulations derived from single cancer cells that exhibit distinct phenotypes while conserving vital pro-survival pathways. We aimed to identify significant drivers of cell fitness in pancreatic adenocarcinoma (PDAC) creating subclones in different nutrient formulations to encourage differential metabolic reprogramming. The genetic and phenotypic expression profiles of each subclone were analyzed relative to a healthy control cell line (hTert-HPNE). The subclones exhibited distinct variations in protein expression and lipid metabolism. Relative to hTert-HPNE, PSN-1 subclones uniformly maintained modified sphingolipid signaling and specifically retained elevated sphingosine-1-phosphate (S1P) relative to C16 ceramide (C16 Cer) ratios. Each clone utilized a different perturbation to this pathway, but maintained this modified signaling to preserve cancerous phenotypes, such as rapid proliferation and defense against mitochondria-mediated apoptosis. Although the subclones were unique in their sensitivity, inhibition of S1P synthesis significantly reduced the ratio of S1P/C16 Cer, slowed cell proliferation, and enhanced sensitivity to apoptotic signals. This reliance on S1P signaling identifies this pathway as a promising drug-sensitizing target that may be used to eliminate cancerous cells consistently across uniquely reprogrammed PDAC clones.}, }
@article {pmid30698308, year = {2019}, author = {El-Sheikh, RM and Mansy, SS and Nessim, IG and Hosni, HN and El Hindawi, A and Hassanein, MH and AbdelFattah, AS}, title = {Carbamoyl phosphate synthetase 1 (CPS1) as a prognostic marker in chronic hepatitis C infection.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {127}, number = {2}, pages = {93-105}, doi = {10.1111/apm.12917}, pmid = {30698308}, issn = {1600-0463}, support = {100//Theodor Bilharz Research Institute (TBRI)/ ; }, mesh = {Adult ; Aged ; Biomarkers/blood ; Carbamoyl-Phosphate Synthase (Ammonia)/*blood ; Female ; Hepatitis C, Chronic/mortality/*pathology ; Humans ; Liver/pathology ; Liver Cirrhosis/*pathology ; Male ; Middle Aged ; Mitochondria/*pathology/ultrastructure ; Prognosis ; Urea/blood ; }, abstract = {This study aims to assess the value of carbamoyl phosphate synthetase 1 (CPS1), as a non-invasive serum marker, for the evolution of chronic HCV infection and hepatic fibrosis. Seventy-two patients with HCV positive serum RNA and 15 health volunteers were enrolled in this study. Out of 72 patients, 10 patients had decompensated liver with ascites. Quantitative analysis of CPS1 was performed in the harvested sera and corresponding liver biopsies using ELISA and immunohistochemistry techniques respectively. Also, mitochondrial count using electron microscopy, urea analysis and conventional liver tests were done. Patients were grouped into (F1 + F2) and (F3 + F4) representing stages of moderate and severe fibrosis respectively. Tissue and serum CPS1 (s.CPS1) correlated significantly in moderate and severe fibrosis. Patients with severe fibrosis showed significantly higher levels of s.CPS1 (p-value ≤ 0.05) and significantly lower mitochondrial counts (p-value = 0.0065) than those with moderate fibrosis. S.urea positively correlated with s.CPS1 only in the decompensated group, at which s.urea reached maximal levels. In conclusion, s.CPS1 is a potential non-invasive marker for the assessment of severity and progression of HCV in relation to mitochondrial dysfunction. Also, increased s.urea with the progression of the disease is mainly due to a concurrent renal malfunction, which needs further investigation.}, }
@article {pmid30446790, year = {2019}, author = {Razzak, MA and Lee, J and Lee, DW and Kim, JH and Yoon, HS and Hwang, I}, title = {Expression of seven carbonic anhydrases in red alga Gracilariopsis chorda and their subcellular localization in a heterologous system, Arabidopsis thaliana.}, journal = {Plant cell reports}, volume = {38}, number = {2}, pages = {147-159}, doi = {10.1007/s00299-018-2356-8}, pmid = {30446790}, issn = {1432-203X}, support = {2016R1E1A1A02922014//Ministry of Fisheries/ ; }, mesh = {Arabidopsis/*genetics ; Carbonic Anhydrases/classification/*metabolism ; Computer Simulation ; Endoplasmic Reticulum/metabolism ; Gene Expression Regulation, Enzymologic ; Glycosylation ; Golgi Apparatus/metabolism ; Green Fluorescent Proteins/metabolism ; Phylogeny ; Plants, Genetically Modified ; Protein Transport ; Protoplasts/metabolism ; Rhodophyta/*enzymology ; Subcellular Fractions/metabolism ; Vacuoles/metabolism ; }, abstract = {KEY MESSAGE: Red alga, Gracilariopsis chorda, contains seven carbonic anhydrases that can be grouped into α-, β- and γ-classes. Carbonic anhydrases (CAHs) are metalloenzymes that catalyze the reversible hydration of CO2. These enzymes are present in all living organisms and play roles in various cellular processes, including photosynthesis. In this study, we identified seven CAH genes (GcCAHs) from the genome sequence of the red alga Gracilariopsis chorda and characterized them at the molecular, cellular and biochemical levels. Based on sequence analysis, these seven isoforms were categorized into four α-class, one β-class, and two γ-class isoforms. RNA sequencing revealed that of the seven CAHs isoforms, six genes were expressed in G. chorda in light at room temperature. In silico analysis revealed that these seven isoforms localized to multiple subcellular locations such as the ER, mitochondria and cytosol. When expressed as green fluorescent protein fusions in protoplasts of Arabidopsis thaliana leaf cells, these seven isoforms showed multiple localization patterns. The four α-class GcCAHs with an N-terminal hydrophobic leader sequence localized to the ER and two of them were further targeted to the vacuole. GcCAHβ1 with no noticeable signal sequence localized to the cytosol. The two γ-class GcCAHs also localized to the cytosol, despite the presence of a predicted presequence. Based on these results, we propose that the red alga G. chorda also employs multiple CAH isoforms for various cellular processes such as photosynthesis.}, }
@article {pmid29579296, year = {2018}, author = {Caspermeyer, J}, title = {Cockroach Ancient Geographic and Genomic History Traced Back to Last Supercontinent.}, journal = {Molecular biology and evolution}, volume = {35}, number = {4}, pages = {1035}, doi = {10.1093/molbev/msy039}, pmid = {29579296}, issn = {1537-1719}, mesh = {Animals ; *Cockroaches ; Genomics ; Mitochondria ; *Phylogeny ; }, }
@article {pmid30060189, year = {2018}, author = {Río Bártulos, C and Rogers, MB and Williams, TA and Gentekaki, E and Brinkmann, H and Cerff, R and Liaud, MF and Hehl, AB and Yarlett, NR and Gruber, A and Kroth, PG and van der Giezen, M}, title = {Mitochondrial Glycolysis in a Major Lineage of Eukaryotes.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2310-2325}, pmid = {30060189}, issn = {1759-6653}, support = {//Wellcome Trust/United Kingdom ; 078566/A/05/Z//Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; Blastocystis/cytology/enzymology/genetics/*metabolism ; Diatoms/cytology/enzymology/genetics/*metabolism ; Energy Metabolism ; Genome, Mitochondrial ; *Glycolysis ; Mitochondria/genetics/*metabolism ; Symbiosis ; Transformation, Genetic ; }, abstract = {The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host's metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.}, }
@article {pmid29959984, year = {2018}, author = {Uribe, JE and Zardoya, R and Puillandre, N}, title = {Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {127}, number = {}, pages = {898-906}, doi = {10.1016/j.ympev.2018.06.037}, pmid = {29959984}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/genetics ; Open Reading Frames/genetics ; *Phylogeny ; Snails/*genetics ; }, abstract = {With more than 5,000 species, Conoidea is one of the most diversified superfamilies of Gastropoda. Recently, the family-level classification of these venomous predator snails has undergone substantial changes, on the basis of a phylogenetic tree reconstructed combining partial mitochondrial and nuclear gene sequences, and up to 16 families are now recognized. However, phylogenetic relationships among these families remain largely unresolved. Here, we sequenced 20 complete or nearly complete mitochondrial (mt) genomes, which were combined with mt genomes available in GenBank to construct a dataset that included representatives of 80% of the known families, although for some we had only one species or genus as representative. Most of the sequenced conoidean mt genomes shared a constant genome organization, and observed rearrangements were limited exclusively to tRNA genes in a few lineages. Phylogenetic trees were reconstructed using probabilistic methods. Two main monophyletic groups, termed &quot;Clade A&quot; and &quot;Clade B&quot;, were recovered with strong support within a monophyletic Conoidea. Clade A (including families Clavatulidae, Horaiclavidae, Turridae s.s., Terebridae, Drilliidae, Pseudomelatomidae, and Cochlespiridae) was composed of four main lineages, one of which was additionally supported by a rearrangement in the gene order. Clade B (including families Conidae, Borsoniidae, Clathurellidae, Mangeliidae, Raphitomidae, and Mitromorphidae) was composed of five main lineages. The reconstructed phylogeny rejected the monophyly of Clavatulidae, Horaiclavidae, Turridae, Pseudomelatomidae, and Conidae, indicating that several of the currently accepted families may be ill-defined. The reconstructed tree also revealed new phylogenetic positions for genera characterized as tentative (Gemmuloborsonia, Lucerapex, and Leucosyrinx), enigmatic (Marshallena) or challenging to place (Fusiturris), which will potentially impact the classification of the Conoidea.}, }
@article {pmid29567505, year = {2018}, author = {O'Connell, KA and Smith, EN}, title = {The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis).}, journal = {Molecular phylogenetics and evolution}, volume = {127}, number = {}, pages = {356-366}, doi = {10.1016/j.ympev.2018.03.018}, pmid = {29567505}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Cell Nucleus/genetics ; Colubridae/*classification ; Cytochromes c/genetics ; Geography ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {A stable alpha taxonomy is essential to understanding evolutionary processes and achieving effective conservation aims. Taxonomy depends on the identification of independently evolving lineages, and the delimitation of these lineages based on multiple lines of evidence. Coalescent species delimitation within an integrative framework has increased the rigor of the delimitation process. Here we use genome-wide SNP data and coalescent species delimitation to explore lineage relationships within several North American whipsnake species, test the species status of several lineages, and test the effect of missing data on species delimitation. We find support for the elevation of several previously recognized subspecies to full species status, and formally elevate two species. This study demonstrates the power of molecular data and model-based delimitation methods to identify evolutionary relationships, and finds that missing data have little impact on the outcome of delimitation analyses.}, }
@article {pmid28743941, year = {2017}, author = {Yum, LK and Baumgarten, S and Röthig, T and Roder, C and Roik, A and Michell, C and Voolstra, CR}, title = {Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6442}, pmid = {28743941}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics/physiology ; Glycolysis/genetics ; Indian Ocean ; Mitochondria/genetics/metabolism ; Oxygen/metabolism ; *Transcriptome ; }, abstract = {Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.}, }
@article {pmid30703566, year = {2019}, author = {Liu, J and Hao, W and Liu, J and Fan, S and Zhao, W and Deng, L and Wang, X and Hu, Z and Hua, W and Wang, H}, title = {A novel chimeric mitochondrial gene confers cytoplasmic effects on seed oil content in polyploid rapeseed (Brassica napus L.).}, journal = {Molecular plant}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molp.2019.01.012}, pmid = {30703566}, issn = {1752-9867}, abstract = {Cytoplasmic effects (CE) are discovered to influence a diverse array of agronomic traits in crops, and understanding the underlying mechanisms can help accelerate breeding programs. Seed oil content (SOC) is of great agricultural, nutritional and economic importance. However, the genetic basis of CE on SOC (CE-SOC) remains enigmatic. Here we employ an optimized approach to sequence cytoplasmic (plastid and mitochondrial) genomes of allotetraploid oilseed rape (Brassica napus L.) 51218 and 56366 cultivars that bear contrasting CE-SOC. By combining comparative genomics and genome-wide transcriptome analysis, we identify mitochondria-encoded orf188 as a potential CE-SOC determinant gene. Functional transgenic analyses in the model system Arabidopsis thaliana and rapeseed indicate that orf188 governs CE-SOC and can significantly increase SOC, strikingly, through promoting the yield of ATP. Further transcriptional profiling with microarray and RNA-Seq consistently reveal transcriptional reprogramming of mitochondrial energy metabolism to facilitate ATP production. Intriguingly, orf188 is a previously uncharacterized chimeric gene in the evolution of genetic novelty that endows rapeseed with positive CE-SOC. Our results sheds light on the molecular basis of CE contributing to a key quantitative trait in polyploidy crops and enrich the theory on maternal control of oil content, providing new scientific guidance for creation of high-oil germplasm resources.}, }
@article {pmid29161481, year = {2017}, author = {Arrivillaga-Henríquez, J and Enríquez, S and Romero, V and Echeverría, G and Pérez-Barrera, J and Poveda, A and Navarro, JC and Warburg, A and Benítez, W}, title = {[Eco-epidemiological aspects, natural detection and molecular identification of Leishmania spp. in Lutzomyia reburra, Lutzomyia barrettoi majuscula and Lutzomyia trapidoi].}, journal = {Biomedica : revista del Instituto Nacional de Salud}, volume = {37}, number = {0}, pages = {83-97}, doi = {10.7705/biomedica.v37i0.3536}, pmid = {29161481}, issn = {0120-4157}, mesh = {Animals ; Cell Nucleus/enzymology ; DNA Topoisomerases, Type II/genetics ; DNA, Protozoan/analysis ; DNA, Ribosomal Spacer/analysis ; Ecuador ; Feeding Behavior ; Female ; Insect Vectors/*parasitology ; Leishmania/genetics/*isolation &amp; purification/physiology ; Leishmaniasis, Cutaneous/parasitology/*transmission ; Mitochondria/enzymology ; Phylogeny ; Phylogeography ; Protozoan Proteins/genetics ; Psychodidae/*parasitology ; Species Specificity ; }, abstract = {INTRODUCTION: The province of Pichincha in Ecuador is an endemic area of cutaneous leishmaniasis, where anthropophilic sand flies with natural infection by Leishmania, have been reported as vectors. However, the role in transmission of zoophilic species has not been evaluated.<br><br>OBJECTIVE: To evaluate natural infection by Leishmania in two zoophilic phlebotomine sand fly species, Lutzomyia reburra and Lu. barrettoi majuscula, and one anthropophilic species, Lu. trapidoi, as well as the endophagy and synanthropism of these species in the northwest of Pichincha.<br><br>MATERIALS AND METHODS: Phlebotomines were collected using CDC light traps in different habitats and altitudes with presence of cutaneous leishmaniasis. Leishmania infection was detected using genomic DNA from females of the collected sand flies. We amplified the internal transcribed spacer gene of ribosomal RNA I (ITS1), the mitochondrial topoisomerase II gene (mtTOPOII), and the nuclear topoisomerase II gene (TopoII). Percentages of positivity for Leishmania, at spatio-temporal scale, proportion of endophagy and synanthropism index were calculated.<br><br>RESULTS: Natural infection was determined for Le. amazonensis in Lu. reburra (9.5%) and Lu. b. majuscula (23.8%), while in Lu. trapidoi we detected Le. amazonensis, Le. brazilienis and Le. naiffi-lainsoni. Phlebotomines were asynanthropic and with low endophagy.<br><br>CONCLUSION: Natural infection with Le. amazonensis was recorded for the first time in Lu. reburra and Lu. b. majuscula, demonstrating the importance of zoophilic phlebotomines in the maintenance of the Leishmania transmission cycle in endemic foci.}, }
@article {pmid29609620, year = {2018}, author = {Hornok, S and Beck, R and Farkas, R and Grima, A and Otranto, D and Kontschán, J and Takács, N and Horváth, G and Szőke, K and Szekeres, S and Majoros, G and Juhász, A and Salant, H and Hofmann-Lehmann, R and Stanko, M and Baneth, G}, title = {High mitochondrial sequence divergence in synanthropic flea species (Insecta: Siphonaptera) from Europe and the Mediterranean.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {221}, pmid = {29609620}, issn = {1756-3305}, support = {115854//OTKA/International ; }, mesh = {Animals ; *Base Sequence ; Ctenocephalides/classification/genetics ; Europe ; Flea Infestations/parasitology ; *Genetic Variation ; Haplotypes ; Humans ; Insect Vectors/classification/genetics ; Mediterranean Region ; Mitochondria/*genetics ; Phylogeny ; Siphonaptera/*classification/*genetics ; }, abstract = {BACKGROUND: Adult fleas are haematophagous ectoparasites of warm-blooded vertebrates, particularly mammals. Among them, the cat flea (Ctenocephalides felis) and the human flea (Pulex irritans) have high veterinary-medical significance, owing to their cosmopolitan distribution and role in the transmission of important vector-borne pathogens. While the taxonomy of Ct. felis has been investigated on a morphological basis during the past decades, its molecular-phylogenetic analyses have been only recently conducted. This study expands the knowledge on Ct. felis from hitherto less studied geographical regions, and includes representatives from additional flea families, less investigated with molecular approaches.<br><br>METHODS: Fleas were collected in four countries of the Mediterranean Basin (Croatia, Italy, Malta and Israel), as well as in Hungary, from domestic and wild carnivores, rodents and humans. The DNA extracts of representative fleas (n = 148), belonging to ten species of eight genera, were used for PCR amplification of part of their cytochrome c oxidase subunits 1, 2 (cox1, cox2) and 18S rRNA genes, followed by sequencing and phylogenetic analyses.<br><br>RESULTS: The majority (65.6%) of Ct. felis felis cox2 sequences showed 99.4-100% similarity to each other (haplogroup A), whereas those from Malta and Israel had 98.1-98.7% sequence similarity (haplogroup B), and a third sequence from Israel (haplotype C) had as low as 96.3% sequence similarity in comparison with a reference sequence from group &quot;A&quot;. Except for the shape of the head, no consistent morphological differences (e.g. in chaetotaxy) were found between haplogroups &quot;A&quot; and &quot;C&quot;. Haplotypes of Ct. canis were genetically more homogenous, with 99.6-100% sequence similarity to each other. However, when P. irritans collected from humans was compared to those from three species of wild carnivores, these only had 96.6% cox2 similarity. The mouse flea, Leptopsylla segnis and the northern rat flea, Nosopsyllus fasciatus were both shown to have haplotypes with low intraspecific cox2 similarities (96.2 and 94.4%, respectively). Taken together, differences between mitochondrial lineages within four flea species exceeded that observed between two Chaetopsylla spp. (which had 97.3% cox2 similarity). The topologies of cox1 and cox2 phylogenetic trees were in line with relevant sequence comparisons. Conversely, 18S rRNA gene analyses only resolved differences above the species level.<br><br>CONCLUSIONS: Ctenocephalides felis felis, P. irritans, L. segnis and N. fasciatus were shown to have such a high level of mitochondrial gene heterogeneity, that the uniformity of these flea taxa should be reconsidered. Although the present results are limited (especially in the case of L. segnis and N. fasciatus), there appears to be no geographical or host restriction, which could explain the divergence of these genetic lineages.}, }
@article {pmid30289547, year = {2019}, author = {Hsu, YW and Juan, CT and Wang, CM and Jauh, GY}, title = {Mitochondrial Heat Shock Protein 60s Interact with What's This Factor 9 to Regulate RNA Splicing of ccmFC and rpl2.}, journal = {Plant &amp; cell physiology}, volume = {60}, number = {1}, pages = {116-125}, doi = {10.1093/pcp/pcy199}, pmid = {30289547}, issn = {1471-9053}, abstract = {Mitochondrial intron splicing is a plant-specific feature that was acquired during the co-evolution of eukaryotic host cells and a-proteobacteria. The elimination of these introns is facilitated by mitochondrial-targeted proteins encoded by its host, nucleus. What's this factor 9 (WTF9), a nuclear-encoded plant organelle RNA recognition (PORR) protein, is involved in the splicing of the mitochondrial group II introns rpl2 and ccmFC. Disruption of WTF9 causes developmental defects associated with the loss of Cyt c and Cyt c1 in Arabidopsis. In the present study, using a co-immunoprecipitation assay, we found that HSP60s interacted with WTF9, which was further confirmed by a pull-down assay. HSP60s are molecular chaperones that assist with protein folding in both eukaryotic and prokaryotic cells. However, accumulating evidence suggests that HSP60s also participate in other biological functions such as RNA metabolism and RNA protection. In this study, we found that consistently with their interaction with WTF9, HSP60s interacted with 48 nucleotides of the ccmFC intron. In mutant studies, the double mutant hsp60-3a1hsp60-3b1 exhibited a small stature phenotype and reduced splicing efficiency for rpl2 and ccmFC. These observations were similar to those in wtf9 mutants and suggest that HSP60s are involved in the RNA splicing of rpl2 and ccmFC introns in mitochondria. Our findings suggest that HSP60s participate in mitochondrial RNA splicing through their RNA-binding ability.}, }
@article {pmid30074999, year = {2018}, author = {Brew-Appiah, RAT and York, ZB and Krishnan, V and Roalson, EH and Sanguinet, KA}, title = {Genome-wide identification and analysis of the ALTERNATIVE OXIDASE gene family in diploid and hexaploid wheat.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0201439}, pmid = {30074999}, issn = {1932-6203}, mesh = {Aegilops/*genetics ; Diploidy ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/physiology ; Genes, Plant/*genetics ; Genome, Plant/genetics ; Herbicide Resistance/genetics ; Mitochondrial Proteins/*genetics ; Multigene Family/*genetics ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins/*genetics ; Polyploidy ; Stress, Physiological/physiology ; Triticum/genetics/*physiology ; Whole Genome Sequencing ; }, abstract = {A comprehensive understanding of wheat responses to environmental stress will contribute to the long-term goal of feeding the planet. ALERNATIVE OXIDASE (AOX) genes encode proteins involved in a bypass of the electron transport chain and are also known to be involved in stress tolerance in multiple species. Here, we report the identification and characterization of the AOX gene family in diploid and hexaploid wheat. Four genes each were found in the diploid ancestors Triticum urartu, and Aegilops tauschii, and three in Aegilops speltoides. In hexaploid wheat (Triticum aestivum), 20 genes were identified, some with multiple splice variants, corresponding to a total of 24 proteins for those with observed transcription and translation. These proteins were classified as AOX1a, AOX1c, AOX1e or AOX1d via phylogenetic analysis. Proteins lacking most or all signature AOX motifs were assigned to putative regulatory roles. Analysis of protein-targeting sequences suggests mixed localization to the mitochondria and other organelles. In comparison to the most studied AOX from Trypanosoma brucei, there were amino acid substitutions at critical functional domains indicating possible role divergence in wheat or grasses in general. In hexaploid wheat, AOX genes were expressed at specific developmental stages as well as in response to both biotic and abiotic stresses such as fungal pathogens, heat and drought. These AOX expression patterns suggest a highly regulated and diverse transcription and expression system. The insights gained provide a framework for the continued and expanded study of AOX genes in wheat for stress tolerance through breeding new varieties, as well as resistance to AOX-targeted herbicides, all of which can ultimately be used synergistically to improve crop yield.}, }
@article {pmid28969942, year = {2018}, author = {Chen, S and Wu, Z and Zhang, J and Wang, M and Jia, R and Zhu, D and Liu, M and Sun, K and Yang, Q and Wu, Y and Zhao, X and Cheng, A}, title = {Duck stimulator of interferon genes plays an important role in host anti-duck plague virus infection through an IFN-dependent signalling pathway.}, journal = {Cytokine}, volume = {102}, number = {}, pages = {191-199}, doi = {10.1016/j.cyto.2017.09.008}, pmid = {28969942}, issn = {1096-0023}, mesh = {Amino Acid Sequence ; Animals ; Avian Proteins/genetics/immunology ; Bird Diseases/*genetics/*immunology/virology ; Ducks/*genetics/*immunology/virology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Immunity, Innate/genetics ; Interferon-beta/genetics ; Mardivirus/*immunology/*pathogenicity/physiology ; Marek Disease/*genetics/*immunology/virology ; NF-kappa B/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Signal Transduction ; Virus Replication ; }, abstract = {The human stimulator of interferon gene (STING) is an important molecule in innate immunity that stimulates type I interferon (IFN) production. However, the role of duck STING (duSTING) in innate immunity has yet to be explained. In this study, the full length of the duSTING cDNA sequence (1149bp), which encodes 382 amino acid (aa) residues, was reported and showed the highest sequence similarity with chicken STINGs. The phylogenetic analysis based on STING aa showed that duSTING was grouped onto the birds clade. According to the tissue distribution spectrum analysis, duSTING was highly present in the bursa of Fabricius, glandular stomach, liver, pancreas, and small intestine of ducklings, as well as in the blood and pancreas of the adult duck. DuSTING mainly colocalized with the endoplasmic reticulum (ER) and mitochondria in transfected Baby Hamster Syrian Kidney (BHK21) and duck embryo fibroblasts (DEF) cells by an indirect immunofluorescence assay. The transfection of the DEFs with duSTING activated NF-κB, which induced the transcription of IFN-β, and the activated IFN induced the interferon-stimulated response element (ISRE). Furthermore, the overexpression of duSTING significantly upregulated the mRNA level of duck IFN-β and IFN-stimulated genes (ISGs), such as duMx and duOASL and inhibited the replication of the double-stranded DNA duck plague virus (DPV) in vitro. In addition, the knockdown of endogenous duSTING by shRNA significantly reduced the poly (I:C) (pIC), poly (dA:dT), and Tembusu virus (TMUV), induced IFN-β production and significantly promoted DPV replication in vitro. In general, these data demonstrate that duSTING is vital for duck type I interferon induction and plays an important role in the host defence of DPV infection.}, }
@article {pmid29949077, year = {2018}, author = {Lu, Y and Liu, N and Xu, L and Fang, J and Wang, S}, title = {The complete mitochondrial genome of Vanessa indica and phylogenetic analyses of the family Nymphalidae.}, journal = {Genes &amp; genomics}, volume = {40}, number = {10}, pages = {1011-1022}, pmid = {29949077}, issn = {2092-9293}, support = {J10118516034//Undergraduate student scientific research innovation projects of Anhui university/International ; }, mesh = {Animals ; Base Composition ; Butterflies/*classification/cytology/genetics ; Evolution, Molecular ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/chemistry ; RNA, Ribosomal, 16S/chemistry ; RNA, Transfer/chemistry ; Sequence Analysis, DNA/*methods ; }, abstract = {Vanessa indica is a small butterfly lacking historical molecular and biological research. Vanessa indica belongs to the family Nymphalidae (Lepidoptera: Papilionoidea), which is the largest group of butterflies and are nearly ubiquitous. However, after more than a century of taxonomic and molecular studies, there is no consensus for family classification, and the phylogenetic relationships within Nymphalidae are controversial. The first objective was to sequence and characterize the complete mitochondrial genome of V. indica. The most important objective was to completely reconstruct the phylogenetic relationships for family members within Nymphalidae. The mitochondrial genomic DNA (mtDNA) of V. indica was extracted and amplified by polymerase chain reaction. The complete mitochondrial sequence was annotated and characterized by analyzing sequences with SeqMan program. The phylogenetic analyses were conducted on thirteen protein coding genes (PCGs) in 95 mtDNA of Nymphalidae downloaded from GenBank for reference using the maximum likelihood method and Bayesian inference to ensure the validity of the results. The complete mitogenome was a circular molecule with 15,191 bp consisting of 13 protein coding genes, two ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA (tRNA) genes, and an A + T-rich region (D-loop). The nucleotide composition of the genome was highly biased for A + T content, which accounts for 80.0% of the nucleotides. All the tRNAs have putative secondary structures that are characteristic of mitochondrial tRNAs, except tRNASer(AGN). All the PCGs started with ATN codons, except cytochrome c oxidase subunit 1 (COX1), which was found to start with an unusual CGA codon. Four genes were observed to have unusual codons: COX1 terminated with atypical TT and the other three genes terminated with a single T. The A + T rich region of 327 bp consisted of repetitive sequences, including a ATAGA motif, a 19-bp poly-T stretch, and two microsatellite-like regions (TA)8. The phylogenetic analyses consistently placed Biblidinae as a sister cluster to Heliconiinae and Calinaginae as a sister clade to Satyrinae. Moreover, the phylogenetic tree identified Libytheinae as a monophyletic group within Nymphalidae. The complete mitogenome of V. indica was 15,191 bp with mitochondrial characterizations common for lepidopteran species, which enriched the mitochondria data of Nymphalid species. And the phylogenetic analysis revealed different classifications and relationships than those previously described. Our results are significant because they would be useful in further understanding of the evolutionary biology of Nymphalidae.}, }
@article {pmid29949074, year = {2018}, author = {Zhang, R and Wang, X}, title = {Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, Sinocyclocheilus multipunctatus (Cypriniformes: Cyprinidae).}, journal = {Genes &amp; genomics}, volume = {40}, number = {10}, pages = {1033-1040}, pmid = {29949074}, issn = {2092-9293}, mesh = {Animals ; Base Composition ; Contig Mapping ; Cyprinidae/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The genus Sinocyclocheilus is a representative group of cave creatures. However, genetic studies on Sinocyclocheilus are rare. The primary objective of this study was to explore the structure and feature of the complete mitochondrial genome of S. multipunctatus, and reconstruct the mitogenomic phylogeny of Sinocyclocheilus. The mitochondrial DNA of S. multipunctatus was amplified by overlapping PCR fragments. The mitogenome was assembled by the SeqMan and annotated using MitoAnnotator. The phylogenetic tree was established using the Bayesian inference and Maximum likelihood methods. The mitogenome of S. multipunctatus is a typical circular molecule of 16,586 bp with base composition A (31.25%), T (25.90%), G (16.35%), and C (26.50%), and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) genes, two ribosomal RNAs, and a 931 bp control region. Phylogenetic analysis reveals two clades in the Sinocyclocheilus with robust support. S. multipunctatus is close to a newly discovered cavefish, S. ronganensis. We obtained and described the complete mitogenome of S. multipunctatus, and investigated its phylogenetic status, which may provide a valuable resource for future phylogenetic analyses and population genetic studies in Sinocyclocheilus.}, }
@article {pmid30670662, year = {2019}, author = {Bloomfield, G and Paschke, P and Okamoto, M and Stevens, TJ and Urushihara, H}, title = {Triparental inheritance in Dictyostelium.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1814425116}, pmid = {30670662}, issn = {1091-6490}, abstract = {Sex promotes the recombination and reassortment of genetic material and is prevalent across eukaryotes, although our knowledge of the molecular details of sexual inheritance is scant in several major lineages. In social amoebae, sex involves a promiscuous mixing of cytoplasm before zygotes consume the majority of cells, but for technical reasons, sexual progeny have been difficult to obtain and study. We report here genome-wide characterization of meiotic progeny in Dictyostelium discoideum We find that recombination occurs at high frequency in pairwise crosses between all three mating types, despite the absence of the Spo11 enzyme that is normally required to initiate crossover formation. Fusions of more than two gametes to form transient syncytia lead to frequent triparental inheritance, with haploid meiotic progeny bearing recombined nuclear haplotypes from two parents and the mitochondrial genome from a third. Cells that do not contribute genetically to the Dictyostelium zygote nucleus thereby have a stake in the next haploid generation. D. discoideum mitochondrial genomes are polymorphic, and our findings raise the possibility that some of this variation might be a result of sexual selection on genes that can promote the spread of individual organelle genomes during sex. This kind of self-interested mitochondrial behavior may have had important consequences during eukaryogenesis and the initial evolution of sex.}, }
@article {pmid30526820, year = {2018}, author = {Ndiaye, PI and Marchand, B and Bâ, CT and Justine, JL and Bray, RA and Quilichini, Y}, title = {Ultrastructure of mature spermatozoa of three Bucephalidae (Prosorhynchus longisaccatus, Rhipidocotyle khalili and Bucephalus margaritae) and phylogenetic implications.}, journal = {Parasite (Paris, France)}, volume = {25}, number = {}, pages = {65}, doi = {10.1051/parasite/2018065}, pmid = {30526820}, issn = {1776-1042}, mesh = {Animals ; Axoneme/ultrastructure ; Cell Nucleus/ultrastructure ; Fish Diseases/parasitology ; Fishes ; Male ; Microscopy, Electron, Transmission ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; New Caledonia ; Pacific Ocean ; *Phylogeny ; Spermatozoa/classification/*ultrastructure ; Trematoda/classification/*ultrastructure ; Trematode Infections/parasitology/veterinary ; }, abstract = {We describe here the mature spermatozoa of three species of bucephalids, namely Bucephalus margaritae, Rhipidocotyle khalili and Prosorhynchus longisaccatus. This study provides the first ultrastructural data on the genera Bucephalus and Rhipidocotyle and enabled us to confirm the model of the mature spermatozoon in the Bucephalinae. The spermatozoon exhibits two axonemes with the 9 + &quot;1&quot; pattern of the Trepaxonemata, one of which is very short, lateral expansion, external ornamentation of the plasma membrane located in the anterior extremity of the spermatozoon and associated with cortical microtubules, spine-like bodies, a mitochondrion, and a nucleus. The maximum number of cortical microtubules is located in the anterior part of the spermatozoon. However, more studies are needed to elucidate if spine-like bodies are present in all the Bucephalinae or not. In the Prosorhynchinae, the mature spermatozoon exhibits a similar ultrastructural pattern. Some differences are observed, particularly the axoneme lengths and the arrangement of the spine-like bodies. The posterior extremity of the spermatozoon in the Bucephalinae exhibits only the nucleus, but prosorhynchines have microtubules.}, }
@article {pmid30668797, year = {2019}, author = {Backes, S and Garg, SG and Becker, L and Peleh, V and Glockshuber, R and Gould, SB and Herrmann, JM}, title = {Development of the mitochondrial intermembrane space disulfide relay represents a critical step in eukaryotic evolution.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msz011}, pmid = {30668797}, issn = {1537-1719}, abstract = {The mitochondrial intermembrane space evolved from the bacterial periplasm. Presumably as a consequence of their common origin, most proteins of these compartments are stabilized by structural disulfide bonds. The molecular machineries that mediate oxidative protein folding in bacteria and mitochondria, however, appear to share no common ancestry. Here we tested whether the enzymes Erv1 and Mia40 of the yeast mitochondrial disulfide relay could be functionally replaced by corresponding components of other compartments. We found that the sulfhydryl oxidase Erv1 could be replaced by the Ero1 oxidase or the protein disulfide isomerase from the endoplasmic reticulum, however at the cost of respiration deficiency. In contrast to Erv1, the mitochondrial oxidoreductase Mia40 proved to be indispensable and could not be replaced by thioredoxin-like enzymes, including the cytoplasmic reductase thioredoxin, the periplasmic dithiol oxidase DsbA and Pdi1. From our studies we conclude that the profound inertness against glutathione, its slow oxidation kinetics and its high affinity to substrates renders Mia40 a unique and essential component of mitochondrial biogenesis. Evidently, the development of a specific mitochondrial disulfide relay system represented a crucial step in the evolution of the eukaryotic cell.}, }
@article {pmid30071112, year = {2018}, author = {Caza, M and Hu, G and Nielson, ED and Cho, M and Jung, WH and Kronstad, JW}, title = {The Sec1/Munc18 (SM) protein Vps45 is involved in iron uptake, mitochondrial function and virulence in the pathogenic fungus Cryptococcus neoformans.}, journal = {PLoS pathogens}, volume = {14}, number = {8}, pages = {e1007220}, pmid = {30071112}, issn = {1553-7374}, support = {MOP13234//Canadian Institutes of Health Research/International ; R01 AI053721/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biological Transport ; Cryptococcosis/metabolism/microbiology/pathology ; *Cryptococcus neoformans/genetics/metabolism/pathogenicity ; Female ; Fungal Proteins/*physiology ; Iron/*metabolism ; Mice ; Mice, Inbred BALB C ; Mitochondria/*physiology ; Organisms, Genetically Modified ; Phylogeny ; Virulence/*genetics ; Virulence Factors/genetics/*physiology ; }, abstract = {The battle for iron between invading microorganisms and mammalian hosts is a pivotal determinant of the outcome of infection. The pathogenic fungus, Cryptococcus neoformans, employs multiple mechanisms to compete for iron during cryptococcosis, a disease primarily of immunocompromised hosts. In this study, we examined the role of endocytic trafficking in iron uptake by characterizing a mutant defective in the Sec1/Munc18 (SM) protein Vps45. This protein is known to regulate the machinery for vesicle trafficking and fusion via interactions with SNARE proteins. As expected, a vps45 deletion mutant was impaired in endocytosis and showed sensitivity to trafficking inhibitors. The mutant also showed poor growth on iron-limited media and a defect in transporting the Cfo1 ferroxidase of the high-affinity iron uptake system from the plasma membrane to the vacuole. Remarkably, we made the novel observation that Vps45 also contributes to mitochondrial function in that a Vps45-Gfp fusion protein associated with mitotracker, and a vps45 mutant showed enhanced sensitivity to inhibitors of electron transport complexes as well as changes in mitochondrial membrane potential. Consistent with mitochondrial function, the vps45 mutant was impaired in calcium homeostasis. To assess the relevance of these defects for virulence, we examined cell surface properties of the vps45 mutant and found increased sensitivity to agents that challenge cell wall integrity and to antifungal drugs. A change in cell wall properties was consistent with our observation of altered capsule polysaccharide attachment, and with attenuated virulence in a mouse model of cryptococcosis. Overall, our studies reveal a novel role for Vps45-mediated trafficking for iron uptake, mitochondrial function and virulence.}, }
@article {pmid29852093, year = {2018}, author = {Li, Z and You, XL and Wang, LL and Yan, ZT and Zhou, ZY}, title = {Spore morphology and ultrastructure of an Ascosphaera apis strain from the honeybees (Apis mellifera) in southwest China.}, journal = {Mycologia}, volume = {110}, number = {2}, pages = {325-338}, doi = {10.1080/00275514.2018.1442084}, pmid = {29852093}, issn = {1557-2536}, mesh = {Animals ; Bees/*microbiology ; Cell Wall/chemistry ; China ; Chitin/analysis ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Microscopy ; Microscopy, Confocal ; Microscopy, Electron, Transmission ; Onygenales/classification/*cytology/isolation &amp; purification/*ultrastructure ; Organelles/ultrastructure ; Phylogeny ; RNA, Ribosomal, 5.8S ; Sequence Analysis, DNA ; Spores, Fungal/*cytology/*ultrastructure ; }, abstract = {Ascosphaera apis is an intestinally infective, spore-forming, filamentous fungus that infects honeybees and causes deadly chalkbrood disease. Although A. apis has been known for 60 y, little is known about the ultrastructure of the spores. In this study, the fine morphology and ultrastructure of an isolate, A. apis CQ1 from southwest China, was comprehensively identified by transmission electron microscopy, confocal laser scanning microscopy, scanning electron microscopy, and optical microscopy. The high sequence similarity and phylogenetic data based on nuc rDNA ITS1-5.8S-ITS2 (ITS) supported the hypothesis that the CQ1 strain is a new member of the A. apis species. Morphological observation indicated that the mature spores are long ovals with an average size of 2 × 1.2 µm and are tightly packed inside spherical spore balls. More than 10 spore balls that were 8-16 µm in diameter were wrapped and formed a spherical, nearly hyaline spore cyst of 50-60 µm in diameter. Ultrastructural analysis showed that mature spores have two nuclei with distinctly different sizes. A large nucleus with double nuclear membranes was found in the center of the spore, whereas the small nucleus was only one-fifth of the large nucleus volume and was located near the end of the spore. Numerous ribosomes filled the cytoplasm, and many mitochondria with well-defined structures were arranged along the inner spore wall. The spore wall consists of an electron-dense outer surface layer, an electron-lucent layer, and an inner plasma membrane. Chitin is the major component of the spore wall. The germinated spore was observed as an empty spore coat, whereas the protoplasts, including the nuclei, mitochondria, and ribosomes, had been discharged. In addition to these typical fungal spore organelles, an unknown electron-dense regular structure might be the growing mycelium, which was arranged close to the inner spore wall and almost covered the entire wall area.}, }
@article {pmid30445187, year = {2018}, author = {Johnston, IG}, title = {Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells.}, journal = {Molecular plant}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molp.2018.11.002}, pmid = {30445187}, issn = {1752-9867}, abstract = {Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.}, }
@article {pmid28646188, year = {2017}, author = {Wang, J and Xiang, H and Liu, L and Kong, M and Yin, T and Zhao, X}, title = {Mitochondrial haplotypes influence metabolic traits across bovine inter- and intra-species cybrids.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4179}, pmid = {28646188}, issn = {2045-2322}, mesh = {Acids/metabolism ; Animals ; Cattle/*genetics ; DNA, Mitochondrial/genetics ; Female ; Gene Dosage ; Gene Expression Regulation ; Genome, Mitochondrial ; Haplotypes/*genetics ; Hybrid Cells/metabolism ; *Hybridization, Genetic ; Lipids/biosynthesis ; Mitochondria/*genetics/*metabolism ; Organelle Biogenesis ; Oxygen Consumption ; Phylogeny ; *Quantitative Trait, Heritable ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {In bovine species, mitochondrial DNA polymorphisms and their correlation to productive or reproductive performances have been widely reported across breeds and individuals. However, experimental evidence of this correlation has never been provided. In order to identify differences among bovine mtDNA haplotypes, transmitochondrial cybrids were generated, with the nucleus from MAC-T cell line, derived from a Holstein dairy cow (Bos taurus) and mitochondria from either primary cell line derived from a domestic Chinese native beef Luxi cattle breed or central Asian domestic yak (Bos grunniens). Yak primary cells illustrated a stronger metabolic capacity than that of Luxi. However, all yak cybrid parameters illustrated a drop in relative yak mtDNA compared to Luxi mtDNA, in line with a mitonuclear imbalance in yak interspecies cybrid. Luxi has 250 divergent variations relative to the mitogenome of Holsteins. In cybrids there were generally higher rates of oxygen consumption (OCR) and extracellular acidification (ECAR), and lower mRNA expression levels of nuclear-encoded mitochondrial genes, potentially reflecting active energy metabolism and cellular stress resistance. The results demonstrate that functional differences exist between bovine cybrid cells. While cybrid viability was similar between Holstein and Luxi breeds, the mitonuclear mismatch caused a marked metabolic dysfunction in cattle:yak cybrid species.}, }
@article {pmid28798357, year = {2017}, author = {Xiang, H and Gao, J and Cai, D and Luo, Y and Yu, B and Liu, L and Liu, R and Zhou, H and Chen, X and Dun, W and Wang, X and Hofreiter, M and Zhao, X}, title = {Origin and dispersal of early domestic pigs in northern China.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5602}, pmid = {28798357}, issn = {2045-2322}, mesh = {Animals ; Animals, Domestic/*genetics ; China ; DNA, Mitochondrial/genetics ; Domestication ; Evolution, Molecular ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sus scrofa/*genetics ; }, abstract = {It is widely accepted that modern pigs were domesticated independently at least twice, and Chinese native pigs are deemed as direct descendants of the first domesticated pigs in the corresponding domestication centers. By analyzing mitochondrial DNA sequences of an extensive sample set spanning 10,000 years, we find that the earliest pigs from the middle Yellow River region already carried the maternal lineages that are dominant in both younger archaeological populations and modern Chinese pigs. Our data set also supports early Neolithic pig utilization and a long-term in situ origin for northeastern Chinese pigs during 8,000-3,500 BP, suggesting a possibly independent domestication in northeast China. Additionally, we observe a genetic replacement in ancient northeast Chinese pigs since 3,500 BP. The results not only provide increasing evidence for pig origin in the middle Yellow River region but also depict an outline for the process of early pig domestication in northeast China.}, }
@article {pmid30649994, year = {2019}, author = {Kraft, LM and Lackner, LL}, title = {A conserved mechanism for mitochondria-dependent dynein anchoring.}, journal = {Molecular biology of the cell}, volume = {}, number = {}, pages = {mbcE18070466}, doi = {10.1091/mbc.E18-07-0466}, pmid = {30649994}, issn = {1939-4586}, abstract = {Mitochondrial anchors have functions that extend beyond simply positioning mitochondria. In budding yeast, mitochondria drive the assembly of the mitochondrial anchor protein Num1 into clusters, which serve to anchor mitochondria as well as dynein to the cell cortex. Here, we explore a conserved role for mitochondria in dynein anchoring by examining the tethering functions of the evolutionarily distant S. pombe Num1 homolog. In addition to its function in dynein anchoring, we find that S. pombe Num1 interacts with and tethers mitochondria to the plasma membrane in S. pombe and S. cerevisiae. Thus, the mitochondria and plasma membrane binding domains of the Num1 homologs, as well as the membrane features these domains recognize, are conserved. In S. pombe, we find that mitochondria impact the assembly and cellular distribution of Num1 clusters and that Num1 clusters actively engaged in mitochondrial tethering serve as cortical attachment sites for dynein. Thus, mitochondria play a critical and conserved role in the formation and distribution of dynein anchoring sites at the cell cortex and, as a consequence, impact dynein function. These findings shed light on an ancient mechanism of mitochondria-dependent dynein anchoring that is conserved over more than 450 million years of evolution, raising the intriguing possibility that the role mitochondria play in dynein anchoring and function extends beyond yeast to higher eukaryotes.}, }
@article {pmid30114187, year = {2018}, author = {Weiss, MC and Preiner, M and Xavier, JC and Zimorski, V and Martin, WF}, title = {The last universal common ancestor between ancient Earth chemistry and the onset of genetics.}, journal = {PLoS genetics}, volume = {14}, number = {8}, pages = {e1007518}, pmid = {30114187}, issn = {1553-7404}, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Code ; Genome ; Mitochondria/genetics ; Nucleic Acid Conformation ; Origin of Life ; *Phylogeny ; Prokaryotic Cells ; }, abstract = {All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust.}, }
@article {pmid29967381, year = {2018}, author = {Pietras, Z and Wojcik, MA and Borowski, LS and Szewczyk, M and Kulinski, TM and Cysewski, D and Stepien, PP and Dziembowski, A and Szczesny, RJ}, title = {Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2558}, pmid = {29967381}, issn = {2041-1723}, support = {UMO-2014/12/W/NZ1/00463 to RJS//Narodowe Centrum Nauki (National Science Centre)/International ; UMO-2014/13/D/NZ2/01114 to RJS//Narodowe Centrum Nauki (National Science Centre)/International ; UMO-2013/11/13/NZ1/00089 to PPS//Narodowe Centrum Nauki (National Science Centre)/International ; 309419 PAPs &amp; PUPs to AD//EC | European Research Council (ERC)/International ; }, mesh = {Animals ; DEAD-box RNA Helicases/metabolism ; Endoribonucleases/metabolism ; Exoribonucleases/genetics/metabolism ; *G-Quadruplexes ; Genome, Mitochondrial/*genetics ; HEK293 Cells ; HeLa Cells ; Humans ; Mitochondria/genetics/*metabolism ; Multienzyme Complexes/metabolism ; Phylogeny ; Poly(A)-Binding Proteins/genetics/*metabolism ; Polyribonucleotide Nucleotidyltransferase/metabolism ; RNA Helicases/metabolism ; RNA, Small Interfering/metabolism ; RNA, Untranslated/genetics/*metabolism ; }, abstract = {The GC skew in vertebrate mitochondrial genomes results in synthesis of RNAs that are prone to form G-quadruplexes (G4s). Such RNAs, although mostly non-coding, are transcribed at high rates and are degraded by an unknown mechanism. Here we describe a dedicated mechanism of degradation of G4-containing RNAs, which is based on cooperation between mitochondrial degradosome and quasi-RNA recognition motif (qRRM) protein GRSF1. This cooperation prevents accumulation of G4-containing transcripts in human mitochondria. In vitro reconstitution experiments show that GRSF1 promotes G4 melting that facilitates degradosome-mediated decay. Among degradosome and GRSF1 regulated transcripts we identified one that undergoes post-transcriptional modification. We show that GRSF1 proteins form a distinct qRRM group found only in vertebrates. The appearance of GRSF1 coincided with changes in the mitochondrial genome, which allows the emergence of G4-containing RNAs. We propose that GRSF1 appearance is an evolutionary adaptation enabling control of G4 RNA.}, }
@article {pmid28657486, year = {2018}, author = {Suk, HY and Lee, MY and Bae, HG and Lee, SJ and Poyarkov, N and Lee, H and Min, MS}, title = {Phylogenetic structure and ancestry of Korean clawed salamander, Onychodactylus koreanus (Caudata: Hynobiidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {650-658}, doi = {10.1080/24701394.2017.1339187}, pmid = {28657486}, issn = {2470-1408}, mesh = {Animals ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial ; *Genetic Speciation ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Republic of Korea ; Species Specificity ; Urodela/*genetics ; }, abstract = {Onychodactylus koreanus, a hynobiid salamander species endemic to the Korean Peninsula, can be regarded as a strict ecological specialist, probably vulnerable to anthropogenic environmental modifications and climate change. We used mitochondrial cytochrome b gene to analyze the genetic diversity and phylogenetic structure of O. koreanus from 19 populations collected in an attempt to cover its major distribution within South Korea. A total of 76 haplotypes of O. koreanus obtained in our analyses could be subdivided into three phylogenetic clades, KR, NE and SE. Clade KR haplotypes occur in most of the regions throughout the Korean Peninsula with four distinct subclades (KR I-IV). Clade NE and SE haplotypes were only observed in two populations YY and YS, respectively. Haplotype sharing was scarce even among populations in geographical proximity, and most of the populations were represented by a single clade or subclade, indicating the low level of gene flow among populations. O. koreanus likely originated from the historical southward dispersal of its ancestral lineages following divergence from Chinese O. zhaoermii that was recovered as the sister of O. koreanus in our phylogenetic analysis. Our results have critical implications for the taxonomic status of O. koreanus and its long-term management plan.}, }
@article {pmid28595493, year = {2018}, author = {Gu, XB and Wang, BJ and Zhao, XB and Li, YF and Yang, GY and Lai, WM and Zhong, ZJ and Peng, GN}, title = {Genetic variation in mitochondrial cox2 of Heterakis gallinarum from poultry in Sichuan, China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {629-634}, doi = {10.1080/24701394.2017.1334771}, pmid = {28595493}, issn = {2470-1408}, mesh = {Animals ; Ascaridida/*genetics/isolation &amp; purification ; Ascaridida Infections/parasitology ; Base Sequence ; Cecum/parasitology ; China ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/enzymology/*genetics ; Phylogeny ; Poultry ; }, abstract = {Heterakis gallinarum is one of the common parasitic nematodes found in the caecum of poultry. To investigate the genetic diversity and genetic structure of the H. gallinarum population in Sichuan, we amplified and sequenced the complete mitochondrial (mt) cytochrome c oxidase subunit II (cox2) gene of 59 H. gallinarum isolates from seven different geographical regions, then analyzed their genetic polymorphisms. All cox2 genes of the 59 H. gallinarum isolates were 696 bp in length, with an average A + T content of 67.1%. Fifty-nine sequences contained 34 variable sites, and were classified into 23 haplotypes (HS1-HS23). The values of haplotype diversity (Hd) and nucleotide diversity (π) were 0.688 and 0.00288, respectively. Based on values of FST and Nm (FST = 0.01929, Nm = 12.71), there was a frequent gene flow but no significant genetic differentiation observed among the populations. The network map showed that the most prominent haplotype was HS1, and the other haplotypes (HS2-HS23) were centered on HS1 with a star-like topology, indicating that H. gallinarum had previously experienced a population expansion. To our knowledge, this is the first research on the population genetics of H. gallinarum based on mitochondrial cox2.}, }
@article {pmid28573928, year = {2018}, author = {Wang, XC and Chen, H and Yang, D and Liu, C}, title = {Diversity of mitochondrial plastid DNAs (MTPTs) in seed plants.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {635-642}, doi = {10.1080/24701394.2017.1334772}, pmid = {28573928}, issn = {2470-1408}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Variation ; Genome, Mitochondrial ; Genome, Plastid ; Mitochondria/*genetics ; Multigene Family ; Phylogeny ; Plants/classification/*genetics ; Plastids/*genetics ; Seeds/genetics ; }, abstract = {Mitochondrial plastid DNAs (MTPTs) refer to plastid-derived DNA fragments in mitochondrial genomes. While the MTPTs have been described for numerous species, its overall patterns have not been examined in details. Here, we carried out a systematic analysis of MTPTs among 73 plant species, including 28 algae, 1 liverwort, 2 moss, 1 lycophyte, 1 gymnosperm, 1 magnoliid, 12 monocots, 26 eudicots and 1 relic angiosperm Amborella trichopoda. A total of 300 MTPT gene clusters were found in 39 seed plants, which represented 144 MTPT gene cluster types. The detected MTPT gene clusters were evaluated in seven aspects, and they were found to be enriched particularly in monocots and asterids of eudicots. Some MTPT gene clusters were found to be shared by closely related species. All chloroplast genes were found in MTPTs, suggesting that there is no functional relevancy for genes that were transferred. However, after calculation of the frequency of the 115 chloroplast genes, five hot spots and three cold spots were discovered in chloroplast genome. In summary, this study demonstrated the high degree of diversity in MTPTs. The discovered MTPTs would facilitate the accurate assembly of chloroplast and mitochondrial genomes as well as the understanding of organelle genome evolution.}, }
@article {pmid28562139, year = {2018}, author = {Sun, P and Tang, B and Yin, F}, title = {Population genetic structure and genetic diversity of Chinese pomfret at the coast of the East China Sea and the South China Sea.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {643-649}, doi = {10.1080/24701394.2017.1334773}, pmid = {28562139}, issn = {2470-1408}, mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Genetics, Population ; Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; }, abstract = {The Chinese pomfret Pampus chinensis is one of the most economic and ecological important marine fish species in China. In the present study, the population genetic structure and genetic diversity of P. chinensis were evaluated from a total sample size of 180 individuals representing six populations from the East China Sea and the South China Sea using mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 24 variable sites (including 3 singleton sites and 21 parsimony information sites) were observed, and 18 haplotypes were defined. The haplotype diversity (Hd) of the populations ranged from 0.559 to 0.775, and the nucleotide diversity (π) ranged from 0.330 to 1.090%. Analysis of molecular variance (AMOVA) reveals that the main variation (66.02%) was among individuals within populations. The average pairwise differences and ϕST values indicated significant genetic differentiation between Dongxing population and the other populations. The results of the present study are helpful for the sustainable management and utilization of this species.}, }
@article {pmid28539070, year = {2018}, author = {Emami-Khoyi, A and Paterson, AM and Hartley, DA and Boren, LJ and Cruickshank, RH and Ross, JG and Murphy, EC and Else, TA}, title = {Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {567-580}, doi = {10.1080/24701394.2017.1325478}, pmid = {28539070}, issn = {2470-1408}, mesh = {Animals ; Breeding ; *Feeding Behavior ; Fur Seals/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; Population Density ; Recreation ; }, abstract = {The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.}, }
@article {pmid28531368, year = {2018}, author = {Kang, L and Zhang, S and Wu, C and Liu, X and Xu, MY and Jiang, L}, title = {Molecular phylogeny of Loliginidae inferred from mitochondrial DNA sequence variation.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {600-605}, doi = {10.1080/24701394.2017.1325482}, pmid = {28531368}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Decapodiformes/classification/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Genes, Mitochondrial ; *Genetic Variation ; Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Loliginidae includes many economically important species in trophic systems worldwide. Here, we investigated genetic relationships and diversity in this family. Sequence comparisons and phylogenetic analyses revealed considerable variations between mitochondrial 16 S rRNA gene and cytochrome coxidase subunit I gene among nine Loliginid species. We identified three similar non-coding regions in eight Loliginid species, but not in Sepioteuthislessoniana. We detected a single extended termination-associated sequence and three conserved sequence blocks among these eight species. Our results suggest that Loliginidae forms a major lineage, with S. lessoniana located at the most basal position and forming an individual clade as sister to the remaining species. Loligobeka, Loliolusjaponica, Loliolusuyii, Loligochinensis, Loligoedulis, Loligoduvauceli, Loligobleekeri, and Loligoopalescensare clustered into a monophyletic group. We identified repetitive elements and repeat numbers in the control regions.}, }
@article {pmid28524717, year = {2018}, author = {Adhikari, P and Han, SH and Kim, YK and Kim, TW and Thapa, TB and Subedi, N and Adhikari, P and Oh, HS}, title = {First molecular evidence of Mus musculus bactrianus in Nepal inferred from the mitochondrial DNA cytochrome B gene sequences.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {561-566}, doi = {10.1080/24701394.2017.1320994}, pmid = {28524717}, issn = {2470-1408}, mesh = {Animals ; *Biological Evolution ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial ; Mice/classification/*genetics ; Mitochondria/*genetics ; Nepal ; Phylogeny ; }, abstract = {To identify the house mice collected in Pokhara and Lumbini of Nepal at the subspecies level, morphological and molecular analyses were carried out. Morphologically, two populations collected in Pokhara and Lumbini were distinguished by fur colour, but there was no significant difference in external measurements (p > .05). The phylogenetic analysis results revealed that the haplotypes sequences of mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene distinguished into two distinct clades on a phylogenetic tree representing two subspecies, Mus musculus bactrianus and M. m. castaneus in Pokhara and Lumbini, respectively. In Nepal, the subspecies M. m. bactrianus was not reported before this study. These findings concluded that at least two subspecies, M. m. bactrianus and M. m. castaneus currently exist in Nepal. We estimated that these two subspecies could have introduced together with human migration, while further study is required to understand their evolutionary history and current distribution.}, }
@article {pmid28407723, year = {2018}, author = {Huang, Z and Ruan, R}, title = {DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {529-534}, doi = {10.1080/24701394.2017.1315569}, pmid = {28407723}, issn = {2470-1408}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial ; Mitochondria/*enzymology ; Passeriformes/*classification/*genetics ; *Phylogeny ; }, abstract = {DNA barcoding has become a promising tool for species identification and phylogeny in a wide range of animal taxa using mitochondrial cytochrome c oxidase subunit I (COI). The Corvidae (Aves: Passeriformes) is a species rich and morphologically diverse family. In the present study, we analyzed the COI barcodes of 39 species from 12 genera of Corvidae. COI gene was also used to examine phylogenetic relationships of Corvidae. Every species possessed a barcode distinct from that of other species. Kimura two-parameter distances were calculated between species barcodes. The average genetic distance between the species was 22 times higher compared to the average genetic distance within species. Maximum likelihood method was used to construct a phylogenetic tree. All the species could be discriminated by their distinct clades in the phylogenetic tree. COI gene data provided good evidence for the monophyly of the Corvidae. Members of Cyanopica and Pyrrhocorax were the first to split from the Corvidae lineage. Analysis of COI genes supported the others genera fell into two clades. DNA barcoding is an effective molecular tool for Corvidae species identification and phylogenetic inference.}, }
@article {pmid30208839, year = {2018}, author = {Bono, JM and Pigage, HK and Wettstein, PJ and Prosser, SA and Pigage, JC}, title = {Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {139}, pmid = {30208839}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetic Variation ; *Genome ; Geography ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Sciuridae/*genetics ; }, abstract = {BACKGROUND: Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert's squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested.<br><br>RESULTS: We used RAD-seq to unravel the complex evolutionary history of the Abert's squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon.<br><br>CONCLUSIONS: Overall, the evolutionary history of Abert's squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories.}, }
@article {pmid29950599, year = {2018}, author = {Burgstaller, JP and Kolbe, T and Havlicek, V and Hembach, S and Poulton, J and Piálek, J and Steinborn, R and Rülicke, T and Brem, G and Jones, NS and Johnston, IG}, title = {Large-scale genetic analysis reveals mammalian mtDNA heteroplasmy dynamics and variance increase through lifetimes and generations.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2488}, doi = {10.1038/s41467-018-04797-2}, pmid = {29950599}, issn = {2041-1723}, support = {MR/J013617/1//Medical Research Council/United Kingdom ; }, mesh = {Age Factors ; Animals ; DNA Copy Number Variations/*genetics ; DNA, Mitochondrial/*genetics ; Datasets as Topic ; Female ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Mice ; Mice, Inbred C57BL ; Mitochondria/metabolism ; Models, Animal ; Oocytes/cytology/immunology ; }, abstract = {Vital mitochondrial DNA (mtDNA) populations exist in cells and may consist of heteroplasmic mixtures of mtDNA types. The evolution of these heteroplasmic populations through development, ageing, and generations is central to genetic diseases, but is poorly understood in mammals. Here we dissect these population dynamics using a dataset of unprecedented size and temporal span, comprising 1947 single-cell oocyte and 899 somatic measurements of heteroplasmy change throughout lifetimes and generations in two genetically distinct mouse models. We provide a novel and detailed quantitative characterisation of the linear increase in heteroplasmy variance throughout mammalian life courses in oocytes and pups. We find that differences in mean heteroplasmy are induced between generations, and the heteroplasmy of germline and somatic precursors diverge early in development, with a haplotype-specific direction of segregation. We develop stochastic theory predicting the implications of these dynamics for ageing and disease manifestation and discuss its application to human mtDNA dynamics.}, }
@article {pmid29385875, year = {2018}, author = {Mustafa, SI and Schwarzacher, T and Heslop-Harrison, JS}, title = {Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {8}, pages = {1180-1193}, doi = {10.1080/24701394.2018.1431226}, pmid = {29385875}, issn = {2470-1408}, mesh = {Animals ; Breeding ; Centromere/*genetics ; *Evolution, Molecular ; Female ; *Genetic Speciation ; *Genome, Mitochondrial ; Male ; Polymorphism, Single Nucleotide ; Sex Chromosomes/genetics ; Sheep/*genetics ; }, abstract = {The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the 'Fertile Crescent'. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (Capra) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (numts). In situ hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of numts, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, numts and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.}, }
@article {pmid28667281, year = {2017}, author = {Yang, F and Jiang, Y and Yang, D and Liu, X}, title = {Mitochondrial genomes of two Australian fishflies with an evolutionary timescale of Chauliodinae.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4481}, pmid = {28667281}, issn = {2045-2322}, mesh = {Animals ; Australia ; Base Composition ; Codon ; Computational Biology/methods ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Genomics/methods ; Insecta/*classification/*genetics ; Mitochondria/genetics ; Nucleic Acid Conformation ; Phylogeny ; }, abstract = {Fishflies (Corydalidae: Chauliodinae) with a total of ca. 130 extant species are one of the major groups of the holometabolous insect order Megaloptera. As a group which originated during the Mesozoic, the phylogeny and historical biogeography of fishflies are of high interest. The previous hypothesis on the evolutionary history of fishflies was based primarily on morphological data. To further test the existing phylogenetic relationships and to understand the divergence pattern of fishflies, we conducted a molecule-based study. We determined the complete mitochondrial (mt) genomes of two Australian fishfly species, Archichauliodes deceptor Kimmins, 1954 and Protochauliodes biconicus Kimmins, 1954, both members of a major subgroup of Chauliodinae with high phylogenetic significance. A phylogenomic analysis was carried out based on 13 mt protein coding genes (PCGs) and two rRNAs genes from the megalopteran species with determined mt genomes. Both maximum likelihood and Bayesian inference analyses recovered the Dysmicohermes clade as the sister group of the Archichauliodes clade + the Protochauliodes clade, which is consistent with the previous morphology-based hypothesis. The divergence time estimation suggested that the divergence among the three major subgroups of fishflies occurred during the Late Jurassic and Early Cretaceous when the supercontinent Pangaea was undergoing sequential breakup.}, }
@article {pmid30621777, year = {2018}, author = {Lynch, M and Marinov, GK}, title = {Response to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {26}, doi = {10.1186/s13062-018-0228-3}, pmid = {30621777}, issn = {1745-6150}, abstract = {A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mitochondrion endowed eukaryotic cells with energetic superiority over prokaryotes. The former point has been addressed previously, with no resultant changes in the conclusions, and the latter point remains inconsistent with multiple lines of empirical data.}, }
@article {pmid28655921, year = {2017}, author = {Liu, H and Li, H and Song, F and Gu, W and Feng, J and Cai, W and Shao, R}, title = {Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4284}, pmid = {28655921}, issn = {2045-2322}, mesh = {Animals ; Evolution, Molecular ; *Gene Rearrangement ; Genes, Mitochondrial ; Genome, Mitochondrial ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Thysanoptera/classification/*genetics ; }, abstract = {We sequenced the mitochondrial (mt) genome of the grass thrips, Anaphothrips obscurus, which is highly rearranged and differs from the four thrips species reported previously in the arrangement of both tRNA genes and a protein-coding gene, nad3, and in the copy number of the control region (CR). We reconstructed the phylogeny of the thrips with mt genome sequences, and used it as a framework to gain insights into mt genome evolution in thrips. It is evident that A. obscurus is less rearranged in mt genome organization than the other four known thrips. nad3 is in its ancestral location in A. obscurus but was translocated in other four thrips. Also, A. obscurus has one CR, which is ancestral to hexapods whereas other thrips have two or three CRs. All of the five thrips whose mt genomes have been sequenced to date are from the subfamily Thripinae, which represents about a quarter of the species richness in the order Thysanoptera. The high variation in mt genome organization observed in a subfamily challenges our knowledge about animal mt genomes. It remains to be investigated why mt genomes evolved so fast in the subfamily Thripinae and how mt genomes evolved in other lineages of thrips.}, }
@article {pmid28655915, year = {2017}, author = {Bernardino, AF and Li, Y and Smith, CR and Halanych, KM}, title = {Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4295}, pmid = {28655915}, issn = {2045-2322}, mesh = {Animals ; Annelida/classification/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Introns ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Wood falls provide episodic fluxes of energy to the sea floor that are degraded by a species-rich benthic fauna. Part of this rich diversity includes annelid polychaetes but unfortunately, our understanding of such fauna is limited and their genetic variability and evolutionary origins remain poorly known. In this study, we sequenced complete mitochondrial genomes from three congeneric Decemunciger (Ampharetidae) individuals that had colonized multiple wood falls in the deep (~1600 m) NE Pacific Ocean. Mitochondrial gene order within Decemunciger was similar to the three other available Terebellomorpha genomes, consistent with the relatively conserved nature of mitochondrial genomes within annelids. Unexpectedly, we found introns within the cox1, nad1 and nad4 genes of all three genomes assembled. This is the greatest number of introns observed in annelid mtDNA genomes, and possibly in bilaterians. Interestingly, the introns were of variable sizes suggesting possible evolutionary differences in the age and origins of introns. The sequence of the introns within cox1 is similar to Group II introns previously identified, suggesting that introns in the mitochondrial genome of annelids may be more widespread then realized. Phylogenetically, Decemunciger appears to be a sister clade among current vent and seep deep-sea Ampharetinae.}, }
@article {pmid30612859, year = {2018}, author = {Adlakha, J and Karamichali, I and Sangwallek, J and Deiss, S and Bär, K and Coles, M and Hartmann, MD and Lupas, AN and Hernandez Alvarez, B}, title = {Characterization of MCU-Binding Proteins MCUR1 and CCDC90B - Representatives of a Protein Family Conserved in Prokaryotes and Eukaryotic Organelles.}, journal = {Structure (London, England : 1993)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.str.2018.11.004}, pmid = {30612859}, issn = {1878-4186}, abstract = {Membrane-bound coiled-coil proteins are important mediators of signaling, fusion, and scaffolding. Here, we delineate a heterogeneous group of trimeric membrane-anchored proteins in prokaryotes and eukaryotic organelles with a characteristic head-neck-stalk-anchor architecture, in which a membrane-anchored coiled-coil stalk projects an N-terminal head domain via a β-layer neck. Based on sequence analysis, we identify different types of head domains and determine crystal structures of two representatives, the archaeal protein Kcr-0859 and the human CCDC90B, which possesses the most widespread head type. Using mitochondrial calcium uniporter regulator 1 (MCUR1), the functionally characterized paralog of CCDC90B, we study the role of individual domains, and find that the head interacts directly with the mitochondrial calcium uniporter (MCU) and is destabilized upon Ca2+ binding. Our data provide structural details of a class of membrane-bound coiled-coil proteins and identify the conserved head domain of the most widespread type as a mediator of their function.}, }
@article {pmid30204084, year = {2018}, author = {Seidi, A and Muellner-Wong, LS and Rajendran, E and Tjhin, ET and Dagley, LF and Aw, VY and Faou, P and Webb, AI and Tonkin, CJ and van Dooren, GG}, title = {Elucidating the mitochondrial proteome of Toxoplasma gondii reveals the presence of a divergent cytochrome c oxidase.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30204084}, issn = {2050-084X}, support = {DP110103144//Australian Research Council/International ; }, mesh = {Animals ; Biotinylation ; Computational Biology ; Electron Transport Complex IV/*metabolism ; Gene Knockdown Techniques ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; Oxygen Consumption ; Parasites/growth &amp; development/metabolism ; Phenotype ; Phylogeny ; Proteome/*metabolism ; Proteomics ; Protozoan Proteins/metabolism ; Toxoplasma/growth &amp; development/*metabolism ; }, abstract = {The mitochondrion of apicomplexan parasites is critical for parasite survival, although the full complement of proteins that localize to this organelle has not been defined. Here we undertake two independent approaches to elucidate the mitochondrial proteome of the apicomplexan Toxoplasma gondii. We identify approximately 400 mitochondrial proteins, many of which lack homologs in the animals that these parasites infect, and most of which are important for parasite growth. We demonstrate that one such protein, termed TgApiCox25, is an important component of the parasite cytochrome c oxidase (COX) complex. We identify numerous other apicomplexan-specific components of COX, and conclude that apicomplexan COX, and apicomplexan mitochondria more generally, differ substantially in their protein composition from the hosts they infect. Our study highlights the diversity that exists in mitochondrial proteomes across the eukaryotic domain of life, and provides a foundation for defining unique aspects of mitochondrial biology in an important phylum of parasites.}, }
@article {pmid29656105, year = {2018}, author = {Dias, C and Lima, KA and Araripe, J and Aleixo, A and Vallinoto, M and Sampaio, I and Schneider, H and Rêgo, PSD}, title = {Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae).}, journal = {Molecular phylogenetics and evolution}, volume = {126}, number = {}, pages = {314-320}, doi = {10.1016/j.ympev.2018.04.017}, pmid = {29656105}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Passeriformes/*classification/*genetics ; *Phylogeny ; }, abstract = {Lepidothrix is the most diverse genus of the family Pipridae, with eight recognized species. Although the genus' monophyly has been supported by both molecular and morphological characters, phylogenetic relationships and species limits within Lepidothrix remain uncertain. In the present study, we combined molecular sequences of mitochondrial (ND2 and COI) and nuclear (MYO, G3PDh and I5BF) markers in a multilocus analysis, to evaluate relationships and inter-specific limits among L. iris, L. nattereri, and L. vilasboasi, which are known to hybridize in eastern Amazonia. The results revealed a complex pattern, whereby events of secondary contact and gene flow after isolation and genetic and phenotypic differentiation prevented the recuperation of reciprocal monophyly among the studied taxa. The mitochondrial data indicate that L. nattereri is divided into two non-sister groups, one monophyletic, and the other, paraphyletic, with L. iris iris being more closely related to one of the two L. nattereri groups, while L. iris eucephala forms an undifferentiated clade with L. vilasboasi, probably resulting from an extensive process of mitochondrial introgression. In agreement with a previous study based on Single Nucleotide Polymorphism (SNP) data, mitochondrial haplotype networks also support that L. vilasboasi does not represent a recent &quot;hybrid swarm&quot; between L. iris and L. nattereri, but instead a genetically divergent lineage with a separate species status. Finally, the sister relationship recovered herein between L. iris iris and some western populations of L. nattereri currently in allopatry is also apparently explained by mitochondrial introgression, as also supported for nuclear genes by SNP data, indicating a complex scenario of past contact and gene flow between currently geographically distant Lepidothrix lineages.}, }
@article {pmid29524652, year = {2018}, author = {Berriman, JS and Ellingson, RA and Awbrey, JD and Rico, DM and Valdés, ÁA and Wilson, NG and Aguilar, A and Herbert, DG and Hirano, YM and Trowbridge, CD and Krug, PJ}, title = {A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume &quot;killer algae&quot;.}, journal = {Molecular phylogenetics and evolution}, volume = {126}, number = {}, pages = {356-370}, pmid = {29524652}, issn = {1095-9513}, support = {R25 GM061331/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Biodiversity ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Eukaryota/*physiology ; Gastropoda/*physiology ; Genetic Variation ; Haplotypes/genetics ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; Tooth/*physiology ; }, abstract = {Predicting biotic resistance to highly invasive strains of &quot;killer algae&quot; (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.}, }
@article {pmid28607415, year = {2017}, author = {Hofmann, S and Stöck, M and Zheng, Y and Ficetola, FG and Li, JT and Scheidt, U and Schmidt, J}, title = {Molecular Phylogenies indicate a Paleo-Tibetan Origin of Himalayan Lazy Toads (Scutiger).}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3308}, pmid = {28607415}, issn = {2045-2322}, mesh = {Animals ; Anura/*classification ; Calibration ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Geography ; Mitochondria/genetics ; *Phylogeny ; Tibet ; Time Factors ; }, abstract = {The Himalaya presents an outstanding geologically active orogen and biodiversity hotspot. However, our understanding of the historical biogeography of its fauna is far from comprehensive. Many taxa are commonly assumed to have originated from China-Indochina and dispersed westward along the Himalayan chain. Alternatively, the &quot;Tibetan-origin hypothesis&quot; suggests primary diversification of lineages in Paleo-Tibet, and secondary diversification along the slopes of the later uplifted Greater Himalaya. We test these hypotheses in high-mountain megophryid anurans (Scutiger). Extensive sampling from High Asia, and analyses of mitochondrial (2839 bp) and nuclear DNA (2208 bp), using Bayesian and Maximum likelihood phylogenetics, suggest that the Himalayan species form a distinct clade, possibly older than those from the eastern Himalaya-Tibet orogen. While immigration from China-Indochina cannot be excluded, our data may indicate that Himalayan Scutiger originated to the north of the Himalaya by colonization from Paleo-Tibet and then date back to the Oligocene. High intraspecific diversity of Scutiger implies limited migration across mountains and drainages along the Himalaya. While our study strengthens support for a &quot;Tibetan-origin hypothesis&quot;, current sampling (10/22 species; 1 revalidated: S. occidentalis) remains insufficient to draw final conclusions on Scutiger but urges comparative phylogeographers to test alternative, geologically supported hypotheses for a true future understanding of Himalayan biogeography.}, }
@article {pmid30612363, year = {2019}, author = {Jelassi, R and Khemaissia, H and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K}, title = {Ecotoxicological effects of trace element contamination in talitrid amphipod Orchestia montagui Audouin, 1826.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-018-3974-y}, pmid = {30612363}, issn = {1614-7499}, abstract = {This study deals with the evaluation of trace element bioaccumulation and histological alterations in the hepatopancreas of the supralittoral amphipod Orchestia montagui Audouin, 1826 due to the exposure to cadmium, copper, and zinc. Orchestia montagui individuals were maintained during 14 days in soils contaminated with different trace elements namely cadmium, copper, and zinc; a control was also prepared. Our results show that the mortality and the body mass vary according to the metal and the nominal concentration used. In general, the mortality increases from the seventh day. However, the body mass shows a decrease with cadmium exposure and an increase with copper and zinc exposures. Furthermore, the concentration factor highlights that this species is considered a macroconcentrator for copper and zinc. The hepatopancreas of unexposed and exposed animals were compared to detect histological changes. Our results show significant alterations in the hepatopancreas of the exposed animals after the experiment. The degree of these alterations was found to be dose-dependent. Among the histological changes in the hepatopancreas in O. montagui, a loss of cell structure was noted, especially cell remoteness and border lyses, the reduction of nuclear volume, an increase in the cytoplasm density with the presence of trace element deposits in both the nucleus and vacuoles, a disorganization and destruction of microvilli, and a condensation of the majority of cell organelles and mitochondria swelling. Through this study, we have confirmed that O. montagui can be a relevant model to assess trace metal element pollution in Tunisian coastal lagoons with the aim of using it in future biomonitoring programs.}, }
@article {pmid30280695, year = {2018}, author = {Önder, Z and İnci, A and Yıldırım, A and Çiloğlu, A and Düzlü, Ö}, title = {Molecular Characterization of Myiasis-Causing Moth Flies (Diptera: Psychodidae).}, journal = {Turkiye parazitolojii dergisi}, volume = {42}, number = {3}, pages = {223-228}, doi = {10.5152/tpd.2018.5943}, pmid = {30280695}, issn = {2146-3077}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry ; Mitochondria/genetics ; Myiasis/*parasitology ; Phylogeny ; Psychodidae/classification/*genetics ; Sequence Alignment ; Turkey ; }, abstract = {OBJECTIVE: The aim of this study is to examine the molecular characterization of moth flies (Diptera: Psychodidae) based on their mitochondrial DNA sequences and determine the vectorial potential and damage caused by moth flies in future researches.<br><br>METHODS: A total of 240 adult moth flies were collected from toilet, bathroom, and basement walls of houses from different locations of the Kayseri region between May 2016 and April 2017. The polymerase chain reaction (PCR) analyses were performed using primer pairs, specificaly targeting the mitochondrial cytochrome oxidase c subunit I (mt-COI) gene of adult flies.<br><br>RESULTS: In total, five isolates were gel purified and sequenced for molecular characterization and phylogenetic analyses. Two species, namely Telmatoscopus albipunctatus (ERU-Telmatos3 and ERU-Telmatos6) and Psychodidae sp. (ERU-Psycho1,4,5), were successfully identified with the sequence alignment of isolates. According to the phylogenetic analysis, it was determined that the ERU-Telmatos3 and ERU-Telmatos6 isolates are clustered in the haplogroup A, while the ERU-Psycho1,4,5 isolate was clustered within the haplogroup B. The ERU-Psycho1 isolate was characterized as a new haplotype within the haplogroup B.<br><br>CONCLUSION: This study represents the first molecular characterization and phylogenetic status of moth flies in Turkey. The obtained findings should be the first step in the future investigation based on detecting the transmission of bacterial pathogens by moth flies.}, }
@article {pmid30604579, year = {2019}, author = {Huang, S and Braun, HP and Gawryluk, RMR and Millar, AH}, title = {Mitochondrial complex II of plants: subunit composition, assembly and function in respiration and signaling.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.14227}, pmid = {30604579}, issn = {1365-313X}, abstract = {Complex II (succinate dehydrogenase [succinate-ubiquinone oxidoreductase]; EC 1.3.5.1; SDH) is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. Complex II in plants is considered unusual due to its accessory subunits (SDH5-8) in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1-4). Here we review compositional and phylogenetic analysis, and biochemical dissection studies to clarify the presence and to propose the role of these subunits. We also consider the wider functional and phylogenetic evidence for SDH assembly factors and the reports from plants on the control of SDH1 flavination and SDH1-SDH2 interaction. Plant Complex II has been shown to influence stomatal opening, the plant defence response and reactive oxygen species-dependent stress responses. Signalling molecules such as salicyclic acid (SA) and nitric oxide (NO) are also reported to interact with the UQ binding site of SDH, influencing signalling transduction in plants. Future directions for SDH research in plants and the specific roles of its different subunits and assembly factors are suggested, including the potential for reverse electron transport to explain succinate-dependent ROS production in plants and new avenues to explore plant mitochondrial Complex II evolution and its utility. This article is protected by copyright. All rights reserved.}, }
@article {pmid30598556, year = {2018}, author = {Rathore, S and Berndtsson, J and Marin-Buera, L and Conrad, J and Carroni, M and Brzezinski, P and Ott, M}, title = {Cryo-EM structure of the yeast respiratory supercomplex.}, journal = {Nature structural &amp; molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41594-018-0169-7}, pmid = {30598556}, issn = {1545-9985}, abstract = {Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III2IV and III2IV2, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.}, }
@article {pmid30598467, year = {2018}, author = {Clergeot, PH and Rode, NO and Glémin, S and Brandström-Durling, M and Ihrmark, K and Olson, Å}, title = {Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1534/genetics.118.301855}, pmid = {30598467}, issn = {1943-2631}, abstract = {Many eukaryote species including taxa such as fungi or algae have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance, a measure that accounts for these two effects, should be close to 0.5 in these species. They also predict that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum, a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.}, }
@article {pmid30595847, year = {2018}, author = {Su-Keene, EJ and Bonilla, MM and Padua, MV and Zeh, DW and Zeh, JA}, title = {Simulated climate warming and mitochondrial haplogroup modulate testicular small non-coding RNA expression in the neotropical pseudoscorpion, Cordylochernes scorpioides.}, journal = {Environmental epigenetics}, volume = {4}, number = {4}, pages = {dvy027}, doi = {10.1093/eep/dvy027}, pmid = {30595847}, issn = {2058-5888}, abstract = {Recent theory suggests that tropical terrestrial arthropods are at significant risk from climate warming. Metabolic rate in such ectothermic species increases exponentially with environmental temperature, and a small temperature increase in a hot environment can therefore have a greater physiological impact than a large temperature increase in a cool environment. In two recent studies of the neotropical pseudoscorpion, Cordylochernes scorpioides, simulated climate warming significantly decreased survival, body size and level of sexual dimorphism. However, these effects were minor compared with catastrophic consequences for male fertility and female fecundity, identifying reproduction as the life stage most vulnerable to climate warming. Here, we examine the effects of chronic high-temperature exposure on epigenetic regulation in C. scorpioides in the context of naturally occurring variation in mitochondrial DNA. Epigenetic mechanisms, including DNA methylation, histone modifications and small non-coding RNA (sncRNA) expression, are particularly sensitive to environmental factors such as temperature, which can induce changes in epigenetic states and phenotypes that may be heritable across generations. Our results indicate that exposure of male pseudoscorpions to elevated temperature significantly altered the expression of >60 sncRNAs in testicular tissue, specifically microRNAs and piwi-interacting RNAs. Mitochondrial haplogroup was also a significant factor influencing both sncRNAs and mitochondrial gene expression. These findings demonstrate that chronic heat stress causes changes in epigenetic profiles that may account for reproductive dysfunction in C. scorpioides males. Moreover, through its effects on epigenetic regulation, mitochondrial DNA polymorphism may provide the potential for an adaptive evolutionary response to climate warming.}, }
@article {pmid30592713, year = {2018}, author = {DiMaio, J and Ruthel, G and Cannon, JJ and Malfara, MF and Povelones, ML}, title = {The single mitochondrion of the kinetoplastid parasite Crithidia fasciculata is a dynamic network.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0202711}, doi = {10.1371/journal.pone.0202711}, pmid = {30592713}, issn = {1932-6203}, abstract = {Mitochondria are central organelles in cellular metabolism. Their structure is highly dynamic, allowing them to adapt to different energy requirements, to be partitioned during cell division, and to maintain functionality. Mitochondrial dynamics, including membrane fusion and fission reactions, are well studied in yeast and mammals but it is not known if these processes are conserved throughout eukaryotic evolution. Kinetoplastid parasites are some of the earliest-diverging eukaryotes to retain a mitochondrion. Each cell has only a single mitochondrial organelle, making them an interesting model for the role of dynamics in controlling mitochondrial architecture. We have investigated the mitochondrial division cycle in the kinetoplastid Crithidia fasciculata. The majority of mitochondrial biogenesis occurs during the G1 phase of the cell cycle, and the mitochondrion is divided symmetrically in a process coincident with cytokinesis. Live cell imaging revealed that the mitochondrion is highly dynamic, with frequent changes in the topology of the branched network. These remodeling reactions include tubule fission, fusion, and sliding, as well as new tubule formation. We hypothesize that the function of this dynamic remodeling is to homogenize mitochondrial contents and to facilitate rapid transport of mitochondria-encoded gene products from the area containing the mitochondrial nucleoid to other parts of the organelle.}, }
@article {pmid30592414, year = {2018}, author = {Li, J and Liu, X and Zhang, H and Ge, X and Tang, Y and Xu, Z and Tian, L and Yuan, X and Mao, X and Liu, Z}, title = {Ferrocenyl-Triphenyltin Complexes as Lysosome-Targeted Imaging and Anticancer Agents.}, journal = {Inorganic chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.inorgchem.8b03305}, pmid = {30592414}, issn = {1520-510X}, abstract = {In this paper, two ferrocenyl-triphenyltin complexes were synthesized and characterized. Complex 2 is constructed as new multifunctional therapeutic platform for lysosome-targeted imaging and displayed much higher cytotoxicity than its analogue 1 by the introduction of a methyl group instead of a hydrogen atom in acylhydrazone. The cyclic voltammograms and reaction with GSH (glutathione) further confirmed that complex 1 has a reversible redox peak and can react with GSH, which indicate that complex 1 might lose its anticancer effect by undergoing reaction with GSH once it enters the cancer cell. Complex 2 could effectively catalyze the oxidation of NADH (the reduced form of nicotinamide adenine dinucleotide) to NAD+ and induce the production of reactive oxygen species (ROS), lead to caspase-dependent apoptosis through damaged mitochondria, simultaneously, accounting for the mitochondrial vacuolization and karyorrhexis. The caspase-3 activation and cytoplasmic vacuolation karyorrhexis induced by complex 2 revealed that the A549 cell lines might undergo cell death primarily mediated by apoptosis and oncosis; however, 1 cannot reproduce this effect. Taken together, these results indicated that complex 2 has more potential for evolution as a new bioimaging and anticancer agent.}, }
@article {pmid30590727, year = {2018}, author = {Tsitsekian, D and Daras, G and Alatzas, A and Templalexis, D and Hatzopoulos, P and Rigas, S}, title = {Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/ery440}, pmid = {30590727}, issn = {1460-2431}, abstract = {The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.}, }
@article {pmid30588726, year = {2018}, author = {Hill, GE and Havird, JC and Sloan, DB and Burton, RS and Greening, C and Dowling, DK}, title = {Assessing the fitness consequences of mitonuclear interactions in natural populations.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.12493}, pmid = {30588726}, issn = {1469-185X}, support = {FT160100022, DP170100165, DE170100310//Australian Research Council/ ; HSF 15/2//Hermon Slade Foundation/ ; R01 GM118046//National Institutes of Health (NIH)/ ; DEB1551466//National Science Foundation (NSF)/ ; }, abstract = {Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.}, }
@article {pmid30059499, year = {2018}, author = {Gao, B and Peng, C and Chen, Q and Zhang, J and Shi, Q}, title = {Mitochondrial genome sequencing of a vermivorous cone snail Conus quercinus supports the correlative analysis between phylogenetic relationships and dietary types of Conus species.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0193053}, pmid = {30059499}, issn = {1932-6203}, mesh = {Animals ; Annelida ; Base Composition ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; Conotoxins/*genetics ; Conus Snail/classification/*genetics ; Food Chain ; Gene Ontology ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Transfer/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Tandem Repeat Sequences ; }, abstract = {Complete mitochondrial genome (mitogenome) sequence of a worm-hunting cone snail, Conus quercinus, was reported in this study. Its mitogenome, the longest one (16,460 bp) among reported Conus specie, is composed of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one D-loop region. The mitochondrial gene arrangement is highly-conserved and identical to other reported. However, the D-loop region of C. quercinus is the longest (943 bp) with the higher A+T content (71.3%) and a long AT tandem repeat stretch (68 bp). Subsequent phylogenetic analysis demonstrated that three different dietary types (vermivorous, molluscivorous and piscivorous) of cone snails are clustered separately, suggesting that the phylogenetics of cone snails is related to their dietary types. In conclusion, our current work improves our understanding of the mitogenomic structure and evolutionary status of the vermivorous C. quercinus, which support the putative hypothesis that the Conus ancestor was vermivorous.}, }
@article {pmid29904051, year = {2018}, author = {Chen, N and Cai, Y and Chen, Q and Li, R and Wang, K and Huang, Y and Hu, S and Huang, S and Zhang, H and Zheng, Z and Song, W and Ma, Z and Ma, Y and Dang, R and Zhang, Z and Xu, L and Jia, Y and Liu, S and Yue, X and Deng, W and Zhang, X and Sun, Z and Lan, X and Han, J and Chen, H and Bradley, DG and Jiang, Y and Lei, C}, title = {Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2337}, pmid = {29904051}, issn = {2041-1723}, support = {31501918//National Natural Science Foundation of China (National Science Foundation of China)/International ; }, mesh = {Animals ; *Breeding ; Cattle/*genetics ; China ; Chromosomes/ultrastructure ; Domestication ; Female ; Genetic Variation ; *Genetics, Population ; *Genome ; Geography ; Haplotypes ; Male ; Mitochondria ; Models, Statistical ; Phylogeny ; Polymorphism, Single Nucleotide ; Species Specificity ; Tibet ; }, abstract = {Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6-49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.}, }
@article {pmid30570818, year = {2018}, author = {Williams, AM and Friso, G and van Wijk, KJ and Sloan, DB}, title = {Extreme variation in rates of evolution in the plastid Clp protease complex.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.14208}, pmid = {30570818}, issn = {1365-313X}, abstract = {Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multisubunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. The clpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history of clpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find that clpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g., loss of introns and RNA-editing sites) within seed plants. Although clpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genus Silene, which has highly elevated and heterogeneous rates of clpP1 evolution. We confirmed that clpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergent Silene species. Additionally, there is a tight correlation between amino-acid substitution rates in clpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting ongoing selection on interactions within this complex. This article is protected by copyright. All rights reserved.}, }
@article {pmid30565720, year = {2018}, author = {Morsi, M and Kobeissy, F and Magdeldin, S and Maher, A and Aboelmagd, O and Johar, D and Bernstein, L}, title = {A shared comparison of diabetes mellitus and neurodegenerative disorders.}, journal = {Journal of cellular biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/jcb.28094}, pmid = {30565720}, issn = {1097-4644}, abstract = {Diabetes mellitus (DM), one of the most prevalent metabolic diseases in the world population, is associated with a number of comorbid conditions including obesity, pancreatic endocrine changes, and renal and cardio-cerebrovascular alterations, coupled with peripheral neuropathy and neurodegenerative disease, some of these disorders are bundled into metabolic syndrome. Type 1 DM (T1DM) is an autoimmune disease that destroys the insulin-secreting islet cells. Type 2 DM (T2DM) is diabetes that is associated with an imbalance in the glucagon/insulin homeostasis that leads to the formation of amyloid deposits in the brain, pancreatic islet cells, and possibly in the kidney glomerulus. There are several layers of molecular pathologic alterations that contribute to the DM metabolic pathophysiology and its associated neuropathic manifestations. In this review, we describe the general signature metabolic features of DM and the cross-talk with neurodegeneration. We will assess the underlying molecular key players associated with DM-induced neuropathic disorders that are associated with both T1DM and T2DM. In this context, we will highlight the role of tau and amyloid protein deposits in the brain as well in the pancreatic islet cells, and possibly in the kidney glomerulus. Furthermore, we will discuss the central role of mitochondria, oxidative stress, and the unfolded protein response in mediating the DM-associated neuropathic degeneration. This study will elucidate the relationship between DM and neurodegeneration which may account for the evolution of other neurodegenerative diseases, particularly Alzheimer's disease and Parkinson's disease as discussed later.}, }
@article {pmid30563833, year = {2018}, author = {Wynn, EL and Christensen, AC}, title = {Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1534/g3.118.200948}, pmid = {30563833}, issn = {2160-1836}, abstract = {Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are not well-conserved between species, and are not always annotated in mitochondrial sequence assemblies. We systematically identified and compared these repeats, which are important clues to mechanisms of DNA maintenance in mitochondria. We developed a tool to find and curate non-tandem repeats larger than 50bp and analyzed the complete mitochondrial sequences from 157 plant species. We observed an interesting difference between taxa: the repeats are larger and more frequent in the vascular plants. Analysis of closely related species also shows that plant mitochondrial genomes evolve in dramatic bursts of breakage and rejoining, complete with DNA sequence gain and loss. We suggest an adaptive explanation for the existence of the repeats and their evolution.}, }
@article {pmid30563453, year = {2018}, author = {Harman, A and Barth, C}, title = {The Dictyostelium discoideum homologue of Twinkle, Twm1, is a mitochondrial DNA helicase, an active primase and promotes mitochondrial DNA replication.}, journal = {BMC molecular biology}, volume = {19}, number = {1}, pages = {12}, doi = {10.1186/s12867-018-0114-7}, pmid = {30563453}, issn = {1471-2199}, abstract = {BACKGROUND: DNA replication requires contributions from various proteins, such as DNA helicases; in mitochondria Twinkle is important for maintaining and replicating mitochondrial DNA. Twinkle helicases are predicted to also possess primase activity, as has been shown in plants; however this activity appears to have been lost in metazoans. Given this, the study of Twinkle in other organisms is required to better understand the evolution of this family and the roles it performs within mitochondria.<br><br>RESULTS: Here we describe the characterization of a Twinkle homologue, Twm1, in the amoeba Dictyostelium discoideum, a model organism for mitochondrial genetics and disease. We show that Twm1 is important for mitochondrial function as it maintains mitochondrial DNA copy number in vivo. Twm1 is a helicase which unwinds DNA resembling open forks, although it can act upon substrates with a single 3' overhang, albeit less efficiently. Furthermore, unlike human Twinkle, Twm1 has primase activity in vitro. Finally, using a novel in bacterio approach, we demonstrated that Twm1 promotes DNA replication.<br><br>CONCLUSIONS: We conclude that Twm1 is a replicative mitochondrial DNA helicase which is capable of priming DNA for replication. Our results also suggest that non-metazoan Twinkle could function in the initiation of mitochondrial DNA replication. While further work is required, this study has illuminated several alternative processes of mitochondrial DNA maintenance which might also be performed by the Twinkle family of helicases.}, }
@article {pmid30313490, year = {2018}, author = {Katoh, TK and Zhang, G and Zhou, CJ and Gao, JJ}, title = {Taxonomy of the Hirtodrosophila melanderi species group (Diptera: Drosophilidae), with descriptions of four new species from southwestern China.}, journal = {Zootaxa}, volume = {4422}, number = {3}, pages = {345-365}, doi = {10.11646/zootaxa.4422.3.2}, pmid = {30313490}, issn = {1175-5334}, mesh = {Animals ; China ; *Diptera ; *Drosophilidae ; Mitochondria ; Phylogeny ; Tibet ; }, abstract = {The Hirtodrosophila melanderi species group contains nine known species recorded from either the Old or the New World. All these species were thought to be strict fungivorous drosophilids. In the present study, we give supplementary descriptions for three of these known species, all recorded from Yunnan, southwestern China, H. furcapenis, H. furcapenisoides, and H. longifurcapenis, by examining respective type specimen(s). We then describe four new species of the same group, H. seticlasper Katoh Gao, sp. nov., H. spinicerca Katoh Gao, sp. nov., H. serratifurcapenis Katoh Gao, sp. nov., and H. truncifurca Katoh Gao, sp. nov., all discovered recently from high altitudes (ca. 3,500 to 3,800 m a.s.l.) in Tibet (Xizang), southwestern China. The delimitation of these new species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI (cytochrome c oxydase, subunits I) gene. In addition, a key to all the species of the species group is provided.}, }
@article {pmid30213880, year = {2018}, author = {Ramrath, DJF and Niemann, M and Leibundgut, M and Bieri, P and Prange, C and Horn, EK and Leitner, A and Boehringer, D and Schneider, A and Ban, N}, title = {Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6413}, pages = {}, doi = {10.1126/science.aau7735}, pmid = {30213880}, issn = {1095-9203}, mesh = {*Evolution, Molecular ; Mitochondrial Ribosomes/*chemistry/ultrastructure ; Models, Molecular ; Protozoan Proteins/*chemistry/ultrastructure ; RNA, Ribosomal/chemistry/ultrastructure ; Ribosomal Proteins/*chemistry/ultrastructure ; Trypanosoma brucei brucei/*ultrastructure ; }, abstract = {Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of Trypanosoma brucei, a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the &quot;minimal&quot; set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.}, }
@article {pmid28903620, year = {2018}, author = {Kim, IH and Park, J and Suk, HY and Bae, HG and Min, MS and Tsai, TS and Park, D}, title = {Phylogenetic relationships of three representative sea krait species (genus Laticauda; elapidae; serpentes) based on 13 mitochondrial genes.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {772-777}, doi = {10.1080/24701394.2017.1357710}, pmid = {28903620}, issn = {2470-1408}, mesh = {Animals ; Biological Evolution ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Elapidae/*genetics ; Genes, Mitochondrial/genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Laticauda/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Snakes/genetics ; }, abstract = {To investigate the phylogenetic relationships of the genus Laticauda to related higher taxa, we compared the sequences of four mitochondrial genes (12S rRNA, 16S rRNA, ND4, Cytb) from three Laticauda species (L. colubrina, L. laticaudata, and L. semifasciata) with those of 55 Asian and Australo-Melanesian elapid species. We also characterized the complete mitogenomes of the three Laticauda species and compared the sequences of 13 mitochondrial genes from Laticauda species with five terrestrial elapid and one viperid species to estimate phylogenetic relationships and divergence times. Our results showed that the genus Laticauda is paraphyletic to terrestrial elapids and diverged from the Asian elapids approximately 16.23 Mya. The mitogenomes of the three Laticauda species commonly encoded 13 proteins, 22 tRNAs, 12S and 16S rRNAs and two control regions and ranged from 17,170 and 17,450 bp in size. The L. colubrina mitogenome was more similar to that of L. laticaudata than that of L. semifasciata. The divergence time among the three Laticauda clades was estimated at 8-10 Mya, and a close phylogenetic relationship between L. colubrina and L. laticaudata was found. Our results contribute to our understanding of the evolutionary history of sea kraits.}, }
@article {pmid28758818, year = {2018}, author = {Manger, A and Behere, GT and Firake, DM and Sharma, B and Deshmukh, NA and Firake, PD and Azad Thakur, NS and Ngachan, SV}, title = {Genetic characterization of Bactrocera fruit flies (Diptera: Tephritidae) from Northeastern India based on DNA barcodes.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {792-799}, doi = {10.1080/24701394.2017.1357713}, pmid = {28758818}, issn = {2470-1408}, mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genome, Mitochondrial/genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tephritidae/*genetics ; }, abstract = {The Northeastern region of India, one of the mega biodiversity hot spots has enormous potential for the production of fruits and vegetables. Fruit flies of the genus Bactrocera Macquart are important pests of fruits and vegetables, and one of the limiting factors in successful production of these commodities. The relationship among some of the species is unclear due to their high molecular and morphological similarities. Moreover, due to the significant morphological resemblance between fruit fly species, reliable identification is very difficult task. We genetically characterized 10 fruit fly species of the genus Bactrocera by using standard DNA barcoding region of COI gene. The characterization and identification of eight species were straight forward. This study was unable to establish the molecular identity of Bactrocera sp. 2. Within the 547 bp region of partial COI gene, there were 157 variable sites of which 110 sites were parsimony informative, 153 were synonymous substitutions and 4 were non-synonymous substitutions. The estimate of genetic divergence among the ten species was in the range of 0-21.9% and the pairwise genetic distance of Bactrocera. (Bactrocera) dorsalis (Hendel) with B. (B.) carambolae was only 0.7%. Phylogenetic analysis formed separate clades for fruit and vegetable infesting fruit flies. B. (B.) aethriobasis Hardy, B. (B.) thailandica and B. (B.) tuberculata (Bezzi) have been reported for the first time from the Northeastern India. The information generated from this study would certainly have implications for pest management, taxonomy, quarantine and trade.}, }
@article {pmid28756720, year = {2018}, author = {Li, YX and Gao, YL and He, XL and Cao, SX}, title = {Exploration of mtDNA control region sequences in Chinese Tibetan Mastiffs.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {800-804}, doi = {10.1080/24701394.2017.1357714}, pmid = {28756720}, issn = {2470-1408}, mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Dogs/*genetics ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tibet ; }, abstract = {The control region of mitochondrial DNA (mtDNA) was obtained from 40 purebred Chinese Tibetan Mastiffs (TMs). Sequence structure and genetic diversity were analyzed, and a phylogenetic tree was constructed. The TM mtDNA control region was composed of ETAS (extended termination associated sequences), CD (a central domain) and CSBs (conserved sequenced blocks) and sequence length showed some diversity, which was mainly caused by the number of 10 nucleotide repeat units [5'-GTA CAC GT (G/A) C-3'] between CSB I and CSB II, which ranged from 27 to 35 among individuals. Seventy-five polymorphic sites were identified, which defined 37 haplotypes; the haplotype diversity was 0.990, and the nucleotide diversity was 1.201. Based on the control region sequences, Chinese TMs were divided into three categories, which were consistent with the origin and geographical classification of TMs. Phylogenetic analysis of 538-bp HVR-I sequences revealed that TMs were most closely related to Labrador Retrievers.}, }
@article {pmid28756717, year = {2018}, author = {Feng, X and He, D and Sui, X and Chen, Y and Chen, Y}, title = {Morphological and genetic divergence between lake and river populations of Triplophysa in Ngangtse Co, Tibet.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {778-784}, doi = {10.1080/24701394.2017.1357711}, pmid = {28756717}, issn = {2470-1408}, mesh = {Animals ; Biological Evolution ; Cypriniformes/*genetics ; DNA ; DNA, Mitochondrial/genetics ; Ecosystem ; Genetic Drift ; Genetic Speciation ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; Lakes ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Rivers ; Tibet ; }, abstract = {Ngangtse Co (4535 m a.s.l., 840 km2) is a typical endorheic lake in Tibet. In 2015, we investigated the fish resource in this lake and its rivers and collected two Triplophysa species, including T. brevicauda and T. stewarti. To understand the evolutionary dynamics of Triplophysa in Ngangtse Co, the adaptive and genetic divergence between river and lake populations were investigated by analysing their morphological characteristics and mitochondrial COI and Cytb sequences. Among all of 277 samples, the ratios of the number of T. brevicauda to T. stewarti were 27:8, 34:11, 14:24, 37:0, 16:23 and 0:83 in river populations RA, RB, RC, RD, lakeside population LSE and lake population L, respectively. For T. brevicauda, a small but significant genetic divergence (mean FST = 0.0890) was detected between population RD and other three river populations, and significant morphological differences of body length/body height and body length/caudal peduncle length were observed between population RD and RA, RB, suggesting an association between differentiation and geographical distance. For T. stewarti, very high levels of genetic differentiation was observed between population L and other populations with the FST values ranging from 0.4737 (L-RA) to 0.7074 (L-RC). In addition, significant differences of most of morphological characteristics were observed between the lake (L) and river (RC) populations, indicating that lake fish of T. stewarti was a population that showed a long-term adaptation to the saltwater lake. These results provide insights on the evolutionary dynamics of Triplophysa in Ngangtse Co and help us to understand the fish speciation in endorheic lakes on the Qinghai-Tibetan Plateau.}, }
@article {pmid28752775, year = {2018}, author = {Wang, ZD and Liao, J and Huang, CQ and Long, SS and Zhang, S and Guo, YS and Liu, L and Liu, CW}, title = {Significant genetic differentiation of Gobiopterus lacustris, a newly recorded transparent goby in China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {785-791}, doi = {10.1080/24701394.2017.1357712}, pmid = {28752775}, issn = {2470-1408}, mesh = {Animals ; China ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Drift ; Genetic Variation/genetics ; Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes ; Mitochondria/genetics ; Perciformes/*genetics ; Phenotype ; Philippines ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/methods ; }, abstract = {In our recent survey, the transparent small Lacustrine goby, Gobiopterus lacustris had reported as the endemic species of Luzon, Philippines, was identified as an abundant species in mangroves of Leizhou Peninsula, China. Here, high diversity and significant differentiation of five sites of samples representing the west and east populations were revealed by mitochondrial DNA sequences. Five haplotypes of 56 cytochrome oxidase subunit I (Cox1) with the lengths of 623 base pairs (bp) have the high pairwise identity (>98.8%). Moreover, a total of 31 haplotypes for 129 partial D-loop regions were clustered into two clades corresponding to the east and west sampling sites. The strong population structure was confirmed (ΦST = 0.43017, p < .0001) with high haplotype diversity (h = 0.880 ± 0.017) and low nucleotide diversity (p=.00484). Moreover, both the mismatch distribution analysis and neutral test of D-loop revealed that the west group might experience a recent demographic expansion. Lastly, the isolation-with-migration analysis supported the expansion and indicated that the east-west split happened at approximately 7.1 kyr ago. Given the distribution and diversity, G. lacustris could be a good model for the study of the sea-level fluctuations and coast evolution of the South China Sea.}, }
@article {pmid28752773, year = {2018}, author = {Koroiva, R and Kvist, S}, title = {Estimating the barcoding gap in a global dataset of cox1 sequences for Odonata: close, but no cigar.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {765-771}, doi = {10.1080/24701394.2017.1357709}, pmid = {28752773}, issn = {2470-1408}, mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We evaluated the extent of intraspecific and interspecific genetic distances for two highly diverse infraorders of Odonata: Anisoptera and Zygoptera. All cytochrome c oxidase subunit I sequences (cox1), the region chosen for zoological DNA barcoding, present in GenBank for each infraorder were downloaded and curated. For Anisoptera, the final dataset consisted of 2,961 individual cox1 sequences for 536 species and the equivalent numbers for Zygoptera were 2,477 sequences for 497 species. More than 7 million individual genetic comparisons were made and the results indicated that there is a tendency towards a barcoding gap, but that the size of the gap may not be sufficient to robustly infer identities for some taxa. DNA barcoding may be of less use for some odonate taxa, perhaps pertaining to misidentifications in global databases. However, at local scales or with more confined taxonomical sampling, this tool may yet be beneficial in identifying these charismatic organisms.}, }
@article {pmid28745560, year = {2018}, author = {Bhatti, S and Abbas, S and Aslamkhan, M and Attimonelli, M and Trinidad, MS and Aydin, HH and de Souza, EMS and Gonzalez, GR}, title = {Genetic perspective of uniparental mitochondrial DNA landscape on the Punjabi population, Pakistan.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {714-726}, doi = {10.1080/24701394.2017.1350951}, pmid = {28745560}, issn = {2470-1408}, mesh = {Adult ; Asian Continental Ancestry Group/genetics ; DNA, Mitochondrial/*genetics ; Ethnic Groups/genetics ; European Continental Ancestry Group/genetics ; Gene Pool ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Pakistan ; Phylogeny ; Phylogeography ; Social Class ; }, abstract = {To investigate the uniparental genetic structure of the Punjabi population from mtDNA aspect and to set up an appropriate mtDNA forensic database, we studied maternally unrelated Punjabi (N = 100) subjects from two caste groups (i.e. Arain and Gujar) belonging to territory of Punjab. The complete control region was elucidated by Sanger sequencing and the subsequent 58 different haplotypes were designated into appropriate haplogroups according to the most recently updated mtDNA phylogeny. We found a homogenous dispersal of Eurasian haplogroup uniformity among the Punjab Province and exhibited a strong connotation with the European populations. Punjabi castes are primarily a composite of substantial South Asian, East Asian and West Eurasian lineages. Moreover, for the first time we have defined the newly sub-haplogroup M52b1 characterized by 16223 T, 16275 G and 16438 A in Gujar caste. The vast array of mtDNA variants displayed in this study suggested that the haplogroup composition radiates signals of extensive genetic conglomeration, population admixture and demographic expansion that was equipped with diverse origin, whereas matrilineal gene pool was phylogeographically homogenous across the Punjab. This context was further fully acquainted with the facts supported by PCA scatterplot that Punjabi population clustered with South Asian populations. Finally, the high power of discrimination (0.8819) and low random match probability (0.0085%) proposed a worthy contribution of mtDNA control region dataset as a forensic database that considered a gold standard of today to get deeper insight into the genetic ancestry of contemporary matrilineal phylogeny.}, }
@article {pmid28745537, year = {2018}, author = {Nakazawa, T and Liu, SV and Sakai, Y and Araki, KS and Tsai, CH and Okuda, N}, title = {Spatial genetic structure and body size divergence in endangered Gymnogobius isaza in ancient Lake Biwa.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {756-764}, doi = {10.1080/24701394.2017.1357708}, pmid = {28745537}, issn = {2470-1408}, mesh = {Animals ; Body Size/*genetics ; DNA, Mitochondrial/genetics ; Endangered Species ; Genetic Variation/genetics ; Genome, Mitochondrial/genetics ; Japan ; Lakes ; Mitochondria/genetics ; Perciformes/*genetics ; Phenotype ; Phylogeny ; }, abstract = {Gymnogobius isaza is a freshwater goby endemic to ancient Lake Biwa, the largest lake in Japan. The species is now listed as 'Critically Endangered' in the Red Data Book of Japan. Nevertheless, it remains subject to fishing without any specific management strategies. Previous studies using mitochondrial DNA markers showed that this fish species has two cryptic lineages. However, little is known about spatial genetic structure and ecological differences across the broad lakescape. In this study, we collected fish samples at nine locations along the lakeshore during the breeding season and tested for the presence of spatial heterogeneity in the lineage's composition while measuring body size as the most fundamental biological trait. The results showed that the major lineage dominated all the sampling locations whereas the minor lineage consisted of only 11% (16/143) of samples. Furthermore, although their spatial distributions overlapped (i.e. the two lineages may be well mixed), we found it possible that the minor lineage may have a potentially narrower distribution than the major lineage. In addition, we found that the two lineages differ in body size; specifically, the minor lineage is smaller in size. From the viewpoint of genetic diversity conservation and sustainable resource use, this fish should be managed as two genetic stocks and spatial and/or body size-based fishery management is desirable, with particular attention to the minor (smaller sized) lineage.}, }
@article {pmid28712321, year = {2018}, author = {Wang, ZL and Yang, XQ and Wang, TZ and Yu, X}, title = {Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {695-702}, doi = {10.1080/24701394.2017.1350949}, pmid = {28712321}, issn = {2470-1408}, mesh = {Animals ; China ; DNA ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/*genetics ; Farms ; Genetic Speciation ; Genetic Variation ; Genome, Insect/*genetics ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Spiders/*genetics ; }, abstract = {DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.}, }
@article {pmid28712317, year = {2018}, author = {Han, CC and Fang, LS and Chang, IM and Lin, HD}, title = {Genetic variation of the land-locked freshwater shrimp Caridina pseudodenticulata (Decapoda: Atyidae: Caridina) in Taiwan.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {687-694}, doi = {10.1080/24701394.2017.1350948}, pmid = {28712317}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Decapoda (Crustacea)/*genetics ; Electron Transport Complex IV/*genetics ; Fresh Water ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; Rivers ; Sequence Analysis, DNA/methods ; Shellfish ; Taiwan ; }, abstract = {Caridina pseudodenticulata is a land-locked freshwater shrimp, which is endemic to North and West Taiwan. It is listed as Vulnerable under criteria A1ce in the IUCN Red List. Our study used mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) gene to examine its genetic structure. In total, 204 sequences were analyzed from 22 populations, and all 39 haplotypes were identified. Our study (1) found that the genetic diversity within population of this species was similar to that of other land-locked freshwater prawn in Taiwan; (2) displayed that during glaciation, the Taiwan Strait was largely above water, an event which created opportunities for colonization Taiwan and dispersal widely; (3) showed that although the phylogenetic analysis showed the lack of a population genetic structure, the AMOVA and haplotypes distribution pattern revealed geographically divided; (4) indicated that C. pseudodenticulata could across to neighbor rivers through the mouths of rivers, which confluent with each other during floods.}, }
@article {pmid28673190, year = {2018}, author = {Koç, H and Bülbül, U and Kurnaz, M and İhsan Eroğlu, A and Kutrup, B}, title = {Phylogenetic relationships of Podarcis siculus (Rafinesque-Schmaltz, 1810) and Podarcis tauricus (Pallas, 1814) in Turkey, based on mitochondrial DNA.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {664-673}, doi = {10.1080/24701394.2017.1342245}, pmid = {28673190}, issn = {2470-1408}, mesh = {Animals ; DNA ; DNA, Mitochondrial/*genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Lizards/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Turkey ; }, abstract = {The Italian wall lizard and the Balkan wall lizard have a series of taxonomic revisions. However, their phylogenetic relationships still remain uncertain in Turkey. In the present study, we have assessed taxonomic relationships, both of Podarcis siculus and Podarcis tauricus through estimation of phylogenetic relationships among 43 and 42 specimens, respectively, using mtDNA (16 S rRNA and cytb) from great main populations in Turkey. The genetic distances among the populations of P. siculus in Turkey were very low and they were ranged from 0.2 to 1.6% in 16 S rRNA while they were ranged from 0.0% to 3.3% in cytb. On the other hand, the p-distances among the populations of P. tauricus were ranged from 0.0 to 0.6% in 16 S rRNA while they were 0.2% cytb in Turkey. Finally, most of the topologically identical trees of phylogenetic analyses and p-distances showed that monophyly was found in extant populations of P. siculus and P. tauricus. The nominate subspecies, P. s. siculus and P. t. tauricus are representatives of these lizards in Turkey.}, }
@article {pmid28622748, year = {2018}, author = {Iswarya Deepti, V and Kandula, S and Khedkar, GD}, title = {DNA barcoding of five species of groupers (Pisces: Serranidae) off Visakhapatnam, central eastern coast of India.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {659-663}, doi = {10.1080/24701394.2017.1339188}, pmid = {28622748}, issn = {2470-1408}, mesh = {Animals ; Bass/*genetics ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; }, abstract = {Grouper species of Epinephelus - E. epistictus, E. heniochus, E. latifasciatus, E. magniscuttis and E. radiatus exhibit overlapping colour pattern that often leads to misidentification in the field. Even the colour pattern of juveniles of these species in different size groups varies considerably with that of adults. DNA barcoding of these five species was carried out to reinforce our knowledge on existing taxonomic relationships derived based on morphological and biochemical genetic studies that were previously done from Indian waters. Mean interspecific genetic distance is in the range 0.079-0.164.The phylogeny tree revealed distinct clades for species that are in concurrence with previous taxonomic and allozyme electrophoretic studies carried out from central eastern coast of India. Barcode sequences generated for the first time for species E. heniochus from Indian waters for E. magniscuttis so far there are no reference sequences in GenBank.}, }
@article {pmid29973152, year = {2018}, author = {Vanhove, MPM and Briscoe, AG and Jorissen, MWP and Littlewood, DTJ and Huyse, T}, title = {The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae).}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {520}, pmid = {29973152}, issn = {1471-2164}, support = {BR/132/PI/TILAPIA//Federaal Wetenschapsbeleid/ ; GB-TAF-2984//SYNTHESYS/ ; GB-TAF-4940//SYNTHESYS/ ; ZRDC2014MP084//Vlaamse Interuniversitaire Raad/ ; P505/12/G112 (ECIP)//Grantová Agentura České Republiky/ ; K220314N//Fonds Wetenschappelijk Onderzoek/ ; Mbisa Congo project//Belgian Development Cooperation/ ; BOF Reserve Fellowship//Universiteit Hasselt/ ; }, mesh = {Animals ; Cichlids/*parasitology ; DNA, Protozoan/chemistry/isolation &amp; purification/metabolism ; Gene Order ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/classification/*genetics ; Phylogeny ; Platyhelminths/*genetics ; Protozoan Proteins/classification/genetics ; RNA, Ribosomal/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective.<br><br>RESULTS: Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines.<br><br>CONCLUSIONS: The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.}, }
@article {pmid30486096, year = {2018}, author = {Agarwal, I and Mahony, S and Giri, VB and Chaitanya, R and Bauer, AM}, title = {Six new Cyrtodactylus (Squamata: Gekkonidae) from northeast India.}, journal = {Zootaxa}, volume = {4524}, number = {5}, pages = {501-535}, pmid = {30486096}, issn = {1175-5334}, mesh = {Animals ; *Color ; India ; *Lizards ; Mitochondria ; Myanmar ; Phylogeny ; }, abstract = {We use mitochondrial sequence data to identify divergent lineages within the gekkonid genus Cyrtodactylus in northeast India and use morphological data to describe six new species from within the Indo-Burma clade of Cyrtodactylus. The new species share an irregular colour pattern but differ from described species from the region in morphology and mitochondrial sequence data (>11 % uncorrected pairwise sequence divergence). Three new species are from along the Brahmaputra River and three are from mountains south of the Brahmaputra, including the largest Cyrtodactylus from India and the fifth gecko to be described from a major Indian city, Guwahati.}, }
@article {pmid29855375, year = {2018}, author = {Amzati, GS and Pelle, R and Muhigwa, JB and Kanduma, EG and Djikeng, A and Madder, M and Kirschvink, N and Marcotty, T}, title = {Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {329}, pmid = {29855375}, issn = {1756-3305}, support = {ABC089//Africa Biosciences Challenge Fund (ABCF) program, BecA-ILRI Hub/ ; S0020***10402//Agence Universitaire de la Francophonie/ ; IFS-92890CA3//International Foundation for Science/ ; Bourses institutionnelles-Ceruna//Université de Namur/ ; 006/014//Communauté économique des pays des Grands Lacs (CEPGL)/ ; }, mesh = {Africa/epidemiology ; Animals ; Arachnid Vectors/*genetics/parasitology ; Cattle ; Genetic Structures ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; Rhipicephalus/*genetics/parasitology ; Theileria parva/*physiology ; Theileriasis/epidemiology/*parasitology ; }, abstract = {BACKGROUND: The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa.<br><br>METHODS: Sequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution.<br><br>RESULTS: Population genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa.<br><br>CONCLUSIONS: Two sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes.}, }
@article {pmid30545443, year = {2018}, author = {Son, JM and Lee, C}, title = {Mitochondria and aging.}, journal = {BMB reports}, volume = {}, number = {}, pages = {}, pmid = {30545443}, issn = {1976-670X}, abstract = {Aging is accompanied by a time-dependent progressive deterioration of multiple factors of the cellular system. The past several decades have witnessed major leaps in our understanding of the biological mechanism of aging using dietary, genetic, pharmacological, and physical interventions. Metabolic processes, including nutrient sensing pathways and mitochondrial function, have emerged as prominent regulators of aging. Mitochondria have been considered to play a key role largely due to their production of reactive oxygen species (ROS), resulting in DNA damage that accumulates over time and ultimately causes cellular failure. This theory, known as the mitochondrial free radical theory of aging (MFRTA), was favored by the aging field, but increasing inconsistent evidence has led to criticism and rejection of this idea. However, MFRTA should not be hastily rejected in its entirety because we now understand that ROS is not simply an undesired toxic metabolic byproduct, but also an important signaling molecule that is vital to cellular fitness. Notably, mitochondrial function, a term traditionally referred to bioenergetics and apoptosis, has since expanded considerably. It encompasses numerous other key biological processes, including the following: (i) complex metabolic processes, (ii) intracellular and endocrine signaling/communication, and (iii) immunity/inflammation. Here, we will discuss shortcomings of previous concepts regarding mitochondria in aging and their emerging roles based on recent advances. We will also discuss how the mitochondrial genome integrates with major theories on the evolution of aging.}, }
@article {pmid30285603, year = {2018}, author = {Chen, G and Zou, Y and Hu, J and Ding, Y}, title = {Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {720}, pmid = {30285603}, issn = {1471-2164}, support = {31471464//National Nature Science Foundation of China/ ; 2013CB126900//&quot;973&quot; Program of China/ ; }, mesh = {Chromosomes, Plant/genetics ; Droughts ; *Gene Expression Profiling ; Genome, Plant/genetics ; *Genomics ; Intracellular Space/metabolism ; MicroRNAs/genetics ; Oryza/drug effects/*genetics/metabolism/*physiology ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Protein Transport ; Salts/pharmacology ; Stress, Physiological/drug effects/*genetics ; Synteny ; }, abstract = {BACKGROUND: Pentatricopeptide-repeat proteins (PPRs) are characterized by tandem arrays of a degenerate 35-amino-acid (PPR motifs), which can bind RNA strands and participate in post-transcription. PPR proteins family is one of the largest families in land plants and play important roles in organelle RNA metabolism and plant development. However, the functions of PPR genes involved in biotic and abiotic stresses of rice (Oryza sativa L.) remain largely unknown.<br><br>RESULTS: In the present study, a comprehensive genome-wide analysis of PPR genes was performed. A total of 491 PPR genes were found in the rice genome, of which 246 PPR genes belong to the P subfamily, and 245 genes belong to the PLS subfamily. Gene structure analysis showed that most PPR genes lack intron. Chromosomal location analysis indicated that PPR genes were widely distributed in all 12 rice chromosomes. Phylogenetic relationship analysis revealed the distinct difference between the P and PLS subfamilies. Many PPR proteins are predicted to target chloroplasts or mitochondria, and a PPR protein (LOC_Os10g34310) was verified to localize in mitochondria. Furthermore, three PPR genes (LOC_Os03g17634,LOC_Os07g40820,LOC_Os04g51350) were verified as corresponding miRNA targets. The expression pattern analysis showed that many PPR genes could be induced under biotic and abiotic stresses. Finally, seven PPR genes were confirmed with their expression patterns under salinity or drought stress.<br><br>CONCLUSIONS: We found 491 PPR genes in the rice genome, and our genes structure analysis and syntenic analysis indicated that PPR genes might be derived from amplification by retro-transposition. The expression pattern present here suggested that PPR proteins have crucial roles in response to different abiotic stresses in rice. Taken together, our study provides a comprehensive analysis of the PPR gene family and will facilitate further studies on their roles in rice growth and development.}, }
@article {pmid30535838, year = {2018}, author = {Kumar, V and Santhosh Kumar, TR and Kartha, CC}, title = {Mitochondrial membrane transporters and metabolic switch in heart failure.}, journal = {Heart failure reviews}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10741-018-9756-2}, pmid = {30535838}, issn = {1573-7322}, abstract = {Mitochondrial dysfunction is widely recognized as a major factor for the progression of cardiac failure. Mitochondrial uptake of metabolic substrates and their utilization for ATP synthesis, electron transport chain activity, reactive oxygen species levels, ion homeostasis, mitochondrial biogenesis, and dynamics as well as levels of reactive oxygen species in the mitochondria are key factors which regulate mitochondrial function in the normal heart. Alterations in these functions contribute to adverse outcomes in heart failure. Iron imbalance and oxidative stress are also major factors for the evolution of cardiac hypertrophy, heart failure, and aging-associated pathological changes in the heart. Mitochondrial ATP-binding cassette (ABC) transporters have a key role in regulating iron metabolism and maintenance of redox status in cells. Deficiency of mitochondrial ABC transporters is associated with an impaired mitochondrial electron transport chain complex activity, iron overload, and increased levels of reactive oxygen species, all of which can result in mitochondrial dysfunction. In this review, we discuss the role of mitochondrial ABC transporters in mitochondrial metabolism and metabolic switch, alterations in the functioning of ABC transporters in heart failure, and mitochondrial ABC transporters as possible targets for therapeutic intervention in cardiac failure.}, }
@article {pmid30527196, year = {2018}, author = {Kazdal, D and Harms, A and Endris, V and Penzel, R and Oliveira, C and Kriegsmann, M and Longuespée, R and Winter, H and Schneider, MA and Muley, T and Pfarr, N and Weichert, W and Stenzinger, A and Warth, A}, title = {Subclonal evolution of pulmonary adenocarcinomas delineated by spatially distributed somatic mitochondrial mutations.}, journal = {Lung cancer (Amsterdam, Netherlands)}, volume = {126}, number = {}, pages = {80-88}, doi = {10.1016/j.lungcan.2018.10.024}, pmid = {30527196}, issn = {1872-8332}, abstract = {OBJECTIVES: The potential role of cancer associated somatic mutations of the mitochondrial genome (mtDNA) is controversial and still poorly understood. Our group and others recently challenged a direct tumorigenic impact and suggested a passenger-like character. In combination with the known increased mutation rate, somatic mtDNA mutations account for an interesting tool to delineate tumor evolution. Here, we comprehensively analyzed the spatial distribution of somatic mtDNA mutations throughout whole tumor sections of pulmonary adenocarcinoma (ADC).<br><br>MATERIALS AND METHODS: Central sections of 19 ADC were analyzed in a segmented manner (11-34 segments/tumor) together with non-neoplastic tissue samples and lymph node metastasis, if present. We performed whole mtDNA sequencing and real-time PCR based quantification of mtDNA copy numbers for all samples. Further, histological growth patterns were determined on H&amp;E sections and the tumor cell content was quantified by digital pathology analyses.<br><br>RESULTS: Somatic mtDNA mutations were present in 96% (18/19) of the analyzed tumors, either ubiquitously or restricted to specific tumor regions. Spatial and histological mapping of the mutations enabled the identification of subclonal structures and phylogenetic relations within a tumor section indicating different progression levels. In this regard, lymph node metastases seem to be related to early events in ADC development. There was no concurrence between histological and mtDNA mutation based clusters. However, micropapillary patterns occurred only in tumors with ubiquitous mutations. ADC with more than two ubiquitous mutations were associated with shorter disease-free survival (p < 0.01).<br><br>CONCLUSION: Cancer related mtDNA mutations are interesting candidates for the understanding of subclonal ADC evolution and perspectively for monitoring tumor progression. Our data reveal a potential prognostic relevance of somatic mtDNA mutations.}, }
@article {pmid30343708, year = {2018}, author = {Tanaka, A and Leung, PSC and Gershwin, ME}, title = {Evolution of our understanding of PBC.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {34-35}, number = {}, pages = {3-9}, doi = {10.1016/j.bpg.2018.05.008}, pmid = {30343708}, issn = {1532-1916}, mesh = {Animals ; Autoantibodies/blood ; Autoantigens/immunology ; Epitopes ; Humans ; Liver Cirrhosis, Biliary/*immunology/*pathology ; Mitochondria/immunology ; }, abstract = {The discovery of mitochondrial autoantigens recognized by antimitochondrial antibodies (AMAs) in 1987 marked the dawn of a new era in primary biliary cholangitis (PBC) research. Since then, there has been substantial progress in our understanding of PBC partly bestowed by the development of innovative technologies in molecular biology, immunology, and genetics. Here, we review this evolutionary progress in understanding PBC. We now recognize that the epitopes of AMAs, CD4+, and CD8+ T cells are all mapped to the same region of the inner lipoyl domain of pyruvate dehydrogenase complex E2 subunit (PDC-E2), and that intrahepatic biliary epithelial cells (BECs) are exclusively targeted in PBC. BECs express PDC-E2 on apotopes in an immunologically intact form during apoptosis, but not other epithelial cells, which could explain the tissue specificity of PBC. In addition, genetic factors, environmental triggers, and epigenetic modifications play crucial roles in the development of PBC. Intact lipoylated PDC-E2, presumably after modification with xenobiotics such as 2-octynamide or 2-nonyamide that are abundantly present in the environment, is endocytosed by antigen-presenting cells and are presented to CD4+ or CD8+ T cells. An immune complex consisting of PDC-E2 and anti-PDC-E2 autoantibodies cross-present autoantigens in a more efficient manner. Finally, an adenylate uridine-rich element (ARE) Del -/- mouse model has been established, which presents a disease modeling human PBC, including female dominance as one of its most important features, and can be used to dissect the immunopathology of PBC. Expanding our knowledge of the pathology from a very early stage of the disease will provide the key to cure PBC.}, }
@article {pmid30309500, year = {2018}, author = {Miquel, J and Poonlaphdecha, S and Ribas, A}, title = {Spermatological characteristics of the family Glypthelminthidae (Digenea, Plagiorchioidea) inferred from the ultrastructural study of Glypthelmins staffordi Tubangui, 1928.}, journal = {Tissue &amp; cell}, volume = {54}, number = {}, pages = {114-119}, doi = {10.1016/j.tice.2018.08.013}, pmid = {30309500}, issn = {1532-3072}, mesh = {Animals ; Male ; Phylogeny ; Spermatozoa/*ultrastructure ; Trematoda/*classification/*ultrastructure ; }, abstract = {The present study describes the ultrastructural organization of the mature spermatozoon of the digenean Glypthelmins staffordi (Glypthelminthidae) by means of transmission electron microscopy. Live digeneans were collected from the Chinese edible frog (Hoplobatrachus rugulosus) in Udon Thani Province (Thailand). The ultrastructural study reveals that the mature spermatozoon of G. staffordi is a filiform cell, which is tapered at both extremities. It exhibits the Bakhoum et al.'s type IV of spermatozoon of digeneans characterized by the 9+'1' axonemes of trepaxonematan Platyhelminthes, the presence of the association &quot;external ornamentation-cortical microtubules&quot;, the external ornamentation located in the posterior part of the anterior region, the arrangement of parallel cortical microtubules in two bundles and with its maximum number located in the anterior part of the sperm cell, and the presence of two mitochondria. Other characteristics are the presence of spine-like bodies, a posterior extremity containing only the nucleus, and the presence of a large amount of glycogen granules. Results of the present study are particularly compared with the existing data in other families of the Plagiorchioidea, namely the Brachycoeliidae, the Haematoloechidae, the Omphalometridae and the Plagiorchiidae.}, }
@article {pmid30158483, year = {2018}, author = {Kozieł, E and Otulak-Kozieł, K and Bujarski, JJ}, title = {Ultrastructural Analysis of Prune DwarfVirus Intercellular Transport and Pathogenesis.}, journal = {International journal of molecular sciences}, volume = {19}, number = {9}, pages = {}, pmid = {30158483}, issn = {1422-0067}, support = {505-10-011100-Q00190-99//Warsaw Univeristy of Life Sciences WULS-SGGW/ ; }, mesh = {Alfalfa mosaic virus/genetics/*pathogenicity/*ultrastructure ; Biological Transport/genetics/physiology ; Phylogeny ; RNA, Viral ; Viral Proteins/metabolism/ultrastructure ; }, abstract = {Prune dwarf virus (PDV) is an important viral pathogen of plum, sweet cherry, peach, and many herbaceous test plants. Although PDV has been intensively investigated, mainly in the context of phylogenetic relationship of its genes and proteins, many gaps exist in our knowledge about the mechanism of intercellular transport of this virus. The aim of this work was to investigate alterations in cellular organelles and the cell-to-cell transport of PDV in Cucumis sativus cv. Polan at ultrastructural level. To analyze the role of viral proteins in local transport, double-immunogold assays were applied to localize PDV coat protein (CP) and movement protein (MP). We observe structural changes in chloroplasts, mitochondria, and cellular membranes. We prove that PDV is transported as viral particles via MP-generated tubular structures through plasmodesmata. Moreover, the computer-run 3D modeling reveals structural resemblances between MPs of PDV and of Alfalfa mosaic virus (AMV), implying similarities of transport mechanisms for both viruses.}, }
@article {pmid30032461, year = {2018}, author = {Sylvester, C and Krishna, MS and Rao, JS and Chandrasekar, A}, title = {Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India.}, journal = {Genetica}, volume = {146}, number = {4-5}, pages = {383-389}, pmid = {30032461}, issn = {1573-6857}, mesh = {Asian Continental Ancestry Group/genetics ; DNA, Mitochondrial/*genetics ; Ethnic Groups/*genetics ; Female ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Humans ; India/ethnology ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Sequence Analysis, DNA/methods ; }, abstract = {The subsequent human migrations that dispersed out of Africa, both prehistoric and historic and colonization of India by modern humans is unanimous, and phylogeny of major mitochondrial DNA haplogroups have played a key role in assessing the genetic origin of people of India. To address more such events, complete mitogenomes of 113 Melakudiya tribe of Southern India were sequenced and 46 individuals showed the presence of west Eurasian autochthonous haplogroups HV14 and U7. Phylogenetic analysis revealed two novel subclades HV14a1b and HV14a1b1 and sequences representing haplogroup U7 were included under previously described subclade U7a3a1a2* specific to India. Moreover, the present analysis on complete mtDNA reveals addition information of the spread and distribution of west Eurasian haplogroups in southern India, in tracing an unexplored genetic link between Melakudiya tribe with the people of Iranian Plateau, South Caucasus, and Central Asia. Coalescence ages of HV14 and U7a3a1a2* trees in the present study dates ~ 16.1 ± 4.3 and ~ 13.4 ± 5.6 kya respectively.}, }
@article {pmid29902489, year = {2018}, author = {Uzarska, MA and Przybyla-Toscano, J and Spantgar, F and Zannini, F and Lill, R and Mühlenhoff, U and Rouhier, N}, title = {Conserved functions of Arabidopsis mitochondrial late-acting maturation factors in the trafficking of iron‑sulfur clusters.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1865}, number = {9}, pages = {1250-1259}, doi = {10.1016/j.bbamcr.2018.06.003}, pmid = {29902489}, issn = {0167-4889}, mesh = {Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cloning, Molecular ; DNA-Binding Proteins/genetics/metabolism ; Evolution, Molecular ; Iron/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*growth &amp; development ; Sulfur/metabolism ; }, abstract = {Numerous proteins require iron‑sulfur (Fe-S) clusters as cofactors for their function. Their biogenesis is a multi-step process occurring in the cytosol and mitochondria of all eukaryotes and additionally in plastids of photosynthetic eukaryotes. A basic model of Fe-S protein maturation in mitochondria has been obtained based on studies achieved in mammals and yeast, yet some molecular details, especially of the late steps, still require investigation. In particular, the late-acting biogenesis factors in plant mitochondria are poorly understood. In this study, we expressed the factors belonging to NFU, BOLA, SUFA/ISCA and IBA57 families in the respective yeast mutant strains. Expression of the Arabidopsis mitochondrial orthologs was usually sufficient to rescue the growth defects observed on specific media and/or to restore the abundance or activity of the defective Fe-S or lipoic acid-dependent enzymes. These data demonstrate that the plant mitochondrial counterparts, including duplicated isoforms, likely retained their ancestral functions. In contrast, the SUFA1 and IBA57.2 plastidial isoforms cannot rescue the lysine and glutamate auxotrophies of the respective isa1-isa2Δ and iba57Δ strains or of the isa1-isa2-iba57Δ triple mutant when expressed in combination. This suggests a specialization of the yeast mitochondrial and plant plastidial factors in these late steps of Fe-S protein biogenesis, possibly reflecting substrate-specific interactions in these different compartments.}, }
@article {pmid29902241, year = {2018}, author = {Yoshino, H and Yamaji, F and Ohsawa, TA}, title = {Genetic structure and dispersal patterns in Limnoria nagatai (Limnoriidae, Isopoda) dwelling in non-buoyant kelps, Eisenia bicyclis and E. arborea, in Japan.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0198451}, pmid = {29902241}, issn = {1932-6203}, mesh = {Animals ; Demography ; Electron Transport Complex IV/*genetics ; Gene Flow ; Isopoda/*classification/physiology ; Japan ; Kelp/*classification/physiology ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; }, abstract = {The marine isopod genus Limnoria contains algae-eating species. Previous phylogeographic studies have suggested that Limnoria species feeding on buoyant kelp underwent low genetic differentiation on a large spatial scale because rafting on floating host kelps promotes high levels of gene flow. In this paper, we survey the genetic structure of Limnoria nagatai, which bores into the non-buoyant kelps Eisenia bicyclis and E. arborea. We analyze the mitochondrial DNA (cytochrome oxidase subunit I [COI] gene) and morphological traits of L. nagatai, and the host kelps E. bicyclis and E. arborea from 14 populations along the Japanese archipelago of the Pacific Ocean and the Sea of Japan. Four major lineages are recognized within L. nagatai: three lineages in the Pacific Ocean, and one lineage in the Sea of Japan which might be a cryptic species. For L. nagatai, we show high genetic differentiation between geographically separated habitats in the Pacific Ocean, while low differentiation is found among continuous host kelps habitats in the Pacific Ocean as well as the Sea of Japan. L. nagatai in E. bicyclis in the Pacific Ocean has experienced large population expansion after the Last Glacial Maximum (LGM), whereas the lineage in E. bicyclis in the Sea of Japan has not. We suggest that Limnoria feeding on non-buoyant kelps, may attain low genetic differentiation because they might be able to disperse long distance if the habitat of host kelps is continuous. The historical events affecting Limnoria after the LGM may differ between the coasts of the Pacific Ocean and the Sea of Japan.}, }
@article {pmid29880721, year = {2018}, author = {Zhang, H and Burr, SP and Chinnery, PF}, title = {The mitochondrial DNA genetic bottleneck: inheritance and beyond.}, journal = {Essays in biochemistry}, volume = {62}, number = {3}, pages = {225-234}, doi = {10.1042/EBC20170096}, pmid = {29880721}, issn = {1744-1358}, support = {101876/Z/13/Z//Wellcome Trust/United Kingdom ; MC_UP_1501/2//Medical Research Council/United Kingdom ; G0601943//Medical Research Council/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Gene-Environment Interaction ; Genetic Drift ; *Genetic Predisposition to Disease ; Humans ; Mitochondria/physiology ; Organelle Biogenesis ; Selection, Genetic ; }, abstract = {mtDNA is a multicopy genome. When mutations exist, they can affect a varying proportion of the mtDNA present within every cell (heteroplasmy). Heteroplasmic mtDNA mutations can be maternally inherited, but the proportion of mutated alleles differs markedly between offspring within one generation. This led to the genetic bottleneck hypothesis, explaining the rapid changes in allele frequency seen during transmission from one generation to the next. Although a physical reduction in mtDNA has been demonstrated in several species, a comprehensive understanding of the molecular mechanisms is yet to be revealed. Several questions remain, including the role of selection for and against specific alleles, whether all bottlenecks are the same, and precisely how the bottleneck is controlled during development. Although originally thought to be limited to the germline, there is evidence that bottlenecks exist in other cell types during development, perhaps explaining why different tissues in the same organism contain different levels of mutated mtDNA. Moreover, tissue-specific bottlenecks may occur throughout life in response to environmental influences, adding further complexity to the situation. Here we review key recent findings, and suggest ways forward that will hopefully advance our understanding of the role of mtDNA in human disease.}, }
@article {pmid29618317, year = {2018}, author = {Doyle, JM and Bell, DA and Bloom, PH and Emmons, G and Fesnock, A and Katzner, TE and LaPré, L and Leonard, K and SanMiguel, P and Westerman, R and Andrew DeWoody, J}, title = {New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus).}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {233}, pmid = {29618317}, issn = {1471-2164}, support = {L12AC20102, L11PX02237, L12AC2010//U.S. Bureau of Land Management/ ; University Faculty Scholar program//Provost's Office at Purdue University/ ; PINN645-21//National Park Service/ ; BIO170038//XSEDE/ ; }, mesh = {Animals ; Avian Proteins/*genetics ; California ; Falconiformes/*classification/genetics ; Female ; Genetics, Population ; Idaho ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Polymorphism, Single Nucleotide ; Whole Genome Sequencing/*veterinary ; }, abstract = {BACKGROUND: Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species' range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.<br><br>RESULTS: We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.<br><br>CONCLUSIONS: Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California's prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole.}, }
@article {pmid29476907, year = {2018}, author = {Layton, KKS and Gosliner, TM and Wilson, NG}, title = {Flexible colour patterns obscure identification and mimicry in Indo-Pacific Chromodoris nudibranchs (Gastropoda: Chromodorididae).}, journal = {Molecular phylogenetics and evolution}, volume = {124}, number = {}, pages = {27-36}, doi = {10.1016/j.ympev.2018.02.008}, pmid = {29476907}, issn = {1095-9513}, mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/genetics ; Gastropoda/genetics/*physiology ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Molecular Mimicry/*genetics ; Phylogeny ; Pigmentation/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Chromodoris is a genus of colourful nudibranchs that feed on sponges and is found across the Indo-Pacific. While this was once the most diverse chromodorid genus, recent work has shown that the genus should be restricted to a monophyletic lineage that contains only 22 species, all of which exhibit black pigmentation and planar spawning behaviour. Earlier phylogenies of this group are poorly resolved and thus additional work is needed to clarify species boundaries within Chromodoris. This study presents a maximum-likelihood phylogeny based on mitochondrial loci (COI, 16S) for 345 Chromodoris specimens, including data from 323 new specimens and 22 from GenBank, from across the Indo-Pacific. Species hypotheses and phylogenetic analysis uncovered 39 taxa in total containing 18 undescribed species, with only five of 39 taxa showing stable colour patterns and distinct morphotypes. This study also presents the first evidence for regional mimicry in this genus, with C. colemani and C. joshi displaying geographically-based variation in colour patterns which appear to match locally abundant congenerics, highlighting the flexibility of these colour patterns in Chromodoris nudibranchs. The current phylogeny contains short branch lengths, polytomies and poor support at interior nodes, which is indicative of a recent radiation. As such, future work will employ a transcriptome-based exon capture approach for resolving the phylogeny of this group. In all, this study included 21 of the 22 described species in the Chromodoris sensu stricto group with broad sampling coverage from across the Indo-Pacific, constituting the most comprehensive sampling of this group to date. This work highlights several cases of undocumented diversity, ultimately expanding our knowledge of species boundaries in this group, while also demonstrating the limitations of colour patterns for species identification in this genus.}, }
@article {pmid29358597, year = {2018}, author = {Eimanifar, A and Kimball, RT and Braun, EL and Ellis, JD}, title = {Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1333}, pmid = {29358597}, issn = {2045-2322}, mesh = {Animals ; Bees/*classification/cytology/genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Introduced Species ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; South Africa ; }, abstract = {Apis mellifera capensis Eschscholtz and A.m. scutellata Lepeletier are subspecies of western honey bees that are indigenous to the Republic of South Africa (RSA). Both subspecies have invasive potential and are organisms of concern for areas outside their native range, though they are important bees to beekeepers, agriculture, and the environment where they are native. The aim of the present study was to examine genetic differentiation among these subspecies and estimate their phylogenetic relationships using complete mitochondrial genomes sequences. We used 25 individuals that were either assigned to one of the subspecies or designated hybrids using morphometric analyses. Phylogenetic analyses of mitogenome sequences by maximum likelihood (ML) and Bayesian inference identified a monophyletic RSA clade, subdivided into two clades. A haplotype network was consistent with the phylogenetic trees. However, members of both subspecies occurred in both clades, indicating that A.m. capensis and A.m. scutellata are neither reciprocally monophyletic nor do they exhibit paraphyly with one subspecies nested within the other subspecies. Furthermore, no mitogenomic features were diagnostic to either subspecies. All bees analyzed from the RSA expressed a substantial level of haplotype diversity (most samples had unique haplotypes) but limited nucleotide diversity. The number of variable codons across protein-coding genes (PCGs) differed among loci, with CO3 exhibiting the most variation and ATP6 the least.}, }
@article {pmid28989067, year = {2018}, author = {Ogedengbe, ME and El-Sherry, S and Ogedengbe, JD and Chapman, HD and Barta, JR}, title = {Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa).}, journal = {International journal for parasitology}, volume = {48}, number = {1}, pages = {59-69}, doi = {10.1016/j.ijpara.2017.07.008}, pmid = {28989067}, issn = {1879-0135}, mesh = {Animals ; Cell Nucleus/*genetics/metabolism ; DNA, Protozoan/*genetics/metabolism ; DNA, Ribosomal/*genetics/metabolism ; Eimeria/classification/*genetics/growth &amp; development/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/*genetics/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Partial mitochondrial (mt) cytochrome c oxidase subunit I (COI) and near-complete nuclear (nu) 18S rDNA sequences were obtained from various eimeriid coccidia infecting vertebrates. New and published sequences were used in phylogenetic reconstructions based on nu 18S rDNA, mt COI and concatenated sequence datasets. Bayesian analyses of nu 18S rDNA sequences used secondary structure-based alignments with a doublet nucleotide substitution model; the codon nucleotide substitution model was applied to COI sequences. Although alignment of the mt COI sequences was unambiguous, substitution saturation was evident for comparisons of COI sequences between ingroup (eimeriid) and outgroup (sarcocystid) taxa. Consequently, a combined dataset applying partition-specific analytical and alignment improvements was used to generate a robust molecular phylogeny. Most eimeriid parasites that infect closely related definitive hosts were found in close proximity on the resulting tree, frequently in a single clade. Whether this represents coevolution or co-accommodation or a combination remains an open point. Unlike host associations, basic oocyst configuration (number of sporocysts per oocyst and sporozoites per sporocyst) was not correlated with phylogeny. Neither 'Eimeria-type' nor 'Isospora-type' oocyst morphotypes formed monophyletic groups. In the combined dataset tree (representing only a tiny fraction of described eimeriid coccidia), at least 10 clades of Eimeria spp. would need to be re-assigned to nine distinct genera to resolve their paraphyly. The apparent lack of congruence between morphotype and genotype will require taxonomists to balance nomenclatural stability and diagnostic ease against the ideal of monophyletic genera. For now, recognition of paraphyletic eimeriid genera defined by basic oocyst configuration may be necessary for reasons of taxonomic stability and diagnostic utility. Future taxonomic revisions to produce monophyletic eimeriid genera will ultimately require the identification of reliable phenotypic characters that agree with the molecular phylogeny of these parasites or, less optimally, acceptance that genotyping may be needed to support monophyletic supraspecific taxonomic groups.}, }
@article {pmid28487526, year = {2017}, author = {Wang, P and Sha, T and Zhang, Y and Cao, Y and Mi, F and Liu, C and Yang, D and Tang, X and He, X and Dong, J and Wu, J and Yoell, S and Yoell, L and Zhang, KQ and Zhang, Y and Xu, J}, title = {Frequent heteroplasmy and recombination in the mitochondrial genomes of the basidiomycete mushroom Thelephora ganbajun.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1626}, pmid = {28487526}, issn = {2045-2322}, mesh = {Agaricales/*genetics/isolation &amp; purification ; Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Gene Amplification ; Genetic Loci ; *Genome, Mitochondrial ; Geography ; Heterozygote ; Homozygote ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {In the majority of sexual eukaryotes, the mitochondrial genomes are inherited uniparentally. As a result, individual organisms are homoplasmic, containing mitochondrial DNA (mtDNA) from a single parent. Here we analyzed the mitochondrial genotypes in Clade I of the gourmet mushroom Thelephora ganbajun from its broad geographic distribution range. A total of 299 isolates from 28 geographic locations were sequenced at three mitochondrial loci: the mitochondrial small ribosomal RNA gene, and the cytochrome c oxidase subunits I (COX1) and III (COX3) genes. Quantitative PCR analyses showed that the strains had about 60-160 copies of mitochondrial genomes per cell. Interestingly, while no evidence of heteroplasmy was found at the 12S rRNA gene, 262 of the 299 isolates had clear evidence of heterogeneity at either the COX1 (261 isolates) or COX3 (12 isolates) gene fragments. The COX1 heteroplasmy was characterized by two types of introns residing at different sites of the same region and at different frequencies among the isolates. Allelic association analyses of the observed mitochondrial polymorphic nucleotide sites suggest that mtDNA recombination is common in natural populations of this fungus. Our results contrast the prevailing view that heteroplasmy, if exists, is only transient in basidiomycete fungi.}, }
@article {pmid30518034, year = {2018}, author = {Derbikova, K and Kuzmenko, A and Levitskii, S and Klimontova, M and Chicherin, I and Baleva, MV and Krasheninnikov, IA and Kamenski, P}, title = {Biological and Evolutionary Significance of Terminal Extensions of Mitochondrial Translation Initiation Factor 3.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123861}, pmid = {30518034}, issn = {1422-0067}, support = {17-14-01005//Russian Science Foundation/ ; 17-54-16005//Russian Foundation for Basic Research/ ; State Assignment AAAA_A16_116021660073_5//Russian Federation Government/ ; }, abstract = {Protein biosynthesis in mitochondria is organized in a bacterial manner. However, during evolution, mitochondrial translation mechanisms underwent many organelle-specific changes. In particular, almost all mitochondrial translation factors, being orthologous to bacterial proteins, are characterized by some unique elements of primary or secondary structure. In the case of the organellar initiation factor 3 (IF3), these elements are several dozen amino acids long N- and C-terminal extensions. This study focused on the terminal extensions of baker's yeast mitochondrial IF3, Aim23p. By in vivo deletion and complementation analysis, we show that at least one extension is necessary for Aim23p function. At the same time, human mitochondrial IF3 is fully functional in yeast mitochondria even without both terminal extensions. While Escherichia coli IF3 itself is poorly active in yeast mitochondria, adding Aim23p terminal extensions makes the resulting chimeric protein as functional as the cognate factor. Our results show that the terminal extensions of IF3 have evolved as the &quot;adaptors&quot; that accommodate the translation factor of bacterial origin to the evolutionary changed protein biosynthesis system in mitochondria.}, }
@article {pmid30517740, year = {2018}, author = {Petrov, AS and Wood, EC and Bernier, CR and Norris, AM and Brown, A and Amunts, A}, title = {Structural Patching Fosters Divergence of Mitochondrial Ribosomes.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msy221}, pmid = {30517740}, issn = {1537-1719}, abstract = {Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data. We generate a map of the acquisition of structural variation and reconstruct the fundamental stages that shaped the evolution of the mitoribosomal large subunit and led to this diversity. Our analysis suggests a critical role for ablation and expansion of rapidly evolving mt-rRNA. These changes cause structural instabilities that are &quot;patched&quot; by the acquisition of pre-existing compensatory elements, thus providing opportunities for rapid evolution. This mechanism underlies the incorporation of mt-tRNA into the central protuberance of the mammalian mitoribosome, and the altered path of the polypeptide exit tunnel of the yeast mitoribosome. We propose that since the toolkits of elements utilized for structural patching differ between mitochondria of different species, it fosters the growing divergence of mitoribosomes.}, }
@article {pmid30484227, year = {2018}, author = {Trosko, JE}, title = {The Role of the Mitochondria in the Evolution of Stem Cells, Including MUSE Stem Cells and Their Biology.}, journal = {Advances in experimental medicine and biology}, volume = {1103}, number = {}, pages = {131-152}, doi = {10.1007/978-4-431-56847-6_7}, pmid = {30484227}, issn = {0065-2598}, abstract = {From the transition of single-cell organisms to multicellularity of metazoans, evolutionary pressures selected new genes and phenotypes to cope with the oxygenation of the Earth's environment, especially via the symbiotic acquisition of the mitochondrial organelle. There were many new genes and phenotypes that appeared, namely, stem cells, low-oxygen-micro-environments to house these genes (&quot;niches&quot;), new epigenetic mechanisms to regulate , selectively, the gene repertoire to control proliferation, differentiation, apoptosis, senescence and DNA protection mechanisms, including antioxidant genes and DNA repair. This transition required a critical regulation of the metabolism of glucose to produce energy for both the stem cell quiescent state and the energy-requiring differentiated state. While the totipotent-, embryonic-, pluripotent-, and a few adult organ-specific stem cells were recognized, only relatively recently, because of the isolation of somatic cell nuclear transfer (SCNT) stem cells and &quot;induced pluripotent stem&quot; cells, challenges to the origin of these &quot;iPS&quot; cells have been made. The isolation and characterization of human MUSE stem cells and more adult organ-specific adult stem cells have indicated that these MUSE cells have many shared characteristics of the &quot;iPS&quot; cells, yet they do not form teratomas but can give rise to the trigeminal cell layers. While the MUSE cells are a subset of human fibroblastic cells, they have not been characterized, yet, for the mitochondrial metabolic genes, either in the stem cell state or during their differentiation processes. A description of other human adult stem cells will be made to set future studies of how the MUSE stem cells compare to all other stem cells.}, }
@article {pmid30246391, year = {2018}, author = {Shibata, D}, title = {Somatic cell evolution: how to improve with age.}, journal = {The Journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/path.5173}, pmid = {30246391}, issn = {1096-9896}, support = {U54CA217376//National Institutes of Health/ ; CA196569//National Institutes of Health/ ; P30CA014089//National Institutes of Health/ ; }, abstract = {A recent article published in this journal illuminates a rare example of somatic evolution where cells improve rather than deteriorate with age. In mitotic intestinal crypts, stem cells with higher levels of a deleterious heteroplasmic germline mitochondrial mutation are purged through time, leading to crypts without the mutation. Similar somatic mitochondrial mutations are not purged from crypts, indicating that special conditions are needed to improve with age. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.}, }
@article {pmid30481564, year = {2018}, author = {Xie, B and Wang, S and Jiang, N and Li, JJ}, title = {Cyclin B1/CDK1-regulated mitochondrial bioenergetics in cell cycle progression and tumor resistance.}, journal = {Cancer letters}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.canlet.2018.11.019}, pmid = {30481564}, issn = {1872-7980}, abstract = {A mammalian cell houses two genomes located separately in the nucleus and mitochondria. During evolution, communications and adaptations between these two genomes occur extensively to achieve and sustain homeostasis for cellular functions and regeneration. Mitochondria provide the major cellular energy and contribute to gene regulation in the nucleus, whereas more than 98% of mitochondrial proteins are encoded by the nuclear genome. Such two-way signaling traffic presents an orchestrated dynamic between energy metabolism and consumption in cells. Recent reports have elucidated the way how mitochondrial bioenergetics synchronizes with the energy consumption for cell cycle progression mediated by cyclin B1/CDK1 as the communicator. This review is to recapitulate cyclin B1/CDK1 mediated mitochondrial activities in cell cycle progression and stress response as well as its potential link to reprogram energy metabolism in tumor adaptive resistance. Cyclin B1/CDK1-mediated mitochondrial bioenergetics is applied as an example to show how mitochondria could timely sense the cellular fuel demand and then coordinate ATP output. Such nucleus-mitochondria oscillation may play key roles in the flexible bioenergetics required for tumor cell survival and compromising the efficacy of anti-cancer therapy. Further deciphering the cyclin B1/CDK1-controlled mitochondrial metabolism may invent effect targets to treat resistant cancers.}, }
@article {pmid29842994, year = {2018}, author = {Weerts, MJA and Timmermans, EC and van de Stolpe, A and Vossen, RHAM and Anvar, SY and Foekens, JA and Sleijfer, S and Martens, JWM}, title = {Tumor-Specific Mitochondrial DNA Variants Are Rarely Detected in Cell-Free DNA.}, journal = {Neoplasia (New York, N.Y.)}, volume = {20}, number = {7}, pages = {687-696}, doi = {10.1016/j.neo.2018.05.003}, pmid = {29842994}, issn = {1476-5586}, mesh = {Aged ; Aged, 80 and over ; Alleles ; *Biomarkers, Tumor ; *Circulating Tumor DNA ; Computational Biology/methods ; *DNA, Mitochondrial ; *DNA, Neoplasm ; Female ; Gene Frequency ; Genetic Heterogeneity ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Neoplasm Staging ; Neoplasms/*genetics/pathology ; Phylogeny ; }, abstract = {The use of blood-circulating cell-free DNA (cfDNA) as a &quot;liquid biopsy&quot; in oncology is being explored for its potential as a cancer biomarker. Mitochondria contain their own circular genomic entity (mitochondrial DNA, mtDNA), up to even thousands of copies per cell. The mutation rate of mtDNA is several orders of magnitude higher than that of the nuclear DNA. Tumor-specific variants have been identified in tumors along the entire mtDNA, and their number varies among and within tumors. The high mtDNA copy number per cell and the high mtDNA mutation rate make it worthwhile to explore the potential of tumor-specific cf-mtDNA variants as cancer marker in the blood of cancer patients. We used single-molecule real-time (SMRT) sequencing to profile the entire mtDNA of 19 tissue specimens (primary tumor and/or metastatic sites, and tumor-adjacent normal tissue) and 9 cfDNA samples, originating from 8 cancer patients (5 breast, 3 colon). For each patient, tumor-specific mtDNA variants were detected and traced in cfDNA by SMRT sequencing and/or digital PCR to explore their feasibility as cancer biomarker. As a reference, we measured other blood-circulating biomarkers for these patients, including driver mutations in nuclear-encoded cfDNA and cancer-antigen levels or circulating tumor cells. Four of the 24 (17%) tumor-specific mtDNA variants were detected in cfDNA, however at much lower allele frequencies compared to mutations in nuclear-encoded driver genes in the same samples. Also, extensive heterogeneity was observed among the heteroplasmic mtDNA variants present in an individual. We conclude that there is limited value in tracing tumor-specific mtDNA variants in blood-circulating cfDNA with the current methods available.}, }
@article {pmid29643269, year = {2018}, author = {Mori, S and Matsunami, M}, title = {Signature of positive selection in mitochondrial DNA in Cetartiodactyla.}, journal = {Genes &amp; genetic systems}, volume = {93}, number = {2}, pages = {65-73}, doi = {10.1266/ggs.17-00015}, pmid = {29643269}, issn = {1880-5779}, mesh = {Amino Acid Substitution ; Animals ; Artiodactyla/*genetics ; Biological Evolution ; Cetacea/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Evolution, Molecular ; Genomics ; Mammals/genetics ; Mitochondria/genetics ; Phylogeny ; Selection, Genetic/genetics ; }, abstract = {Acceleration of the amino acid substitution rate is a good indicator of positive selection in adaptive evolutionary changes of functional genes. Genomic information about mammals has become readily available in recent years, as many researchers have attempted to clarify the adaptive evolution of mammals by examining evolutionary rate change based on multiple loci. The order Cetartiodactyla (Artiodactyla and Cetacea) is one of the most diverse orders of mammals. Species in this order are found throughout all continents and seas, except Antarctica, and they exhibit wide variation in morphology and habitat. Here, we focused on the metabolism-related genes of mitochondrial DNA (mtDNA) in species of the order Cetartiodactyla using 191 mtDNA sequences available in databases. Based on comparisons of the dN/dS ratio (ω) in 12 protein-coding genes, ATP8 was shown to have a higher ω value (ω = 0.247) throughout Cetartiodactyla than the other 11 genes (ω < 0.05). In a branch-site analysis of ATP8 sequences, a markedly higher ω value of 0.801 was observed in the ancestral lineage of the clade of Cetacea, which is indicative of adaptive evolution. Through efforts to detect positively selected amino acids, codon positions 52 and 54 of ATP8 were shown to have experienced positive selective pressure during the course of evolution; multiple substitutions have occurred at these sites throughout the cetacean lineage. At position 52, glutamic acid was replaced with asparagine, and, at position 54, lysine was replaced with non-charged amino acids. These sites are conserved in most Artiodactyla. These results imply that the ancestor of cetaceans underwent accelerated amino acid changes in ATP8 and replacements at codons 52 and 54, which adjusted metabolism to adapt to the marine environment.}, }
@article {pmid29362421, year = {2018}, author = {Carreras, C and Pascual, M and Tomás, J and Marco, A and Hochscheid, S and Castillo, JJ and Gozalbes, P and Parga, M and Piovano, S and Cardona, L}, title = {Sporadic nesting reveals long distance colonisation in the philopatric loggerhead sea turtle (Caretta caretta).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1435}, doi = {10.1038/s41598-018-19887-w}, pmid = {29362421}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Ecosystem ; Mediterranean Sea ; *Microsatellite Repeats ; Mitochondria/genetics ; *Nesting Behavior ; Population Dynamics ; Sequence Analysis, DNA/*methods ; Temperature ; Turtles/genetics/*physiology ; }, abstract = {The colonisation of new suitable habitats is crucial for species survival at evolutionary scale under changing environmental conditions. However, colonisation potential may be limited by philopatry that facilitates exploiting successful habitats across generations. We examine the mechanisms of long distance dispersal of the philopatric loggerhead sea turtle (Caretta caretta) by analysing 40 sporadic nesting events in the western Mediterranean. The analysis of a fragment of the mitochondrial DNA and 7 microsatellites of 121 samples from 18 of these nesting events revealed that these nests were colonising events associated with juveniles from distant populations feeding in nearby foraging grounds. Considering the temperature-dependent sex determination of the species, we simulated the effect of the incubation temperature and propagule pressure on a potential colonisation scenario. Our results indicated that colonisation will succeed if warm temperature conditions, already existing in some of the beaches in the area, extend to the whole western Mediterranean. We hypothesize that the sporadic nesting events in developmental foraging grounds may be a mechanism to overcome philopatry limitations thus increasing the dispersal capabilities of the species and the adaptability to changing environments. Sporadic nesting in the western Mediterranean can be viewed as potential new populations in a scenario of rising temperatures.}, }
@article {pmid30466434, year = {2018}, author = {Petrů, M and Wideman, J and Moore, K and Alcock, F and Palmer, T and Doležal, P}, title = {Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria.}, journal = {BMC biology}, volume = {16}, number = {1}, pages = {141}, doi = {10.1186/s12915-018-0607-3}, pmid = {30466434}, issn = {1741-7007}, support = {13-29423S//Grantová Agentura České Republiky (CZ)/ ; 1215//Grantová Agentura, Univerzita Karlova/ ; LH15253//Ministerstvo Školství, Mládeže a Tělovýchovy (CZ)/ ; LQ1604//Ministerstvo Školství, Mládeže a Tělovýchovy (CZ)/ ; CZ.1.05/1.1.00/02.0109//European Regional Development Fund ()/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//European Regional Development Fund ()/ ; }, abstract = {BACKGROUND: Bacteria and mitochondria contain translocases that function to transport proteins across or insert proteins into their inner and outer membranes. Extant mitochondria retain some bacterial-derived translocases but have lost others. While BamA and YidC were integrated into general mitochondrial protein transport pathways (as Sam50 and Oxa1), the inner membrane TAT translocase, which uniquely transports folded proteins across the membrane, was retained sporadically across the eukaryote tree.<br><br>RESULTS: We have identified mitochondrial TAT machinery in diverse eukaryotic lineages and define three different types of eukaryote-encoded TatABC-derived machineries (TatAC, TatBC and TatC-only). Here, we investigate TatAC and TatC-only machineries, which have not been studied previously. We show that mitochondria-encoded TatAC of the jakobid Andalucia godoyi represent the minimal functional pathway capable of substituting for the Escherichia coli TatABC complex and can transport at least one substrate. However, selected TatC-only machineries, from multiple eukaryotic lineages, were not capable of supporting the translocation of this substrate across the bacterial membrane. Despite the multiple losses of the TatC gene from the mitochondrial genome, the gene was never transferred to the cell nucleus. Although the major constraint preventing nuclear transfer of mitochondrial TatC is likely its high hydrophobicity, we show that in chloroplasts, such transfer of TatC was made possible due to modifications of the first transmembrane domain.<br><br>CONCLUSIONS: At its origin, mitochondria inherited three inner membrane translocases Sec, TAT and Oxa1 (YidC) from its bacterial ancestor. Our work shows for the first time that mitochondrial TAT has likely retained its unique function of transporting folded proteins at least in those few eukaryotes with TatA and TatC subunits encoded in the mitochondrial genome. However, mitochondria, in contrast to chloroplasts, abandoned the machinery multiple times in evolution. The overall lower hydrophobicity of the Oxa1 protein was likely the main reason why this translocase was nearly universally retained in mitochondrial biogenesis pathways.}, }
@article {pmid30464337, year = {2018}, author = {Chen, YL and Chen, LJ and Chu, CC and Huang, PK and Wen, JR and Li, HM}, title = {TIC236 links the outer and inner membrane translocons of the chloroplast.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-018-0713-y}, pmid = {30464337}, issn = {1476-4687}, abstract = {The two-membrane envelope is a defining feature of chloroplasts. Chloroplasts evolved from a Gram-negative cyanobacterial endosymbiont. During evolution, genes of the endosymbiont have been transferred to the host nuclear genome. Most chloroplast proteins are synthesized in the cytosol as higher-molecular-mass preproteins with an N-terminal transit peptide. Preproteins are transported into chloroplasts by the TOC and TIC (translocons at the outer- and inner-envelope membranes of chloroplasts, respectively) machineries1,2, but how TOC and TIC are assembled together is unknown. Here we report the identification of the TIC component TIC236; TIC236 is an integral inner-membrane protein that projects a 230-kDa domain into the intermembrane space, which binds directly to the outer-membrane channel TOC75. The knockout mutation of TIC236 is embryonically lethal. In TIC236-knockdown mutants, a smaller amount of the inner-membrane channel TIC20 was associated with TOC75; the amount of TOC-TIC supercomplexes was also reduced. This resulted in a reduced import rate into the stroma, though outer-membrane protein insertion was unaffected. The size and the essential nature of TIC236 indicate that-unlike in mitochondria, in which the outer- and inner-membrane translocons exist as separate complexes and a supercomplex is only transiently assembled during preprotein translocation3,4-a long and stable protein bridge in the intermembrane space is required for protein translocation into chloroplasts. Furthermore, TIC236 and TOC75 are homologues of bacterial inner-membrane TamB5 and outer-membrane BamA, respectively. Our evolutionary analyses show that, similar to TOC75, TIC236 is preserved only in plants and has co-evolved with TOC75 throughout the plant lineage. This suggests that the backbone of the chloroplast protein-import machinery evolved from the bacterial TamB-BamA protein-secretion system.}, }
@article {pmid29069345, year = {2017}, author = {Christy, SF and Wernick, RI and Lue, MJ and Velasco, G and Howe, DK and Denver, DR and Estes, S}, title = {Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3008-3022}, doi = {10.1093/gbe/evx222}, pmid = {29069345}, issn = {1759-6653}, mesh = {Adaptation, Physiological/genetics ; Animals ; *Biological Evolution ; Caenorhabditis elegans/*genetics ; Genes, Helminth/*genetics ; *Genetic Drift ; Genetic Fitness ; Mitochondria/genetics ; Models, Genetic ; Mutation Accumulation ; Mutation Rate ; Oxidative Stress/*genetics ; Polymorphism, Single Nucleotide ; Selection, Genetic ; }, abstract = {A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1. The original intent of the study was to assess the effect of electron transport chain dysfunction involving elevated reactive oxygen species production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared with their ancestor. Likewise, the gas-1 MA lines experienced partial recovery to wildtype reactive oxygen species levels. Whole-genome sequencing and analysis revealed that the molecular spectrum but not the overall rate of nuclear DNA mutation differed from wildtype patterns. Further analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome, and could be classified into a small number of functional-genomic categories. Characterization of a backcrossed four-mutation set isolated from one gas-1 MA line revealed this combination to be beneficial on both gas-1 mutant and wildtype genetic backgrounds. Our combined results suggest that selection favoring beneficial mutations can be powerful even under unfavorable population genetic conditions, and agree with fitness landscape theory predicting an inverse relationship between population fitness and the likelihood of adaptation.}, }
@article {pmid30056805, year = {2018}, author = {Seixas, FA and Boursot, P and Melo-Ferreira, J}, title = {The genomic impact of historical hybridization with massive mitochondrial DNA introgression.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {91}, doi = {10.1186/s13059-018-1471-8}, pmid = {30056805}, issn = {1474-760X}, support = {FCT-ANR/BIA-EVF/0250/2012//Fundação para a Ciência e a Tecnologia/International ; IF/00033/2014/CP1256/CT0005//Fundação para a Ciência e a Tecnologia/International ; SFRH/BD/87126/2012//Fundação para a Ciência e a Tecnologia/International ; ANR-12-ISV7-0002-01//Agence Nationale de la Recherche/International ; NORTE-01-0145-FEDER-000007//NORTE2020, ERDF/International ; }, mesh = {Adaptation, Biological/genetics ; *Animal Migration ; Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Europe ; Genetics, Population ; *Genome ; *Hybridization, Genetic ; Lagomorpha/classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; Recombination, Genetic ; Selection, Genetic ; Whole Genome Sequencing ; X Chromosome/chemistry ; }, abstract = {BACKGROUND: The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA.<br><br>RESULTS: Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions.<br><br>CONCLUSIONS: General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.}, }
@article {pmid29339819, year = {2018}, author = {Sharma, I and Sharma, V and Khan, A and Kumar, P and Rai, E and Bamezai, RNK and Vilar, M and Sharma, S}, title = {Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {851}, doi = {10.1038/s41598-017-18893-8}, pmid = {29339819}, issn = {2045-2322}, mesh = {DNA, Mitochondrial/chemistry/classification/metabolism ; Female ; Genetic Variation ; Haplotypes ; *Human Migration ; Humans ; India ; Male ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Jammu and Kashmir (J&amp;K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.}, }
@article {pmid30443184, year = {2018}, author = {Dou, X and Chen, L and Lei, M and Zellmer, L and Jia, Q and Ling, P and He, Y and Yang, W and Liao, DJ}, title = {Evaluating the Remote Control of Programmed Cell Death, with or without a Compensatory Cell Proliferation.}, journal = {International journal of biological sciences}, volume = {14}, number = {13}, pages = {1800-1812}, doi = {10.7150/ijbs.26962}, pmid = {30443184}, issn = {1449-2288}, abstract = {Organisms and their different component levels, whether organelle, cellular or other, come by birth and go by death, and the deaths are often balanced by new births. Evolution on the one hand has built demise program(s) in cells of organisms but on the other hand has established external controls on the program(s). For instance, evolution has established death program(s) in animal cells so that the cells can, when it is needed, commit apoptosis or senescent death (SD) in physiological situations and stress-induced cell death (SICD) in pathological situations. However, these programmed cell deaths are not predominantly regulated by the cells that do the dying but, instead, are controlled externally and remotely by the cells' superior(s), i.e. their host tissue or organ or even the animal's body. Currently, it is still unclear whether a cell has only one death program or has several programs respectively controlling SD, apoptosis and SICD. In animals, apoptosis exterminates, in a physiological manner, healthy but no-longer needed cells to avoid cell redundancy, whereas suicidal SD and SICD, like homicidal necrosis, terminate ill but useful cells, which may be followed by regeneration of the live cells and by scar formation to heal the damaged organ or tissue. Therefore, &quot;who dies&quot; clearly differentiates apoptosis from SD, SICD and necrosis. In animals, apoptosis can occur only in those cell types that retain a lifelong ability of proliferation and never occurs in those cell types that can no longer replicate in adulthood. In cancer cells, SICD is strengthened, apoptosis is dramatically weakened while SD has been lost. Most published studies professed to be about apoptosis are actually about SICD, which has four basic and well-articulated pathways involving caspases or involving pathological alterations in the mitochondria, endoplasmic reticula, or lysosomes.}, }
@article {pmid29428509, year = {2018}, author = {Sahoo, RK and Lohman, DJ and Wahlberg, N and Müller, CJ and Brattström, O and Collins, SC and Peggie, D and Aduse-Poku, K and Kodandaramaiah, U}, title = {Evolution of Hypolimnas butterflies (Nymphalidae): Out-of-Africa origin and Wolbachia-mediated introgression.}, journal = {Molecular phylogenetics and evolution}, volume = {123}, number = {}, pages = {50-58}, doi = {10.1016/j.ympev.2018.02.001}, pmid = {29428509}, issn = {1095-9513}, mesh = {Africa ; Animals ; Base Sequence ; Bayes Theorem ; Biodiversity ; *Biological Evolution ; Butterflies/*genetics/*microbiology ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Larva/physiology ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Wolbachia/*physiology ; }, abstract = {Hypolimnas butterflies (Nymphalidae), commonly known as eggflies, are a popular model system for studying a wide range of ecological questions including mimicry, polymorphism, wing pattern evolution, and Wolbachia-host interactions. The lack of a time-calibrated phylogeny for this group has precluded understanding its evolutionary history. We reconstruct a species-level phylogeny using a nine gene dataset and estimate species divergence times. Based on the resulting tree, we investigate the taxon's historical biogeography, examine the evolution of host plant preferences, and test the hypothesis that the endosymbiotic bacterium Wolbachia mediates gene transfer between species. Our analyses indicate that the species are grouped within three strongly supported, deeply divergent clades. However, relationships among these three clades are uncertain. In addition, many Hypolimnas species are not monophyletic or monophyletic with weak support, suggesting widespread incomplete lineage sorting and/or introgression. Biogeographic analysis strongly indicates that the genus diverged from its ancestor in Africa and subsequently dispersed to Asia; the strength of this result is not affected by topological uncertainties. While the larvae of African species feed almost exclusively on Urticaceae, larvae of species found further east often feed on several additional families. Interestingly, we found an identical mitochondrial haplotype in two Hypolimnas species, H. bolina and H. alimena, and a strong association between this mitotype and the Wolbachia strain wBol1a. Future investigations should explore the plausibility of Wolbachia-mediated introgression between species.}, }
@article {pmid30421421, year = {2018}, author = {Patten, MM}, title = {The X chromosome favors males under sexually antagonistic selection.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1111/evo.13646}, pmid = {30421421}, issn = {1558-5646}, abstract = {The X chromosome is found twice as often in females as males. This has led to an intuition that X-linked genes for traits experiencing sexually antagonistic selection should tend to evolve toward the female optimum. However, this intuition has never been formally examined. In this paper, I present a simple mathematical model and ask whether the X chromosome is indeed biased toward effecting female-optimal phenotypes. Counter to the intuition, I find that the exact opposite bias exists; the X chromosome is revealed to be a welcome spot for mutations that benefit males at the expense of females. Not only do male-beneficial alleles have an easier time of invading and spreading through a population, but they also achieve higher equilibrium frequencies than comparable female-beneficial alleles. The X chromosome is therefore expected over evolutionary time to nudge phenotypes closer to the male optimum. Consequently, the X chromosome should find itself engaged in perpetual intragenomic conflicts with the autosomes and the mitochondria over developmental outcomes. The X chromosome's male bias and the intragenomic conflicts that ensue bear on the evolution of gene regulation, speciation, and our concept of organismality. This article is protected by copyright. All rights reserved.}, }
@article {pmid30419142, year = {2018}, author = {Muthye, V and Lavrov, DV}, title = {Characterization of mitochondrial proteomes of nonbilaterian animals.}, journal = {IUBMB life}, volume = {}, number = {}, pages = {}, doi = {10.1002/iub.1961}, pmid = {30419142}, issn = {1521-6551}, support = {//Iowa State University/ ; }, abstract = {Mitochondria require ~1,500 proteins for their maintenance and proper functionality, which constitute the mitochondrial proteome (mt-proteome). Although a few of these proteins, mostly subunits of the electron transport chain complexes, are encoded in mitochondrial DNA (mtDNA), the vast majority are encoded in the nuclear genome and imported to the organelle. Previous studies have shown a continuous and complex evolution of mt-proteome among eukaryotes. However, there was less attention paid to mt-proteome evolution within Metazoa, presumably because animal mtDNA and, by extension, animal mitochondria are often considered to be uniform. In this analysis, two bioinformatic approaches (Orthologue-detection and Mitochondrial Targeting Sequence prediction) were used to identify mt-proteins in 23 species from four nonbilaterian phyla: Cnidaria, Ctenophora, Placozoa, and Porifera, as well as two choanoflagellates, the closest animal relatives. Our results revealed a large variation in mt-proteome in nonbilaterian animals in size and composition. Myxozoans, highly reduced cnidarian parasites, possessed the smallest inferred mitochondrial proteomes, while calcareous sponges possessed the largest. About 513 mitochondrial orthologous groups were present in all nonbilaterian phyla and human. Interestingly, 42 human mitochondrial proteins were not identified in any nonbilaterian species studied and represent putative innovations along the bilaterian branch. Several of these proteins were involved in apoptosis and innate immunity, two processes known to evolve within Metazoa. Conversely, several proteins identified as mitochondrial in nonbilaterian phyla and animal outgroups were absent in human, representing cases of possible loss. Finally, a few human cytosolic proteins, such as histones and cytosolic ribosomal proteins, were predicted to be targeted to mitochondria in nonbilaterian animals. Overall, our analysis provides the first step in characterization of mt-proteomes in nonbilaterian animals and understanding evolution of animal mt-proteome. © 2018 IUBMB Life, 2018.}, }
@article {pmid30417348, year = {2018}, author = {Lasne, C and Van Heerwaarden, B and Sgrò, CM and Connallon, T}, title = {Quantifying the relative contributions of the X chromosome, autosomes and mitochondrial genome to local adaptation.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1111/evo.13647}, pmid = {30417348}, issn = {1558-5646}, abstract = {During local adaptation with gene flow, some regions of the genome are inherently more responsive to selection than others. Recent theory predicts that X-linked genes should disproportionately contribute to local adaptation relative to other genomic regions, yet this prediction remains to be tested. We carried out a multi-generation crossing scheme, using two cline-end populations of Drosophila melanogaster, to estimate the relative contributions of the X chromosome, autosomes and mitochondrial genome to adaptive divergence in four traits involved in local adaptation (wing size, and resistance to heat, desiccation, and starvation stresses). We found that the mitochondrial genome and autosomes contributed significantly to clinal divergence in three of the four traits. In contrast, the X made no significant contribution to divergence in these traits. Given the small size of the mitochondrial genome, our results indicate that it plays a surprisingly large role in clinal adaptation. In contrast, the X, which represents roughly 20% of the Drosophila genome, contributes negligibly - a pattern that conflicts with theoretical predictions. These patterns reinforce recent work implying a central role of mitochondria in climatic adaptation, and suggest that different genomic regions may play fundamentally different roles in processes of divergence with gene flow. This article is protected by copyright. All rights reserved.}, }
@article {pmid30316921, year = {2019}, author = {Gao, XM and Mu, DL and Hou, CC and Zhu, JQ and Jin, S and Wang, CL}, title = {Expression and putative functions of KIFC1 for nuclear reshaping and midpiece formation during spermiogenesis of Phascolosoma esculenta.}, journal = {Gene}, volume = {683}, number = {}, pages = {169-183}, doi = {10.1016/j.gene.2018.10.021}, pmid = {30316921}, issn = {1879-0038}, mesh = {Animals ; Binding Sites ; Cell Nucleus/metabolism ; Gene Expression Regulation ; Kinesin/chemistry/*genetics/*metabolism ; Male ; Microtubules/metabolism ; Models, Molecular ; Phylogeny ; Polychaeta/genetics/*physiology ; Protein Conformation ; Protein Domains ; Protein Transport ; *Spermatogenesis ; }, abstract = {Kinesin-14 KIFC1 plays an important role in vesicular transport, microtubule organization, and spermiogenesis. In this study, we first investigated the microtubule distribution and expression pattern of KIFC1 during spermiogenesis of P. esculenta. Microtubules are abundant during spermiogenesis of P. esculenta and may be related to the generation and maintenance of pseudopodia-like cytoplasmic protrusions and nuclear reshaping. The Pe-KIFC1 protein is conserved with a motor domain where microtubule and ATP binding sites are predicted, a coiled-coil domain and a divergent tail domain. The Pe-kifc1 gene was extensively expressed and showed the highest expression in coelomic fluid where spermiogenesis occurs. We further observed the expression of kifc1 mRNA and protein and found that Pe-KIFC1 protein primarily co-localized with microtubules during spermiogenesis, indicating that KIFC1 might play several roles during this process via its cargo transport and/or microtubule organization function. In addition, co-localization of mitochondria and KIFC1 was also detected during spermiogenesis, which were located in the midpiece in mature sperm, suggesting that mitochondria might be a cargo of Pe-KIFC1 that participates in the intracellular distribution of mitochondria and formation of the midpiece. Based on our detailed observations of the dynamic distribution of microtubules, KIFC1, and mitochondria during spermiogenesis and the conserved function of KIFC1 in cargo transport and microtubule organization, functional models of Pe-KIFC1 during spermiogenesis are proposed, including the participation of KIFC1 in nuclear reshaping and midpiece formation.}, }
@article {pmid29916730, year = {2018}, author = {Chang, CH and Dai, WY and Chen, TY and Lee, AH and Hou, HY and Liu, SH and Jang-Liaw, NH}, title = {DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens.}, journal = {Genome}, volume = {61}, number = {8}, pages = {615-624}, doi = {10.1139/gen-2017-0264}, pmid = {29916730}, issn = {1480-3321}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genetic Markers ; Government ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; Taiwan ; Turtles/classification/*genetics ; }, abstract = {Compared to traditional morphological identification, DNA barcoding-molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)-provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding. To increase the accuracy of DNA barcoding, Taipei Zoo will continue to enrich the BOLD database and also establish a genetic database, to include additional genetic markers, by using government-seized chelonian specimens. A fast and accurate method to authenticate seized samples could assist law enforcement agencies to prosecute criminals and restrict illegal exploitation of wild chelonian resources.}, }
@article {pmid29913080, year = {2018}, author = {Wilkerson, CD and Mahoney, SP and Carr, SM}, title = {Post-glacial recolonization of insular Newfoundland across the Strait of Belle Isle gave rise to an endemic subspecies of woodland caribou, Rangifer tarandus terranovae (Bangs, 1896): evidence from mtDNA haplotypes.}, journal = {Genome}, volume = {61}, number = {8}, pages = {575-585}, doi = {10.1139/gen-2017-0199}, pmid = {29913080}, issn = {1480-3321}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Forests ; *Genetic Speciation ; Haplotypes/genetics ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Newfoundland and Labrador ; Reindeer/*genetics ; }, abstract = {Post-glacial origins of woodland caribou (Rangifer tarandus subsp.) on the island of Newfoundland and their relationship to mainland populations have been uncertain. Sequence analysis of 2223 bp of the mitochondrial DNA control region and cytochrome b gene from 233 Newfoundland caribou identified 32 haplotypes in four major clades. Comparison with other Nearctic caribou confirms a closer affinity of the basal Clade A with animals from the mainland, and as an outgroup to Clades B, C, and D that are endemic to the island. This indicates re-entry of caribou to post-glacial Newfoundland across the Strait of Belle Isle from Labrador, rather than from southern coastal refugia. Newfoundland caribou are a distinct subspecies, Rangifer tarandus terranovae (Bangs, 1896). Hierarchical AMOVA shows significant clinal differentiation of the major clades from northwest to southeast across the island. The isolated Avalon Peninsula population in the extreme southeast is genetically depauperate. Founder effects are evident in herds introduced to previously unoccupied areas by wildlife managers over the past 40-50 years. Reindeer introduced in the early 20th century have not contributed to mtDNA diversity in Newfoundland caribou.}, }
@article {pmid29794164, year = {2018}, author = {Ries, LNA and José de Assis, L and Rodrigues, FJS and Caldana, C and Rocha, MC and Malavazi, I and Bayram, Ö and Goldman, GH}, title = {The Aspergillus nidulans Pyruvate Dehydrogenase Kinases Are Essential To Integrate Carbon Source Metabolism.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {7}, pages = {2445-2463}, doi = {10.1534/g3.118.200411}, pmid = {29794164}, issn = {2160-1836}, mesh = {Aspergillus nidulans/classification/genetics/*metabolism ; Carbon/*metabolism ; Catabolite Repression ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Glucose/metabolism ; Hydrolysis ; Metabolic Networks and Pathways ; Metabolome ; Metabolomics/methods ; Multigene Family ; Phylogeny ; Protein Interaction Mapping ; Protein Interaction Maps ; Protein Transport ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; }, abstract = {The pyruvate dehydrogenase complex (PDH), that converts pyruvate to acetyl-coA, is regulated by pyruvate dehydrogenase kinases (PDHK) and phosphatases (PDHP) that have been shown to be important for morphology, pathogenicity and carbon source utilization in different fungal species. The aim of this study was to investigate the role played by the three PDHKs PkpA, PkpB and PkpC in carbon source utilization in the reference filamentous fungus Aspergillus nidulans, in order to unravel regulatory mechanisms which could prove useful for fungal biotechnological and biomedical applications. PkpA and PkpB were shown to be mitochondrial whereas PkpC localized to the mitochondria in a carbon source-dependent manner. Only PkpA was shown to regulate PDH activity. In the presence of glucose, deletion of pkpA and pkpC resulted in reduced glucose utilization, which affected carbon catabolite repression (CCR) and hydrolytic enzyme secretion, due to de-regulated glycolysis and TCA cycle enzyme activities. Furthermore, PkpC was shown to be required for the correct metabolic utilization of cellulose and acetate. PkpC negatively regulated the activity of the glyoxylate cycle enzyme isocitrate lyase (ICL), required for acetate metabolism. In summary, this study identified PDHKs important for the regulation of central carbon metabolism in the presence of different carbon sources, with effects on the secretion of biotechnologically important enzymes and carbon source-related growth. This work demonstrates how central carbon metabolism can affect a variety of fungal traits and lays a basis for further investigation into these characteristics with potential interest for different applications.}, }
@article {pmid28937858, year = {2018}, author = {Kramer, P and Bressan, P}, title = {Our (Mother's) Mitochondria and Our Mind.}, journal = {Perspectives on psychological science : a journal of the Association for Psychological Science}, volume = {13}, number = {1}, pages = {88-100}, doi = {10.1177/1745691617718356}, pmid = {28937858}, issn = {1745-6924}, mesh = {Animals ; Biological Evolution ; Humans ; Mental Disorders/physiopathology ; Mental Processes/*physiology ; Mitochondria/genetics/*physiology ; }, abstract = {Most of the energy we get to spend is furnished by mitochondria, minuscule living structures sitting inside our cells or dispatched back and forth within them to where they are needed. Mitochondria produce energy by burning down what remains of our meal after we have digested it, but at the cost of constantly corroding themselves and us. Here we review how our mitochondria evolved from invading bacteria and have retained a small amount of independence from us; how we inherit them only from our mother; and how they are heavily implicated in learning, memory, cognition, and virtually every mental or neurological affliction. We discuss why counteracting mitochondrial corrosion with antioxidant supplements is often unwise, and why our mitochondria, and therefore we ourselves, benefit instead from exercise, meditation, sleep, sunshine, and particular eating habits. Finally, we describe how malfunctioning mitochondria force rats to become socially subordinate to others, how such disparity can be evened off by a vitamin, and why these findings are relevant to us.}, }
@article {pmid28327596, year = {2017}, author = {Shen, CM and Hu, L and Yang, CH and Yin, CY and Li, ZD and Meng, HT and Guo, YX and Mei, T and Chen, F and Zhu, BF}, title = {Genetic polymorphisms of 54 mitochondrial DNA SNP loci in Chinese Xibe ethnic minority group.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44407}, doi = {10.1038/srep44407}, pmid = {28327596}, issn = {2045-2322}, mesh = {Alleles ; China ; DNA, Mitochondrial/*genetics ; *Ethnic Groups ; Gene Frequency ; Genetic Loci ; *Genetics, Population ; Haplotypes ; Humans ; Microsatellite Repeats ; Minority Groups ; Mitochondria/*genetics ; *Phylogeny ; *Polymorphism, Single Nucleotide ; }, abstract = {We analyzed the genetic polymorphisms of 54 mitochondrial DNA (mtDNA) variants in Chinese Xibe ethnic minority group. A total of 137 unrelated healthy volunteers from Chinese Xibe group were the objects of our study. Among the selected loci, there were 51 variable positions including transitions and transversions, and single nucleotide transitions were common (83.93%) versus transversions. These variations defined 64 different mtDNA haplotypes exclusive of (CA)n and 9 bp deletion variation. The haplotype diversity and discrimination power in Xibe population were 0.9800 ± 0.004 and 0.9699, respectively. Besides, we compared Xibe group with 18 other populations and reconstructed a phylogenetic tree using Neighbor-Joining method. The result revealed that Xibe group was a close to Xinjiang Han and Yanbian Korean groups. Our data also indicated that Xibe group has a close relationship with Daur and Ewenki groups, which is reflected by the history that Xibe was influenced by Daur and Ewenki groups during the development of these groups. In conclusion, the variants we studied are polymorphic and could be used as informative genetic markers for forensic and population genetic application.}, }
@article {pmid30395972, year = {2018}, author = {Fan, PC and Zhang, Y and Wang, Y and Wei, W and Zhou, YX and Xie, Y and Wang, X and Qi, YZ and Chang, L and Jia, ZP and Zhou, Z and Guan, H and Zhang, H and Xu, P and Zhou, PK}, title = {Quantitative proteomics reveals mitochondrial respiratory chain as a dominant target for carbon ion radiation: delayed reactive oxygen species generation caused DNA damage.}, journal = {Free radical biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2018.10.449}, pmid = {30395972}, issn = {1873-4596}, abstract = {Heavy ion radiotherapy has shown great promise for cancer therapy. Understanding the cellular response mechanism to heavy ion radiation is required to explore measures of overcoming devastating side effects. Here, we performed a quantitative proteomic analysis to investigate the mechanism of carbon ion irradiation on human AHH-1 lymphoblastoid cells. We identified 4602 proteins and quantified 4569 proteins showing high coverage in the mitochondria. Data are available via ProteomeXchange with identifier PXD008351. After stringent filtering, 290 proteins were found to be significantly up-regulated and 16 proteins were down-regulated. Functional analysis revealed that these up-regulated proteins were enriched in the process of DNA damage repair, mitochondrial ribosome, and particularly mitochondrial respiratory chain, accounting for approximately 50% of the accumulated proteins. Bioinformatics and functional analysis demonstrated that these up-regulated mitochondrial respiratory chain proteins enhanced ATP production and simultaneously reactive oxygen species release. More importantly, increased reactive oxygen species led to secondary organelle injury and lagged DNA double-strand breaks. Consistently, the expression of antioxidant enzymes was up-regulated for free radical scavenging. The mechanism of lagged secondary injury originated from disturbances in the mitochondrial respiratory chain. Our results provided a novel target for cell self-repair against heavy ion radiation-induced cellular damage.}, }
@article {pmid30394643, year = {2018}, author = {Rand, DM and Mossman, JA and Zhu, L and Biancani, LM and Ge, JY}, title = {Mitonuclear epistasis, genotype-by-environment interactions, and personalized genomics of complex traits in Drosophila.}, journal = {IUBMB life}, volume = {}, number = {}, pages = {}, doi = {10.1002/iub.1954}, pmid = {30394643}, issn = {1521-6551}, support = {NIA grant 1R01AG027849NIH grant 2R01GM067862/GF/NIH HHS/United States ; 1R01AG027849/GF/NIH HHS/United States ; 2R01GM067862/GF/NIH HHS/United States ; //Brown University/ ; }, abstract = {Mitochondrial function requires the coordinated expression of dozens of gene products from the mitochondrial genome and hundreds from the nuclear genomes. The systems that emerge from these interactions convert the food we eat and the oxygen we breathe into energy for life, while regulating a wide range of other cellular processes. These facts beg the question of whether the gene-by-gene interactions (G x G) that enable mitochondrial function are distinct from the gene-by-environment interactions (G x E) that fuel mitochondrial activity. We examine this question using a Drosophila model of mitonuclear interactions in which experimental combinations of mtDNA and nuclear chromosomes generate pairs of mitonuclear genotypes to test for epistatic interactions (G x G). These mitonuclear genotypes are then exposed to altered dietary or oxygen environments to test for G x E interactions. We use development time to assess dietary effects, and genome wide RNAseq analyses to assess hypoxic effects on transcription, which can be partitioned in to mito, nuclear, and environmental (G x G x E) contributions to these complex traits. We find that mitonuclear epistasis is universal, and that dietary and hypoxic treatments alter the epistatic interactions. We further show that the transcriptional response to alternative mitonuclear interactions has significant overlap with the transcriptional response to alternative oxygen environments. Gene coexpression analyses suggest that these shared genes are more central in networks of gene interactions, implying some functional overlap between epistasis and genotype by environment interactions. These results are discussed in the context of evolutionary fitness, the genetic basis of complex traits, and the challenge of achieving precision in personalized medicine. © 2018 IUBMB Life, :1-14, 2018.}, }
@article {pmid30391331, year = {2018}, author = {Xu, L and Peng, L and Gu, T and Yu, D and Yao, YG}, title = {The 3'UTR of human MAVS mRNA contains multiple regulatory elements for the control of protein expression and subcellular localization.}, journal = {Biochimica et biophysica acta. Gene regulatory mechanisms}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbagrm.2018.10.017}, pmid = {30391331}, issn = {1876-4320}, abstract = {Post-transcriptional regulation controls the mRNA stability, translation efficiency, and subcellular localization of a protein. The mitochondrial antiviral signaling protein (MAVS) plays a vital role in innate antiviral immunity. The MAVS mRNA has a long 3' untranslated region (UTR, >9 kb) and an understanding of this region may help to explain the post-transcriptional regulation in a key protein. In this study, we aimed to characterize the role of the MAVS 3'UTR during MAVS expression by truncating the 3'UTR into different fragments so as to identify the regulatory elements. We found that the different fragments (H1-H5) of the MAVS 3'UTR play different roles in regulating the subcellular localization and function of MAVS. Three AU-rich elements (AREs) in the MAVS 3'UTR H1 fragment (region 1-3445 in the 3'UTR) repressed MAVS expression by interacting with HuR to destabilize its mRNA. The MAVS 3'UTR H5 fragment (region 5955-7687 in the 3'UTR) affected the cellular localization of MAVS in mitochondria and influenced the subsequent antiviral function. Four miR-27a binding sites were recognized in the MAVS 3'UTR, and treatment of miR-27a inhibited MAVS expression and promoted the replication of the vesicular stomatitis virus (VSV). The identification of multiple regulatory elements in the MAVS 3'UTR offers new insights into the precise control of MAVS expression in innate immunity.}, }
@article {pmid30390623, year = {2018}, author = {Portugez, S and Martin, WF and Hazkani-Covo, E}, title = {Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {162}, doi = {10.1186/s12862-018-1279-x}, pmid = {30390623}, issn = {1471-2148}, support = {I-1321-203.13/2015//German-Israeli Foundation for Scientific Research and Development/ ; I-1321-203.13/2015//German-Israeli Foundation for Scientific Research and Development/ ; 666053//European Research Council/International ; }, abstract = {BACKGROUND: Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts and nupts are classified as simple if they are composed of a single organelle fragment or as complex if they are composed of multiple fragments. Mosaic insertions are complex insertions composed of fragments of both mitochondrial and plastid DNA. Simple numts and nupts in eukaryotes have been extensively studied, their mechanism of insertion involves non-homologous end joining (NHEJ). Mosaic insertions have been less well-studied and their mechanisms of integration are unknown.<br><br>RESULTS: Here we estimated the number of nuclear mosaic insertions (numins) in nine plant genomes. We show that numins compose up to 10% of the total nuclear insertions of organelle DNA in these plant genomes. The NHEJ hallmarks typical for numts and nupts were also identified in mosaic insertions. However, the number of identified insertions that integrated via NHEJ mechanism is underestimated, as NHEJ signatures are conserved only in recent insertions and mutationally eroded in older ones. A few complex insertions show signatures of long homology that cannot be attributed to NHEJ, a novel observation that implicates gene conversion or single strand annealing mechanisms in organelle nuclear insertions.<br><br>CONCLUSIONS: The common NHEJ signature that was identified here reveals that, in plant cells, mitochondria and plastid fragments in numins must meet during or prior to integration into the nuclear genome.}, }
@article {pmid29374514, year = {2018}, author = {Godahewa, GI and Perera, NCN and Nam, BH and Lee, J}, title = {Antioxidative properties and structural features of atypical 2-Cys peroxiredoxin from Sebastes schlegelii.}, journal = {Developmental and comparative immunology}, volume = {82}, number = {}, pages = {152-164}, doi = {10.1016/j.dci.2018.01.015}, pmid = {29374514}, issn = {1879-0089}, mesh = {Animals ; Antioxidants ; Cloning, Molecular ; Cysteine/genetics ; Fish Proteins/*genetics/metabolism ; Fishes/*metabolism ; Gills/*metabolism ; Insulin/metabolism ; Liver/*metabolism ; Mitochondria/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Peroxiredoxins/*genetics/metabolism ; Phylogeny ; Reactive Oxygen Species/metabolism ; Streptococcal Infections/*immunology ; Streptococcus iniae/*immunology ; Structure-Activity Relationship ; Transcriptome ; Vertebrates ; }, abstract = {Atypical 2-Cys peroxiredoxin (Prx5) is an antioxidant protein that exerts its antioxidant function by detoxifying different reactive oxygen species (ROS). Here, we identified mitochondrial Prx5 from rockfish (SsPrx5) and described its specific structural and functional characteristics. The open reading frame (ORF) of SsPrx5 (570 bp) was translated into a 190-amino acid polypeptide that contained a mitochondrial targeting sequence (MTS), thioredoxin 2 domain, two Prx-specific signature motifs, and three conserved cysteine residues. Sequence comparison indicated that the SsPrx5 protein sequence shared greatest identity with teleost orthologs, where the phylogenetic results showed an evolutionary position within the fish Prx5. The coding sequence of SsPrx5 was scattered in six exons as found in other vertebrates. Additionally, the potent antioxidant functions of recombinantly expressed SsPrx5 protein was demonstrated by insulin reduction and extracellular H2O2 scavenging both in vitro and in vivo. Quantitative real time PCR (qPCR) detected ubiquitous mRNA expression of SsPrx5 in healthy rockfish tissues, with remarkable expression observed in gill, liver, and reproductive tissues. Prompt transcription of SsPrx5 was shown in the immune-stimulated gill and liver tissues against Streptococcus iniae and lipopolysaccharide injection. Taken together, present results suggest the indispensable role of SsPrx5 in the rockfish antioxidant defense system against oxidative stresses and its role in maintaining redox balance upon pathogen invasion.}, }
@article {pmid30385634, year = {2018}, author = {Loell, K and Nanda, V}, title = {Marginal protein stability drives subcellular proteome isoelectric point.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1809098115}, pmid = {30385634}, issn = {1091-6490}, abstract = {There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome-a highly acidic compartment in the cell-have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.}, }
@article {pmid29787733, year = {2018}, author = {Younas, F and Soltanmohammadi, N and Knapp, O and Benz, R}, title = {The major outer membrane protein of Legionella pneumophila Lpg1974 shows pore-forming characteristics similar to the human mitochondrial outer membrane pore, hVDAC1.}, journal = {Biochimica et biophysica acta. Biomembranes}, volume = {1860}, number = {8}, pages = {1544-1553}, doi = {10.1016/j.bbamem.2018.05.008}, pmid = {29787733}, issn = {0005-2736}, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/chemistry/classification/genetics/*metabolism ; Escherichia coli/metabolism ; Humans ; Legionella pneumophila/*metabolism ; Lipid Bilayers/chemistry/metabolism ; Phylogeny ; Protein Structure, Secondary ; Recombinant Proteins/biosynthesis/chemistry/isolation &amp; purification ; Sequence Alignment ; Voltage-Dependent Anion Channel 1/chemistry/*metabolism ; }, abstract = {Legionella pneumophila is an aerobic and nonspore-forming pathogenic Gram-negative bacterium of the genus Legionella. It is the causative agent of Legionnaires' disease, also known as Legionellosis. The hosts of this organism are diverse, ranging from simple water borne protozoans such as amoebae to more complex hosts such as macrophages in humans. Genome analyses have shown the presence of genes coding for eukaryotic like proteins in several Legionella species. The presence of these proteins may assist L. pneumophila in its adaptation to the eukaryotic host. We studied the characteristics of a protein (Lpg1974) of L. pneumophila that shows remarkable homologies in length of the primary sequence and for the identity/homology of many amino acids to the voltage dependent anion channel (human VDAC1, Porin 31HL) of human mitochondria. Two different forms of Lpg1974 were overexpressed in Escherichia coli and purified to homogeneity: the one containing a putative N-terminal signal sequence and one without it. Reconstituted protein containing the signal sequence formed ion-permeable pores in lipid bilayer membranes with a conductance of approximately 5.4 nS in 1 M KCl. When the predicted N-terminal signal peptide of Lpg1974 comprising an α-helical structure similar to that at the N-terminus of hVDAC1 was removed, the channels formed in reconstitution experiments had a conductance of 7.6 nS in 1 M KCl. Both Lpg1974 proteins formed pores that were voltage-dependent and anion-selective similar to the pores formed by hVDAC1. These results suggest that Lpg1974 of L. pneumophila is indeed a structural and functional homologue to hVDAC1.}, }
@article {pmid28256554, year = {2017}, author = {Tong, W and He, Q and Park, YJ}, title = {Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43327}, doi = {10.1038/srep43327}, pmid = {28256554}, issn = {2045-2322}, mesh = {Biological Evolution ; DNA, Plant/*genetics ; Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Oryza/classification/*genetics ; *Phylogeny ; Plant Breeding/methods ; Plant Weeds/classification/*genetics ; Polymorphism, Single Nucleotide ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.}, }
@article {pmid30378025, year = {2018}, author = {Gabaldón, T}, title = {Evolution of the Peroxisomal Proteome.}, journal = {Sub-cellular biochemistry}, volume = {89}, number = {}, pages = {221-233}, doi = {10.1007/978-981-13-2233-4_9}, pmid = {30378025}, issn = {0306-0225}, abstract = {Peroxisomes are single-membrane bound intracellular organelles that can be found in organisms across the tree of eukaryotes, and thus are likely to derive from an ancestral peroxisome in the last eukaryotic common ancestor (LECA). Yet, peroxisomes in different lineages can present a large diversity in terms of their metabolic capabilities, which reflects a highly variable proteomic content. Theories on the evolutionary origin of peroxisomes have shifted in the last decades from scenarios involving an endosymbiotic origin, similar to those of mitochondria and plastids, towards hypotheses purporting an endogenous origin from within the endomembrane system. The peroxisomal proteome is highly dynamic in evolutionary terms, and can evolve via differential loss and gain of proteins, as well as via relocalization of proteins from and to other sub-cellular compartments. Here, I review current knowledge and discussions on the diversity, origin, and evolution of the peroxisomal proteome.}, }
@article {pmid30377874, year = {2018}, author = {Cai, C and Liu, F and Jiang, T and Wang, L and Jia, R and Zhou, L and Gu, K and Ren, J and He, P}, title = {Comparative study on mitogenomes of green tide algae.}, journal = {Genetica}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10709-018-0046-7}, pmid = {30377874}, issn = {1573-6857}, support = {18ZR1417400//Shanghai Natural Science Fund/ ; 41576163//National Natural Science Foundation of China/ ; 2016YFC1402105//National Key R&amp;D Program of China/ ; MATHAB2017010//Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, S.O.A./ ; }, abstract = {Since 2007, the annual green tide disaster in the Yellow Sea has brought serious economic losses to China. There is no research on the genetic similarities of four constituent species of green tide algae at the genomic level. We previously determined the mitochondrial genomes of Ulva prolifera, Ulva linza and Ulva flexuosa. In the present work, the mitochondrial genome of another green tide (Ulva compressa) was sequenced and analyzed. With the length of 62,311 bp, it contained 29 encoding genes, 26 tRNAs and 10 open reading frames. By comparing these four mitochondrial genomes, we found that U. compressa was quite different from the other three types of Ulva species. However, there were similarities between U. prolifera and U. linza in the number, distribution and homology of open reading frames, evolutionary and codon variation of tRNA, evolutionary relationship and selection pressure of coding genes. Repetitive sequence analysis of simple sequence repeats, tandem repeat and forward repeats further supposed that they have evolved from the same origin. In addition, we directly analyzed gene homologies and translocation of four green tide algae by Mauve alignment. There were gene order rearrangements among them. With fast-evolving genomes, these four green algal mitochondria have both conservatism and variation, thus opening another window for the understanding of origin and evolution of Ulva.}, }
@article {pmid28262720, year = {2017}, author = {Gandini, CL and Sanchez-Puerta, MV}, title = {Foreign Plastid Sequences in Plant Mitochondria are Frequently Acquired Via Mitochondrion-to-Mitochondrion Horizontal Transfer.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43402}, doi = {10.1038/srep43402}, pmid = {28262720}, issn = {2045-2322}, mesh = {Arecaceae/classification/genetics ; Base Sequence ; DNA, Mitochondrial ; Evolution, Molecular ; Fagaceae/classification/genetics ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plastid ; Lamiaceae/classification/genetics ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Plastids/*genetics ; Rosaceae/classification/genetics ; }, abstract = {Angiosperm mitochondrial genomes (mtDNA) exhibit variable quantities of alien sequences. Many of these sequences are acquired by intracellular gene transfer (IGT) from the plastid. In addition, frequent events of horizontal gene transfer (HGT) between mitochondria of different species also contribute to their expanded genomes. In contrast, alien sequences are rarely found in plastid genomes. Most of the plant-to-plant HGT events involve mitochondrion-to-mitochondrion transfers. Occasionally, foreign sequences in mtDNAs are plastid-derived (MTPT), raising questions about their origin, frequency, and mechanism of transfer. The rising number of complete mtDNAs allowed us to address these questions. We identified 15 new foreign MTPTs, increasing significantly the number of those previously reported. One out of five of the angiosperm species analyzed contained at least one foreign MTPT, suggesting a remarkable frequency of HGT among plants. By analyzing the flanking regions of the foreign MTPTs, we found strong evidence for mt-to-mt transfers in 65% of the cases. We hypothesize that plastid sequences were initially acquired by the native mtDNA via IGT and then transferred to a distantly-related plant via mitochondrial HGT, rather than directly from a foreign plastid to the mitochondrial genome. Finally, we describe three novel putative cases of mitochondrial-derived sequences among angiosperm plastomes.}, }
@article {pmid30373839, year = {2018}, author = {Mehta, AP and Supekova, L and Chen, JH and Pestonjamasp, K and Webster, P and Ko, Y and Henderson, SC and McDermott, G and Supek, F and Schultz, PG}, title = {Engineering yeast endosymbionts as a step toward the evolution of mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1813143115}, pmid = {30373839}, issn = {1091-6490}, abstract = {It has been hypothesized that mitochondria evolved from a bacterial ancestor that initially became established in an archaeal host cell as an endosymbiont. Here we model this first stage of mitochondrial evolution by engineering endosymbiosis between Escherichia coli and Saccharomyces cerevisiae An ADP/ATP translocase-expressing E. coli provided ATP to a respiration-deficient cox2 yeast mutant and enabled growth of a yeast-E. coli chimera on a nonfermentable carbon source. In a reciprocal fashion, yeast provided thiamin to an endosymbiotic E. coli thiamin auxotroph. Expression of several SNARE-like proteins in E. coli was also required, likely to block lysosomal degradation of intracellular bacteria. This chimeric system was stable for more than 40 doublings, and GFP-expressing E. coli endosymbionts could be observed in the yeast by fluorescence microscopy and X-ray tomography. This readily manipulated system should allow experimental delineation of host-endosymbiont adaptations that occurred during evolution of the current, highly reduced mitochondrial genome.}, }
@article {pmid29892953, year = {2018}, author = {Liu, W and Hu, C and Xie, W and Chen, P and Zhang, Y and Yao, R and Li, K and Chang, Q}, title = {The mitochondrial genome of red-necked phalarope Phalaropus lobatus (Charadriiformes: Scolopacidae) and phylogeny analysis among Scolopacidae.}, journal = {Genes &amp; genomics}, volume = {40}, number = {5}, pages = {455-463}, doi = {10.1007/s13258-017-0632-6}, pmid = {29892953}, issn = {2092-9293}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Birds/genetics ; Charadriiformes/*genetics ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {The red-necked phalarope is a wonderful species with specific morphological characters and lifestyles. Mitochondrial genomes, encoding necessary proteins involved in the system of energy metabolism, are important for the evolution and adaption of species. In this study, we determined the complete mitogenome sequence of Phalaropus lobatus (Charadriiformes: Scolopacidae). The circular genome is 16714 bp in size, containing 13 PCGs, two ribosomal RNAs and 22 tRNAs and a high AT-rich control region. The AT skew and GC skew of major strand is positive and negative respectively. Most of PCGs are biased towards A-rich except ND1. A codon usage analysis shows that 3 start codons (ATG, GTG and ATA), 4 stop codons (TAA, TAG, AGG, AGA) and two incomplete terminate codons (T-). Twenty two transfer RNAs have the typical cloverleaf structure, and a total of ten base pairs are mismatched throughout the nine tRNA genes. The phylogenetic tree based on 13 PCGs and 2 rRNA genes indicates that monophyly of the family and genus Phalaropus is close to genus Xenus plus Tringa. The analysis of selective pressure shows 13 protein-coding genes are evolving under the purifying selection and P. lobatus is different from other Scolopacidae species on the selective pressure of gene ND4. This study helps us know the inherent mechanism of mitochondrial structure and natural selection.}, }
@article {pmid29850800, year = {2018}, author = {Guillory, WX and Onyshchenko, A and Ruck, EC and Parks, M and Nakov, T and Wickett, NJ and Alverson, AJ}, title = {Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta).}, journal = {Genome biology and evolution}, volume = {10}, number = {6}, pages = {1504-1515}, doi = {10.1093/gbe/evy103}, pmid = {29850800}, issn = {1759-6653}, mesh = {DNA, Mitochondrial/genetics ; Diatoms/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial/*genetics ; Introns/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.}, }
@article {pmid29171872, year = {2017}, author = {Luévano-Martínez, LA and Kowaltowski, AJ}, title = {Topological characterization of the mitochondrial phospholipid scramblase 3.}, journal = {FEBS letters}, volume = {591}, number = {24}, pages = {4056-4066}, doi = {10.1002/1873-3468.12917}, pmid = {29171872}, issn = {1873-3468}, mesh = {Animals ; Cardiolipins/chemistry/metabolism ; Crystallography, X-Ray ; Intracellular Membranes/metabolism ; Male ; Mitochondria/*enzymology ; Models, Molecular ; Phospholipid Transfer Proteins/*chemistry/genetics/metabolism ; Phylogeny ; Rats ; Rats, Sprague-Dawley ; Saccharomyces cerevisiae ; }, abstract = {Scramblases redistribute phospholipids in biological membranes. Phospholipid scramblase 3 (PLSCR3), which is located in mitochondria, has been reported to be involved in cardiolipin distribution from the inner to the outer membrane, thus regulating cellular processes such as apoptosis or mitophagy. However, the localization and topology of this protein has not been convincingly addressed to support a role in intermembrane phospholipid transfer. Here, we studied PLSCR3 topology within mitochondria. We show that PLSCR3 inserts in the inner membrane (IM) via its C-terminal transmembrane helix, whereas its N-terminal portion is oriented toward the intermembrane space where it is activated by calcium. Our results suggest that PLSCR3, via its C-terminal transmembrane domain, participates in the bidirectional movement of phospholipids within the IM.}, }
@article {pmid28059116, year = {2017}, author = {Wang, Q and Zhang, C and Wang, C and Qian, Y and Li, Z and Hong, J and Zhou, X}, title = {Further characterization of Maize chlorotic mottle virus and its synergistic interaction with Sugarcane mosaic virus in maize.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {39960}, doi = {10.1038/srep39960}, pmid = {28059116}, issn = {2045-2322}, mesh = {China ; Chloroplasts/physiology/virology ; Gammaherpesvirinae/classification/genetics/isolation &amp; purification/*pathogenicity ; Mitochondria/virology ; Photosynthesis ; Phylogeny ; Plant Diseases/*virology ; Potyvirus/classification/genetics/isolation &amp; purification/*pathogenicity ; Zea mays/*virology ; }, abstract = {Maize chlorotic mottle virus (MCMV) was first reported in maize in China in 2009. In this study we further analyzed the epidemiology of MCMV and corn lethal necrosis disease (CLND) in China. We determined that CLND observed in China was caused by co-infection of MCMV and sugarcane mosaic virus (SCMV). Phylogenetic analysis using four full-length MCMV cDNA sequences obtained in this study and the available MCMV sequences retrieved from GenBank indicated that Chinese MCMV isolates were derived from the same source. To screen for maize germplasm resistance against MCMV infection, we constructed an infectious clone of MCMV isolate YN2 (pMCMV) and developed an Agrobacterium-mediated injection procedure to allow high throughput inoculations of maize with the MCMV infectious clone. Electron microscopy showed that chloroplast photosynthesis in leaves was significantly impeded by the co-infection of MCMV and SCMV. Mitochondria in the MCMV and SCMV co-infected cells were more severely damaged than in MCMV-infected cells. The results of this study provide further insight into the epidemiology of MCMV in China and shed new light on physiological and cytopathological changes related to CLND in maize.}, }
@article {pmid30368957, year = {2018}, author = {Olsson, M and Friesen, CR and Rollings, N and Sudyka, J and Lindsay, W and Whittingtion, CM and Wilson, M}, title = {Long term effects of superoxide and DNA repair on lizard telomeres.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.14913}, pmid = {30368957}, issn = {1365-294X}, abstract = {Telomeres are the non-coding protein-nucleotide 'caps' at chromosome ends that contribute to chromosomal stability by protecting the coding parts of the linear DNA from shortening at cell division, and from erosion by reactive molecules. Recently, there has been some controversy between molecular and cell biologists, on the one hand, and evolutionary ecologists on the other, regarding whether reactive molecules erode telomeres during oxidative stress. Many studies of biochemistry and medicine have verified these relationships in cell culture, but other researchers have failed to find such effects in free-living vertebrates. Here we use a novel approach to measure free radicals (superoxide), mitochondrial 'content' (a combined measure of mitochondrial number and size in cells), telomere length and DNA damage at two primary time points during the mating season of an annual lizard species (Ctenophorus pictus). Superoxide levels early in the mating season vary widely and elevated levels predict shorter telomeres both at that time as well as several months later. These effects are likely driven by mitochondrial content, which significantly impacts late season superoxide (cells with more mitochondria have more superoxide), but superoxide effects on telomeres are counteracted by DNA repair as revealed by 8-hydroxy-2'-deoxyguanosine assays. We conclude that reactive oxygen species and DNA repair are fundamental for both short- and long-term regulation of lizard telomere length with pronounced effects of early-season cellular stress detectable on telomere length near lizard death. This article is protected by copyright. All rights reserved.}, }
@article {pmid30358111, year = {2018}, author = {Yu, J and Zhang, L and Li, Y and Zhu, X and Xu, S and Zhou, XM and Wang, H and Zhang, H and Liang, B and Liu, P}, title = {The Adrenal Lipid Droplet is a New Site for Steroid Hormone Metabolism.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e1800136}, doi = {10.1002/pmic.201800136}, pmid = {30358111}, issn = {1615-9861}, abstract = {Steroid hormones play essential roles for living organisms. It has been long and well established that the endoplasmic reticulum (ER) and mitochondria are essential sites for steroid hormone biosynthesis because several steroidogenic enzymes are located in these organelles. The adrenal gland lipid droplet (LD) proteomes from human, macaque monkey, and rodent were analyzed, revealing that steroidogenic enzymes are also present in abundance on LDs. The enzymes found include 3β-hydroxysteroid dehydrogenase (HSD3B), and estradiol 17β-dehydrogenase 11 (HSD17B11). Analyses by Western blot and subcellular localization consistently demonstrated that HSD3B2 was localized on LDs. Furthermore, in vitro experiments confirmed that the isolated LDs from HeLa cell stably expressing HSD3B2 or from rat adrenal glands had the capacity to convert pregnenolone to progesterone. Collectively, these data suggest that LDs may be important sites of steroid hormone metabolism. These findings may bring novel insights into the biosynthesis and metabolism of steroid hormones and the development of treatments for adrenal disorders. This article is protected by copyright. All rights reserved.}, }
@article {pmid30358065, year = {2018}, author = {Paris, Z and Alfonzo, JD}, title = {How the intracellular partitioning of tRNA and tRNA modification enzymes affects mitochondrial function.}, journal = {IUBMB life}, volume = {}, number = {}, pages = {}, doi = {10.1002/iub.1957}, pmid = {30358065}, issn = {1521-6551}, support = {AI131348/GF/NIH HHS/United States ; GM084065/GF/NIH HHS/United States ; CZ.02.1.01/0.0/0.0/16_019/0000759//ERDF/ESF project Centre for Research of Pathogenicity and Virulence of Parasites/ ; }, abstract = {Organisms have evolved different strategies to seclude certain molecules to specific locations of the cell. This is most pronounced in eukaryotes with their extensive intracellular membrane systems. Intracellular compartmentalization is particularly critical in genome containing organelles, which because of their bacterial evolutionary ancestry still maintain protein-synthesis machinery that resembles more their evolutionary origin than the extant eukaryotic cell they once joined as an endosymbiont. Despite this, it is clear that genome-containing organelles such as the mitochondria are not in isolation and many molecules make it across the mitochondrial membranes from the cytoplasm. In this realm the import of tRNAs and the enzymes that modify them prove most consequential. In this review, we discuss two recent examples of how modifications typically found in cytoplasmic tRNAs affect mitochondrial translation in organisms that forcibly import all their tRNAs from the cytoplasm. In our view, the combination of tRNA import and the compartmentalization of modification enzymes must have played a critical role in the evolution of the organelle. © 2018 IUBMB Life, 2018.}, }
@article {pmid30358047, year = {2018}, author = {Gabaldón, T}, title = {Relative timing of mitochondrial endosymbiosis and the &quot;pre-mitochondrial symbioses&quot; hypothesis.}, journal = {IUBMB life}, volume = {}, number = {}, pages = {}, doi = {10.1002/iub.1950}, pmid = {30358047}, issn = {1521-6551}, support = {ERC-2016-724173//H2020 European Research Council/ ; H2020-MSCA-ITN-2014-642095//H2020 Marie Skłodowska-Curie Actions/ ; BFU2015-67107//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; H2020-MSCA-ITN-2014-642095//Marie Sklodowska-Curie/ ; ERC-2016-724173//European Union's Horizon 2020/ ; SGR857//Catalan Research Agency/ ; //CERCA Programme/Generalitat de Catalunya/ ; //European Regional Development Fund/ ; BFU2015-67107//Spanish Ministry of Economy, Industry, and Competitiveness/ ; SEV-2012-0208//Spanish Ministry of Economy, Industry, and Competitiveness/ ; }, abstract = {The origin of eukaryotes stands as a major open question in biology. Central to this question is the nature and timing of the origin of the mitochondrion, an ubiquitous eukaryotic organelle originated by the endosymbiosis of an alphaproteobacterial ancestor. Different hypotheses disagree, among other aspects, on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host is debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Here, I will discuss recent findings from phylogenomics analyses of extant genomes that are shedding light into the evolutionary origins of the eukaryotic ancestor, and which suggest a later acquisition of alpha-proteobacterial derived proteins as compared to those with different bacterial ancestries. I argue that simple eukaryogenesis models that assume a binary symbiosis between an archaeon host and an alpha-proteobacterial proto-mitochondrion cannot explain the complex chimeric nature that is inferred for the eukaryotic ancestor. To reconcile existing hypotheses with the new data, I propose the &quot;pre-mitochondrial symbioses&quot; hypothesis that provides a framework for eukaryogenesis scenarios involving alternative symbiotic interactions that predate the acquisition of mitochondria. © 2018 IUBMB Life, 2018.}, }
@article {pmid30347487, year = {2018}, author = {Ligas, J and Pineau, E and Bock, R and Huynen, MA and Meyer, EH}, title = {The assembly pathway of Complex I in Arabidopsis thaliana.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.14133}, pmid = {30347487}, issn = {1365-313X}, abstract = {All present-day mitochondria originate from a single endosymbiotic event that gave rise to the last eukaryotic common ancestor (LECA) more than a billion years ago. However, to date, many aspects of mitochondrial evolution have remained unresolved. Comparative genomics and proteomics have revealed a complex evolutionary origin of many mitochondrial components. To understand the evolution of the respiratory chain, we have examined both the components and the mechanisms of the assembly pathway of complex I. Complex I represents the first enzyme of the respiratory chain, and complex I deficiencies have dramatic consequences in both animals and plants. The complex is located in the mitochondrial inner membrane and possesses two arms: one embedded in the inner membrane and one protruding in the matrix. Here, we describe the assembly pathway of complex I in the model plant Arabidopsis thaliana. Using a proteomic approach called complexome profiling, we have resolved the different steps in the assembly process in plants. We are proposing a model for the stepwise assembly of complex I including every subunit. We then compared this pathway with the corresponding pathway in humans and found that complex I assembly in plants follows a different, and likely ancestral, pathway compared to the one in humans. We show that the main evolutionary changes in complex I structure and assembly in humans occurred at the level of the membrane arm, whereas the matrix arm remained rather conserved. This article is protected by copyright. All rights reserved.}, }
@article {pmid30341492, year = {2018}, author = {Arakawa, T and Ue, S and Sano, C and Matsunaga, M and Kagami, H and Yoshida, Y and Kuroda, Y and Taguchi, K and Kitazaki, K and Kubo, T}, title = {Identification and characterization of a semi-dominant restorer-of-fertility 1 allele in sugar beet (Beta vulgaris).}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00122-018-3211-6}, pmid = {30341492}, issn = {1432-2242}, support = {18K05564//Japan Society for the Promotion of Science/ ; 16J01146//Japan Society for the Promotion of Science/ ; Research program on development of innovative technology//Bio-oriented Technology Research Advancement Institution/ ; Grant Number 30001A//Bio-oriented Technology Research Advancement Institution/ ; }, abstract = {KEY MESSAGE: The sugar beet Rf1 locus has a number of molecular variants. We found that one of the molecular variants is a weak allele of a previously identified allele. Male sterility (MS) caused by nuclear-mitochondrial interaction is called cytoplasmic male sterility (CMS) in which MS-inducing mitochondria are suppressed by a nuclear gene, restorer-of-fertility. Rf and rf are the suppressing and non-suppressing alleles, respectively. This dichotomic view, however, seems somewhat unsatisfactory to explain the recently discovered molecular diversity of Rf loci. In the present study, we first identified sugar beet line NK-305 as a new source of Rf1. Our crossing experiment revealed that NK-305 Rf1 is likely a semi-dominant allele that restores partial fertility when heterozygous but full fertility when homozygous, whereas Rf1 from another sugar beet line appeared to be a dominant allele. Proper degeneration of anther tapetum is a prerequisite for pollen development; thus, we compared tapetal degeneration in the NK-305 Rf1 heterozygote and the homozygote. Degeneration occurred in both genotypes but to a lesser extent in the heterozygote, suggesting an association between NK-305 Rf1 dose and incompleteness of tapetal degeneration leading to partial fertility. Our protein analyses revealed a quantitative correlation between NK-305 Rf1 dose and a reduction in the accumulation of a 250 kDa mitochondrial protein complex consisting of a CMS-specific mitochondrial protein encoded by MS-inducing mitochondria. The abundance of Rf1 transcripts correlated with NK-305 Rf1 dose. The molecular organization of NK-305 Rf1 suggested that this allele evolved through intergenic recombination. We propose that the sugar beet Rf1 locus has a series of multiple alleles that differ in their ability to restore fertility and are reflective of the complexity of Rf evolution.}, }
@article {pmid30333973, year = {2018}, author = {Lou, E and Zhai, E and Sarkari, A and Desir, S and Wong, P and Iizuka, Y and Yang, J and Subramanian, S and McCarthy, J and Bazzaro, M and Steer, CJ}, title = {Cellular and Molecular Networking Within the Ecosystem of Cancer Cell Communication via Tunneling Nanotubes.}, journal = {Frontiers in cell and developmental biology}, volume = {6}, number = {}, pages = {95}, doi = {10.3389/fcell.2018.00095}, pmid = {30333973}, issn = {2296-634X}, abstract = {Intercellular communication is vital to the ecosystem of cancer cell organization and invasion. Identification of key cellular cargo and their varied modes of transport are important considerations in understanding the basic mechanisms of cancer cell growth. Gap junctions, exosomes, and apoptotic bodies play key roles as physical modalities in mediating intercellular transport. Tunneling nanotubes (TNTs)-narrow actin-based cytoplasmic extensions-are unique structures that facilitate direct, long distance cell-to-cell transport of cargo, including microRNAs, mitochondria, and a variety of other sub cellular components. The transport of cargo via TNTs occurs between malignant and stromal cells and can lead to changes in gene regulation that propagate the cancer phenotype. More notably, the transfer of these varied molecules almost invariably plays a critical role in the communication between cancer cells themselves in an effort to resist death by chemotherapy and promote the growth and metastases of the primary oncogenic cell. The more traditional definition of &quot;Systems Biology&quot; is the computational and mathematical modeling of complex biological systems. The concept, however, is now used more widely in biology for a variety of contexts, including interdisciplinary fields of study that focus on complex interactions within biological systems and how these interactions give rise to the function and behavior of such systems. In fact, it is imperative to understand and reconstruct components in their native context rather than examining them separately. The long-term objective of evaluating cancer ecosystems in their proper context is to better diagnose, classify, and more accurately predict the outcome of cancer treatment. Communication is essential for the advancement and evolution of the tumor ecosystem. This interplay results in cancer progression. As key mediators of intercellular communication within the tumor ecosystem, TNTs are the central topic of this article.}, }
@article {pmid30326913, year = {2018}, author = {Zhu, Y and Gu, X and Xu, C}, title = {Mitochondrial DNA 7908-8816 region mutations in maternally inherited essential hypertensive subjects in China.}, journal = {BMC medical genomics}, volume = {11}, number = {1}, pages = {89}, doi = {10.1186/s12920-018-0408-0}, pmid = {30326913}, issn = {1755-8794}, support = {BL2013022//special fund for clinical medicine of Jiangsu province/ ; JS2006038//Health Department of Jiangsu Province (CN)/ ; }, abstract = {BACKGROUND: Nuclear genes or family-based mitochondrial screening have been the focus of genetic studies into essential hypertension. Studies into the role of mitochondria in sporadic Chinese hypertensives are lacking. The objective of the study was to explore the relationship between mitochondrial DNA (mtDNA) variations and the development of maternally inherited essential hypertension (MIEH) in China.<br><br>METHODS: Yangzhou residents who were outpatients or in-patients at the Department of Cardiology in Northern Jiangsu People's Hospital (Jiangsu, China) from June 2009 to June 2015 were recruited in a 1:1 case control study of 600 gender-matched Chinese MIEH subjects and controls. Genomic DNA was isolated from whole blood cells. The most likely sites for hypertension were screened using oligodeoxynucleotides at positions 7908-8816, purified and subsequently analyzed by direct sequencing according to the revised consensus Cambridge sequence. The frequency, density, type and conservative evolution of mtDNA variations were comprehensively analyzed.<br><br>RESULTS: We found a statistical difference between the two groups for body mass index, waist circumference, abdominal circumference, triglyceride, low-density lipoprotein cholesterol, fasting blood glucose, uric acid, creatinine and blood urea nitrogen (P < 0.05). More amino-acid changes and RNA variants were found in MIEH subjects than the controls (P < 0.01). The detection system simultaneously identified 40 different heteroplasmic or homoplasmic mutations in 4 genes: COXII, tRNALys, ATP8 and ATP 6. The mtDNA variations were mainly distributed in regions of ATP6 binding sites, and the site of highest mutation frequency was m. 8414C > T. Three changes in single bases (C8414T in ATP8, A8701G in ATP6 and G8584A in ATP6) were significantly different in the MIEH patients and the controls (P < 0.001). The m.8273_8281del mutation was identified from 59 MIEH patients.<br><br>CONCLUSIONS: Our results indicate that novel mtDNA mutations may be involved in the pathological process of MIEH, and mitochondrial genetic characteristics were identified in MIEH individuals.}, }
@article {pmid30304578, year = {2018}, author = {Burger, G and Valach, M}, title = {Perfection of eccentricity: Mitochondrial genomes of diplonemids.}, journal = {IUBMB life}, volume = {}, number = {}, pages = {}, doi = {10.1002/iub.1927}, pmid = {30304578}, issn = {1521-6551}, support = {MOP-79309//Canadian Institutes of Health Research/Canada ; GBMF-4983//Gordon and Betty Moore Foundation/ ; RGPIN-2014-05286//NSERC/ ; }, abstract = {Mitochondria are the sandbox of evolution as exemplified most particularly by the diplonemids, a group of marine microeukaryotes. These protists are uniquely characterized by their highly multipartite mitochondrial genome and systematically fragmented genes whose pieces are spread out over several dozens of chromosomes. The type species Diplonema papillatum was the first member of this group in which the expression of fragmented mitochondrial genes was investigated experimentally. We now know that gene expression involves separate transcription of gene pieces (modules), RNA editing of module transcripts, and module joining to mature mRNAs and rRNAs. The mechanism of cognate module recognition and ligation is distinct from known intron splicing and remains to be uncovered. Here, we review the current status of research on mitochondrial genome architecture, as well as gene complement, structure, and expression modes in diplonemids. Further, we discuss the potential molecular mechanisms of posttranscriptional processing, and finally reflect on the evolutionary trajectories and trends of mtDNA evolution as seen in this protist group. © 2018 IUBMB Life, 2018.}, }
@article {pmid30304531, year = {2018}, author = {Urantowka, AD and Kroczak, A and Silva, T and Padrón, RZ and Gallardo, NF and Blanch, J and Blanch, B and Mackiewicz, P}, title = {New insight into parrots' mitogenomes indicates that their ancestor contained a duplicated region.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msy189}, pmid = {30304531}, issn = {1537-1719}, abstract = {Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate PCR strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups.}, }
@article {pmid30281911, year = {2018}, author = {van Esveld, SL and Huynen, MA}, title = {Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins?.}, journal = {IUBMB life}, volume = {}, number = {}, pages = {}, doi = {10.1002/iub.1940}, pmid = {30281911}, issn = {1521-6551}, support = {//Radboud Institute for Molecular Life Sciences/ ; R0002792//Radboudumc/ ; }, abstract = {Most eukaryotic cells contain mitochondria with a genome that evolved from their α-proteobacterial ancestor. In the course of eukaryotic evolution, the mitochondrial genome underwent a dramatic reduction in size, caused by the loss and translocation of genes. This required adjustments in mitochondrial gene expression mechanisms and resulted in a complex collaborative system of mitochondrially encoded transfer RNAs and ribosomal RNAs with nuclear encoded proteins to express the mitochondrial encoded oxidative phosphorylation (OXPHOS) proteins. In this review, we examine mitochondrial gene expression from an evolutionary point of view: to what extent can we correlate changes in the mitochondrial genome in the evolutionary lineage leading to human with the origin of new nuclear encoded proteins. We dated the evolutionary origin of mitochondrial proteins that interact with mitochondrial DNA or its RNA and/or protein products in a systematic manner and compared them with documented changes in the mitochondrial DNA. We find anecdotal but accumulating evidence that metazoan RNA-interacting proteins arose in conjunction with changes of the mitochondrial DNA. We find no substantial evidence for such compensatory evolution in new OXPHOS proteins, which appear to be constrained by the ability to form supercomplexes. © 2018 IUBMB Life, 1-11, 2018.}, }
@article {pmid30281880, year = {2018}, author = {Harborne, SPD and Kunji, ERS}, title = {Calcium-regulated mitochondrial ATP-Mg/Pi carriers evolved from a fusion of an EF-hand regulatory domain with a mitochondrial ADP/ATP carrier-like domain.}, journal = {IUBMB life}, volume = {}, number = {}, pages = {}, doi = {10.1002/iub.1931}, pmid = {30281880}, issn = {1521-6551}, support = {MC_UU_00015/1//Medical Research Council/United Kingdom ; }, abstract = {The mitochondrial ATP-Mg/Pi carrier is responsible for the calcium-dependent regulation of adenosine nucleotide concentrations in the mitochondrial matrix, which allows mitochondria to respond to changing energy requirements of the cell. The carrier is expressed in mitochondria of fungi, plants and animals and belongs to the family of mitochondrial carriers. The carrier is unusual as it consists of three separate domains: (i) an N-terminal regulatory domain with four calcium-binding EF-hands similar to calmodulin, (ii) a loop domain containing an amphipathic α-helix and (iii) a mitochondrial carrier domain related to the mitochondrial ADP/ATP carrier. This striking example of three domains coming together from different origins to provide new functions represents an interesting quirk of evolution. In this review, we outline how the carrier was identified and how its physiological role was established with a focus on human isoforms. We exploit the sequence and structural information of the domains to explore the similarities and differences to their closest counterparts; mitochondrial ADP/ATP carriers and proteins with four EF-hands. We discuss how their combined function has led to a mechanism for calcium-regulated transport of adenosine nucleotides. Finally, we compare the ATP-Mg/Pi carrier with the mitochondrial aspartate/glutamate carrier, the only other mitochondrial carrier regulated by calcium, and we will argue that they have arisen by convergent rather than divergent evolution. © 2018 The Authors IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 2018.}, }
@article {pmid30265295, year = {2018}, author = {Pereira, J and Lupas, AN}, title = {The Origin of Mitochondria-Specific Outer Membrane β-Barrels from an Ancestral Bacterial Fragment.}, journal = {Genome biology and evolution}, volume = {10}, number = {10}, pages = {2759-2765}, doi = {10.1093/gbe/evy216}, pmid = {30265295}, issn = {1759-6653}, abstract = {Outer membrane β-barrels (OMBBs) are toroidal arrays of antiparallel β-strands that span the outer membrane of Gram-negative bacteria and eukaryotic organelles. Although homologous, most families of bacterial OMBBs evolved through the independent amplification of an ancestral ββ-hairpin. In mitochondria, one family (SAM50) has a clear bacterial ancestry; the origin of the other family, consisting of 19-stranded OMBBs found only in mitochondria (MOMBBs), is substantially unclear. In a large-scale comparison of mitochondrial and bacterial OMBBs, we find evidence that the common ancestor of all MOMBBs emerged by the amplification of a double ββ-hairpin of bacterial origin, probably at the time of the Last Eukaryotic Common Ancestor. Thus, MOMBBs are indeed descended from bacterial OMBBs, but their fold formed independently in the proto-mitochondria, possibly in response to the need for a general-purpose polypeptide importer. This occurred by a process of amplification, despite the final fold having a prime number of strands.}, }
@article {pmid30258733, year = {2018}, author = {Huang, Y and Zheng, S and Mei, X and Yu, B and Sun, B and Li, B and Wei, J and Chen, J and Li, T and Pan, G and Zhou, Z and Li, C}, title = {A secretory hexokinase plays an active role in the proliferation of Nosema bombycis.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5658}, doi = {10.7717/peerj.5658}, pmid = {30258733}, issn = {2167-8359}, abstract = {The microsporidian Nosema bombycis is an obligate intracellular parasite of Bombyx mori, that lost its intact tricarboxylic acid cycle and mitochondria during evolution but retained its intact glycolysis pathway. N. bombycis hexokinase (NbHK) is not only a rate-limiting enzyme of glycolysis but also a secretory protein. Indirect immunofluorescence assays and recombinant HK overexpressed in BmN cells showed that NbHK localized in the nucleus and cytoplasm of host cell during the meront stage. When N. bombycis matured, NbHK tended to concentrate at the nuclei of host cells. Furthermore, the transcriptional profile of NbHK implied it functioned during N. bombycis' proliferation stages. A knock-down of NbHK effectively suppressed the proliferation of N. bombycis indicating that NbHK is an important protein for parasite to control its host.}, }
@article {pmid30256727, year = {2018}, author = {McClelland, GB and Scott, GR}, title = {Evolved Mechanisms of Aerobic Performance and Hypoxia Resistance in High-Altitude Natives.}, journal = {Annual review of physiology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-physiol-021317-121527}, pmid = {30256727}, issn = {1545-1585}, abstract = {Comparative physiology studies of high-altitude species provide an exceptional opportunity to understand naturally evolved mechanisms of hypoxia resistance. Aerobic capacity (VO2max) is a critical performance trait under positive selection in some high-altitude taxa, and several high-altitude natives have evolved to resist the depressive effects of hypoxia on VO2max. This is associated with enhanced flux capacity through the O2 transport cascade and attenuation of the maladaptive responses to chronic hypoxia that can impair O2 transport. Some highlanders exhibit elevated rates of carbohydrate oxidation during exercise, taking advantage of its high ATP yield per mole of O2. Certain highland native animals have also evolved more oxidative muscles and can sustain high rates of lipid oxidation to support thermogenesis. The underlying mechanisms include regulatory adjustments of metabolic pathways and to gene expression networks. Therefore, the evolution of hypoxia resistance in high-altitude natives involves integrated functional changes in the pathways for O2 and substrate delivery and utilization by mitochondria. Expected final online publication date for the Annual Review of Physiology Volume 81 is February 10, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid30211573, year = {2018}, author = {Geary, DC}, title = {Efficiency of mitochondrial functioning as the fundamental biological mechanism of general intelligence (g).}, journal = {Psychological review}, volume = {}, number = {}, pages = {}, doi = {10.1037/rev0000124}, pmid = {30211573}, issn = {1939-1471}, abstract = {General intelligence or g is one of the most thoroughly studied concepts in the behavioral sciences. Measures of intelligence are predictive of a wide range of educational, occupational, and life outcomes, including creative productivity and are systematically related to physical health and successful aging. The nexus of relations suggests 1 or several fundamental biological mechanisms underlie g, health, and aging, among other outcomes. Cell-damaging oxidative stress has been proposed as 1 of many potential mechanisms, but the proposal is underdeveloped and does not capture other important mitochondrial functions. I flesh out this proposal and argue that the overall efficiency of mitochondrial functioning is a core component of g; the most fundamental biological mechanism common to all brain and cognitive processes and that contributes to the relations among intelligence, health, and aging. The proposal integrates research on intelligence with models of the centrality of mitochondria to brain development and functioning, neurological diseases, and health more generally. Moreover, the combination of the maternal inheritance of mitochondrial DNA (mtDNA), the evolution of compensatory nuclear DNA, and the inability of evolutionary processes to purge deleterious mtDNA in males may contribute to the sex difference in variability in intelligence and in other cognitive domains. The proposal unifies many now disparate literatures and generates testable predictions for future studies. (PsycINFO Database Record}, }
@article {pmid30209549, year = {2018}, author = {Sandor, S and Zhang, Y and Xu, J}, title = {Fungal mitochondrial genomes and genetic polymorphisms.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-018-9350-5}, pmid = {30209549}, issn = {1432-0614}, support = {531998//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Mitochondria are the powerhouses of eukaryotic cells, responsible for ATP generation and playing a role in a diversity of cellular and organismal functions. Different from the majority of other intracellular membrane structures, mitochondria contain their own genetic materials that are capable of independent replication and inheritance. In this mini-review, we provide brief summaries of fungal mitochondrial genome structure, size, gene content, inheritance, and genetic variation. We pay special attention to the relative genetic polymorphisms of the mitochondrial vs nuclear genomes at the population level within individual fungal species. Among the 20 species/groups of species reviewed here, there is a range of variation among genes and species in the relative nuclear and mitochondrial genetic polymorphisms. Interestingly, most (15/20) showed a greater genetic diversity for nuclear genes and genomes than for mitochondrial genes and genomes, with the remaining five showing similar or slower nuclear genome genetic variations. This fungal pattern is different from the dominant pattern in animals, but more similar to that in plants. At present, the mechanisms for the variations among fungal species and the overall low level of mitochondrial sequence polymorphisms are not known. The increasing availability of population genomic data should help us reveal the potential genetic and ecological factors responsible for the observed variations.}, }
@article {pmid30206380, year = {2018}, author = {Jebb, D and Foley, NM and Whelan, CV and Touzalin, F and Puechmaille, SJ and Teeling, EC}, title = {Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13634}, doi = {10.1038/s41598-018-31093-2}, pmid = {30206380}, issn = {2045-2322}, support = {ERC-2012-StG311000//EC | European Research Council (ERC)/ ; }, abstract = {Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The &quot;Free Radical Theory of Ageing&quot; (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria deep-sequenced, with a subset sampled over multiple years. The majority of heteroplasmies were at a low frequency and were transitions. Oxidative mutations were present in only a small number of individuals, suggesting local oxidative stress events. Cohort data showed no significant increase in heteroplasmy with age, while longitudinal data from recaptured individuals showed heteroplasmy is dynamic, and does not increase uniformly over time. We show that bats do not suffer from the predicted, inevitable increase in heteroplasmy as posited by the FRTA, instead heteroplasmy was found to be dynamic, questioning its presumed role as a primary driver of ageing.}, }
@article {pmid30196672, year = {2018}, author = {Eom, KS and Park, H and Lee, D and Choe, S and Kang, Y and Bia, MM and Lee, SH and Keyyu, J and Fyumagwa, R and Jeon, HK}, title = {Molecular and Morphologic Identification of Spirometra ranarum Found in the Stool of African Lion, Panthera leo in the Serengeti Plain of Tanzania.}, journal = {The Korean journal of parasitology}, volume = {56}, number = {4}, pages = {379-383}, doi = {10.3347/kjp.2018.56.4.379}, pmid = {30196672}, issn = {1738-0006}, support = {2017R1D1A3B03035976//National Research Foundation of Korea/ ; PRB000720//Parasite Resource Bank of Korea/ ; }, mesh = {Animals ; Cyclooxygenase 1/genetics ; Feces/*parasitology ; Host-Parasite Interactions ; Lions/*parasitology ; Male ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Spirometra/anatomy &amp; histology/*genetics/*isolation &amp; purification ; Tanzania ; }, abstract = {The present study was performed with morphological and molecular analysis (cox1 and nad1 mitochondrial genes) to identify the proglottids of spirometrid tapeworm found in the stool of an African lion, Panthera leo, in the Serengeti plain of Tanzania. A strand of tapeworm strobila, about 75 cm in length, was obtained in the stool of a male African lion in the Serengeti National Park (34˚ 50' E, 02˚ 30' S), Tanzania, in February 2012. The morphological features of the adult worm examined exhibited 3 uterine coils with a bow tie appearance and adopted a diagonal direction in the second turn. The posterior uterine coils are larger than terminal uterine ball and the feature of uteri are swirling rather than spirally coiling. The sequence difference between the Spirometra species (Tanzania origin) and S. erinaceieuropaei (GenBank no. KJ599680) was 9.4% while those of S. decipiens (GenBank no. KJ599679) differed by 2.1% in the cox1 and nad1 genes. Phylogenetic tree topologies generated using the 2 analytic methods were identical and presented high level of confidence values for the 3 major branches of the 3 Spirometra species in the cox1 gene. The morphological and molecular findings obtained in this study were nearly coincided with those of S. ranarum. Therefore, we can know for the first time that the African lion, Panthera leo, is to the definitive host of this tapeworm.}, }
@article {pmid30195322, year = {2018}, author = {Verechshagina, NA and Konstantinov, YM and Kamenski, PA and Mazunin, IO}, title = {Import of Proteins and Nucleic Acids into Mitochondria.}, journal = {Biochemistry. Biokhimiia}, volume = {83}, number = {6}, pages = {643-661}, doi = {10.1134/S0006297918060032}, pmid = {30195322}, issn = {1608-3040}, mesh = {Biopolymers/metabolism ; Eukaryota/genetics/*metabolism ; Mitochondria/*genetics ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Nucleic Acids/*metabolism ; RNA, Transfer/metabolism ; }, abstract = {Many mitochondrial genes have been transferred to the nucleus in course of evolution. The products of expression of these genes, being still necessary for organelle function, are imported there from the cytosol. Molecular mechanisms of protein import are studied much deeper than those of nucleic acids. The latter, it seems to us, retards the development of mitochondrial genome editing technologies. In this review, we describe mechanisms of DNA, RNA, and protein import into mitochondria of different eukaryotes. The description is given for the natural processes, as well as for artificial targeting of macromolecules into mitochondria for therapy. Also, we discuss different approaches to introduce changes into the mitochondrial DNA sequence.}, }
@article {pmid30179526, year = {2018}, author = {Haenel, GJ and Del Gaizo Moore, V}, title = {Functional Divergence of Mitochondria and Coevolution of Genomes: Cool Mitochondria in Hot Lizards.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {91}, number = {5}, pages = {1068-1081}, doi = {10.1086/699918}, pmid = {30179526}, issn = {1537-5293}, abstract = {Mitochondria play a key role in the ecology and evolution of species through their influence on aerobic metabolism. Mitochondrial DNA (mtDNA) and nuclear genomes must interact for optimal functioning of oxidative phosphorylation to produce ATP, and breakdown of coadaptation components from each may have important evolutionary consequences for hybridization. Introgression of mitochondria in natural populations through hybridization with unidirectional backcrossing allows the testing of coadaptation of mitochondria to different nuclear backgrounds. We compared the function of mitochondria isolated from two species of Urosaurus lizards and hybrid populations. Due to past introgression, hybrids contain the nuclear genome of the &quot;hot-adapted&quot; species (U. graciosus) but the mtDNA of the less heat-tolerant species (U. ornatus). It was found that the function of the parental forms of mitochondria had significantly diverged with the hot-adapted species. There was significant genotype × genotype × environment interactions for mitochondrial membrane potential and genotype × genotype interactions for ATP production. Membrane potential decreased less at a higher temperature, while ATP production was higher at both temperatures in introgressed mitochondria. Oxygen consumption was lower in U. graciosus than in U. ornatus parental-type mitochondria, indicating a likely response to living in hotter environments. Respiratory control ratio values, which provide an indication of the functional quality of isolated mitochondria, were lower in introgressed mitochondria than in parental U. ornatus types, indicating a negative impact on biological function in introgressed mitochondria.}, }
@article {pmid30176805, year = {2018}, author = {Matthee, CA and Engelbrecht, A and Matthee, S}, title = {Comparative phylogeography of parasitic Laelaps mites contribute new insights into the specialist-generalist variation hypothesis (SGVH).}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {131}, doi = {10.1186/s12862-018-1245-7}, pmid = {30176805}, issn = {1471-2148}, support = {Incentive Funding//National Research Foundation/International ; }, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; Geography ; Haplotypes/genetics ; Host Specificity ; Mites/*classification/genetics ; Mitochondria/genetics ; *Models, Biological ; Murinae/genetics/parasitology ; Parasites/*classification/genetics ; *Phylogeography ; }, abstract = {BACKGROUND: The specialist-generalist variation hypothesis (SGVH) in parasites suggests that, due to patchiness in habitat (host availability), specialist species will show more subdivided population structure when compared to generalist species. In addition, since specialist species are more prone to local stochastic extinction events with their hosts, they will show lower levels of intraspecific genetic diversity when compared to more generalist.<br><br>RESULTS: To test the wider applicability of the SGVH we compared 337 cytochrome oxidase I mitochondrial DNA and 268 nuclear tropomyosin DNA sequenced fragments derived from two co-distributed Laelaps mite species and compared the data to 294 COI mtDNA sequences derived from the respective hosts Rhabdomys dilectus, R. bechuanae, Mastomys coucha and M. natalensis. In support of the SGVH, the generalist L. muricola was characterized by a high mtDNA haplotypic diversity of 0.97 (±0.00) and a low level of population differentiation (mtDNA Fst = 0.56, p < 0.05; nuDNA Fst = 0.33, P < 0.05) while the specialist L. giganteus was overall characterized by a lower haplotypic diversity of 0.77 (±0.03) and comparatively higher levels of population differentiation (mtDNA Fst = 0.87, P < 0.05; nuDNA Fst = 0.48, P < 0.05). When the two specialist L. giganteus lineages, which occur on two different Rhabdomys species, are respectively compared to the generalist parasite, L. muricola, the SGVH is not fully supported. One of the specialist L. giganteus species occurring on R. dilectus shows similar low levels of population differentiation (mtDNA Fst = 0.53, P < 0.05; nuDNA Fst = 0.12, P < 0.05) than that found for the generalist L. muricola. This finding can be correlated to differences in host dispersal: R. bechuanae populations are characterized by a differentiated mtDNA Fst of 0.79 (P < 0.05) while R. dilectus populations are less structured with a mtDNA Fst = 0.18 (P < 0.05).<br><br>CONCLUSIONS: These findings suggest that in ectoparasites, host specificity and the vagility of the host are both important drivers for parasite dispersal. It is proposed that the SGHV hypothesis should also incorporate reference to host dispersal since in our case only the specialist species who occur on less mobile hosts showed more subdivided population structure when compared to generalist species.}, }
@article {pmid30176793, year = {2018}, author = {Yin, M and Wang, X and Ma, X and Gießler, S and Petrusek, A and Griebel, J and Hu, W and Wolinska, J}, title = {Cytonuclear diversity and shared mitochondrial haplotypes among Daphnia galeata populations separated by seven thousand kilometres.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {130}, doi = {10.1186/s12862-018-1256-4}, pmid = {30176793}, issn = {1471-2148}, support = {31670380//National Natural Science Foundation of China/International ; 16ZR1402900//Natural Science Foundation of Shanghai/International ; WO 1587/6-1//German Science Foundation/International ; }, mesh = {Alleles ; Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; China ; DNA/genetics ; DNA, Mitochondrial/genetics ; Daphnia/*genetics ; Europe ; Genes, Mitochondrial ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/*genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; Zooplankton/genetics ; }, abstract = {BACKGROUND: The zooplanktonic cladocerans Daphnia, present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing eggs carried by waterfowl, Daphnia often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species, D. galeata, we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci.<br><br>RESULTS: Mitochondrial DNA demonstrated relatively shallow divergence within D. galeata, with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European D. galeata populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for D. galeata populations in China but not in Europe.<br><br>CONCLUSIONS: Our results indicate relatively recent spread of D. galeata across wide expanses of the Palaearctic, with one mtDNA lineage of D. galeata successfully establishing over large distances. Despite a clear differentiation of Chinese and European D. galeata at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.}, }
@article {pmid30176236, year = {2018}, author = {Virji, AZ and Thekkiniath, J and Ma, W and Lawres, L and Knight, J and Swei, A and Roch, KL and Mamoun, CB}, title = {Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2018.05.008}, pmid = {30176236}, issn = {1879-0135}, support = {R01 AI123321/AI/NIAID NIH HHS/United States ; }, abstract = {Babesia microti and Babesia duncani are the main causative agents of human babesiosis in the United States. While significant knowledge about B. microti has been gained over the past few years, nothing is known about B. duncani biology, pathogenesis, mode of transmission or sensitivity to currently recommended therapies. Studies in immunocompetent wild type mice and hamsters have shown that unlike B. microti, infection with B. duncani results in severe pathology and ultimately death. The parasite factors involved in B. duncani virulence remain unknown. Here we report the first known completed sequence and annotation of the apicoplast and mitochondrial genomes of B. duncani. We found that the apicoplast genome of this parasite consists of a 34 kb monocistronic circular molecule encoding functions that are important for apicoplast gene transcription as well as translation and maturation of the organelle's proteins. The mitochondrial genome of B. duncani consists of a 5.9 kb monocistronic linear molecule with two inverted repeats of 48 bp at both ends. Using the conserved cytochrome b (Cytb) and cytochrome c oxidase subunit I (coxI) proteins encoded by the mitochondrial genome, phylogenetic analysis revealed that B. duncani defines a new lineage among apicomplexan parasites distinct from B. microti, Babesia bovis, Theileria spp. and Plasmodium spp. Annotation of the apicoplast and mitochondrial genomes of B. duncani identified targets for development of effective therapies. Our studies set the stage for evaluation of the efficacy of these drugs alone or in combination against B. duncani in culture as well as in animal models.}, }
@article {pmid30165810, year = {2018}, author = {Galen, SC and Nunes, R and Sweet, PR and Perkins, SL}, title = {Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {128}, doi = {10.1186/s12862-018-1242-x}, pmid = {30165810}, issn = {1471-2148}, support = {1358465//National Science Foundation/International ; }, mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetic Loci ; *Genetic Variation ; Haemosporida/*genetics ; Haplotypes/genetics ; *Host Specificity ; Malaria/*parasitology ; Mitochondria/*genetics ; Parasites/*genetics ; Phylogeny ; Songbirds/parasitology ; Species Specificity ; }, abstract = {BACKGROUND: Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used for the study of microbial groups that are likely to harbor many unrecognized species. Among microbial symbionts, integrating genetic species delimitation methods with trait data that could indicate reproductive isolation, such as host specificity data, has rarely been used despite its potential to inform species limits. Here we test the ability of an integrative approach combining genetic and host specificity data to delimit species within the avian malaria parasite genus Leucocytozoon in central Alaska.<br><br>RESULTS: We sequenced seven nuclear loci for 69 Leucocytozoon samples and used multiple species delimitation methods (GMYC and BPP models), tested for differences in host infection patterns among putative species based on 406 individual infections, and characterized parasite morphology. We found that cryptic morphology has masked a highly diverse Leucocytozoon assemblage, with most species delimitation methods recovering support for at least 21 separate species that occur sympatrically and have divergent host infection patterns. Reproductive isolation among putative species appears to have evolved despite low mtDNA divergence, and in one instance two Leucocytozoon cytb haplotypes that differed by a single base pair (~ 0.2% divergence) were supported as separate species. However, there was no consistent association between mtDNA divergence and species limits. Among cytb haplotypes that differed by one to three base pairs we observed idiosyncratic patterns of nuclear and ecological divergence, with cytb haplotype pairs found to be either conspecific, reproductively isolated with no divergence in host specificity, or reproductively isolated with divergent patterns of host specialization.<br><br>CONCLUSION: Integrating multi-locus genetic species delimitation methods and non-traditional ecological data types such as host specificity provide a novel view of the diversity of avian malaria parasites that has been missed previously using morphology and mtDNA barcodes. Species delimitation methods show that Leucocytozoon is highly species-rich in Alaska, and the genus is likely to harbor extraordinary species-level diversity worldwide. Integrating genetic and ecological data will be an important approach for understanding the diversity and evolutionary history of microbial symbionts moving forward.}, }
@article {pmid30154842, year = {2018}, author = {Berzabá-Evoli, E and Zazueta, C and Cruz Hernández, JH and Gómez-Crisóstomo, NP and Juárez-Rojop, IE and De la Cruz-Hernández, EN and Martínez-Abundis, E}, title = {Leptin Modifies the Rat Heart Performance Associated with Mitochondrial Dysfunction Independently of Its Prohypertrophic Effects.}, journal = {International journal of endocrinology}, volume = {2018}, number = {}, pages = {6081415}, doi = {10.1155/2018/6081415}, pmid = {30154842}, issn = {1687-8337}, abstract = {Background: Functional receptors for leptin were described on the surface of cardiomyocytes, and there was a prohypertrophic effect with high concentrations of the cytokine. Therefore, leptin could be a link between obesity and the prevalence of cardiovascular diseases. On the other hand, a deleterious effect of leptin on mitochondrial performance was described, which was also associated with the evolution of cardiac hypertrophy to heart failure. The goal of our study was to analyze the effect of the exposure of rat hearts to a high concentration of leptin on cardiac and mitochondrial function.<br><br>Methods: Rat hearts were perfused continuously with or without 3.1 nM leptin for 1, 2, 3, or 4 hours. Homogenates and mitochondria were prepared by centrifugation and analyzed for cardiac actin, STAT3, and pSTAT3 by Western blotting, as well as for mitochondrial oxidative phosphorylation, membrane potential, swelling, calcium transport, and content of oxidized lipids.<br><br>Results: In our results, leptin induced an increased rate-pressure product as a result of increased heart rate and contraction force, as well oxidative stress. In addition, mitochondrial dysfunction expressed as a loss of membrane potential, decreased ability for calcium transport and retention, faster swelling, and less respiratory control was observed.<br><br>Conclusions: Our results support the role of leptin as a deleterious factor for cardiac function and indicates that mitochondrial dysfunction could be a trigger for cardiac hypertrophy and failure.}, }
@article {pmid30144423, year = {2018}, author = {Pustylnikov, S and Costabile, F and Beghi, S and Facciabene, A}, title = {Targeting mitochondria in cancer: current concepts and immunotherapy approaches.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trsl.2018.07.013}, pmid = {30144423}, issn = {1878-1810}, abstract = {An essential advantage during eukaryotic cell evolution was the acquisition of a network of mitochondria as a source of energy for cell metabolism and contrary to conventional wisdom, functional mitochondria are essential for the cancer cell. Multiple aspects of mitochondrial biology beyond bioenergetics support transformation including mitochondrial biogenesis, fission and fusion dynamics, cell death susceptibility, oxidative stress regulation, metabolism, and signaling. In cancer, the metabolism of cells is reprogrammed for energy generation from oxidative phosphorylation to aerobic glycolysis and impacts cancer mitochondrial function. Furthermore cancer cells can also modulate energy metabolism within the cancer microenvironment including immune cells and induce &quot;metabolic anergy&quot; of antitumor immune response. Classical approaches targeting the mitochondria of cancer cells usually aim at inducing changing energy metabolism or directly affecting functions of mitochondrial antiapoptotic proteins but most of such approaches miss the required specificity of action and carry important side effects. Several types of cancers harbor somatic mitochondrial DNA mutations and specific immune response to mutated mitochondrial proteins has been observed. An attractive alternative way to target the mitochondria in cancer cells is the induction of an adaptive immune response against mutated mitochondrial proteins. Here, we review the cancer cell-intrinsic and cell-extrinsic mechanisms through which mitochondria influence all steps of oncogenesis, with a focus on the therapeutic potential of targeting mitochondrial DNA mutations or Tumor Associated Mitochondria Antigens using the immune system.}, }
@article {pmid30141728, year = {2018}, author = {Boratyński, JS and Szafrańska, PA}, title = {Does Basal Metabolism Set the Limit for Metabolic Downregulation during Torpor?.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {91}, number = {5}, pages = {1057-1067}, doi = {10.1086/699917}, pmid = {30141728}, issn = {1537-5293}, abstract = {The evolution of endothermic thermoregulation is rooted in the processes involving high metabolism, which allows the maintenance of high and stable body temperatures (Tb). In turn, selection for high endothermic metabolism correlates with increased size of metabolically active organs and thus with high basal metabolic rate (BMR). Endothermic animals are characterized by an MR several times that of similar-sized ectotherms. However, many small mammals are temporally heterothermic and are able to temporally decrease Tb and MR by entering daily torpor or hibernation. Both BMR and minimum MR during torpor (TMRmin) likely result from oxidative respiration in mitochondria of the same tissues. It should be expected that these two MRs are positively correlated, suggesting that the evolution of endothermy and higher BMR set the limit for the ability to reduce MR while entering torpor. Using published data for 96 mammal species, we tested the hypothesis that, among heterothermic mammals, the processes leading to the evolution of higher BMR limit the ability to downregulate metabolism during torpor. We found that body mass (mb)-adjusted BMR was positively correlated with mb- and Tb-adjusted TMRmin, in a phylogenetically corrected analysis. Phylogenetic path modeling indicated that the mechanisms underlying the evolutionary increase of BMR in endotherms most likely constrain their ability to reduce MR during torpor. Given that heterothermy is considered an ancestral state in mammals, these results suggest an increase in BMR during the evolution of endothermy in homeothermic animals, which leads to the loss of their ability to enter torpor.}, }
@article {pmid30139961, year = {2018}, author = {Liu, J and Kim, SY and Shin, S and Jung, SH and Yim, SH and Lee, JY and Lee, SH and Chung, YJ}, title = {Overexpression of TFF3 is involved in prostate carcinogenesis via blocking mitochondria-mediated apoptosis.}, journal = {Experimental &amp; molecular medicine}, volume = {50}, number = {8}, pages = {110}, doi = {10.1038/s12276-018-0137-7}, pmid = {30139961}, issn = {2092-6413}, support = {2012R1A5A2047939//National Research Foundation of Korea (NRF)/ ; 2012R1A1A3002027//National Research Foundation of Korea (NRF)/ ; }, abstract = {The overexpression of trefoil factor family 3 (TFF3) is observed in a variety of cancers, including prostate cancer (PCa), and its potential role in carcinogenesis, such as activating the PI3K/AKT pathway, is suggested. However, its role and its related mechanisms in prostate tumorigenesis remain unknown. To elucidate the role of TFF3 overexpression in PCa, we silenced TFF3 in two PCa cell lines that overexpressed TFF3 and explored the molecular mechanism behind its antiapoptotic role. We also examined TFF3 expression in 108 Korean PCa specimens and 106 normal prostate tissues by immunohistochemistry (IHC) analysis. The mean TFF3 IHC score in the tumor tissues was significantly higher than that in the normal tissues (4.702 vs. 0.311, P = 2.52 × 10-24). TFF3-silenced cells showed suppressed tumor cell growth and migration. TFF3 silencing decreased BCL2 and increased BAX expression. The translocation of BAX to the mitochondria was also confirmed. After TFF3 silencing, the expression of the mitochondrial proapoptotic proteins, cytochrome C and Smac/DIABLO, was elevated, and these proteins were released from the mitochondria to the cytosol. Downstream mediators of mitochondrial apoptosis, including cleaved caspase-3, caspase-9, and PARP, were also elevated. Accordingly, the proportion of apoptotic cells was significantly higher among TFF3-silenced cells. There was no difference in extrinsic apoptosis-related molecules after TFF3 silencing. All the results support that TFF3 silencing induces the downstream signaling pathway of mitochondria-mediated apoptosis. This study provides a better understanding of the mechanism of prostate tumorigenesis, suggesting TFF3 as a potential biomarker and therapeutic target of PCa.}, }
@article {pmid30137656, year = {2018}, author = {Kagda, MS and Vu, AL and Ah-Fong, AMV and Judelson, HS}, title = {Phosphagen kinase function in flagellated spores of the oomycete Phytophthora infestans integrates transcriptional regulation, metabolic dynamics and protein retargeting.}, journal = {Molecular microbiology}, volume = {110}, number = {2}, pages = {296-308}, doi = {10.1111/mmi.14108}, pmid = {30137656}, issn = {1365-2958}, support = {161339//National Science Foundation/ ; }, abstract = {Flagellated spores play important roles in the infection of plants and animals by many eukaryotic microbes. The oomycete Phytophthora infestans, which causes potato blight, expresses two phosphagen kinases (PKs). These enzymes store energy in taurocyamine, and are hypothesized to resolve spatial and temporal imbalances between rates of ATP creation and use in zoospores. A dimeric PK is found at low levels in vegetative mycelia, but high levels in ungerminated sporangia and zoospores. In contrast, a monomeric PK protein is at similar levels in all tissues, although is transcribed primarily in mycelia. Subcellular localization studies indicate that the monomeric PK is mitochondrial. In contrast, the dimeric PK is cytoplasmic in mycelia and sporangia but is retargeted to flagellar axonemes during zoosporogenesis. This supports a model in which PKs shuttle energy from mitochondria to and through flagella. Metabolite analysis indicates that deployment of the flagellar PK is coordinated with a large increase in taurocyamine, synthesized by sporulation-induced enzymes that were lost during the evolution of zoospore-lacking oomycetes. Thus, PK function is enabled by coordination of the transcriptional, metabolic and protein targeting machinery during the life cycle. Since plants lack PKs, the enzymes may be useful targets for inhibitors of oomycete plant pathogens.}, }
@article {pmid30127539, year = {2018}, author = {Betts, HC and Puttick, MN and Clark, JW and Williams, TA and Donoghue, PCJ and Pisani, D}, title = {Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {10}, pages = {1556-1562}, doi = {10.1038/s41559-018-0644-x}, pmid = {30127539}, issn = {2397-334X}, abstract = {Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth's history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053-1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.}, }
@article {pmid30121730, year = {2018}, author = {Radzinski, M and Reichmann, D}, title = {Variety is the spice of life: how to explore a redox-dependent heterogeneity in genomically identical cellular populations.}, journal = {Current genetics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00294-018-0878-9}, pmid = {30121730}, issn = {1432-0983}, support = {1765/13//Israel Science Foundation/ ; 1649/16//legacy Heritage Biomedical Science Partnership/ ; CDA00064/2014//Human Frontier Science Program/ ; 2015056//United States - Israel Binational Science Foundation/ ; }, abstract = {Cellular heterogeneity is a widespread phenomenon, existing across organisms and serving a crucial role in evolution and cell survival. Genetically identical cells may as a result present in a variety of forms with different gene and protein expressions, as well as oxidation level. As a result, a wide range of methodologies and techniques for dissecting different types of genetic, proteomic, and phenotypic heterogeneous traits have emerged in recent years in an effort to better understand how diversity exists within a single population and its effects therein. A key area of interest seeks to establish the ways in which cellular heterogeneity and aging processes interact with each other. Here, we discuss recent developments in defining cellular heterogeneity, specifically focusing on redox-dependent heterogeneity, its characterization, quantification, and behavior. We further expand on potential applications of a cell sorting-based methodology for distinguishing between cells harboring different redox statuses. As an example, we use organelle-specific fluorescence protein-based probes to examine the crosstalk between cytosol and mitochondria in a yeast strain lacking glutathione reductase. Together, these may have wide-reaching implications for future research into redox-associated factors, as well as mechanisms of redox-dependent heterogeneity and its influence on organelles and the cell at large.}, }
@article {pmid30110634, year = {2018}, author = {Vazquez, JM and Sulak, M and Chigurupati, S and Lynch, VJ}, title = {A Zombie LIF Gene in Elephants Is Upregulated by TP53 to Induce Apoptosis in Response to DNA Damage.}, journal = {Cell reports}, volume = {24}, number = {7}, pages = {1765-1776}, doi = {10.1016/j.celrep.2018.07.042}, pmid = {30110634}, issn = {2211-1247}, abstract = {Large-bodied organisms have more cells that can potentially turn cancerous than small-bodied organisms, imposing an increased risk of developing cancer. This expectation predicts a positive correlation between body size and cancer risk; however, there is no correlation between body size and cancer risk across species (&quot;Peto's paradox&quot;). Here, we show that elephants and their extinct relatives (proboscideans) may have resolved Peto's paradox in part through refunctionalizing a leukemia inhibitory factor pseudogene (LIF6) with pro-apoptotic functions. LIF6 is transcriptionally upregulated by TP53 in response to DNA damage and translocates to the mitochondria where it induces apoptosis. Phylogenetic analyses of living and extinct proboscidean LIF6 genes indicates that its TP53 response element evolved coincident with the evolution of large body sizes in the proboscidean stem lineage. These results suggest that refunctionalizing of a pro-apoptotic LIF pseudogene may have been permissive (although not sufficient) for the evolution of large body sizes in proboscideans.}, }
@article {pmid30109028, year = {2018}, author = {Wideman, JG and Balacco, DL and Fieblinger, T and Richards, TA}, title = {PDZD8 is not the 'functional ortholog' of Mmm1, it is a paralog.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {1088}, doi = {10.12688/f1000research.15523.1}, pmid = {30109028}, issn = {2046-1402}, abstract = {Authors of a recent paper demonstrate that, like ERMES (ER-mitochondria encounter structure) in fungal cells, PDZD8 (PDZ domain containing 8) tethers mitochondria to the ER in mammalian cells. However, identifying PDZD8 as a &quot;functional ortholog&quot; of yeast Mmm1 (maintenance of mitochondrial morphology protein 1) is at odds with the phylogenetic data. PDZD8 and Mmm1 are paralogs, not orthologs, which affects the interpretation of the data with respect to the evolution of ER-mitochondria tethering. Our phylogenetic analyses show that PDZD8 co-occurs with ERMES components in lineages closely related to animals solidifying its identity as a paralog of Mmm1. Additionally, we identify two related paralogs, one specific to flagellated fungi, and one present only in unicellular relatives of animals. These results point to a complex evolutionary history of ER-mitochondria tethering involving multiple gene gains and losses in the lineage leading to animals and fungi.}, }
@article {pmid30107780, year = {2018}, author = {Dong, S and Zhao, C and Chen, F and Liu, Y and Zhang, S and Wu, H and Zhang, L and Liu, Y}, title = {The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {614}, doi = {10.1186/s12864-018-4991-4}, pmid = {30107780}, issn = {1471-2164}, support = {31470314//National Natural Science Foundation of China/ ; 31600171//National Natural Science Foundation of China/ ; FLSF2017-03//National Natural Science Foundation of China/ ; 201520//Shenzhen Urban Management Bureau Fund/ ; DEB-1240045//National Science Foundation/ ; JCYJ20150529150409546//Shenzhen Municipal Government of China/ ; }, mesh = {*Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/*genetics ; Nymphaea/*genetics/growth &amp; development ; *Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms.<br><br>RESULTS: Assembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195 bp with an average depth of 601×. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome.<br><br>CONCLUSIONS: The Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.}, }
@article {pmid30107223, year = {2018}, author = {Reyes-Ramos, CA and Peregrino-Uriarte, AB and Cota-Ruiz, K and Valenzuela-Soto, EM and Leyva-Carrillo, L and Yepiz-Plascencia, G}, title = {Phosphoenolpyruvate carboxykinase cytosolic and mitochondrial isoforms are expressed and active during hypoxia in the white shrimp Litopenaeus vannamei.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {226}, number = {}, pages = {1-9}, doi = {10.1016/j.cbpb.2018.08.001}, pmid = {30107223}, issn = {1879-1107}, mesh = {Amino Acid Sequence ; Animals ; Aquaculture ; Conserved Sequence ; Cytosol/*enzymology/metabolism ; Databases, Protein ; *Gene Expression Regulation, Developmental ; Gills/enzymology/growth &amp; development/metabolism ; Hepatopancreas/enzymology/growth &amp; development/metabolism ; Hypoxia/*enzymology/metabolism ; Isoenzymes/genetics/metabolism ; Mitochondria/*enzymology/metabolism ; Muscle, Skeletal/enzymology/growth &amp; development/metabolism ; Organ Specificity ; Penaeidae/growth &amp; development/*physiology ; Phosphoenolpyruvate Carboxykinase (GTP)/chemistry/genetics/*metabolism ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Hypoxic zones in marine environments are spreading around the world affecting the survival of many organisms. Marine animals have several strategies to respond to hypoxia, including the regulation of gluconeogenesis. Phosphoenolpyruvate carboxykinase (PEPCK) is a key regulatory enzyme of gluconeogenesis. The objective of this work was to study two isoforms of PEPCK, one mitochondrial (PEPKC-M) and one cytosolic (PEPCK-C), from the white shrimp Litopenaeus vannamei and the response to hypoxia. Both PEPCK isoforms are 72 kDa proteins and have 92% identity at the amino acid level. The mitochondrial isoform has a N-terminal signal peptide for mitochondrial import. Gene expression and enzymatic activity in subcellular fractions were detected in gills, hepatopancreas and muscle in normoxic and hypoxic conditions. Expression of PEPCK-C was higher than PEPCK-M in all the tissues and induced in response to hypoxia at 48 h in hepatopancreas, while the enzymatic activity of PEPCK-M was higher than PEPCK-C in gills and hepatopancreas, but not in muscle and also increased in response to hypoxia in hepatopancreas but decreased in gills and muscle. During limiting oxygen conditions, shrimp tissues obtain energy by inducing anaerobic glycolysis, and although gluconeogenesis implies energy investment, due to the need to maintain glucose homeostasis, these gluconeogenic enzymes are active with contrasting behaviors in the cytosol and mitochondrial cell compartments and appear to be up-regulated in hepatopancreas indicating this tissue pivotal role in gluconeogenesis during the response to hypoxia.}, }
@article {pmid30097722, year = {2018}, author = {Ding, CQ and Ng, S and Wang, L and Wang, YC and Li, NN and Hao, XY and Zeng, JM and Wang, XC and Yang, YJ}, title = {Genome-wide identification and characterization of ALTERNATIVE OXIDASE genes and their response under abiotic stresses in Camellia sinensis (L.) O. Kuntze.}, journal = {Planta}, volume = {248}, number = {5}, pages = {1231-1247}, doi = {10.1007/s00425-018-2974-y}, pmid = {30097722}, issn = {1432-2048}, support = {1610212017003//Central Public-interest Scientific Institution Basal Research Fund/ ; CARS-19//Earmarked Fund for China Agriculture Research System/ ; 2016C02053-4//The Major Project of Agricultural Science and Technology in Breeding of Tea Plant Variety in Zhejiang Province/ ; ALTF1239-2015//European Molecular Biology Organization/ ; LTFCOFUND2013//FP PEOPLE: Marie cutie actions/ ; GA-2013-609409//FP PEOPLE: Marie cutie actions/ ; }, mesh = {Camellia sinensis/enzymology/*genetics/physiology ; Cloning, Molecular ; Conserved Sequence/genetics ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Mitochondrial Proteins/*genetics/physiology ; Oxidoreductases/*genetics/physiology ; Phylogeny ; Plant Proteins/*genetics/physiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Stress, Physiological ; Transcriptome ; }, abstract = {MAIN CONCLUSION: Four typical ALTERNATIVE OXIDASE genes have been identified in tea plants, and their sequence features and gene expression profiles have provided useful information for further studies on function and regulation. Alternative oxidase (AOX) is a terminal oxidase located in the respiratory electron transport chain. AOX catalyzes the oxidation of quinol and the reduction of oxygen into water. In this study, a genome-wide search and subsequent DNA cloning were performed to identify and characterize AOX genes in tea plant (Camellia sinensis (L.) O. Kuntze cv. Longjing43). Our results showed that tea plant possesses four AOX genes, i.e., CsAOX1a, CsAOX1d, CsAOX2a and CsAOX2b. Gene structure and protein sequence analyses revealed that all CsAOXs share a four-exon/three-intron structure with highly conserved regions and amino acid residues, which are necessary for AOX secondary structures, catalytic activities and post-translational regulations. All CsAOX were shown to localize in mitochondria using the green fluorescent protein (GFP)-targeting assay. Both CsAOX1a and CsAOX1d were induced by cold, salt and drought stresses, and with different expression patterns in young and mature leaves. Reactive oxygen species (ROS) accumulated strongly after 72 and 96 h cold treatments in both young and mature leaves, while the polyphenol and total catechin decreased significantly only in mature leaves. In comparison to AtAOX1a in Arabidopsis thaliana, CsAOX1a lost almost all of the stress-responsive cis-acting regulatory elements in its promoter region (1500 bp upstream), but possesses a flavonoid biosynthesis-related MBSII cis-acting regulatory element. These results suggest a link between CsAOX1a function and the metabolism of some secondary metabolites in tea plant. Our studies provide a basis for the further elucidation of the biological function and regulation of the AOX pathway in tea plants.}, }
@article {pmid30086701, year = {2018}, author = {Skoracka, A and Lopes, LF and Alves, MJ and Miller, A and Lewandowski, M and Szydło, W and Majer, A and Różańska, E and Kuczyński, L}, title = {Genetics of lineage diversification and the evolution of host usage in the economically important wheat curl mite, Aceria tosichella Keifer, 1969.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {122}, doi = {10.1186/s12862-018-1234-x}, pmid = {30086701}, issn = {1471-2148}, support = {No. 01/KNOW2/2014//Funding for open access charge: Ministry of Science and Higher Education of the Republic of Poland, from the quality promoting subsidy, under the Leading National Research Centre (KNOW) program for the years 2014-2019/International ; 2011/03/B/NZ8/00129//Narodowe Centrum Nauki/International ; 2011/01/N/NZ8/04540//Narodowe Centrum Nauki/International ; UID/BIA/00329/2013//Fundação para a Ciência e a Tecnologia/International ; UID/BIA/00329/2013//Fundação para a Ciência e a Tecnologia/International ; }, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Calibration ; DNA, Mitochondrial/genetics ; Demography ; Gene Flow ; Genetic Variation ; Host-Pathogen Interactions/*genetics ; Mites/*classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Plant Diseases/*parasitology ; Time Factors ; Triticum/*parasitology ; }, abstract = {BACKGROUND: Understanding the mechanisms that underlie the diversification of herbivores through interactions with their hosts is important for their diversity assessment and identification of expansion events, particularly in a human-altered world where evolutionary processes can be exacerbated. We studied patterns of host usage and genetic structure in the wheat curl mite complex (WCM), Aceria tosichella, a major pest of the world's grain industry, to identify the factors behind its extensive diversification.<br><br>RESULTS: We expanded on previous phylogenetic research, demonstrating deep lineage diversification within the taxon, a complex of distinctive host specialist and generalist lineages more diverse than previously assumed. Time-calibrated phylogenetic reconstruction inferred from mitochondrial DNA sequence data suggests that lineage diversification pre-dates the influence of agricultural practices, and lineages started to radiate in the mid Miocene when major radiations of C4 grasses is known to have occurred. Furthermore, we demonstrated that host specificity is not phylogenetically constrained, while host generalization appears to be a more derived trait coinciding with the expansion of the world's grasslands. Demographic history of specialist lineages have been more stable when compared to generalists, and their expansion pre-dated all generalist lineages. The lack of host-associated genetic structure of generalists indicates gene flow between mite populations from different hosts.<br><br>CONCLUSIONS: Our analyses demonstrated that WCM is an unexpectedly diverse complex of genetic lineages and its differentiation is likely associated with the time of diversification and expansion of its hosts. Signatures of demographic histories and expansion of generalists are consistent with the observed proliferation of the globally most common lineages. The apparent lack of constrains on host use, coupled with a high colonization potential, hinders mite management, which may be further compromised by host range expansion. This study provides a significant contribution to the growing literature on host-association and diversification in herbivorous invertebrates.}, }
@article {pmid30055249, year = {2018}, author = {Torrezan-Nitao, E and Figueiredo, RCBQ and Marques-Santos, LF}, title = {Mitochondrial permeability transition pore in sea urchin female gametes.}, journal = {Mechanisms of development}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mod.2018.07.008}, pmid = {30055249}, issn = {1872-6356}, abstract = {Mitochondrial permeability transition pore (MPTP) has been associated to calcium homeostasis and reactive oxygen species (ROS) generation in several cell types. While extensively investigated in somatic cells, there are few data regarding MPTP phenomenon in gametes. The aim of the present work was to investigate MPTP occurrence in sea urchin female gametes. The protonophores CCCP and FCCP, and the Ca2+ ionophore ionomycin, were used as pore inductors. Pore opening was monitored by mitochondrial potential sensitive probes and cobalt-quenched calcein assay. The pore desensitizer cyclosporin A (CsA) prevented the loss of mitochondrial inner membrane potential (ΔΨm) and pore opening induced by MPTP activators. The disruption of ΔΨm led to an increase in ROS generation, which was completely prevented by CsA. Our data also demonstrated that the increase in ROS production induced by MPTP opening requires extracellular Ca2+. In summary, the current study provides evidence about the occurrence of MPTP in sea urchin eggs in a similar manner as described in vertebrate somatic cells - CsA-sensitive, voltage- and Ca2+-triggered - and shows MPTP as a highly conserved physiological event through the evolution.}, }
@article {pmid30046113, year = {2018}, author = {Dhir, A and Dhir, S and Borowski, LS and Jimenez, L and Teitell, M and Rötig, A and Crow, YJ and Rice, GI and Duffy, D and Tamby, C and Nojima, T and Munnich, A and Schiff, M and de Almeida, CR and Rehwinkel, J and Dziembowski, A and Szczesny, RJ and Proudfoot, NJ}, title = {Mitochondrial double-stranded RNA triggers antiviral signalling in humans.}, journal = {Nature}, volume = {560}, number = {7717}, pages = {238-242}, doi = {10.1038/s41586-018-0363-0}, pmid = {30046113}, issn = {1476-4687}, abstract = {Mitochondria are descendants of endosymbiotic bacteria and retain essential prokaryotic features such as a compact circular genome. Consequently, in mammals, mitochondrial DNA is subjected to bidirectional transcription that generates overlapping transcripts, which are capable of forming long double-stranded RNA structures1,2. However, to our knowledge, mitochondrial double-stranded RNA has not been previously characterized in vivo. Here we describe the presence of a highly unstable native mitochondrial double-stranded RNA species at single-cell level and identify key roles for the degradosome components mitochondrial RNA helicase SUV3 and polynucleotide phosphorylase PNPase in restricting the levels of mitochondrial double-stranded RNA. Loss of either enzyme results in massive accumulation of mitochondrial double-stranded RNA that escapes into the cytoplasm in a PNPase-dependent manner. This process engages an MDA5-driven antiviral signalling pathway that triggers a type I interferon response. Consistent with these data, patients carrying hypomorphic mutations in the gene PNPT1, which encodes PNPase, display mitochondrial double-stranded RNA accumulation coupled with upregulation of interferon-stimulated genes and other markers of immune activation. The localization of PNPase to the mitochondrial inter-membrane space and matrix suggests that it has a dual role in preventing the formation and release of mitochondrial double-stranded RNA into the cytoplasm. This in turn prevents the activation of potent innate immune defence mechanisms that have evolved to protect vertebrates against microbial and viral attack.}, }
@article {pmid30042786, year = {2018}, author = {Riggs, CL and Summers, A and Warren, DE and Nilsson, GE and Lefevre, S and Dowd, WW and Milton, S and Podrabsky, JE}, title = {Small Non-coding RNA Expression and Vertebrate Anoxia Tolerance.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {230}, doi = {10.3389/fgene.2018.00230}, pmid = {30042786}, issn = {1664-8021}, abstract = {Background: Extreme anoxia tolerance requires a metabolic depression whose modulation could involve small non-coding RNAs (small ncRNAs), which are specific, rapid, and reversible regulators of gene expression. A previous study of small ncRNA expression in embryos of the annual killifish Austrofundulus limnaeus, the most anoxia-tolerant vertebrate known, revealed a specific expression pattern of small ncRNAs that could play important roles in anoxia tolerance. Here, we conduct a comparative study on the presence and expression of small ncRNAs in the most anoxia-tolerant representatives of several major vertebrate lineages, to investigate the evolution of and mechanisms supporting extreme anoxia tolerance. The epaulette shark (Hemiscyllium ocellatum), crucian carp (Carassius carassius), western painted turtle (Chrysemys picta bellii), and leopard frog (Rana pipiens) were exposed to anoxia and recovery, and small ncRNAs were sequenced from the brain (one of the most anoxia-sensitive tissues) prior to, during, and following exposure to anoxia. Results: Small ncRNA profiles were broadly conserved among species under normoxic conditions, and these expression patterns were largely conserved during exposure to anoxia. In contrast, differentially expressed genes are mostly unique to each species, suggesting that each species may have evolved distinct small ncRNA expression patterns in response to anoxia. Mitochondria-derived small ncRNAs (mitosRNAs) which have a robust response to anoxia in A. limnaeus embryos, were identified in the other anoxia tolerant vertebrates here but did not display a similarly robust response to anoxia. Conclusion: These findings support an overall stabilization of the small ncRNA transcriptome during exposure to anoxic insults, but also suggest that multiple small ncRNA expression pathways may support anoxia tolerance, as no conserved small ncRNA response was identified among the anoxia-tolerant vertebrates studied. This may reflect divergent strategies to achieve the same endpoint: anoxia tolerance. However, it may also indicate that there are multiple cellular pathways that can trigger the same cellular and physiological survival processes, including hypometabolism.}, }
@article {pmid30022808, year = {2018}, author = {Lang, SA and Shain, DH}, title = {Atypical Evolution of the F1Fo Adenosine Triphosphate Synthase Regulatory ATP6 subunit in Glacier Ice Worms (Annelida: Clitellata: Mesenchytraeus).}, journal = {Evolutionary bioinformatics online}, volume = {14}, number = {}, pages = {1176934318788076}, doi = {10.1177/1176934318788076}, pmid = {30022808}, issn = {1176-9343}, abstract = {The glacier ice worm, Mesenchytraeus solifugus, is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction. Furthermore, sequence analysis suggests that this insertion is not of metazoan origin, but rather is a product of horizontal gene transfer from a microbial dietary source, and may act as a proton shuttle to accelerate the rate of ATP synthesis.}, }
@article {pmid30021129, year = {2018}, author = {Sun, S and Sha, Z and Wang, Y}, title = {Complete mitochondrial genome of the first deep-sea spongicolid shrimp Spongiocaris panglao (Decapoda: Stenopodidea): Novel gene arrangement and the phylogenetic position and origin of Stenopodidea.}, journal = {Gene}, volume = {676}, number = {}, pages = {123-138}, doi = {10.1016/j.gene.2018.07.026}, pmid = {30021129}, issn = {1879-0038}, mesh = {Animals ; Base Composition ; Decapoda (Crustacea)/*genetics ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry ; Sequence Analysis, DNA/*methods ; }, abstract = {Stenopodidea Claus, 1872 (Crustacea: Decapoda) is one of the major groups of decapods crustaceans. Hitherto, only one complete mitochondrial genome (mitogenome) from the family Stenopodidae is available for the infraorder Stenopodidea. Here, we determined the complete mitogenome of Spongiocaris panglao de Grave and Saito, 2016 using Illumina sequencing, representing the first species from the family Spongicolidae. The 15,909 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. Although the overall genome organization is typical for metazoans, the mitogenome of S. panglao shows some derived characters. A + T content of 77.42% in S. pamglao mitogenome is second-highest among the dacapods described to date. The trnR gene exhibit modified secondary structure with the TψC loop completely missing, which might be a putative autapomorphy of S. pamglao mitogenome. Compared with the shallow-water stenopodidean species S. hispidus, the control region of S. pamglao exhibits three characteristics: larger size, higher A + T content, and more tandem repeat sequences. The gene order exhibited difference from the ancestral mitogenome pattern of the Pancrustacea, with 5 tRNA genes rearrangement. The result from BI was agreed with most morphological characters and molecular evidences, revealing that Stenopodidea and Reptantia had the closest relationship, as the sister group of Caridea. Still, the alternative hypothesis supported from ML topology cannot be completely rejected based on the current data. Estimated times revealed that the two stenopodideans families Stenopodidae and Spongicolidae diverged from each other around 122 Mya. The divergence time of spongicolid shrimp is in good agreement with the origin of their hexactinellid hosts (78-144 Mya).}, }
@article {pmid30003876, year = {2018}, author = {Katane, M and Ariyoshi, M and Tateishi, S and Koiwai, S and Takaku, K and Nagai, K and Nakayama, K and Saitoh, Y and Miyamoto, T and Sekine, M and Mita, M and Hamase, K and Matoba, S and Homma, H}, title = {Structural and enzymatic properties of mammalian d-glutamate cyclase.}, journal = {Archives of biochemistry and biophysics}, volume = {654}, number = {}, pages = {10-18}, doi = {10.1016/j.abb.2018.07.005}, pmid = {30003876}, issn = {1096-0384}, abstract = {d-Glutamate cyclase (DGLUCY) is a unique enzyme that reversibly converts free d-glutamate to 5-oxo-d-proline and H2O. Mammalian DGLUCY is highly expressed in the mitochondrial matrix in the heart, and its downregulation disrupts d-glutamate and/or 5-oxo-d-proline levels, contributing to the onset and/or exacerbation of heart failure. However, detailed characterisation of DGLUCY has not yet been performed. Herein, the structural and enzymatic properties of purified recombinant mouse DGLUCY were examined. The results revealed a dimeric oligomerisation state, and both d-glutamate-to-5-oxo-d-proline and 5-oxo-d-proline-to-d-glutamate reactions were catalysed in a stereospecific manner. Catalytic activity is modulated by divalent cations and nucleotides including ATP and ADP. Interestingly, the presence of Mn2+ completely abolished the 5-oxo-d-proline-to-d-glutamate reaction but stimulated the d-glutamate-to-5-oxo-d-proline reaction. The optimum pH is ∼8.0, similar to that in the mitochondrial matrix, and the catalytic efficiency for d-glutamate is markedly higher than that for 5-oxo-d-proline. These findings suggest that DGLUCY functions as a metalloenzyme that degrades d-glutamate in the mitochondrial matrix in mammalian cells. The results also provide insight into the correlation between DGLUCY enzyme activity and the physiological and pathological roles of d-glutamate and 5-oxo-d-proline in cardiac function, which is of relevance to the risk of onset of heart failure.}, }
@article {pmid29992378, year = {2018}, author = {Kasperski, A and Kasperska, R}, title = {Bioenergetics of life, disease and death phenomena.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12064-018-0266-5}, pmid = {29992378}, issn = {1611-7530}, abstract = {In this article, some new aspects of unified cell bioenergetics are presented. From the perspective of unified cell bioenergetics certain subsequent stages of cancer development, from initiation stage, through transformation to metastasis, are analyzed. Here we show that after transformation, cancer cells are permanently exposed to reactive oxygen species, that causes continual random DNA mutations and as a result genome and chromosomal destabilizations. The modern cancer attractor hypothesis has been extended in explaining cancer development. Discussion is conducted in light of current cancerogenesis research, including bioenergetic cancer initiation, the somatic mutation theory and the tissue organization field theory. In the article reasons complicating the discovery of patterns of cancer genome changes and cancer evolution are presented. In addition certain cancer therapeutic aspects are given attention to.}, }
@article {pmid29989670, year = {2018}, author = {Iha, C and Grassa, CJ and Lyra, GM and Davis, CC and Verbruggen, H and Oliveira, MC}, title = {Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta).}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.12765}, pmid = {29989670}, issn = {1529-8817}, support = {152939/2014-8//CNPq/ ; 301491/2013-5//CNPq/ ; 406351/2016-3//CNPq/ ; 88881.134422/2016-01//CAPES/ ; TO INT0001/2016//FAPESB/ ; 2013/11833-3//Biota-FAPESP/ ; 2015/50078-1//FAPESP/ ; }, abstract = {Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from 10 species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny, Melanthalia intermedia is sister to a monophyletic clade including Gracilaria and Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes cob and trnL, and trnA and trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between psdD and rrs genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial leuC/leuD operon was found in chloroplast genomes of Gracilaria tenuistipitata, G. chilensis, and M. intermedia, and in extrachromosomal plasmid of G. vermiculophylla. Phylogenetic trees show two different origins of leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.}, }
@article {pmid29987715, year = {2018}, author = {Rolland, N and Bouchnak, I and Moyet, L and Salvi, D and Kuntz, M}, title = {The Main Functions of Plastids.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {73-85}, doi = {10.1007/978-1-4939-8654-5_5}, pmid = {29987715}, issn = {1940-6029}, abstract = {Plastids are semiautonomous organelles like mitochondria, and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.}, }
@article {pmid29987711, year = {2018}, author = {Maréchal, E}, title = {Primary Endosymbiosis: Emergence of the Primary Chloroplast and the Chromatophore, Two Independent Events.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {3-16}, doi = {10.1007/978-1-4939-8654-5_1}, pmid = {29987711}, issn = {1940-6029}, abstract = {The emergence of semiautonomous organelles, such as the mitochondrion, the chloroplast, and more recently, the chromatophore, are critical steps in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and finally the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter describes our current understanding of primary endosymbiosis, with a specific focus on primary chloroplasts considered to have emerged more than one billion years ago, and on the chromatophore, having emerged about one hundred million years ago.}, }
@article {pmid29984192, year = {2018}, author = {MacDonald, JA and Fowle, WH and Shin, E and Woods, DC}, title = {A method for freeze-fracture and scanning electron microscopy of isolated mitochondria.}, journal = {MethodsX}, volume = {5}, number = {}, pages = {593-598}, doi = {10.1016/j.mex.2018.05.006}, pmid = {29984192}, issn = {2215-0161}, abstract = {Electron microscopy as a methodology for the study of mitochondria based on morphological features is a standard technique that has experienced little evolution over the course of several decades. This technology has identified heterogeneity of mitochondria populations across both whole tissues, as well between individual cells, using primarily ultrathin sections for transmission electron microscopy (TEM). However, this technique constrains the evaluation of a sample to a single two-dimensional plane. To overcome this limitation, scanning electron microscopy (SEM) has been successfully utilized to observe three-dimensional mitochondria structures within the complex microenvironment containing total cellular components. In response to these dual technical caveats of existing electron microscopy protocols, we developed a methodology to evaluate the three-dimensional ultrastructure of isolated mitochondria, utilizing a freeze-fracture step and rigorous preservation of sample morphology. This protocol allows for a more high-throughput analysis of mitochondria populations from a specimen of interest, as the sample has been previously purified, as well as a finer resolution of complex intra-mitochondrial structures, using the depth of field created by SEM. •Protocol designed for SEM of isolated mitochondria samples.•SEM visualizes mitochondria ultrastructure in 3-D.•Freeze-fracture creates cross-sectional plane for view of interior organelle structures.}, }
@article {pmid29976842, year = {2018}, author = {He, K and Chen, X and Chen, P and He, SW and Cheng, F and Jiang, XL and Campbell, K}, title = {A new genus of Asiatic short-tailed shrew (Soricidae, Eulipotyphla) based on molecular and morphological comparisons.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {321-334}, doi = {10.24272/j.issn.2095-8137.2018.058}, pmid = {29976842}, issn = {2095-8137}, mesh = {Animals ; Biological Evolution ; China ; Mitochondria/genetics ; North America ; Sequence Analysis, DNA ; Shrews/*anatomy &amp; histology/classification/genetics ; Skull/anatomy &amp; histology ; }, abstract = {Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiatic short-tailed shrew genus Blarinella currently persist (mostly in southwestern China and adjacent areas). Only three forms of Blarinella have been recognized as either species or subspecies. However, recent molecular studies indicated a strikingly deep divergence within the genus, implying the existence of a distinct genus-level lineage. We sequenced the complete mitochondrial genomes and one nuclear gene of three Asiatic short-tailed and two North American shrews and analyzed them morphometrically and morphologically. Our molecular analyses revealed that specimens ascribed to B. griselda formed two deeply diverged lineages, one a close relative to B. quadraticauda, whereas the other - comprised of topotype specimens from southern Gansu - diverged from other Blarinella in the middle Miocene (ca. 18.2 million years ago (Ma), 95% confidence interval=13.4-23.6 Ma). Although the skulls were similarly shaped in both lineages, we observed several diagnostic characteristics, including the shape of the upper P4. In consideration of the molecular and morphological evidence, we recognize B. griselda as the sole species of a new genus, namely, Pantherina gen. nov. Interestingly, some characteristics of Pantherina griselda are more similar to fossil genera, suggesting it represents an evolutionarily more primitive form than Blarinella. Recognition of this new genus sheds light on the systematics and evolutionary history of the tribe Blarinellini throughout Eurasia and North America.}, }
@article {pmid29970001, year = {2018}, author = {Lenz, H and Hein, A and Knoop, V}, title = {Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {255}, doi = {10.1186/s12859-018-2244-9}, pmid = {29970001}, issn = {1471-2105}, abstract = {BACKGROUND: Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encoded in the organelle genomes. Predicting and analyzing RNA editing, which ranges from only few sites in some species to thousands in other taxa, is bioinformatically demanding.<br><br>RESULTS: Here, we present major enhancements and extensions of PREPACT, a WWW-based service for analysing, predicting and cataloguing plant-type RNA editing. New features in PREPACT's core include direct GenBank accession query input and options to restrict searches to candidate U-to-C editing or to sites where editing has been documented previously in the references. The reference database has been extended by 20 new organelle editomes. PREPACT 3.0 features new modules &quot;EdiFacts&quot; and &quot;TargetScan&quot;. EdiFacts integrates information on pentatricopeptide repeat (PPR) proteins characterized as site-specific RNA editing factors. PREPACT's editome references connect into EdiFacts, linking editing events to specific co-factors where known. TargetScan allows position-weighted querying for sequence motifs in the organelle references, optionally restricted to coding regions or sequences around editing sites, or in queries uploaded by the user. TargetScan is mainly intended to evaluate and further refine the proposed PPR-RNA recognition code but may be handy for other tasks as well. We present an analysis for the immediate sequence environment of more than 15,000 documented editing sites finding strong and different bias in the editome data sets.<br><br>CONCLUSIONS: We exemplarily present the novel features of PREPACT 3.0 aimed to enhance the analyses of plant-type RNA editing, including its new modules EdiFacts integrating information on characterized editing factors and TargetScan aimed to analyse RNA editing site recognition specificities.}, }
@article {pmid29955026, year = {2018}, author = {Liu, SY and He, K and Chen, SD and Jin, W and Murphy, RW and Tang, MK and Liao, R and Li, FJ}, title = {How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {309-320}, doi = {10.24272/j.issn.2095-8137.2018.053}, pmid = {29955026}, issn = {2095-8137}, mesh = {Animals ; China ; Cytochromes b/*genetics ; Mitochondria/*genetics ; Murinae/anatomy &amp; histology/*genetics ; Phylogeny ; Rats/anatomy &amp; histology/*genetics ; Skull/anatomy &amp; histology ; Surveys and Questionnaires ; Tooth/anatomy &amp; histology ; }, abstract = {Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.}, }
@article {pmid29953866, year = {2018}, author = {Woodling, NS and Partridge, L}, title = {Parkinson's Disease: Mitochondria Parked at the ER Hit the Snooze Button.}, journal = {Neuron}, volume = {98}, number = {6}, pages = {1059-1061}, doi = {10.1016/j.neuron.2018.06.025}, pmid = {29953866}, issn = {1097-4199}, abstract = {Parkinson's disease patients report sleep disturbances well ahead of motor symptoms. In this issue of Neuron, Valadas et al. (2018) report that the disease genes pink1 and parkin exert novel, cell-type-specific effects to modulate ER-mitochondria contacts, neuropeptidergic transmission, and sleep patterns.}, }
@article {pmid29950419, year = {2018}, author = {Bilz, NC and Jahn, K and Lorenz, M and Lüdtke, A and Hübschen, JM and Geyer, H and Mankertz, A and Hübner, D and Liebert, UG and Claus, C}, title = {Rubella Viruses Shift Cellular Bioenergetics to a More Oxidative and Glycolytic Phenotype with a Strain-Specific Requirement for Glutamine.}, journal = {Journal of virology}, volume = {92}, number = {17}, pages = {}, doi = {10.1128/JVI.00934-18}, pmid = {29950419}, issn = {1098-5514}, mesh = {A549 Cells ; Endothelial Cells/metabolism/virology ; *Energy Metabolism ; Glucose/metabolism/pharmacology ; Glutamine/*metabolism/pharmacology ; Glycolysis/*drug effects ; Homeostasis ; Humans ; Kynurenine/metabolism ; Metabolic Networks and Pathways/drug effects ; Mitochondria/metabolism ; Nucleotides/biosynthesis ; Oxidation-Reduction ; Oxidative Stress ; Oxygen Consumption/drug effects/*physiology ; Phenotype ; Pyruvic Acid/metabolism/pharmacology ; Rubella virus/*metabolism ; Virus Replication/drug effects ; }, abstract = {The flexible regulation of cellular metabolic pathways enables cellular adaptation to changes in energy demand under conditions of stress such as posed by a virus infection. To analyze such an impact on cellular metabolism, rubella virus (RV) was used in this study. RV replication under selected substrate supplementation with glucose, pyruvate, and glutamine as essential nutrients for mammalian cells revealed its requirement for glutamine. The assessment of the mitochondrial respiratory (based on the oxygen consumption rate) and glycolytic (based on the extracellular acidification rate) rate and capacity by respective stress tests through Seahorse technology enabled determination of the bioenergetic phenotype of RV-infected cells. Irrespective of the cellular metabolic background, RV infection induced a shift of the bioenergetic state of epithelial cells (Vero and A549) and human umbilical vein endothelial cells to a higher oxidative and glycolytic level. Interestingly there was a RV strain-specific, but genotype-independent demand for glutamine to induce a significant increase in metabolic activity. While glutaminolysis appeared to be rather negligible for RV replication, glutamine could serve as donor of its amide nitrogen in biosynthesis pathways for important metabolites. This study suggests that the capacity of RVs to induce metabolic alterations could evolve differently during natural infection. Thus, changes in cellular bioenergetics represent an important component of virus-host interactions and could complement our understanding of the viral preference for a distinct host cell population.IMPORTANCE RV pathologies, especially during embryonal development, could be connected with its impact on mitochondrial metabolism. With bioenergetic phenotyping we pursued a rather novel approach in virology. For the first time it was shown that a virus infection could shift the bioenergetics of its infected host cell to a higher energetic state. Notably, the capacity to induce such alterations varied among different RV isolates. Thus, our data add viral adaptation of cellular metabolic activity to its specific needs as a novel aspect to virus-host evolution. In addition, this study emphasizes the implementation of different viral strains in the study of virus-host interactions and the use of bioenergetic phenotyping of infected cells as a biomarker for virus-induced pathological alterations.}, }
@article {pmid29948488, year = {2018}, author = {Yoshida, Y}, title = {The cellular machineries responsible for the division of endosymbiotic organelles.}, journal = {Journal of plant research}, volume = {131}, number = {5}, pages = {727-734}, doi = {10.1007/s10265-018-1050-9}, pmid = {29948488}, issn = {1618-0860}, support = {Career Development Award/CDA00049/2018-C//Human Frontier Science Program/ ; KAKENHI/JP18K06325//Japan Society for the Promotion of Science/ ; }, abstract = {Chloroplasts (plastids) and mitochondria evolved from endosymbiotic bacteria. These organelles perform vital functions in photosynthetic eukaryotes, such as harvesting and converting energy for use in biological processes. Consistent with their evolutionary origins, plastids and mitochondria proliferate by the binary fission of pre-existing organelles. Here, I review the structures and functions of the supramolecular machineries driving plastid and mitochondrial division, which were discovered and first studied in the primitive red alga Cyanidioschyzon merolae. In the past decade, intact division machineries have been isolated from plastids and mitochondria and examined to investigate their underlying structure and molecular mechanisms. A series of studies has elucidated how these division machineries assemble and transform during the fission of these organelles, and which of the component proteins generate the motive force for their contraction. Plastid- and mitochondrial-division machineries have important similarities in their structures and mechanisms despite sharing no component proteins, implying that these division machineries evolved in parallel. The establishment of these division machineries might have enabled the host eukaryotic ancestor to permanently retain these endosymbiotic organelles by regulating their binary fission and the equal distribution of resources to daughter cells. These findings provide key insights into the establishment of endosymbiotic organelles and have opened new avenues of research into their evolution and mechanisms of proliferation.}, }
@article {pmid29948332, year = {2018}, author = {van der Sluis, R}, title = {Analyses of the genetic diversity and protein expression variation of the acyl: CoA medium-chain ligases, ACSM2A and ACSM2B.}, journal = {Molecular genetics and genomics : MGG}, volume = {293}, number = {5}, pages = {1279-1292}, doi = {10.1007/s00438-018-1460-3}, pmid = {29948332}, issn = {1617-4623}, support = {Self-Initiated research grant//South African Medical Research Council/ ; 99323//National Research Foundation/ ; }, mesh = {Coenzyme A Ligases/*genetics/metabolism ; *Genetic Variation ; Glycine/metabolism ; *Haplotypes ; Humans ; Mitochondria, Liver/*enzymology ; Phylogeny ; Substrate Specificity ; Xenobiotics/*metabolism ; }, abstract = {Benzoate (found in milk and widely used as preservative), salicylate (present in fruits and the active component of aspirin), dietary polyphenols produced by gut microbiota, metabolites from organic acidemias, and medium-chain fatty acids (MCFAs) are all metabolised/detoxified by the glycine conjugation pathway. Xenobiotics are first activated to an acyl-CoA by the mitochondrial xenobiotic/medium-chain fatty acid: CoA ligases (ACSMs) and subsequently conjugated to glycine by glycine N-acyltransferase (GLYAT). The MCFAs are activated to acyl-CoA by the ACSMs before entering mitochondrial β-oxidation. This two-step enzymatic pathway has, however, not been thoroughly investigated and the biggest gap in the literature remains the fact that studies continuously characterise the pathway as a one-step reaction. There are no studies available on the interaction/competition of the various substrates involved in the pathway, whilst very little research has been done on the ACSM ligases. To identify variants/haplotypes that should be characterised in future detoxification association studies, this study assessed the naturally observed sequence diversity and protein expression variation of ACSM2A and ACSM2B. The allelic variation, haplotype diversity, Tajima's D values, and phylogenetic analyses indicated that ACSM2A and ACSM2B are highly conserved. This confirmed an earlier hypothesis that the glycine conjugation pathway is highly conserved and essential for life as it maintains the CoA and glycine homeostasis in the liver mitochondria. The protein expression analyses showed that ACSM2A is the predominant transcript in liver. Future studies should investigate the effect of the variants identified in this study on the substrate specificity of these proteins.}, }
@article {pmid29946965, year = {2018}, author = {Sharma, M and Bennewitz, B and Klösgen, RB}, title = {Rather rule than exception? How to evaluate the relevance of dual protein targeting to mitochondria and chloroplasts.}, journal = {Photosynthesis research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11120-018-0543-7}, pmid = {29946965}, issn = {1573-5079}, abstract = {Dual targeting of a nuclearly encoded protein into two different cell organelles is an exceptional event in eukaryotic cells. Yet, the frequency of such dual targeting is remarkably high in case of mitochondria and chloroplasts, the two endosymbiotic organelles of plant cells. In most instances, it is mediated by &quot;ambiguous&quot; transit peptides, which recognize both organelles as the target. A number of different approaches including in silico, in organello as well as both transient and stable in vivo assays are established to determine the targeting specificity of such transit peptides. In this review, we will describe and compare these approaches and discuss the potential role of this unusual targeting process. Furthermore, we will present a hypothetical scenario how dual targeting might have arisen during evolution.}, }
@article {pmid29945721, year = {2018}, author = {Barshad, G and Marom, S and Cohen, T and Mishmar, D}, title = {Mitochondrial DNA Transcription and Its Regulation: An Evolutionary Perspective.}, journal = {Trends in genetics : TIG}, volume = {34}, number = {9}, pages = {682-692}, doi = {10.1016/j.tig.2018.05.009}, pmid = {29945721}, issn = {0168-9525}, abstract = {The bacterial heritage of mitochondria, as well as its independent genome [mitochondrial DNA (mtDNA)] and polycistronic transcripts, led to the view that mitochondrial transcriptional regulation relies on an evolutionarily conserved, prokaryotic-like system that is separated from the rest of the cell. Indeed, mtDNA transcription was previously thought to be governed by a few dedicated direct regulators, namely, the mitochondrial RNA polymerase (POLRMT), two transcription factors (TFAM and TF2BM), one transcription elongation (TEFM), and one known transcription termination factor (mTERF1). Recent findings have, however, revealed that known nuclear gene expression regulators are also involved in mtDNA transcription and have identified novel transcriptional features consistent with adaptation of the mitochondria to the regulatory environment of the precursor of the eukaryotic cell. Finally, whereas mammals follow the human mtDNA transcription pattern, other organisms notably diverge in terms of mtDNA transcriptional regulation. Hence, mtDNA transcriptional regulation is likely more evolutionary diverse than once thought.}, }
@article {pmid29945248, year = {2018}, author = {Bize, P and Lowe, I and Lehto Hürlimann, M and Heckel, G}, title = {Effects of the Mitochondrial and Nuclear Genomes on Nonshivering Thermogenesis in a Wild Derived Rodent.}, journal = {Integrative and comparative biology}, volume = {58}, number = {3}, pages = {532-543}, doi = {10.1093/icb/icy072}, pmid = {29945248}, issn = {1557-7023}, abstract = {A key adaptation of mammals to their environment is their ability to maintain a constant high body temperature, even at rest, under a wide range of ambient temperatures. In cold climates, this is achieved by an adaptive production of endogenous heat, known as nonshivering thermogenesis (NST), in the brown adipose tissue (BAT). This organ, unique to mammals, contains a very high density of mitochondria, and BAT correct functioning relies on the correct functioning of its mitochondria. Mitochondria enclose proteins encoded both in the maternally inherited mitochondrial genome and in the biparentally inherited nuclear genome, and one overlooked hypothesis is that both genomes and their interaction may shape NST. By housing under standardized conditions wild-derived common voles (Microtus arvalis) from two distinct evolutionary lineages (Western [W] and Central [C]), we show that W voles had greater NST than C voles. By introgressing those two lineages over at least nine generations, we then experimentally tested the influence of the nuclear and mitochondrial genomes on NST and related phenotypic traits. We found that between-lineage variation in NST and BAT size were significantly influenced by the mitochondrial and nuclear genomes, respectively, with the W mitochondrial genotype being associated with higher NST and the W nuclear genotype with a larger BAT. There were significant mito-nuclear interactions on whole animal body weight and resting metabolic rate (RMR). Hybrid voles were lighter and had higher RMR. Overall, our findings turn new light on the influence of the mitochondrial and nuclear genomes on thermogenesis and building adaptation to the environment in mammals.}, }
@article {pmid29944924, year = {2018}, author = {Chakrabarty, S and Kabekkodu, SP and Singh, RP and Thangaraj, K and Singh, KK and Satyamoorthy, K}, title = {Mitochondria in health and disease.}, journal = {Mitochondrion}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mito.2018.06.006}, pmid = {29944924}, issn = {1872-8278}, abstract = {Mitochondrial biology has become an area of intense research owing to the unique physiology of the organelle and its role in several types of cancers and other disorders. It has been found that mitochondria-encoded proteins, mitochondrial DNA and even RNA influence the functioning of the cell in more ways than were previously imagined. This may contribute to disease phenotypes which require detailed investigation and communication to the community health care providers. Additionally, this provides several novel avenues in drug designing against various cancers, neurodegenerative diseases and other metabolic disorders. The sixth annual conference of the Society for Mitochondrial Research and Medicine - India (SMRM) titled, 'Mitochondria in Health and Disease' was organized by Rana P. Singh at the School of Life Sciences, Jawaharlal Nehru University in New Delhi, India from 10th to 11th February 2017. The underlying objective of the conference was to provide a platform to discuss the recent advances in basic and translational research in mitochondrial biology and diseases. The conference aimed to translate academic research into clinical practice by providing a forum for basic researchers and clinicians to share their knowledge and build collaborations towards development of advanced therapeutic in mitochondrial diseases. To facilitate the knowledge-sharing, six major themes for the scientific sessions were (1) understanding of mitochondrial biology in disease progression, (2) advances in basic and translational mitochondrial research, (3) mitochondria in evolution and development, (4) targeting mitochondria for cancer prevention and treatment, (5) mitochondria in metabolic and neurological disorders and (6) mitochondria in stem cell and regeneration biology. This report summarizes the major outcomes of the discussions at the conference.}, }
@article {pmid29940392, year = {2018}, author = {Wang, Q and Lu, W and Yang, J and Jiang, L and Zhang, Q and Kan, X and Yang, X}, title = {Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {28}, number = {}, pages = {27-36}, doi = {10.1016/j.cbd.2018.06.002}, pmid = {29940392}, issn = {1878-0407}, abstract = {Recent studies have shown that mitochondria play a crucial role in cellular energy production through the oxidative phosphorylation (OXPHOS) system. Complex I (NADH:ubiquinone oxidoreductase), the first and largest enzyme complex of the OXPHOS system, includes both nuclear- and mitochondrial-encoded proteins. However, the patterns of natural selection and phylogenetic implications of complex I in birds still remain unclear. In this study, we combined transcriptomic and phylogenetic analyses to comprehensively determine the evolution of avian complex I. The transcriptomes of three Passerida species (Leiothrix lutea, Spodiopsar sericeus, and Passer montanus) were obtained using the Illumina HiSeq™ 2500 system. More than 192,000,000 clean reads were assembled in a total of 828,267 transcripts. Evolutionary selection analysis suggested that six genes of the core subunits in avian complex I may have undergone putative positive selection. Notably, we found that the mean dN/dS (ω) ratio for mitochondrial genes of core subunits was significantly lower than that for nuclear genes of non-core subunits within complex I. The constructed maximum-parsimony, maximum-likelihood, and Bayesian inference phylogenetic trees were based on 44 complex I genes. We verified that the family Paridae (represented by Parus major and Pseudopodoces humilis) was clustered with Musicicapoidea. Our results provide new insights into the evolution of avian mitochondrial complex I.}, }
@article {pmid29934612, year = {2018}, author = {Lajbner, Z and Pnini, R and Camus, MF and Miller, J and Dowling, DK}, title = {Experimental evidence that thermal selection shapes mitochondrial genome evolution.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9500}, doi = {10.1038/s41598-018-27805-3}, pmid = {29934612}, issn = {2045-2322}, abstract = {Mitochondria are essential organelles, found within eukaryotic cells, which contain their own DNA. Mitochondrial DNA (mtDNA) has traditionally been used in population genetic and biogeographic studies as a maternally-inherited and evolutionary-neutral genetic marker. However, it is now clear that polymorphisms within the mtDNA sequence are routinely non-neutral, and furthermore several studies have suggested that such mtDNA polymorphisms are also sensitive to thermal selection. These observations led to the formulation of the &quot;mitochondrial climatic adaptation&quot; hypothesis, for which all published evidence to date is correlational. Here, we use laboratory-based experimental evolution in the fruit fly, Drosophila melanogaster, to test whether thermal selection can shift population frequencies of two mtDNA haplogroups whose natural frequencies exhibit clinal associations with latitude along the Australian east-coast. We present experimental evidence that the thermal regime in which the laboratory populations were maintained drove changes in haplogroup frequencies across generations. Our results strengthen the emerging view that intra-specific mtDNA variants are sensitive to selection, and suggest spatial distributions of mtDNA variants in natural populations of metazoans might reflect adaptation to climatic environments rather than within-population coalescence and diffusion of selectively-neutral haplotypes across populations.}, }
@article {pmid29923829, year = {2018}, author = {Vitali, DG and Käser, S and Kolb, A and Dimmer, KS and Schneider, A and Rapaport, D}, title = {Independent evolution of functionally exchangeable mitochondrial outer membrane import complexes.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, doi = {10.7554/eLife.34488}, pmid = {29923829}, issn = {2050-084X}, support = {ITN TAMPting, 607072//H2020 Marie Skłodowska-Curie Actions/ ; 138355//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; RA 1028/7-1,RA 1028/10-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Assembly and/or insertion of a subset of mitochondrial outer membrane (MOM) proteins, including subunits of the main MOM translocase, require the fungi-specific Mim1/Mim2 complex. So far it was unclear which proteins accomplish this task in other eukaryotes. Here, we show by reciprocal complementation that the MOM protein pATOM36 of trypanosomes is a functional analogue of yeast Mim1/Mim2 complex, even though these proteins show neither sequence nor topological similarity. Expression of pATOM36 rescues almost all growth, mitochondrial biogenesis, and morphology defects in yeast cells lacking Mim1 and/or Mim2. Conversely, co-expression of Mim1 and Mim2 restores the assembly and/or insertion defects of MOM proteins in trypanosomes ablated for pATOM36. Mim1/Mim2 and pATOM36 form native-like complexes when heterologously expressed, indicating that additional proteins are not part of these structures. Our findings indicate that Mim1/Mim2 and pATOM36 are the products of convergent evolution and arose only after the ancestors of fungi and trypanosomatids diverged.}, }
@article {pmid29923828, year = {2018}, author = {Tokatlidis, K}, title = {Shaping the import system of mitochondria.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, doi = {10.7554/eLife.38209}, pmid = {29923828}, issn = {2050-084X}, abstract = {Evidence is accumulating that unrelated species have independently evolved the same way of importing proteins in their mitochondria.}, }
@article {pmid29913250, year = {2018}, author = {Seligmann, H}, title = {Giant viruses as protein-coated amoeban mitochondria?.}, journal = {Virus research}, volume = {253}, number = {}, pages = {77-86}, doi = {10.1016/j.virusres.2018.06.004}, pmid = {29913250}, issn = {1872-7492}, mesh = {Acanthamoeba/genetics/metabolism/*virology ; *Biological Evolution ; Gene Order ; Genome Size ; Genome, Viral ; Giant Viruses/*genetics/physiology ; Mitochondria/genetics/metabolism/*virology ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; }, abstract = {Mimivirus' genome includes parts of 5S, 16S and 23S ribosomal RNAs encoded by Acanthamoeba's mitogenome, the giant virus' host. Two non-exclusive hypotheses for rRNA remnants in giant viruses are examined: 1. mitogenomes invade viral genomes as they do for nuclear chromosomes (producing numts); 2. megaviral genomes evolved from an ancestral mitogenome. Alignment analyses confirm mitochondrial, rather than alphaproteobacterial origins of megaviral rRNAs. Other mitogenes have likely megaviral homologues. These megaviral homologues coevolve to much larger extents than candidate rRNA homologues, suggesting rRNA decay in viruses. Megaviral mitogene homologues overall follow mitochondrial gene order, suggesting mitogenome ancestry. Ancestral synteny decreases with megaviral genome size, suggesting that subsequent mitogene insertions blur ancestral gene order. Putative defenses against DNA invasion conserve mitogene order in short megaviral genomes. Synteny between mitogenome and megaviral genomes confirms the RNA/DNA polymerase-homologies-based hypothesis that giant viruses have mitochondrial-like ancestors, viral rRNA remnants are corollary of mitogenomic origins of megaviral genomes. Note that giant viruses, mitochondria and bacterial spores all have double membranes, spores and viruses have protein coats. Mitochondria might occasionally form spore-like structures that drifted into megaviruses. These missing links could confirm mitogenome ancestry of giant viruses rather than giant virus ancestry of mitochondria.}, }
@article {pmid29897900, year = {2018}, author = {Chadha, S and Vijayan, R and Gupta, S and Munde, M and Gourinath, S and Madhubala, R}, title = {Genetic manipulation of Leishmania donovani threonyl tRNA synthetase facilitates its exploration as a potential therapeutic target.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {6}, pages = {e0006575}, doi = {10.1371/journal.pntd.0006575}, pmid = {29897900}, issn = {1935-2735}, mesh = {Drug Delivery Systems ; Escherichia coli/enzymology/genetics ; Fatty Alcohols/pharmacology ; Gene Expression ; Humans ; Leishmania donovani/drug effects/*enzymology/genetics/pathogenicity ; Leishmaniasis, Visceral/*parasitology ; Organisms, Genetically Modified ; Phylogeny ; Protein Domains ; Protein Transport ; Protozoan Proteins/antagonists &amp; inhibitors/genetics/isolation &amp; purification/metabolism ; Recombinant Proteins ; Sequence Deletion ; Threonine-tRNA Ligase/antagonists &amp; inhibitors/*genetics/isolation &amp; purification/metabolism ; }, abstract = {BACKGROUND: Aminoacyl tRNA synthetases are central enzymes required for protein synthesis. These enzymes are the known drug targets in bacteria and fungi. Here, we for the first time report the functional characterization of threonyl tRNA synthetase (LdThrRS) of Leishmania donovani, a protozoan parasite, the primary causative agent of visceral leishmaniasis.<br><br>METHODOLOGY: Recombinant LdThrRS (rLdThrRS) was expressed in E. coli and purified. The kinetic parameters for rLdThrRS were determined. The subcellular localization of LdThrRS was done by immunofluorescence analysis. Heterozygous mutants of LdThrRS were generated in Leishmania promastigotes. These genetically manipulated parasites were checked for their proliferation, virulence, aminoacylation activity and sensitivity to the known ThrRS inhibitor, borrelidin. An in silico generated structural model of L. donovani ThrRS was compared to that of human.<br><br>CONCLUSIONS: Recombinant LdThrRS displayed aminoacylation activity, and the protein is possibly localized to both the cytosol and mitochondria. The comparison of the 3D-model of LdThrRS to human ThrRS displayed considerable similarity. Heterozygous parasites showed restrictive growth phenotype and had attenuated infectivity. These heterozygous parasites were more susceptible to inhibition by borrelidin. Several attempts to obtain ThrRS homozygous null mutants were not successful, indicating its essentiality for the Leishmania parasite. Borrelidin showed a strong affinity for LdThrRS (KD: 0.04 μM) and was effective in inhibiting the aminoacylation activity of the rLdThrRS (IC50: 0.06 μM). Borrelidin inhibited the promastigotes (IC50: 21 μM) stage of parasites. Our data shows that LdThrRS is essential for L. donovani survival and is likely to bind with small drug-like molecules with strong affinity, thus making it a potential target for drug discovery efforts.}, }
@article {pmid29879897, year = {2018}, author = {Hein, A and Knoop, V}, title = {Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {85}, doi = {10.1186/s12862-018-1203-4}, pmid = {29879897}, issn = {1471-2148}, mesh = {Arabidopsis/genetics ; Base Sequence ; Cell Nucleus/metabolism ; Chloroplasts/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; *Phylogeny ; Plant Proteins/*genetics/metabolism ; Poaceae/*genetics ; RNA Editing/*genetics ; RNA, Messenger/genetics/metabolism ; RNA, Plant/*genetics/metabolism ; RNA-Binding Proteins/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: C-to-U RNA editing in mitochondria and chloroplasts and the nuclear-encoded, RNA-binding PPR proteins acting as editing factors present a wide field of co-evolution between the different genetic systems in a plant cell. Recent studies on chloroplast editing factors RARE1 and CRR28 addressing one or two chloroplast editing sites, respectively, found them strictly conserved among 65 flowering plants as long as one of their RNA editing targets remained present.<br><br>RESULTS: Extending the earlier sampling to 117 angiosperms with high-quality genome or transcriptome data, we find more evidence confirming previous conclusions but now also identify cases for expected evolutionary transition states such as retention of RARE1 despite loss of its editing target or the degeneration of CRR28 truncating its carboxyterminal DYW domain. The extended angiosperm set was now used to explore CLB19, an &quot;E+&quot;-type PPR editing factor targeting two chloroplast editing sites, rpoAeU200SF and clpPeU559HY, in Arabidopsis thaliana. We found CLB19 consistently conserved if one of the two targets was retained and three independent losses of CLB19 after elimination of both targets. The Ericales show independent regains of the ancestrally lost clpPeU559HY editing, further explaining why multiple-target editing factors are lost much more rarely than single target factors like RARE1. The retention of CLB19 despite loss of both editing targets in some Ericaceae, Apocynaceae and in Camptotheca (Nyssaceae) likely represents evolutionary transitions. However, the retention of CLB19 after a phylogenetic deep loss in the Poaceae rather suggests a yet unrecognized further editing target, for which we suggest editing event ndhAeU473SL.<br><br>CONCLUSION: Extending the scope of studies on plant organelle RNA editing to further taxa and additional nuclear cofactors reveals expected evolutionary transitions, strikingly different evolutionary dynamics for multiple-target editing factors like CLB19 and CRR28 and suggests additional functions for editing factor CLB19 among the Poaceae.}, }
@article {pmid29875327, year = {2018}, author = {Bonsack, F and Sukumari-Ramesh, S}, title = {TSPO: An Evolutionarily Conserved Protein with Elusive Functions.}, journal = {International journal of molecular sciences}, volume = {19}, number = {6}, pages = {}, doi = {10.3390/ijms19061694}, pmid = {29875327}, issn = {1422-0067}, mesh = {Animals ; Conserved Sequence ; Disease Susceptibility ; Evolution, Molecular ; Humans ; Ligands ; Mitochondria/genetics/metabolism ; Molecular Targeted Therapy ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Receptors, GABA/chemistry/*genetics/*metabolism ; Steroids/biosynthesis ; }, abstract = {TSPO (18 kDa translocator protein) was identified decades ago in a search for peripheral tissue binding sites for benzodiazepines, and was formerly called the peripheral benzodiazepine receptor. TSPO is a conserved protein throughout evolution and it is implicated in the regulation of many cellular processes, including inflammatory responses, oxidative stress, and mitochondrial homeostasis. TSPO, apart from its broad expression in peripheral tissues, is highly expressed in neuroinflammatory cells, such as activated microglia. In addition, emerging studies employing the ligands of TSPO suggest that TSPO plays an important role in neuropathological settings as a biomarker and therapeutic target. However, the precise molecular function of this protein in normal physiology and neuropathology remains enigmatic. This review provides an overview of recent advances in our understanding of this multifaceted molecule and identifies the knowledge gap in the field for future functional studies.}, }
@article {pmid29873740, year = {2018}, author = {Scott, GR and Guo, KH and Dawson, NJ}, title = {The Mitochondrial Basis for Adaptive Variation in Aerobic Performance in High-Altitude Deer Mice.}, journal = {Integrative and comparative biology}, volume = {58}, number = {3}, pages = {506-518}, doi = {10.1093/icb/icy056}, pmid = {29873740}, issn = {1557-7023}, abstract = {Mitochondria play a central role in aerobic performance. Studies aimed at elucidating how evolved variation in mitochondrial physiology contributes to adaptive variation in aerobic performance can therefore provide a unique and powerful lens to understanding the evolution of complex physiological traits. Here, we review our ongoing work on the importance of changes in mitochondrial quantity and quality to adaptive variation in aerobic performance in high-altitude deer mice. Whole-organism aerobic capacity in hypoxia (VO2max) increases in response to hypoxia acclimation in this species, but high-altitude populations have evolved consistently greater VO2max than populations from low altitude. The evolved increase in VO2max in highlanders is associated with an evolved increase in the respiratory capacity of the gastrocnemius muscle. This appears to result from highlanders having more mitochondria in this tissue, attributed to a higher proportional abundance of oxidative fiber-types and a greater mitochondrial volume density within oxidative fibers. The latter is primarily caused by an over-abundance of subsarcolemmal mitochondria in high-altitude mice, which is likely advantageous for mitochondrial O2 supply because more mitochondria are situated adjacent to the cell membrane and close to capillaries. Evolved changes in gastrocnemius phenotype appear to be underpinned by population differences in the expression of genes involved in energy metabolism, muscle development, and vascular development. Hypoxia acclimation has relatively little effect on respiratory capacity of the gastrocnemius, but it increases respiratory capacity of the diaphragm. However, the mechanisms responsible for this increase differ between populations: lowlanders appear to adjust mitochondrial quantity and quality (i.e., increases in citrate synthase [CS] activity, and mitochondrial respiration relative to CS activity) and they exhibit higher rates of mitochondrial release of reactive oxygen species, whereas highlanders only increase mitochondrial quantity in response to hypoxia acclimation. In contrast to the variation in skeletal muscles, the respiratory capacity of cardiac muscle does not appear to be affected by hypoxia acclimation and varies little between populations. Therefore, evolved changes in mitochondrial quantity and quality make important tissue-specific contributions to adaptive variation in aerobic performance in high-altitude deer mice.}, }
@article {pmid29857468, year = {2018}, author = {Avelange-Macherel, MH and Candat, A and Neveu, M and Tolleter, D and Macherel, D}, title = {Decoding the Divergent Subcellular Location of Two Highly Similar Paralogous LEA Proteins.}, journal = {International journal of molecular sciences}, volume = {19}, number = {6}, pages = {}, doi = {10.3390/ijms19061620}, pmid = {29857468}, issn = {1422-0067}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Multigene Family ; Mutation ; Plant Proteins/chemistry/*genetics/*metabolism ; Protein Binding ; Protein Transport ; Proteolysis ; Structure-Activity Relationship ; }, abstract = {Many mitochondrial proteins are synthesized as precursors in the cytosol with an N-terminal mitochondrial targeting sequence (MTS) which is cleaved off upon import. Although much is known about import mechanisms and MTS structural features, the variability of MTS still hampers robust sub-cellular software predictions. Here, we took advantage of two paralogous late embryogenesis abundant proteins (LEA) from Arabidopsis with different subcellular locations to investigate structural determinants of mitochondrial import and gain insight into the evolution of the LEA genes. LEA38 and LEA2 are short proteins of the LEA_3 family, which are very similar along their whole sequence, but LEA38 is targeted to mitochondria while LEA2 is cytosolic. Differences in the N-terminal protein sequences were used to generate a series of mutated LEA2 which were expressed as GFP-fusion proteins in leaf protoplasts. By combining three types of mutation (substitution, charge inversion, and segment replacement), we were able to redirect the mutated LEA2 to mitochondria. Analysis of the effect of the mutations and determination of the LEA38 MTS cleavage site highlighted important structural features within and beyond the MTS. Overall, these results provide an explanation for the likely loss of mitochondrial location after duplication of the ancestral gene.}, }
@article {pmid29852202, year = {2018}, author = {Wang, M and Teng, Y}, title = {Genome-wide identification and analysis of MICU genes in land plants and their potential role in calcium stress.}, journal = {Gene}, volume = {670}, number = {}, pages = {174-181}, doi = {10.1016/j.gene.2018.05.102}, pmid = {29852202}, issn = {1879-0038}, mesh = {Calcium/metabolism ; Calcium-Binding Proteins/chemistry/*genetics/metabolism ; Down-Regulation ; Embryophyta/classification/genetics/*metabolism ; Evolution, Molecular ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Domains ; Signal Transduction ; *Stress, Physiological ; }, abstract = {Mitochondrial calcium uptake (MICU) plays a vital role in the regulation of mitochondrial calcium homeostasis, and, consequently, influences calcium signaling transduction. Although genes involved in mitochondrial calcium uptake have been well studied in animals, less is known about their ubiquity and function in plants. In this study, we identified 96 MICU genes in land plants. On the basis of phylogenetic analysis of MICU proteins, they were classified into three clades: MICU from eudicots (Clade I), from monocots (Clade II), and from a basal angiosperm, a bryophyte, and a lycophyte (Clade III). Pairwise identity analysis across all MICU proteins showed that they are highly conserved among land plants at the protein level. Conserved motif analysis showed that most MICU proteins contained three EF-hands, and an additional EF-hand motif first identified in the MICU of Arabidopsis thaliana but not mammals was found in all 96 putative MICU proteins. This suggests that a cellular pathway of calcium uptake and signaling that requires three EF-hand motifs is evolutionarily conserved in plants. In addition, we discovered that MICU-defective mutants of Arabidopsis thaliana exhibited longer roots than wild-type under high calcium stress. Concurrently, the mRNA transcription levels of MICU were decreased under high calcium conditions. These results suggest that loss-of-function mutations of MICU may have potential roles in helping plants resist high calcium stress. This study provides clues to the possible role of plant MICU in mitochondrial calcium uptake, as well as useful information to support further studies on MICU function in plants.}, }
@article {pmid29851233, year = {2018}, author = {Solari, KA and Hadly, EA}, title = {Evolution for extreme living: variation in mitochondrial cytochrome c oxidase genes correlated with elevation in pikas (genus Ochotona).}, journal = {Integrative zoology}, volume = {13}, number = {5}, pages = {517-535}, doi = {10.1111/1749-4877.12332}, pmid = {29851233}, issn = {1749-4877}, mesh = {Adaptation, Physiological/*genetics ; Altitude ; Animals ; *Biological Evolution ; Ecosystem ; Electron Transport Complex IV/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Lagomorpha/genetics/*physiology ; Mitochondria/*enzymology ; Phylogeny ; }, abstract = {The genus Ochotona (pikas) is a clade of cold-tolerant lagomorphs that includes many high-elevation species. Pikas offer a unique opportunity to study adaptations and potential limitations of an ecologically important mammal to high-elevation hypoxia. We analyzed the evolution of 3 mitochondrial genes encoding the catalytic core of cytochrome c oxidase (COX) in 10 pika species occupying elevations from sea level to 5000 m. COX is an enzyme highly reliant on oxygen and essential for cell function. One amino acid property, the equilibrium constant (ionization of COOH), was found to be under selection in the overall protein complex. We observed a strong relationship between the net value change in this property and the elevation each species occupies, with higher-elevation species having potentially more efficient proteins. We also found evidence of selection in low-elevation species for potentially less efficient COX, perhaps trading efficiency for heat production in the absence of hypoxia. Our results suggest that different pika species may have evolved elevation-specific COX proteins, specialization that may indicate limitations in their ability to shift their elevational ranges in response to future climate change.}, }
@article {pmid29848319, year = {2018}, author = {Bronstein, O and Kroh, A and Haring, E}, title = {Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {80}, doi = {10.1186/s12862-018-1198-x}, pmid = {29848319}, issn = {1471-2148}, support = {P 29508//Austrian Science Fund FWF/Austria ; P 29508-B25//Austrian Science Fund/International ; }, mesh = {Algorithms ; Animals ; Base Sequence ; DNA Primers/metabolism ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Genetic Markers ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; Sea Urchins/*genetics ; }, abstract = {BACKGROUND: In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region.<br><br>RESULTS: Here we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids.<br><br>CONCLUSIONS: Our target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.}, }
@article {pmid29848286, year = {2018}, author = {Darbani, B and Kell, DB and Borodina, I}, title = {Energetic evolution of cellular Transportomes.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {418}, doi = {10.1186/s12864-018-4816-5}, pmid = {29848286}, issn = {1471-2164}, support = {NNF10CC1016517//The Novo Nordisk Foundation Center for Biosustainability/ ; BB/M006891/1, BB/M017702/1 and BB/P009042/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 757384//H2020 European Research Council/ ; }, abstract = {BACKGROUND: Transporter proteins mediate the translocation of substances across the membranes of living cells. Many transport processes are energetically expensive and the cells use 20 to 60% of their energy to power the transportomes. We hypothesized that there may be an evolutionary selection pressure for lower energy transporters.<br><br>RESULTS: We performed a genome-wide analysis of the compositional reshaping of the transportomes across the kingdoms of bacteria, archaea, and eukarya. We found that the share of ABC transporters is much higher in bacteria and archaea (ca. 27% of the transportome) than in primitive eukaryotes (13%), algae and plants (10%) and in fungi and animals (5-6%). This decrease is compensated by an increased occurrence of secondary transporters and ion channels. The share of ion channels is particularly high in animals (ca. 30% of the transportome) and algae and plants with (ca. 13%), when compared to bacteria and archaea with only 6-7%. Therefore, our results show a move to a preference for the low-energy-demanding transporters (ion channels and carriers) over the more energy-costly transporter classes (ATP-dependent families, and ABCs in particular) as part of the transition from prokaryotes to eukaryotes. The transportome analysis also indicated seven bacterial species, including Neorickettsia risticii and Neorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, based on the phylogenetically restricted presence therein of clear homologues of modern mitochondrial solute carriers.<br><br>CONCLUSIONS: The results indicate that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. These changes have likely been important in the development of tissues performing energetically costly cellular functions.}, }
@article {pmid29843612, year = {2018}, author = {Hartmann, T and Bernt, M and Middendorf, M}, title = {EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {192}, doi = {10.1186/s12859-018-2170-x}, pmid = {29843612}, issn = {1471-2105}, support = {PhD student fellowship//Universit?t Leipzig/ ; }, abstract = {BACKGROUND: To study the differences between two unichromosomal circular genomes, e.g., mitochondrial genomes, under the tandem duplication random loss (TDRL) rearrangement it is important to consider the whole set of potential TDRL rearrangement events that could have taken place. The reason is that for two given circular gene orders there can exist different TDRL rearrangements that transform one of the gene orders into the other. Hence, a TDRL event cannot always be reconstructed only from the knowledge of the circular gene order before a TDRL event and the circular gene order after it.<br><br>RESULTS: We present the program EqualTDRL that computes and illustrates the complete set of TDRLs for pairs of circular gene orders that differ by only one TDRL. EqualTDRL considers the circularity of the given genomes and certain restrictions on the TDRL rearrangements. Examples for the latter are sequences of genes that have to be conserved during a TDRL or pairs of genes that frame intergenic regions which might represent remnants of duplicated genes. Additionally, EqualTDRL allows to determine the set of TDRLs that are minimum with respect to the number of duplicated genes.<br><br>CONCLUSION: EqualTDRL supports scientists to study the complete set of TDRLs that possibly could have taken place in the evolution of mitochondrial genomes. EqualTDRL is implemented in C++ using the ggplot2 package of the open source programming language R and is freely available from http://pacosy.informatik.uni-leipzig.de/equaltdrl .}, }
@article {pmid29843598, year = {2018}, author = {Perry, KD and Baker, GJ and Powis, KJ and Kent, JK and Ward, CM and Baxter, SW}, title = {Cryptic Plutella species show deep divergence despite the capacity to hybridize.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {77}, doi = {10.1186/s12862-018-1183-4}, pmid = {29843598}, issn = {1471-2148}, support = {UA00146//University of Adelaide/International ; DAS00094//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DP120100047//Australian Research Council/International ; FT140101303//Australian Research Council/International ; }, mesh = {Animals ; Australia ; Biological Assay ; Crosses, Genetic ; DNA, Mitochondrial/genetics ; Female ; Fertility ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Heterozygote ; *Hybridization, Genetic/drug effects ; Insecticide Resistance/drug effects/genetics ; Insecticides/toxicity ; Likelihood Functions ; Male ; Mitochondria/genetics ; Moths/*genetics/microbiology ; Phylogeny ; Species Specificity ; Sympatry ; Wolbachia/drug effects/physiology ; }, abstract = {BACKGROUND: Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world's most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry &amp; Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected Plutella from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and Wolbachia infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays.<br><br>RESULTS: The two Plutella species coexisted on wild brassicas and canola crops, but only 10% of Plutella individuals were P. australiana. This species was not found on commercial Brassica vegetable crops, which are routinely sprayed with insecticides. Bioassays found that P. australiana was 19-306 fold more susceptible to four commonly-used insecticides than P. xylostella. Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in P. australiana, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5% of P. xylostella.<br><br>CONCLUSIONS: Despite sympatric distributions and the capacity to hybridize, strong genomic and phenotypic divergence exists between these Plutella species that is consistent with contrasting colonization histories and reproductive isolation after secondary contact. Although P. australiana is a potential pest of brassicaceous crops, it is of secondary importance to P. xylostella.}, }
@article {pmid29808012, year = {2018}, author = {Yuan, L and Zhai, L and Qian, L and Huang,  and Ding, Y and Xiang, H and Liu, X and Thompson, JW and Liu, J and He, YH and Chen, XQ and Hu, J and Kong, QP and Tan, M and Wang, XF}, title = {Switching off IMMP2L signaling drives senescence via simultaneous metabolic alteration and blockage of cell death.}, journal = {Cell research}, volume = {28}, number = {6}, pages = {625-643}, doi = {10.1038/s41422-018-0043-5}, pmid = {29808012}, issn = {1748-7838}, support = {R01 CA154586/CA/NCI NIH HHS/United States ; UL1 TR001117/TR/NCATS NIH HHS/United States ; }, abstract = {Cellular senescence is a fundamental cell fate playing a significant role throughout the natural aging process. However, the molecular determinants distinguishing senescence from other cell-cycle arrest states such as quiescence and post-mitotic state, and the specified mechanisms underlying cell-fate decisions towards senescence versus cell death in response to cellular stress stimuli remain less understood. Employing multi-omics approaches, we revealed that switching off the specific mitochondrial processing machinery involving the peptidase IMMP2L serves as the foundation of the senescence program, which was also observed during the mammalian aging process. Mechanistically, we demonstrate that IMMP2L processes and thus activates at least two substrates, mitochondrial metabolic enzyme glycerol-3-phosphate dehydrogenase (GPD2) and cell death regulator apoptosis-inducing factor (AIF). For cells destined to senesce, concerted shutdown of the IMMP2L-GPD2 and IMMP2L-AIF signaling axes collaboratively drives the senescent process by reprogramming mitochondria-associated redox status, phospholipid metabolism and signaling network, and simultaneously blocking cell death under oxidative stress conditions.}, }
@article {pmid29806019, year = {2018}, author = {Taborsky, M and Schütz, D and Goffinet, O and van Doorn, GS}, title = {Alternative male morphs solve sperm performance/longevity trade-off in opposite directions.}, journal = {Science advances}, volume = {4}, number = {5}, pages = {eaap8563}, doi = {10.1126/sciadv.aap8563}, pmid = {29806019}, issn = {2375-2548}, abstract = {Males pursuing alternative reproductive tactics have been predicted to face a trade-off between maximizing either swimming performance or endurance of their sperm. However, empirical evidence for this trade-off is equivocal, which may be due to simplistic assumptions. In the shell-brooding cichlid fish Lamprologus callipterus, two Mendelian male morphs compete for fertilization by divergent means: Bourgeois nest males ejaculate sperm, on average, about six times farther from the unfertilized ova than do parasitic dwarf males. This asymmetry is opposite to the usual situation, in which bourgeois males typically benefit from superior fertilization opportunities, suggesting that nest males' sperm should persist longer than dwarf male sperm. The assumed trade-off between sperm swimming performance and longevity predicts that, in turn, sperm of dwarf males should outperform that of nest males in swimming efficiency. Measurement of sperm performance and endurance reveals that dwarf male spermatozoa swim straighter initially than those of nest males, but their motility declines earlier and their velocity slows down more abruptly. Nest male sperm survives longer, which relates to a larger sperm head plus midpiece, implying more mitochondria. Thus, the trade-off between sperm performance and endurance is optimized in opposite directions by alternative male morphs. We argue that the relative success of alternative sperm performance strategies can be influenced strongly by environmental factors such as the time window between gamete release and fertilization, and the position of gamete release. This is an important yet little understood aspect of gametic adaptations to sperm competition.}, }
@article {pmid29802659, year = {2018}, author = {Tilquin, A and Christie, JR and Kokko, H}, title = {Mitochondrial complementation: a possible neglected factor behind early eukaryotic sex.}, journal = {Journal of evolutionary biology}, volume = {31}, number = {8}, pages = {1152-1164}, doi = {10.1111/jeb.13293}, pmid = {29802659}, issn = {1420-9101}, abstract = {Sex is ancestral in eukaryotes. Meiotic sex differs from bacterial ways of exchanging genetic material by involving the fusion of two cells. We examine the hypothesis that fusion evolved in early eukaryotes because it was directly beneficial, rather than a passive side effect of meiotic sex. We assume that the uptake of (proto)mitochondria into eukaryotes preceded the evolution of cell fusion and that Muller's ratchet operating within symbiont lineages led to the accumulation of lineage-specific sets of mutations in asexual host cells. We examine whether cell fusion, and the consequent biparental inheritance of symbionts, helps to mitigate the effects of this mutational meltdown of mitochondria. In our model, host cell fitness improves when two independently evolved mitochondrial strains co-inhabit a single cytoplasm, mirroring mitochondrial complementation found in modern eukaryotes. If fusion incurs no cost, we find that an allele coding for fusion can invade a population of nonfusers. If fusion is costly, there are two thresholds. The first describes a maximal fusing rate (probability of fusion per round of cell division) that is able to fix. An allele that codes for a rate above this threshold can reach a polymorphic equilibrium with nonfusers, as long as the rate is below the second threshold, above which the fusion allele is counter-selected. Whenever it evolves, fusion increases the population-wide level of heteroplasmy, which allows mitochondrial complementation and increases population fitness. We conclude that beneficial interactions between mitochondria are a potential factor that selected for cell fusion in early eukaryotes.}, }
@article {pmid29799088, year = {2018}, author = {Li, Q and Chen, C and Xiong, C and Jin, X and Chen, Z and Huang, W}, title = {Comparative mitogenomics reveals large-scale gene rearrangements in the mitochondrial genome of two Pleurotus species.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {14}, pages = {6143-6153}, doi = {10.1007/s00253-018-9082-6}, pmid = {29799088}, issn = {1432-0614}, support = {2016NZ0042//The National Science &amp; Technology Pillar Program of Sichuan/ ; 2016NZ0103//the Crop Molecular Breeding Platform in Sichuan/ ; }, mesh = {DNA, Mitochondrial/genetics ; Gene Rearrangement/*genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; Pleurotus/classification/*genetics ; Species Specificity ; }, abstract = {In the present study, we assembled the mitogenomes of Pleurotus citrinopileatus and Pleurotus platypus. The circular mitogenome of the two Pleurotus species comprises a set of 14 conserved protein-encoding genes (PEGs), 2 RNA genes (small subunit ribosomal RNA and large subunit ribosomal RNA), and 24 tRNAs, with sizes of 60,694 and 73,807 bp, respectively. They contain 4 and 10 introns with 3 and 10 intronic open reading frames (ORFs), respectively. Thirteen position classes (Pcls) of introns were found in the cox1 gene of four Pleurotus species. The number and class of Pcl varied among different Pleurotus species, indicating that numerous events of loss and gain occurred during evolution of Pleurotus. Comparative mitogenomic and collinearity analyses reveal that large-scale gene rearrangements may have occurred during the evolution of Pleurotus citrinopileatus and Pleurotus platypus, including gene rearrangements and inversions, which may be related to the observed high amounts of repetitive DNA elements (5.62 and 5.45%, respectively). Phylogenetic analysis based on concatenated mitochondrial protein sequences reveals that concatenated mitochondrial genes are suitable as molecular markers for phylogenetic analysis. This serves as the first report on large-scale rearrangements in the mitochondria of the genus Pleurotus, thereby improving our understanding of the evolution of the Pleurotus genus and other macrofungi.}, }
@article {pmid29794041, year = {2018}, author = {Camus, MF and Dowling, DK}, title = {Mitochondrial genetic effects on reproductive success: signatures of positive intrasexual, but negative intersexual pleiotropy.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1879}, pages = {}, doi = {10.1098/rspb.2018.0187}, pmid = {29794041}, issn = {1471-2954}, abstract = {Theory predicts that maternal inheritance of mitochondria will facilitate the accumulation of mtDNA mutations that are male biased, or even sexually antagonistic, in effect. While there are many reported cases of mtDNA mutations conferring cytoplasmic male sterility in plants, historically it was assumed such mutations would not persist in the streamlined mitochondrial genomes of bilaterian metazoans. Intriguingly, recent cases of mitochondrial variants exerting male biases in effect have come to light in bilaterians. These cases aside, it remains unknown whether the mitochondrial genetic variation affecting phenotypic expression, and in particular reproductive performance, in bilaterians is routinely composed of sex-biased or sex-specific variation. If selection consistently favours mtDNA variants that augment female fitness, but at cost to males, this could shape patterns of pleiotropy and lead to negative intersexual correlations across mtDNA haplotypes. Here, we show that genetic variation across naturally occurring mitochondrial haplotypes affects components of reproductive success in both sexes, in the fruit fly Drosophila melanogaster We find that intrasexual correlations across mitochondrial haplotypes, for components of reproductive success, are generally positive, while intersexual correlations are negative. These results accord with theoretical predictions, suggesting that maternal inheritance has led to the fixation of numerous mutations of sexually antagonistic effect.}, }
@article {pmid29792772, year = {2018}, author = {Xia, C and Wang, M and Yin, C and Cornejo, OE and Hulbert, SH and Chen, X}, title = {Genome Sequence Resources for the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) and the Barley Stripe Rust Pathogen (Puccinia striiformis f. sp. hordei).}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {31}, number = {11}, pages = {1117-1120}, doi = {10.1094/MPMI-04-18-0107-A}, pmid = {29792772}, issn = {0894-0282}, abstract = {Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interactions.}, }
@article {pmid29787825, year = {2018}, author = {Long, Z and Li, H and Du, Y and Han, B}, title = {Congenital sideroblastic anemia: Advances in gene mutations and pathophysiology.}, journal = {Gene}, volume = {668}, number = {}, pages = {182-189}, doi = {10.1016/j.gene.2018.05.074}, pmid = {29787825}, issn = {1879-0038}, mesh = {Anemia, Sideroblastic/congenital/*genetics/metabolism ; Heme/biosynthesis ; Humans ; Iron/metabolism ; Mitochondrial Proteins/biosynthesis ; *Mutation ; }, abstract = {Congenital sideroblastic anemia (CSA) is a series of rare, heterogeneous disorders, characterized by iron overload in the mitochondria of erythroblasts and ringed sideroblasts in bone marrow. In recent years, rapid development of next-generation sequencing technology brings great advance in understanding of genetic and pathophysiologic features of CSA. Based on the pathophysiology of mitochondrial iron metabolism, causative genes of CSA can be divided into three subtypes: heme biosynthesis related; iron‑sulfur cluster biosynthesis and transportation related; and mitochondrial respiratory chain synthesis related. Patients with CSA present various clinical manifestation due to relevant mutation gene and require different treatment strategies. The recognition of the causative genes and evolution of pathogenicity is critical. In this review, we summarize the recent progress in mutation genes of CSA, and its potential role in the pathogenesis, diagnosis and treatment.}, }
@article {pmid29779502, year = {2018}, author = {Buysse, M and Duron, O}, title = {Multi-locus phylogenetics of the Midichloria endosymbionts reveals variable specificity of association with ticks.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-10}, doi = {10.1017/S0031182018000793}, pmid = {29779502}, issn = {1469-8161}, abstract = {Candidatus Midichloria mitochondrii is a maternally inherited bacterium of ticks with a unique intra-mitochondrial lifestyle. Here, we investigate on the evolutionary history of these associations and the degree of Midichloria-tick specificity. While previous surveys used the 16S rRNA gene as an exclusive molecular marker, we rather developed a multi-locus typing method based on four more variable housekeeping genes (groEL, rpoB, dnaK and ftsZ) and on one flagellum gene (fliC) present in Midichloria genomes. Using this method, multi-locus phylogenetic analyses revealed the structuring of a wide Midichloria genetic diversity into three distinct lineages associated with ticks. Overall, two distinct evolutionary strategies are obvious depending on lineage: two Midichloria lineages are generalists with infections acquired through horizontal transfers between distantly related tick species but one other Midichloria lineage rather show a high specificity degree to the Ixodes tick genus. This pattern suggests a capacity of certain Midichloria strains to maintain infections in only limited range of related tick species. These different infection strategies of Midichloria highlight an unexpected variability in their dependency to their tick hosts. We further conjecture that this pattern is also likely to indicate variability in their effects on ticks.}, }
@article {pmid29770661, year = {2018}, author = {Cang-Lin, Z and Jia, P and Zhen, R and Jin-Rong, Z and Ya-Ming, Y}, title = {[Genotyping and polymorphism analysis of cytochrome c oxidase subunit Ⅰ gene of Pomacea canaliculata from Lincang City in Yunnan Province].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {30}, number = {2}, pages = {179-183}, doi = {10.16250/j.32.1374.2017163}, pmid = {29770661}, issn = {1005-6661}, mesh = {Angiostrongylus cantonensis ; Animals ; China ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Gastropoda/enzymology/*genetics ; Genotype ; Haplotypes ; Phylogeny ; }, abstract = {OBJECTIVE: To analyze the genetic diversity of Pomacea canaliculata based on the mitochondria DNA cytochrome c oxidase subunit Ⅰ (mtDNA COⅠ) gene as a molecular marker in Lincang City of Yunnan Province, so as to provide the scientific data for monitoring Angiostrongylus cantonensis in local areas.<br><br>METHODS: The genotypes and polymorphisms of 38 specimens of P. canaliculata collected from Mengding Town of Lincang City were analyzed by sequencing COⅠ gene. The phylogenetic tree and genetic distances were produced based on the haplotypes from GenBank and the present study by using the neighbourjoining method with the software MEGA version 6.06.<br><br>RESULTS: Totally 31 sequences were acquired in the present study and they produced 3 unique haplotypes. Haplotype 1 showed a higher frequency compared to the others and it accounted for 83.9 % (26/31). The data showed that the least genetic distances ranged from 0 to 0.052 between P. canaliculata and 3 haplotypes, as well as the largest genetic distances ranged from 0.021 to 0.239 between Pila conica and 3 haplotypes. Otherwise, the analysis of the phylogenetic trees based on COⅠ gene sequences of P. canaliculata indicated that all of 3 haplotypes clustered into one big clade with that from Japan (GenBank accession number: AB433769), China (GenBank accession number: KT313034) and USA (GenBank accession number: EU523129), which owned the closet relationship amongst them. Their genetic relationships were distantly related to the GenBank's reference sequences of P. insularum (GenBank accession number: EF514942), P. camena (GenBank accession number: EF515059) and so on.<br><br>CONCLUSIONS: There is a P. canaliculata species in Lincang City of Yunnan Province as well as a high genetic diversity amongst the acquired 3 haplotypes in this study.}, }
@article {pmid29769322, year = {2018}, author = {Krah, A and Zarco-Zavala, M and McMillan, DGG}, title = {Insights into the regulatory function of the ɛ subunit from bacterial F-type ATP synthases: a comparison of structural, biochemical and biophysical data.}, journal = {Open biology}, volume = {8}, number = {5}, pages = {}, doi = {10.1098/rsob.170275}, pmid = {29769322}, issn = {2046-2441}, abstract = {ATP synthases catalyse the formation of ATP, the most common chemical energy storage unit found in living cells. These enzymes are driven by an electrochemical ion gradient, which allows the catalytic evolution of ATP by a binding change mechanism. Most ATP synthases are capable of catalysing ATP hydrolysis to varying degrees, and to prevent wasteful ATP hydrolysis, bacteria and mitochondria have regulatory mechanisms such as ADP inhibition. Additionally, ɛ subunit inhibition has also been described in three bacterial systems, Escherichia coli, Bacillus PS3 and Caldalkalibacillus thermarum TA2.A1. Previous studies suggest that the ɛ subunit is capable of undergoing an ATP-dependent conformational change from the ATP hydrolytic inhibitory 'extended' conformation to the ATP-induced non-inhibitory 'hairpin' conformation. A recently published crystal structure of the F1 domain of the C. thermarum TA2.A1 F1Fo ATP synthase revealed a mutant ɛ subunit lacking the ability to bind ATP in a hairpin conformation. This is a surprising observation considering it is an organism that performs no ATP hydrolysis in vivo, and appears to challenge the current dogma on the regulatory role of the ɛ subunit. This has prompted a re-examination of present knowledge of the ɛ subunits role in different organisms. Here, we compare published biochemical, biophysical and structural data involving ɛ subunit-mediated ATP hydrolysis regulation in a variety of organisms, concluding that the ɛ subunit from the bacterial F-type ATP synthases is indeed capable of regulating ATP hydrolysis activity in a wide variety of bacteria, making it a potentially valuable drug target, but its exact role is still under debate.}, }
@article {pmid29761268, year = {2018}, author = {Edera, AA and Gandini, CL and Sanchez-Puerta, MV}, title = {Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria.}, journal = {Plant molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11103-018-0734-9}, pmid = {29761268}, issn = {1573-5028}, abstract = {KEY MESSAGE: Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites. By means of publicly available RNA-seq data, this study identified 10,217 editing sites in mitochondrial protein-coding genes of 17 diverse angiosperms. Even though other types of mismatches were also identified, we did not find evidence of non-canonical editing processes. The results showed an uneven distribution of editing sites among species, genes, and codon positions. The analyses revealed that editing sites were conserved across angiosperms but there were some species-specific sites. Non-synonymous editing sites were particularly highly conserved (~ 80%) across the plant species and were efficiently edited (80% editing extent). In contrast, editing sites at third codon positions were poorly conserved (~ 30%) and only partially edited (~ 40% editing extent). We found that the loss of editing sites along angiosperm evolution is mainly occurring by replacing editing sites with thymidines, instead of a degradation of the editing recognition motif around editing sites. Consecutive and highly conserved editing sites had been replaced by thymidines as result of retroprocessing, by which edited transcripts are reverse transcribed to cDNA and then integrated into the genome by homologous recombination. This phenomenon was more pronounced in eudicots, and in the gene cox1. These results suggest that retroprocessing is a widespread driving force underlying the loss of editing sites in angiosperm mitochondria.}, }
@article {pmid29760081, year = {2018}, author = {Sharp, NP and Sandell, L and James, CG and Otto, SP}, title = {The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {E5046-E5055}, doi = {10.1073/pnas.1801040115}, pmid = {29760081}, issn = {1091-6490}, mesh = {DNA Breaks, Double-Stranded ; DNA Repair/genetics ; DNA Replication/genetics ; DNA, Fungal/*genetics ; *Diploidy ; Genes, Fungal/genetics ; *Haploidy ; Mitochondria/genetics ; Mutation/*genetics ; Mutation Rate ; Saccharomyces cerevisiae/*genetics ; }, abstract = {By altering the dynamics of DNA replication and repair, alternative ploidy states may experience different rates and types of new mutations, leading to divergent evolutionary outcomes. We report a direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploids and diploids following a mutation-accumulation experiment in the budding yeast Saccharomyces cerevisiae Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide mutations (SNMs) and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that mutations would have weaker effects, due to masking, in diploids. Haploidy is expected to reduce the opportunity for conservative DNA repair involving homologous chromosomes, increasing the insertion-deletion rate, but we found little support for this idea. Instead, haploids were more susceptible to SNMs in late-replicating genomic regions, resulting in a ploidy difference in the spectrum of substitutions. In diploids, we detect mutation rate variation among chromosomes in association with centromere location, a finding that is supported by published polymorphism data. Diploids are not simply doubled haploids; instead, our results predict that the spectrum of spontaneous mutations will substantially shape the dynamics of genome evolution in haploid and diploid populations.}, }
@article {pmid29747566, year = {2018}, author = {Oetjens, MT and Martin, A and Veeramah, KR and Kidd, JM}, title = {Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {350}, doi = {10.1186/s12864-018-4749-z}, pmid = {29747566}, issn = {1471-2164}, support = {R01 GM103961/GM/NIGMS NIH HHS/United States ; R01GM103961//National Institute of General Medical Sciences/ ; }, abstract = {BACKGROUND: Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs.<br><br>RESULTS: We identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700-7000 years old) belong to distinct clades.<br><br>CONCLUSIONS: We estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68-151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs.}, }
@article {pmid29743632, year = {2018}, author = {Sinha, S and Bheemsetty, VA and Inamdar, MS}, title = {A double helical motif in OCIAD2 is essential for its localization, interactions and STAT3 activation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7362}, doi = {10.1038/s41598-018-25667-3}, pmid = {29743632}, issn = {2045-2322}, abstract = {The Ovarian Carcinoma Immunoreactive Antigen domain (OCIAD) - containing proteins OCIAD1/Asrij and OCIAD2, are implicated in several cancers and neurodegenerative diseases. While Asrij has a conserved role in facilitating STAT3 activation for JAK/STAT signaling, the expression and function of OCIAD2 in non-cancerous contexts remains unknown. Here, we report that ociad2 neighbors ociad1/asrij in most vertebrate genomes, and the two genes likely arose by tandem gene duplication, probably somewhere between the Ordovician and Silurian eras. We show that ociad2 expression is higher in the mouse kidney, liver and brain relative to other tissues. OCIAD2 localizes to early endosomes and mitochondria, and interacts with Asrij and STAT3. Knockdown and overexpression studies showed that OCIAD2 is essential for STAT3 activation and cell migration, which could contribute to its role in tumor metastasis. Structure prediction programs, protein disruption studies, biochemical and functional assays revealed a double helical motif in the OCIA domain that is necessary and sufficient for its localization, interactions and STAT3 activation. Given the importance of JAK/STAT signaling in development and disease, our studies shed light on the evolution and conserved function of the OCIA domain in regulating this pathway and will be critical for understanding this clinically important protein family.}, }
@article {pmid29738865, year = {2018}, author = {Feng, S and Stejskal, V and Wang, Y and Li, Z}, title = {The mitochondrial genomes of the barklice, Lepinotus reticulatus and Dorypteryx domestica (Psocodea: Trogiomorpha): Insight into phylogeny of the order Psocodea.}, journal = {International journal of biological macromolecules}, volume = {116}, number = {}, pages = {247-254}, doi = {10.1016/j.ijbiomac.2018.05.021}, pmid = {29738865}, issn = {1879-0003}, mesh = {Animals ; Base Sequence ; Evolution, Molecular ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Insecta/*genetics ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The order Psocodea which has incorporated the two former orders Psocoptera (barklice and booklice) and Phthiraptera (parasitic lice) attracts much attention for its unusual mitochondrial (mt) genome rearrangements. Available phylogenetic analysis for Psocodea is subjected to partial taxa and a complete one is needed. To further explore the genome rearrangement and phylogeny in Psocodea, we sequenced the mt genomes of two barklice, Lepinotus reticulatus (collected from China) and Dorypteryx domestica (collected from Czech Republic). Both of newly sequenced barklice had typical one-chromosome mt genomes and the same mt gene arrangement with the reported Lepidopsocidae sp. The mt genomes of L. reticulatus and D. domestica contained 37 genes typical of bilateral animals. In contrast with the recent report mt genome of D. domestica, our strain was found with many single nucleotide polymorphisms in intra-specific difference. Phylogenetic relationships were inferred from all available mt genomes of Psocodea data using Maximum Likelihood and Bayesian methods. The mt genome of L. reticulatus is the first representative with complete sequences of the family Trogiidae and our D. domestica data enriched the family Psyllipsocidae, which will contribute to the further study of mt gene rearrangement and phylogeny of Psocodea.}, }
@article {pmid29731304, year = {2018}, author = {Maclean, AE and Hertle, AP and Ligas, J and Bock, R and Balk, J and Meyer, EH}, title = {Absence of Complex I Is Associated with Diminished Respiratory Chain Function in European Mistletoe.}, journal = {Current biology : CB}, volume = {28}, number = {10}, pages = {1614-1619.e3}, doi = {10.1016/j.cub.2018.03.036}, pmid = {29731304}, issn = {1879-0445}, abstract = {Parasitism is a life history strategy found across all domains of life whereby nutrition is obtained from a host. It is often associated with reductive evolution of the genome, including loss of genes from the organellar genomes [1, 2]. In some unicellular parasites, the mitochondrial genome (mitogenome) has been lost entirely, with far-reaching consequences for the physiology of the organism [3, 4]. Recently, mitogenome sequences of several species of the hemiparasitic plant mistletoe (Viscum sp.) have been reported [5, 6], revealing a striking loss of genes not seen in any other multicellular eukaryotes. In particular, the nad genes encoding subunits of respiratory complex I are all absent and other protein-coding genes are also lost or highly diverged in sequence, raising the question what remains of the respiratory complexes and mitochondrial functions. Here we show that oxidative phosphorylation (OXPHOS) in European mistletoe, Viscum album, is highly diminished. Complex I activity and protein subunits of complex I could not be detected. The levels of complex IV and ATP synthase were at least 5-fold lower than in the non-parasitic model plant Arabidopsis thaliana, whereas alternative dehydrogenases and oxidases were higher in abundance. Carbon flux analysis indicates that cytosolic reactions including glycolysis are greater contributors to ATP synthesis than the mitochondrial tricarboxylic acid (TCA) cycle. Our results describe the extreme adjustments in mitochondrial functions of the first reported multicellular eukaryote without complex I.}, }
@article {pmid29730527, year = {2018}, author = {van der Hoek, MD and Madsen, O and Keijer, J and van der Leij, FR}, title = {Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of CPT2 versus CPT1 and related variants.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {1863}, number = {8}, pages = {909-918}, doi = {10.1016/j.bbalip.2018.05.001}, pmid = {29730527}, issn = {1879-2618}, abstract = {Carnitine/choline acyltransferases play diverse roles in energy metabolism and neuronal signalling. Our knowledge of their evolutionary relationships, important for functional understanding, is incomplete. Therefore, we aimed to determine the evolutionary relationships of these eukaryotic transferases. We performed extensive phylogenetic and intron position analyses. We found that mammalian intramitochondrial CPT2 is most closely related to cytosolic yeast carnitine transferases (Sc-YAT1 and 2), whereas the other members of the family are related to intraorganellar yeast Sc-CAT2. Therefore, the cytosolically active CPT1 more closely resembles intramitochondrial ancestors than CPT2. The choline acetyltransferase is closely related to carnitine acetyltransferase and shows lower evolutionary rates than long chain acyltransferases. In the CPT1 family several duplications occurred during animal radiation, leading to the isoforms CPT1A, CPT1B and CPT1C. In addition, we found five CPT1-like genes in Caenorhabditis elegans that strongly group to the CPT1 family. The long branch leading to mammalian brain isoform CPT1C suggests that either strong positive or relaxed evolution has taken place on this node. The presented evolutionary delineation of carnitine/choline acyltransferases adds to current knowledge on their functions and provides tangible leads for further experimental research.}, }
@article {pmid29728774, year = {2018}, author = {Gong, S and Vamberger, M and Auer, M and Praschag, P and Fritz, U}, title = {Millennium-old farm breeding of Chinese softshell turtles (Pelodiscus spp.) results in massive erosion of biodiversity.}, journal = {Die Naturwissenschaften}, volume = {105}, number = {5-6}, pages = {34}, doi = {10.1007/s00114-018-1558-9}, pmid = {29728774}, issn = {1432-1904}, support = {31471966//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Biodiversity ; *Breeding ; China ; DNA, Mitochondrial/genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Turtles/*classification/*genetics ; }, abstract = {Chinese softshell turtles (Pelodiscus spp.) are widely distributed, ranging from the Amur and Ussuri Rivers in the Russian Far East through the Korean Peninsula, Japan, and eastern, central, and southern China to southern Vietnam. In East and Southeast Asia, Chinese softshell turtles are traditionally exploited for food and have been farm-bred in China since the Spring and Autumn Period, more than 2400 years ago. Currently, the annual production of Pelodiscus amounts to 340,000 t in China alone. Using mitochondrial DNA (2428 bp) and five nuclear loci (3704 bp), we examined broad sampling of wild and farm-bred Pelodiscus to infer genetic and taxonomic differentiation. We discovered four previously unknown mitochondrial lineages, all from China. One lineage from Jiangxi is deeply divergent and sister to the mitochondrial lineage of Pelodiscus axenaria. The nuclear loci supported species status for P. axenaria and the new lineage from Jiangxi. Pelodiscus maackii and P. parviformis, both harboring distinct mitochondrial lineages, were not differentiated from P. sinensis in the studied nuclear markers. The same is true for two new mitochondrial lineages from Zhejiang, China, represented by only one individual each, and another new lineage from Anhui, Guangdong, Jiangxi and Zhejiang, China. However, Vietnamese turtles yielding a mitochondrial lineage clustering within P. sinensis were distinct in nuclear markers, suggesting that these populations could represent another unknown species with introgressed mitochondria. Its species status is also supported by the syntopic occurrence with P. sinensis in northern Vietnam and by morphology. In addition, we confirmed sympatry of P. axenaria and P. parviformis in Guangxi, China, and found evidence for sympatry of P. sinensis and the new putative species from Jiangxi, China. We also discovered evidence for hybridization in turtle farms and for the occurrence of alien lineages in the wild (Zhejiang, China), highlighting the risk of genetic pollution of native stock. In the face of the large-scale breeding of Pelodiscus, we claim that the long-term survival of distinct genetic lineages and species can only be assured when an upscale market segment for pure-bred softshell turtles is established, making the breeding of pure lineages lucrative for turtle farms. Our findings underline that the diversity of Pelodiscus is currently underestimated and threatened by anthropogenic admixture. We recommend mass screening of genetic and morphological variation of Chinese softshell turtles as a first step to understand and preserve their diversity.}, }
@article {pmid29724860, year = {2018}, author = {Garg, SG and Martin, WF}, title = {Asking endosymbionts to do an enzyme's job.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {20}, pages = {E4543-E4544}, doi = {10.1073/pnas.1804397115}, pmid = {29724860}, issn = {1091-6490}, mesh = {*Biological Evolution ; Enzymes/*metabolism ; Mitochondria ; *Symbiosis ; }, }
@article {pmid29723685, year = {2018}, author = {Samuilov, VD and Kiselevsky, DB and Oleskin, AV}, title = {Mitochondria-targeted quinones suppress the generation of reactive oxygen species, programmed cell death and senescence in plants.}, journal = {Mitochondrion}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mito.2018.04.008}, pmid = {29723685}, issn = {1872-8278}, abstract = {This work focuses on the effect of mitochondria-targeted quinones (SkQs) on plants. SkQs with antioxidant properties are accumulated in the mitochondria of pea cells and suppress the generation of reactive oxygen species. At nanomolar concentrations, SkQs prevented the death of pea leaf epidermal or guard cells caused by chitosan, bacterial lipopolysaccharide or KCN. The protective effect of SkQs was removed by a protonophoric uncoupler. SkQs at micromolar concentrations inhibited the O2 evolution by illuminated chloroplasts and stimulated the respiration of mitochondria. SkQs slowed down the senescence and the death of Arabidopsis thaliana leaves and improved the wheat crop structure.}, }
@article {pmid29720079, year = {2018}, author = {Dufresnes, C and Lymberakis, P and Kornilios, P and Savary, R and Perrin, N and Stöck, M}, title = {Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {67}, doi = {10.1186/s12862-018-1179-0}, pmid = {29720079}, issn = {1471-2148}, support = {STO 493/2-2//Deutsche Forschungsgemeinschaft/International ; P2LAP3_171818//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/International ; }, mesh = {Animals ; Base Sequence ; *Biodiversity ; Bufonidae/*classification ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Drift ; Genetics, Population ; Genome ; Greece ; *Islands ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Reproductive Isolation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs.<br><br>RESULTS: We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids.<br><br>CONCLUSIONS: The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia.}, }
@article {pmid29718949, year = {2018}, author = {Lv, C and Li, Q and Kong, L}, title = {Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196466}, doi = {10.1371/journal.pone.0196466}, pmid = {29718949}, issn = {1932-6203}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Bayes Theorem ; Bivalvia/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.}, }
@article {pmid29706933, year = {2018}, author = {Goetzman, ES and Prochownik, EV}, title = {The Role for Myc in Coordinating Glycolysis, Oxidative Phosphorylation, Glutaminolysis, and Fatty Acid Metabolism in Normal and Neoplastic Tissues.}, journal = {Frontiers in endocrinology}, volume = {9}, number = {}, pages = {129}, doi = {10.3389/fendo.2018.00129}, pmid = {29706933}, issn = {1664-2392}, support = {R01 CA174713/CA/NCI NIH HHS/United States ; R01 DK090242/DK/NIDDK NIH HHS/United States ; }, abstract = {That cancer cells show patterns of metabolism different from normal cells has been known for over 50 years. Yet, it is only in the past decade or so that an appreciation of the benefits of these changes has begun to emerge. Altered cancer cell metabolism was initially attributed to defective mitochondria. However, we now realize that most cancers do not have mitochondrial mutations and that normal cells can transiently adopt cancer-like metabolism during periods of rapid proliferation. Indeed, an encompassing, albeit somewhat simplified, conceptual framework to explain both normal and cancer cell metabolism rests on several simple premises. First, the metabolic pathways used by cancer cells and their normal counterparts are the same. Second, normal quiescent cells use their metabolic pathways and the energy they generate largely to maintain cellular health and organelle turnover and, in some cases, to provide secreted products necessary for the survival of the intact organism. By contrast, undifferentiated cancer cells minimize the latter functions and devote their energy to producing the anabolic substrates necessary to maintain high rates of unremitting cellular proliferation. Third, as a result of the uncontrolled proliferation of cancer cells, a larger fraction of the metabolic intermediates normally used by quiescent cells purely as a source of energy are instead channeled into competing proliferation-focused and energy-consuming anabolic pathways. Fourth, cancer cell clones with the most plastic and rapidly adaptable metabolism will eventually outcompete their less well-adapted brethren during tumor progression and evolution. This attribute becomes increasingly important as tumors grow and as their individual cells compete in a constantly changing and inimical environment marked by nutrient, oxygen, and growth factor deficits. Here, we review some of the metabolic pathways whose importance has gained center stage for tumor growth, particularly those under the control of the c-Myc (Myc) oncoprotein. We discuss how these pathways differ functionally between quiescent and proliferating normal cells, how they are kidnapped and corrupted during the course of transformation, and consider potential therapeutic strategies that take advantage of common features of neoplastic and metabolic disorders.}, }
@article {pmid29703131, year = {2018}, author = {Arafat, H and Alamaru, A and Gissi, C and Huchon, D}, title = {Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {65}, doi = {10.1186/s12862-018-1186-1}, pmid = {29703131}, issn = {1471-2148}, support = {161/15//Israel Science Foundation/International ; }, mesh = {Animals ; Biological Evolution ; Conserved Sequence/genetics ; Ctenophora/*genetics ; DNA, Mitochondrial/genetics ; Gene Order ; *Gene Rearrangement ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {BACKGROUND: Complete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. Ctenophora (comb jellies) is one such example, with only two complete mt sequences determined hitherto for this phylum, which encompasses ca. 150-200 described species. This lack of data derives from the extremely fast mt evolutionary rate in this lineage, complicating primer design and DNA amplification. Indeed, in the two ctenophore mt genomes sequenced to date, i.e. those of Mnemiopsis leidyi (order Lobata) and Pleurobrachia bachei (order Cydippida), both rRNA and protein coding genes exhibit an extraordinary size reduction and have highly derived sequences. Additionally, all tRNAs, and the atp6 and atp8 genes are absent. In order to determine whether these characteristics are shared by other ctenophores, we obtained the complete mt genomes of three benthic ctenophores belonging to the so far unsampled order of Platyctenida: Coeloplana loyai, Coeloplana yulianicorum and Vallicula multiformis.<br><br>RESULTS: The mt genomes of benthic ctenophores reveal the same peculiarities found in Mnemiopsis and Pleurobrachia, demonstrating that the fast evolutionary rate is a general trait of the ctenophore mt genomes. Our results also indicate that this high evolutionary rate not only affects the nucleotide substitution but also gene rearrangements. Indeed, gene order was highly rearranged among representatives of the different taxonomic orders in which it was close to random, but also quite variable within Platyctenida, in which the genera Coeloplana and Vallicula share only four conserved synteny blocks. However, the two congeneric Coeloplana species display exactly the same gene order. Because of the extreme evolutionary rate, our phylogenetic analyses were unable to resolve the phylogenetic position of ctenophores within metazoans or the relationships among the different Ctenophora orders. Comparative sequence-analyses allowed us to correct the annotation of the Pleurobrachia mt genome, confirming the absence of tRNAs, the presence of both rRNA genes, and the existence of a reassignment of codon TGA from tryptophan to serine for this species.<br><br>CONCLUSIONS: Since Platyctenida is an early diverging lineage among Ctenophora, our findings suggest that the mt traits described above are ancestral characteristics of this phylum.}, }
@article {pmid29698456, year = {2018}, author = {Peña-Diaz, P and Mach, J and Kriegová, E and Poliak, P and Tachezy, J and Lukeš, J}, title = {Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0196474}, doi = {10.1371/journal.pone.0196474}, pmid = {29698456}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Down-Regulation ; Electron Transport Complex IV/metabolism ; Metalloendopeptidases/antagonists &amp; inhibitors/classification/genetics/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*enzymology ; Phylogeny ; Protein Subunits/antagonists &amp; inhibitors/genetics/metabolism ; RNA Interference ; RNA, Small Interfering/metabolism ; Substrate Specificity ; Trypanosoma brucei brucei/*metabolism ; }, abstract = {Upon their translocation into the mitochondrial matrix, the N-terminal pre-sequence of nuclear-encoded proteins undergoes cleavage by mitochondrial processing peptidases. Some proteins require more than a single processing step, which involves several peptidases. Down-regulation of the putative Trypanosoma brucei mitochondrial intermediate peptidase (MIP) homolog by RNAi renders the cells unable to grow after 48 hours of induction. Ablation of MIP results in the accumulation of the precursor of the trypanosomatid-specific trCOIV protein, the largest nuclear-encoded subunit of the cytochrome c oxidase complex in this flagellate. However, the trCOIV precursor of the same size accumulates also in trypanosomes in which either alpha or beta subunits of the mitochondrial processing peptidase (MPP) have been depleted. Using a chimeric protein that consists of the N-terminal sequence of a putative subunit of respiratory complex I fused to a yellow fluorescent protein, we assessed the accumulation of the precursor protein in trypanosomes, in which RNAi was induced against the alpha or beta subunits of MPP or MIP. The observed accumulation of precursors indicates MIP depletion affects the activity of the cannonical MPP, or at least one of its subunits.}, }
@article {pmid29697049, year = {2018}, author = {Stairs, CW and Eme, L and Muñoz-Gómez, SA and Cohen, A and Dellaire, G and Shepherd, JN and Fawcett, JP and Roger, AJ}, title = {Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, doi = {10.7554/eLife.34292}, pmid = {29697049}, issn = {2050-084X}, support = {MOP 341174//Canadian Institutes of Health Research/Canada ; MOP 142349//Canadian Institutes of Health Research/Canada ; R15 GM096398/GM/NIGMS NIH HHS/United States ; 1R15GM096398-01//National Institutes of Health/ ; NSERC-CGS-D//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN 05616//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Under hypoxic conditions, some organisms use an electron transport chain consisting of only complex I and II (CII) to generate the proton gradient essential for ATP production. In these cases, CII functions as a fumarate reductase that accepts electrons from a low electron potential quinol, rhodoquinol (RQ). To clarify the origins of RQ-mediated fumarate reduction in eukaryotes, we investigated the origin and function of rquA, a gene encoding an RQ biosynthetic enzyme. RquA is very patchily distributed across eukaryotes and bacteria adapted to hypoxia. Phylogenetic analyses suggest lateral gene transfer (LGT) of rquA from bacteria to eukaryotes occurred at least twice and the gene was transferred multiple times amongst protists. We demonstrate that RquA functions in the mitochondrion-related organelles of the anaerobic protist Pygsuia and is correlated with the presence of RQ. These analyses reveal the role of gene transfer in the evolutionary remodeling of mitochondria in adaptation to hypoxia.}, }
@article {pmid29695865, year = {2018}, author = {Martijn, J and Vosseberg, J and Guy, L and Offre, P and Ettema, TJG}, title = {Deep mitochondrial origin outside the sampled alphaproteobacteria.}, journal = {Nature}, volume = {557}, number = {7703}, pages = {101-105}, doi = {10.1038/s41586-018-0059-5}, pmid = {29695865}, issn = {1476-4687}, mesh = {Alphaproteobacteria/*cytology/*genetics ; Atlantic Ocean ; Genome, Bacterial/genetics ; Genomics ; Metagenome/genetics ; Mitochondria/*genetics/*metabolism ; Pacific Ocean ; *Phylogeny ; }, abstract = {Mitochondria are ATP-generating organelles, the endosymbiotic origin of which was a key event in the evolution of eukaryotic cells 1 . Despite strong phylogenetic evidence that mitochondria had an alphaproteobacterial ancestry 2 , efforts to pinpoint their closest relatives among sampled alphaproteobacteria have generated conflicting results, complicating detailed inferences about the identity and nature of the mitochondrial ancestor. While most studies support the idea that mitochondria evolved from an ancestor related to Rickettsiales3-9, an order that includes several host-associated pathogenic and endosymbiotic lineages10,11, others have suggested that mitochondria evolved from a free-living group12-14. Here we re-evaluate the phylogenetic placement of mitochondria. We used genome-resolved binning of oceanic metagenome datasets and increased the genomic sampling of Alphaproteobacteria with twelve divergent clades, and one clade representing a sister group to all Alphaproteobacteria. Subsequent phylogenomic analyses that specifically address long branch attraction and compositional bias artefacts suggest that mitochondria did not evolve from Rickettsiales or any other currently recognized alphaproteobacterial lineage. Rather, our analyses indicate that mitochondria evolved from a proteobacterial lineage that branched off before the divergence of all sampled alphaproteobacteria. In light of this new result, previous hypotheses on the nature of the mitochondrial ancestor6,15,16 should be re-evaluated.}, }
@article {pmid29689791, year = {2018}, author = {Sadasivan, K and Ramesh, MB and Palot, MJ and Ambekar, M and Mirza, ZA}, title = {A new species of fan-throated lizard of the genus Sitana Cuvier, 1829 from coastal Kerala, southern India.}, journal = {Zootaxa}, volume = {4374}, number = {4}, pages = {545-564}, doi = {10.11646/zootaxa.4374.4.5}, pmid = {29689791}, issn = {1175-5334}, mesh = {Animals ; India ; *Lizards ; Mitochondria ; Phylogeny ; }, abstract = {We here describe Sitana attenboroughii sp. nov., a new species of fan-throated lizard of the genus Sitana Cuvier, 1829 from coastal Kerala in southern India. The new species morphologically is closer to Sitana visiri Deepak, 2016 (in Deepak et al. 2016a), however, differs in having higher numbers of ventral scales and a comparatively short but richly colored dewlap. Genetically the new species shows affinity to Sitana marudhamneydhal Deepak, Khandekar, Varma Chaitanya, 2016 from which it differs in an uncorrected pairwise sequence divergence of 2.2% for a fragment of mitochondrial Nicotinamide adenine dinucleotide dehydrogenase (NADH) subunit 2 gene.}, }
@article {pmid29678141, year = {2018}, author = {Beltrán-López, RG and Domínguez-Domínguez, O and Pérez-Rodríguez, R and Piller, K and Doadrio, I}, title = {Evolving in the highlands: the case of the Neotropical Lerma live-bearing Poeciliopsis infans (Woolman, 1894) (Cyprinodontiformes: Poeciliidae) in Central Mexico.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {56}, doi = {10.1186/s12862-018-1172-7}, pmid = {29678141}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Climate ; Cyprinodontiformes/genetics/*physiology ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Fresh Water ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Mexico ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; Time Factors ; *Tropical Climate ; }, abstract = {BACKGROUND: Volcanic and tectonic activities in conjunction with Quaternary climate are the main events that shaped the geographical distribution of genetic variation of many lineages. Poeciliopsis infans is the only poeciliid species that was able to colonize the temperate highlands of central Mexico. We inferred the phylogenetic relationships, biogeographic history, and historical demography in the widespread Neotropical species P. infans and correlated this with geological events and the Quaternary glacial-interglacial climate in the highlands of central Mexico, using the mitochondrial genes Cytochrome b and Cytochrome oxidase I and two nuclear loci, Rhodopsin and ribosomal protein S7.<br><br>RESULTS: Populations of P. infans were recovered in two well-differentiated clades. The maximum genetic distances between the two clades were 3.3% for cytb, and 1.9% for coxI. The divergence of the two clades occurred ca. 2.83 Myr. Ancestral area reconstruction revealed a complex biogeographical history for P. infans. The Bayesian Skyline Plot showed a demographic decline, although more visible for clade A, and more recently showed a population expansion in the last 0.025 Myr. Finally, the habitat suitability modelling showed that during the LIG, clade B had more areas with high probabilities of presence in comparison to clade A, whereas for the LGM, clade A showed more areas with high probabilities of presence in comparisons to clade B.<br><br>CONCLUSIONS: Poeciliopsis infans has had a complex evolutionary and biogeographic history, which, as in other co-distributed freshwater fishes, seems to be linked to the volcanic and tectonic activities during the Pliocene or early Pleistocene. Populations of P. infans distributed in lowlands showed a higher level of genetic diversity than populations distributed in highlands, which could be linked to more stable and higher temperatures in lowland areas. The fluctuations in population size through time are in agreement with the continuous fluctuations of the climate of central Mexico.}, }
@article {pmid29665772, year = {2018}, author = {Padilla-Jacobo, G and Cano-Camacho, H and López-Zavala, R and Cornejo-Pérez, ME and Zavala-Páramo, MG}, title = {Evolutionary history of Mexican domesticated and wild Meleagris gallopavo.}, journal = {Genetics, selection, evolution : GSE}, volume = {50}, number = {1}, pages = {19}, doi = {10.1186/s12711-018-0388-8}, pmid = {29665772}, issn = {1297-9686}, support = {Scholarship No. 359650//Consejo Nacional de Ciencia y Tecnología/International ; Scholarship//Consejo Nacional de Ciencia y Tecnología/International ; 2004-C01-201//Consejo Nacional de Ciencia y Tecnología-SAGARPA (MX)/International ; 2009-05-115938//Fondos Mixtos Consejo Nacional de Ciencia y Tecnología Gobierno del Estado de Michoacán (MX)/International ; }, mesh = {Animals ; Animals, Domestic/*genetics ; Animals, Wild/genetics ; Canada ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Variation ; Guatemala ; Haplotypes ; Mexico ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; Turkeys/classification/*genetics ; }, abstract = {BACKGROUND: The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mitochondrial D-loop, we investigated the genetic diversity and structure, genealogical relationships, divergence time and demographic history of M. gallopavo populations including domesticated individuals.<br><br>RESULTS: Analyses of 612 wild and domesticated turkey mitochondrial D-loop sequences, including 187 that were collected for this study and 425 from databases, revealed 64 haplotypes with few mutations, some of which are shared between domesticated and wild turkeys. We found a high level of haplotype and nucleotide diversity, which suggests that the total population of this species is large and stable with an old evolutionary history. The results of genetic differentiation, haplotype network, and genealogical relationships analyses revealed three main genetic groups within the species: mexicana as a population relict (C1), merriami (C2), and mexicana/intermedia/silvestris/osceola (C3). Haplotypes detected in domesticated turkeys belong to group C3. Estimates of divergence times agree with range expansion and diversification events of the relict population of M. gallopavo in northwestern Mexico during the Pliocene-Pleistocene and Pleistocene-Holocene boundaries. Demographic reconstruction showed that an expansion of the population occurred 110,000 to 130,000 years ago (Kya), followed by a stable period 100 Kya and finally a decline ~ 10 Kya (Pleistocene-Holocene boundary). In Mexico, the Trans-Mexican Volcanic Belt may be responsible for the range expansion of the C3 group. Two haplotypes with different divergence times, MGMDgoB/MICH1 and MICH2, are dominant in domesticated and commercial turkeys.<br><br>CONCLUSIONS: During the Pleistocene, a large and stable population of M. gallopavo covered a wide geographic distribution from the north to the center of America (USA and Mexico). The mexicana, merriami, and mexicana/intermedia/silvestris/osceola genetic groups originated after divergence and range expansion from northwestern Mexico during the Pliocene-Pleistocene and Pleistocene-Holocene boundaries. Old and new maternal lines of the mexicana/intermedia/silvestris/osceola genetic group were distributed within the Trans-Mexican Volcanic Belt where individuals were captured for domestication. Two haplotypes are the main founder maternal lines of domesticated turkeys.}, }
@article {pmid29664320, year = {2018}, author = {Nakano, M}, title = {16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products.}, journal = {Journal of food protection}, volume = {81}, number = {5}, pages = {848-859}, doi = {10.4315/0362-028X.JFP-17-346}, pmid = {29664320}, issn = {1944-9097}, abstract = {High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.}, }
@article {pmid29654216, year = {2018}, author = {Reichold, M and Klootwijk, ED and Reinders, J and Otto, EA and Milani, M and Broeker, C and Laing, C and Wiesner, J and Devi, S and Zhou, W and Schmitt, R and Tegtmeier, I and Sterner, C and Doellerer, H and Renner, K and Oefner, PJ and Dettmer, K and Simbuerger, JM and Witzgall, R and Stanescu, HC and Dumitriu, S and Iancu, D and Patel, V and Mozere, M and Tekman, M and Jaureguiberry, G and Issler, N and Kesselheim, A and Walsh, SB and Gale, DP and Howie, AJ and Martins, JR and Hall, AM and Kasgharian, M and O'Brien, K and Ferreira, CR and Atwal, PS and Jain, M and Hammers, A and Charles-Edwards, G and Choe, CU and Isbrandt, D and Cebrian-Serrano, A and Davies, B and Sandford, RN and Pugh, C and Konecki, DS and Povey, S and Bockenhauer, D and Lichter-Konecki, U and Gahl, WA and Unwin, RJ and Warth, R and Kleta, R}, title = {Glycine Amidinotransferase (GATM), Renal Fanconi Syndrome, and Kidney Failure.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {29}, number = {7}, pages = {1849-1858}, doi = {10.1681/ASN.2017111179}, pmid = {29654216}, issn = {1533-3450}, abstract = {Background For many patients with kidney failure, the cause and underlying defect remain unknown. Here, we describe a novel mechanism of a genetic order characterized by renal Fanconi syndrome and kidney failure.Methods We clinically and genetically characterized members of five families with autosomal dominant renal Fanconi syndrome and kidney failure. We performed genome-wide linkage analysis, sequencing, and expression studies in kidney biopsy specimens and renal cells along with knockout mouse studies and evaluations of mitochondrial morphology and function. Structural studies examined the effects of recognized mutations.Results The renal disease in these patients resulted from monoallelic mutations in the gene encoding glycine amidinotransferase (GATM), a renal proximal tubular enzyme in the creatine biosynthetic pathway that is otherwise associated with a recessive disorder of creatine deficiency. In silico analysis showed that the particular GATM mutations, identified in 28 members of the five families, create an additional interaction interface within the GATM protein and likely cause the linear aggregation of GATM observed in patient biopsy specimens and cultured proximal tubule cells. GATM aggregates-containing mitochondria were elongated and associated with increased ROS production, activation of the NLRP3 inflammasome, enhanced expression of the profibrotic cytokine IL-18, and increased cell death.Conclusions In this novel genetic disorder, fully penetrant heterozygous missense mutations in GATM trigger intramitochondrial fibrillary deposition of GATM and lead to elongated and abnormal mitochondria. We speculate that this renal proximal tubular mitochondrial pathology initiates a response from the inflammasome, with subsequent development of kidney fibrosis.}, }
@article {pmid29653091, year = {2018}, author = {Islam, W and Lin, W and Qasim, M and Islam, SU and Ali, H and Adnan, M and Arif, M and Du, Z and Wu, Z}, title = {A nation-wide genetic survey revealed a complex population structure of Bemisia tabaci in Pakistan.}, journal = {Acta tropica}, volume = {183}, number = {}, pages = {119-125}, doi = {10.1016/j.actatropica.2018.04.015}, pmid = {29653091}, issn = {1873-6254}, mesh = {Agriculture ; Animals ; Base Sequence ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genetic Variation ; Hemiptera/*genetics ; Insect Proteins/genetics ; Mitochondria/genetics ; *Molecular Epidemiology ; Pakistan ; *Phylogeny ; }, abstract = {The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex distributed worldwide. In Pakistan, B. tabaci poses a serious threat to agriculture production. To understand its diversity in Pakistan, a large-scale sampling was conducted from various locations of all four provinces of the country and Mitochondrial cytochrome oxidase I (mtCOI) gene sequencing was used to determine the whiteflies genetically. The study revealed the presence of five different cryptic species in Pakistan namely Asia II-1, Asia II-5, Asia II-7, Asia II-8 and MEAM-1, respectively. Among them, Asia II-1, which was previously reported from a few areas in the country, had been found now to be prevalent all over the country covering 88.7% of all the sequenced samples. Based on the mtCOI sequences and genetic distance analyses, the diversity of Asia II-1 was much greater than all other cryptic species, which exist only in small patches.}, }
@article {pmid29636759, year = {2018}, author = {Shibata, S and Arimura, SI and Ishikawa, T and Awai, K}, title = {Alterations of Membrane Lipid Content Correlated With Chloroplast and Mitochondria Development in Euglena gracilis.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {370}, doi = {10.3389/fpls.2018.00370}, pmid = {29636759}, issn = {1664-462X}, abstract = {Euglenoids are unique protists that can grow photoautotrophically, photomixotrophically, and heterotrophically. Here we grew Euglena gracilis under these different growth conditions and determined cellular contents of seven membrane lipids and one storage lipid (triacylglycerol), which account for more than 94 mol% of total membrane lipids. We also describe the relationship among chloroplast and mitochondria developments with lipid contents, protein contents, and oxygen evolution/consumption rates. In photoautotrophic growth conditions, E. gracilis cells accumulated chlorophyll, photosynthetic proteins, and glycolipids typical to thylakoid membranes. The same occurred for the cells grown under photomixotrophic conditions with higher respiration rates. In heterotrophic conditions, E. gracilis cells had higher respiration rates compared to cells grown in other conditions with the accumulation of pyruvate: NADP+ oxidoreductase, a mitochondrial protein and phospholipid common in mitochondria. Cells were also observed using a confocal laser scanning microscope and found to show more chlorophyll autofluorescence when grown photoautotrophically and photomixotrophycally, and fluorescence of MitoTracker when grown photomixotrophically and heterotrophically. These results suggest that under illumination, E. gracilis develops functional thylakoid membranes with membrane lipids and proteins for photosynthesis. In the medium with glucose, the cells develop mitochondria with phospholipids and proteins for respiration. Possible application based on lipid analysis for the enhancement of wax ester or alkene synthesis is discussed.}, }
@article {pmid29623424, year = {2018}, author = {Peña-Diaz, P and Lukeš, J}, title = {Fe-S cluster assembly in the supergroup Excavata.}, journal = {Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry}, volume = {23}, number = {4}, pages = {521-541}, doi = {10.1007/s00775-018-1556-6}, pmid = {29623424}, issn = {1432-1327}, abstract = {The majority of established model organisms belong to the supergroup Opisthokonta, which includes yeasts and animals. While enlightening, this focus has neglected protists, organisms that represent the bulk of eukaryotic diversity and are often regarded as primitive eukaryotes. One of these is the &quot;supergroup&quot; Excavata, which comprises unicellular flagellates of diverse lifestyles and contains species of medical importance, such as Trichomonas, Giardia, Naegleria, Trypanosoma and Leishmania. Excavata exhibits a continuum in mitochondrial forms, ranging from classical aerobic, cristae-bearing mitochondria to mitochondria-related organelles, such as hydrogenosomes and mitosomes, to the extreme case of a complete absence of the organelle. All forms of mitochondria house a machinery for the assembly of Fe-S clusters, ancient cofactors required in various biochemical activities needed to sustain every extant cell. In this review, we survey what is known about the Fe-S cluster assembly in the supergroup Excavata. We aim to bring attention to the diversity found in this group, reflected in gene losses and gains that have shaped the Fe-S cluster biogenesis pathways.}, }
@article {pmid29621569, year = {2018}, author = {Seligmann, H}, title = {Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.}, journal = {Bio Systems}, volume = {167}, number = {}, pages = {33-46}, doi = {10.1016/j.biosystems.2018.03.002}, pmid = {29621569}, issn = {1872-8324}, mesh = {Amino Acid Sequence ; Amino Acids/*genetics ; Animals ; Anticodon/genetics ; Cell Nucleus/*genetics ; Codon, Terminator/*genetics ; Data Interpretation, Statistical ; Evolution, Molecular ; Genetic Code/*genetics ; Humans ; Mitochondria/*genetics ; }, abstract = {Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Hence short-term protein evolution models reconstruct long-term genetic code evolution. Mitochondria reassign stops to amino acids otherwise inserted at stops by codon-anticodon mismatches (near-cognate tRNAs). Hence dual function (translation termination and translation by codon-anticodon mismatch) precedes mitochondrial reassignments of stops to amino acids. Stop ambiguity increases coded information, compensates endocellular mitogenome reduction. Mitochondrial codon reassignments might prevent viral infections.}, }
@article {pmid29618295, year = {2018}, author = {Derbikova, KS and Levitsky, SA and Chicherin, IV and Vinogradova, EN and Kamenski, PA}, title = {Activation of Yeast Mitochondrial Translation: Who Is in Charge?.}, journal = {Biochemistry. Biokhimiia}, volume = {83}, number = {2}, pages = {87-97}, doi = {10.1134/S0006297918020013}, pmid = {29618295}, issn = {1608-3040}, mesh = {Cytochromes b/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Transcriptional Activation ; }, abstract = {Mitochondrial genome has undergone significant reduction in a course of evolution; however, it still contains a set of protein-encoding genes and requires translational machinery for their expression. Mitochondrial translation is of the prokaryotic type with several remarkable differences. This review is dedicated to one of the most puzzling features of mitochondrial protein synthesis, namely, the system of translational activators, i.e., proteins that specifically regulate translation of individual mitochondrial mRNAs and couple protein biosynthesis with the assembly of mitochondrial respiratory chain complexes. The review does not claim to be a comprehensive analysis of all published data; it is rather focused on the idea of the &quot;core component&quot; of the translational activator system.}, }
@article {pmid29616678, year = {2018}, author = {Nie, WH and Wang, JH and Su, WT and Hu, Y and He, SW and Jiang, XL and He, K}, title = {Species identification of crested gibbons (Nomascus) in captivity in China using karyotyping- and PCR-based approaches.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {356-363}, doi = {10.24272/j.issn.2095-8137.2018.036}, pmid = {29616678}, issn = {2095-8137}, mesh = {Animals ; Animals, Zoo ; Cell Nucleus/genetics ; China ; Endangered Species ; Genes/genetics ; Hylobates/classification/*genetics ; In Situ Hybridization, Fluorescence ; Karyotype ; Karyotyping ; Mitochondria/genetics ; Polymerase Chain Reaction ; }, abstract = {Gibbons and siamangs (Hylobatidae) are well-known for their rapid chromosomal evolution, which has resulted in high speciation rate within the family. On the other hand, distinct karyotypes do not prevent speciation, allowing interbreeding between individuals in captivity, and the unwanted hybrids are ethically problematic as all gibbon species are endangered or critically endangered. Thus, accurate species identification is crucial for captive breeding, particularly in China where studbooks are unavailable. Identification based on external morphology is difficult, especially for hybrids, because species are usually similar in appearance. In this study, we employed G-banding karyotyping and fluorescence in situ hybridization (FISH) as well as a PCR-based approach to examine karyotypic characteristics and identify crested gibbons of the genus Nomascus from zoos and nature reserves in China. We characterized and identified five karyotypes from 21 individuals of Nomascus. Using karyotypes and mitochondrial and nuclear genes, we identified three purebred species and three hybrids, including one F2 hybrid between N. gabriellae and N. siki. Our results also supported that N. leucogenys and N. siki shared the same inversion on chromosome 7, which resolves arguments from previous studies. Our results demonstrated that both karyotyping and DNA-based approaches were suitable for identifying purebred species, though neither was ideal for hybrid identification. The advantages and disadvantages of both approaches are discussed. Our results further highlight the importance of animal ethics and welfare, which are critical for endangered species in captivity.}, }
@article {pmid29614345, year = {2018}, author = {Fan, Z and Zhou, A and Osada, N and Yu, J and Jiang, J and Li, P and Du, L and Niu, L and Deng, J and Xu, H and Xing, J and Yue, B and Li, J}, title = {Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {127}, number = {}, pages = {376-386}, doi = {10.1016/j.ympev.2018.03.038}, pmid = {29614345}, issn = {1095-9513}, abstract = {The evolutionary history of the stump-tailed macaque (Macaca arctoides) and its genetic relationship to other macaques is a subject of continuing controversy. Here, we have reported the first genome sequences of two stump-tailed macaques and one Assamese macaque (M. assamensis). Additionally, we have investigated the genetic diversity between macaque species and analyzed ancient hybridization events. Genome-wide analyses demonstrated that the stump-tailed macaque is more closely related to sinica species than to fascicularis/mulatta species. This topology contradicts the mitochondrial sequence-based phylogeny that places the stump-tailed macaque into the fascicularis/mulatta group. However, our results further show that stump-tailed macaques have genetic backgrounds distinct from sinica species, and present evidence of gene flows with rhesus macaques. We suggest that an ancient introgression occurred after stump-tailed macaques diverged from sinica species. The distinct gene flow between proto-arctoides and proto-mulatta resulted in the transfer of rhesus macaque-type mitochondria into proto-arctoides. The rhesus macaque-type mitochondria remained in populations because of genetic drift during the bottleneck. The PSMC results and morphological and geographic evidence are consistent with the mitochondria capture pattern in the stump-tailed macaque. The molecular clock estimates suggest that the mitochondrial transference into stump-tailed macaques occurred 0.4-1.4 million years ago. Furthermore, we detected extensive admixtures between different macaque species, indicating that gene flow has played an important role in the evolutionary history of the genus Macaca.}, }
@article {pmid29587633, year = {2018}, author = {Chase, EE and Robicheau, BM and Veinot, S and Breton, S and Stewart, DT}, title = {The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {221}, doi = {10.1186/s12864-018-4583-3}, pmid = {29587633}, issn = {1471-2164}, support = {217175//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Animals ; Computer Simulation ; DNA, Mitochondrial/genetics ; Disorders of Sex Development/*genetics ; Female ; Fresh Water ; *Genome, Mitochondrial ; Male ; Mitochondrial Proteins/genetics ; *Open Reading Frames ; Phylogeny ; Sex Factors ; Unionidae/classification/*genetics ; }, abstract = {BACKGROUND: Doubly uniparental inheritance (DUI) of mitochondrial DNA in bivalves is a fascinating exception to strictly maternal inheritance as practiced by all other animals. Recent work on DUI suggests that there may be unique regions of the mitochondrial genomes that play a role in sex determination and/or sexual development in freshwater mussels (order Unionoida). In this study, one complete mitochondrial genome of the hermaphroditic swan mussel, Anodonta cygnea, is sequenced and compared to the complete mitochondrial genome of the gonochoric duck mussel, Anodonta anatina. An in silico assessment of novel proteins found within freshwater bivalve species (known as F-, H-, and M-open reading frames or ORFs) is conducted, with special attention to putative transmembrane domains (TMs), signal peptides (SPs), signal cleavage sites (SCS), subcellular localization, and potential control regions. Characteristics of TMs are also examined across freshwater mussel lineages.<br><br>RESULTS: In silico analyses suggests the presence of SPs and SCSs and provides some insight into possible function(s) of these novel ORFs. The assessed confidence in these structures and functions was highly variable, possibly due to the novelty of these proteins. The number and topology of putative TMs appear to be maintained among both F- and H-ORFs, however, this is not the case for M-ORFs. There does not appear to be a typical control region in H-type mitochondrial DNA, especially given the loss of tandem repeats in unassigned regions when compared to F-type mtDNA.<br><br>CONCLUSION: In silico analyses provides a useful tool to discover patterns in DUI and to navigate further in situ analyses related to DUI in freshwater mussels. In situ analysis will be necessary to further explore the intracellular localizations and possible role of these open reading frames in the process of sex determination in freshwater mussel.}, }
@article {pmid29563878, year = {2018}, author = {Zeth, K and Zachariae, U}, title = {Ten Years of High Resolution Structural Research on the Voltage Dependent Anion Channel (VDAC)-Recent Developments and Future Directions.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {108}, doi = {10.3389/fphys.2018.00108}, pmid = {29563878}, issn = {1664-042X}, abstract = {Mitochondria are evolutionarily related to Gram-negative bacteria and both comprise two membrane systems with strongly differing protein composition. The major protein in the outer membrane of mitochondria is the voltage-dependent anion channel (VDAC), which mediates signal transmission across the outer membrane but also the exchange of metabolites, most importantly ADP and ATP. More than 30 years after its discovery three identical high-resolution structures were determined in 2008. These structures show a 19-stranded anti-parallel beta-barrel with an N-terminal helix located inside. An odd number of beta-strands is also shared by Tom40, another member of the VDAC superfamily. This indicates that this superfamily is evolutionarily relatively young and that it has emerged in the context of mitochondrial evolution. New structural information obtained during the last decade on Tom40 can be used to cross-validate the structure of VDAC and vice versa. Interpretation of biochemical and biophysical studies on both protein channels now rests on a solid basis of structural data. Over the past 10 years, complementary structural and functional information on proteins of the VDAC superfamily has been collected from in-organello, in-vitro, and in silico studies. Most of these findings have confirmed the validity of the original structures. This short article briefly reviews the most important advances on the structure and function of VDAC superfamily members collected during the last decade and summarizes how they enhanced our understanding of the channel.}, }
@article {pmid29555947, year = {2018}, author = {Islam, T and Ghosh, A}, title = {Genome-wide dissection and expression profiling of unique glyoxalase III genes in soybean reveal the differential pattern of transcriptional regulation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4848}, doi = {10.1038/s41598-018-23124-9}, pmid = {29555947}, issn = {2045-2322}, abstract = {Reactive carbonyl species, such as methylglyoxal and glyoxal are very toxic in nature and can inactivate various cellular macromolecules such as DNA, RNA, and protein by forming advanced glycation end products. Conventional glyoxalase pathway with two enzymes- glyoxalase I and glyoxalase II, detoxify MG into D-lactate with the help of reduced glutathione. However, DJ-1/PfpI domain(s) containing DJ-1/ Hsp31 proteins do the same in a single step, and thus termed as &quot;glyoxalase III&quot;. A comprehensive genome-wide analysis of soybean identified eleven putative glyoxalase III proteins with DJ-1/PfpI domain encoded by seven genes. Most of these proteins are predicted to be mitochondria and chloroplast localized. In spite of similar function, a differential evolution pattern was observed between Hsp31 and DJ-1 proteins. Expression of GmDJ-1A, GmDJ-1B, and GmDJ-1D2 transcripts was found to be constitutive in different tissues and developmental stages. Transcript profiling revealed the strong substrate-specific upregulation of GmDJ-1 genes in response to exogenous methylglyoxal exposure. Out of seven genes, GmDJ-1D1 and GmDJ-1D2 showed maximum upregulation against salinity, dehydration, and oxidative stresses. Moreover, GmDJ-1D2 showed functional glyoxalase III enzyme activity by utilizing MG as a substrate. Overall, this study identifies some novel tissue-specific and abiotic stress-responsive GmDJ-1 genes that could be investigated further.}, }
@article {pmid29554738, year = {2018}, author = {Braz-Mota, S and Campos, DF and MacCormack, TJ and Duarte, RM and Val, AL and Almeida-Val, VMF}, title = {Mechanisms of toxic action of copper and copper nanoparticles in two Amazon fish species: Dwarf cichlid (Apistogramma agassizii) and cardinal tetra (Paracheirodon axelrodi).}, journal = {The Science of the total environment}, volume = {630}, number = {}, pages = {1168-1180}, doi = {10.1016/j.scitotenv.2018.02.216}, pmid = {29554738}, issn = {1879-1026}, mesh = {Animals ; Characidae/*physiology ; Cichlids/*physiology ; Copper/*toxicity ; Metal Nanoparticles/*toxicity ; Mitochondria/drug effects ; Stress, Physiological/drug effects ; Toxicity Tests ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Copper oxide nanoparticles (nCuO) are widely used in boat antifouling paints and are released into the environment, potentially inducing toxicity to aquatic organisms. The present study aimed to understand the effects of nCuO and dissolved copper (Cu) on two ornamental Amazon fish species: dwarf cichlid (Apistogramma agassizii) and cardinal tetra (Paracheirodon axelrodi). Fish were exposed to 50% of the LC50 for nCuO (dwarf cichlid 58.31μgL-1 and cardinal tetra 69.6μgL-1) and Cu (dwarf cichlid 20μgL-1 and cardinal tetra 22.9μgL-1) for 24, 48, 72 and 96h. Following exposure, aerobic metabolic rate (ṀO2), gill osmoregulatory physiology and mitochondrial function, oxidative stress markers, and morphological damage were evaluated. Our results revealed species specificity in metabolic stress responses. An increase of ṀO2 was noted in cardinal tetra exposed to Cu, but not nCuO, whereas ṀO2 in dwarf cichlid showed little change with either treatment. In contrast, mitochondria from dwarf cichlid exhibited increased proton leak and a resulting decrease in respiratory control ratios in response to nCuO and Cu exposure. This uncoupling was directly related to an increase in reactive oxygen species (ROS) levels. Our findings reveal different metabolic responses between these two species in response to nCuO and Cu, which are probably caused by the differences between species natural histories, indicating that different mechanisms of toxic action of the contaminants are associated to differential osmoregulatory strategies among species.}, }
@article {pmid29551757, year = {2018}, author = {McLean, BS and Nyamsuren, B and Tchabovsky, A and Cook, JA}, title = {Impacts of late Quaternary environmental change on the long-tailed ground squirrel (Urocitellus undulatus) in Mongolia.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {364-372}, doi = {10.24272/j.issn.2095-8137.2018.042}, pmid = {29551757}, issn = {2095-8137}, mesh = {Animals ; Climate Change ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Environment ; Genotyping Techniques ; Mitochondria/genetics ; Mongolia ; Phylogeny ; Phylogeography ; Sciuridae/classification/*genetics ; }, abstract = {Impacts of Quaternary environmental changes on mammal faunas of central Asia remain poorly understood due to a lack of geographically comprehensive phylogeographic sampling for most species. To help address this knowledge gap, we conducted the most extensive molecular analysis to date of the long-tailed ground squirrel (Urocitellus undulatus Pallas 1778) in Mongolia, a country that comprises the southern core of this species' range. Drawing on material from recent collaborative field expeditions, we genotyped 128 individuals at 2 mitochondrial genes (cytochrome b and cytochrome oxidase I; 1 797 bp total). Phylogenetic inference supports the existence of two deeply divergent infraspecific lineages (corresponding to subspecies U. u. undulatus and U. u. eversmanni), a result in agreement with previous molecular investigations but discordant with patterns of range-wide craniometric and external phenotypic variation. In the widespread westerneversmanni lineage, we recovered geographically-associated clades from the: (a) Khangai, (b) Mongolian Altai, and (c) Govi Altai mountain ranges. Phylogeographic structure in U. u. eversmanni is consistent with an isolation-by-distance model; however, genetic distances are significantly lower than among subspecies, and intra-clade relationships are largely unresolved. The latter patterns, as well as the relatively higher nucleotide polymorphism of populations from the Great Lakes Depression of northwestern Mongolia, suggest a history of range shifts into these lowland areas in response to Pleistocene glaciation and environmental change, followed by upslope movements and mitochondrial lineage sorting with Holocene aridification. Our study illuminates possible historical mechanisms responsible for U. undulatus genetic structure and contributes to a framework for ongoing exploration of mammalian response to past and present climate change in central Asia.}, }
@article {pmid29547666, year = {2018}, author = {Oxusoff, L and Préa, P and Perez, Y}, title = {A complete logical approach to resolve the evolution and dynamics of mitochondrial genome in bilaterians.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194334}, doi = {10.1371/journal.pone.0194334}, pmid = {29547666}, issn = {1932-6203}, mesh = {Algorithms ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genomics/methods ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {Investigating how recombination might modify gene order during the evolution has become a routine part of mitochondrial genome analysis. A new method of genomic maps analysis based on formal logic is described. The purpose of this method is to 1) use mitochondrial gene order of current taxa as datasets 2) calculate rearrangements between all mitochondrial gene orders and 3) reconstruct phylogenetic relationships according to these calculated rearrangements within a tree under the assumption of maximum parsimony. Unlike existing methods mainly based on the probabilistic approach, the main strength of this new approach is that it calculates all the exact tree solutions with completeness and provides logical consequences as highly robust results. Moreover, this method infers all possible hypothetical ancestors and reconstructs character states for all internal nodes of the trees. We started by testing our method using the deuterostomes as a study case. Then, with sponges as an outgroup, we investigated the evolutionary history of mitochondrial genomes of 47 bilaterian phyla and emphasised the peculiar case of chaetognaths. This pilot work showed that the use of formal logic in a hypothetico-deductive background such as phylogeny (where experimental testing of hypotheses is impossible) is very promising to explore mitochondrial gene order in deuterostomes and should be applied to many other bilaterian clades.}, }
@article {pmid29543917, year = {2018}, author = {Visser, JH and Bennett, NC and Jansen van Vuuren, B}, title = {Spatial genetic diversity in the Cape mole-rat, Georychus capensis: Extreme isolation of populations in a subterranean environment.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194165}, doi = {10.1371/journal.pone.0194165}, pmid = {29543917}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Cytochromes b/genetics ; Ecosystem ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Mole Rats/*genetics ; Phylogeny ; Phylogeography ; South Africa ; }, abstract = {The subterranean niche harbours animals with extreme adaptations. These adaptations decrease the vagility of taxa and, along with other behavioural adaptations, often result in isolated populations characterized by small effective population sizes, high inbreeding, population bottlenecks, genetic drift and consequently, high spatial genetic structure. Although information is available for some species, estimates of genetic diversity and whether this variation is spatially structured, is lacking for the Cape mole-rat (Georychus capensis). By adopting a range-wide sampling regime and employing two variable mitochondrial markers (cytochrome b and control region), we report on the effects that life-history, population demography and geographic barriers had in shaping genetic variation and population genetic patterns in G. capensis. We also compare our results to information available for the sister taxon of the study species, Bathyergus suillus. Our results show that Georychus capensis exhibits low genetic diversity relative to the concomitantly distributed B. suillus, most likely due to differences in habitat specificity, habitat fragmentation and historical population declines. In addition, the isolated nature of G. capensis populations and low levels of population connectivity has led to small effective population sizes and genetic differentiation, possibly aided by genetic drift. Not surprisingly therefore, G. capensis exhibits pronounced spatial structure across its range in South Africa. Along with geographic distance and demography, other factors shaping the genetic structure of G. capensis include the historical and contemporary impacts of mountains, rivers, sea-level fluctuations and elevation. Given the isolation and differentiation among G. capensis populations, the monotypic genus Georychus may represent a species complex.}, }
@article {pmid29543844, year = {2018}, author = {Bekker, EI and Karabanov, DP and Galimov, YR and Haag, CR and Neretina, TV and Kotov, AA}, title = {Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194045}, doi = {10.1371/journal.pone.0194045}, pmid = {29543844}, issn = {1932-6203}, mesh = {Animals ; Cell Lineage/*genetics ; Cladocera/*genetics ; DNA, Mitochondrial/genetics ; Daphnia/*genetics ; Europe ; Far East ; Haplotypes/genetics ; Lakes ; Mitochondria/*genetics ; North America ; Phylogeny ; Phylogeography/methods ; Siberia ; }, abstract = {Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.}, }
@article {pmid29543809, year = {2018}, author = {Abdollahi, N and Albani, A and Anthony, E and Baud, A and Cardon, M and Clerc, R and Czernecki, D and Conte, R and David, L and Delaune, A and Djerroud, S and Fourgoux, P and Guiglielmoni, N and Laurentie, J and Lehmann, N and Lochard, C and Montagne, R and Myrodia, V and Opuu, V and Parey, E and Polit, L and Privé, S and Quignot, C and Ruiz-Cuevas, M and Sissoko, M and Sompairac, N and Vallerix, A and Verrecchia, V and Delarue, M and Guérois, R and Ponty, Y and Sacquin-Mora, S and Carbone, A and Froidevaux, C and Le Crom, S and Lespinet, O and Weigt, M and Abboud, S and Bernardes, J and Bouvier, G and Dequeker, C and Ferré, A and Fuchs, P and Lelandais, G and Poulain, P and Richard, H and Schweke, H and Laine, E and Lopes, A}, title = {Meet-U: Educating through research immersion.}, journal = {PLoS computational biology}, volume = {14}, number = {3}, pages = {e1005992}, doi = {10.1371/journal.pcbi.1005992}, pmid = {29543809}, issn = {1553-7358}, mesh = {Computational Biology/*education/*methods ; Humans ; Research/*education ; Research Design ; Students ; Universities ; }, abstract = {We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4-5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes &quot;coopetition,&quot; as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master's students in bioinformatics and modeling, with protein-protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.}, }
@article {pmid29540429, year = {2018}, author = {Czarnoleski, M and Labecka, AM and Dragosz-Kluska, D and Pis, T and Pawlik, K and Kapustka, F and Kilarski, WM and Kozłowski, J}, title = {Concerted evolution of body mass and cell size: similar patterns among species of birds (Galliformes) and mammals (Rodentia).}, journal = {Biology open}, volume = {7}, number = {4}, pages = {}, doi = {10.1242/bio.029603}, pmid = {29540429}, issn = {2046-6390}, abstract = {Cell size plays a role in body size evolution and environmental adaptations. Addressing these roles, we studied body mass and cell size in Galliformes birds and Rodentia mammals, and collected published data on their genome sizes. In birds, we measured erythrocyte nuclei and basal metabolic rates (BMRs). In birds and mammals, larger species consistently evolved larger cells for five cell types (erythrocytes, enterocytes, chondrocytes, skin epithelial cells, and kidney proximal tubule cells) and evolved smaller hepatocytes. We found no evidence that cell size differences originated through genome size changes. We conclude that the organism-wide coordination of cell size changes might be an evolutionarily conservative characteristic, and the convergent evolutionary body size and cell size changes in Galliformes and Rodentia suggest the adaptive significance of cell size. Recent theory predicts that species evolving larger cells waste less energy on tissue maintenance but have reduced capacities to deliver oxygen to mitochondria and metabolize resources. Indeed, birds with larger size of the abovementioned cell types and smaller hepatocytes have evolved lower mass-specific BMRs. We propose that the inconsistent pattern in hepatocytes derives from the efficient delivery system to hepatocytes, combined with their intense involvement in supracellular function and anabolic activity.}, }
@article {pmid29538419, year = {2018}, author = {Bocak, L and Motyka, M and Bocek, M and Bocakova, M}, title = {Incomplete sclerotization and phylogeny: The phylogenetic classification of Plastocerus (Coleoptera: Elateroidea).}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194026}, doi = {10.1371/journal.pone.0194026}, pmid = {29538419}, issn = {1932-6203}, mesh = {Animals ; Coleoptera/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; Luminescence ; Male ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The relationships of the monogeneric family Plastoceridae Crowson, 1972 (Coleoptera: Elateroidea) have remained contentious due to its modified morphology, incorrect information on incomplete metamorphosis of females and the absence of molecular data. We produced the sequences for P. angulosus (Germar, 1844) (the type-species of Plastocerus Schaum, 1852) and performed molecular phylogenetic analyses to estimate its position. The analyses of Elateroidea (186 spp.) and Elateridae (110 spp.) molecular datasets of two mitochondrial and two nuclear gene fragments repeatedly placed Plastocerus Schaum, 1852 in relationships with the elaterid genera Oxynopterus Hope, 1842 and Pectocera Hope, 1842. Alternative topologies were rejected by likelihood tests. Therefore, Plastoceridae Crowson, 1972 are down-ranked to the subfamily Plastocerinae in Elateridae Leach, 1815. We suggest that the morphology-based placement and high rank for some elateroid lineages were inferred from the presence of homoplasies which evolved due to incomplete sclerotization. Distantly related soft-bodied elateroids share freely movable and transverse coxae, a shortened prosternum, and a weakly sclerotized abdomen with free ventrites. Importantly, the apomorphic structures characteristic for their closest relatives, such as the prosternal process, mesoventral cavity, and intercoxal keel in the first abdominal ventrite are regularly absent. Consequently, morphology-based phylogenetic analyses suggest deeply rooted positions for lineages without expressed apomorphic character states. Molecular data represent an independent character system that is not affected by the convergent morphological evolution, and therefore molecular phylogenies can elucidate the relationships of incompletely sclerotized lineages.}, }
@article {pmid29533769, year = {2018}, author = {Marsit, S and Dion-Côté, AM and Barbash, DA}, title = {Did Mitochondria Kill the Frog?.}, journal = {Developmental cell}, volume = {44}, number = {5}, pages = {539-541}, doi = {10.1016/j.devcel.2018.02.020}, pmid = {29533769}, issn = {1878-1551}, mesh = {*Genome ; Genomics ; Hybridization, Genetic ; Mitochondria ; *Reproductive Isolation ; }, abstract = {Genomic divergence can cause reproductive isolation between species. The molecular mechanisms underlying reproductive isolation can thus reveal which genomic features evolve rapidly and become unstable or incompatible in hybrids. In a recent paper in Nature, Gibeaux et al. (2018) report paternal genome instability and metabolic imbalance in hybrids between frog species.}, }
@article {pmid29531011, year = {2018}, author = {Wolters, JF and Charron, G and Gaspary, A and Landry, CR and Fiumera, AC and Fiumera, HL}, title = {Mitochondrial Recombination Reveals Mito-Mito Epistasis in Yeast.}, journal = {Genetics}, volume = {209}, number = {1}, pages = {307-319}, doi = {10.1534/genetics.117.300660}, pmid = {29531011}, issn = {1943-2631}, support = {R01 GM101320/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Mitochondrial ; *Epistasis, Genetic ; Genotype ; Haplotypes ; Mitochondria/*genetics ; Quantitative Trait Loci ; *Recombination, Genetic ; Stress, Physiological ; Yeasts/*genetics ; }, abstract = {Genetic variation in mitochondrial DNA (mtDNA) provides adaptive potential although the underlying genetic architecture of fitness components within mtDNAs is not known. To dissect functional variation within mtDNAs, we first identified naturally occurring mtDNAs that conferred high or low fitness in Saccharomyces cerevisiae by comparing growth in strains containing identical nuclear genotypes but different mtDNAs. During respiratory growth under temperature and oxidative stress conditions, mitotype effects were largely independent of nuclear genotypes even in the presence of mito-nuclear interactions. Recombinant mtDNAs were generated to determine fitness components within high- and low-fitness mtDNAs. Based on phenotypic distributions of isogenic strains containing recombinant mtDNAs, we found that multiple loci contributed to mitotype fitness differences. These mitochondrial loci interacted in epistatic, nonadditive ways in certain environmental conditions. Mito-mito epistasis (i.e., nonadditive interactions between mitochondrial loci) influenced fitness in progeny from four different crosses, suggesting that mito-mito epistasis is a widespread phenomenon in yeast and other systems with recombining mtDNAs. Furthermore, we found that interruption of coadapted mito-mito interactions produced recombinant mtDNAs with lower fitness. Our results demonstrate that mito-mito epistasis results in functional variation through mitochondrial recombination in fungi, providing modes for adaptive evolution and the generation of mito-mito incompatibilities.}, }
@article {pmid29530548, year = {2018}, author = {Zhang, P and Liu, Y and Wang, M and Dong, M and Liu, Z and Jia, Z and Wang, W and Zhang, A and Wang, L and Song, L}, title = {Chinese mitten crab (Eriocheir sinensis) iron-sulphur cluster assembly protein 2 (EsIscA2) is differentially regulated after immune and oxidative stress challenges.}, journal = {Developmental and comparative immunology}, volume = {84}, number = {}, pages = {343-352}, doi = {10.1016/j.dci.2018.03.007}, pmid = {29530548}, issn = {1879-0089}, abstract = {Iron-sulphur clusters (ISCs), one of the oldest and most versatile cofactors of proteins, are involved in catalysis reactions, electron transport reactions, regulation processes as well as sensing of ambient conditions. Iron-sulphur cluster assembly protein (IscA) is a scaffold protein member of ISC formation system, which plays a significant role in the assembly and maturation process of ISC proteins. In the present study, the cDNA sequence of iron-sulphur cluster assembly protein 2 (designated as EsIscA2) was cloned from Eriocheir sinensis. The open reading frame (ORF) of EsIscA2 was of 507 bp, encoding a peptide of 168 amino acids with a typically conserved Fe-S domain. A tetrameric form was predicated by the SWISS-MODEL prediction algorithm, and three conserved cysteine residues (Cys-93, Cys-158, Cys-160) from each IscA monomer were predicted to form a 'cysteine pocket'. The deduced amino acid sequence of EsIscA2 shared over 50% similarity with that of other IscAs. EsIscA2 was clustered with IscA2 proteins from invertebrates and vertebrates, indicating that the protein was highly conservative in the evolution. rEsIscA2 exhibited a high iron binding affinity in the concentration ranging from 2 to 200 μM. EsIscA2 transcripts were detected in all the tested tissues including gonad, hemocytes, gill, muscle, heart, hepatopancreas and eyestalk, and EsIscA2 protein was detected in the mitochondria of hemocytes. The highest mRNA expression level of EsIscA2 was detected in muscle and hepatopancreas, which was about 34.66-fold (p < 0.05) and 27.07-fold (p < 0.05) of that in hemocytes, respectively. After Aeromonas hydrophila and lipopolysaccharide (LPS) stimulations, the mRNA expression of EsIscA2 in hemocytes was down-regulated and reached the lowest level at 24 h (0.31-fold, p < 0.05) and 48 h (0.29-fold, p < 0.05) compared to control group, respectively. And the expression of EsIscA2 mRNA in hepatopancreas was repressed from 6 h to 48 h post stimulation (p < 0.05). When the primary cultured crab hemocytes were incubated with different concentrations of H2O2 for 15 min, the expression level of EsIscA2 mRNA was significantly repressed to the 0.34-0.44-fold of that in the control group. After A. hydrophila stimulation, the mRNA expression of EsGrx2 was up-regulated at 3 h (3.22-fold compared to control group, p < 0.05) and reached the peak at 12 h (4.88-fold, p < 0.05). All these results suggested that EsIscA2 had iron-binding capabilities as observed in IscA proteins from other organisms, supporting the role of EsIscA2 as a mitochondrial iron donor for ISC synthesis in Chinese mitten crab. Its differential mRNA expression after immune and oxidative stress challenges suggested the adaptations of ISC synthesis rates to these stress conditions.}, }
@article {pmid29529094, year = {2018}, author = {Bourret, TB and Choudhury, RA and Mehl, HK and Blomquist, CL and McRoberts, N and Rizzo, DM}, title = {Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0192502}, doi = {10.1371/journal.pone.0192502}, pmid = {29529094}, issn = {1932-6203}, mesh = {Cell Nucleus/genetics ; Likelihood Functions ; Mitochondria/genetics ; Peronospora/*genetics ; *Phylogeny ; Phytophthora/*genetics ; Plant Diseases/parasitology ; }, abstract = {Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the &quot;subgeneric&quot; clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.}, }
@article {pmid29529025, year = {2018}, author = {Tas, D and Stickley, L and Miozzo, F and Koch, R and Loncle, N and Sabado, V and Gnägi, B and Nagoshi, E}, title = {Parallel roles of transcription factors dFOXO and FER2 in the development and maintenance of dopaminergic neurons.}, journal = {PLoS genetics}, volume = {14}, number = {3}, pages = {e1007271}, doi = {10.1371/journal.pgen.1007271}, pmid = {29529025}, issn = {1553-7404}, mesh = {Animals ; Autophagy ; Basic Helix-Loop-Helix Transcription Factors/genetics/*metabolism ; Cell Survival ; Dopaminergic Neurons/*metabolism/*pathology ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster ; Forkhead Transcription Factors/genetics/*metabolism ; Mitochondria/metabolism ; Mutation ; *Neuroprotection ; Parkinson Disease/metabolism/*pathology ; }, abstract = {Forkhead box (FOXO) proteins are evolutionarily conserved, stress-responsive transcription factors (TFs) that can promote or counteract cell death. Mutations in FOXO genes are implicated in numerous pathologies, including age-dependent neurodegenerative disorders, such as Parkinson's disease (PD). However, the complex regulation and downstream mechanisms of FOXOs present a challenge in understanding their roles in the pathogenesis of PD. Here, we investigate the involvement of FOXO in the death of dopaminergic (DA) neurons, the key pathological feature of PD, in Drosophila. We show that dFOXO null mutants exhibit a selective loss of DA neurons in the subgroup crucial for locomotion, the protocerebral anterior medial (PAM) cluster, during development as well as in adulthood. PAM neuron-targeted adult-restricted knockdown demonstrates that dFOXO in adult PAM neurons tissue-autonomously promotes neuronal survival during aging. We further show that dFOXO and the bHLH-TF 48-related-2 (FER2) act in parallel to protect PAM neurons from different forms of cellular stress. Remarkably, however, dFOXO and FER2 share common downstream processes leading to the regulation of autophagy and mitochondrial morphology. Thus, overexpression of one can rescue the loss of function of the other. These results indicate a role of dFOXO in neuroprotection and highlight the notion that multiple genetic and environmental factors interact to increase the risk of DA neuron degeneration and the development of PD.}, }
@article {pmid29523798, year = {2018}, author = {Fu, YB}, title = {Oat evolution revealed in the maternal lineages of 25 Avena species.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4252}, doi = {10.1038/s41598-018-22478-4}, pmid = {29523798}, issn = {2045-2322}, abstract = {Cultivated hexaploid oat has three different sets of nuclear genomes (A, C, D), but its evolutionary history remains elusive. A multiplexed shotgun sequencing procedure was explored to acquire maternal phylogenetic signals from chloroplast and mitochondria genomes of 25 Avena species. Phylogenetic analyses of the acquired organelle SNP data revealed a new maternal pathway towards hexaploids of oat genome evolution involving three diploid species (A. ventricosa, A. canariensis and A. longiglumis) and two tetraploid species (A. insularis and A. agadiriana). Cultivated hexaploid A. sativa acquired its maternal genome from an AC genome tetraploid close to A. insularis. Both AC genome A. insularis and AB genome A. agadiriana obtained a maternal genome from an ancient A, not C, genome diploid close to A. longiglumis. Divergence dating showed the major divergences of C genome species 19.9-21.2 million years ago (Mya), of the oldest A genome A. canariensis 13-15 Mya, and of the clade with hexaploids 8.5-9.5 Mya. These findings not only advance our knowledge on oat genome evolution, but also have implications for oat germplasm conservation and utilization in breeding.}, }
@article {pmid29521101, year = {2018}, author = {Wyżewski, Z and Gregorczyk, KP and Szczepanowska, J and Szulc-Dąbrowska, L}, title = {Functional role of Hsp60 as a positive regulator of human viral infection progression.}, journal = {Acta virologica}, volume = {62}, number = {1}, pages = {33-40}, doi = {10.4149/av_2018_104}, pmid = {29521101}, issn = {0001-723X}, mesh = {Chaperonin 60/genetics/*metabolism ; HIV Infections/*metabolism ; Hepatitis B/*metabolism ; Humans ; Influenza, Human/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; }, abstract = {Heat shock proteins (Hsps) are a family of proteins highly conserved in evolution. Members of the Hsp family are mainly responsible for proper protein folding, however they perform many other functions in living organisms. Hsp60 is a molecular chaperone that is present in mitochondria and cytosol of eukaryotic cells, as well as on their surface. It is also found in the extracellular space and in the peripheral blood. Apart from its role in assisting protein folding in cooperation with Hsp10, Hsp60 contributes to regulation of apoptosis, as well as participates in modulation of the immune system activity. Hsp60 may favor oncogenesis by promoting survival or growth of some tumor cell types. Hsp60 is a subject of medical research due to its role in pathogenesis of certain tumors and infectious diseases. In this review we discuss mechanisms by which Hsp60 promotes development and progression of infections caused by three human viruses: hepatitis B virus (HBV), human immunodeficiency virus (HIV) and influenza A virus.}, }
@article {pmid29515095, year = {2018}, author = {Suwannapoom, C and Wu, YJ and Chen, X and Adeola, AC and Chen, J and Wang, WZ}, title = {Complete mitochondrial genome of the Thai Red Junglefowl (Gallus gallus) and phylogenetic analysis.}, journal = {Zoological research}, volume = {39}, number = {2}, pages = {127-129}, doi = {10.24272/j.issn.2095-8137.2017.028}, pmid = {29515095}, issn = {2095-8137}, mesh = {Animals ; Chickens/*genetics ; DNA, Mitochondrial/genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Thailand ; }, abstract = {In this study, we sequenced the complete mitochondrial genome (mitogenome) of the Thai Red Junglefowl (RJF; Gallus gallus) using the next-generation sequencing (NGS) platform of the Ion Torrent PGM. Samples were taken from Mae Wang District, Chiang Mai Province, northern Thailand. Our data showed the complete mitogenome to be 16 785 bp in length, composed by 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The genome nucleotide composition was 30.3% A, 23.7% T, 32.5% C, and 13.5% G, resulting in a high percentage of A+T (50.4%). Phylogenetic analysis revealed that the mitogenome belonged to haplogroup X, whereas those of all domestic chickens belong to haplogroups A to G. This newly released mitogenome sequence will advance further evolutionary and population genetics study of the RJF and domestic chicken. The availability of the G. gallus mitogenome will also contribute to further conservation genetics research of a unique species, listed as 'data deficient' in Thailand.}, }
@article {pmid29511984, year = {2018}, author = {Zhao, YQ and Mu, DL and Wang, D and Han, YL and Hou, CC and Zhu, JQ}, title = {Analysis of the function of KIF3A and KIF3B in the spermatogenesis in Boleophthalmus pectinirostris.}, journal = {Fish physiology and biochemistry}, volume = {44}, number = {3}, pages = {769-788}, doi = {10.1007/s10695-017-0461-1}, pmid = {29511984}, issn = {1573-5168}, support = {No. 31272642//National Natural Science Foundation of China (CN)/ ; No. 2015C110005//Scientific and Technical Project of Ningbo/ ; No.2016A610081//Ningbo Natural Science Foundation/ ; }, mesh = {Animals ; *Fish Proteins/chemistry/genetics/metabolism ; Gills/metabolism ; Kidney/metabolism ; *Kinesin/chemistry/genetics/metabolism ; Liver/metabolism ; Male ; Microscopy, Electron, Transmission ; Muscles/metabolism ; Myocardium/metabolism ; *Perciformes ; Phylogeny ; RNA, Messenger/metabolism ; Sequence Analysis, DNA ; Spermatogenesis/genetics/*physiology ; Spermatozoa/metabolism/ultrastructure ; Spleen/metabolism ; Testis/metabolism ; }, abstract = {Spermatogenesis represents one of the most complicated morphological transformation procedures. During this process, the assembly and maintenance of the flagella and intracellular transport of membrane-bound organelles required KIF3A and KIF3B. Our main goal was to test KIF3A and KIF3B location during spermatogenesis of Boleophthalmus pectinirostris. We cloned complete cDNA of KIF3A/3B from the testis of B. pectinirostris by PCR and rapid amplification of cDNA ends (RACE). The predicted secondary and tertiary structures of B. pectinirostris KIF3A/3B contained three domains: (a) the head region, (b) the stalk region, and (c) the tail region. Real-time quantitative PCR (qPCR) results revealed that KIF3A and KIF3B mRNA were presented in all the tissues examined, with the highest expression seen in the testis. In situ hybridization (ISH) showed that KIF3A and KIF3B were distributed in the periphery of the nuclear in the spermatocyte and the early spermatid. In the late spermatid and mature sperm, the KIF3A and KIF3B mRNA were gradually gathered to one side where the flagella formed. Immunofluorescence (IF) showed that KIF3A, tubulin, and mitochondria were co-localized in different stages during spermiogenesis in B. pectinirostris. The temporal and spatial expression dynamics of KIF3A/3B indicate that KIF3A and KIF3B might be involved in flagellar assembly and maintenance at the mRNA and protein levels. Moreover, these proteins may transport the mitochondria resulting in flagellum formation in B. pectinirostris.}, }
@article {pmid29495437, year = {2018}, author = {Mansilla, N and Racca, S and Gras, DE and Gonzalez, DH and Welchen, E}, title = {The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants.}, journal = {International journal of molecular sciences}, volume = {19}, number = {3}, pages = {}, doi = {10.3390/ijms19030662}, pmid = {29495437}, issn = {1422-0067}, mesh = {Animals ; Catalytic Domain ; Electron Transport Complex IV/chemistry/genetics/*metabolism ; *Energy Metabolism ; Enzyme Activation ; Gene Expression Regulation, Plant ; Humans ; Mammals/genetics/metabolism ; Mitochondria/genetics/*metabolism ; Mutation ; Plant Development ; Plant Physiological Phenomena ; Plants/genetics/*metabolism ; Protein Subunits ; Yeasts/genetics/metabolism ; }, abstract = {Mitochondrial respiration is an energy producing process that involves the coordinated action of several protein complexes embedded in the inner membrane to finally produce ATP. Complex IV or Cytochrome c Oxidase (COX) is the last electron acceptor of the respiratory chain, involved in the reduction of O₂ to H₂O. COX is a multimeric complex formed by multiple structural subunits encoded in two different genomes, prosthetic groups (heme a and heme a₃), and metallic centers (CuA and CuB). Tens of accessory proteins are required for mitochondrial RNA processing, synthesis and delivery of prosthetic groups and metallic centers, and for the final assembly of subunits to build a functional complex. In this review, we perform a comparative analysis of COX composition and biogenesis factors in yeast, mammals and plants. We also describe possible external and internal factors controlling the expression of structural proteins and assembly factors at the transcriptional and post-translational levels, and the effect of deficiencies in different steps of COX biogenesis to infer the role of COX in different aspects of plant development. We conclude that COX assembly in plants has conserved and specific features, probably due to the incorporation of a different set of subunits during evolution.}, }
@article {pmid29487229, year = {2018}, author = {Weiss, AKH and Loeffler, JR and Liedl, KR and Gstach, H and Jansen-Dürr, P}, title = {The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria.}, journal = {Biochemical Society transactions}, volume = {46}, number = {2}, pages = {295-309}, doi = {10.1042/BST20170518}, pmid = {29487229}, issn = {1470-8752}, mesh = {Amino Acid Sequence ; Carboxy-Lyases/metabolism ; Humans ; Hydrolases/chemistry/*metabolism ; *Microbiota ; Mitochondria/*enzymology ; Sequence Homology, Amino Acid ; Tyrosine/metabolism ; }, abstract = {Prokaryotic and eukaryotic fumarylacetoacetate hydrolase (FAH) superfamily members, sharing conserved regions that form the so-called FAH-domain, catalyze a remarkable variety of reactions. These enzymes are essential in the metabolic pathways to degrade aromatic compounds in prokaryotes and eukaryotes. It appears that prokaryotic FAH superfamily members evolved mainly to allow microbes to generate energy and useful metabolites from complex carbon sources. We review recent findings, indicating that both prokaryotic and eukaryotic members of the FAH superfamily also display oxaloacetate decarboxylase (ODx) activity. The identification of human FAH domain-containing protein 1 as mitochondrial ODx regulating mitochondrial function supports the new concept that, during evolution, eukaryotic FAH superfamily members have acquired important regulatory functions beyond catabolism of complex carbon sources. Molecular studies on the evolution and function of FAH superfamily members are expected to provide new mechanistic insights in their physiological roles.}, }
@article {pmid29486692, year = {2017}, author = {Skulachev, MV and Skulachev, VP}, title = {Programmed Aging of Mammals: Proof of Concept and Prospects of Biochemical Approaches for Anti-aging Therapy.}, journal = {Biochemistry. Biokhimiia}, volume = {82}, number = {12}, pages = {1403-1422}, doi = {10.1134/S000629791712001X}, pmid = {29486692}, issn = {1608-3040}, mesh = {Aging/drug effects/*physiology ; Animals ; Antioxidants/pharmacology ; Humans ; Longevity/drug effects ; Mitochondria/metabolism ; Mole Rats ; Plastoquinone/analogs &amp; derivatives/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {(i) In 2015-2017 we compared possible reasons for longevity of two mammalian highly social species, i.e. naked mole rats and humans. We proposed that in both cases longevity is a result of neoteny, prolongation of youth by deceleration of late ontogeny (Skulachev, V. P. (2015) Abst. 11th Conf. on Mitochondrial Physiology (MiP2015), Lucni Bouda, Czech Republic, pp. 64-66; Skulachev, V. P., Holtze, S., Vyssokikh, M. Y., Bakeeva, L. E., Skulachev, M. V., Markov, A. V., Hildebrandt, T. B., and Sadovnichii, V. A. (2017) Physiol. Rev., 97, 699-720). Both naked mole rats and humans strongly decreased the pressure of natural selection, although in two different manners. Naked mole rats preferred an &quot;aristocratic&quot; pathway when reproduction (and, hence, involvement in evolution) is monopolized by the queen and her several husbands. Huge number of subordinates who have no right to take part in reproduction and hence in evolution serves the small queen's family. Humans used an alternative, &quot;democratic&quot; pathway, namely technical progress facilitating adaptation to the changing environmental conditions. This pathway is open to all humankind. (ii) As a result, aging as a mechanism increasing evolvability by means of facilitation of natural selection became unnecessary for naked mole rats and humans due to strong attenuation of this selection. This is apparently why aging became a counterproductive atavism for these two species and was strongly shifted to late ages. This shift is direct evidence of the hypothesis that aging is programmed, being the last step of late ontogeny. (iii) Further deceleration of aging for humans by means of neoteny is unrealistic since the development of neoteny probably takes million years. (iv) However, if biological aging is a program, an alternative and much simpler way to avoid it seems possible. We mean inhibition of an essential step of this program. (v) At present, the most probable scheme of the aging program assumes that it is a mechanism of slow poisoning of an organism by reactive oxygen species produced by mitochondria. If this is the case, a mitochondria-targeted antioxidant might be an inhibitor of the aging program. During the last 12 years, such an antioxidant, namely SkQ1, was synthesized and studied in detail in our group. It consists of plastoquinone and decyltriphenylphosphonium (a penetrating cation responsible for electrophoretic accumulation of SkQ1 in mitochondria). It was shown that long-term treatment with SkQ1 increased the lifespan of plants, fungi, invertebrates, fish, and mammals. Moreover, SkQ1 is effective in the therapy of various age-related diseases. It was also shown that a single SkQ1 injection could save life in certain models of sudden death of animals. (vi) A tentative scheme is proposed considering aging as a process of chronic phenoptosis, which eventually results in initiation of acute phenoptosis and death. This scheme also suggests that under certain conditions chronic phenoptosis can be neutralized by an anti-aging program that is activated by food restriction regarded by an organism as a signal of starvation. As for acute phenoptosis, it is apparently controlled by receptors responsible for measuring key parameters of homeostasis. The first experimental indications have been already obtained indicating that both chronic and acute phenoptosis are suppressed by SkQ1.}, }
@article {pmid29486209, year = {2018}, author = {Kenny, NJ and Noreña, C and Damborenea, C and Grande, C}, title = {Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources.}, journal = {Genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ygeno.2018.02.009}, pmid = {29486209}, issn = {1089-8646}, abstract = {For their apparent morphological simplicity, the Platyhelminthes or &quot;flatworms&quot; are a diverse clade found in a broad range of habitats. Their body plans have however made them difficult to robustly classify. Molecular evidence is only beginning to uncover the true evolutionary history of this clade. Here we present nine novel mitochondrial genomes from the still undersampled orders Polycladida and Rhabdocoela, assembled from short Illumina reads. In particular we present for the first time in the literature the mitochondrial sequence of a Rhabdocoel, Bothromesostoma personatum (Typhloplanidae, Mesostominae). The novel mitochondrial genomes examined generally contained the 36 genes expected in the Platyhelminthes, with all possessing 12 of the 13 protein-coding genes normally found in metazoan mitochondrial genomes (ATP8 being absent from all Platyhelminth mtDNA sequenced to date), along with two ribosomal RNA genes. The majority presented possess 22 transfer RNA genes, and a single tRNA gene was absent from two of the nine assembled genomes. By comparison of mitochondrial gene order and phylogenetic analysis of the protein coding and ribosomal RNA genes contained within these sequences with those of previously sequenced species we are able to gain a firm molecular phylogeny for the inter-relationships within this clade. Our phylogenetic reconstructions, using both nucleotide and amino acid sequences under several models and both Bayesian and Maximum Likelihood methods, strongly support the monophyly of Polycladida, and the monophyly of Acotylea and Cotylea within that clade. They also allow us to speculate on the early emergence of Macrostomida, the monophyly of a &quot;Turbellarian-like&quot; clade, the placement of Rhabditophora, and that of Platyhelminthes relative to the Lophotrochozoa (=Spiralia). The data presented here therefore represent a significant advance in our understanding of platyhelminth phylogeny, and will form the basis of a range of future research in the still-disputed classifications within this taxon.}, }
@article {pmid29483657, year = {2018}, author = {Curson, ARJ and Williams, BT and Pinchbeck, BJ and Sims, LP and Martínez, AB and Rivera, PPL and Kumaresan, D and Mercadé, E and Spurgin, LG and Carrión, O and Moxon, S and Cattolico, RA and Kuzhiumparambil, U and Guagliardo, P and Clode, PL and Raina, JB and Todd, JD}, title = {DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton.}, journal = {Nature microbiology}, volume = {3}, number = {4}, pages = {430-439}, doi = {10.1038/s41564-018-0119-5}, pmid = {29483657}, issn = {2058-5276}, abstract = {Dimethylsulfoniopropionate (DMSP) is a globally important organosulfur molecule and the major precursor for dimethyl sulfide. These compounds are important info-chemicals, key nutrients for marine microorganisms, and are involved in global sulfur cycling, atmospheric chemistry and cloud formation1-3. DMSP production was thought to be confined to eukaryotes, but heterotrophic bacteria can also produce DMSP through the pathway used by most phytoplankton 4 , and the DsyB enzyme catalysing the key step of this pathway in bacteria was recently identified 5 . However, eukaryotic phytoplankton probably produce most of Earth's DMSP, yet no DMSP biosynthesis genes have been identified in any such organisms. Here we identify functional dsyB homologues, termed DSYB, in many phytoplankton and corals. DSYB is a methylthiohydroxybutryate methyltransferase enzyme localized in the chloroplasts and mitochondria of the haptophyte Prymnesium parvum, and stable isotope tracking experiments support these organelles as sites of DMSP synthesis. DSYB transcription levels increased with DMSP concentrations in different phytoplankton and were indicative of intracellular DMSP. Identification of the eukaryotic DSYB sequences, along with bacterial dsyB, provides the first molecular tools to predict the relative contributions of eukaryotes and prokaryotes to global DMSP production. Furthermore, evolutionary analysis suggests that eukaryotic DSYB originated in bacteria and was passed to eukaryotes early in their evolution.}, }
@article {pmid29472284, year = {2018}, author = {Raina, JB and Eme, L and Pollock, FJ and Spang, A and Archibald, JM and Williams, TA}, title = {Symbiosis in the microbial world: from ecology to genome evolution.}, journal = {Biology open}, volume = {7}, number = {2}, pages = {}, doi = {10.1242/bio.032524}, pmid = {29472284}, issn = {2046-6390}, abstract = {The concept of symbiosis - defined in 1879 by de Bary as 'the living together of unlike organisms' - has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists' workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.}, }
@article {pmid29466431, year = {2018}, author = {Ravago-Gotanco, R and de la Cruz, TL and Pante, MJ and Borsa, P}, title = {Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0193220}, doi = {10.1371/journal.pone.0193220}, pmid = {29466431}, issn = {1932-6203}, mesh = {Animals ; Fishes/classification/*genetics ; *Genetic Loci ; *Genotype ; *Microsatellite Repeats ; Mitochondria/*genetics ; Oceans and Seas ; *Phylogeny ; }, abstract = {The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.}, }
@article {pmid29464567, year = {2018}, author = {Schlattner, U and Kay, L and Tokarska-Schlattner, M}, title = {Mitochondrial Proteolipid Complexes of Creatine Kinase.}, journal = {Sub-cellular biochemistry}, volume = {87}, number = {}, pages = {365-408}, doi = {10.1007/978-981-10-7757-9_13}, pmid = {29464567}, issn = {0306-0225}, mesh = {Animals ; *Creatine Kinase/chemistry/metabolism ; Cytosol/chemistry/metabolism ; Humans ; *Mitochondria/chemistry/metabolism ; *Mitochondrial Membranes/chemistry/metabolism ; *Mitochondrial Proteins/chemistry/metabolism ; *Phospholipids/chemistry/metabolism ; Reactive Oxygen Species/chemistry/metabolism ; Thermogenesis/physiology ; }, abstract = {Isoforms of creatine kinase (CK) generate and use phosphocreatine, a concentrated and highly diffusible cellular &quot;high energy&quot; intermediate, for the main purpose of energy buffering and transfer in order to maintain cellular energy homeostasis. The mitochondrial CK isoform (mtCK) localizes to the mitochondrial intermembrane and cristae space, where it assembles into peripherally membrane-bound, large cuboidal homooctamers. These are part of proteolipid complexes wherein mtCK directly interacts with cardiolipin and other anionic phospholipids, as well as with the VDAC channel in the outer membrane. This leads to a stabilization and cross-linking of inner and outer mitochondrial membrane, forming so-called contact sites. Also the adenine nucleotide translocator of the inner membrane can be recruited into these proteolipid complexes, probably mediated by cardiolipin. The complexes have functions mainly in energy transfer to the cytosol and stimulation of oxidative phosphorylation, but also in restraining formation of reactive oxygen species and apoptosis. In vitro evidence indicates a putative role of mtCK in mitochondrial phospholipid distribution, and most recently a role in thermogenesis has been proposed. This review summarizes the essential structural and functional data of these mtCK complexes and describes in more detail the more recent advances in phospholipid interaction, thermogenesis, cancer and evolution of mtCK.}, }
@article {pmid29463212, year = {2018}, author = {Wagner, JT and Singh, PP and Romney, AL and Riggs, CL and Minx, P and Woll, SC and Roush, J and Warren, WC and Brunet, A and Podrabsky, JE}, title = {The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {155}, doi = {10.1186/s12864-018-4539-7}, pmid = {29463212}, issn = {1471-2164}, support = {IOS-1354549//National Science Foundation/International ; CEHG Fellowship//Stanford University/International ; }, mesh = {Adaptation, Biological/*genetics ; Animals ; Base Composition ; Biological Evolution ; Chickens ; Embryo, Nonmammalian ; Embryonic Development/*genetics ; Gene Expression Regulation ; *Genome ; Genome Size ; Genomics/methods ; Killifishes/*embryology/genetics/*physiology ; Mitochondria/genetics/metabolism ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Stress, Physiological/*genetics ; Vertebrates ; Zebrafish ; }, abstract = {BACKGROUND: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system.<br><br>RESULTS: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection.<br><br>CONCLUSION: The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution.}, }
@article {pmid29460123, year = {2018}, author = {Larsen, PA and Hunnicutt, KE and Larsen, RJ and Yoder, AD and Saunders, AM}, title = {Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {26}, number = {1-2}, pages = {93-111}, doi = {10.1007/s10577-018-9573-4}, pmid = {29460123}, issn = {1573-6849}, support = {S10 OD018164/OD/NIH HHS/United States ; }, abstract = {Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the benefits that Alus provide, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders. In particular, neurological networks are potentially vulnerable to the epigenetic dysregulation of Alu elements operating across the suite of nuclear-encoded mitochondrial genes that are critical for both mitochondrial and CNS function. Here, we highlight the beneficial neurological aspects of Alu elements as well as their potential to cause disease by disrupting key cellular processes across the CNS. We identify at least 37 neurological and neurodegenerative disorders wherein deleterious Alu activity has been implicated as a contributing factor for the manifestation of disease, and for many of these disorders, this activity is operating on genes that are essential for proper mitochondrial function. We conclude that the epigenetic dysregulation of Alu elements can ultimately disrupt mitochondrial homeostasis within the CNS. This mechanism is a plausible source for the incipient neuronal stress that is consistently observed across a spectrum of sporadic neurological and neurodegenerative disorders.}, }
@article {pmid29455315, year = {2018}, author = {Caparroz, R and Rocha, AV and Cabanne, GS and Tubaro, P and Aleixo, A and Lemmon, EM and Lemmon, AR}, title = {Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes.}, journal = {Molecular biology reports}, volume = {45}, number = {3}, pages = {279-285}, doi = {10.1007/s11033-018-4160-5}, pmid = {29455315}, issn = {1573-4978}, support = {564036/2010-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 445025/2014-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 457444/2012-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 202796/2014-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; PIP 2012-2014 0862//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PICT 2014-2154//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, mesh = {Animals ; Base Sequence/genetics ; Gene Order ; Genes, Mitochondrial ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined. We also estimated how often duplication events occurred in Passeriformes and if the two CR copies demonstrate a pattern of concerted evolution in Sylvioidea. One tissue sample for each species was used to obtain the mitogenomes as a byproduct using next generation sequencing. The evolutionary history of mitogenome rearrangements was reconstructed mapping these characters onto a mitogenome Bayesian phylogenetic tree of Passeriformes. Finally, we performed a Bayesian analysis for both CRs from some Sylvioidea species in order to evaluate the evolutionary process involving these two copies. Both mitogenomes described comprise 2 rRNAs, 22 tRNAs, 13 protein-codon genes and the CR. However, S. olivascens has 16,768 bp showing the ancestral avian arrangement, while L. angustirostris has 16,973 bp and the remnant CR2 arrangement. Both species showed the expected gene order compared to their closest relatives. The ancestral state reconstruction suggesting at least six independent duplication events followed by partial deletions or loss of one copy in some lineages. Our results also provide evidence that both CRs in some Sylvioidea species seem to be maintained in an apparently functional state, perhaps by concerted evolution, and that this mechanism may be important for the evolution of the bird mitogenome.}, }
@article {pmid29449618, year = {2018}, author = {Shinde, P and Sarkar, C and Jalan, S}, title = {Codon based co-occurrence network motifs in human mitochondria.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3060}, doi = {10.1038/s41598-018-21454-2}, pmid = {29449618}, issn = {2045-2322}, abstract = {The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies. The diversity observed in the mtDNA was compared with mutations, co-occurring mutations, network motifs considering codon positions as causing agent. This comparison showed that long-range nucleotide co-occurrences have a large effect on genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analysis also showed that variable nucleotide positions of different human sub-populations implemented the independent mtDNA evolution to its geographical dispensation. Ergo, this study has provided both a network framework and a codon glance to investigate co-occurring genomic variations that are critical in underlying complex mitochondrial evolution.}, }
@article {pmid29447215, year = {2018}, author = {Keleher, MR and Zaidi, R and Shah, S and Oakley, ME and Pavlatos, C and El Idrissi, S and Xing, X and Li, D and Wang, T and Cheverud, JM}, title = {Maternal high-fat diet associated with altered gene expression, DNA methylation, and obesity risk in mouse offspring.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192606}, doi = {10.1371/journal.pone.0192606}, pmid = {29447215}, issn = {1932-6203}, support = {P30 CA91842/NH/NIH HHS/United States ; UL1TR000448/NH/NIH HHS/United States ; P30 DK020579/NH/NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; *DNA Methylation ; *Diet, High-Fat ; Female ; *Gene Expression ; Mice ; *Mothers ; Obesity/*epidemiology ; Risk Factors ; }, abstract = {We investigated maternal obesity in inbred SM/J mice by assigning females to a high-fat diet or a low-fat diet at weaning, mating them to low-fat-fed males, cross-fostering the offspring to low-fat-fed SM/J nurses at birth, and weaning the offspring onto a high-fat or low-fat diet. A maternal high-fat diet exacerbated obesity in the high-fat-fed daughters, causing them to weigh more, have more fat, and have higher serum levels of leptin as adults, accompanied by dozens of gene expression changes and thousands of DNA methylation changes in their livers and hearts. Maternal diet particularly affected genes involved in RNA processing, immune response, and mitochondria. Between one-quarter and one-third of differentially expressed genes contained a differentially methylated region associated with maternal diet. An offspring high-fat diet reduced overall variation in DNA methylation, increased body weight and organ weights, increased long bone lengths and weights, decreased insulin sensitivity, and changed the expression of 3,908 genes in the liver. Although the offspring were more affected by their own diet, their maternal diet had epigenetic effects lasting through adulthood, and in the daughters these effects were accompanied by phenotypic changes relevant to obesity and diabetes.}, }
@article {pmid29440651, year = {2018}, author = {Petit, D and Teppa, E and Cenci, U and Ball, S and Harduin-Lepers, A}, title = {Reconstruction of the sialylation pathway in the ancestor of eukaryotes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2946}, doi = {10.1038/s41598-018-20920-1}, pmid = {29440651}, issn = {2045-2322}, abstract = {The biosynthesis of sialylated molecules of crucial relevance for eukaryotic cell life is achieved by sialyltransferases (ST) of the CAZy family GT29. These enzymes are widespread in the Deuterostoma lineages and more rarely described in Protostoma, Viridiplantae and various protist lineages raising the question of their presence in the Last eukaryotes Common Ancestor (LECA). If so, it is expected that the main enzymes associated with sialic acids metabolism are also present in protists. We conducted phylogenomic and protein sequence analyses to gain insights into the origin and ancient evolution of ST and sialic acid pathway in eukaryotes, Bacteria and Archaea. Our study uncovered the unreported occurrence of bacterial GT29 ST and evidenced the existence of 2 ST groups in the LECA, likely originating from the endosymbiotic event that generated mitochondria. Furthermore, distribution of the major actors of the sialic acid pathway in the different eukaryotic phyla indicated that these were already present in the LECA, which could also access to this essential monosaccharide either endogenously or via a sialin/sialidase uptake mechanism involving vesicles. This pathway was lost in several basal eukaryotic lineages including Archaeplastida despite the presence of two different ST groups likely assigned to other functions.}, }
@article {pmid29438872, year = {2018}, author = {Nibert, ML and Vong, M and Fugate, KK and Debat, HJ}, title = {Evidence for contemporary plant mitoviruses.}, journal = {Virology}, volume = {518}, number = {}, pages = {14-24}, doi = {10.1016/j.virol.2018.02.005}, pmid = {29438872}, issn = {1096-0341}, mesh = {Crops, Agricultural/*virology ; Evolution, Molecular ; Gene Expression Regulation, Viral/physiology ; Phylogeny ; Plant Diseases/*virology ; Plant Viruses/*classification/physiology ; RNA Viruses/*classification ; RNA, Viral/genetics ; Viral Proteins/genetics/metabolism ; }, abstract = {Mitoviruses have small RNA(+) genomes, replicate in mitochondria, and have been shown to infect only fungi to date. For this report, sequences that appear to represent nearly complete plant mitovirus genomes were recovered from publicly available transcriptome data. Twenty of the refined sequences, 2684-2898 nt long and derived from 10 different species of land plants, appear to encompass the complete coding regions of contemporary plant mitoviruses, which furthermore constitute a monophyletic cluster within genus Mitovirus. Complete coding sequences of several of these viruses were recovered from multiple transcriptome (but not genome) studies of the same plant species and also from multiple plant tissues. Crop plants among implicated hosts include beet and hemp. Other new results suggest that such genuine plant mitoviruses were immediate ancestors to endogenized mitovirus elements now widespread in land plant genomes. Whether these mitoviruses are wholly cryptic with regard to plant health remains to be investigated.}, }
@article {pmid29435647, year = {2018}, author = {Karmi, O and Marjault, HB and Pesce, L and Carloni, P and Onuchic, JN and Jennings, PA and Mittler, R and Nechushtai, R}, title = {The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease.}, journal = {Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry}, volume = {23}, number = {4}, pages = {599-612}, doi = {10.1007/s00775-018-1538-8}, pmid = {29435647}, issn = {1432-1327}, support = {1613462//Division of Molecular and Cellular Biosciences/ ; 1427654//Division of Physics/ ; GM101467//National Institute of Health/ ; 2015831//NSF and US-Israel Binational Science Foundation (BSF)/ ; R01 GM101467/GM/NIGMS NIH HHS/United States ; 1614101//Division of Chemistry/ ; }, abstract = {NEET proteins comprise a new class of [2Fe-2S] cluster proteins. In human, three genes encode for NEET proteins: cisd1 encodes mitoNEET (mNT), cisd2 encodes the Nutrient-deprivation autophagy factor-1 (NAF-1) and cisd3 encodes MiNT (Miner2). These recently discovered proteins play key roles in many processes related to normal metabolism and disease. Indeed, NEET proteins are involved in iron, Fe-S, and reactive oxygen homeostasis in cells and play an important role in regulating apoptosis and autophagy. mNT and NAF-1 are homodimeric and reside on the outer mitochondrial membrane. NAF-1 also resides in the membranes of the ER associated mitochondrial membranes (MAM) and the ER. MiNT is a monomer with distinct asymmetry in the molecular surfaces surrounding the clusters. Unlike its paralogs mNT and NAF-1, it resides within the mitochondria. NAF-1 and mNT share similar backbone folds to the plant homodimeric NEET protein (At-NEET), while MiNT's backbone fold resembles a bacterial MiNT protein. Despite the variation of amino acid composition among these proteins, all NEET proteins retained their unique CDGSH domain harboring their unique 3Cys:1His [2Fe-2S] cluster coordination through evolution. The coordinating exposed His was shown to convey the lability to the NEET proteins' [2Fe-2S] clusters. In this minireview, we discuss the NEET fold and its structural elements. Special attention is given to the unique lability of the NEETs' [2Fe-2S] cluster and the implication of the latter to the NEET proteins' cellular and systemic function in health and disease.}, }
@article {pmid29433421, year = {2018}, author = {Li, Q and Dong, K and Xu, L and Jia, X and Wu, J and Sun, W and Zhang, X and Fu, S}, title = {The distribution of three candidate cold-resistant SNPs in six minorities in North China.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {134}, doi = {10.1186/s12864-018-4524-1}, pmid = {29433421}, issn = {1471-2164}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological/*genetics ; Asian Continental Ancestry Group/genetics ; Carnitine O-Palmitoyltransferase/genetics ; China ; *Cold Temperature ; Ethnic Groups/classification/*genetics ; Fatty Acid Desaturases/genetics ; Gene Frequency ; Genotype ; Humans ; Linkage Disequilibrium ; Phylogeny ; *Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Heilongjiang Province located in northeast China is a multi-ethnic region with people who have lived in cold conditions for several generations. Fatty acids are important to people with cold resistance. CPT1A encodes a protein that imports long-chain fatty acids into the mitochondria for fatty-acid oxidation. FADS is an essential enzyme for the synthesis of long-chain polyunsaturated fatty acids.<br><br>RESULTS: In the present study, we investigated the distributions of three cold resistance-related SNPs (rs80356779 G > A in CPT1A, rs7115739 T > G in FADS3 and rs174570 C > T in FADS2) from six populations that included 1093 individuals who have lived in Heilongjiang Province for at least three generations. The frequencies of rs174570 and rs7115739 were different in our six north minorities compared to the Chinese Dai in Xishuangbanna (CDX) in southern China. All the SNPs in Hezhen were significantly different from other five studied populations. In addition, the genetic distribution of rs174570 in Daur was significantly different from Manchu and Korea, and the frequency of rs7115739 in Ewenki was significantly different from the other populations. The results also showed that the frequencies of the three SNPs in the six minorities were different from those of Greenlandic Inuit and Siberian population.<br><br>CONCLUSIONS: Our results showed the distributions of the three cold resistance-related SNPs from six populations that included 1093 individuals in northern China. Distributions of the allele frequencies for the cold resistance-related SNPs in northern China were statistically different from those in southern China. These data help to establish the DNA genome database for the six populations and fully preserve existing minority genetic information.}, }
@article {pmid29432738, year = {2018}, author = {Qin, Q and Jin, J and He, F and Zheng, Y and Li, T and Zhang, Y and He, J}, title = {Humanin promotes mitochondrial biogenesis in pancreatic MIN6 β-cells.}, journal = {Biochemical and biophysical research communications}, volume = {497}, number = {1}, pages = {292-297}, doi = {10.1016/j.bbrc.2018.02.071}, pmid = {29432738}, issn = {1090-2104}, mesh = {Animals ; Cell Line ; Insulin-Secreting Cells/cytology/*drug effects/*physiology ; Intracellular Signaling Peptides and Proteins/*administration &amp; dosage/*metabolism ; Mice ; Mitochondria/*drug effects/*physiology/ultrastructure ; *Organelle Biogenesis ; Treatment Outcome ; }, abstract = {Mitochondrial dysfunction is associated with β-cell failure and insulin resistance in diabetes. Humanin is an endogenous cytoprotective peptide. In the current study, we aimed to define the effects of Humanin on mitochondrial biogenesis in pancreatic β-cells. Our findings demonstrated that Humanin treatment significantly increased the expression of PGC-1α and its downstream target genes NRF1 and TFAM in MIN6 β-cells. Notably, Humanin treatment significantly promoted mitochondrial biogenesis by increasing mitochondrial mass, elevating mtDNA/nDNA ratio, and stimulating the expression of cytochrome B, which were suppressed by the specific AMPK inhibitor compound C. Indeed, Humanin treatment caused the phosphorylation of AMPK, which was involved in the induction of PGC-1α, NRF1, and TFAM by Humanin. Importantly, our findings indicate that Humanin treatment led to a possible functional gain of the mitochondria by increasing ATP levels and respiratory rate. Our findings provided a new insight into the molecular mechanisms of action by which Humanin improves pancreatic β-cell function via enhanced mitochondrial mass and performance.}, }
@article {pmid29426933, year = {2018}, author = {Allu, PK and Boggula, Y and Karri, S and Marada, A and Krishnamoorthy, T and Sepuri, NBV}, title = {A conserved R type Methionine Sulfoxide Reductase reverses oxidized GrpEL1/Mge1 to regulate Hsp70 chaperone cycle.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2716}, doi = {10.1038/s41598-018-21083-9}, pmid = {29426933}, issn = {2045-2322}, abstract = {Cells across evolution employ reversible oxidative modification of methionine and cysteine amino acids within proteins to regulate responses to redox stress. Previously we have shown that mitochondrial localized methionine sulfoxide reductase (Mxr2) reversibly regulates oxidized yeast Mge1 (yMge1), a co-chaperone of Hsp70/Ssc1 to maintain protein homeostasis during oxidative stress. However, the specificity and the conservation of the reversible methionine oxidation mechanism in higher eukaryotes is debatable as human GrpEL1 (hGrpEL1) unlike its homolog yMge1 harbors two methionine residues and multiple cysteines besides the mammalian mitochondria hosting R and S types of Mxrs/Msrs. In this study, using yeast as a surrogate system, we show that hGRPEL1 and R type MSRs but not the S type MSRs complement the deletion of yeast MGE1 or MXR2 respectively. Our investigations show that R type Msrs interact selectively with oxidized hGrpEL1/yMge1 in an oxidative stress dependent manner, reduce the conserved hGrpEL1-Met146-SO and rescue the Hsp70 ATPase activity. In addition, a single point mutation in hGrpEL1-M146L rescues the slow growth phenotype of yeast MXR2 deletion under oxidative duress. Our study illustrates the evolutionarily conserved formation of specific Met-R-SO in hGrpEL1/yMge1 and the essential and canonical role of R type Msrs/Mxrs in mitochondrial redox mechanism.}, }
@article {pmid29424926, year = {2018}, author = {Sweetman, C and Soole, KL and Jenkins, CLD and Day, DA}, title = {Genomic structure and expression of alternative oxidase genes in legumes.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.13161}, pmid = {29424926}, issn = {1365-3040}, abstract = {Mitochondria isolated from chickpea (Cicer arietinum) possess substantial alternative oxidase (AOX) activity, even in non-stressed plants, and one or two AOX protein bands were detected immunologically, depending on the organ. Four different AOX isoforms were identified in the chickpea genome: CaAOX1 and CaAOX2A, B and D. CaAOX2A was the most highly expressed form and was strongly expressed in photosynthetic tissues, whereas CaAOX2D was found in all organs examined. These results are very similar to those of previous studies with soybean and siratro. Searches of available databases showed that this pattern of AOX genes and their expression was common to at least 16 different legume species. The evolution of the legume AOX gene family is discussed, as is the in vivo impact of an inherently high AOX capacity in legumes on growth and responses to environmental stresses.}, }
@article {pmid29417658, year = {2018}, author = {Pogoda, CS and Keepers, KG and Lendemer, JC and Kane, NC and Tripp, EA}, title = {Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses.}, journal = {Molecular ecology}, volume = {27}, number = {5}, pages = {1155-1169}, doi = {10.1111/mec.14519}, pmid = {29417658}, issn = {1365-294X}, abstract = {Symbioses among co-evolving taxa are often marked by genome reductions such as a loss of protein-coding genes in at least one of the partners as a means of reducing redundancy or intergenomic conflict. To explore this phenomenon in an iconic yet under-studied group of obligate symbiotic organisms, mitochondrial genomes of 22 newly sequenced and annotated species of lichenized fungi were compared to 167 mitochondrial genomes of nonlichenized fungi. Our results demonstrate the first broad-scale loss of atp9 from mitochondria of lichenized fungi. Despite key functions in mitochondrial energy production, we show that atp9 has been independently lost in three different lineages spanning 10 of the 22 studied species. A search for predicted, functional copies of atp9 among genomes of other symbionts involved in each lichen revealed the full-length, presumably functional copies of atp9 in either the photosynthetic algal partner or in other symbiotic fungi in all 10 instances. Together, these data yield evidence of an obligate symbiotic relationship in which core genomic processes have been streamlined, likely due to co-evolution.}, }
@article {pmid29410353, year = {2018}, author = {Rose, JP and Kleist, TJ and Löfstrand, SD and Drew, BT and Schönenberger, J and Sytsma, KJ}, title = {Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections.}, journal = {Molecular phylogenetics and evolution}, volume = {122}, number = {}, pages = {59-79}, doi = {10.1016/j.ympev.2018.01.014}, pmid = {29410353}, issn = {1095-9513}, mesh = {Animals ; *Biodiversity ; Chloroplasts/genetics ; Far East ; Fossils/history ; Genetic Speciation ; History, Ancient ; Magnoliopsida/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Phylogeography/history ; Ribosomes/genetics ; }, abstract = {Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.}, }
@article {pmid29408286, year = {2018}, author = {Yuan, ML and Zhang, QL and Zhang, L and Jia, CL and Li, XP and Yang, XZ and Feng, RQ}, title = {Mitochondrial phylogeny, divergence history and high-altitude adaptation of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) inhabiting the Tibetan Plateau.}, journal = {Molecular phylogenetics and evolution}, volume = {122}, number = {}, pages = {116-124}, doi = {10.1016/j.ympev.2018.01.016}, pmid = {29408286}, issn = {1095-9513}, mesh = {*Adaptation, Physiological/genetics ; *Altitude ; Animals ; Biodiversity ; DNA/chemistry/isolation &amp; purification/metabolism ; Grassland ; Mitochondria/*genetics ; Moths/*classification/genetics ; Open Reading Frames/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Tibet ; }, abstract = {Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most important pests in alpine meadows of the Tibetan Plateau (TP) and have well adapted to high-altitude environments. To further understand the evolutionary history and their adaptation to the TP, we newly determined seven complete TP Gynaephora mitogenomes. Compared to single genes, whole mitogenomes provided the best phylogenetic signals and obtained robust results, supporting the monophyly of the TP Gynaephora species and a phylogeny of Arctiinae + (Aganainae + Lymantriinae). Incongruent phylogenetic signals were found among single mitochondrial genes, none of which recovered the same phylogeny as the whole mitogenome. We identified six best-performing single genes using Shimodaira-Hasegawa tests and found that the combinations of rrnS and either cox1 or cox3 generated the same phylogeny as the whole mitogenome, indicating the phylogenetic potential of these three genes for future evolutionary studies of Gynaephora. The TP Gynaephora species were estimated to radiate on the TP during the Pliocene and Quaternary, supporting an association of the diversification and speciation of the TP Gynaephora species with the TP uplifts and associated climate changes during this time. Selection analyses revealed accelerated evolutionary rates of the mitochondrial protein-coding genes in the TP Gynaephora species, suggesting that they accumulated more nonsynonymous substitutions that may benefit their adaptation to high altitudes. Furthermore, signals of positive selection were detected in nad5 of two Gynaephora species with the highest altitude-distributions, indicating that this gene may contribute to Gynaephora's adaptation to divergent altitudes. This study adds to the understanding of the TP Gynaephora evolutionary relationships and suggests a link between mitogenome evolution and ecological adaptation to high-altitude environments in grassland caterpillars.}, }
@article {pmid29404746, year = {2018}, author = {Jaleta, TG and Rödelsperger, C and Abanda, B and Eisenbarth, A and Achukwi, MD and Renz, A and Streit, A}, title = {Full mitochondrial and nuclear genome comparison confirms that Onchocerca sp. &quot;Siisa&quot; is Onchocerca ochengi.}, journal = {Parasitology research}, volume = {117}, number = {4}, pages = {1069-1077}, doi = {10.1007/s00436-018-5783-0}, pmid = {29404746}, issn = {1432-1955}, support = {AOBJ:602317//Deutsche Forschungsgemeinschaft/ ; N/A//Max-Planck-Gesellschaft/ ; }, mesh = {Animals ; Cattle/parasitology ; Cattle Diseases/parasitology ; Genome, Mitochondrial/*genetics ; Genome, Protozoan/*genetics ; Humans ; Insect Vectors/parasitology ; Mitochondria/genetics ; Onchocerca/*classification/*genetics/isolation &amp; purification ; Onchocerciasis/parasitology ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Simuliidae/parasitology ; Skin/parasitology ; }, abstract = {Onchocerca ochengi is a nodule-forming filarial nematode parasite of cattle. It is the closest known relative of the human parasite Onchocerca volvulus, with which it shares the black fly vector Simulium damnosum. Onchocerca sp. &quot;Siisa&quot; was described in black flies and in cattle and, based on limited mitochondrial sequence information, appeared to be about equally phylogenetically distant from O. ochengi and O. volvulus. Based on molecular genetic markers and apparent interbreeding, we later proposed that O. sp. &quot;Siisa&quot; belongs to the species O. ochengi. However, we did not demonstrate directly that the hybrids were fertile, and we were still unable to resolve the phylogenetic relationship of O. ochengi, O. sp. &quot;Siisa,&quot; and O. volvulus, leaving some concerns with the conclusion mentioned above. Here, we present fully assembled, manually curated mitochondrial genomes of O. ochengi and O. sp. &quot;Siisa,&quot; and we compare multiple individuals of these two taxa with respect to their whole mitochondrial and nuclear genomes. Based on the mitochondrial genomes, O. ochengi and O. sp. &quot;Siisa&quot; are phylogenetically much closer to each other than to O. volvulus. The differences between them are well within the range of what is expected for within-species variation. The nuclear genome comparison provided no indication of genetic separation of O. ochengi and O. sp. &quot;Siisa.&quot; From this, in combination with the earlier literature, we conclude that O. ochengi and O. sp. &quot;Siisa&quot; should be considered one species.}, }
@article {pmid29401406, year = {2018}, author = {Abboud, TG and Zubaer, A and Wai, A and Hausner, G}, title = {The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi.}, journal = {Canadian journal of microbiology}, volume = {64}, number = {5}, pages = {339-348}, doi = {10.1139/cjm-2017-0605}, pmid = {29401406}, issn = {1480-3275}, mesh = {Base Sequence ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Fungal Proteins/genetics ; Genes, Fungal ; *Genome, Mitochondrial ; Mitochondria/genetics ; Open Reading Frames ; Ophiostoma/*genetics ; Phylogeny ; Plant Diseases/*microbiology ; Ulmus/microbiology ; }, abstract = {Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.}, }
@article {pmid29383422, year = {2018}, author = {Yu, H and Wang, D and Zou, L and Zhang, Z and Xu, H and Zhu, F and Ren, X and Xu, B and Yuan, J and Liu, J and Spencer, PS and Yang, X}, title = {Proteomic alterations of brain subcellular organelles caused by low-dose copper exposure: implication for Alzheimer's disease.}, journal = {Archives of toxicology}, volume = {92}, number = {4}, pages = {1363-1382}, doi = {10.1007/s00204-018-2163-6}, pmid = {29383422}, issn = {1432-0738}, support = {2014A030313715//National Natural Science Foundation of China/ ; }, abstract = {Excessive copper intake can lead to neurotoxicity, but there is a lack of comprehensive understanding on the potential impact of copper exposure especially at a low-dose on brain. We used 3xTg-AD mice to explore the potential neurotoxicity of chronic, low-dose copper treatment (0.13 ppm copper chloride in drinking water) on behavior and the brain hippocampal mitochondrial and nuclear proteome. Low-dose copper increased the spatial memory impairment of these animals, increased accumulation of intracellular amyloid 1-42 (Aβ1-42), decreased ATP content, increased the positive staining of 8-hydroxyguanosine (8-OHdG), a marker of DNA oxidative damage, and caused apoptosis and a decrease in synaptic proteins. Mitochondrial proteomic analysis by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) revealed modulation of 24 hippocampal mitochondrial proteins (14 increased and 10 decreased) in copper-treated vs. untreated 3xTg-AD mice. Nuclear proteomic analysis revealed 43 modulated hippocampal nuclear proteins (25 increased and 18 decreased) in copper-treated 3xTg-AD vs. untreated mice. Classification of modulated mitochondrial and nuclear proteins included functional categories such as energy metabolism, synaptic-related proteins, DNA damage and apoptosis-related proteins, and oxidative stress-related proteins. Among these differentially expressed mitochondrial and nuclear proteins, nine proteins were abnormally expressed in both hippocampus mitochondria and nuclei, including electron transport chain-related proteins NADH dehydrogenase 1 alpha subcomplex subunit 10 (NDUAA), cytochrome b-c1 complex subunit Rieske (UCRI), cytochrome c oxidase subunit 5B (COX5B), and ATP synthase subunit d (ATP5H), glycolytic-related pyruvate kinase PKM (KPYM) and pyruvate dehydrogenase E1 component subunit alpha (ODPA). Furthermore, we found coenzyme Q10 (CoQ10), an endogenous mitochondrial protective factor/antioxidant, modulated the expression of 12 differentially expressed hippocampal proteins (4 increased and 8 decreased), which could be classified in functional categories such as glycolysis and synaptic-related proteins, oxidative stress-related proteins, implying that CoQ10 improved synaptic function, suppress oxidative stress, and regulate glycolysis. For the proteomics study, we validated the expression of several proteins related to synapses, DNA and apoptosis. The data confirmed that synapsin-2, a synaptic-related protein, was significantly decreased in both mitochondria and nuclei of copper-exposed 3xTg-AD mice. In mitochondria, dynamin-1 (DYN1), an apoptosis-related proteins, was significantly decreased. In the cellular nuclei, paraspeckle protein 1 (PSPC1) and purin-rich element-binding protein alpha (Purα), two DNA damage-related proteins, were significantly decreased and increased, respectively. We conclude that low-dose copper exposure exacerbates the spatial memory impairment of 3xTg-AD mice and perturbs multiple biological/pathogenic processes by dysregulating the mitochondrial and nuclear proteome. Exposure to copper might therefore contribute to the evolution of AD.}, }
@article {pmid29382768, year = {2018}, author = {Zachar, I and Szilágyi, A and Számadó, S and Szathmáry, E}, title = {Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {7}, pages = {E1504-E1510}, doi = {10.1073/pnas.1718707115}, pmid = {29382768}, issn = {1091-6490}, support = {294332//European Research Council/International ; }, mesh = {Animals ; Bacteria/pathogenicity ; *Biological Evolution ; Computational Biology ; Erythrocytes/*microbiology ; Eukaryota ; Humans ; Mitochondria/*physiology ; *Models, Biological ; Predatory Behavior ; *Selection, Genetic ; Symbiosis/*physiology ; }, abstract = {The origin of mitochondria was a major evolutionary transition leading to eukaryotes, and is a hotly debated issue. It is unknown whether mitochondria were acquired early or late, and whether it was captured via phagocytosis or syntrophic integration. We present dynamical models to directly simulate the emergence of mitochondria in an ecoevolutionary context. Our results show that regulated farming of prey bacteria and delayed digestion can facilitate the establishment of stable endosymbiosis if prey-rich and prey-poor periods alternate. Stable endosymbiosis emerges without assuming any initial metabolic benefit provided by the engulfed partner, in a wide range of parameters, despite that during good periods farming is costly. Our approach lends support to the appearance of mitochondria before any metabolic coupling has emerged, but after the evolution of primitive phagocytosis by the urkaryote.}, }
@article {pmid29381758, year = {2018}, author = {Song, N and Lin, A and Zhao, X}, title = {Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191826}, doi = {10.1371/journal.pone.0191826}, pmid = {29381758}, issn = {1932-6203}, mesh = {Animals ; Genes, Insect ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Neoptera/*classification/genetics ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).}, }
@article {pmid29374209, year = {2018}, author = {Giordano, L and Sillo, F and Garbelotto, M and Gonthier, P}, title = {Mitonuclear interactions may contribute to fitness of fungal hybrids.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1706}, doi = {10.1038/s41598-018-19922-w}, pmid = {29374209}, issn = {2045-2322}, abstract = {Hybridization between species is being recognized as a major force in the rapid adaptive evolution of fungal plant pathogens. The first stages of interspecific hybridization necessarily involve nuclear-mitochondrial chimeras. In their 2001 publication, Olson and Stenlid reported that mitochondria control the virulence of first generation hybrids between the North American fungal pathogen Heterobasidion irregulare and its congeneric H. occidentale. By assessing saprobic ability and gene expression of H. irregulare × H. annosum sensu stricto hybrids and of their parental genotypes, we demonstrate that mitochondria also influence saprobic growth of hybrids. Moreover, gene expression data suggest that fungal fitness is modulated by an intimate interplay between nuclear genes and mitochondrial type, and is dependent on the specific mitonuclear combination.}, }
@article {pmid29370159, year = {2018}, author = {Lane, N}, title = {Hot mitochondria?.}, journal = {PLoS biology}, volume = {16}, number = {1}, pages = {e2005113}, doi = {10.1371/journal.pbio.2005113}, pmid = {29370159}, issn = {1545-7885}, abstract = {Mitochondria generate most of the heat in endotherms. Given some impedance of heat transfer across protein-rich bioenergetic membranes, mitochondria must operate at a higher temperature than body temperature in mammals and birds. But exactly how much hotter has been controversial, with physical calculations suggesting that maximal heat gradients across cells could not be greater than 10-5 K. Using the thermosensitive mitochondrial-targeted fluorescent dye Mito Thermo Yellow (MTY), Chrétien and colleagues suggest that mitochondria are optimised to nearly 50 °C, 10 °C hotter than body temperature. This extreme value questions what temperature really means in confined far-from-equilibrium systems but encourages a reconsideration of thermal biology.}, }
@article {pmid29360606, year = {2018}, author = {Hou, CC and Gao, XM and Ni, J and Mu, DL and Yang, HY and Liu, C and Zhu, JQ}, title = {The expression pattern and potential functions of PHB in the spermiogenesis of Phascolosoma esculenta.}, journal = {Gene}, volume = {652}, number = {}, pages = {25-38}, doi = {10.1016/j.gene.2018.01.056}, pmid = {29360606}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genetic Vectors/chemistry/metabolism ; Male ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Models, Molecular ; Phylogeny ; Polychaeta/classification/*genetics/growth &amp; development/metabolism ; Polyubiquitin/genetics/metabolism ; Protein Domains ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/genetics/metabolism ; Repressor Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Spermatogenesis/*genetics ; Spermatozoa/growth &amp; development/*metabolism ; }, abstract = {Prohibitin (PHB) is a ubiquitous, evolutionarily conserved protein that is mainly localized in the inner mitochondrial membrane and exerts various mitochondrial functions. Here, we first cloned the phb gene from P. esculenta. The Pe-PHB protein has high homology and a similar protein structure to that of other animals, and it can be divided into the N-terminal hydrophobic/transmembrane domain, SPFH domain, and C-terminal coiled-coil domain. The Pe-phb gene is widely expressed, and the gene expression of phb is highest in coelomic fluid where spermiogenesis occurs, indicating a specific function in the coelom. We further observed continuous expression of the phb gene and localization of PHB proteins in mitochondria during spermiogenesis, indicating that PHB, as a mitochondrial component, may play a role during this process via its mitochondrial function. In addition, ubiquitination of mitochondria was detected, and the PHB signal was co-localized with the poly-ubiquitin signal during spermiogenesis. Mature sperm also showed ubiquitination of mitochondria and PHB. Therefore, PHB may be a substrate of poly-ubiquitin to regulate the ubiquitination of mitochondria and even subsequent elimination during P. esculenta spermiogenesis, and it has a potential role in guaranteeing the maternal inheritance of mitochondria. Taken together, these results support the hypothesis that PHB participates in the spermiogenesis of P. esculenta by maintaining the normal function of mitochondria and regulating the degradation of mitochondria.}, }
@article {pmid29359358, year = {2018}, author = {Zhang, MY and Wei, D and Li, R and Jia, HT and Liu, YW and Taning, CNT and Wang, JJ and Smagghe, G}, title = {Cytoplasmic glutamine synthetase gene expression regulates larval development in Bactrocera dorsalis (Hendel).}, journal = {Archives of insect biochemistry and physiology}, volume = {97}, number = {4}, pages = {}, doi = {10.1002/arch.21447}, pmid = {29359358}, issn = {1520-6327}, mesh = {Amino Acid Sequence ; Animals ; Female ; Glutamate-Ammonia Ligase/genetics/*metabolism ; Insect Proteins/metabolism ; Larva/enzymology/growth &amp; development ; Methionine Sulfoximine ; Phylogeny ; RNA Interference ; Tephritidae/*enzymology/genetics/*growth &amp; development ; }, abstract = {In insects, glutamine synthetase (GS), a key enzyme in the synthesis of glutamine, has been reported to be associated with embryonic development, heat shock response, and fecundity regulation. However, little is known about the influence of GS on postembryonic development. In this study, we demonstrate that blocking the activity of GS in the oriental fruit fly (Bactrocera dorsalis) with use of a GS-specific inhibitor (L-methionine S-sulfoximine), led to a significant delay in larval development, pupal weight loss, and inhibition of pupation. We further identify cloned and characterized two GS genes (BdGS-c and BdGS-m) from B. dorsalis. The two GS genes identified in B. dorsalis were predicted to be located in the cytosol (BdGS-c) and mitochondria (BdGS-m), and homology analysis indicated that both genes were similar to homologs from other Dipterans, such as Drosophila melanogaster and Aedes aegypti. BdGS-c was highly expressed in the larval stages, suggesting that cytosolic GS plays a predominant role in larval development. Furthermore, RNA interference experiments against BdGS-c, to specifically decrease the expression of cytosolic GS, resulted in delay in larval development as well as pupal weight loss. This study presents the prominent role played by BdGS-c in regulating larval development and suggests that the observed effect could have been modulated through ecdysteroid synthesis, agreeing with the reduced expression of the halloween gene spook. Also, the direct effects of BdGS-c silencing on B. dorsalis, such as larval lethality, delayed pupation, and late emergence, can be further exploited as novel insecticide target in the context of pest management.}, }
@article {pmid29359182, year = {2018}, author = {Shevade, A and Strogolova, V and Orlova, M and Yeo, CT and Kuchin, S}, title = {Mitochondrial Voltage-Dependent Anion Channel Protein Por1 Positively Regulates the Nuclear Localization of Saccharomyces cerevisiae AMP-Activated Protein Kinase.}, journal = {mSphere}, volume = {3}, number = {1}, pages = {}, doi = {10.1128/mSphere.00482-17}, pmid = {29359182}, issn = {2379-5042}, abstract = {Snf1 protein kinase of the yeast Saccharomyces cerevisiae is a member of the highly conserved eukaryotic AMP-activated protein kinase (AMPK) family, which is involved in regulating responses to energy limitation. Under conditions of carbon/energy stress, such as during glucose depletion, Snf1 is catalytically activated and enriched in the nucleus to regulate transcription. Snf1 catalytic activation requires phosphorylation of its conserved activation loop threonine (Thr210) by upstream kinases. Catalytic activation is also a prerequisite for Snf1's subsequent nuclear enrichment, a process that is mediated by Gal83, one of three alternate β-subunits of the Snf1 kinase complex. We previously reported that the mitochondrial voltage-dependent anion channel (VDAC) proteins Por1 and Por2 play redundant roles in promoting Snf1 catalytic activation by Thr210 phosphorylation. Here, we show that the por1Δ mutation alone, which by itself does not affect Snf1 Thr210 phosphorylation, causes defects in Snf1 and Gal83 nuclear enrichment and Snf1's ability to stimulate transcription. We present evidence that Por1 promotes Snf1 nuclear enrichment by promoting the nuclear enrichment of Gal83. Overexpression of Por2, which is not believed to have channel activity, can suppress the localization and transcription activation defects of the por1Δ mutant, suggesting that the regulatory role played by Por1 is separable from its channel function. Thus, our findings expand the positive roles of the yeast VDACs in carbon/energy stress signaling upstream of Snf1. Since AMPK/Snf1 and VDAC proteins are conserved in evolution, our findings in yeast may have implications for AMPK regulation in other eukaryotes, including humans. IMPORTANCE AMP-activated protein kinases (AMPKs) sense energy limitation and regulate transcription and metabolism in eukaryotes from yeast to humans. In mammals, AMPK responds to increased AMP-to-ATP or ADP-to-ATP ratios and is implicated in diabetes, heart disease, and cancer. Mitochondria produce ATP and are generally thought to downregulate AMPK. Indeed, some antidiabetic drugs activate AMPK by affecting mitochondrial respiration. ATP release from mitochondria is mediated by evolutionarily conserved proteins known as voltage-dependent anion channels (VDACs). One would therefore expect VDACs to serve as negative regulators of AMPK. However, our experiments in yeast reveal the existence of an opposite relationship. We previously showed that Saccharomyces cerevisiae VDACs Por1 and Por2 positively regulate AMPK/Snf1 catalytic activation. Here, we show that Por1 also plays an important role in promoting AMPK/Snf1 nuclear localization. Our counterintuitive findings could inform research in areas ranging from diabetes to cancer to fungal pathogenesis.}, }
@article {pmid29356455, year = {2017}, author = {Antunes, CD and Lucena, MN and Garçon, DP and Leone, FA and McNamara, JC}, title = {Low salinity-induced alterations in epithelial ultrastructure, Na+/K+-ATPase immunolocalization and enzyme kinetic characteristics in the gills of the thinstripe hermit crab, Clibanarius vittatus (Anomura, Diogenidae).}, journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology}, volume = {327}, number = {6}, pages = {380-397}, doi = {10.1002/jez.2109}, pmid = {29356455}, issn = {2471-5646}, abstract = {Fresh caught Clibanarius vittatus [SW, 31‰ salinity (S)] were acclimated to a dilute medium (15‰ S) for 10 days, employing silver staining to locate gill ion transporting tissue, immunofluorescence to localize the Na+/K+-ATPase α-subunit in the lamellae, and electron microscopy to portray ultrastructural changes in the gill epithelia. Na+/K+-ATPase activity was characterized kinetically in a gill microsomal fraction, including synergistic stimulation by NH4+ plus K+. Silver staining revealed that all 26 phyllobranchiate arthro- and pleurobranchiae participate in ion transport. Na+/K+-ATPase α-subunit staining was weak in SW crabs and distributed exclusively and irregularly within the intralamellar septal cells, particularly at the septal-pillar cell body junctions, and septal cell cytoplasm facing the hemolymph space. In 15‰ S crabs, α-subunit localization was intense, occupying the entire thickened septum. Pillar cells and flanges did not stain. Mitochondria and membrane foldings increased in the pillar cell flanges and intralamellar septal cells, greatly amplifying surface area. Only a single ATP binding site (VM = 130.8 ± 10.5 nmol min-1 mg protein-1; K0.5 = 55.3 ± 1.7 μmol l-1) obeying Michaelis-Menten kinetics was disclosed. Na+/K+-ATPase activity was modulated by Mg2+, Na+, and NH4+, exhibiting site-site interactions; K+ modulation showed Michaelis-Menten kinetics. K+ plus NH4+ synergistically stimulated activity ≈ 1.7-fold. Ouabain inhibited total ATPase activity by ≈ 70% (KI = 220-300 μmol l-1), revealing phosphohydrolytic activities other than the Na+/K+-ATPase. Despite ample phylogenetic separation, the phyllobranchiate lamellae of the Anomura and Caridea share many ultrastructural features, that is, an intralamellar septum and opposed abutting pillar cells, similar Na+/K+-ATPase distribution, and comparable kinetic characteristics. These findings suggest either convergent evolution at the structural and biochemical levels, or preservation of traits present in a remote common ancestor.}, }
@article {pmid29343698, year = {2018}, author = {Li, X and Zhou, TC and Wu, CH and Tao, LL and Bi, R and Chen, LJ and Deng, DY and Liu, C and Otecko, NO and Tang, Y and Lai, X and Zhang, L and Wei, J}, title = {Correlations between mitochondrial DNA haplogroup D5 and chronic hepatitis B virus infection in Yunnan, China.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {869}, doi = {10.1038/s41598-018-19184-6}, pmid = {29343698}, issn = {2045-2322}, abstract = {Mitochondrial abnormality is frequently reported in individuals with hepatitis B virus (HBV) infection, but the associated hosts' mitochondrial genetic factors remain obscure. We hypothesized that mitochondria may affect host susceptibility to HBV infection. In this study, we aimed to detect the association between chronic HBV infection and mitochondrial DNA in Chinese from Yunnan, Southwest China. A total of 272 individuals with chronic HBV infection (CHB), 310 who had never been infected by HBV (healthy controls, HC) and 278 with a trace of HBV infection (spontaneously recovered, SR) were analysed for mtDNA sequence variations and classified into respective haplogroups. Haplogroup frequencies were compared between HBV infected patients, HCs and SRs. Haplogroup D5 presented a higher frequency in CHBs than in HCs (P = 0.017, OR = 2.87, 95% confidence interval [CI] = (1.21-6.81)) and SRs (P = 0.049, OR = 2.90, 95% CI = 1.01-8.35). The network of haplogroup D5 revealed a distinct distribution pattern between CHBs and non-CHBs. A trend of higher viral load among CHBs with haplogroup D5 was observed. Our results indicate the risk potential of mtDNA haplogroup D5 in chronic HBV infection in Yunnan, China.}, }
@article {pmid29343499, year = {2018}, author = {Wilton, PR and Zaidi, A and Makova, K and Nielsen, R}, title = {A Population Phylogenetic View of Mitochondrial Heteroplasmy.}, journal = {Genetics}, volume = {208}, number = {3}, pages = {1261-1274}, doi = {10.1534/genetics.118.300711}, pmid = {29343499}, issn = {1943-2631}, support = {R01 GM116044/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bayes Theorem ; Computer Simulation ; *Genetics, Population ; Mitochondria/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {The mitochondrion has recently emerged as an active player in myriad cellular processes. Additionally, it was recently shown that >200 diseases are known to be linked to variants in mitochondrial DNA or in nuclear genes interacting with mitochondria. This has reinvigorated interest in its biology and population genetics. Mitochondrial heteroplasmy, or genotypic variation of mitochondria within an individual, is now understood to be common in humans and important in human health. However, it is still not possible to make quantitative predictions about the inheritance of heteroplasmy and its proliferation within the body, partly due to the lack of an appropriate model. Here, we present a population-genetic framework for modeling mitochondrial heteroplasmy as a process that occurs on an ontogenetic phylogeny, with genetic drift and mutation changing heteroplasmy frequencies during the various developmental processes represented in the phylogeny. Using this framework, we develop a Bayesian inference method for inferring rates of mitochondrial genetic drift and mutation at different stages of human life. Applying the method to previously published heteroplasmy frequency data, we demonstrate a severe effective germline bottleneck comprised of the cumulative genetic drift occurring between the divergence of germline and somatic cells in the mother, and the separation of germ layers in the offspring. Additionally, we find that the two somatic tissues we analyze here undergo tissue-specific bottlenecks during embryogenesis, less severe than the effective germline bottleneck, and that these somatic tissues experience little additional genetic drift during adulthood. We conclude with a discussion of possible extensions of the ontogenetic phylogeny framework and its possible applications to other ontogenetic processes in addition to mitochondrial heteroplasmy.}, }
@article {pmid29338715, year = {2018}, author = {Ramos, B and González-Acuña, D and Loyola, DE and Johnson, WE and Parker, PG and Massaro, M and Dantas, GPM and Miranda, MD and Vianna, JA}, title = {Landscape genomics: natural selection drives the evolution of mitogenome in penguins.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {53}, doi = {10.1186/s12864-017-4424-9}, pmid = {29338715}, issn = {1471-2164}, support = {11110060 and 1150517//Fondo Nacional de Desarrollo Científico y Tecnológico (CL)/International ; INACH T12-13//Instituto Antártico Chileno/International ; DI-410-13/I//Universidad Andres Bello/International ; 482501/2013-8 and 490403/2008-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)/International ; 2009/08624//Fundação de Amparo à Pesquisa do Estado de São Paulo/International ; ANT 0944411//Directorate for Biological Sciences/International ; C01X1001//Ministry of Science and Innovation, New Zealand/International ; }, mesh = {Animals ; DNA, Mitochondrial/chemistry ; *Evolution, Molecular ; Gene-Environment Interaction ; *Genome, Mitochondrial ; Genomics ; *Selection, Genetic ; Spheniscidae/*genetics ; }, abstract = {BACKGROUND: Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes and Aptenodytes). The genetic data were correlated with environmental data obtained through remote sensing (sea surface temperature [SST], chlorophyll levels [Chl] and a combination of SST and Chl [COM]) through the distribution of these species.<br><br>RESULTS: We identified the complete mtDNA genomes of several penguin species, including ND6 and 8 tRNAs on the light strand and 12 protein coding genes, 14 tRNAs and two rRNAs positioned on the heavy strand. The highest diversity was found in NADH dehydrogenase genes and the lowest in COX genes. The lowest evolutionary divergence among species was between Humboldt (Spheniscus humboldti) and Galapagos (S. mendiculus) penguins (0.004), while the highest was observed between little penguin (Eudyptula minor) and Adélie penguin (Pygoscelis adeliae) (0.097). We identified a signature of purifying selection (Ka/Ks < 1) across the mitochondrial genome, which is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain Oxidative phosphorylation (OXPHOS) proteins and functionality. Pairwise species maximum-likelihood analyses of selection at codon sites suggest positive selection has occurred on ATP8 (Fixed-Effects Likelihood, FEL) and ND4 (Single Likelihood Ancestral Counting, SLAC) in all penguins. In contrast, COX1 had a signature of strong negative selection. ND4 Ka/Ks ratios were highly correlated with SST (Mantel, p-value: 0.0001; GLM, p-value: 0.00001) and thus may be related to climate adaptation throughout penguin speciation.<br><br>CONCLUSIONS: These results identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of penguins to their environment. Such knowledge may be particularly useful for developing predictive models of how these species may respond to severe climatic changes in the future.}, }
@article {pmid29337274, year = {2018}, author = {Ballesteros, JA and Hormiga, G}, title = {Species delimitation of the North American orchard-spider Leucauge venusta (Walckenaer, 1841) (Araneae, Tetragnathidae).}, journal = {Molecular phylogenetics and evolution}, volume = {121}, number = {}, pages = {183-197}, doi = {10.1016/j.ympev.2018.01.002}, pmid = {29337274}, issn = {1095-9513}, mesh = {Animals ; Brazil ; Calibration ; Canada ; Ecosystem ; Florida ; Geography ; Male ; Mexico ; Mitochondria/genetics ; North America ; *Phylogeny ; Probability ; Species Specificity ; Spiders/classification/*genetics ; Time Factors ; United States ; }, abstract = {The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through the southeastern USA to investigate the observed genetic divide. The dataset, complemented with additional samples from Mexico, and Brazil was analyzed for species delimitation using STACEY and bGMYC based on sequences from one nuclear (ITS2) and one mitochondrial marker (COI). The analyses clearly separate USA samples into two deeply divergent and geographically structured groups (north-south) which we interpret as two different species. We generated ecological niche models for these two groups rejecting a niche equivalence hypothesis for these lineages. Taxonomic changes are proposed based on these findings, Leucauge venusta is restricted to denote the northern clade, and its known distribution restricted to the USA. Leucauge argyrobapta (White, 1841) is removed from synonymy to denote the populations in Florida, Mexico and Brazil. Although the delimitation analyses suggest each of these geographic clusters within the L. argyrobapta samples represent different species, more specimens from Central and South America are needed to properly test the cohesion of L. argyrobapta populations.}, }
@article {pmid29335382, year = {2018}, author = {Aviv, A}, title = {The mitochondrial genome, paternal age and telomere length in humans.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {373}, number = {1741}, pages = {}, doi = {10.1098/rstb.2017.0210}, pmid = {29335382}, issn = {1471-2970}, abstract = {Telomere length (TL) in humans is highly heritable and undergoes progressive age-dependent shortening in somatic cells. By contrast, sperm donated by older men display comparatively long telomeres, presumably because in the male germline, telomeres become longer with age. This puzzling phenomenon might explain why TL in the offspring correlates positively with paternal age. The present communication proposes that mitochondrial DNA polymorphisms and heteroplasmy cause variation in the production of reactive oxygen species, which, in turn, mediate age-dependent selection of germ stem cells with long telomeres and hence sperm with long telomeres. These long telomeres are then inherited by the offspring. The effect of paternal age on the offspring TL might be an evolutionarily driven mechanism that helps regulate TL across the human population.This article is part of the theme issue 'Understanding diversity in telomere dynamics'.}, }
@article {pmid29312883, year = {2017}, author = {Lemasters, JJ}, title = {Evolution of Voltage-Dependent Anion Channel Function: From Molecular Sieve to Governator to Actuator of Ferroptosis.}, journal = {Frontiers in oncology}, volume = {7}, number = {}, pages = {303}, doi = {10.3389/fonc.2017.00303}, pmid = {29312883}, issn = {2234-943X}, support = {R01 AA021191/AA/NIAAA NIH HHS/United States ; P30 CA138313/CA/NCI NIH HHS/United States ; P20 GM103542/GM/NIGMS NIH HHS/United States ; R01 DK073336/DK/NIDDK NIH HHS/United States ; R01 CA184456/CA/NCI NIH HHS/United States ; R01 DE016572/DE/NIDCR NIH HHS/United States ; }, abstract = {The voltage-dependent anion channel (VDAC) is well known as the pathway for passive diffusion of anionic hydrophilic mitochondrial metabolites across the outer membrane, but a more complex functionality of the three isoforms of VDAC has emerged, as addressed in the Frontiers in Oncology Research Topic on &quot;Uncovering the Function of the Mitochondrial Protein VDAC in Health and Disease: from Structure-Function to Novel Therapeutic Strategies.&quot; VDAC as the single most abundant protein in mitochondrial outer membranes is typically involved in isoform-specific interactions of the mitochondrion with its surroundings as, for example, during mitochondria-dependent pathways of cell death. VDAC closure can also act as an adjustable limiter (governator) of global mitochondrial metabolism, as during hepatic ethanol metabolism to promote selective oxidation of membrane-permeant acetaldehyde. In cancer cells, high free tubulin inhibits VDAC1 and VDAC2, contributing to suppression of mitochondrial function in the Warburg phenomenon. Erastin, the canonical inducer of ferroptosis, opens VDAC in the presence of tubulin and hyperpolarizes mitochondria, leading to mitochondrial production of reactive oxygen species, mitochondrial dysfunction, and cell death. Our understanding of VDAC function continues to evolve.}, }
@article {pmid29307851, year = {2018}, author = {Bai, J and Xu, S and Nie, Z and Wang, Y and Zhu, C and Wang, Y and Min, W and Cai, Y and Zou, J and Zhou, X}, title = {The complete mitochondrial genome of Huananpotamon lichuanense (Decapoda: Brachyura) with phylogenetic implications for freshwater crabs.}, journal = {Gene}, volume = {646}, number = {}, pages = {217-226}, doi = {10.1016/j.gene.2018.01.015}, pmid = {29307851}, issn = {1879-0038}, mesh = {Animals ; Brachyura/*genetics ; Evolution, Molecular ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Male ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; }, abstract = {In the present study, we determined the complete mitochondrial genome of Huananpotamon lichuanense (Decapoda: Brachyura) for the first time. The genome is 15,380bp in length and typically consists of 37 genes. When the gene order was compared to the ancestral crustacean type, two tRNA genes (tRNAHis and tRNAGln) were rearranged in H. lichuanense, and the translocation of tRNAGln appeared only in Potamoidea crabs, such as Geothelphusa dehaani and Sinopotamon xiushuiense, supporting the monophyly of the Potamoidea superfamily. Thirteen protein-coding genes and 2 rRNA genes were divided into five complexes to perform the phylogenetic analysis, and the results showed that the trees constructed by complex I (ND1-ND6 and ND4L), complex IV (COX1-COX3) and rRNA genes better accord with the morphological classification system, suggesting that molecular markers of higher-level phylogeny can be developed in these three complexes in the future. The estimated divergence time for freshwater crabs is approximately 133.58Ma, and G. dehaani from Japan diverged from the freshwater crabs of mainland China approximately 60.66Ma. A selective pressure analysis based on current data revealed obviously increasing dN/dS ratios (except for ATP6 and ND4L) of freshwater crabs, and the accumulation of nonsynonymous mutations suggests that terrestrial habitats provide a relatively relaxed selective pressure environment for this group.}, }
@article {pmid29301905, year = {2018}, author = {Dai, D and Luan, S and Chen, X and Wang, Q and Feng, Y and Zhu, C and Qi, W and Song, R}, title = {Maize Dek37 Encodes a P-type PPR Protein That Affects cis-Splicing of Mitochondrial nad2 Intron 1 and Seed Development.}, journal = {Genetics}, volume = {208}, number = {3}, pages = {1069-1082}, doi = {10.1534/genetics.117.300602}, pmid = {29301905}, issn = {1943-2631}, mesh = {Cloning, Molecular ; *Gene Expression Regulation, Plant ; *Introns ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Mutation ; NADH Dehydrogenase/metabolism ; Phenotype ; Phylogeny ; Plant Proteins/*genetics ; Protein Transport ; *RNA Splicing ; Seeds/*genetics ; Zea mays/*genetics ; }, abstract = {Mitochondrial group II introns require the participation of numerous nucleus-encoded general and specific factors to achieve efficient splicing in vivo Pentatricopeptide repeat (PPR) proteins have been implicated in assisting group II intron splicing. Here, we identified and characterized a new maize seed mutant, defective kernel 37 (dek37), which has significantly delayed endosperm and embryo development. Dek37 encodes a classic P-type PPR protein that targets mitochondria. The dek37 mutation causes no detectable DEK37 protein in mutant seeds. Mitochondrial transcripts analysis indicated that dek37 mutation decreases splicing efficiency of mitochondrial nad2 intron 1, leading to reduced assembly and NADH dehydrogenase activity of complex I. Transmission Electron Microscopy (TEM) revealed severe morphological defects of mitochondria in dek37 Transcriptome analysis of dek37 endosperm indicated enhanced expression in the alternative respiratory pathway and extensive differentially expressed genes related to mitochondrial function. These results indicated that Dek37 is involved in cis-splicing of mitochondrial nad2 intron 1 and is required for complex I assembly, mitochondrial function, and seed development in maize.}, }
@article {pmid29299440, year = {2017}, author = {Awadi, A}, title = {Host species and pathogenicity effects in the evolution of the mitochondrial genomes of Eimeria species (Apicomplexa; Coccidia; Eimeriidae).}, journal = {Journal of biological research (Thessalonike, Greece)}, volume = {24}, number = {}, pages = {13}, doi = {10.1186/s40709-017-0070-2}, pmid = {29299440}, issn = {1790-045X}, abstract = {Background: Mitochondria are fundamental organelles responsible for cellular metabolism and energy production in eukaryotes via the oxidative phosphorylation pathway. Mitochondrial DNA is often used in population and species studies with the assumption of neutral evolution. However, evidence of positive selection in mitochondrial coding genes of various animal species has accumulated suggesting that amino acid changes in mtDNA might be adaptive. The functional and physiological implications of the inferred positively selected sites are usually unknown and are only evaluated based on available structural and functional models. Such studies are absent in unicellular organisms that show several crucial differences to the electron transport chain of animal mitochondria. In the present study, we explored Eimeria mitogenomes for positive selection. We also tested for association between mtDNA polymorphism and environmental variation (i.e. host species), parasite life cycle (i.e. sporulation period), and efficient host cell invasion (i.e. pathogenicity, prepatent period).<br><br>Findings: We used site- and branch-site tests to estimate the extent of purifying and positive selection at each site and each lineage of several Eimeria parasite mitogenomes retrieved from GenBank. We founded sixteen codons in the three mtDNA-encoded proteins to be under positive selection compared to a strong purifying selection. Variation in the ratios of non-synonymous to synonymous changes of the studied parasites was associated with their different host species (F = 13.748; p < 0.001), whereas pathogenicity levels were associated with both synonymous and non-synonymous changes. This association was also confirmed by the multiple regression analysis.<br><br>Conclusions: Our results suggest that host species and pathogenicity are important factors that might shape mitochondrial variation in Eimeria parasites. This supports the important role of mtDNA variations in the evolution and adaptation of these parasites.}, }
@article {pmid29297348, year = {2017}, author = {Logacheva, MD and Krinitsina, AA and Belenikin, MS and Khafizov, K and Konorov, EA and Kuptsov, SV and Speranskaya, AS}, title = {Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions.}, journal = {BMC plant biology}, volume = {17}, number = {Suppl 2}, pages = {255}, doi = {10.1186/s12870-017-1195-z}, pmid = {29297348}, issn = {1471-2229}, mesh = {DNA, Plant/genetics ; Genes, Plant/genetics ; Genome, Plant/genetics ; Inverted Repeat Sequences/*genetics ; Phylogeny ; Plastids/*genetics ; Pteridophyta/*genetics ; }, abstract = {BACKGROUND: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes.<br><br>RESULTS: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns. We also sequenced the plastome of Adianthum hispidulum (Pteridaceae). Unexpectedly, we found high variability in the IR region, including duplication of rrn16 in D. blanfordii, complete loss of trnI-GAU in D. filix-mas, its pseudogenization due to the loss of an exon in D. blanfordii. Analysis of previously reported plastomes of Polypodiales demonstrated that Woodwardia unigemmata and Lepisorus clathratus have unusual insertions in the IR region. The sequence of these inserted regions has high similarity to several LSC fragments of ferns outside of Polypodiales and to spacer between tRNA-CGA and tRNA-TTT genes of mitochondrial genome of Asplenium nidus. We suggest that this reflects the ancient DNA transfer from mitochondrial to plastid genome occurred in a common ancestor of ferns. We determined the marked conservation of gene content and relative evolution rate of genes and intergenic spacers in the IRs of Polypodiales. Faster evolution of the four intergenic regions had been demonstrated (trnA- orf42, rrn16-rps12, rps7-psbA and ycf2-trnN).<br><br>CONCLUSIONS: IRs of Polypodiales plastomes are dynamic, driven by such events as gene loss, duplication and putative lateral transfer from mitochondria.}, }
@article {pmid29294404, year = {2018}, author = {Qu, M and Tang, W and Liu, Q and Wang, D and Ding, S}, title = {Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker.}, journal = {Molecular phylogenetics and evolution}, volume = {121}, number = {}, pages = {46-51}, doi = {10.1016/j.ympev.2017.12.031}, pmid = {29294404}, issn = {1095-9513}, mesh = {Animals ; Biomarkers/*metabolism ; Cell Nucleus/genetics ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; *Genetic Variation ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Oceans and Seas ; Phylogeny ; Ryanodine Receptor Calcium Release Channel/*genetics ; Species Specificity ; }, abstract = {Groupers (family Epinephelidae) are an assemblage of coral reef fishes comprising more than 160 species in 16 genera, many of which are both environmentally and economically valuable. Because of their similar morphology, variable color patterns, and tendency for interspecies hybridization, morphological identification of groupers usually leads to taxonomic confusion. To find an effective method for identifying different grouper species and hybrids, evaluate genetic diversity and uncover any synonymous or cryptic species, we sampled a total of 221 specimens representing 57 species in 9 genera in the China Seas. Both mitochondrial (mt) cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) were found to be effective barcoding genes. We also developed an efficient protocol for identifying hybrid groupers using mt markers and the nuclear RYR3 gene and found the first record of wide interspecies hybridization in genus Epinephelus. This barcoding study revealed high genetic divergence in many widespread species and possible synonyms. In addition to providing a molecular method for identifying grouper species, this study offers important resources for the further study of grouper conservation genetics, speciation, hybridization and other evolutionary traits.}, }
@article {pmid29293597, year = {2018}, author = {Silva, SR and Michael, TP and Meer, EJ and Pinheiro, DG and Varani, AM and Miranda, VFO}, title = {Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190321}, doi = {10.1371/journal.pone.0190321}, pmid = {29293597}, issn = {1932-6203}, mesh = {Chloroplasts/*genetics ; *Genome, Chloroplast ; Magnoliopsida/classification/*genetics ; NADPH Dehydrogenase/*genetics ; Phylogeny ; }, abstract = {In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.}, }
@article {pmid29284403, year = {2017}, author = {Wojtkowska, M and Buczek, D and Suzuki, Y and Shabardina, V and Makałowski, W and Kmita, H}, title = {The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {997}, doi = {10.1186/s12864-017-4383-1}, pmid = {29284403}, issn = {1471-2164}, support = {MPD/2010/3//Fundacja na rzecz Nauki Polskiej/International ; 01/KNOW2/2014//Polish Ministry of Science and Higher Education/International ; }, mesh = {Acanthamoeba castellanii/genetics ; Amoebozoa/classification/*genetics ; Cells, Cultured ; Dictyostelium/genetics ; Gene Expression Profiling ; Genomics ; Mitochondrial Membrane Transport Proteins/classification/*genetics ; Phylogeny ; Protein Subunits/genetics ; }, abstract = {BACKGROUND: The existence of mitochondria-related organelles (MROs) is proposed for eukaryotic organisms. The Amoebozoa includes some organisms that are known to have mitosomes but also organisms that have aerobic mitochondria. However, the mitochondrial protein apparatus of this supergroup remains largely unsampled, except for the mitochondrial outer membrane import complexes studied recently. Therefore, in this study we investigated the mitochondrial inner membrane and intermembrane space complexes, using the available genome and transcriptome sequences.<br><br>RESULTS: When compared with the canonical cognate complexes described for the yeast Saccharomyces cerevisiae, amoebozoans with aerobic mitochondria, display lower differences in the number of subunits predicted for these complexes than the mitochondrial outer membrane complexes, although the predicted subunits appear to display different levels of diversity in regard to phylogenetic position and isoform numbers. For the putative mitosome-bearing amoebozoans, the number of predicted subunits suggests the complex elimination distinctly more pronounced than in the case of the outer membrane ones.<br><br>CONCLUSION: The results concern the problem of mitochondrial and mitosome protein import machinery structural variability and the reduction of their complexity within the currently defined supergroup of Amoebozoa. This results are crucial for better understanding of the Amoebozoa taxa of both biomedical and evolutionary importance.}, }
@article {pmid29281973, year = {2017}, author = {Chong, RA and Mueller, RL}, title = {Polymorphic duplicate genes and persistent non-coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {992}, doi = {10.1186/s12864-017-4358-2}, pmid = {29281973}, issn = {1471-2164}, support = {1210900//Division of Environmental Biology/International ; 1021489//Division of Environmental Biology/International ; }, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Intergenic/chemistry ; DNA, Mitochondrial/*chemistry ; *Evolution, Molecular ; Gene Duplication ; *Gene Order ; *Genes, Duplicate ; *Genes, Mitochondrial ; Genes, rRNA ; Genetic Variation ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Transfer/genetics ; Urodela/classification/*genetics ; }, abstract = {BACKGROUND: Mitochondria are the site of the citric acid cycle and oxidative phosphorylation (OXPHOS). In metazoans, the mitochondrial genome is a small, circular molecule averaging 16.5 kb in length. Despite evolutionarily conserved gene content, metazoan mitochondrial genomes show a diversity of gene orders most commonly explained by the duplication-random loss (DRL) model. In the DRL model, (1) a sequence of genes is duplicated in tandem, (2) one paralog sustains a loss-of-function mutation, resulting in selection to retain the other copy, and (3) the non-functional paralog is eventually deleted from the genome. Despite its apparent role in generating mitochondrial gene order diversity, little is known about the tempo and mode of random gene loss after duplication events. Here, we determine mitochondrial gene order across the salamander genus Aneides, which was previously shown to include at least two DRL-mediated rearrangement events. We then analyze these gene orders in a phylogenetic context to reveal patterns of DNA loss after mitochondrial gene duplication.<br><br>RESULTS: We identified two separate duplication events that resulted in mitochondrial gene rearrangements in Aneides; one occurred at the base of the clade tens of millions of years ago, while the other occurred much more recently (i.e. within a single species), resulting in gene order polymorphism and paralogs that are readily identifiable. We demonstrate that near-complete removal of duplicate rRNA genes has occurred since the recent duplication event, whereas duplicate protein-coding genes persist as pseudogenes and duplicate tRNAs persist as functionally intact paralogs. In addition, we show that non-coding DNA duplicated at the base of the clade has persisted across species for tens of millions of years.<br><br>CONCLUSIONS: The evolutionary history of the mitochondrial genome, from its inception as a bacterial endosymbiont, includes massive genomic reduction. Consistent with this overall trend, selection for efficiency of mitochondrial replication and transcription has been hypothesized to favor elimination of extra sequence. Our results, however, suggest that there may be no strong disadvantage to extraneous sequences in salamander mitochondrial genomes, although duplicate rRNA genes may be deleterious.}, }
@article {pmid29280079, year = {2018}, author = {de Brito Vieira, WH and Ferraresi, C and Schwantes, MLB and de Andrade Perez, SE and Baldissera, V and Cerqueira, MS and Parizotto, NA}, title = {Photobiomodulation increases mitochondrial citrate synthase activity in rats submitted to aerobic training.}, journal = {Lasers in medical science}, volume = {33}, number = {4}, pages = {803-810}, doi = {10.1007/s10103-017-2424-2}, pmid = {29280079}, issn = {1435-604X}, mesh = {Animals ; Citrate (si)-Synthase/*metabolism ; Infrared Rays ; L-Lactate Dehydrogenase/metabolism ; Low-Level Light Therapy ; Male ; Mitochondria, Muscle/*enzymology/radiation effects ; Muscle, Skeletal/enzymology/radiation effects ; Myocardium/enzymology ; Physical Conditioning, Animal ; Rats ; Rats, Wistar ; Running ; }, abstract = {This study investigated the effects of photobiomodulation by low-laser laser therapy (LLLT) on the activities of citrate synthase (CS) and lactate dehydrogenase (LDH) and the anaerobic threshold (AT) in rats submitted to treadmill exercise. Fifty-four rats were allocated into four groups: rest control (RCG), rest laser (RLG), exercise control (ECG), and exercise laser (ELG). The infrared LLLT was applied daily on the quadriceps, gluteus maximum, soleus, and tibialis anterior muscles. Muscle samples (soleus, tibialis anterior, and cardiac muscles) were removed 48 h after the last exercise session for spectrophotometric analysis of the CS and LDH. The CS activity (μmol/protein) in ELG (16.02 and 0.49) was significantly greater (P < 0.05) than RCG (2.34 and 0.24), RLG (6.25 and 0.17), and ECG (6.76 and 0.26) in the cardiac and soleus muscles, respectively. The LDH activity (in 1 Mm/protein) in soleus muscle was smaller (P < 0.05) for ELG (0.33) compared to ECG (0.97), RLG (0.79), and RCG (1.07). For cardiac muscle, the LDH activity was smaller (P < 0.05) in ELG (1.38) compared to ECG (1.91) and RCG (2.55). The ECG and ELG showed increases in the maximum speed and a shift of the AT to higher effort levels after the training period, but no differences occurred between the exercised groups. In conclusion, the aerobic treadmill training combined with LLLT promotes an increase of oxidative capacity in this rat model, mainly in muscles with greater aerobic capacity.}, }
@article {pmid29279407, year = {2018}, author = {Łukasik, P and Nazario, K and Van Leuven, JT and Campbell, MA and Meyer, M and Michalik, A and Pessacq, P and Simon, C and Veloso, C and McCutcheon, JP}, title = {Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {2}, pages = {E226-E235}, doi = {10.1073/pnas.1712321115}, pmid = {29279407}, issn = {1091-6490}, mesh = {Animals ; Bacteria/*classification/*genetics ; Bacterial Physiological Phenomena/*genetics ; Biological Evolution ; Chile ; Genetic Variation ; Genome, Bacterial ; Hemiptera/*microbiology ; Phylogeny ; Symbiosis/*physiology ; }, abstract = {Bacterial endosymbionts that provide nutrients to hosts often have genomes that are extremely stable in structure and gene content. In contrast, the genome of the endosymbiont Hodgkinia cicadicola has fractured into multiple distinct lineages in some species of the cicada genus Tettigades To better understand the frequency, timing, and outcomes of Hodgkinia lineage splitting throughout this cicada genus, we sampled cicadas over three field seasons in Chile and performed genomics and microscopy on representative samples. We found that a single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over the last 4 million years, resulting in complexes of between two and six distinct Hodgkinia lineages per host. Individual genomes in these symbiotic complexes differ dramatically in relative abundance, genome size, organization, and gene content. Each Hodgkinia lineage retains a small set of core genes involved in genetic information processing, but the high level of gene loss experienced by all genomes suggests that extensive sharing of gene products among symbiont cells must occur. In total, Hodgkinia complexes that consist of multiple lineages encode nearly complete sets of genes present on the ancestral single lineage and presumably perform the same functions as symbionts that have not undergone splitting. However, differences in the timing of the splits, along with dissimilar gene loss patterns on the resulting genomes, have led to very different outcomes of lineage splitting in extant cicadas.}, }
@article {pmid29277086, year = {2018}, author = {Hagström, E and Andersson, SG}, title = {The challenges of integrating two genomes in one cell.}, journal = {Current opinion in microbiology}, volume = {41}, number = {}, pages = {89-94}, doi = {10.1016/j.mib.2017.12.003}, pmid = {29277086}, issn = {1879-0364}, abstract = {Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single genome. Functional gene transfers to the host nuclear genome is uncommon in mutualistic bacteria and lost gene functions are rather rescued by co-symbiotic bacteria. Recent findings suggest that the mitochondrial genome is retained to avoid conflicting signals between protein targeting pathways in the cell. However, if the selective pressure for oxygenic respiration is lost, the mitochondrial genome will start to deteriorate and soon be lost.}, }
@article {pmid29271525, year = {2018}, author = {Corrêa-da-Silva, F and Pereira, JAS and de Aguiar, CF and de Moraes-Vieira, PMM}, title = {Mitoimmunity-when mitochondria dictates macrophage function.}, journal = {Cell biology international}, volume = {42}, number = {6}, pages = {651-655}, doi = {10.1002/cbin.10921}, pmid = {29271525}, issn = {1095-8355}, mesh = {Animals ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Inflammasomes/metabolism ; Inflammation/metabolism/*pathology ; Macrophages/cytology/*immunology/metabolism ; Mitochondria/*metabolism ; Mitochondrial Dynamics ; NADP/metabolism ; Reactive Oxygen Species/metabolism ; Succinate Dehydrogenase/metabolism ; }, abstract = {In the past decade, several reports have appointed the importance of mitochondria in the immune response. Our understanding of mitochondria evolved from a simple supplier of energy into a platform necessary for immunorregulation. Proinflammatory responses are associated with enhanced glycolytic activity and breakdown of the TCA cycle. Mitochondrial reactive species of oxygen (mROS) are key regulators of classically activated macrophages, with substantial impact in the anti-microbicidal activity and pro-inflammatory cytokine secretion of macrophages. The inflammasome activation in macrophages is dependent on mROS production and mitochondrial regulation and mitochondrial dynamics and functionality direct impact inflammatory responses. Alternative activated macrophage metabolism relies on fatty acid oxidation, and the mechanism responsible for this phenotype is not fully elucidated. Thus, cellular metabolism and mitochondria function is a key immunoregulatory feature of macrophage biology. In this review, we will provide insights into recently reported evidences of mitochondria-related metabolic nodes, which are important for macrophage physiology.}, }
@article {pmid29262786, year = {2017}, author = {Dai, C and Hao, Y and He, Y and Lei, F}, title = {The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {266}, doi = {10.1186/s12862-017-1114-9}, pmid = {29262786}, issn = {1471-2148}, support = {31401965//National Natural Science Foundation of China/International ; }, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; *Genetic Loci ; Genetic Speciation ; Genetic Variation ; Geography ; Haplotypes/genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Passeriformes/*genetics ; *Phylogeny ; Probability ; *Reproductive Isolation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: A deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses.<br><br>RESULTS: ND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids.<br><br>CONCLUSIONS: Isolation for 2.4 Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.}, }
@article {pmid29253894, year = {2017}, author = {Wei, W and Gomez-Duran, A and Hudson, G and Chinnery, PF}, title = {Background sequence characteristics influence the occurrence and severity of disease-causing mtDNA mutations.}, journal = {PLoS genetics}, volume = {13}, number = {12}, pages = {e1007126}, doi = {10.1371/journal.pgen.1007126}, pmid = {29253894}, issn = {1553-7404}, mesh = {Alleles ; Base Sequence ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Founder Effect ; Gene Frequency ; Genetic Variation ; Haplotypes ; Humans ; Mitochondria/genetics ; *Mutation ; Optic Atrophy, Hereditary, Leber/*genetics ; Phylogeny ; }, abstract = {Inherited mitochondrial DNA (mtDNA) mutations have emerged as a common cause of human disease, with mutations occurring multiple times in the world population. The clinical presentation of three pathogenic mtDNA mutations is strongly associated with a background mtDNA haplogroup, but it is not clear whether this is limited to a handful of examples or is a more general phenomenon. To address this, we determined the characteristics of 30,506 mtDNA sequences sampled globally. After performing several quality control steps, we ascribed an established pathogenicity score to the major alleles for each sequence. The mean pathogenicity score for known disease-causing mutations was significantly different between mtDNA macro-haplogroups. Several mutations were observed across all haplogroup backgrounds, whereas others were only observed on specific clades. In some instances this reflected a founder effect, but in others, the mutation recurred but only within the same phylogenetic cluster. Sequence diversity estimates showed that disease-causing mutations were more frequent on young sequences, and genomes with two or more disease-causing mutations were more common than expected by chance. These findings implicate the mtDNA background more generally in recurrent mutation events that have been purified through natural selection in older populations. This provides an explanation for the low frequency of mtDNA disease reported in specific ethnic groups.}, }
@article {pmid29250469, year = {2017}, author = {Klink, GV and Golovin, AV and Bazykin, GA}, title = {Substitutions into amino acids that are pathogenic in human mitochondrial proteins are more frequent in lineages closely related to human than in distant lineages.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4143}, doi = {10.7717/peerj.4143}, pmid = {29250469}, issn = {2167-8359}, abstract = {Propensities for different amino acids within a protein site change in the course of evolution, so that an amino acid deleterious in a particular species may be acceptable at the same site in a different species. Here, we study the amino acid-changing variants in human mitochondrial genes, and analyze their occurrence in non-human species. We show that substitutions giving rise to such variants tend to occur in lineages closely related to human more frequently than in more distantly related lineages, indicating that a human variant is more likely to be deleterious in more distant species. Unexpectedly, substitutions giving rise to amino acids that correspond to alleles pathogenic in humans also more frequently occur in more closely related lineages. Therefore, a pathogenic variant still tends to be more acceptable in human mitochondria than a variant that may only be fit after a substantial perturbation of the protein structure.}, }
@article {pmid29247559, year = {2018}, author = {Lee, K and Lee, HY and Back, K}, title = {Rice histone deacetylase 10 and Arabidopsis histone deacetylase 14 genes encode N-acetylserotonin deacetylase, which catalyzes conversion of N-acetylserotonin into serotonin, a reverse reaction for melatonin biosynthesis in plants.}, journal = {Journal of pineal research}, volume = {64}, number = {2}, pages = {}, doi = {10.1111/jpi.12460}, pmid = {29247559}, issn = {1600-079X}, mesh = {Arabidopsis/*metabolism ; Arylalkylamine N-Acetyltransferase/metabolism ; Histone Deacetylases/*metabolism ; Melatonin/*biosynthesis ; Oryza/*metabolism ; Phylogeny ; Plant Proteins/*metabolism ; Serotonin/analogs &amp; derivatives/metabolism ; }, abstract = {In plants, melatonin production is strictly regulated, unlike the production of its precursor, serotonin, which is highly inducible in response to stimuli, such as senescence and pathogen exposure. Exogenous serotonin treatment does not greatly induce the production of N-acetylserotonin (NAS) and melatonin in plants, which suggests the possible existence of one or more regulatory genes in the pathway for the biosynthesis of melatonin from serotonin. In this report, we found that NAS was rapidly and abundantly converted into serotonin in rice seedlings, indicating the presence of an N-acetylserotonin deacetylase (ASDAC). To clone the putative ASDAC gene, we screened 4 genes that were known as histone deacetylase (HDAC) genes, but encoded proteins targeted into chloroplasts or mitochondria rather than nuclei. Of 4 recombinant Escherichia coli strains expressing these genes, one E. coli strain expressing the rice HDAC10 gene was found to be capable of producing serotonin in response to treatment with NAS. The recombinant purified rice HDAC10 (OsHDAC10) protein exhibited ASDAC enzyme activity toward NAS, N-acetyltyramine (NAT), N-acetyltryptamine, and melatonin, with the highest ASDAC activity for NAT. In addition, its Arabidopsis ortholog, AtHDAC14, showed similar ASDAC activity to that of OsHDAC10. Both OsHDAC10 and AtHDAC14 were found to be expressed in chloroplasts. Phylogenetic analysis indicated that ASDAC homologs were present in archaea, but not in cyanobacteria, which differs from the distribution of serotonin N-acetyltransferase (SNAT). This suggests that SNAT and ASDAC may have evolved differently from ancestral eukaryotic cells.}, }
@article {pmid29245571, year = {2017}, author = {Pickersgill, M and Zimkus, BM and Raw, LRG}, title = {A new species of Phrynobatrachus (Anura: Phrynobatrachidae) from the Eastern Arc Mountians of Tanzania.}, journal = {Zootaxa}, volume = {4350}, number = {1}, pages = {151-163}, doi = {10.11646/zootaxa.4350.1.9}, pmid = {29245571}, issn = {1175-5334}, mesh = {Animals ; *Anura ; Male ; Mitochondria ; Phylogeny ; RNA, Ribosomal, 16S ; Tanzania ; }, abstract = {Phrynobatrachus discogularis sp. nov. (Anura, Phrynobatrachidae) is described from the Eastern Arc Mountains in Tanzania. It occupies upland grasslands and while it morphologically most resembles West and Central African P. gutturosus (Chabanaud, 1921), P. rungwensis (Loveridge, 1932), and P. anotis Schmidt and Inger, 1959, preliminary analysis of mitochondrial 16S rRNA indicates that the new species differs from all other species with published sequence data by a minimum distance of 4.1% and has affinities with P. rungwensis, P. uzungwensis Grandison and Howell, 1983 and P. keniensis Barbour and Loveridge, 1928-all diminutive upland eastern African taxa. The shape and colour of the male's external gular apparatus distinguish this species from all other described Phrynobatrachus species. Although geographically either sympatric or closely allopatric with P. uzungwensis, the lack of overlapping morphological characters indicates the two forms are distinct species. The new taxon is compared with other species from the region.}, }
@article {pmid29244187, year = {2017}, author = {Salinas-Giegé, T and Cavaiuolo, M and Cognat, V and Ubrig, E and Remacle, C and Duchêne, AM and Vallon, O and Maréchal-Drouard, L}, title = {Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii.}, journal = {Nucleic acids research}, volume = {45}, number = {22}, pages = {12963-12973}, doi = {10.1093/nar/gkx903}, pmid = {29244187}, issn = {1362-4962}, mesh = {Base Sequence ; Chlamydomonas reinhardtii/*genetics/metabolism ; Chlorophyta/classification/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics/metabolism ; Phylogeny ; Poly C/metabolism ; RNA, Messenger/*genetics/metabolism ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic ; }, abstract = {The unicellular photosynthetic organism, Chlamydomonas reinhardtii, represents a powerful model to study mitochondrial gene expression. Here, we show that the 5'- and 3'-extremities of the eight Chlamydomonas mitochondrial mRNAs present two unusual characteristics. First, all mRNAs start primarily at the AUG initiation codon of the coding sequence which is often marked by a cluster of small RNAs. Second, unusual tails are added post-transcriptionally at the 3'-extremity of all mRNAs. The nucleotide composition of the tails is distinct from that described in any other systems and can be partitioned between A/U-rich tails, predominantly composed of Adenosine and Uridine, and C-rich tails composed mostly of Cytidine. Based on 3' RACE experiments, 22% of mRNAs present C-rich tails, some of them composed of up to 20 consecutive Cs. Polycytidylation is specific to mitochondria and occurs primarily on mRNAs. This unprecedented post-transcriptional modification seems to be a specific feature of the Chlorophyceae class of green algae and points out the existence of novel strategies in mitochondrial gene expression.}, }
@article {pmid29241459, year = {2017}, author = {Carrie, C and Soll, J}, title = {To Mia or not to Mia: stepwise evolution of the mitochondrial intermembrane space disulfide relay.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {119}, doi = {10.1186/s12915-017-0468-1}, pmid = {29241459}, issn = {1741-7007}, abstract = {The disulfide relay system found in the intermembrane space (IMS) of mitochondria is an essential pathway for the import and oxidative folding of IMS proteins. Erv1, an essential member of this pathway, has been previously found to be ubiquitously present in mitochondria-containing eukaryotes. However, the other essential protein, Mia40, was found to be absent or not required in some organisms, raising questions about how the disulfide relay functions in these organisms. A recent study published in BMC Biology demonstrates for the first time that some Erv1 proteins can function in oxidative folding independently of a Mia40 protein, providing for the first time strong evidence that the IMS disulfide relay evolved in a stepwise manner.See research article: 10.1186/s12915-017-0445-8.}, }
@article {pmid29241457, year = {2017}, author = {Yalvac, ME and Amornvit, J and Braganza, C and Chen, L and Hussain, SA and Shontz, KM and Montgomery, CL and Flanigan, KM and Lewis, S and Sahenk, Z}, title = {Impaired regeneration in calpain-3 null muscle is associated with perturbations in mTORC1 signaling and defective mitochondrial biogenesis.}, journal = {Skeletal muscle}, volume = {7}, number = {1}, pages = {27}, doi = {10.1186/s13395-017-0146-6}, pmid = {29241457}, issn = {2044-5040}, mesh = {AMP-Activated Protein Kinases/metabolism ; Animals ; Calpain/genetics/*metabolism ; Cells, Cultured ; Disease Models, Animal ; Genetic Therapy ; Mechanistic Target of Rapamycin Complex 1/*metabolism ; Mice, Inbred C57BL ; Mice, Knockout ; MicroRNAs/metabolism ; Muscle Proteins/genetics/*metabolism ; Muscle, Skeletal/metabolism/pathology/*physiology ; Muscular Dystrophies, Limb-Girdle/metabolism/physiopathology ; *Organelle Biogenesis ; Proto-Oncogene Proteins c-akt/metabolism ; *Regeneration ; Signal Transduction ; Transforming Growth Factor beta/metabolism ; }, abstract = {BACKGROUND: Previous studies in patients with limb-girdle muscular dystrophy type 2A (LGMD2A) have suggested that calpain-3 (CAPN3) mutations result in aberrant regeneration in muscle.<br><br>METHODS: To gain insight into pathogenesis of aberrant muscle regeneration in LGMD2A, we used a paradigm of cardiotoxin (CTX)-induced cycles of muscle necrosis and regeneration in the CAPN3-KO mice to simulate the early features of the dystrophic process in LGMD2A. The temporal evolution of the regeneration process was followed by assessing the oxidative state, size, and the number of metabolic fiber types at 4 and 12 weeks after last CTX injection. Muscles isolated at these time points were further investigated for the key regulators of the pathways involved in various cellular processes such as protein synthesis, cellular energy status, metabolism, and cell stress to include Akt/mTORC1 signaling, mitochondrial biogenesis, and AMPK signaling. TGF-β and microRNA (miR-1, miR-206, miR-133a) regulation were also assessed. Additional studies included in vitro assays for quantifying fusion index of myoblasts from CAPN3-KO mice and development of an in vivo gene therapy paradigm for restoration of impaired regeneration using the adeno-associated virus vector carrying CAPN3 gene in the muscle.<br><br>RESULTS: At 4 and 12 weeks after last CTX injection, we found impaired regeneration in CAPN3-KO muscle characterized by excessive numbers of small lobulated fibers belonging to oxidative metabolic type (slow twitch) and increased connective tissue. TGF-β transcription levels in the regenerating CAPN3-KO muscles were significantly increased along with microRNA dysregulation compared to wild type (WT), and the attenuated radial growth of muscle fibers was accompanied by perturbed Akt/mTORC1 signaling, uncoupled from protein synthesis, through activation of AMPK pathway, thought to be triggered by energy shortage in the CAPN3-KO muscle. This was associated with failure to increase mitochondria content, PGC-1α, and ATP5D transcripts in the regenerating CAPN3-KO muscles compared to WT. In vitro studies showed defective myotube fusion in CAPN3-KO myoblast cultures. Replacement of CAPN3 by gene therapy in vivo increased the fiber size and decreased the number of small oxidative fibers.<br><br>CONCLUSION: Our findings provide insights into understanding of the impaired radial growth phase of regeneration in calpainopathy.}, }
@article {pmid29221178, year = {2017}, author = {Díaz-Carballo, D and Klein, J and Acikelli, AH and Wilk, C and Saka, S and Jastrow, H and Wennemuth, G and Dammann, P and Giger-Pabst, U and Khosrawipour, V and Rassow, J and Nienen, M and Strumberg, D}, title = {Cytotoxic stress induces transfer of mitochondria-associated human endogenous retroviral RNA and proteins between cancer cells.}, journal = {Oncotarget}, volume = {8}, number = {56}, pages = {95945-95964}, doi = {10.18632/oncotarget.21606}, pmid = {29221178}, issn = {1949-2553}, abstract = {About 8 % of the human genome consists of human endogenous retroviruses (HERVs), which are relicts of ancient exogenous retroviral infections incurred during evolution. Although the majority of HERVs have functional gene defects or epigenetic modifications, many of them are still able to produce retroviral proteins that have been proposed to be involved in cellular transformation and cancer development. We found that, in chemo-resistant U87RETO glioblastoma cells, cytotoxic stress induced by etoposide promotes accumulation and large-scale fission of mitochondria, associated with the detection of HERV-WE1 (syncytin-1) and HERV-FRD1 (syncytin-2) in these organelles. In addition, mitochondrial preparations also contained the corresponding receptors, i.e. ASCT2 and MFSD2. We clearly demonstrated that mitochondria associated with HERV-proteins were shuttled between adjacent cancer cells not only via tunneling tubes, but also by direct cellular uptake across the cell membrane. Furthermore, anti-syncytin-1 and anti-syncytin-2 antibodies were able to specifically block this direct cellular uptake of mitochondria even more than antibodies targeting the cognate receptors. Here, we suggest that the association of mitochondria with syncytin-1/syncytin-2 together with their respective receptors could represent a novel mechanism of cell-to-cell transfer. In chemotherapy-refractory cancer cells, this might open up attractive avenues to novel mitochondria-targeting therapies.}, }
@article {pmid29210936, year = {2018}, author = {Litts, KM and Zhang, Y and Freund, KB and Curcio, CA}, title = {OPTICAL COHERENCE TOMOGRAPHY AND HISTOLOGY OF AGE-RELATED MACULAR DEGENERATION SUPPORT MITOCHONDRIA AS REFLECTIVITY SOURCES.}, journal = {Retina (Philadelphia, Pa.)}, volume = {38}, number = {3}, pages = {445-461}, doi = {10.1097/IAE.0000000000001946}, pmid = {29210936}, issn = {1539-2864}, support = {R01 EY006109/EY/NEI NIH HHS/United States ; }, mesh = {Bruch Membrane/pathology ; Humans ; Macular Degeneration/diagnostic imaging/*pathology ; Mitochondria/*ultrastructure ; Retinal Cone Photoreceptor Cells/pathology ; Retinal Photoreceptor Cell Outer Segment/*pathology ; Retinal Pigment Epithelium/pathology ; Tomography, Optical Coherence/*methods ; }, abstract = {PURPOSE: Widespread adoption of optical coherence tomography has revolutionized the diagnosis and management of retinal disease. If the cellular and subcellular sources of reflectivity in optical coherence tomography can be identified, the value of this technology will be advanced even further toward precision medicine, mechanistic thinking, and molecular discovery. Four hyperreflective outer retinal bands are created by the exquisite arrangement of photoreceptors, Müller cells, retinal pigment epithelium, and Bruch membrane. Because of massed effects of these axially compartmentalized and transversely aligned cells, reflectivity can be localized to the subcellular level. This review focuses on the second of the four bands, called ellipsoid zone in a consensus clinical lexicon, with the central thesis that mitochondria in photoreceptor inner segments are a major independent reflectivity source in this band, because of Mie scattering and waveguiding.<br><br>METHODS: We review the evolution of Band 2 nomenclature in published literature and discuss the origins of imaging signals from photoreceptor mitochondria that could make these organelles visible in vivo.<br><br>RESULTS: Our recent data pertain to outer retinal tubulation, a unique neurodegenerative and gliotic structure with a highly reflective border, prominent in late age-related macular degeneration. High-resolution histology and multimodal imaging of outer retinal tubulation together provide evidence that inner segment mitochondria undergoing fission and translocation toward the nucleus provide the reflectivity signal.<br><br>CONCLUSION: Our data support adoption of the ellipsoid zone nomenclature. Identifying subcellular signal sources will newly inform clinical.}, }
@article {pmid29207267, year = {2017}, author = {Petitjean, C and Williams, TA}, title = {Evolution: New Gene-Rich Mitochondria Found across the Eukaryotic Tree.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {R1270-R1271}, doi = {10.1016/j.cub.2017.10.028}, pmid = {29207267}, issn = {1879-0445}, abstract = {Mitochondria are the energy-generating organelles that power eukaryotic cells. Originally descended from endosymbiotic bacteria, their genomes have shrunk during evolution. New analyses suggest that large, gene-rich mitochondrial genomes are more common than previously thought, with interesting implications for eukaryotic genome evolution.}, }
@article {pmid29202688, year = {2017}, author = {Abrahamian, M and Kagda, M and Ah-Fong, AMV and Judelson, HS}, title = {Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {241}, doi = {10.1186/s12862-017-1087-8}, pmid = {29202688}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Cytosol ; Eukaryotic Cells/*metabolism ; Genes ; *Glycolysis ; Mitochondria/genetics/*metabolism ; Oomycetes/metabolism ; Phosphorylation ; Phylogeny ; Phytophthora infestans/metabolism ; Serine/*biosynthesis ; Stramenopiles/*enzymology/*metabolism ; }, abstract = {BACKGROUND: An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides.<br><br>RESULTS: Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides. The predicted mitochondrial targeting was confirmed by using fluorescent tags to localize phosphoglycerate kinase, phosphoglycerate mutase, and pyruvate kinase in Phytophthora infestans, the oomycete that causes potato blight. A genome-wide search for other enzymes with atypical mitochondrial locations identified phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which form a pathway for generating serine from the glycolytic intermediate 3-phosphoglycerate. Fluorescent tags confirmed the delivery of these serine biosynthetic enzymes to P. infestans mitochondria. A cytosolic form of this serine biosynthetic pathway, which occurs in most eukaryotes, is missing from oomycetes and most other stramenopiles. The glycolysis and serine metabolism pathways of oomycetes appear to be mosaics of enzymes with different ancestries. While some of the noncanonical oomycete mitochondrial enzymes have the closest affinity in phylogenetic analyses with proteins from other stramenopiles, others cluster with bacterial, plant, or animal proteins. The genes encoding the mitochondrial phosphoglycerate kinase and serine-forming enzymes are physically linked on oomycete chromosomes, which suggests a shared origin.<br><br>CONCLUSIONS: Stramenopile metabolism appears to have been shaped through the acquisition of genes by descent and lateral or endosymbiotic gene transfer, along with the targeting of the proteins to locations that are novel compared to other eukaryotes. Colocalization of the glycolytic and serine biosynthesis enzymes in mitochondria is apparently necessary since they share a common intermediate. The results indicate that descriptions of metabolism in textbooks do not cover the full diversity of eukaryotic biology.}, }
@article {pmid29202174, year = {2018}, author = {Wragg, D and Techer, MA and Canale-Tabet, K and Basso, B and Bidanel, JP and Labarthe, E and Bouchez, O and Le Conte, Y and Clémencet, J and Delatte, H and Vignal, A}, title = {Autosomal and Mitochondrial Adaptation Following Admixture: A Case Study on the Honeybees of Reunion Island.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {220-238}, doi = {10.1093/gbe/evx247}, pmid = {29202174}, issn = {1759-6653}, mesh = {Acclimatization ; Adaptation, Physiological ; Animals ; Bees/*genetics/physiology ; DNA, Mitochondrial/genetics ; Female ; Genome, Insect ; Genome, Mitochondrial ; Male ; Mitochondria/*genetics/metabolism ; Reunion ; }, abstract = {The honeybee population of the tropical Reunion Island is a genetic admixture of the Apis mellifera unicolor subspecies, originally described in Madagascar, and of European subspecies, mainly A. m. carnica and A. m. ligustica, regularly imported to the island since the late 19th century. We took advantage of this population to study genetic admixing of the tropical-adapted indigenous and temperate-adapted European genetic backgrounds. Whole genome sequencing of 30 workers and 6 males from Reunion, compared with samples from Europe, Madagascar, Mauritius, Rodrigues, and the Seychelles, revealed the Reunion honeybee population to be composed on an average of 53.2 ± 5.9% A. m. unicolor nuclear genomic background, the rest being mainly composed of A. m. carnica and to a lesser extent A. m. ligustica. In striking contrast to this, only 1 out of the 36 honeybees from Reunion had a mitochondrial genome of European origin, suggesting selection has favored the A. m. unicolor mitotype, which is possibly better adapted to the island's bioclimate. Local ancestry was determined along the chromosomes for all Reunion samples, and a test for preferential selection for the A. m. unicolor or European background revealed 15 regions significantly associated with the A. m. unicolor lineage and 9 regions with the European lineage. Our results provide insights into the long-term consequences of introducing exotic specimen on the nuclear and mitochondrial genomes of locally adapted populations.}, }
@article {pmid29199107, year = {2018}, author = {Solano-Zavaleta, I and Nieto-Montes de Oca, A}, title = {Species limits in the Morelet's Alligator lizard (Anguidae: Gerrhonotinae).}, journal = {Molecular phylogenetics and evolution}, volume = {120}, number = {}, pages = {16-27}, doi = {10.1016/j.ympev.2017.11.011}, pmid = {29199107}, issn = {1095-9513}, mesh = {Alligators and Crocodiles/*physiology ; Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Central America ; DNA, Mitochondrial/genetics ; Lizards/genetics/*physiology ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Species Specificity ; Time Factors ; }, abstract = {The widely distributed, Central American anguid lizard Mesaspis moreletii is currently recognized as a polytypic species with five subspecies (M. m. fulvus, M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis). We reevaluated the species limits within Mesaspis moreletii using DNA sequences of one mitochondrial and three nuclear genes. The multi-locus data set included samples of all of the subspecies of M. moreletii, the other species of Mesaspis in Central America (M. cuchumatanus and M. monticola), and some populations assignable to M. moreletii but of uncertain subspecific identity from Honduras and Nicaragua. We first used a tree-based method for delimiting species based on mtDNA data to identify potential evolutionary independent lineages, and then analized the multilocus dataset with two species delimitation methods that use the multispecies coalescent model to evaluate different competing species delimitation models: the Bayes factors species delimitation method (BFD) implemented in ∗BEAST, and the Bayesian Phylogenetics and Phylogeography (BP&amp;P) method. Our results suggest that M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis represent distinct evolutionary independent lineages, and that the populations of uncertain status from Honduras and Nicaragua may represent additional undescribed species. Our results also suggest that M. m. fulvus is a synonym of M. m. moreletii. The biogeography of the Central American lineages of Mesaspis is discussed.}, }
@article {pmid29196205, year = {2018}, author = {Medina, CD and Avila, LJ and Sites, JW and Santos, J and Morando, M}, title = {Alternative methods of phylogenetic inference for the Patagonian lizard group Liolaemus elongatus-kriegi (Iguania: Liolaemini) based on mitochondrial and nuclear markers.}, journal = {Molecular phylogenetics and evolution}, volume = {120}, number = {}, pages = {158-169}, doi = {10.1016/j.ympev.2017.11.017}, pmid = {29196205}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; Cytochromes b/classification/genetics/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Lizards/*classification/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/chemistry/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {We present different approaches to a multi-locus phylogeny for the Liolaemus elongatus-kriegi group, including almost all species and recognized lineages. We sequenced two mitochondrial and five nuclear gene regions for 123 individuals from 35 taxa, and compared relationships resolved from concatenated and species tree methods. The L. elongatus-kriegi group was inferred as monophyletic in three of the five analyses (concatenated mitochondrial, concatenated mitochondrial + nuclear gene trees, and SVD quartet species tree). The mitochondrial gene tree resolved four haploclades, three corresponding to the previously recognized complexes: L. elongatus, L. kriegi and L. petrophilus complexes, and the L. punmahuida group. The BEAST species tree approach included the L. punmahuida group within the L. kriegi complex, but the SVD quartet method placed it as sister to the L. elongatus-kriegi group. BEAST inferred species of the L. elongatus and L. petrophilus complexes as one clade, while SVDquartet inferred these two complexes as monophyletic (although with no statistical support for the L. petrophilus complex). The species tree approach also included the L. punmahuida group as part of the L. elongatus-kriegi group. Our study provides detailed multilocus phylogenetic hypotheses for the L. elongatus-kriegi group, and we discuss possible reasons for differences in the concatenation and species tree methods.}, }
@article {pmid29195856, year = {2018}, author = {Chakraborty, S and Uddin, A and Mazumder, TH and Choudhury, MN and Malakar, AK and Paul, P and Halder, B and Deka, H and Mazumder, GA and Barbhuiya, RA and Barbhuiya, MA and Devi, WJ}, title = {Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents.}, journal = {Mitochondrion}, volume = {42}, number = {}, pages = {64-76}, doi = {10.1016/j.mito.2017.11.006}, pmid = {29195856}, issn = {1872-8278}, abstract = {The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes. The codon usage bias was low as revealed from high ENC value. Correlation between codon usage and GC3 suggested that all the codons ending with G/C were positively correlated with GC3 but vice versa for A/T ending codons with the exception of ND4L and ND5 genes. Neutrality plot revealed that for the genes ATP6, COI, COIII, CYB, ND4 and ND4L, natural selection might have played a major role while mutation pressure might have played a dominant role in the codon usage bias of ATP8, COII, ND1, ND2, ND3, ND5 and ND6 genes. Phylogenetic analysis indicated that evolutionary relationships in each of 13 protein coding genes of human mitochondria were different across six continents and further suggested that geographical distance was an important factor for the origin and evolution of 13 protein coding genes of human mitochondria.}, }
@article {pmid29193148, year = {2018}, author = {Damerau, M and Freese, M and Hanel, R}, title = {Multi-gene phylogeny of jacks and pompanos (Carangidae), including placement of monotypic vadigo Campogramma glaycos.}, journal = {Journal of fish biology}, volume = {92}, number = {1}, pages = {190-202}, doi = {10.1111/jfb.13509}, pmid = {29193148}, issn = {1095-8649}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus ; DNA, Mitochondrial ; Fishes/*genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {In this study, the phylogenetic trees of jacks and pompanos (Carangidae), an ecologically and morphologically diverse, globally distributed fish family, are inferred from a complete, concatenated data set of two mitochondrial (cytochrome c oxidase I, cytochrome b) loci and one nuclear (myosin heavy chain 6) locus. Maximum likelihood and Bayesian inferences are largely congruent and show a clear separation of Carangidae into the four subfamilies: Scomberoidinae, Trachinotinae, Naucratinae and Caranginae. The inclusion of the carangid sister lineages Coryphaenidae (dolphinfishes) and Rachycentridae (cobia), however, render Carangidae paraphyletic. The phylogenetic trees also show with high statistical support that the monotypic vadigo Campogramma glaycos is the sister to all other species within the Naucratinae.}, }
@article {pmid29191733, year = {2018}, author = {Chatterjee, K and Nostramo, RT and Wan, Y and Hopper, AK}, title = {tRNA dynamics between the nucleus, cytoplasm and mitochondrial surface: Location, location, location.}, journal = {Biochimica et biophysica acta. Gene regulatory mechanisms}, volume = {1861}, number = {4}, pages = {373-386}, doi = {10.1016/j.bbagrm.2017.11.007}, pmid = {29191733}, issn = {1874-9399}, support = {R01 GM027930/GM/NIGMS NIH HHS/United States ; R01 GM122884/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Transport ; Cell Nucleus/*metabolism ; Cytoplasm/*metabolism ; Endoribonucleases/metabolism ; Evolution, Molecular ; Fungal Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondrial Membranes/*metabolism ; Nuclear Pore Complex Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/*metabolism ; Plant Proteins/metabolism ; RNA Precursors/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Transfer/*metabolism ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription, Genetic ; Vertebrates/metabolism ; Yeasts/metabolism ; }, abstract = {Although tRNAs participate in the essential function of protein translation in the cytoplasm, tRNA transcription and numerous processing steps occur in the nucleus. This subcellular separation between tRNA biogenesis and function requires that tRNAs be efficiently delivered to the cytoplasm in a step termed &quot;primary tRNA nuclear export&quot;. Surprisingly, tRNA nuclear-cytoplasmic traffic is not unidirectional, but, rather, movement is bidirectional. Cytoplasmic tRNAs are imported back to the nucleus by the &quot;tRNA retrograde nuclear import&quot; step which is conserved from budding yeast to vertebrate cells and has been hijacked by viruses, such as HIV, for nuclear import of the viral reverse transcription complex in human cells. Under appropriate environmental conditions cytoplasmic tRNAs that have been imported into the nucleus return to the cytoplasm via the 3rd nuclear-cytoplasmic shuttling step termed &quot;tRNA nuclear re-export&quot;, that again is conserved from budding yeast to vertebrate cells. We describe the 3 steps of tRNA nuclear-cytoplasmic movements and their regulation. There are multiple tRNA nuclear export and import pathways. The different tRNA nuclear exporters appear to possess substrate specificity leading to the tantalizing possibility that the cellular proteome may be regulated at the level of tRNA nuclear export. Moreover, in some organisms, such as budding yeast, the pre-tRNA splicing heterotetrameric endonuclease (SEN), which removes introns from pre-tRNAs, resides on the cytoplasmic surface of the mitochondria. Therefore, we also describe the localization of the SEN complex to mitochondria and splicing of pre-tRNA on mitochondria, which occurs prior to the participation of tRNAs in protein translation. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.}, }
@article {pmid29187976, year = {2017}, author = {Conner, WR and Blaxter, ML and Anfora, G and Ometto, L and Rota-Stabelli, O and Turelli, M}, title = {Genome comparisons indicate recent transfer of wRi-like Wolbachia between sister species Drosophila suzukii and D. subpulchrella.}, journal = {Ecology and evolution}, volume = {7}, number = {22}, pages = {9391-9404}, doi = {10.1002/ece3.3449}, pmid = {29187976}, issn = {2045-7758}, abstract = {Wolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full-length copies of 703 of the 734 single-copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014%-0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar-by at least a factor of 100-to be plausible candidates for cladogenic transmission. These three wRi-like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria, and Wolbachia.}, }
@article {pmid29182013, year = {2017}, author = {Dickerson, T and Jauregui, CE and Teng, Y}, title = {Friend or foe? Mitochondria as a pharmacological target in cancer treatment.}, journal = {Future medicinal chemistry}, volume = {9}, number = {18}, pages = {2197-2210}, doi = {10.4155/fmc-2017-0110}, pmid = {29182013}, issn = {1756-8927}, mesh = {ATPases Associated with Diverse Cellular Activities/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; DNA, Mitochondrial/drug effects/metabolism ; Energy Metabolism/drug effects ; Humans ; Membrane Proteins/metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/metabolism ; Neoplasms/*drug therapy/metabolism/pathology ; Reactive Oxygen Species/metabolism ; Signal Transduction/drug effects ; }, abstract = {Mitochondria have acquired numerous functions over the course of evolution, such as those involved in controlling energy production, cellular metabolism, cell survival, apoptosis and autophagy within host cells. Tumor cells can develop defects in mitochondrial function, presenting a potential strategy for designing selective anticancer therapies. Therefore, cancer has been the main focus of recent research to uncover possible mitochondrial targets for therapeutic benefit. This comprehensive review covers not only the recent discoveries of the roles of mitochondria in cancer development, progression and therapeutic implications but also the findings regarding emerging mitochondrial therapeutic targets and mitochondria-targeted agents. Current challenges and future directions for developments and applications of mitochondrial-targeted therapeutics are also discussed.}, }
@article {pmid29179728, year = {2017}, author = {Li, D and Du, X and Guo, X and Zhan, L and Li, X and Yin, C and Chen, C and Li, M and Li, B and Yang, H and Xing, J}, title = {Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations.}, journal = {Journal of experimental &amp; clinical cancer research : CR}, volume = {36}, number = {1}, pages = {168}, doi = {10.1186/s13046-017-0638-6}, pmid = {29179728}, issn = {1756-9966}, mesh = {Amino Acids/genetics ; Codon/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Databases, Genetic ; Humans ; Mitochondria/chemistry/*genetics ; Mutation Rate ; Neoplasms/*genetics ; *Point Mutation ; Selection, Genetic ; }, abstract = {BACKGROUND: Previous studies have indicated that tumor mitochondrial DNA (mtDNA) mutations are primarily shaped by relaxed negative selection, which is contradictory to the critical roles of mtDNA mutations in tumorigenesis. Therefore, we hypothesized that site-specific selection may influence tumor mtDNA mutations.<br><br>METHODS: To test our hypothesis, we developed the largest collection of tumor mtDNA mutations to date and evaluated how natural selection shaped mtDNA mutation patterns.<br><br>RESULTS: Our data demonstrated that both positive and negative selections acted on specific positions or functional units of tumor mtDNAs, although the landscape of these mutations was consistent with the relaxation of negative selection. In particular, mutation rate (mutation number in a region/region bp length) in complex V and tRNA coding regions, especially in ATP8 within complex V and in loop and variable regions within tRNA, were significantly lower than those in other regions. While the mutation rate of most codons and amino acids were consistent with the expectation under neutrality, several codons and amino acids had significantly different rates. Moreover, the mutations under selection were enriched for changes that are predicted to be deleterious, further supporting the evolutionary constraints on these regions.<br><br>CONCLUSION: These results indicate the existence of site-specific selection and imply the important role of the mtDNA mutations at some specific sites in tumor development.}, }
@article {pmid29178068, year = {2017}, author = {Wang, L and Liebmen, MN and Wang, X}, title = {Roles of Mitochondrial DNA Signaling in Immune Responses.}, journal = {Advances in experimental medicine and biology}, volume = {1038}, number = {}, pages = {39-53}, doi = {10.1007/978-981-10-6674-0_4}, pmid = {29178068}, issn = {0065-2598}, mesh = {Animals ; *Autophagy/genetics/immunology ; *CRISPR-Cas Systems ; *DNA, Mitochondrial/genetics/immunology ; *Gene Editing ; Humans ; *Immune System Diseases/genetics/immunology/therapy ; *Mitochondria/genetics/immunology/pathology ; Toll-Like Receptor 9/genetics/immunology ; }, abstract = {Mitochondrial DNA (mtDNA) plays an important role in immune responses during the evolution. The present chapter systemically describes its role on immune-related diseases and its interaction on immune responses. It is important to explore the main function and mechanisms of mtDNA in immune responses by which mtDNA regulates the signaling pathways of Toll-like receptor 9, autophagy, and STING. There are potentials to discover therapeutic targets of mtDNA in immune diseases and inflammation. It will be more exciting if the CRISPR-Cas9 method can be applied for mtDNA gene editing to cure diseases and provide a novel insight of mtDNA in immune responses as well as new therapies.}, }
@article {pmid29177973, year = {2017}, author = {Niu, Y and Moghimyfiroozabad, S and Safaie, S and Yang, Y and Jonas, EA and Alavian, KN}, title = {Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules.}, journal = {Journal of molecular evolution}, volume = {85}, number = {5-6}, pages = {219-233}, doi = {10.1007/s00239-017-9819-3}, pmid = {29177973}, issn = {1432-1432}, mesh = {Adenosine Triphosphate/biosynthesis ; Evolution, Molecular ; Humans ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mitochondrial Proton-Translocating ATPases/*genetics/*metabolism ; Phylogeny ; Protein Domains ; Protein Structural Elements/genetics ; Transcription, Genetic/genetics ; }, abstract = {ATP synthase is a complex universal enzyme responsible for ATP synthesis across all kingdoms of life. The F-type ATP synthase has been suggested to have evolved from two functionally independent, catalytic (F1) and membrane bound (Fo), ancestral modules. While the modular evolution of the synthase is supported by studies indicating independent assembly of the two subunits, the presence of intermediate assembly products suggests a more complex evolutionary process. We analyzed the phylogenetic profiles of the human mitochondrial proteins and bacterial transcription units to gain additional insight into the evolution of the F-type ATP synthase complex. In this study, we report the presence of intermediary modules based on the phylogenetic profiles of the human mitochondrial proteins. The two main intermediary modules comprise the α3β3 hexamer in the F1 and the c-subunit ring in the Fo. A comprehensive analysis of bacterial transcription units of F1Fo ATP synthase revealed that while a long and constant order of F1Fo ATP synthase genes exists in a majority of bacterial genomes, highly conserved combinations of separate transcription units are present among certain bacterial classes and phyla. Based on our findings, we propose a model that includes the involvement of multiple modules in the evolution of F1Fo ATP synthase. The central and peripheral stalk subunits provide a link for the integration of the F1/Fo modules.}, }
@article {pmid29176839, year = {2017}, author = {Peçanha, WT and Althoff, SL and Galiano, D and Quintela, FM and Maestri, R and Gonçalves, GL and Freitas, TRO}, title = {Pleistocene climatic oscillations in Neotropical open areas: Refuge isolation in the rodent Oxymycterus nasutus endemic to grasslands.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0187329}, doi = {10.1371/journal.pone.0187329}, pmid = {29176839}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Brazil ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Genetic Markers ; Genetic Variation ; Geography ; *Grassland ; Haplotypes/genetics ; Mitochondria/genetics ; Models, Theoretical ; *Paleontology ; Phylogeny ; Rodentia/genetics/*physiology ; Skull/anatomy &amp; histology ; Species Specificity ; Time Factors ; *Tropical Climate ; Uruguay ; }, abstract = {Pleistocene climatic oscillations favoured the expansion of grassland ecosystems and open vegetation landscapes throughout the Neotropics, and influenced the evolutionary history of species adapted to such environments. In this study, we sampled populations of the rodent Oxymycterus nasutus endemic to open areas in the Pampas and Atlantic Forest biomes to assess the tempo and mode of population divergence using an integrative approach, including coalescence theory, ecological niche models, and morphometry. Our results indicated that these O. nasutus populations exhibited high levels of genetic structure. Six major mtDNA clades were found, structuring these biomes into distinct groups. Estimates of their divergence times was indicated to be 0.571 myr. The high degree of genetic structure is reflected in the analyses of geometric morphometric; skull differences between lineages in the two ecoregions were detected. During the last glacial maximum, there was a strong increase in suitable abiotic conditions for O. nasutus. Distinct molecular markers revealed a population expansion over time, with a possible demographic retraction during the post-glacial period. Considering that all clades coalesce with the last interglacial maximum, our results indicated that reduction in suitable conditions during this period may have resulted in a possible vicariance associated with refuge isolation.}, }
@article {pmid29174633, year = {2017}, author = {Praefcke, GJK}, title = {Regulation of innate immune functions by guanylate-binding proteins.}, journal = {International journal of medical microbiology : IJMM}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijmm.2017.10.013}, pmid = {29174633}, issn = {1618-0607}, abstract = {Guanylate-binding proteins (GBP) are a family of dynamin-related large GTPases which are expressed in response to interferons and other pro-inflammatory cytokines. GBPs mediate a broad spectrum of innate immune functions against intracellular pathogens ranging from viruses to bacteria and protozoa. Several binding partners for individual GBPs have been identified and several different mechanisms of action have been proposed depending on the organisms, the cell type and the pathogen used. Many of these anti-pathogenic functions of GBPs involve the recruitment to and the subsequent destruction of pathogen containing vacuolar compartments, the assembly of large oligomeric innate immune complexes such as the inflammasome, or the induction of autophagy. Furthermore, GBPs often cooperate with immunity-related GTPases (IRGs), another family of dynamin-related GTPases, to exert their anti-pathogenic function, but since most IRGs have been lost in the evolution of higher primates, the anti-pathogenic function of human GBPs seems to be IRG-independent. GBPs and IRGs share biochemical and structural properties with the other members of the dynamin superfamily such as low nucleotide affinity and a high intrinsic GTPase activity which can be further enhanced by oligomerisation. Furthermore, GBPs and IRGs can interact with lipid membranes. In the case of three human and murine GBP isoforms this interaction is mediated by C-terminal isoprenylation. Based on cell biological studies, and in analogy to the function of other dynamins in membrane scission events, it has been postulated that both GBPs and IRGs might actively disrupt the outer membrane of pathogen-containing vacuole leading to the detection and destruction of the pathogen by the cytosolic innate immune system of the host. Recent evidence, however, indicates that GBPs might rather function by mediating membrane tethering events similar to the dynamin-related atlastin and mitofusin proteins, which mediate fusion of the ER and mitochondria, respectively. The aim of this review is to highlight the current knowledge on the function of GBPs in innate immunity and to combine it with the recent progress in the biochemical characterisation of this protein family.}, }
@article {pmid29171834, year = {2017}, author = {Quandt, CA and Beaudet, D and Corsaro, D and Walochnik, J and Michel, R and Corradi, N and James, TY}, title = {The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, doi = {10.7554/eLife.29594}, pmid = {29171834}, issn = {2050-084X}, mesh = {*Adaptation, Biological ; Amoeba/microbiology ; Animals ; Fungi/*genetics ; *Genome, Fungal ; *Host-Parasite Interactions ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; }, abstract = {Intracellular parasitism often results in gene loss, genome reduction, and dependence upon the host for cellular functioning. Rozellomycota is a clade comprising many such parasites and is related to the diverse, highly reduced, animal parasites, Microsporidia. We sequenced the nuclear and mitochondrial genomes of Paramicrosporidium saccamoebae [Rozellomycota], an intranuclear parasite of amoebae. A canonical fungal mitochondrial genome was recovered from P. saccamoebae that encodes genes necessary for the complete oxidative phosphorylation pathway including Complex I, differentiating it from most endoparasites including its sequenced relatives in Rozellomycota and Microsporidia. Comparative analysis revealed that P. saccamoebae shares more gene content with distantly related Fungi than with its closest relatives, suggesting that genome evolution in Rozellomycota and Microsporidia has been affected by repeated and independent gene losses, possibly as a result of variation in parasitic strategies (e.g. host and subcellular localization) or due to multiple transitions to parasitism.}, }
@article {pmid29168500, year = {2017}, author = {Bohnert, KA and Kenyon, C}, title = {A lysosomal switch triggers proteostasis renewal in the immortal C. elegans germ lineage.}, journal = {Nature}, volume = {551}, number = {7682}, pages = {629-633}, doi = {10.1038/nature24620}, pmid = {29168500}, issn = {1476-4687}, support = {P40 OD010440/OD/NIH HHS/United States ; R01 AG011816/AG/NIA NIH HHS/United States ; R37 AG011816/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Caenorhabditis elegans/*cytology/*metabolism ; Caenorhabditis elegans Proteins/metabolism ; *Cell Lineage ; Female ; Fertilization ; Hormones/metabolism/secretion ; Hydrogen-Ion Concentration ; Lysosomes/*metabolism ; Male ; Mitochondria/metabolism ; Oocytes/*cytology/enzymology/*metabolism ; Oogenesis ; Protein Aggregation, Pathological/metabolism ; *Proteostasis ; Signal Transduction ; Spermatozoa/metabolism/secretion ; Vacuolar Proton-Translocating ATPases/biosynthesis/metabolism ; Xenopus ; }, abstract = {Although individuals age and die with time, an animal species can continue indefinitely, because of its immortal germ-cell lineage. How the germline avoids transmitting damage from one generation to the next remains a fundamental question in biology. Here we identify a lysosomal switch that enhances germline proteostasis before fertilization. We find that Caenorhabditis elegans oocytes whose maturation is arrested by the absence of sperm exhibit hallmarks of proteostasis collapse, including protein aggregation. Remarkably, sperm-secreted hormones re-establish oocyte proteostasis once fertilization becomes imminent. Key to this restoration is activation of the vacuolar H+-ATPase (V-ATPase), a proton pump that acidifies lysosomes. Sperm stimulate V-ATPase activity in oocytes by signalling the degradation of GLD-1, a translational repressor that blocks V-ATPase synthesis. Activated lysosomes, in turn, promote a metabolic shift that mobilizes protein aggregates for degradation, and reset proteostasis by enveloping and clearing the aggregates. Lysosome acidification also occurs during Xenopus oocyte maturation; thus, a lysosomal switch that enhances oocyte proteostasis in anticipation of fertilization may be conserved in other species.}, }
@article {pmid29162845, year = {2017}, author = {Chatre, L and Fernandes, J and Michel, V and Fiette, L and Avé, P and Arena, G and Jain, U and Haas, R and Wang, TC and Ricchetti, M and Touati, E}, title = {Helicobacter pylori targets mitochondrial import and components of mitochondrial DNA replication machinery through an alternative VacA-dependent and a VacA-independent mechanisms.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15901}, doi = {10.1038/s41598-017-15567-3}, pmid = {29162845}, issn = {2045-2322}, abstract = {Targeting mitochondria is a powerful strategy for pathogens to subvert cell physiology and establish infection. Helicobacter pylori is a bacterial pathogen associated with gastric cancer development that is known to target mitochondria directly and exclusively through its pro-apoptotic and vacuolating cytotoxin VacA. By in vitro infection of gastric epithelial cells with wild-type and VacA-deficient H. pylori strains, treatment of cells with purified VacA proteins and infection of a mouse model, we show that H. pylori deregulates mitochondria by two novel mechanisms, both rather associated with host cell survival. First, early upon infection VacA induces transient increase of mitochondrial translocases and a dramatic accumulation of the mitochondrial DNA replication and maintenance factors POLG and TFAM. These events occur when VacA is not detected intracellularly, therefore do not require the direct interaction of the cytotoxin with the organelle, and are independent of the toxin vacuolating activity. In vivo, these alterations coincide with the evolution of gastric lesions towards severity. Second, H. pylori also induces VacA-independent alteration of mitochondrial replication and import components, suggesting the involvement of additional H. pylori activities in mitochondria-mediated effects. These data unveil two novel mitochondrial effectors in H. pylori-host interaction with links on gastric pathogenesis.}, }
@article {pmid29160602, year = {2018}, author = {Guedes-Monteiro, RF and Ferreira-Junior, JR and Bleicher, L and Nóbrega, FG and Barrientos, A and Barros, MH}, title = {Mitochondrial ribosome bL34 mutants present diminished translation of cytochrome c oxidase subunits.}, journal = {Cell biology international}, volume = {42}, number = {6}, pages = {630-642}, doi = {10.1002/cbin.10913}, pmid = {29160602}, issn = {1095-8355}, support = {R35 GM118141/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Electron Transport Complex IV/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mitochondrial Ribosomes/*metabolism ; Mutagenesis, Site-Directed ; Protein Biosynthesis ; RGS Proteins/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Sequence Alignment ; }, abstract = {Saccharomyces cerevisiae mitoribosomes are specialized in the translation of a few number of highly hydrophobic membrane proteins, components of the oxidative phosphorylation system. Mitochondrial characteristics, such as the membrane system and its redox state driven mitoribosomes evolution through great diversion from their bacterial and cytosolic counterparts. Therefore, mitoribosome presents a considerable number of mitochondrial-specific proteins, as well as new protein extensions. In this work we characterize temperature sensitive mutants of the subunit bL34 present in the 54S large subunit. Although bL34 has bacterial homologs, in yeast it has a long 65 aminoacids mitochondrial N-terminal addressing sequence, here we demonstrate that it can be replaced by the mitochondrial addressing sequence of Neurospora crassa ATP9 gene. The bL34 temperature sensitive mutants present lowered translation of mitochondrial COX1 and COX3, which resulted in reduced cytochrome c oxidase activity and respiratory growth deficiency. The sedimentation properties of bL34 in sucrose gradients suggest that similarly to its bacterial homolog, bL34 is also a later participant in the process of mitoribosome biogenesis.}, }
@article {pmid29155472, year = {2018}, author = {Wang, D and Gu, J and David, R and Wang, Z and Yang, S and Searle, IR and Zhu, JK and Timmis, JN}, title = {Experimental reconstruction of double-stranded break repair-mediated plastid DNA insertion into the tobacco nucleus.}, journal = {The Plant journal : for cell and molecular biology}, volume = {93}, number = {2}, pages = {227-234}, doi = {10.1111/tpj.13769}, pmid = {29155472}, issn = {1365-313X}, mesh = {Cell Nucleus/genetics ; *DNA Breaks, Double-Stranded ; *DNA Repair ; DNA, Chloroplast/genetics ; Genome, Plant/*genetics ; Plastids/genetics ; Symbiosis ; Tobacco/*genetics ; }, abstract = {The mitochondria and plastids of eukaryotic cells evolved from endosymbiotic prokaryotes. DNA from the endosymbionts has bombarded nuclei since the ancestral prokaryotes were engulfed by a precursor of the nucleated eukaryotic host. An experimental confirmation regarding the molecular mechanisms responsible for organelle DNA incorporation into nuclei has not been performed until the present analysis. Here we introduced double-stranded DNA breaks into the nuclear genome of tobacco through inducible expression of I-SceI, and showed experimentally that tobacco chloroplast DNAs insert into nuclear genomes through double-stranded DNA break repair. Microhomology-mediated linking of disparate segments of chloroplast DNA occurs frequently during healing of induced nuclear double-stranded breaks (DSB) but the resulting nuclear integrants are often immediately unstable. Non-Mendelian inheritance of a selectable marker (neo), used to identify plastid DNA transfer, was observed in the progeny of about 50% of lines emerging from the screen. The instability of these de novo nuclear insertions of plastid DNA (nupts) was shown to be associated with deletion not only of the nupt itself but also of flanking nuclear DNA within one generation of transfer. This deletion of pre-existing nuclear DNA suggests that the genetic impact of organellar DNA transfer to the nucleus is potentially far greater than previously thought.}, }
@article {pmid29155008, year = {2018}, author = {McDonald, AE and Pichaud, N and Darveau, CA}, title = {&quot;Alternative&quot; fuels contributing to mitochondrial electron transport: Importance of non-classical pathways in the diversity of animal metabolism.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {224}, number = {}, pages = {185-194}, doi = {10.1016/j.cbpb.2017.11.006}, pmid = {29155008}, issn = {1879-1107}, mesh = {Animals ; Citric Acid Cycle/*physiology ; Electron Transport/physiology ; Glycolysis/*physiology ; Humans ; Mitochondria/*physiology ; *Oxidative Phosphorylation ; }, abstract = {The study of glycolysis, the TCA cycle, and oxidative phosphorylation in animals has yielded a wealth of information about bioenergetics. Less is known about how animals use fuels other than glucose and less characterized enzymes that are also used to provide electrons to the electron transport system. It has become clear that bioenergetic flexibility is employed by a wide variety of animals in order to successfully grow, maintain cells, and reproduce, and has contributed to the exploitation of new environments and ecological niches through evolution. In most cases, the discovery of these &quot;alternative&quot; fuels and non-classical pathways is relatively recent, but is starting to call into question long believed paradigms about the diversity of animal bioenergetics. We present several specific examples of these &quot;alternatives&quot; and the animals that use them and present some implications for animal mitochondrial physiology research.}, }
@article {pmid29154412, year = {2018}, author = {Shaw, RE and Banks, SC and Peakall, R}, title = {The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers.}, journal = {Molecular ecology}, volume = {27}, number = {1}, pages = {66-82}, doi = {10.1111/mec.14433}, pmid = {29154412}, issn = {1365-294X}, abstract = {For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure.}, }
@article {pmid29149282, year = {2017}, author = {Skibinski, DOF and Ghiselli, F and Diz, AP and Milani, L and Mullins, JGL}, title = {Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3265-3281}, doi = {10.1093/gbe/evx235}, pmid = {29149282}, issn = {1759-6653}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Substitution ; Animals ; Bivalvia/cytology/enzymology/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*chemistry/classification/genetics ; *Evolution, Molecular ; Female ; Inheritance Patterns ; Male ; Membrane Potential, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Subunits ; Sequence Analysis, DNA ; }, abstract = {Many bivalve species have two types of mitochondrial DNA passed independently through the female line (F genome) and male line (M genome). Here we study the cytochrome oxidase I protein in such bivalve species and provide evidence for differences between the F and M proteins in amino acid property values, particularly relating to hydrophobicity and helicity. The magnitude of these differences varies between different regions of the protein and the change from the ancestor is most marked in the M protein. The observed changes occur in parallel and in the same direction in the different species studied. Two possible causes are considered, first relaxation of purifying selection with drift and second positive selection. These may operate in different ways in different regions of the protein. Many different amino acid substitutions contribute in a small way to the observed variation, but substitutions involving alanine and serine have a quantitatively large effect. Some of these substitutions are potential targets for phosphorylation and some are close to residues of functional importance in the catalytic mechanism. We propose that the observed changes in the F and M proteins might contribute to functional differences between them relating to ATP production and mitochondrial membrane potential with implications for sperm function.}, }
@article {pmid29145028, year = {2018}, author = {Sun, S and Hui, M and Wang, M and Sha, Z}, title = {The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {25}, number = {}, pages = {42-52}, doi = {10.1016/j.cbd.2017.11.002}, pmid = {29145028}, issn = {1878-0407}, abstract = {Deep-sea hydrothermal vent is one of the most extreme environments on Earth with low oxygen and high levels of toxins. Decapod species from the family Alvinocarididae have colonized and successfully adapted to this extremely harsh environment. Mitochondria plays a vital role in oxygen usage and energy metabolism, thus it may be under selection in the adaptive evolution of the hydrothermal vent shrimps. In this study, the mitochondrial genome (mitogenome) of alvinocaridid shrimp Shinkaicaris leurokolos (Kikuchi &amp; Hashimoto, 2000) was determined through Illumina sequencing. The mitogenome of S. leurokolos was 15,903bp in length, containing 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of sequenced alvinocaridids. It has the longest concatenated sequences of protein-coding genes, tRNAs and shortest pooled rRNAs among the alvinocaridids. The control regions (CRs) of alvinocaridid were significantly longer (p<0.01) than those of the other caridaen. The alignment of the alvinocaridid CRs revealed two conserved sequence blocks (CSBs), and each of the CSBs included a noncanonical open reading frame (ORF), which may be involved in adjusting mitochondrial energy metabolism to adapt to the hydrothermal environment. Phylogenetic analysis supported that the deep-sea hydrothermal vent shrimps may have originated from those living in shallow area. Positive selection analysis reveals the evidence of adaptive change in the mitogenome of Alvinocarididae. Thirty potentially important adaptive residues were identified, which were located in atp6, cox1, cox3, cytb and nad1-5. This study explores the mitochondrial genetic basis of hydrothermal vent adaptation in alvinocaridid for the first time, and provides valuable clues regarding the adaptation.}, }
@article {pmid29141880, year = {2017}, author = {Lague, SL and Chua, B and Alza, L and Scott, GR and Frappell, PB and Zhong, Y and Farrell, AP and McCracken, KG and Wang, Y and Milsom, WK}, title = {Divergent respiratory and cardiovascular responses to hypoxia in bar-headed geese and Andean birds.}, journal = {The Journal of experimental biology}, volume = {220}, number = {Pt 22}, pages = {4186-4194}, doi = {10.1242/jeb.168799}, pmid = {29141880}, issn = {1477-9145}, mesh = {*Altitude ; Anaerobiosis ; Animal Migration ; Animals ; Biological Evolution ; Ducks/*physiology ; Female ; Geese/*physiology ; *Life History Traits ; Male ; *Oxygen Consumption ; Phylogeny ; *Respiration ; Species Specificity ; }, abstract = {Many high-altitude vertebrates have evolved increased capacities in their oxygen transport cascade (ventilation, pulmonary diffusion, circulation and tissue diffusion), enhancing oxygen transfer from the atmosphere to mitochondria. However, the extent of interspecies variation in the control processes that dictate hypoxia responses remains largely unknown. We compared the metabolic, cardiovascular and respiratory responses to progressive decreases in inspired oxygen levels of bar-headed geese (Anser indicus), birds that biannually migrate across the Himalayan mountains, with those of Andean geese (Chloephaga melanoptera) and crested ducks (Lophonetta specularioides), lifelong residents of the high Andes. We show that Andean geese and crested ducks have evolved fundamentally different mechanisms for maintaining oxygen supply during low oxygen (hypoxia) from those of bar-headed geese. Bar-headed geese respond to hypoxia with robust increases in ventilation and heart rate, whereas Andean species increase lung oxygen extraction and cardiac stroke volume. We propose that transient high-altitude performance has favoured the evolution of robust convective oxygen transport recruitment in hypoxia, whereas life-long high-altitude residency has favoured the evolution of structural enhancements to the lungs and heart that increase lung diffusion and stroke volume.}, }
@article {pmid29141015, year = {2017}, author = {Bozler, J and Kacsoh, BZ and Bosco, G}, title = {Nematocytes: Discovery and characterization of a novel anculeate hemocyte in Drosophila falleni and Drosophila phalerata.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0188133}, doi = {10.1371/journal.pone.0188133}, pmid = {29141015}, issn = {1932-6203}, support = {DP1 MH110234/MH/NIMH NIH HHS/United States ; P30 CA023108/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Drosophila/*classification/immunology ; *Hemocytes ; Immunity, Innate ; Microscopy, Fluorescence ; Phylogeny ; Species Specificity ; }, abstract = {Immune challenges, such as parasitism, can be so pervasive and deleterious that they constitute an existential threat to a species' survival. In response to these ecological pressures, organisms have developed a wide array of novel behavioral, cellular, and molecular adaptations. Research into these immune defenses in model systems has resulted in a revolutionary understanding of evolution and functional biology. As the field has expanded beyond the limited number of model organisms our appreciation of evolutionary innovation and unique biology has widened as well. With this in mind, we have surveyed the hemolymph of several non-model species of Drosophila. Here we identify and describe a novel hemocyte, type-II nematocytes, found in larval stages of numerous Drosophila species. Examined in detail in Drosophila falleni and Drosophila phalerata, we find that these remarkable cells are distinct from previously described hemocytes due to their anucleate state (lacking a nucleus) and unusual morphology. Type-II nematocytes are long, narrow cells with spindle-like projections extending from a cell body with high densities of mitochondria and microtubules, and exhibit the ability to synthesize proteins. These properties are unexpected for enucleated cells, and together with our additional characterization, we demonstrate that these type-II nematocytes represent a biological novelty. Surprisingly, despite the absence of a nucleus, we observe through live cell imaging that these cells remain motile with a highly dynamic cellular shape. Furthermore, these cells demonstrate the ability to form multicellular structures, which we suggest may be a component of the innate immune response to macro-parasites. In addition, live cell imaging points to a large nucleated hemocyte, type-I nematocyte, as the progenitor cell, leading to enucleation through a budding or asymmetrical division process rather than nuclear ejection: This study is the first to report such a process of enucleation. Here we describe these cells in detail for the first time and examine their evolutionary history in Drosophila.}, }
@article {pmid29138502, year = {2017}, author = {Pannek, M and Simic, Z and Fuszard, M and Meleshin, M and Rotili, D and Mai, A and Schutkowski, M and Steegborn, C}, title = {Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1513}, doi = {10.1038/s41467-017-01701-2}, pmid = {29138502}, issn = {2041-1723}, mesh = {Acylation ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Lysine/*chemistry/genetics/metabolism ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Sirtuins/*chemistry/genetics/metabolism ; Xenopus ; Xenopus Proteins/*chemistry/genetics/metabolism ; }, abstract = {Sirtuins are evolutionary conserved NAD+-dependent protein lysine deacylases. The seven human isoforms, Sirt1-7, regulate metabolism and stress responses and are considered therapeutic targets for aging-related diseases. Sirt4 locates to mitochondria and regulates fatty acid metabolism and apoptosis. In contrast to the mitochondrial deacetylase Sirt3 and desuccinylase Sirt5, no prominent deacylase activity and structural information are available for Sirt4. Here we describe acyl substrates and crystal structures for Sirt4. The enzyme shows isoform-specific acyl selectivity, with significant activity against hydroxymethylglutarylation. Crystal structures of Sirt4 from Xenopus tropicalis reveal a particular acyl binding site with an additional access channel, rationalizing its activities. The structures further identify a conserved, isoform-specific Sirt4 loop that folds into the active site to potentially regulate catalysis. Using these results, we further establish efficient Sirt4 activity assays, an unusual Sirt4 regulation by NADH, and Sirt4 effects of pharmacological modulators.}, }
@article {pmid29137980, year = {2018}, author = {El Haddad, S and Serrano, A and Normand, T and Robin, C and Dubois, M and Brulé-Morabito, F and Mollet, L and Charpentier, S and Legrand, A}, title = {Interaction of Alpha-synuclein with Cytogaligin, a protein encoded by the proapoptotic gene GALIG.}, journal = {Biochemical and biophysical research communications}, volume = {495}, number = {1}, pages = {787-792}, doi = {10.1016/j.bbrc.2017.11.078}, pmid = {29137980}, issn = {1090-2104}, mesh = {Apoptosis ; Apoptosis Regulatory Proteins ; Blood Proteins/*metabolism/*secretion ; Extracellular Fluid/*metabolism ; Galectins/*metabolism/*secretion ; HeLa Cells ; Humans ; Protein Binding ; Protein Interaction Mapping ; Subcellular Fractions/*metabolism ; alpha-Synuclein/*metabolism ; }, abstract = {GALIG, an internal gene to the human galectin-3 gene, encodes two distinct proteins, Mitogaligin and Cytogaligin through translation of a unique mRNA in two overlapping alternative reading frames. When overexpressed GALIG induces apoptosis. In cultured cells, Mitogaligin destabilizes mitochondria membranes through interaction with cardiolipin. Little is known regarding the role of Cytogaligin. This protein displays multiple subcellular localizations; cytosol, nucleus, and mitochondria. We illustrate here that Cytogaligin is also secreted in the extracellular medium. Cytogaligin is shown to interact with α-Synuclein, the major component of Lewy bodies in Parkinson's disease. Overexpression of Cytogaligin reduces α-Synuclein dimerization raising a possible role in the evolution of α-Synuclein aggregation, a key molecular event underlying the pathogenesis of Parkinson's disease.}, }
@article {pmid29137957, year = {2018}, author = {Saunders, GW and Jackson, C and Salomaki, ED}, title = {Phylogenetic analyses of transcriptome data resolve familial assignments for genera of the red-algal Acrochaetiales-Palmariales Complex (Nemaliophycidae).}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {151-159}, doi = {10.1016/j.ympev.2017.11.002}, pmid = {29137957}, issn = {1095-9513}, mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Rhodophyta/*classification/*genetics ; Transcriptome/*genetics ; }, abstract = {Phylogenetic analyses of transcriptome data for representatives of the red algal Acrochaetiales-Palmariales Complex provided robust support for the assignment of genera to the constituent families. In the Acrochaetiales, the genera Acrochaetium, Grania, and an unnamed genus-level lineage (Acrochaetiac sp._1Aus) were assigned to the Acrochaetiaceae, while Audouinella is placed in a resurrected Audouinellaceae and Rhodochorton and Rhododrewia constitute the resurrected Rhodochortonaceae. For the Palmariales, transcriptome data solidly support the inclusion of Camontagnea and Rhodothamniella in the Rhodothamniellaceae, Meiodiscus and Rubrointrusa in the Meiodiscaceae, Rhodonematella and Rhodophysema in the Rhodophysemataceae, while Devaleraea and Palmaria remained in the Palmariaceae. These analyses, however, questioned the monophyly of Palmaria, which prompted a second round of analyses using eight common red algal phylogenetic markers and including a broader sampling of red algal genera in our analyses. These results supported transfer of Palmaria callophylloides and P. mollis to the genus Devaleraea necessitating new combinations, and further added the genus Halosaccion to the Palmariaceae and the genera Kallymenicola and Rhodophysemopsis to the Meiodiscaceae. Finally, DNA barcode (mitochondrial COI-5P) and ITS data were explored and supported the continued recognition of Palmaria palmata as a single species in the North Atlantic.}, }
@article {pmid29129605, year = {2018}, author = {Pogozheva, ID and Lomize, AL}, title = {Evolution and adaptation of single-pass transmembrane proteins.}, journal = {Biochimica et biophysica acta. Biomembranes}, volume = {1860}, number = {2}, pages = {364-377}, doi = {10.1016/j.bbamem.2017.11.002}, pmid = {29129605}, issn = {0005-2736}, mesh = {*Adaptation, Physiological ; Arabidopsis/genetics/metabolism ; Cell Membrane/*metabolism ; Databases, Protein ; Dictyostelium/genetics/metabolism ; Escherichia coli/genetics/metabolism ; *Evolution, Molecular ; Humans ; Membrane Proteins/chemistry/genetics/*metabolism ; Methanocaldococcus/genetics/metabolism ; Protein Conformation, alpha-Helical ; Protein Multimerization ; Proteome/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Species Specificity ; }, abstract = {A comparative analysis of 6039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the Membranome database. The observed repertoire of bitopic proteins is significantly enlarged in eukaryotic cells and especially in multicellular organisms due to the diversification of enzymes, emergence of proteins involved in vesicular trafficking, and expansion of receptors, structural, and adhesion proteins. The majority of bitopic proteins in multicellular organisms are located in the plasma membrane (PM) and involved in cell communication. Bitopic proteins from different membranes significantly diverge in terms of their biological functions, size, topology, domain architecture, physical properties of transmembrane (TM) helices and propensity to form homodimers. Most proteins from eukaryotic PM and endoplasmic reticulum (ER) have the N-out topology. The predicted lengths of TM helices and hydrophobic thicknesses, stabilities and hydrophobicities of TM α-helices are the highest for proteins from eukaryotic PM, intermediate for proteins from prokaryotic cells, ER and Golgi apparatus, and lowest for proteins from mitochondria, chloroplasts, and peroxisomes. Tyr and Phe residues accumulate at the cytoplasmic leaflet of PM and at the outer leaflet of membranes of bacteria, Golgi apparatus, and nucleus. The propensity for dimerization increases from unicellular to multicellular eukaryotes, from enzymes to receptors, and from intracellular membrane proteins to PM proteins. More than half of PM proteins form homodimers with a 2:1 ratio of right-handed to left-handed helix packing arrangements. The inverse ratio (1:2) was observed for dimers from the ER, Golgi and vesicles.}, }
@article {pmid29129532, year = {2017}, author = {Campbell, MA and Łukasik, P and Simon, C and McCutcheon, JP}, title = {Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas.}, journal = {Current biology : CB}, volume = {27}, number = {22}, pages = {3568-3575.e3}, doi = {10.1016/j.cub.2017.10.008}, pmid = {29129532}, issn = {1879-0445}, mesh = {Animals ; Bacteria/genetics ; Biological Evolution ; DNA, Circular/genetics ; Genome, Bacterial ; Genomics ; Hemiptera/*genetics/*microbiology ; Phylogeny ; Sequence Analysis, DNA/methods ; Symbiosis/*genetics ; }, abstract = {When a free-living bacterium transitions to a host-beneficial endosymbiotic lifestyle, it almost invariably loses a large fraction of its genome [1, 2]. The resulting small genomes often become stable in size, structure, and coding capacity [3-5], as exemplified by Sulcia muelleri, a nutritional endosymbiont of cicadas. Sulcia's partner endosymbiont, Hodgkinia cicadicola, similarly remains co-linear in some cicadas diverged by millions of years [6, 7]. But in the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has split into dozens of tiny, gene-sparse circles that sometimes reside in distinct Hodgkinia cells [8]. Previous data suggested that all other Magicicada species harbor complex Hodgkinia populations, but the timing, number of origins, and outcomes of the splitting process were unknown. Here, by sequencing Hodgkinia metagenomes from the remaining six Magicicada and two sister species, we show that each Magicicada species harbors Hodgkinia populations of at least 20 genomic circles. We find little synteny among the 256 Hodgkinia circles analyzed except between the most closely related cicada species. Gene phylogenies show multiple Hodgkinia lineages in the common ancestor of Magicicada and its closest known relatives but that most splitting has occurred within Magicicada and has given rise to highly variable Hodgkinia gene dosages among species. These data show that Hodgkinia genome degradation has proceeded down different paths in different Magicicada species and support a model of genomic degradation that is stochastic in outcome and nonadaptive for the host. These patterns mirror the genomic instability seen in some mitochondria.}, }
@article {pmid29126122, year = {2018}, author = {Pacheco, MA and Matta, NE and Valkiunas, G and Parker, PG and Mello, B and Stanley, CE and Lentino, M and Garcia-Amado, MA and Cranfield, M and Kosakovsky Pond, SL and Escalante, AA}, title = {Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites.}, journal = {Molecular biology and evolution}, volume = {35}, number = {2}, pages = {383-403}, doi = {10.1093/molbev/msx285}, pmid = {29126122}, issn = {1537-1719}, support = {R01 GM080586/GM/NIGMS NIH HHS/United States ; R01 GM093939/GM/NIGMS NIH HHS/United States ; }, abstract = {Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites' diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes' evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium. Contrary to previous assertions, the mtDNA is phylogenetically informative. The inferred phylogeny showed that, like the genus Plasmodium, the Leucocytozoon and Haemoproteus genera are not monophyletic groups. Although sensitive to the assumptions of the molecular dating method used, the estimated times indicate that the diversification of the avian haemosporidian subgenera/genera took place after the Cretaceous-Paleogene boundary following the radiation of modern birds. Furthermore, parasite clade differences in mtDNA substitution rates and strength of negative selection were detected. These differences may affect the biological interpretation of mtDNA gene lineages used as a proxy to species in ecological and parasitological investigations. Given that the mitochondria are critically important in the parasite life cycle stages that take place in the vector and that the transmission of parasites belonging to particular clades has been linked to specific insect families/subfamilies, this study suggests that differences in vectors have affected the mode of evolution of haemosporidian mtDNA genes. The observed patterns also suggest that the radiation of haemosporidian parasites may be the result of community-level evolutionary processes between their vertebrate and invertebrate hosts.}, }
@article {pmid29123225, year = {2017}, author = {Eme, L and Spang, A and Lombard, J and Stairs, CW and Ettema, TJG}, title = {Archaea and the origin of eukaryotes.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {12}, pages = {711-723}, doi = {10.1038/nrmicro.2017.133}, pmid = {29123225}, issn = {1740-1534}, mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; Pharmacogenomic Variants ; }, abstract = {Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor.}, }
@article {pmid29122550, year = {2018}, author = {VandenBrooks, JM and Gstrein, G and Harmon, J and Friedman, J and Olsen, M and Ward, A and Parker, G}, title = {Supply and demand: How does variation in atmospheric oxygen during development affect insect tracheal and mitochondrial networks?.}, journal = {Journal of insect physiology}, volume = {106}, number = {Pt 3}, pages = {217-223}, doi = {10.1016/j.jinsphys.2017.11.001}, pmid = {29122550}, issn = {1879-1611}, abstract = {Atmospheric oxygen is one of the most important atmospheric component for all terrestrial organisms. Variation in atmospheric oxygen has wide ranging effects on animal physiology, development, and evolution. This variation in oxygen has the potential to affect both respiratory systems (the supply side) and mitochondrial networks (the demand side) in animals. Insect respiratory systems supplying oxygen to tissues in the gas phase through blind ended tracheal systems are particularly susceptible to this variation. While the large conducting tracheae have previously been shown to respond developmentally to changes in rearing oxygen, the effect of oxygen on the tracheolar network has been relatively unexplored, especially in adult insects. Similarly, mitochondrial networks that meet energy demand in insects and other animals are dynamic and their enzyme activities have been shown to vary in the presence of oxygen. These two systems together should be under selective pressure to meet the aerobic metabolic requirements of insects. To test this hypothesis, we reared Mito-YFP Drosophila under three different oxygen concentrations hypoxia (12%), normoxia (21%), and hyperoxia (31%) and imaged their tracheolar and mitochondrial networks within their flight muscle using confocal microscopy. In terms of oxygen supply, hypoxia increased mean (mid-length) tracheolar diameters, tracheolar tip diameters, the number of tracheoles per main branch and affected tracheal branching patterns, while the opposite was observed in hyperoxia. In terms of oxygen demand, hypoxia increased mitochondrial investment and mitochondrial to tracheolar volume ratios; while the opposite was observed in hyperoxia. Generally, hypoxia had a stronger effect on both systems than hyperoxia. These results show that insects are capable of developmentally changing investment in both their supply and demand networks to increase overall fitness.}, }
@article {pmid29117860, year = {2017}, author = {Peleh, V and Zannini, F and Backes, S and Rouhier, N and Herrmann, JM}, title = {Erv1 of Arabidopsis thaliana can directly oxidize mitochondrial intermembrane space proteins in the absence of redox-active Mia40.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {106}, doi = {10.1186/s12915-017-0445-8}, pmid = {29117860}, issn = {1741-7007}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Mitochondrial Membrane Transport Proteins/*genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Oxidation-Reduction ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {BACKGROUND: Many proteins of the mitochondrial intermembrane space (IMS) contain structural disulfide bonds formed by the mitochondrial disulfide relay. In fungi and animals, the sulfhydryl oxidase Erv1 'generates' disulfide bonds that are passed on to the oxidoreductase Mia40, which oxidizes substrate proteins. A different structural organization of plant Erv1 proteins compared to that of animal and fungal orthologs was proposed to explain its inability to complement the corresponding yeast mutant.<br><br>RESULTS: Herein, we have revisited the biochemical and functional properties of Arabidopsis thaliana Erv1 by both in vitro reconstituted activity assays and complementation of erv1 and mia40 yeast mutants. These mutants were viable, however, they showed severe defects in the biogenesis of IMS proteins. The plant Erv1 was unable to oxidize yeast Mia40 and rather even blocked its activity. Nevertheless, it was able to mediate the import and folding of mitochondrial proteins.<br><br>CONCLUSIONS: We observed that plant Erv1, unlike its homologs in fungi and animals, can promote protein import and oxidative protein folding in the IMS independently of the oxidoreductase Mia40. In accordance to the absence of Mia40 in many protists, our study suggests that the mitochondrial disulfide relay evolved in a stepwise reaction from an Erv1-only system to which Mia40 was added in order to improve substrate specificity. Graphical Abstract The mitochondrial disulfide relay evolved in a step-wise manner from an Erv1-only system.}, }
@article {pmid29117562, year = {2017}, author = {Redrejo-Rodríguez, M and Ordóñez, CD and Berjón-Otero, M and Moreno-González, J and Aparicio-Maldonado, C and Forterre, P and Salas, M and Krupovic, M}, title = {Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements.}, journal = {Cell reports}, volume = {21}, number = {6}, pages = {1574-1587}, doi = {10.1016/j.celrep.2017.10.039}, pmid = {29117562}, issn = {2211-1247}, support = {340440//European Research Council/International ; }, mesh = {Amino Acid Sequence ; Bacteriophage M13/genetics ; DNA/*biosynthesis ; DNA Primers/*metabolism ; DNA, Single-Stranded/biosynthesis ; DNA-Directed DNA Polymerase/chemistry/classification/genetics/*metabolism ; Databases, Genetic ; Escherichia coli/enzymology ; Phylogeny ; Plasmids/genetics/metabolism ; Recombinant Proteins/biosynthesis/isolation &amp; purification ; Sequence Alignment ; Transcription, Genetic ; }, abstract = {Family B DNA polymerases (PolBs) play a central role during replication of viral and cellular chromosomes. Here, we report the discovery of a third major group of PolBs, which we denote primer-independent PolB (piPolB), that might be a link between the previously known protein-primed and RNA/DNA-primed PolBs. PiPolBs are encoded by highly diverse mobile genetic elements, pipolins, integrated in the genomes of diverse bacteria and also present as circular plasmids in mitochondria. Biochemical characterization showed that piPolB displays efficient DNA polymerization activity that can use undamaged and damaged templates and is endowed with proofreading and strand displacement capacities. Remarkably, the protein is also capable of template-dependent de novo DNA synthesis, i.e., DNA-priming activity, thereby breaking the long-standing dogma that replicative DNA polymerases require a pre-existing primer for DNA synthesis. We suggest that piPolBs are involved in self-replication of pipolins and may also contribute to bacterial DNA damage tolerance.}, }
@article {pmid29117555, year = {2017}, author = {Labbadia, J and Brielmann, RM and Neto, MF and Lin, YF and Haynes, CM and Morimoto, RI}, title = {Mitochondrial Stress Restores the Heat Shock Response and Prevents Proteostasis Collapse during Aging.}, journal = {Cell reports}, volume = {21}, number = {6}, pages = {1481-1494}, doi = {10.1016/j.celrep.2017.10.038}, pmid = {29117555}, issn = {2211-1247}, support = {P01 AG049665/AG/NIA NIH HHS/United States ; R37 AG026647/AG/NIA NIH HHS/United States ; }, mesh = {*Aging ; Animals ; Caenorhabditis elegans/*metabolism ; Caenorhabditis elegans Proteins/antagonists &amp; inhibitors/genetics/metabolism ; Cytoplasm/metabolism ; Electron Transport Chain Complex Proteins/antagonists &amp; inhibitors/metabolism ; Heat-Shock Proteins/genetics/metabolism ; Heat-Shock Response/*genetics ; Longevity ; Mitochondria/drug effects/*metabolism ; Protein Binding ; Proteostasis/physiology ; RNA Interference ; RNA Polymerase II/genetics/metabolism ; RNA, Small Interfering/metabolism ; Reactive Oxygen Species/metabolism ; Stress, Physiological ; Temperature ; Transcription Factors/genetics/metabolism ; Xenobiotics/pharmacology ; }, abstract = {In Caenorhabditis elegans, the programmed repression of the heat shock response (HSR) accompanies the transition to reproductive maturity, leaving cells vulnerable to environmental stress and protein aggregation with age. To identify the factors driving this event, we performed an unbiased genetic screen for suppressors of stress resistance and identified the mitochondrial electron transport chain (ETC) as a central regulator of the age-related decline of the HSR and cytosolic proteostasis. Mild downregulation of ETC activity, either by genetic modulation or exposure to mitochondria-targeted xenobiotics, maintained the HSR in adulthood by increasing HSF-1 binding and RNA polymerase II recruitment at HSF-1 target genes. This resulted in a robust restoration of cytoplasmic proteostasis and increased vitality later in life, without detrimental effects on fecundity. We propose that low levels of mitochondrial stress regulate cytoplasmic proteostasis and healthspan during aging by coordinating the long-term activity of HSF-1 with conditions preclusive to optimal fitness.}, }
@article {pmid29117544, year = {2017}, author = {Nave, KA and Tzvetanova, ID and Schirmeier, S}, title = {Glial Cell Evolution: The Origins of a Lipid Store.}, journal = {Cell metabolism}, volume = {26}, number = {5}, pages = {701-702}, doi = {10.1016/j.cmet.2017.10.011}, pmid = {29117544}, issn = {1932-7420}, abstract = {In Drosophila, neuronal mitochondria that lack OXPHOS generate ROS-protective fatty acids and lipid droplets in associated glia. In this issue, Liu et al. (2017) demonstrate that neuronal lipid synthesis is driven by the glial lactate shuttle. This lipoprotein-dependent deposition of lipids may be at the origin of glial specializations evolving in vertebrates.}, }
@article {pmid29112874, year = {2017}, author = {Roger, AJ and Muñoz-Gómez, SA and Kamikawa, R}, title = {The Origin and Diversification of Mitochondria.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {R1177-R1192}, doi = {10.1016/j.cub.2017.09.015}, pmid = {29112874}, issn = {1879-0445}, mesh = {Adenosine Triphosphate/biosynthesis/metabolism ; Alphaproteobacteria/*genetics/growth &amp; development ; *Biological Evolution ; Eukaryotic Cells/*metabolism ; Genome, Mitochondrial/genetics ; Membrane Transport Proteins/genetics ; *Mitochondria/genetics/metabolism/physiology ; Protein Transport/genetics/physiology ; Symbiosis/genetics/physiology ; }, abstract = {Mitochondria are best known for their role in the generation of ATP by aerobic respiration. Yet, research in the past half century has shown that they perform a much larger suite of functions and that these functions can vary substantially among diverse eukaryotic lineages. Despite this diversity, all mitochondria derive from a common ancestral organelle that originated from the integration of an endosymbiotic alphaproteobacterium into a host cell related to Asgard Archaea. The transition from endosymbiotic bacterium to permanent organelle entailed a massive number of evolutionary changes including the origins of hundreds of new genes and a protein import system, insertion of membrane transporters, integration of metabolism and reproduction, genome reduction, endosymbiotic gene transfer, lateral gene transfer and the retargeting of proteins. These changes occurred incrementally as the endosymbiont and the host became integrated. Although many insights into this transition have been gained, controversy persists regarding the nature of the original endosymbiont, its initial interactions with the host and the timing of its integration relative to the origin of other features of eukaryote cells. Since the establishment of the organelle, proteins have been gained, lost, transferred and retargeted as mitochondria have specialized into the spectrum of functional types seen across the eukaryotic tree of life.}, }
@article {pmid29107619, year = {2018}, author = {Chueca, LJ and Gómez-Moliner, BJ and Madeira, MJ and Pfenninger, M}, title = {Molecular phylogeny of Candidula (Geomitridae) land snails inferred from mitochondrial and nuclear markers reveals the polyphyly of the genus.}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {357-368}, doi = {10.1016/j.ympev.2017.10.022}, pmid = {29107619}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; Electron Transport Complex IV/chemistry/genetics ; Evolution, Molecular ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 28S/chemistry/genetics ; RNA, Ribosomal, 5.8S/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Snails/*classification/genetics ; }, abstract = {The genus Candidula (Geomitridae), consisting of 28 species in Western Europe as currently described, has a disjunct distribution in the Iberian Peninsula, Italy, the Balkans, the Aegean Islands, and one species on the Canary Islands. Although the genus is seemingly well defined by characters of the reproductive system, the relationships within the genus are still unclear and some authors have indicated a possible subgeneric division based on the internal morphology of the dart sac. Despite substantial phylogenetic incongruence, we present a well-resolved molecular phylogeny of Candidula based on two mitochondrial genes (COI and 16S rRNA), the nuclear rDNA region (5.8S rNRA + ITS2 + 28S rRNA) and seven additional nuclear DNA regions developed specifically for this genus (60SL13, 60SL17, 60SL7, RPL14, 40SS6, 60SL9, 60SL13a), in total 5595 bp. Six reciprocally monophyletic entities including Candidula species were recovered, grouping into two major clades. The incorporation of additional geomitrid genera allowed us to unequivocally demonstrate the polyphyly of the genus Candidula. One major clade grouped species from southern France and Italy with the widely distributed species C. unifasciata. The second major clade grouped all the species from the Iberian Peninsula, including C. intersecta and C. gigaxii. Candidula ultima from the Canary Islands was recovered as separated lineage within the latter clade and related to African taxa. The six monophyla were defined as six new genera belonging to different tribes within the Helicellinae. Thus, we could show that similar structures of the stimulatory apparatus of the genital system in different taxa do not necessarily indicate a close phylogenetic relationship in the Geomitridae. More genera of the family are needed to clarify their evolutionary relationships, and to fully understand the evolution of the stimulatory apparatus of the genital system within the Geomitridae.}, }
@article {pmid29107618, year = {2018}, author = {da Cruz, MOR and Weksler, M}, title = {Impact of tree priors in species delimitation and phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae).}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {1-12}, doi = {10.1016/j.ympev.2017.10.021}, pmid = {29107618}, issn = {1095-9513}, mesh = {Animals ; Arvicolinae/*classification ; Bayes Theorem ; Mitochondria/metabolism ; *Phylogeny ; Probability ; Species Specificity ; Time Factors ; }, abstract = {The use of genetic data and tree-based algorithms to delimit evolutionary lineages is becoming an important practice in taxonomic identification, especially in morphologically cryptic groups. The effects of different phylogenetic and/or coalescent models in the analyses of species delimitation, however, are not clear. In this paper, we assess the impact of different evolutionary priors in phylogenetic estimation, species delimitation, and molecular dating of the genus Oligoryzomys (Mammalia: Rodentia), a group with complex taxonomy and morphological cryptic species. Phylogenetic and coalescent analyses included 20 of the 24 recognized species of the genus, comprising of 416 Cytochrome b sequences, 26 Cytochrome c oxidase I sequences, and 27 Beta-Fibrinogen Intron 7 sequences. For species delimitation, we employed the General Mixed Yule Coalescent (GMYC) and Bayesian Poisson tree processes (bPTP) analyses, and contrasted 4 genealogical and phylogenetic models: Pure-birth (Yule), Constant Population Size Coalescent, Multiple Species Coalescent, and a mixed Yule-Coalescent model. GMYC analyses of trees from different genealogical models resulted in similar species delimitation and phylogenetic relationships, with incongruence restricted to areas of poor nodal support. bPTP results, however, significantly differed from GMYC for 5 taxa. Oligoryzomys early diversification was estimated to have occurred in the Early Pleistocene, between 0.7 and 2.6 MYA. The mixed Yule-Coalescent model, however, recovered younger dating estimates for Oligoryzomys diversification, and for the threshold for the speciation-coalescent horizon in GMYC. Eight of the 20 included Oligoryzomys species were identified as having two or more independent evolutionary units, indicating that current taxonomy of Oligoryzomys is still unsettled.}, }
@article {pmid29106540, year = {2017}, author = {Degli Esposti, M}, title = {A Journey across Genomes Uncovers the Origin of Ubiquinone in Cyanobacteria.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3039-3053}, doi = {10.1093/gbe/evx225}, pmid = {29106540}, issn = {1759-6653}, abstract = {Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochondria and bacteria. Nonorthologous proteins can also contribute to some biochemical steps as originally uncovered in Escherichia coli, which is the best studied organism for Q biosynthesis in prokaryotes. However, the origin of the biosynthetic pathway of Q has remained obscure. Here, I show by genome analysis that Q biosynthesis originated in cyanobacteria and then diversified in anaerobic alpha proteobacteria which have extant relatives in members of the Rhodospirillaceae family. Two distinct biochemical pathways diverged when ambient oxygen reached current levels on earth, one leading to the well-known series of Ubi genes found in E. coli, and the other containing CoQ proteins originally found in eukaryotes. Extant alpha proteobacteria show Q biosynthesis pathways that are more similar to that present in mitochondria than to that of E. coli. Hence, this work clarifies not only the origin but also the evolution of Q biosynthesis from bacteria to mitochondria.}, }
@article {pmid29106528, year = {2017}, author = {Ostersetzer-Biran, O and Lane, N and Pomiankowski, A and Burton, R and Arnqvist, G and Filipovska, A and Huchon, D and Mishmar, D}, title = {The First Mitochondrial Genomics and Evolution SMBE-Satellite Meeting: A New Scientific Symbiosis.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3054-3058}, doi = {10.1093/gbe/evx227}, pmid = {29106528}, issn = {1759-6653}, abstract = {The central role of the mitochondrion for cellular and organismal metabolism is well known, yet its functional role in evolution has rarely been featured in leading international conferences. Moreover, the contribution of mitochondrial genetics to complex disease phenotypes is particularly important, and although major advances have been made in the field of genomics, mitochondrial genomic data have in many cases been overlooked. Accumulating data and new knowledge support a major contribution of this maternally inherited genome, and its interactions with the nucleus, to both major evolutionary processes and diverse disease phenotypes. These advances encouraged us to assemble the first Mitochondrial Genomics and Evolution (MGE) meeting-an SMBE satellite and Israeli Science foundation international conference (Israel, September 2017). Here, we report the content and outcome of the MGE meeting (https://www.mge2017.com/; last accessed November 5, 2017).}, }
@article {pmid29104545, year = {2017}, author = {Dobson, GP and Arsyad, A and Letson, HL}, title = {The Adenosine Hypothesis Revisited: Modulation of Coupling between Myocardial Perfusion and Arterial Compliance.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {824}, doi = {10.3389/fphys.2017.00824}, pmid = {29104545}, issn = {1664-042X}, abstract = {For over four decades the thoracic aortic ring model has become one of the most widely used methods to study vascular reactivity and electromechanical coupling. A question that is rarely asked, however, is what function does a drug-mediated relaxation (or contraction) in this model serve in the intact system? The physiological significance of adenosine relaxation in rings isolated from large elastic conduit arteries from a wide range of species remains largely unknown. We propose that adenosine relaxation increases aortic compliance in acute stress states and facilitates ventricular-arterial (VA) coupling, and thereby links compliance and coronary artery perfusion to myocardial energy metabolism. In 1963 Berne argued that adenosine acts as a local negative feedback regulator between oxygen supply and demand in the heart during hypoxic/ischemic stress. The adenosine VA coupling hypothesis extends and enhances Berne's &quot;adenosine hypothesis&quot; from a local regulatory scheme in the heart to include conduit arterial function. In multicellular organisms, evolution may have selected adenosine, nitric oxide, and other vascular mediators, to modulate VA coupling for optimal transfer of oxygen (and nutrients) from the lung, heart, large conduit arteries, arterioles and capillaries to respiring mitochondria. Finally, a discussion of the potential clinical significance of adenosine modulation of VA coupling is extended to vascular aging and disease, including hypertension, diabetes, obesity, coronary artery disease and heart failure.}, }
@article {pmid29104141, year = {2018}, author = {Lüddecke, T and Krehenwinkel, H and Canning, G and Glaw, F and Longhorn, SJ and Tänzler, R and Wendt, I and Vences, M}, title = {Discovering the silk road: Nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies.}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {63-70}, doi = {10.1016/j.ympev.2017.10.015}, pmid = {29104141}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Silk/*genetics ; Spiders/*classification/*genetics ; }, abstract = {The mygalomorph spiders in the family Theraphosidae, also known as &quot;tarantulas&quot;, are one of the most popular and diverse groups of arachnids, but their evolutionary history remains poorly understood because morphological analyses have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of the Theraphosidae and of most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of the previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.}, }
@article {pmid29100916, year = {2018}, author = {Krishnan, R and Girish Babu, P and Jeena, K and Tripathi, G and Pani Prasad, K}, title = {Molecular characterization, ontogeny and expression profiling of mitochondrial antiviral signaling adapter, MAVS from Asian seabass Lates calcarifer, Bloch (1790).}, journal = {Developmental and comparative immunology}, volume = {79}, number = {}, pages = {175-185}, doi = {10.1016/j.dci.2017.10.019}, pmid = {29100916}, issn = {1879-0089}, mesh = {Adaptor Proteins, Signal Transducing/*genetics ; Animals ; Bass/*immunology ; Cloning, Molecular ; Fish Diseases/*immunology ; Fish Proteins ; Gene Expression Profiling ; Immunity, Innate ; Mitochondria/*metabolism ; Nodaviridae/*physiology ; Phylogeny ; RNA Virus Infections/*immunology ; Signal Transduction ; Spleen/*metabolism ; Zebrafish Proteins/genetics ; }, abstract = {Mitochondrial antiviral signaling protein (MAVS), an innate immune signaling adapter coordinates the signals received from two independent cytosolic pathogen recognition receptors (RIG-1 and MDA5) to induce antiviral genes. In the present study the MAVS gene of Lates calcarifer (LcMAVS) was cloned and characterized. The complete cDNA sequence of LcMAVS was 3160 bp and encodes a poly peptide of 577 amino acids. Structural analysis of LcMAVS revealed an N-terminal CARD-like domain, central proline-rich domain and a C-terminal transmembrane domain. Phylogenetic analysis indicated that LcMAVS exhibited the closest relationship to P. olivaceous MAVS. LcMAVS was ubiquitously expressed in all tested tissues of healthy fish viz., brain, gill, heart, liver, spleen, kidney and intestine, with highest transcript level in spleen. The mRNA transcript level of LcMAVS in different developmental stages showed constitutive expression in all the stages tested suggesting the maternal transfer of the gene. Significant up regulation in MAVS expression was observed post nervous necrosis virus (NNV) challenge in vivo in all the selected tissues. Further, time course analysis showed that LcMAVS transcripts significantly increased in the brain and spleen tissues after NNV infection. These findings provide useful information for further elucidating the function of LcMAVS in antiviral innate immune response against NNV in Asian seabass.}, }
@article {pmid29099633, year = {2017}, author = {Kotarska, K and Doniec, A and Bednarska, M and Polański, Z and Styrna, J}, title = {Aging deteriorates quality of sperm produced by male mice with partial Yq deletion.}, journal = {Systems biology in reproductive medicine}, volume = {63}, number = {6}, pages = {360-363}, doi = {10.1080/19396368.2017.1391888}, pmid = {29099633}, issn = {1939-6376}, mesh = {Aging/*physiology ; Animals ; Azoospermia/genetics ; *Chromosome Deletion ; Fertilization ; Infertility, Male/genetics ; Male ; Mice ; Mice, Congenic/genetics ; Mitochondria/physiology ; Sperm Motility/genetics ; Spermatogenesis/genetics ; Spermatozoa/*physiology/ultrastructure ; Y Chromosome/*genetics ; }, abstract = {The aim of the study was to assess the cumulative effects of aging and Y-chromosome long arm deletion on sperm quality parameters. Motility, mitochondrial activity, and head morphology were evaluated for sperm of 3- and 12-month-old males from B10.BR-Ydel and B10.BR congenic mouse strains. The study revealed that quality and fertilizing potential of sperm produced by younger and older B10.BR males persist on similar levels, but worsen significantly with age of B10.BR-Ydel males. The findings imply that partial Yq deletions might be more harmful for spermiogenesis in advancing age and may be applicable to other species including humans.<br><br>ABBREVIATIONS: AZF: azoospermia factor; MSYq: male-specific region of the Y-chromosome long arm.}, }
@article {pmid29080362, year = {2018}, author = {Fernandez-Martell, A and Johari, YB and James, DC}, title = {Metabolic phenotyping of CHO cells varying in cellular biomass accumulation and maintenance during fed-batch culture.}, journal = {Biotechnology and bioengineering}, volume = {115}, number = {3}, pages = {645-660}, doi = {10.1002/bit.26485}, pmid = {29080362}, issn = {1097-0290}, abstract = {CHO cell lines capable of high-level recombinant protein product biosynthesis during fed-batch culture are still generally obtained by intensive empirical screening of transfected cells rather than knowledge-guided cellular engineering. In this study, we investigate how CHO cell lines create and maintain cellular biosynthetic capacity during fed-batch culture to achieve the optimal combination of rapid exponential proliferation and extended maintenance of high cell biomass concentration. We perform a comparative meta-analysis of mitochondrial and glycolytic functions of 22 discrete parental CHO cell lineages varying in fed-batch culture performance to test the hypotheses that (i) &quot;biomass-intensive&quot; CHO cells exhibit conserved differences in metabolic programming and (ii) it is possible to isolate parental CHO cell lines with a biomass-intensive phenotype to support fed-batch bioproduction processes. We show that for most parental CHO cell lines, rapid proliferation and high late-stage culture performance are mutually exclusive objectives. However, quantitative dissection of mitochondrial and glycolytic functions revealed that a small proportion of clones utilize a conserved metabolic program that significantly enhances cellular glycolytic and mitochondrial oxidative capacity at the onset of late-stage culture. We reveal the central importance of dynamic metabolic re-programming to activate oxidative mitochondrial function as a necessary mechanism to support CHO cell biosynthetic performance during culture.}, }
@article {pmid29079378, year = {2018}, author = {Yoshizawa, K and Johnson, KP and Sweet, AD and Yao, I and Ferreira, RL and Cameron, SL}, title = {Mitochondrial phylogenomics and genome rearrangements in the barklice (Insecta: Psocodea).}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {118-127}, doi = {10.1016/j.ympev.2017.10.014}, pmid = {29079378}, issn = {1095-9513}, mesh = {Animals ; Evolution, Molecular ; *Gene Order ; *Genome, Mitochondrial ; Insecta/*classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial genome arrangement in the insect order Psocodea (booklice, barklice, and parasitic lice) is extremely variable. Genome organization ranges from the rearrangement of a few tRNAs and protein coding genes, through extensive tRNA and protein coding gene rearrangements, to subdivision into multiple mini-chromosomes. Evolution of the extremely modified mitochondrial genome in parasitic lice (Phthiraptera) has been the subject of several studies, but limited information is available regarding the mitochondrial genome organization of the more plesiomorphic, free-living Psocodea (formerly known as the &quot;Psocoptera&quot;). In particular, the ancestral state of the psocodean mitochondrial genome arrangement and the evolutionary pathway to the rearranged conditions are still unknown. In this study, we addressed mitochondrial evolutionary questions within the Psocodea by using mitochondrial genome sequences obtained from a wide range of Psocoptera, covering all three suborders. We identified seven types of mitochondrial genome arrangements in Psocoptera, including the first example in Psocodea of retention of the ancestral pancrustacean condition in Prionoglaris (Prionoglarididae). Two methods (condition-based parsimony reconstruction and common-interval genome distances) were applied to estimate the ancestral mitochondrial arrangement in Psocodea, and both provided concordant results. Specifically, the common ancestor of Psocodea retained the ancestral pancrustacean condition, and most of the gene arrangement types have originated independently from this ancestral condition. We also utilized the genomic data for phylogenetic estimation. The tree estimated from the mitochondrial genomic data was well resolved, strongly supported, and in agreement with previously estimated phylogenies. It also provided the first robust support for the family Prionoglarididae, as its monophyly was uncertain in previous morphological and molecular studies.}, }
@article {pmid29075935, year = {2017}, author = {Glasgow, RIC and Thompson, K and Barbosa, IA and He, L and Alston, CL and Deshpande, C and Simpson, MA and Morris, AAM and Neu, A and Löbel, U and Hall, J and Prokisch, H and Haack, TB and Hempel, M and McFarland, R and Taylor, RW}, title = {Novel GFM2 variants associated with early-onset neurological presentations of mitochondrial disease and impaired expression of OXPHOS subunits.}, journal = {Neurogenetics}, volume = {18}, number = {4}, pages = {227-235}, doi = {10.1007/s10048-017-0526-4}, pmid = {29075935}, issn = {1364-6753}, support = {FKZ 01ZX1405C//German Federal Ministry of Education and Research (BMBF)/ ; 01GM1603, 01GM1207//German Bundesministerium für Bildung und Forschung (BMBF) and Horizon2020/ ; 203105/Z/16/Z//Wellcome Centre for Mitochondrial Research/ ; 633974//EU Horizon2020 Collaborative Research Project SOUND/ ; G0800674//Mitochondrial Disease Patient Cohort (UK)/ ; NIHR-HCS-D12-03-04//NIHR/CSO Healthcare Science Research Fellowship/ ; NIHR-HCS-D12-03-04//Department of Health/United Kingdom ; }, mesh = {Child ; Exome/genetics ; Female ; Homozygote ; Humans ; Male ; Mitochondria/*genetics/metabolism ; Mitochondrial Diseases/*genetics ; Mitochondrial Proteins/genetics/*metabolism ; Mutation/genetics ; Pedigree ; Peptide Elongation Factor G/*genetics ; Phenotype ; }, abstract = {Mitochondrial diseases are characterised by clinical, molecular and functional heterogeneity, reflecting their bi-genomic control. The nuclear gene GFM2 encodes mtEFG2, a protein with an essential role during the termination stage of mitochondrial translation. We present here two unrelated patients harbouring different and previously unreported compound heterozygous (c.569G>A, p.(Arg190Gln); c.636delA, p.(Glu213Argfs*3)) and homozygous (c.275A>C, p.(Tyr92Ser)) recessive variants in GFM2 identified by whole exome sequencing (WES) together with histochemical and biochemical findings to support the diagnoses of pathological GFM2 variants in each case. Both patients presented similarly in early childhood with global developmental delay, raised CSF lactate and abnormalities on cranial MRI. Sanger sequencing of familial samples confirmed the segregation of bi-allelic GFM2 variants with disease, while investigations into steady-state mitochondrial protein levels revealed respiratory chain subunit defects and loss of mtEFG2 protein in muscle. These data demonstrate the effects of defective mtEFG2 function, caused by previously unreported variants, confirming pathogenicity and expanding the clinical phenotypes associated with GFM2 variants.}, }
@article {pmid29074460, year = {2018}, author = {Smith, CH and Johnson, NA and Pfeiffer, JM and Gangloff, MM}, title = {Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus).}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {50-62}, doi = {10.1016/j.ympev.2017.10.018}, pmid = {29074460}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Bivalvia/*anatomy &amp; histology/*genetics ; Florida ; *Fresh Water ; *Genetic Speciation ; Geography ; Haplotypes/genetics ; Louisiana ; Mitochondria/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent 'Strophitus' connasaugaensis and 'Strophitus' subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.}, }
@article {pmid29073898, year = {2017}, author = {Radzvilavicius, AL and Lane, N and Pomiankowski, A}, title = {Sexual conflict explains the extraordinary diversity of mechanisms regulating mitochondrial inheritance.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {94}, doi = {10.1186/s12915-017-0437-8}, pmid = {29073898}, issn = {1741-7007}, mesh = {Animals ; *Evolution, Molecular ; Female ; *Genes, Mitochondrial ; *Inheritance Patterns ; Male ; Spermatogenesis ; }, abstract = {BACKGROUND: Mitochondria are predominantly inherited from the maternal gamete, even in unicellular organisms. Yet an extraordinary array of mechanisms enforce uniparental inheritance, which implies shifting selection pressures and multiple origins.<br><br>RESULTS: We consider how this high turnover in mechanisms controlling uniparental inheritance arises using a novel evolutionary model in which control of mitochondrial transmission occurs either during spermatogenesis (by paternal nuclear genes) or at/after fertilization (by maternal nuclear genes). The model treats paternal leakage as an evolvable trait. Our evolutionary analysis shows that maternal control consistently favours strict uniparental inheritance with complete exclusion of sperm mitochondria, whereas some degree of paternal leakage of mitochondria is an expected outcome under paternal control. This difference arises because mito-nuclear linkage builds up with maternal control, allowing the greater variance created by asymmetric inheritance to boost the efficiency of purifying selection and bring benefits in the long term. In contrast, under paternal control, mito-nuclear linkage tends to be much weaker, giving greater advantage to the mixing of cytotypes, which improves mean fitness in the short term, even though it imposes a fitness cost to both mating types in the long term.<br><br>CONCLUSIONS: Sexual conflict is an inevitable outcome when there is competition between maternal and paternal control of mitochondrial inheritance. If evolution has led to complete uniparental inheritance through maternal control, it creates selective pressure on the paternal nucleus in favour of subversion through paternal leakage, and vice versa. This selective divergence provides a reason for the repeated evolution of novel mechanisms that regulate the transmission of paternal mitochondria, both in the fertilized egg and spermatogenesis. Our analysis suggests that the widespread occurrence of paternal leakage and prevalence of heteroplasmy are natural outcomes of this sexual conflict.}, }
@article {pmid29070589, year = {2017}, author = {Cantarero, A and Alonso-Alvarez, C}, title = {Mitochondria-targeted molecules determine the redness of the zebra finch bill.}, journal = {Biology letters}, volume = {13}, number = {10}, pages = {}, doi = {10.1098/rsbl.2017.0455}, pmid = {29070589}, issn = {1744-957X}, mesh = {Animals ; Beak/*physiology ; Carotenoids/*metabolism ; Finches/*physiology ; Male ; Mitochondria/*metabolism ; Onium Compounds/metabolism ; Organophosphorus Compounds/metabolism ; *Pigmentation ; Ubiquinone/analogs &amp; derivatives/metabolism ; }, abstract = {The evolution and production mechanisms of red carotenoid-based ornaments in animals are poorly understood. Recently, it has been suggested that enzymes transforming yellow carotenoids to red pigments (ketolases) in animal cells may be positioned in the inner mitochondrial membrane (IMM) intimately linked to the electron transport chain. These enzymes may mostly synthesize coenzyme Q10 (coQ10), a key redox-cycler antioxidant molecularly similar to yellow carotenoids. It has been hypothesized that this shared pathway favours the evolution of red traits as sexually selected individual quality indices by revealing a well-adjusted oxidative metabolism. We administered mitochondria-targeted molecules to male zebra finches (Taeniopygia guttata) measuring their bill redness, a trait produced by transforming yellow carotenoids. One molecule included coQ10 (mitoquinone mesylate, MitoQ) and the other one (decyl-triphenylphosphonium; dTPP) has the same structure without the coQ10 aromatic ring. At the highest dose, the bill colour of MitoQ and dTPP birds strongly differed: MitoQ birds' bills were redder and dTPP birds showed paler bills even compared to birds injected with saline only. These results suggest that ketolases are indeed placed at the IMM and that coQ10 antioxidant properties may improve their efficiency. The implications for evolutionary theories of sexual signalling are discussed.}, }
@article {pmid29068466, year = {2017}, author = {Martin, WF}, title = {Too Much Eukaryote LGT.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700115}, pmid = {29068466}, issn = {1521-1878}, mesh = {Animals ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Mitochondria/genetics ; Phylogeny ; Plants/classification/genetics ; Plastids/genetics ; Prokaryotic Cells/cytology/metabolism ; Symbiosis/*genetics ; }, abstract = {The realization that prokaryotes naturally and frequently disperse genes across steep taxonomic boundaries via lateral gene transfer (LGT) gave wings to the idea that eukaryotes might do the same. Eukaryotes do acquire genes from mitochondria and plastids and they do transfer genes during the process of secondary endosymbiosis, the spread of plastids via eukaryotic algal endosymbionts. From those observations it, however, does not follow that eukaryotes transfer genes either in the same ways as prokaryotes do, or to a quantitatively similar degree. An important illustration of the difference is that eukaryotes do not exhibit pangenomes, though prokaryotes do. Eukaryotes reveal no detectable cumulative effects of LGT, though prokaryotes do. A critical analysis suggests that something is deeply amiss with eukaryote LGT theories.}, }
@article {pmid29064673, year = {2018}, author = {Li, S and Shen, G and Li, W}, title = {Intramembrane Thiol Oxidoreductases: Evolutionary Convergence and Structural Controversy.}, journal = {Biochemistry}, volume = {57}, number = {3}, pages = {258-266}, doi = {10.1021/acs.biochem.7b00876}, pmid = {29064673}, issn = {1520-4995}, support = {R01 HL121718/HL/NHLBI NIH HHS/United States ; R21 EY028705/EY/NEI NIH HHS/United States ; }, mesh = {Catalysis ; Conserved Sequence ; Disulfides/chemistry ; *Evolution, Molecular ; Humans ; Isomerism ; Oxidoreductases Acting on Sulfur Group Donors/*chemistry ; Protein Folding ; Protein Structure, Secondary ; Sulfhydryl Compounds/*chemistry ; Vitamin K Epoxide Reductases/*chemistry ; }, abstract = {During oxidative protein folding, disulfide bond formation is catalyzed by thiol oxidoreductases. Through dedicated relay pathways, the disulfide is generated in donor enzymes, passed to carrier enzymes, and subsequently delivered to target proteins. The eukaryotic disulfide donors are flavoenzymes, Ero1 in the endoplasmic reticulum and Erv1 in mitochondria. In prokaryotes, disulfide generation is coupled to quinone reduction, catalyzed by intramembrane donor enzymes, DsbB and VKOR. To catalyze de novo disulfide formation, these different disulfide donors show striking structural convergence at several levels. They share a four-helix bundle core structure at their active site, which contains a CXXC motif at a helical end. They have also evolved a flexible loop with shuttle cysteines to transfer electrons to the active site and relay the disulfide bond to the carrier enzymes. Studies of the prokaryotic VKOR, however, have stirred debate about whether the human homologue adopts the same topology with four transmembrane helices and uses the same electron-transfer mechanism. The controversies have recently been resolved by investigating the human VKOR structure and catalytic process in living cells with a mass spectrometry-based approach. Structural convergence between human VKOR and the disulfide donors is found to underlie cofactor reduction, disulfide generation, and electron transfer.}, }
@article {pmid29061908, year = {2017}, author = {Yang, Y and Zhu, G and Li, R and Yan, S and Fu, D and Zhu, B and Tian, H and Luo, Y and Zhu, H}, title = {The RNA Editing Factor SlORRM4 Is Required for Normal Fruit Ripening in Tomato.}, journal = {Plant physiology}, volume = {175}, number = {4}, pages = {1690-1702}, doi = {10.1104/pp.17.01265}, pmid = {29061908}, issn = {1532-2548}, mesh = {CRISPR-Cas Systems ; Fruit/*physiology ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/*physiology ; Gene Silencing ; Lycopersicon esculentum/genetics/*physiology ; Mitochondria ; Mutation ; Phylogeny ; Plant Development/genetics/physiology ; Plant Proteins/genetics/*metabolism ; RNA Editing/genetics/*physiology ; }, abstract = {RNA editing plays a key posttranscriptional role in gene expression. Existing studies on cytidine-to-uridine RNA editing in plants have focused on maize (Zea mays), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana). However, the importance and regulation of RNA editing in several critical agronomic processes are not well understood, a notable example of which is fruit ripening. Here, we analyzed the expression profile of 33 RNA editing factors and identified 11 putative tomato (Solanum lycopersicum) fruit ripening-related factors. A rapid virus-induced gene silencing assay indicated that the organelle RNA recognition motif-containing protein SlORRM4 affected tomato fruit ripening. Knocking out SlORRM4 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy delayed tomato fruit ripening by lowering respiratory rate and ethylene production. Additionally, the expression of numerous genes associated with fruit ripening and mitochondrial functions changed significantly when SlORRM4 was knocked out. Moreover, the loss of SlORRM4 function significantly reduced RNA editing of many mitochondrial transcripts, leading to low-level expression of some core subunits that are critical for mitochondrial complex assembly (i.e. Nad3, Cytc1, and COX II). Taken together, these results indicate that SlORRM4 is involved in RNA editing of transcripts in ripening fruit that influence mitochondrial function and key aspects of fruit ripening.}, }
@article {pmid29056456, year = {2017}, author = {Wang, P and Khoshravesh, R and Karki, S and Tapia, R and Balahadia, CP and Bandyopadhyay, A and Quick, WP and Furbank, R and Sage, TL and Langdale, JA}, title = {Re-creation of a Key Step in the Evolutionary Switch from C3 to C4 Leaf Anatomy.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {3278-3287.e6}, doi = {10.1016/j.cub.2017.09.040}, pmid = {29056456}, issn = {1879-0445}, mesh = {Biological Evolution ; Chloroplasts/*genetics/physiology ; Mitochondria/genetics ; Oryza/*genetics ; Photosynthesis/*genetics ; Plant Leaves/anatomy &amp; histology/genetics/*metabolism ; Plant Proteins/*genetics ; Transcription Factors/*genetics ; Zea mays/*genetics ; }, abstract = {The C4 photosynthetic pathway accounts for ∼25% of primary productivity on the planet despite being used by only 3% of species. Because C4 plants are higher yielding than C3 plants, efforts are underway to introduce the C4 pathway into the C3 crop rice. This is an ambitious endeavor; however, the C4 pathway evolved from C3 on multiple independent occasions over the last 30 million years, and steps along the trajectory are evident in extant species. One approach toward engineering C4 rice is to recapitulate this trajectory, one of the first steps of which was a change in leaf anatomy. The transition from C3 to so-called &quot;proto-Kranz&quot; anatomy requires an increase in organelle volume in sheath cells surrounding leaf veins. Here we induced chloroplast and mitochondrial development in rice vascular sheath cells through constitutive expression of maize GOLDEN2-LIKE genes. Increased organelle volume was accompanied by the accumulation of photosynthetic enzymes and by increased intercellular connections. This suite of traits reflects that seen in &quot;proto-Kranz&quot; species, and, as such, a key step toward engineering C4 rice has been achieved.}, }
@article {pmid29048531, year = {2017}, author = {Wu, B and Macielog, AI and Hao, W}, title = {Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2658-2667}, doi = {10.1093/gbe/evx211}, pmid = {29048531}, issn = {1759-6653}, mesh = {Ascomycota/*genetics ; DNA Transposable Elements ; DNA, Intergenic/genetics ; *Evolution, Molecular ; Genome, Fungal ; *Introns ; Spliceosomes/*genetics ; }, abstract = {Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species. Within the genome, spliceosomal introns can proliferate in unrelated genes and intergenic regions. Among conspecific strains, spliceosomal introns undergo rapid turnover (gains and losses) and frequent sequence exchange between geographically distinct strains. Furthermore, spliceosomal introns could undergo introgression between distinct species, which can further promote intron invasion and proliferation. The dynamic invasion and proliferation processes of spliceosomal introns resemble the life cycles of mobile selfish (group I/II) introns, and these intron movements, at least in part, account for the dramatic processes of intron gain and intron loss during eukaryotic evolution.}, }
@article {pmid29048527, year = {2017}, author = {Sayadi, A and Immonen, E and Tellgren-Roth, C and Arnqvist, G}, title = {The Evolution of Dark Matter in the Mitogenome of Seed Beetles.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2697-2706}, doi = {10.1093/gbe/evx205}, pmid = {29048527}, issn = {1759-6653}, mesh = {Animals ; Coleoptera/classification/*genetics ; DNA, Intergenic/genetics ; *Evolution, Molecular ; *Genome, Insect ; *Genome, Mitochondrial ; Phylogeny ; Selection, Genetic ; Tandem Repeat Sequences ; *Transcriptome ; }, abstract = {Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114-10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution. The LIGSs have been retained for at least some 45 my but must have undergone repeated reductions and expansions, despite strong purifying selection on protein coding mtDNA genes. The LIGSs are located in two intergenic sites where a few recent studies of insects have also reported shorter LIGSs (>200 bp). These sites may represent spaces that tolerate neutral repeat array expansions or, alternatively, the LIGSs may function to allow a more economic translational machinery. Mitochondrial respiration in adult seed beetles is based almost exclusively on fatty acids, which reduces the need for building complex I of the oxidative phosphorylation pathway (NADH dehydrogenase). One possibility is thus that the LIGSs may allow depressed transcription of NAD genes. RNA sequencing showed that LIGSs are partly transcribed and transcriptional profiling suggested that all seven mtDNA NAD genes indeed show low levels of transcription and co-regulation of transcription across sexes and tissues.}, }
@article {pmid29036556, year = {2018}, author = {Kang, C and Badr, MA and Kyrychenko, V and Eskelinen, EL and Shirokova, N}, title = {Deficit in PINK1/PARKIN-mediated mitochondrial autophagy at late stages of dystrophic cardiomyopathy.}, journal = {Cardiovascular research}, volume = {114}, number = {1}, pages = {90-102}, doi = {10.1093/cvr/cvx201}, pmid = {29036556}, issn = {1755-3245}, support = {R01 HL093342/HL/NHLBI NIH HHS/United States ; }, abstract = {Aims: Duchenne muscular dystrophy (DMD) is an inherited devastating muscle disease with severe and often lethal cardiac complications. Emerging evidence suggests that the evolution of the pathology in DMD is accompanied by the accumulation of mitochondria with defective structure and function. Here, we investigate whether defects in the housekeeping autophagic pathway contribute to mitochondrial and metabolic dysfunctions in dystrophic cardiomyopathy.<br><br>Methods and results: We employed various biochemical and imaging techniques to assess mitochondrial structure and function as well as to evaluate autophagy, and specific mitochondrial autophagy (mitophagy), in hearts of mdx mice, an animal model of DMD. Our results indicate substantial structural damage of mitochondria and a significant decrease in ATP production in hearts of mdx animals, which developed cardiomyopathy. In these hearts, we also detected enhanced autophagy but paradoxically, mitophagy appeared to be suppressed. In addition, we found decreased levels of several proteins involved in the PINK1/PARKIN mitophagy pathway as well as an insignificant amount of PARKIN protein phosphorylation at the S65 residue upon induction of mitophagy.<br><br>Conclusions: Our results suggest faulty mitophagy in dystrophic hearts due to defects in the PINK1/PARKIN pathway.}, }
@article {pmid29032499, year = {2017}, author = {Hu, L and Yang, Y and Zhao, Y and Niu, D and Yang, R and Wang, R and Lu, Z and Li, X}, title = {DNA barcoding for molecular identification of Demodex based on mitochondrial genes.}, journal = {Parasitology research}, volume = {116}, number = {12}, pages = {3285-3290}, doi = {10.1007/s00436-017-5641-5}, pmid = {29032499}, issn = {1432-1955}, support = {81471972//National Natural Science Foundation of China/ ; 81271856//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Dog Diseases ; Dogs ; *Genes, Mitochondrial ; Mite Infestations/parasitology/veterinary ; Mites/*classification ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {There has been no widely accepted DNA barcode for species identification of Demodex. In this study, we attempted to solve this issue. First, mitochondrial cox1-5' and 12S gene fragments of Demodex folloculorum, D. brevis, D. canis, and D. caprae were amplified, cloned, and sequenced for the first time; intra/interspecific divergences were computed and phylogenetic trees were reconstructed. Then, divergence frequency distribution plots of those two gene fragments were drawn together with mtDNA cox1-middle region and 16S obtained in previous studies. Finally, their identification efficiency was evaluated by comparing barcoding gap. Results indicated that 12S had the higher identification efficiency. Specifically, for cox1-5' region of the four Demodex species, intraspecific divergences were less than 2.0%, and interspecific divergences were 21.1-31.0%; for 12S, intraspecific divergences were less than 1.4%, and interspecific divergences were 20.8-26.9%. The phylogenetic trees demonstrated that the four Demodex species clustered separately, and divergence frequency distribution plot showed that the largest intraspecific divergence of 12S (1.4%) was less than cox1-5' region (2.0%), cox1-middle region (3.1%), and 16S (2.8%). The barcoding gap of 12S was 19.4%, larger than cox1-5' region (19.1%), cox1-middle region (11.3%), and 16S (13.0%); the interspecific divergence span of 12S was 6.2%, smaller than cox1-5' region (10.0%), cox1-middle region (14.1%), and 16S (11.4%). Moreover, 12S has a moderate length (517 bp) for sequencing at once. Therefore, we proposed mtDNA 12S was more suitable than cox1 and 16S to be a DNA barcode for classification and identification of Demodex at lower category level.}, }
@article {pmid29024751, year = {2018}, author = {Mokodongan, DF and Montenegro, J and Mochida, K and Fujimoto, S and Ishikawa, A and Kakioka, R and Yong, L and Mulis,  and Hadiaty, RK and Mandagi, IF and Masengi, KWA and Wachi, N and Hashiguchi, Y and Kitano, J and Yamahira, K}, title = {Phylogenomics reveals habitat-associated body shape divergence in Oryzias woworae species group (Teleostei: Adrianichthyidae).}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {194-203}, doi = {10.1016/j.ympev.2017.10.005}, pmid = {29024751}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Female ; *Genomics ; Geography ; Indonesia ; Male ; Mitochondria/genetics ; Oryzias/*anatomy &amp; histology/*genetics ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; }, abstract = {The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations. Second, their phylogenetic relationships did not support the presence of three species; phylogenies using mitochondrial DNA and genomic data obtained from RNA-Seq revealed that the eight populations could not be sorted into three different clades representing three described species. Third, phylogenetic corrections of body shape variations and ancestral state reconstruction of body shapes demonstrated that body shape divergence between riverine and lacustrine populations persisted even if the phylogenies were considered and that body shape evolved rapidly irrespective of phylogeny. Sexual dimorphism in body shape was also evident, but the degree of dimorphism did not significantly differ between riverine and lacustrine populations after phylogenetic corrections, suggesting that sexual selection may not substantially contribute to geographical variations in body shape. Overall, these results indicate that the deep-elongated body shape divergence of the O. woworae species group evolved locally in response to habitat environments, such as water currents, and that a thorough taxonomic reexamination of the O. woworae species group may be necessary.}, }
@article {pmid29021915, year = {2017}, author = {Klein, KA and Warren, AK and Baumal, CR and Hedges, TR}, title = {Optical coherence tomography findings in methanol toxicity.}, journal = {International journal of retina and vitreous}, volume = {3}, number = {}, pages = {36}, doi = {10.1186/s40942-017-0089-4}, pmid = {29021915}, issn = {2056-9920}, abstract = {BACKGROUND: Methanol toxicity poses a significant public health problem in developing countries, and in Southeast Asia, where the most common source of poisoning is via adulterated liquor in local drinks. Methanol toxicity can have devastating visual consequences and retinal specialists should be aware of the features of this toxic optic neuropathy. The authors report a case of severe systemic methanol toxicity and relatively mild optic neuropathy demonstrating unique retinal changes on optical coherence tomography (OCT).<br><br>CASE PRESENTATION: A previously healthy student developed ataxia, difficulty breathing and loss of consciousness hours after drinking homemade alcohol while traveling in Indonesia. She was found to have a serum pH of 6.79 and elevated methanol levels. She was treated with intravenous ethanol, methylprednisolone and sodium bicarbonate. When she awoke she had bilateral central scotomas. At presentation, she had central depression on visual field testing. OCT of the retinal nerve fiber layer (RNFL) was normal but ganglion cell layer analysis (GCL) showed highly selective loss of the nasal fibers in both eyes. Further, OCT of the macula demonstrated inner nuclear layer (INL) microcysts in the corresponding area of selective GCL loss in both eyes.<br><br>CONCLUSIONS: The selective involvement of the papillomacular bundle fibers is common in toxic optic neuropathies and represents damage to the small caliber axons rich in mitochondria. Despite severe systemic toxicity, the relative sparing of the optic nerve in this case enabled characterization of the evolution of methanol toxicity with segmental GCL involvement and preservation of the RNFL, corresponding to the papillomacular bundle. This is the first reported case of INL microcysts in methanol optic neuropathy and supports that they are a non-specific finding, and may represent preferential damage to the papillomacular bundle.}, }
@article {pmid28993269, year = {2017}, author = {Bombaça, ACS and Dias, FA and Ennes-Vidal, V and Garcia-Gomes, ADS and Sorgine, MHF and d'Avila-Levy, CM and Menna-Barreto, RFS}, title = {Hydrogen peroxide resistance in Strigomonas culicis: Effects on mitochondrial functionality and Aedes aegypti interaction.}, journal = {Free radical biology &amp; medicine}, volume = {113}, number = {}, pages = {255-266}, doi = {10.1016/j.freeradbiomed.2017.10.006}, pmid = {28993269}, issn = {1873-4596}, mesh = {Adenosine Triphosphate/biosynthesis ; Aedes/*parasitology ; Animals ; Antioxidants/metabolism ; Betaproteobacteria/metabolism ; Biological Evolution ; Drug Resistance ; Electron Transport Chain Complex Proteins/*genetics/metabolism ; Energy Metabolism/*genetics ; Gastrointestinal Tract/parasitology ; Gene Expression Regulation ; *Host-Parasite Interactions ; Hydrogen Peroxide/*pharmacology ; Mitochondria/drug effects/genetics/metabolism ; Oxidation-Reduction ; Oxidative Stress ; Protozoan Proteins/*genetics/metabolism ; Signal Transduction ; Symbiosis/physiology ; Trypanosomatina/drug effects/genetics/*metabolism/microbiology ; }, abstract = {Reactive oxygen species (ROS) are toxic molecules involved in several biological processes such as cellular signaling, proliferation, differentiation and cell death. Adaptations to oxidative environments are crucial for the success of the colonization of insects by protozoa. Strigomonas culicis is a monoxenic trypanosomatid found in the midgut of mosquitoes and presenting a life cycle restricted to the epimastigote form. Among S. culicis peculiarities, there is an endosymbiotic bacterium in the cytoplasm, which completes essential biosynthetic routes of the host cell and may represent an intermediary evolutive step in organelle origin, thus constituting an interesting model for evolutive researches. In this work, we induced ROS resistance in wild type S. culicis epimastigotes by the incubation with increasing concentrations of hydrogen peroxide (H2O2), and compared the oxidative and energetic metabolisms among wild type, wild type-H2O2 resistant and aposymbiotic strains. Resistant protozoa were less sensitive to the oxidative challenge and more dependent on oxidative phosphorylation, which was demonstrated by higher oxygen consumption and mitochondrial membrane potential, increased activity of complexes II-III and IV, increased complex II gene expression and higher ATP production. Furthermore, the wild type-H2O2 resistant strain produced reduced ROS levels and showed lower lipid peroxidation, as well as an increase in gene expression of antioxidant enzymes and thiol-dependent peroxidase activity. On the other hand, the aposymbiotic strain showed impaired mitochondrial function, higher H2O2 production and deficient antioxidant response. The induction of H2O2 resistance also led to a remarkable increase in Aedes aegypti midgut binding in vitro and colonization in vivo, indicating that both the pro-oxidant environment in the mosquito gut and the oxidative stress susceptibility regulate S. culicis population in invertebrates.}, }
@article {pmid28988150, year = {2017}, author = {Semenova, GA and Fomina, IR and Kosobryukhov, AA and Lyubimov, VY and Nadezhkina, ES and Balakhnina, TI}, title = {Mesophyll cell ultrastructure of wheat leaves etiolated by lead and selenium.}, journal = {Journal of plant physiology}, volume = {219}, number = {}, pages = {37-44}, doi = {10.1016/j.jplph.2017.09.008}, pmid = {28988150}, issn = {1618-1328}, mesh = {Chlorophyll/*metabolism ; *Etiolation ; Hydrogen Peroxide/*metabolism ; Lead/*metabolism ; Mesophyll Cells/drug effects/ultrastructure ; Oxygen/*metabolism ; Plant Leaves/drug effects/growth &amp; development/metabolism/ultrastructure ; Selenium/*metabolism ; Stress, Physiological ; Triticum/drug effects/*growth &amp; development/metabolism/ultrastructure ; }, abstract = {The ultrastructure of mesophyll cells was studied in leaves of the Triticum aestivum L. cv. &quot;Trizo&quot; seedlings after two weeks of growth on soil contaminated by Pb and/or Se. The soil treatments: control; (Pb1) 50mgkg-1; (Pb2) 100mgkg-1; (Se1) 0.4mgkg-1; (Se2) 0.8mgkg-1; (Pb1+Se1); (Pb1+Se2); (P2+Se1); and (Pb2+Se2) were used. Light and other conditions were optimal for plant growth. The (Se1)-plants showed enhanced growth and biomass production; (Pb1+Se1)-plants did not lag behind the controls, though O2 evolution decreased; chlorophyll content did not differ statistically in these treatments. Other treatments led to statistically significant growth suppression, chlorophyll content reduction, inhibition of photosynthesis, stress development tested by H2O2 and leaf etiolation at the end of 14-days experiment. The tops of etiolated leaves remained green, while the main leaf parts were visually white. Plastids in mesophyll cells of etiolated parts of leaves were mainly represented by etioplasts and an insignificant amount of degraded chloroplasts. Other cellular organelles remained intact in most mesophyll cells of the plants, except (Pb2+Se2)-plants. Ruptured tonoplast and etioplast envelope, swelled cytoplasm and mitochondria, and electron transparent matrix of gialoplasm were observed in the mesophyll cells at (Pb2+Se2)-treatment, that caused maximal inhibition of plant growth. The results indicate that Pb and Se effects on growth of wheat leaves are likely to target meristem in which the development of proplastids to chloroplasts under the light is determined by chlorophyll biosynthesis. Antagonistic effect of low concentration of Se and Pb in combination may retard etiolation process.}, }
@article {pmid28986237, year = {2018}, author = {Liu, Y and Song, F and Jiang, P and Wilson, JJ and Cai, W and Li, H}, title = {Compositional heterogeneity in true bug mitochondrial phylogenomics.}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {135-144}, doi = {10.1016/j.ympev.2017.09.025}, pmid = {28986237}, issn = {1095-9513}, mesh = {Animals ; Base Composition ; Base Sequence ; Bayes Theorem ; Genetic Variation ; *Genome, Mitochondrial ; Heteroptera/*genetics ; Likelihood Functions ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {Mitochondrial phylogenomics is often controversial, in particular for inferring deep relationships. The recent rapid increase of mitochondrial genome data provides opportunities for better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and mutation rates. Here, we gathered 76 mitochondrial genome sequences for Heteroptera representing all seven infraorders, including 17 newly sequenced mitochondrial genomes. We found strong heterogeneity in base composition and contrasting evolutionary rates among heteropteran mitochondrial genomes, which affected analyses with various datasets and partitioning schemes under site-homogeneous models and produced false groupings of unrelated taxa exhibiting similar base composition and accelerated evolutionary rates. Bayesian analyses using a site-heterogeneous mixture CAT+GTR model showed high congruence of topologies with the currently accepted phylogeny of Heteroptera. The results confirm the monophyly of the six infraorders within Heteroptera, except for Cimicomorpha which was recovered as two paraphyletic clades. The monophyly of Terheteroptera (Cimicomorpha and Pentatomomorpha) and Panheteroptera (Nepomorpha, Leptopodomorpha and Terheteroptera) was recovered demonstrating a significant improvement over previous studies using mitochondrial genome data. Our study shows the power of the site-heterogeneous mixture models for resolving phylogenetic relationships with Heteroptera and provides one more case showing that model adequacy is critical for accurate tree reconstruction in mitochondrial phylogenomics.}, }
@article {pmid28986236, year = {2018}, author = {Matenaar, D and Fingerle, M and Heym, E and Wirtz, S and Hochkirch, A}, title = {Phylogeography of the endemic grasshopper genus Betiscoides (Lentulidae) in the South African Cape Floristic Region.}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {318-329}, doi = {10.1016/j.ympev.2017.09.024}, pmid = {28986236}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Biological Evolution ; DNA/chemistry/isolation &amp; purification/metabolism ; Genetic Variation ; Grasshoppers/*classification/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Alignment ; Sequence Analysis, DNA ; South Africa ; }, abstract = {Vicariance and dispersal are two important processes shaping biodiversity patterns. The South African Cape Floristic Region (CFR) is known for its high biotic diversity and endemism. However, studies on the phylogeography of endemic invertebrates in this biodiversity hotspot are still scarce. Here, we present a phylogenetic study of the flightless grasshopper genus Betiscoides, which is endemic to the CFR and strongly associated with restio plants (Restionaceae). We hypothesized that the genus originated in the southwestern part of the CFR, that differentiation within the genus is mainly an effect of vicariance and that the three known species only represent a minor fraction of the real genetic diversity of the genus. We inferred the phylogeny based on sequences of three mitochondrial and two nuclear genes from 99 Betiscoides specimens collected across the CFR. Furthermore, we conducted a SDIVA analysis to detect distributions of ancestral nodes and the possible spatial origin of these lineages. Strong differentiation among genetic lineages was shown. The ancestor of this genus was most likely distributed in the southwestern CFR. Five major lineages were detected, three of which were ancestrally distributed in the southwestern CFR. The ancestors of the two other lineages were distributed in the northern and eastern margins of the CFR. A total of 24 divergent evolutionary lineages were found, reflecting the geographical isolation of restio-dominated fynbos habitats. Dispersal played a more prominent role than expected in differentiation of Betiscoides. While the five main lineages were separated during a first phase via dispersal, differentiation occurred later and on smaller spatial scale, predominantly driven by isolation in montane refugia (i.e. vicariance). Our study also suggests that flightless insect taxa likely show high levels of differentiation in biodiversity hotspots with their taxonomy often being incomplete.}, }
@article {pmid28985476, year = {2017}, author = {Court, DA and Khetoo, S and Shuvo, SR and Reitmeier, SD and Hausner, G}, title = {In silico analysis of coevolution among ERMES proteins, Pex11, and Lam6.}, journal = {Canadian journal of microbiology}, volume = {63}, number = {12}, pages = {984-997}, doi = {10.1139/cjm-2017-0460}, pmid = {28985476}, issn = {1480-3275}, mesh = {Antiporters/genetics ; *Computer Simulation ; *Evolution, Molecular ; Membrane Proteins/genetics ; Peroxins/genetics ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {In eukaryotic cells, communication and dynamic interactions among different organelles are important for maintaining cellular homeostasis. The endoplasmic reticulum (ER) mitochondria encounter structure (ERMES) complex establishes membrane contact sites between ER and mitochondria and is essential for phospholipid transport, protein import, and mitochondrial dynamics and inheritance. In this work, in silico analyses were used to probe the intramolecular interactions in ERMES proteins and the interactions that support the ERMES complex. Based on mutual information (MI), sites of intramolecular coevolution are predicted in the core proteins Mmm1, Mdm10, Mdm12, Mdm34, the peroxisomal protein Pex11, and cytoplasmic Lam6; these sites are linked to structural features of the proteins. Intermolecular coevolution is predicted among the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domains of Mmm1, Mdm12, and Mdm34. Segments of Pex11 and Lam6 also share MI with the SMP domains of Mmm1 and Mdm12 and with the N terminus of Mdm34, implicating Mdm34 as part of a hub for interactions between ERMES and other complexes. In contrast, evidence of limited intermolecular coevolution involving the outer membrane protein Mdm10 was detected only with Mmm1 and Pex11. The results support models for the organization of these interacting proteins and suggest roles for Pex11 and Lam6 in regulating complex formation.}, }
@article {pmid28985295, year = {2017}, author = {Eslamieh, M and Williford, A and Betrán, E}, title = {Few Nuclear-Encoded Mitochondrial Gene Duplicates Contribute to Male Germline-Specific Functions in Humans.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2782-2790}, doi = {10.1093/gbe/evx176}, pmid = {28985295}, issn = {1759-6653}, support = {R01 GM071813/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/*genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Gene Duplication/*genetics ; Gene Expression Profiling ; Gene Ontology ; Genes, Insect/genetics ; Genes, Mitochondrial/*genetics ; Genome, Human/*genetics ; Humans ; Male ; Mitochondria/genetics/metabolism/physiology ; Species Specificity ; Spermatogenesis/genetics ; Spermatozoa/metabolism/*physiology ; Testis/physiology ; }, abstract = {Most of the genes encoding proteins that function in the mitochondria are located in the nucleus and are called nuclear-encoded mitochondrial genes, or N-mt genes. In Drosophila melanogaster , about 23% of N-mt genes fall into gene families, and all duplicates with tissue-biased expression (76%) are testis biased. These genes are enriched for energy-related functions and tend to be older than other duplicated genes in the genome. These patterns reveal strong selection for the retention of new genes for male germline mitochondrial functions. The two main forces that are likely to drive changes in mitochondrial functions are maternal inheritance of mitochondria and male-male competition for fertilization. Both are common among animals, suggesting similar N-mt gene duplication patterns in different species. To test this, we analyzed N-mt genes in the human genome. We find that about 18% of human N-mt genes fall into gene families, but unlike in Drosophila , only 28% of the N-mt duplicates have tissue-biased expression and only 36% of these have testis-biased expression. In addition, human testis-biased duplicated genes are younger than other duplicated genes in the genome and have diverse functions. These contrasting patterns between species might reflect either differences in selective pressures for germline energy-related or other mitochondrial functions during spermatogenesis and fertilization, or differences in the response to similar pressures.}, }
@article {pmid28981721, year = {2017}, author = {Allio, R and Donega, S and Galtier, N and Nabholz, B}, title = {Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker.}, journal = {Molecular biology and evolution}, volume = {34}, number = {11}, pages = {2762-2772}, doi = {10.1093/molbev/msx197}, pmid = {28981721}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Biomarkers ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome/genetics ; Mitochondria/genetics ; Mutation ; *Mutation Rate ; Phylogeny ; Polymorphism, Genetic/genetics ; Population Density ; Selection, Genetic/genetics ; }, abstract = {It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear DNA (nuDNA) in animals. This has contributed to the popularity of mtDNA as a molecular marker in evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic data sets encompassing 4,676 species of animals, we demonstrate that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa. In nonvertebrates, such as insects and arachnids, the ratio of mtDNA over nuDNA mutation rate varies between 2 and 6, whereas it is above 20, on average, in vertebrates such as scaled reptiles and birds. Interestingly, this variation is sufficient to explain the previous report of a similar level of mitochondrial polymorphism, on average, between vertebrates and nonvertebrates, which was originally interpreted as reflecting the effect of pervasive positive selection. Our analysis rather indicates that the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection. Finally, we explore the variation in the absolute per-year mutation rate of both mtDNA and nuDNA using a reduced data set for which fossil calibration is available, and discuss the potential determinants of mutation rate variation across genomes and taxa. This study has important implications regarding DNA-based identification methods in predicting that mtDNA barcoding should be less reliable in nonvertebrates than in vertebrates.}, }
@article {pmid28979209, year = {2017}, author = {Gaudry, MJ and Campbell, KL}, title = {Evolution of UCP1 Transcriptional Regulatory Elements Across the Mammalian Phylogeny.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {670}, doi = {10.3389/fphys.2017.00670}, pmid = {28979209}, issn = {1664-042X}, abstract = {Uncoupling protein 1 (UCP1) permits non-shivering thermogenesis (NST) when highly expressed in brown adipose tissue (BAT) mitochondria. Exclusive to placental mammals, BAT has commonly been regarded to be advantageous for thermoregulation in hibernators, small-bodied species, and the neonates of larger species. While numerous regulatory control motifs associated with UCP1 transcription have been proposed for murid rodents, it remains unclear whether these are conserved across the eutherian mammal phylogeny and hence essential for UCP1 expression. To address this shortcoming, we conducted a broad comparative survey of putative UCP1 transcriptional regulatory elements in 139 mammals (135 eutherians). We find no evidence for presence of a UCP1 enhancer in monotremes and marsupials, supporting the hypothesis that this control region evolved in a stem eutherian ancestor. We additionally reveal that several putative promoter elements (e.g., CRE-4, CCAAT) identified in murid rodents are not conserved among BAT-expressing eutherians, and together with the putative regulatory region (PRR) and CpG island do not appear to be crucial for UCP1 expression. The specificity and importance of the upTRE, dnTRE, URE1, CRE-2, RARE-2, NBRE, BRE-1, and BRE-2 enhancer elements first described from rats and mice are moreover uncertain as these motifs differ substantially-but generally remain highly conserved-in other BAT-expressing eutherians. Other UCP1 enhancer motifs (CRE-3, PPRE, and RARE-3) as well as the TATA box are also highly conserved in nearly all eutherian lineages with an intact UCP1. While these transcriptional regulatory motifs are generally also maintained in species where this gene is pseudogenized, the loss or degeneration of key basal promoter (e.g., TATA box) and enhancer elements in other UCP1-lacking lineages make it unlikely that the enhancer region is pleiotropic (i.e., co-regulates additional genes). Importantly, differential losses of (or mutations within) putative regulatory elements among the eutherian lineages with an intact UCP1 suggests that the transcriptional control of gene expression is not highly conserved in this mammalian clade.}, }
@article {pmid28978045, year = {2017}, author = {Ozsvari, B and Fiorillo, M and Bonuccelli, G and Cappello, AR and Frattaruolo, L and Sotgia, F and Trowbridge, R and Foster, R and Lisanti, MP}, title = {Mitoriboscins: Mitochondrial-based therapeutics targeting cancer stem cells (CSCs), bacteria and pathogenic yeast.}, journal = {Oncotarget}, volume = {8}, number = {40}, pages = {67457-67472}, doi = {10.18632/oncotarget.19084}, pmid = {28978045}, issn = {1949-2553}, abstract = {The &quot;endo-symbiotic theory of mitochondrial evolution&quot; states that mitochondrial organelles evolved from engulfed aerobic bacteria, after millions of years of symbiosis and adaptation. Here, we have exploited this premise to design new antibiotics and novel anti-cancer therapies, using a convergent approach. First, virtual high-throughput screening (vHTS) and computational chemistry were used to identify novel compounds binding to the 3D structure of the mammalian mitochondrial ribosome. The resulting library of ∼880 compounds was then subjected to phenotypic drug screening on human cancer cells, to identify which compounds functionally induce ATP-depletion, which is characteristic of mitochondrial inhibition. Notably, the top ten &quot;hit&quot; compounds define four new classes of mitochondrial inhibitors. Next, we further validated that these novel mitochondrial inhibitors metabolically target mitochondrial respiration in cancer cells and effectively inhibit the propagation of cancer stem-like cells in vitro. Finally, we show that these mitochondrial inhibitors possess broad-spectrum antibiotic activity, preventing the growth of both gram-positive and gram-negative bacteria, as well as C. albicans - a pathogenic yeast. Remarkably, these novel antibiotics also were effective against methicillin-resistant Staphylococcus aureus (MRSA). Thus, this simple, yet systematic, approach to the discovery of mitochondrial ribosome inhibitors could provide a plethora of anti-microbials and anti-cancer therapies, to target drug-resistance that is characteristic of both i) tumor recurrence and ii) infectious disease. In summary, we have successfully used vHTS combined with phenotypic drug screening of human cancer cells to identify several new classes of broad-spectrum antibiotics that target both bacteria and pathogenic yeast. We propose the new term &quot;mitoriboscins&quot; to describe these novel mitochondrial-related antibiotics. Thus far, we have identified four different classes of mitoriboscins, such as: 1) mitoribocyclines, 2) mitoribomycins, 3) mitoribosporins and 4) mitoribofloxins. However, we broadly define mitoriboscins as any small molecule(s) or peptide(s) that bind to the mitoribosome (large or small subunits) and, as a consequence, inhibit mitochondrial function, i.e., mitoribosome inhibitors.}, }
@article {pmid28977708, year = {2017}, author = {Cariou, M and Duret, L and Charlat, S}, title = {The global impact of Wolbachia on mitochondrial diversity and evolution.}, journal = {Journal of evolutionary biology}, volume = {30}, number = {12}, pages = {2204-2210}, doi = {10.1111/jeb.13186}, pmid = {28977708}, issn = {1420-9101}, mesh = {Animals ; Arthropods/*genetics/microbiology ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation ; Male ; Phylogeny ; Wolbachia/*physiology ; }, abstract = {The spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. While documented in several host species, it is currently unclear if such a scenario is common enough to globally impact the diversity and evolution of mitochondria in Wolbachia-infected lineages. Here, we address this question using a mapping of Wolbachia acquisition/extinction events on a large mitochondrial DNA tree, including over 1000 species. Our analyses indicate that on a large phylogenetic scale, other sources of variation, such as mutation rates, tend to hide the effects of Wolbachia. However, paired comparisons between closely related infected and uninfected taxa reveal that Wolbachia is associated with a twofold reduction in silent mitochondrial polymorphism, and a 13% increase in nonsynonymous substitution rates. These findings validate the conjecture that the widespread distribution of Wolbachia infections throughout arthropods impacts the effective population size of mitochondria. These effects might in part explain the disconnection between genetic diversity and demographic population size in mitochondria, and also fuel red-queen-like cytonuclear co-evolution through the fixation of deleterious mitochondrial alleles.}, }
@article {pmid28967179, year = {2018}, author = {Dayan, FE and Barker, A and Tranel, PJ}, title = {Origins and structure of chloroplastic and mitochondrial plant protoporphyrinogen oxidases: implications for the evolution of herbicide resistance.}, journal = {Pest management science}, volume = {74}, number = {10}, pages = {2226-2234}, doi = {10.1002/ps.4744}, pmid = {28967179}, issn = {1526-4998}, mesh = {Amaranthus/drug effects/enzymology/genetics ; Chloroplast Proteins/genetics/metabolism ; *Evolution, Molecular ; Glycine/analogs &amp; derivatives/pharmacology ; Herbicide Resistance/*genetics ; Herbicides/*pharmacology ; Mitochondrial Proteins/genetics/metabolism ; Plant Weeds/drug effects/enzymology/*genetics ; Protoporphyrinogen Oxidase/*genetics/metabolism ; }, abstract = {Protoporphyrinogen IX oxidase (PPO)-inhibiting herbicides are effective tools to control a broad spectrum of weeds, including those that have evolved resistance to glyphosate. Their utility is being threatened by the appearance of biotypes that are resistant to PPO inhibitors. While the chloroplastic PPO1 isoform is thought to be the primary target of PPO herbicides, evolved resistance mechanisms elucidated to date are associated with changes to the mitochondrial PPO2 isoform, suggesting that the importance of PPO2 has been underestimated. Our investigation of the evolutionary and structural biology of plant PPOs provides some insight into the potential reasons why PPO2 is the preferred target for evolution of resistance. The most common target-site mutation imparting resistance involved the deletion of a key glycine codon. The genetic environment that facilitates this deletion is apparently only present in the gene encoding PPO2 in a few species. Additionally, both species with this mutation (Amaranthus tuberculatus and Amaranthus palmeri) have dual targeting of PPO2 to both the chloroplast and the mitochondria, which might be a prerequisite to impart herbicide resistance. The most recent target-site mutations have substituted a key arginine residue involved in stabilizing the substrate in the catalytic domain of PPO2. This arginine is highly conserved across all plant PPOs, suggesting that its substitution could be equally likely on PPO1 and PPO2, yet it has only occurred on PPO2, underscoring the importance of this isoform for the evolution of herbicide resistance. © 2017 Society of Chemical Industry.}, }
@article {pmid28966595, year = {2017}, author = {Wiens, L and Banh, S and Sotiri, E and Jastroch, M and Block, BA and Brand, MD and Treberg, JR}, title = {Comparison of Mitochondrial Reactive Oxygen Species Production of Ectothermic and Endothermic Fish Muscle.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {704}, doi = {10.3389/fphys.2017.00704}, pmid = {28966595}, issn = {1664-042X}, support = {R01 AG033542/AG/NIA NIH HHS/United States ; }, abstract = {Recently we demonstrated that the capacity of isolated muscle mitochondria to produce reactive oxygen species, measured as H2O2 efflux, is temperature-sensitive in isolated muscle mitochondria of ectothermic fish and the rat, a representative endothermic mammal. However, at physiological temperatures (15° and 37°C for the fish and rat, respectively), the fraction of total mitochondrial electron flux that generated H2O2, the fractional electron leak (FEL), was far lower in the rat than in fish. Those results suggested that the elevated body temperatures associated with endothermy may lead to a compensatory decrease in mitochondrial ROS production relative to respiratory capacity. To test this hypothesis we compare slow twitch (red) muscle mitochondria from the endothermic Pacific bluefin tuna (Thunnus orientalis) with mitochondria from three ectothermic fishes [rainbow trout (Oncorhynchus mykiss), common carp (Cyprinus carpio), and the lake sturgeon (Acipenser fulvescens)] and the rat. At a common assay temperature (25°C) rates of mitochondrial respiration and H2O2 efflux were similar in tuna and the other fishes. The thermal sensitivity of fish mitochondria was similar irrespective of ectothermy or endothermy. Comparing tuna to the rat at a common temperature, respiration rates were similar, or lower depending on mitochondrial substrates. FEL was not different across fish species at a common assay temperature (25°C) but was markedly higher in fishes than in rat. Overall, endothermy and warming of Pacific Bluefin tuna red muscle may increase the potential for ROS production by muscle mitochondria but the evolution of endothermy in this species is not necessarily associated with a compensatory reduction of ROS production relative to the respiratory capacity of mitochondria.}, }
@article {pmid28963083, year = {2018}, author = {Eldridge, RA and Achmadi, AS and Giarla, TC and Rowe, KC and Esselstyn, JA}, title = {Geographic isolation and elevational gradients promote diversification in an endemic shrew on Sulawesi.}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {306-317}, doi = {10.1016/j.ympev.2017.09.018}, pmid = {28963083}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; DNA/chemistry/isolation &amp; purification/metabolism ; Gene Flow ; Genetic Variation ; Genetics, Population ; Indonesia ; Islands ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Alignment ; Sequence Analysis, DNA ; Shrews/*classification ; }, abstract = {Phylogeographic research on endemic primates and amphibians inhabiting the Indonesian island of Sulawesi revealed the existence of seven areas of endemism (AoEs). Here, we use phylogenetic and population genetic analyses of one mitochondrial gene and 15 nuclear loci to assess geographic patterns of genetic partitioning in a shrew (Crocidura elongata) that is endemic to Sulawesi, but occurs across the island. We uncover substantial genetic diversity in this species both between and within AoEs, but we also identify close relationships between populations residing in different AoEs. One of the earliest divergences within C. elongata distinguishes a high-elevation clade from low-elevation clades. In addition, on one mountain, we observe three distinct genetic groups from low, middle, and high elevations, suggesting divergence along a single elevational gradient. In general, our results show that C. elongata, like several other Sulawesi endemic taxa, harbors extensive genetic diversity. This diversity is structured in part by known AoE boundaries, but also by elevational gradients and geographic isolation within AoEs.}, }
@article {pmid28961859, year = {2017}, author = {Cheng, J and Guo, X and Cai, P and Cheng, X and Piškur, J and Ma, Y and Jiang, H and Gu, Z}, title = {Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation.}, journal = {Molecular biology and evolution}, volume = {34}, number = {11}, pages = {2870-2878}, doi = {10.1093/molbev/msx220}, pmid = {28961859}, issn = {1537-1719}, mesh = {Aerobiosis/*genetics/physiology ; Anaerobiosis/genetics ; Biological Evolution ; Chromatin/*genetics/physiology ; Dekkera/genetics/metabolism ; Evolution, Molecular ; Fermentation/genetics ; Gene Expression/genetics ; Glucose/metabolism ; Phylogeny ; Promoter Regions, Genetic/genetics ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Parallel evolution occurs when a similar trait emerges in independent evolutionary lineages. Although changes in protein coding and gene transcription have been investigated as underlying mechanisms for parallel evolution, parallel changes in chromatin structure have never been reported. Here, Saccharomyces cerevisiae and a distantly related yeast species, Dekkera bruxellensis, are investigated because both species have independently evolved the capacity of aerobic fermentation. By profiling and comparing genome sequences, transcriptomic landscapes, and chromatin structures, we revealed that parallel changes in nucleosome occupancy in the promoter regions of mitochondria-localized genes led to concerted suppression of mitochondrial functions by glucose, which can explain the metabolic convergence in these two independent yeast species. Further investigation indicated that similar mutational processes in the promoter regions of these genes in the two independent evolutionary lineages underlay the parallel changes in chromatin structure. Our results indicate that, despite several hundred million years of separation, parallel changes in chromatin structure, can be an important adaptation mechanism for different organisms. Due to the important role of chromatin structure changes in regulating gene expression and organism phenotypes, the novel mechanism revealed in this study could be a general phenomenon contributing to parallel adaptation in nature.}, }
@article {pmid28952250, year = {2017}, author = {Chen, YJ and Rong, QX and Jiang, D and Shen, Y and Huang, LQ}, title = {[Bioinformatics analysis of geranylgeranyl pyrophosphate synthase coding gene and amino acid sequence in Lamiaceae].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {3}, pages = {465-472}, doi = {10.19540/j.cnki.cjcmm.20170103.030}, pmid = {28952250}, issn = {1001-5302}, mesh = {Amino Acid Sequence ; Computational Biology ; Geranylgeranyl-Diphosphate Geranylgeranyltransferase/*genetics ; Lamiaceae/enzymology/*genetics ; Phylogeny ; Plant Proteins/*genetics ; }, abstract = {Geranylgeranyl pyrophosphate synthase enzyme is one of the key enzymes in the synthesis pathway of diterpenoid. Nine Lamiaceae genus GGPS synthase in Genebank was analyzed in this article. GGPS synthase the nucleic acid sequences and amino acid sequences, physicochemical properties, the signal peptide, leader peptides, transmembrane topological structure, hydrophobic, hydrophilic, subcellular localization, secondary structure, function domain, tertiary structure and evolutional relationship were predicted by using bioinformatics methods.Phylogenetic tree was constructed for the geranylgeranyl pyrophosphate synthase enzyme protein family. The results showed that GGPS amino acid sequence of the physical and chemical properties were basically identical, mainly hydrophilic protein, there existed chloroplast transit peptide, and no signal peptide and membrane structure domain, which mainly located in the chloroplast, the minor part located in mitochondria. The main secondary structures of the proteins are alpha helix and random coil. All these proteins have catalytic residues, aspartate-rich region, active site lid residues, substrate-Mg2+ binding site. The results provide theoretical reference for study on both the enzymatic characteristics of GGPS and the biosynthesis pathway of diterpenoid.}, }
@article {pmid28947489, year = {2017}, author = {Majsec, K and Bhuiyan, NH and Sun, Q and Kumari, S and Kumar, V and Ware, D and van Wijk, KJ}, title = {The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis.}, journal = {The Plant cell}, volume = {29}, number = {11}, pages = {2687-2710}, doi = {10.1105/tpc.17.00481}, pmid = {28947489}, issn = {1532-298X}, mesh = {Arabidopsis Proteins/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Gene Regulatory Networks/genetics ; Mitochondria/*enzymology/genetics ; Peptide Hydrolases/classification/genetics/*metabolism ; Phylogeny ; Plastids/*enzymology/genetics ; Proteome/genetics/metabolism ; Proteostasis/genetics ; }, abstract = {Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.}, }
@article {pmid28943271, year = {2017}, author = {Chaturvedi, D and Mahalakshmi, R}, title = {Transmembrane β-barrels: Evolution, folding and energetics.}, journal = {Biochimica et biophysica acta. Biomembranes}, volume = {1859}, number = {12}, pages = {2467-2482}, doi = {10.1016/j.bbamem.2017.09.020}, pmid = {28943271}, issn = {0005-2736}, support = {IA/I/14/1/501305//Wellcome Trust-DBT India Alliance/India ; }, mesh = {Amino Acid Sequence ; Bacteria/genetics/*metabolism ; Bacterial Outer Membrane Proteins/*chemistry/genetics/metabolism ; *Biological Evolution ; Eukaryota/genetics/metabolism ; Gene Expression ; Mitochondria/chemistry/*metabolism ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Molecular Chaperones/*chemistry/genetics/metabolism ; Protein Binding ; Protein Conformation, beta-Strand ; Protein Folding ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Sequence Homology, Amino Acid ; Thermodynamics ; }, abstract = {The biogenesis of transmembrane β-barrels (outer membrane proteins, or OMPs) is an elaborate multistep orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. Several theories exist that describe the mechanism of chaperone-assisted OMP assembly in vivo and unassisted (spontaneous) folding in vitro. Structurally, OMPs of bacterial origin possess even-numbered strands, while mitochondrial β-barrels are even- and odd-stranded. Several underlying similarities between prokaryotic and eukaryotic β-barrels and their folding machinery are known; yet, the link in their evolutionary origin is unclear. While OMPs exhibit diversity in sequence and function, they share similar biophysical attributes and structure. Similarly, it is important to understand the intricate OMP assembly mechanism, particularly in eukaryotic β-barrels that have evolved to perform more complex functions. Here, we deliberate known facets of β-barrel evolution, folding, and stability, and attempt to highlight outstanding questions in β-barrel biogenesis and proteostasis.}, }
@article {pmid28942768, year = {2017}, author = {Bakhoum, AJS and Miquel, J and Ndiaye, PI and Justine, JL and Falchi, A and Bâ, CT and Marchand, B and Quilichini, Y}, title = {Advances in Spermatological Characters in the Digenea: Review and Proposal of Spermatozoa Models and Their Phylogenetic Importance.}, journal = {Advances in parasitology}, volume = {98}, number = {}, pages = {111-165}, doi = {10.1016/bs.apar.2017.04.001}, pmid = {28942768}, issn = {2163-6079}, mesh = {Animals ; Axoneme/*ultrastructure ; Male ; Microtubules ; *Phylogeny ; Spermatozoa/*ultrastructure ; Trematoda/*classification/cytology ; }, abstract = {The wide biodiversity and economic importance of digeneans have motivated a great deal of research in the last decade, focussing on their phylogenetic positions. Molecular research was instrumental for our understanding of phylogeny in the Digenea, but spermatological studies have also provided many results, which are potentially useful for phylogeny; however, the complete spermatological data set has never been reviewed in a whole phylogenetic perspective. Spermatological data are now available for more than 100 species, belonging to 15 superfamilies and 46 families. In this paper, we try to summarize the current knowledge about sperm structure in the digeneans and propose a classification of digenean spermatozoa into five basic models. The main ultrastructural characters used are (1) the type of axoneme, (2) the lateral expansion, (3) the association 'external ornamentation of the plasma membrane + cortical microtubules', (4) the field of cortical microtubules and its number, (5) the location of the external ornamentation, (6) the location of the maximum number of cortical microtubules and (7) the number of mitochondria. We also outline the most interesting features for phylogenetic inference and their possible value in the context of digenean systematics, phylogeny and evolution. Associations between sperm models and superfamilies were found as follows: Type 1 in the Schistosomatoidea; Type 2 in the Hemiuroidea; Type 3 in the Opecoeloidea, Lepocreadioidea, Haploporoidea and Opisthorchioidea; Type 4 in the Gorgoderoidea, Microphalloidea, Plagiorchioidea and Gymnophalloidea; Type 5 in the Echinostomatoidea, Microscaphidioidea, Paramphistomoidea, Pronocephaloidea and Brachylaimoidea.}, }
@article {pmid28938742, year = {2017}, author = {Wells, D and Ravichandran, K and McCaffrey, C and Grifo, J and Morales, A and Perloe, M and Munne, S and Fragouli, E}, title = {Reply: Mitochondrial DNA Quantification-the devil in the detail.}, journal = {Human reproduction (Oxford, England)}, volume = {32}, number = {10}, pages = {2150-2151}, doi = {10.1093/humrep/dex279}, pmid = {28938742}, issn = {1460-2350}, mesh = {*DNA, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria ; Phylogeny ; }, }
@article {pmid28932931, year = {2018}, author = {Gorgulho, R and Jacinto, R and Lopes, SS and Pereira, SA and Tranfield, EM and Martins, GG and Gualda, EJ and Derks, RJE and Correia, AC and Steenvoorden, E and Pintado, P and Mayboroda, OA and Monteiro, EC and Morello, J}, title = {Usefulness of zebrafish larvae to evaluate drug-induced functional and morphological renal tubular alterations.}, journal = {Archives of toxicology}, volume = {92}, number = {1}, pages = {411-423}, doi = {10.1007/s00204-017-2063-1}, pmid = {28932931}, issn = {1432-0738}, support = {Gulbenkian Professorship 121986/2012//Fundação Calouste Gulbenkian/ ; ANR/BEX-BID/0153/2012//Foundation for Science and Technology/ ; IF/00951/2012//Foundation for Science and Technology/ ; PD/BD/52420/2013//Foundation for Science and Technology/ ; SFRH/BSAB/114291/2016//Foundation for Science and Technology/ ; LISBOA-01-0145-FEDER-007344//iNOVA Health Research Unit/ ; }, abstract = {Prediction and management of drug-induced renal injury (DIRI) rely on the knowledge of the mechanisms of drug insult and on the availability of appropriate animal models to explore it. Zebrafish (Danio rerio) offers unique advantages for assessing DIRI because the larval pronephric kidney has a high homology with its human counterpart and it is fully mature at 3.5 days post-fertilization. Herein, we aimed to evaluate the usefulness of zebrafish larvae as a model of renal tubular toxicity through a comprehensive analysis of the renal alterations induced by the lethal concentrations for 10% of the larvae for gentamicin, paracetamol and tenofovir. We evaluated drug metabolic profile by mass spectrometry, renal function with the inulin clearance assay, the 3D morphology of the proximal convoluted tubule by two-photon microscopy and the ultrastructure of proximal convoluted tubule mitochondria by transmission electron microscopy. Paracetamol was metabolized by conjugation and oxidation with further detoxification with glutathione. Renal clearance was reduced with gentamicin and paracetamol. Proximal tubules were enlarged with paracetamol and tenofovir. All drugs induced mitochondrial alterations including dysmorphic shapes (&quot;donuts&quot;, &quot;pancakes&quot; and &quot;rods&quot;), mitochondrial swelling, cristae disruption and/or loss of matrix granules. These results are in agreement with the tubular effects of gentamicin, paracetamol and tenofovir in man and demonstrate that zebrafish larvae might be a good model to assess functional and structural damage associated with DIRI.}, }
@article {pmid28918565, year = {2017}, author = {Scala, A and Mirabella, R and Goedhart, J and de Vries, M and Haring, MA and Schuurink, RC}, title = {Forward genetic screens identify a role for the mitochondrial HER2 in E-2-hexenal responsiveness.}, journal = {Plant molecular biology}, volume = {95}, number = {4-5}, pages = {399-409}, doi = {10.1007/s11103-017-0659-8}, pmid = {28918565}, issn = {1573-5028}, support = {818.02.017//NWO/ ; }, mesh = {Aldehydes/*pharmacology ; Arabidopsis/cytology/drug effects/*genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Mitochondria/drug effects/metabolism ; Mutation ; Oxidation-Reduction/drug effects ; Phylogeny ; Plant Leaves/cytology/drug effects/genetics/physiology ; Plant Roots/cytology/drug effects/genetics/physiology ; Receptor, ErbB-2/genetics/*metabolism ; Seedlings/cytology/drug effects/genetics/physiology ; Signal Transduction/drug effects ; }, abstract = {KEY MESSAGE: This work adds a new player, HER2, downstream of the perception of E-2-hexenal, a green leaf volatile, and shows that E-2-hexenal specifically changes the redox status of the mitochondria. It is widely accepted that plants produce and respond to green leaf volatiles (GLVs), but the molecular components involved in transducing their perception are largely unknown. The GLV E-2-hexenal inhibits root elongation in seedlings and, using this phenotype, we isolated E-2-hexenal response (her) Arabidopsis thaliana mutants. Using map-based cloning we positioned the her2 mutation to the At5g63620 locus, resulting in a phenylalanine instead of serine on position 223. Knockdown and overexpression lines of HER2 confirmed the role of HER2, which encodes an oxidoreductase, in the responsiveness to E-2-hexenal. Since E-2-hexenal is a reactive electrophile species, which are known to influence the redox status of cells, we utilized redox sensitive GFP2 (roGFP2) to determine the redox status of E-2-hexenal-treated root cells. Since the signal peptide of HER2 directed mCherry to the mitochondria, we targeted the expression of roGFP2 to this organelle besides the cytosol. E-2-hexenal specifically induced a change in the redox status in the mitochondria. We did not see a difference in the redox status in her2 compared to wild-type Arabidopsis. Still, the mitochondrial redox status did not change with Z-3-hexenol, another abundant GLV. These results indicate that HER2 is involved in transducing the perception of E-2-hexenal, which changes the redox status of the mitochondria.}, }
@article {pmid28916841, year = {2017}, author = {Dunn, CD}, title = {Some Liked It Hot: A Hypothesis Regarding Establishment of the Proto-Mitochondrial Endosymbiont During Eukaryogenesis.}, journal = {Journal of molecular evolution}, volume = {85}, number = {3-4}, pages = {99-106}, doi = {10.1007/s00239-017-9809-5}, pmid = {28916841}, issn = {1432-1432}, support = {637649//European Research Council/International ; }, mesh = {Archaea/*genetics/metabolism ; Bacteria/genetics ; *Biological Evolution ; Energy Metabolism ; Eukaryota/*genetics/metabolism ; *Hot Temperature ; Mitochondria/genetics/*metabolism/physiology ; *Symbiosis ; }, abstract = {Eukaryotic cells are characterized by a considerable increase in subcellular compartmentalization when compared to prokaryotes. Most evidence suggests that the earliest eukaryotes consisted of mitochondria derived from an α-proteobacterial ancestor enclosed within an archaeal host cell. However, what benefits the archaeal host and the proto-mitochondrial endosymbiont might have obtained at the beginning of this endosymbiotic relationship remains unclear. In this work, I argue that heat generated by the proto-mitochondrion initially permitted an archaeon living at high temperatures to colonize a cooler environment, thereby removing apparent limitations on cellular complexity. Furthermore, heat generation by the endosymbiont would have provided phenotypic flexibility not available through fixed alleles selected for fitness at specific temperatures. Finally, a role for heat production by the proto-mitochondrion bridges a conceptual gap between initial endosymbiont entry to the archaeal host and a later role for mitochondrial ATP production in permitting increased cellular complexity.}, }
@article {pmid28911184, year = {2017}, author = {Xia, L and Liang, H and Xu, L and Chen, J and Bekaert, M and Zhang, H and Lu, Y}, title = {Subcellular localization and function study of a secreted phospholipase C from Nocardia seriolae.}, journal = {FEMS microbiology letters}, volume = {364}, number = {17}, pages = {}, doi = {10.1093/femsle/fnx143}, pmid = {28911184}, issn = {1574-6968}, mesh = {Animals ; Apoptosis ; Cell Line ; Cloning, Molecular ; Cyprinidae/*microbiology ; Cytoplasm/*enzymology ; Epithelial Cells/cytology/microbiology/ultrastructure ; Escherichia coli/genetics ; Gene Expression ; Green Fluorescent Proteins/genetics ; Host-Pathogen Interactions ; Microscopy, Fluorescence ; Mitochondria/enzymology/ultrastructure ; Nocardia/cytology/*enzymology/genetics ; Phylogeny ; Recombinant Fusion Proteins/metabolism ; Transfection ; Type C Phospholipases/*chemistry/genetics/*metabolism ; Virulence Factors/chemistry/*metabolism ; }, abstract = {Fish nocardiosis is a chronic systemic granulomatous disease, and Nocardia seriolae is the main pathogen that causes it. The pathogenesis and virulence factors of N. seriolae are not fully understood. A phospholipase C (PLC), which is likely to be a secreted protein targeting host cell mitochondria, was found by a bioinformatics analysis of the whole genome sequence of N. seriolae. In order to determine the subcellular localization and study the preliminary function of PLC from N. seriolae (NsPLC), in this study gene cloning, secreted protein identification, subcellular localization in host cells and apoptosis detection of NsPLC were carried out. Mass spectrometry analysis of extracellular products from N. seriolae showed that NsPLC was a secreted protein. Subcellular localization of NsPLC-GFP fusion protein in fathead minnow (FHM) cells revealed that the green fluorescence exhibited a punctate distribution near the nucleus and did not co-localize with mitochondria. In addition, an apoptosis assay suggested that apoptosis was induced in FHM cells by the overexpression of NsPLC. This study may lay the foundations for further studies on the function of NsPLC and promote the understanding of the virulence factors and pathogenic mechanism of N. seriolae.}, }
@article {pmid28910691, year = {2017}, author = {Tyml, T and Dyková, I}, title = {Phylogeny and taxonomy of new and re-examined strains of Tubulinea (Amoebozoa).}, journal = {European journal of protistology}, volume = {61}, number = {Pt A}, pages = {41-47}, doi = {10.1016/j.ejop.2017.08.002}, pmid = {28910691}, issn = {1618-0429}, mesh = {Lobosea/*classification/cytology ; Norway ; *Phylogeny ; Species Specificity ; }, abstract = {Morphological and molecular characterizations of three newly isolated tubulinean strains and re-examination of five strains formerly considered representatives of Saccamoeba and one strain formerly considered as Trichamoeba resulted in (a) the determination of strain BA02, isolated from a dripping rock ledge in Skansbukta (Billefjorden, Svalbard), as a new representative of Ptolemeba bulliensis Brown et al., 2014; (b) identification of strain ATCC® 50249™, deposited in the American Type Culture Collection as Trichamoeba, as the same species (P. bulliensis); (c) characterization of the new strain POHL into the Saccamoeba clade as a member closely related to S. lacustris; and (d) changing the generic residence of three strains formerly considered as representatives of Saccamoeba (strain PV67 to the P. bulliensis clade, and W187G and DP7 into the sister group of Ptolemeba noxubium Brown et al., 2014) whereas two other strains (MSED6, NTSHR) retain their original Saccamoeba clade position. Within the individual clades, the ultrastructure (especially the inner architecture of mitochondria) is congruent and thus of superior taxonomic value to that of light microscopic (morphometric) features.}, }
@article {pmid28902190, year = {2017}, author = {Lindsey, ARI and Stouthamer, R}, title = {The effects of outbreeding on a parasitoid wasp fixed for infection with a parthenogenesis-inducing Wolbachia symbiont.}, journal = {Heredity}, volume = {119}, number = {6}, pages = {411-417}, doi = {10.1038/hdy.2017.53}, pmid = {28902190}, issn = {1365-2540}, mesh = {Animals ; Biological Coevolution ; Crosses, Genetic ; Female ; Fertility ; Heterozygote ; Homozygote ; Male ; Models, Genetic ; *Parthenogenesis ; *Sex Ratio ; Symbiosis ; Wasps/*genetics/microbiology ; *Wolbachia ; }, abstract = {Trichogramma wasps can be rendered asexual by infection with the maternally inherited symbiont Wolbachia. Previous studies indicate the Wolbachia strains infecting Trichogramma wasps are host-specific, inferred by failed horizontal transfer of Wolbachia to novel Trichogramma hosts. Additionally, Trichogramma can become dependent upon their Wolbachia infection for the production of female offspring, leaving them irreversibly asexual, further linking host and symbiont. We hypothesized Wolbachia strains infecting irreversibly asexual, resistant to horizontal transfer Trichogramma would show adaptation to a particular host genetic background. To test this, we mated Wolbachia-dependent females with males from a Wolbachia-naïve population to create heterozygous wasps. We measured sex ratios and fecundity, a proxy for Wolbachia fitness, produced by heterozygous wasps, and by their recombinant offspring. We find a heterozygote advantage, resulting in higher fitness for Wolbachia, as wasps will produce more offspring without any reduction in the proportion of females. While recombinant wasps did not differ in total fecundity after 10 days, recombinants produced fewer offspring early on, leading to an increased female-biased sex ratio for the whole brood. Despite the previously identified barriers to horizontal transfer of Wolbachia to and from Trichogramma pretiosum, there were no apparent barriers for Wolbachia to induce parthenogenesis in these non-native backgrounds. This is likely due to the route of infection being introgression rather than horizontal transfer, and possibly the co-evolution of Wolbachia with the mitochondria rather than the nuclear genome. These results help to elucidate the mechanisms by which Wolbachia adapt to hosts and the evolution of host-symbiont phenotypes.}, }
@article {pmid28893855, year = {2017}, author = {Radzvilavicius, AL and Kokko, H and Christie, JR}, title = {Mitigating Mitochondrial Genome Erosion Without Recombination.}, journal = {Genetics}, volume = {207}, number = {3}, pages = {1079-1088}, doi = {10.1534/genetics.117.300273}, pmid = {28893855}, issn = {1943-2631}, mesh = {Eukaryota ; Genome, Mitochondrial/*genetics ; Maternal Inheritance ; Mitochondrial Dynamics ; *Models, Genetic ; *Mutation Accumulation ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Mitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller's ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question. Occasional paternal leakage could in principle promote recombination, but it would also compromise the purifying selection benefits of uniparental inheritance. We assess this tradeoff using a stochastic population-genetic model. In the absence of recombination, uniparental inheritance of freely-segregating genomes mitigates mutational erosion, while paternal leakage exacerbates the ratchet effect. Mitochondrial fusion-fission cycles ensure independent genome segregation, improving purifying selection. Paternal leakage provides opportunity for recombination to slow down the mutation accumulation, but always at a cost of increased steady-state mutation load. Our findings indicate that random segregation of mitochondrial genomes under uniparental inheritance can effectively combat the mutational meltdown, and that homologous recombination under paternal leakage might not be needed.}, }
@article {pmid28889978, year = {2017}, author = {Singer, A and Poschmann, G and Mühlich, C and Valadez-Cano, C and Hänsch, S and Hüren, V and Rensing, SA and Stühler, K and Nowack, ECM}, title = {Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora.}, journal = {Current biology : CB}, volume = {27}, number = {18}, pages = {2763-2773.e5}, doi = {10.1016/j.cub.2017.08.010}, pmid = {28889978}, issn = {1879-0445}, mesh = {Cercozoa/*physiology ; Chromatophores/*physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mass Spectrometry ; Metabolic Networks and Pathways ; Proteome/*analysis ; Protozoan Proteins/*analysis ; Sequence Analysis, Protein ; Symbiosis ; }, abstract = {The endosymbiotic acquisition of mitochondria and plastids more than 1 Ga ago profoundly impacted eukaryote evolution. At the heart of understanding organelle evolution is the re-arrangement of the endosymbiont proteome into a host-controlled organellar proteome. However, early stages in this process as well as the timing of events that underlie organelle integration remain poorly understood. The amoeba Paulinella chromatophora contains cyanobacterium-derived photosynthetic organelles, termed &quot;chromatophores,&quot; that were acquired more recently (around 100 Ma ago). To explore the re-arrangement of an organellar proteome during its integration into a eukaryotic host cell, here we characterized the chromatophore proteome by protein mass spectrometry. Apparently, genetic control over the chromatophore has shifted substantially to the nucleus. Two classes of nuclear-encoded proteins-which differ in protein length-are imported into the chromatophore, most likely through independent pathways. Long imported proteins carry a putative, conserved N-terminal targeting signal, and many specifically fill gaps in chromatophore-encoded metabolic pathways or processes. Surprisingly, upon heterologous expression in a plant cell, the putative chromatophore targeting signal conferred chloroplast localization. This finding suggests common features in the protein import pathways of chromatophores and plastids, two organelles that evolved independently and more than 1 Ga apart from each other. By combining experimental data with in silico predictions, we provide a comprehensive catalog of almost 450 nuclear-encoded, chromatophore-targeted proteins. Interestingly, most imported proteins seem to derive from ancestral host genes, suggesting that the re-targeting of nuclear-encoded proteins that resulted from endosymbiotic gene transfers plays only a minor role at the onset of chromatophore integration.}, }
@article {pmid28882896, year = {2017}, author = {Sultana, S and Solotchi, M and Ramachandran, A and Patel, SS}, title = {Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {44}, pages = {18145-18160}, doi = {10.1074/jbc.M117.797480}, pmid = {28882896}, issn = {1083-351X}, support = {R35 GM118086/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophage T7/enzymology ; Base Pair Mismatch ; DNA Damage ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Deoxyguanosine/analogs &amp; derivatives/metabolism ; Fluorescence Polarization ; Humans ; Mitochondrial Proteins/genetics/*metabolism ; *Mutation ; Mutation Rate ; Oxidation-Reduction ; Recombinant Fusion Proteins/metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Substrate Specificity ; *Transcription Elongation, Genetic ; Transcription Factors/metabolism ; Viral Proteins/genetics/*metabolism ; }, abstract = {Single-subunit RNA polymerases (RNAPs) are present in phage T7 and in mitochondria of all eukaryotes. This RNAP class plays important roles in biotechnology and cellular energy production, but we know little about its fidelity and error rates. Herein, we report the error rates of three single-subunit RNAPs measured from the catalytic efficiencies of correct and all possible incorrect nucleotides. The average error rates of T7 RNAP (2 × 10-6), yeast mitochondrial Rpo41 (6 × 10-6), and human mitochondrial POLRMT (RNA polymerase mitochondrial) (2 × 10-5) indicate high accuracy/fidelity of RNA synthesis resembling those of replicative DNA polymerases. All three RNAPs exhibit a distinctly high propensity for GTP misincorporation opposite dT, predicting frequent A→G errors in RNA with rates of ∼10-4 The A→C, G→A, A→U, C→U, G→U, U→C, and U→G errors mostly due to pyrimidine-purine mismatches were relatively frequent (10-5-10-6), whereas C→G, U→A, G→C, and C→A errors from purine-purine and pyrimidine-pyrimidine mismatches were rare (10-7-10-10). POLRMT also shows a high C→A error rate on 8-oxo-dG templates (∼10-4). Strikingly, POLRMT shows a high mutagenic bypass rate, which is exacerbated by TEFM (transcription elongation factor mitochondrial). The lifetime of POLRMT on terminally mismatched elongation substrate is increased in the presence of TEFM, which allows POLRMT to efficiently bypass the error and continue with transcription. This investigation of nucleotide selectivity on normal and oxidatively damaged DNA by three single-subunit RNAPs provides the basic information to understand the error rates in mitochondria and, in the case of T7 RNAP, to assess the quality of in vitro transcribed RNAs.}, }
@article {pmid28878314, year = {2017}, author = {Sun, S and Li, Q and Kong, L and Yu, H}, title = {Limited locomotive ability relaxed selective constraints on molluscs mitochondrial genomes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10628}, doi = {10.1038/s41598-017-11117-z}, pmid = {28878314}, issn = {2045-2322}, abstract = {Mollusca are the second largest phylum in the animal kingdom with different types of locomotion. Some molluscs are poor-migrating, while others are free-moving or fast-swimming. Most of the energy required for locomotion is provided by mitochondria via oxidative phosphorylation. Here, we conduct a comparative genomic analysis of 256 molluscs complete mitochondrial genomes and evaluate the role of energetic functional constraints on the protein-coding genes, providing a new insight into mitochondrial DNA (mtDNA) evolution. The weakly locomotive molluscs, compared to strongly locomotive molluscs, show significantly higher Ka/Ks ratio, which suggest they accumulated more nonsynonymous mutations in mtDNA and have experienced more relaxed evolutionary constraints. Eleven protein-coding genes (CoxI, CoxII, ATP6, Cytb, ND1-6, ND4L) show significant difference for Ka/Ks ratios between the strongly and weakly locomotive groups. The relaxation of selective constraints on Atp8 arise in the common ancestor of bivalves, and the further relaxation occurred in marine bivalves lineage. Our study thus demonstrates that selective constraints relevant to locomotive ability play an essential role in evolution of molluscs mtDNA.}, }
@article {pmid28870618, year = {2017}, author = {Sato, N}, title = {Revisiting the theoretical basis of the endosymbiotic origin of plastids in the original context of Lynn Margulis on the origin of mitosing, eukaryotic cells.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {104-113}, doi = {10.1016/j.jtbi.2017.08.028}, pmid = {28870618}, issn = {1095-8541}, mesh = {Chromosomes ; DNA Replication ; History, 20th Century ; Mitosis/*genetics ; *Models, Theoretical ; Plastids ; *Symbiosis ; }, abstract = {Fifty years ago, Lynn Margulis proposed a comprehensive hypothesis on the origin of eukaryotic cells with an emphasis on the origin of mitosis. This hypothesis postulated that the eukaryotic cell is a composite of different parts as a result of the symbiosis of various different bacteria. In this hypothesis, she integrated previously proposed ideas that mitochondria and chloroplasts were descendants of endosymbionts that originated from aerobic bacteria and blue-green algae (now cyanobacteria), respectively. However, the major part of her hypothesis, which she believed to be original, was the origin of mitosis. The core of her postulate involved a chromosome partition mechanism dependent on DNA-microtubule binding, which originated from a hypothetical centriole-DNA complex, with an ability to replicate. Surprisingly, her complete lack of real experimental works in the cytoskeleton, cell motility, or paleontology did not prevent this 29-year-old junior scientist from assembling archival knowledge and constructing a narrative on the evolution of all organisms. Whether the centriole-DNA complex originated from a spirochete or not was a minor anecdote in this initial postulate. Unfortunately, this hypothesis on the origin of mitosis, which she believed to be a holistic unity, testable by experiments, was entirely refuted. Despite falsification of her original narrative as a whole, her success as a founder of endosymbiotic theory on the origin of mitochondria and chloroplasts is undoubted. We will discuss the reasons for her success in terms of the historical situation in the latter half of the 20th century.}, }
@article {pmid28870165, year = {2017}, author = {Kollmar, M and Mühlhausen, S}, title = {Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {211}, doi = {10.1186/s12862-017-1056-2}, pmid = {28870165}, issn = {1471-2148}, mesh = {Eukaryota/*classification/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome ; Introns ; Myosins/chemistry/*genetics ; Phylogeny ; Spliceosomes ; }, abstract = {BACKGROUND: The last eukaryotic common ancestor already had an amazingly complex cell possessing genomic and cellular features such as spliceosomal introns, mitochondria, cilia-dependent motility, and a cytoskeleton together with several intracellular transport systems. In contrast to the microtubule-based dyneins and kinesins, the actin-filament associated myosins are considerably divergent in extant eukaryotes and a unifying picture of their evolution has not yet emerged.<br><br>RESULTS: Here, we manually assembled and annotated 7852 myosins from 929 eukaryotes providing an unprecedented dense sequence and taxonomic sampling. For classification we complemented phylogenetic analyses with gene structure comparisons resulting in 79 distinct myosin classes. The intron pattern analysis and the taxonomic distribution of the classes suggest two myosins in the last eukaryotic common ancestor, a class-1 prototype and another myosin, which is most likely the ancestor of all other myosin classes. The sparse distribution of class-2 and class-4 myosins outside their major lineages contradicts their presence in the last eukaryotic common ancestor but instead strongly suggests early eukaryote-eukaryote horizontal gene transfer.<br><br>CONCLUSIONS: By correlating the evolution of myosin diversity with the history of Earth we found that myosin innovation occurred in independent major &quot;burst&quot; events in the major eukaryotic lineages. Most myosin inventions happened in the Mesoproterozoic era. In the late Neoproterozoic era, a process of extensive independent myosin loss began simultaneously with further eukaryotic diversification. Since the Cambrian explosion, myosin repertoire expansion is driven by lineage- and species-specific gene and genome duplications leading to subfunctionalization and fine-tuning of myosin functions.}, }
@article {pmid28864909, year = {2017}, author = {Reiter, RJ and Rosales-Corral, S and Tan, DX and Jou, MJ and Galano, A and Xu, B}, title = {Melatonin as a mitochondria-targeted antioxidant: one of evolution's best ideas.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {74}, number = {21}, pages = {3863-3881}, doi = {10.1007/s00018-017-2609-7}, pmid = {28864909}, issn = {1420-9071}, mesh = {Animals ; Antioxidants/*pharmacology ; Free Radicals/*metabolism ; Humans ; Melatonin/*pharmacology ; Mitochondria/drug effects/*metabolism ; Oxidation-Reduction ; }, abstract = {Melatonin is an ancient antioxidant. After its initial development in bacteria, it has been retained throughout evolution such that it may be or may have been present in every species that have existed. Even though it has been maintained throughout evolution during the diversification of species, melatonin's chemical structure has never changed; thus, the melatonin present in currently living humans is identical to that present in cyanobacteria that have existed on Earth for billions of years. Melatonin in the systemic circulation of mammals quickly disappears from the blood presumably due to its uptake by cells, particularly when they are under high oxidative stress conditions. The measurement of the subcellular distribution of melatonin has shown that the concentration of this indole in the mitochondria greatly exceeds that in the blood. Melatonin presumably enters mitochondria through oligopeptide transporters, PEPT1, and PEPT2. Thus, melatonin is specifically targeted to the mitochondria where it seems to function as an apex antioxidant. In addition to being taken up from the circulation, melatonin may be produced in the mitochondria as well. During evolution, mitochondria likely originated when melatonin-forming bacteria were engulfed as food by ancestral prokaryotes. Over time, engulfed bacteria evolved into mitochondria; this is known as the endosymbiotic theory of the origin of mitochondria. When they did so, the mitochondria retained the ability to synthesize melatonin. Thus, melatonin is not only taken up by mitochondria but these organelles, in addition to many other functions, also probably produce melatonin as well. Melatonin's high concentrations and multiple actions as an antioxidant provide potent antioxidant protection to these organelles which are exposed to abundant free radicals.}, }
@article {pmid28863891, year = {2017}, author = {Lu, L and Wang, X and Wu, S and Song, X and Zou, Z and Xie, X and Xiao, J and Chen, S and Feng, H}, title = {Black carp STING functions importantly in innate immune defense against RNA virus.}, journal = {Fish &amp; shellfish immunology}, volume = {70}, number = {}, pages = {13-24}, doi = {10.1016/j.fsi.2017.08.037}, pmid = {28863891}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Carps/*genetics/*immunology ; Fish Diseases/*immunology ; Fish Proteins/chemistry/genetics/immunology ; Gene Expression Profiling ; Gene Expression Regulation/*immunology ; Immunity, Innate/*genetics ; Membrane Proteins/chemistry/*genetics/*immunology ; Phylogeny ; Reoviridae/physiology ; Reoviridae Infections/immunology ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology ; }, abstract = {Stimulator of interferon genes (STING) is a central and multifaceted mediator in the innate immune response of higher vertebrates. To explore its role in teleost fish, the STING homolog of black carp (Mylopharyngodon piceus) (bcSTING) has been cloned and characterized in this paper. bcSTING transcription in Mylopharyngodon piceus fin (MPF) cells increased remarkably in response to GCRV and SVCV infection, or poly (I:C) stimulation. bcSTING migrated around 42 KDa in immunoblot assay and was identified as a cytosolic protein locating on ER majorly through immunofluorescence staining. Under condition of SVCV/GCRV infection or poly (I:C) stimulation, the subcellular distribution of bcSTING majorly displayed on mitochondria, which overlapped with that of bcMAVS. HA-bcSTING instead of bcSTING-HA presented strong IFN-inducing activity in reporter assay and antiviral ability against both SVCV and GCRV in plaque assay. Site mutation of serine (S) on C-terminus of bcSTING demonstrated that both S371 and S379 were crucial for its mediated signaling. Taken together, our study support the conclusion that bcSTING plays an important role in host innate immune defense against RNA virus such as SVCV and GCRV, in which its C-terminus functions crucially.}, }
@article {pmid28859174, year = {2017}, author = {Hudson, W}, title = {Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0184309}, doi = {10.1371/journal.pone.0184309}, pmid = {28859174}, issn = {1932-6203}, mesh = {Agriculture ; Animals ; DNA, Mitochondrial/*genetics ; Egypt ; Haplotypes/genetics ; Horses/*genetics ; Mitochondria/genetics ; Pedigree ; *Phylogeny ; }, abstract = {BACKGROUND: Egyptian Arabian horses have been maintained in a state of genetic isolation for over a hundred years. There is only limited genetic proof that the studbook records of female lines of Egyptian Arabian pedigrees are reliable. This study characterized the mitochondrial DNA (mtDNA) signatures of 126 horses representing 14 matrilines in the Egyptian Agricultural Organization (EAO) horse-breeding program.<br><br>FINDINGS: Analysis of the whole D-loop sequence yielded additional information compared to hypervariable region-1 (HVR1) analysis alone, with 42 polymorphic sites representing ten haplotypes compared to 16 polymorphic sites representing nine haplotypes, respectively. Most EAO haplotypes belonged to ancient haplogroups, suggesting origin from a wide geographical area over many thousands of years, although one haplotype was novel.<br><br>CONCLUSIONS: Historical families share haplotypes and some individuals from different strains belonged to the same haplogroup: the classical EAO strain designation is not equivalent to modern monophyletic matrilineal groups. Phylogenetic inference showed that the foundation mares of the historical haplotypes were highly likely to have the same haplotypes as the animals studied (p > 0.998 in all cases), confirming the reliability of EAO studbook records and providing the opportunity for breeders to confirm the ancestry of their horses.}, }
@article {pmid28855414, year = {2017}, author = {Sloan, DB}, title = {Nuclear and mitochondrial RNA editing systems have opposite effects on protein diversity.}, journal = {Biology letters}, volume = {13}, number = {8}, pages = {}, doi = {10.1098/rsbl.2017.0314}, pmid = {28855414}, issn = {1744-957X}, mesh = {Base Sequence ; Inosine ; Phylogeny ; Proteins ; RNA ; *RNA Editing ; }, abstract = {RNA editing can yield protein products that differ from those directly encoded by genomic DNA. This process is pervasive in the mitochondria of many eukaryotes, where it predominantly results in the restoration of ancestral protein sequences. Nuclear mRNAs in metazoans also undergo editing (adenosine-to-inosine or 'A-to-I' substitutions), and most of these edits appear to be nonadaptive 'misfirings' of adenosine deaminases. However, recent analysis of cephalopod transcriptomes found that many editing sites are shared by anciently divergent lineages within this group, suggesting they play some adaptive role. Recent discoveries have also revealed that some fungi have an independently evolved A-to-I editing mechanism, resulting in extensive recoding of their nuclear mRNAs. Here, phylogenetic comparisons were used to determine whether RNA editing generally restores ancestral protein sequences or creates derived variants. Unlike in mitochondrial systems, RNA editing in metazoan and fungal nuclear transcripts overwhelmingly leads to novel sequences not found in inferred ancestral proteins. Even for the subset of RNA editing sites shared by deeply divergent cephalopod lineages, the primary effect of nuclear editing is an increase-not a decrease-in protein divergence. These findings suggest fundamental differences in the forces responsible for the evolution of RNA editing in nuclear versus mitochondrial systems.}, }
@article {pmid28854633, year = {2017}, author = {Park, S and Ruhlman, TA and Weng, ML and Hajrah, NH and Sabir, JSM and Jansen, RK}, title = {Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1766-1780}, doi = {10.1093/gbe/evx124}, pmid = {28854633}, issn = {1759-6653}, mesh = {Base Sequence ; *Evolution, Molecular ; *Genome, Mitochondrial ; Genome, Plant ; *Genome, Plastid ; Geranium/chemistry/classification/*genetics ; Mitochondria/genetics ; Mutation ; Phylogeny ; Plastids/genetics ; }, abstract = {Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species. This study reports on rates and patterns of nucleotide substitutions in plastomes and mitogenomes of 17 species of Geranium and representatives of other Geraniaceae. As detected across other angiosperms, substitution rates in the plastome are 3.5 times higher than the mitogenome in most Geranium. However, in the branch leading to Geranium brycei/Geranium incanum mitochondrial genes experienced significantly higher dN and dS than plastid genes, a pattern that has only been detected in one other angiosperm. Furthermore, rate accelerations differ in the two organelle genomes with plastomes having increased dN and mitogenomes with increased dS. In the Geranium phaeum/Geranium reflexum clade, duplicate copies of clpP and rpoA genes that experienced asymmetric rate divergence were detected in the single copy region of the plastome. In the case of rpoA, the branch leading to G. phaeum/G. reflexum experienced positive selection or relaxation of purifying selection. Finally, the evolution of acetyl-CoA carboxylase is unusual in Geraniaceae because it is only the second angiosperm family where both prokaryotic and eukaryotic ACCases functionally coexist in the plastid.}, }
@article {pmid28854623, year = {2017}, author = {Marlétaz, F and Le Parco, Y and Liu, S and Peijnenburg, KTCA}, title = {Extreme Mitogenomic Variation in Natural Populations of Chaetognaths.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1374-1384}, doi = {10.1093/gbe/evx090}, pmid = {28854623}, issn = {1759-6653}, support = {268513//European Research Council/International ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Eukaryota/classification/*genetics ; Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus. Additionally, based on 54 complete mitogenomes, we observed mitochondrial gene order differences between several of these lineages. We examined nuclear divergence patterns (18S, 28S, and an intron) to determine the possible origin of these lineages, but did not find congruent patterns between mitochondrial and nuclear markers. We also show that extreme mitochondrial divergence in chaetognaths is not driven by positive selection. Hence, we propose that the extreme levels of mitochondrial variation could be the result of either a complex scenario of reproductive isolation, or a combination of large population size and accelerated mitochondrial mutation rate. These findings emphasize the importance of characterizing genome-wide levels of nuclear variation in these species and promote chaetognaths as a remarkable model to study mitochondrial evolution.}, }
@article {pmid28854615, year = {2017}, author = {Mak, SST and Gopalakrishnan, S and Carøe, C and Geng, C and Liu, S and Sinding, MS and Kuderna, LFK and Zhang, W and Fu, S and Vieira, FG and Germonpré, M and Bocherens, H and Fedorov, S and Petersen, B and Sicheritz-Pontén, T and Marques-Bonet, T and Zhang, G and Jiang, H and Gilbert, MTP}, title = {Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.}, journal = {GigaScience}, volume = {6}, number = {8}, pages = {1-13}, doi = {10.1093/gigascience/gix049}, pmid = {28854615}, issn = {2047-217X}, support = {681396//European Research Council/International ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Base Composition ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; Genomics/*methods/*standards ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction-amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.}, }
@article {pmid28854599, year = {2017}, author = {Rauch, C and Christa, G and de Vries, J and Woehle, C and Gould, SB}, title = {Mitochondrial Genome Assemblies of Elysia timida and Elysia cornigera and the Response of Mitochondrion-Associated Metabolism during Starvation.}, journal = {Genome biology and evolution}, volume = {9}, number = {7}, pages = {1873-1879}, doi = {10.1093/gbe/evx129}, pmid = {28854599}, issn = {1759-6653}, mesh = {Animals ; Chloroplasts/metabolism ; DNA, Mitochondrial/genetics ; Gastropoda/classification/*genetics/*metabolism ; *Genome, Mitochondrial ; Mitochondria/genetics/metabolism ; Photosynthesis ; Plastids/metabolism ; }, abstract = {Some sacoglossan sea slugs sequester functional plastids (kleptoplasts) from their food, which continue to fix CO2 in a light dependent manner inside the animals. In plants and algae, plastid and mitochondrial metabolism are linked in ways that reach beyond the provision of energy-rich carbon compounds through photosynthesis, but how slug mitochondria respond to starvation or alterations in plastid biochemistry has not been explored. We assembled the mitochondrial genomes of the plastid-sequestering sea slugs Elysia timida and Elysia cornigera from RNA-Seq data that was complemented with standard sequencing of mitochondrial DNA through primer walking. Our data confirm the sister species relationship of the two Sacoglossa and from the analysis of changes in mitochondrial-associated metabolism during starvation we speculate that kleptoplasts might aid in the rerouting or recycling of reducing power independent of, yet maybe improved by, photosynthesis.}, }
@article {pmid28848044, year = {2017}, author = {Srivastava, S and Savanur, MA and Sinha, D and Birje, A and R, V and Saha, PP and D'Silva, P}, title = {Regulation of mitochondrial protein import by the nucleotide exchange factors GrpEL1 and GrpEL2 in human cells.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {44}, pages = {18075-18090}, doi = {10.1074/jbc.M117.788463}, pmid = {28848044}, issn = {1083-351X}, mesh = {Biomarkers/metabolism ; Genetic Complementation Test ; Green Fluorescent Proteins/genetics/metabolism ; HEK293 Cells ; HSP70 Heat-Shock Proteins/chemistry/*metabolism ; HeLa Cells ; Humans ; Immunoprecipitation ; Intracellular Signaling Peptides and Proteins/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Ligands ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; *Models, Molecular ; Molecular Chaperones/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Oxidative Stress ; Phylogeny ; Protein Isoforms/metabolism ; Protein Multimerization ; Protein Stability ; Protein Transport ; RNA Interference ; Recombinant Fusion Proteins/chemistry/metabolism ; }, abstract = {Mitochondria are organelles indispensable for maintenance of cellular energy homeostasis. Most mitochondrial proteins are nuclearly encoded and are imported into the matrix compartment where they are properly folded. This process is facilitated by the mitochondrial heat shock protein 70 (mtHsp70), a chaperone contributing to mitochondrial protein quality control. The affinity of mtHsp70 for its protein clients and its chaperone function are regulated by binding of ATP/ADP to mtHsp70's nucleotide-binding domain. Nucleotide exchange factors (NEFs) play a crucial role in exchanging ADP for ATP at mtHsp70's nucleotide-binding domain, thereby modulating mtHsp70's chaperone activity. A single NEF, Mge1, regulates mtHsp70's chaperone activity in lower eukaryotes, but the mammalian orthologs are unknown. Here, we report that two putative NEF orthologs, GrpE-like 1 (GrpEL1) and GrpEL2, modulate mtHsp70's function in human cells. We found that both GrpEL1 and GrpEL2 associate with mtHsp70 as a hetero-oligomeric subcomplex and regulate mtHsp70 function. The formation of this subcomplex was critical for conferring stability to the NEFs, helped fine-tune mitochondrial protein quality control, and regulated crucial mtHsp70 functions, such as import of preproteins and biogenesis of Fe-S clusters. Our results also suggested that GrpEL2 has evolved as a possible stress resistance protein in higher vertebrates to maintain chaperone activity under stress conditions. In conclusion, our findings support the idea that GrpEL1 has a role as a stress modulator in mammalian cells and highlight that multiple NEFs are involved in controlling protein quality in mammalian mitochondria.}, }
@article {pmid28846455, year = {2017}, author = {Bock, R}, title = {Witnessing Genome Evolution: Experimental Reconstruction of Endosymbiotic and Horizontal Gene Transfer.}, journal = {Annual review of genetics}, volume = {51}, number = {}, pages = {1-22}, doi = {10.1146/annurev-genet-120215-035329}, pmid = {28846455}, issn = {1545-2948}, mesh = {Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Speciation ; *Genome, Plant ; Genomics/methods ; Mitochondria/genetics/metabolism ; Plant Cells/metabolism ; Plants/*genetics ; Symbiosis/*genetics ; }, abstract = {Present day mitochondria and plastids (chloroplasts) evolved from formerly free-living bacteria that were acquired through endosymbiosis more than a billion years ago. Conversion of the bacterial endosymbionts into cell organelles involved the massive translocation of genetic material from the organellar genomes to the nucleus. The development of transformation technologies for organellar genomes has made it possible to reconstruct this endosymbiotic gene transfer in laboratory experiments and study the mechanisms involved. Recently, the horizontal transfer of genetic information between organisms has also become amenable to experimental investigation. It led to the discovery of horizontal genome transfer as an asexual process generating new species and new combinations of nuclear and organellar genomes. This review describes experimental approaches towards studying endosymbiotic and horizontal gene transfer processes, discusses the new knowledge gained from these approaches about both the evolutionary significance of gene transfer and the underlying molecular mechanisms, and highlights exciting possibilities to exploit gene and genome transfer in biotechnology and synthetic biology.}, }
@article {pmid28842472, year = {2017}, author = {Kraus, F and Ryan, MT}, title = {The constriction and scission machineries involved in mitochondrial fission.}, journal = {Journal of cell science}, volume = {130}, number = {18}, pages = {2953-2960}, doi = {10.1242/jcs.199562}, pmid = {28842472}, issn = {1477-9137}, mesh = {Actins/metabolism ; Animals ; Endoplasmic Reticulum/metabolism ; Humans ; Lipids/chemistry ; *Mitochondrial Dynamics ; Mitochondrial Proteins/metabolism ; Models, Biological ; }, abstract = {A key event in the evolution of eukaryotic cells was the engulfment of an aerobic bacterium by a larger anaerobic archaebacterium, leading to a close relationship between the host and the newly formed endosymbiont. Mitochondria, originating from this event, have evolved to be the main place of cellular ATP production. Maintaining elements of their independence, mitochondria undergo growth and division in the cell, thereby ensuring that new daughter cells inherit a mitochondrial complement. Mitochondrial division is also important for other processes, including quality control, mitochondrial (mt)DNA inheritance, transport and cell death. However, unlike bacterial fission, which uses a dynamin-related protein to constrict the membrane at its inner face, mitochondria use dynamin and dynamin-related proteins to constrict the outer membrane from the cytosolic face. In this Review, we summarize the role of proteins from the dynamin superfamily in mitochondrial division. This includes recent findings highlighting that dynamin-2 (Dnm2) is involved in mitochondrial scission, which led to the reappraisal of the role of dynamin-related protein 1 (Drp1; also known as Dnm1l) and its outer membrane adaptors as components of the mitochondrial constriction machinery along with ER components and actin.}, }
@article {pmid28837072, year = {2017}, author = {Hikmat, O and Eichele, T and Tzoulis, C and Bindoff, LA}, title = {Understanding the Epilepsy in POLG Related Disease.}, journal = {International journal of molecular sciences}, volume = {18}, number = {9}, pages = {}, doi = {10.3390/ijms18091845}, pmid = {28837072}, issn = {1422-0067}, mesh = {Animals ; Cerebral Cortex/pathology ; DNA Polymerase gamma/*genetics/*metabolism ; Disease Susceptibility ; Electroencephalography ; Epilepsy/diagnosis/*etiology/*metabolism/therapy ; Humans ; Magnetic Resonance Imaging/methods ; Neurons/metabolism ; }, abstract = {Epilepsy is common in polymerase gamma (POLG) related disease and is associated with high morbidity and mortality. Epileptiform discharges typically affect the occipital regions initially and focal seizures, commonly evolving to bilateral convulsive seizures which are the most common seizure types in both adults and children. Our work has shown that mtDNA depletion-i.e., the quantitative loss of mtDNA-in neurones is the earliest and most important factor of the subsequent development of cellular dysfunction. Loss of mtDNA leads to loss of mitochondrial respiratory chain (MRC) components that, in turn, progressively disables energy metabolism. This critically balanced neuronal energy metabolism leads to both a chronic and continuous attrition (i.e., neurodegeneration) and it leaves the neurone unable to cope with increased demand that can trigger a potentially catastrophic cycle that results in acute focal necrosis. We believe that it is the onset of epilepsy that triggers the cascade of damage. These events can be identified in the stepwise evolution that characterizes the clinical, Electroencephalography (EEG), neuro-imaging, and neuropathology findings. Early recognition with prompt and aggressive seizure management is vital and may play a role in modifying the epileptogenic process and improving survival.}, }
@article {pmid28830831, year = {2017}, author = {Banker, SE and Wade, EJ and Simon, C}, title = {The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia.}, journal = {Molecular phylogenetics and evolution}, volume = {116}, number = {}, pages = {172-181}, doi = {10.1016/j.ympev.2017.08.009}, pmid = {28830831}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Hemiptera/*genetics ; *Hybridization, Genetic ; Mitochondria/genetics ; New Zealand ; *Phylogeny ; Species Specificity ; }, abstract = {Phylogenetic studies of multiple independently inherited nuclear genes considered in combination with patterns of inheritance of organelle DNA have provided considerable insight into the history of species evolution. In particular, investigations of cicadas in the New Zealand genus Kikihia have identified interesting cases where mitochondrial DNA (mtDNA) crosses species boundaries in some species pairs but not others. Previous phylogenetic studies focusing on mtDNA largely corroborated Kikihia species groups identified by song, morphology and ecology with the exception of a unique South Island mitochondrial haplotype clade-the Westlandica group. This newly identified group consists of diverse taxa previously classified as belonging to three different sub-generic clades. We sequenced five nuclear loci from multiple individuals from every species of Kikihia to assess the nuclear gene concordance for this newly-identified mtDNA lineage. Bayes Factor analysis of the constrained phylogeny suggests some support for the mtDNA-based hypotheses, despite the fact that neither concatenation nor multiple species tree methods resolve the Westlandica group as monophyletic. The nuclear analyses suggest a geographic distinction between clearly defined monophyletic North Island clades and unresolved South Island clades. We suggest that more extreme habitat modification on South Island during the Pliocene and Pleistocene resulted in secondary contact and hybridization between species pairs and a series of mitochondrial capture events followed by subsequent lineage evolution.}, }
@article {pmid28829360, year = {2017}, author = {Vasileiou, PVS and Mourouzis, I and Pantos, C}, title = {Principal Aspects Regarding the Maintenance of Mammalian Mitochondrial Genome Integrity.}, journal = {International journal of molecular sciences}, volume = {18}, number = {8}, pages = {}, doi = {10.3390/ijms18081821}, pmid = {28829360}, issn = {1422-0067}, mesh = {Animals ; DNA Damage ; DNA Repair ; DNA, Mitochondrial ; Evolution, Molecular ; *Genome, Mitochondrial ; Genomic Instability ; Genomic Structural Variation ; *Genomics/methods ; *Homeostasis ; Humans ; Mammals/*genetics ; Mitochondrial Degradation/genetics ; Mitochondrial Dynamics/genetics ; }, abstract = {Mitochondria have emerged as key players regarding cellular homeostasis not only due to their contribution regarding energy production through oxidative phosphorylation, but also due to their involvement in signaling, ion regulation, and programmed cell death. Indeed, current knowledge supports the notion that mitochondrial dysfunction is a hallmark in the pathogenesis of various diseases. Mitochondrial biogenesis and function require the coordinated action of two genomes: nuclear and mitochondrial. Unfortunately, both intrinsic and environmental genotoxic insults constantly threaten the integrity of nuclear as well as mitochondrial DNA. Despite the extensive research that has been made regarding nuclear genome instability, the importance of mitochondrial genome integrity has only recently begun to be elucidated. The specific architecture and repair mechanisms of mitochondrial DNA, as well as the dynamic behavior that mitochondria exert regarding fusion, fission, and autophagy participate in mitochondrial genome stability, and therefore, cell homeostasis.}, }
@article {pmid28822138, year = {2017}, author = {Khoshravesh, R and Lundsgaard-Nielsen, V and Sultmanis, S and Sage, TL}, title = {Light Microscopy, Transmission Electron Microscopy, and Immunohistochemistry Protocols for Studying Photorespiration.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1653}, number = {}, pages = {243-270}, doi = {10.1007/978-1-4939-7225-8_17}, pmid = {28822138}, issn = {1940-6029}, mesh = {Arabidopsis/*physiology/ultrastructure ; Carbon Dioxide/metabolism ; Chloroplasts/metabolism/ultrastructure ; Cytosol/metabolism/ultrastructure ; Glycolates/metabolism ; Immunohistochemistry/*methods ; Microscopy, Electron, Transmission/instrumentation/*methods ; Microtomy/instrumentation/methods ; Mitochondria/metabolism/ultrastructure ; Oxygen/metabolism ; Oxygen Consumption/*physiology ; Peroxisomes/metabolism/ultrastructure ; Photosynthesis/*physiology ; Plant Leaves/*physiology/ultrastructure ; Ribulose-Bisphosphate Carboxylase/metabolism ; Staining and Labeling/instrumentation/methods ; Tissue Embedding/methods ; Tissue Fixation/methods ; }, abstract = {High-resolution images obtained from plant tissues processed for light microscopy, transmission electron microscopy, and immunohistochemistry have provided crucial links between plant subcellular structure and physiology during photorespiration as well as the impact of photorespiration on plant evolution and development. This chapter presents established protocols to guide researchers in the preparation of plant tissues for high-resolution imaging with a light and transmission electron microscope and detection of proteins using immunohistochemistry. Discussion of concepts and theory behind each step in the process from tissue preservation to staining of resin-embedded tissues is included to enhance the understanding of all steps in the procedure. We also include a brief protocol for quantification of cellular parameters from high-resolution images to help researchers rigorously test hypotheses.}, }
@article {pmid28821609, year = {2017}, author = {Lyons, A and Coleman, M and Riis, S and Favre, C and O'Flanagan, CH and Zhdanov, AV and Papkovsky, DB and Hursting, SD and O'Connor, R}, title = {Insulin-like growth factor 1 signaling is essential for mitochondrial biogenesis and mitophagy in cancer cells.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {41}, pages = {16983-16998}, doi = {10.1074/jbc.M117.792838}, pmid = {28821609}, issn = {1083-351X}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; }, mesh = {Carrier Proteins/genetics/metabolism ; Cell Survival/genetics ; Humans ; Insulin-Like Growth Factor I/genetics/*metabolism ; MCF-7 Cells ; Membrane Proteins/genetics/metabolism ; Mitochondria/genetics/*metabolism ; *Mitochondrial Degradation ; *Mitochondrial Dynamics ; NF-E2-Related Factor 2/genetics/metabolism ; Neoplasm Proteins/genetics/*metabolism ; Neoplasms/genetics/*metabolism/pathology ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics/metabolism ; Proto-Oncogene Proteins/genetics/metabolism ; Receptors, Somatomedin/genetics/metabolism ; *Signal Transduction ; Tumor Suppressor Proteins/genetics/metabolism ; }, abstract = {Mitochondrial activity and metabolic reprogramming influence the phenotype of cancer cells and resistance to targeted therapy. We previously established that an insulin-like growth factor 1 (IGF-1)-inducible mitochondrial UTP carrier (PNC1/SLC25A33) promotes cell growth. This prompted us to investigate whether IGF signaling is essential for mitochondrial maintenance in cancer cells and whether this contributes to therapy resistance. Here we show that IGF-1 stimulates mitochondrial biogenesis in a range of cell lines. In MCF-7 and ZR75.1 breast cancer cells, IGF-1 induces peroxisome proliferator-activated receptor γ coactivator 1β (PGC-1β) and PGC-1α-related coactivator (PRC). Suppression of PGC-1β and PRC with siRNA reverses the effects of IGF-1 and disrupts mitochondrial morphology and membrane potential. IGF-1 also induced expression of the redox regulator nuclear factor-erythroid-derived 2-like 2 (NFE2L2 alias NRF-2). Of note, MCF-7 cells with acquired resistance to an IGF-1 receptor (IGF-1R) tyrosine kinase inhibitor exhibited reduced expression of PGC-1β, PRC, and mitochondrial biogenesis. Interestingly, these cells exhibited mitochondrial dysfunction, indicated by reactive oxygen species expression, reduced expression of the mitophagy mediators BNIP3 and BNIP3L, and impaired mitophagy. In agreement with this, IGF-1 robustly induced BNIP3 accumulation in mitochondria. Other active receptor tyrosine kinases could not compensate for reduced IGF-1R activity in mitochondrial protection, and MCF-7 cells with suppressed IGF-1R activity became highly dependent on glycolysis for survival. We conclude that IGF-1 signaling is essential for sustaining cancer cell viability by stimulating both mitochondrial biogenesis and turnover through BNIP3 induction. This core mitochondrial protective signal is likely to strongly influence responses to therapy and the phenotypic evolution of cancer.}, }
@article {pmid28818345, year = {2017}, author = {Novikova, O and Belfort, M}, title = {Mobile Group II Introns as Ancestral Eukaryotic Elements.}, journal = {Trends in genetics : TIG}, volume = {33}, number = {11}, pages = {773-783}, doi = {10.1016/j.tig.2017.07.009}, pmid = {28818345}, issn = {0168-9525}, support = {R01 GM039422/GM/NIGMS NIH HHS/United States ; R01 GM044844/GM/NIGMS NIH HHS/United States ; R37 GM039422/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Eukaryotic Cells ; Interspersed Repetitive Sequences ; *Introns ; RNA, Catalytic/genetics ; Spliceosomes ; }, abstract = {The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes. Although there is no doubt that prokaryotic and organellar group II introns are evolutionary related, there are remarkable differences in survival strategies between them. Furthermore, an evolutionary relationship of group II introns to eukaryotic retroelements, including telomeres, and spliceosomes is unmistakable.}, }
@article {pmid28812460, year = {2017}, author = {Martín-Hernández, E and García-Silva, MT and Quijada-Fraile, P and Rodríguez-García, ME and Rivera, H and Hernández-Laín, A and Coca-Robinot, D and Fernández-Toral, J and Arenas, J and Martín, MA and Martínez-Azorín, F}, title = {Myopathic mtDNA Depletion Syndrome Due to Mutation in TK2 Gene.}, journal = {Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society}, volume = {20}, number = {5}, pages = {416-420}, doi = {10.1177/1093526616686439}, pmid = {28812460}, issn = {1093-5266}, abstract = {Whole-exome sequencing was used to identify the disease gene(s) in a Spanish girl with failure to thrive, muscle weakness, mild facial weakness, elevated creatine kinase, deficiency of mitochondrial complex III and depletion of mtDNA. With whole-exome sequencing data, it was possible to get the whole mtDNA sequencing and discard any pathogenic variant in this genome. The analysis of whole exome uncovered a homozygous pathogenic mutation in thymidine kinase 2 gene (TK2; NM_004614.4:c.323 C>T, p.T108M). TK2 mutations have been identified mainly in patients with the myopathic form of mtDNA depletion syndromes. This patient presents an atypical TK2-related myopathic form of mtDNA depletion syndromes, because despite having a very low content of mtDNA (<20%), she presents a slower and less severe evolution of the disease. In conclusion, our data confirm the role of TK2 gene in mtDNA depletion syndromes and expanded the phenotypic spectrum.}, }
@article {pmid28806979, year = {2017}, author = {Zachar, I and Szathmáry, E}, title = {Breath-giving cooperation: critical review of origin of mitochondria hypotheses : Major unanswered questions point to the importance of early ecology.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {19}, doi = {10.1186/s13062-017-0190-5}, pmid = {28806979}, issn = {1745-6150}, mesh = {*Biological Evolution ; Energy Metabolism ; Genome, Mitochondrial ; *Mitochondria ; *Models, Biological ; Phagocytosis ; Phylogeny ; }, abstract = {The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. We have objectively compared contending hypotheses under these questions to find the most plausible course of events and to draw insight on missing pieces of the puzzle. Since endosymbiosis borders evolution and ecology, and since a realistic theory has to comply with both domains' constraints, the conclusion is that the most important aspect to clarify is the initial ecological relationship of partners. Metabolic benefits are largely irrelevant at this initial phase, where ecological costs could be more disruptive. There is no single theory capable of answering all questions indicating a severe lack of ecological considerations. A new theory, compliant with recent phylogenomic results, should adhere to these criteria.<br><br>REVIEWERS: This article was reviewed by Michael W. Gray, William F. Martin and Purificación López-García.}, }
@article {pmid28801771, year = {2017}, author = {Schmitt, C and Betz, O}, title = {Morphology and ultrastructure of the tarsal adhesive organs of the Madagascar hissing cockroach Gromphadorhina portentosa.}, journal = {Cell and tissue research}, volume = {370}, number = {2}, pages = {243-265}, doi = {10.1007/s00441-017-2661-5}, pmid = {28801771}, issn = {1432-0878}, mesh = {Adhesives/*analysis ; Animals ; Cockroaches/*anatomy &amp; histology/cytology/*ultrastructure ; Cryoelectron Microscopy ; Epidermis/anatomy &amp; histology/cytology/ultrastructure ; Female ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Walking ; }, abstract = {The present transmission and scanning electron microscopic study of the ultramorphology of the pliable attachment pads (arolium, euplantulae) of the Madagascar hissing cockroach Gromphadorhina portentosa reveals structural evidence for their function in producing, storing, and secreting an adhesion-mediating secretion and releasing it to the exterior. The exocrine epidermal tissue of both the arolium and the euplantula is significantly enlarged by numerous invaginations stretching into the hemolymph cavity. Its cells show large nuclei, numerous mitochondria, Golgi complexes, and a prominent rough-surfaced endoplasmic reticulum integrated within an electron-dense cytoplasm that contains numerous vesicles of diverse electron density and size. Invaginations of the cell membrane provide evidence for strong membrane turnover. The glandular epithelium of both the arolium and the euplantula releases the adhesion-mediating secretion into a subcuticular void from which it has to permeate the thick cuticle of the adhesive pads. The subcuticular void is compartmentalized by cuticle bands through which the adhesion-mediating secretion permeates via small canals. The secretion subsequently enters a larger storage reservoir before being received by a prominent sponge-like cuticle. The structural differences between the arolium and the euplantula consist of the number and length of the interdigitations spanning the hemolymph cavity, of the subdivision of the subcuticular reservoir by cuticle bands, and of the thickness of the sponge-like cuticle. The structural results are discussed with respect to the production of a chemically complex (emulsion-like) adhesive, its controlled release to the exterior, and the micromechanical properties of the cuticle of the pliable pad.}, }
@article {pmid28798696, year = {2017}, author = {Wu, X and Wu, FH and Wu, Q and Zhang, S and Chen, S and Sima, M}, title = {Phylogenetic and Molecular Evolutionary Analysis of Mitophagy Receptors under Hypoxic Conditions.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {539}, doi = {10.3389/fphys.2017.00539}, pmid = {28798696}, issn = {1664-042X}, abstract = {As animals evolved to use oxygen as the main strategy to produce ATP through the process of mitochondrial oxidative phosphorylation, the ability to adapt to fluctuating oxygen concentrations is a crucial component of evolutionary pressure. Three mitophagy receptors, FUNDC1, BNIP3 and NIX, induce the removal of dysfunctional mitochondria (mitophagy) under prolonged hypoxic conditions in mammalian cells, to maintain oxygen homeostasis and prevent cell death. However, the evolutionary origins and structure-function relationships of these receptors remain poorly understood. Here, we found that FUN14 domain-containing proteins are present in archaeal, bacterial and eukaryotic genomes, while the family of BNIP3 domain-containing proteins evolved from early animals. We investigated conservation patterns of the critical amino acid residues of the human mitophagy receptors. These residues are involved in receptor regulation, mainly through phosphorylation, and in interaction with LC3 on the phagophore. Whereas FUNDC1 may be able to bind to LC3 under the control of post-translational regulations during the early evolution of vertebrates, BINP3 and NIX had already gained the ability for LC3 binding in early invertebrates. Moreover, FUNDC1 and BNIP3 each lack a layer of phosphorylation regulation in fishes that is conserved in land vertebrates. Molecular evolutionary analysis revealed that BNIP3 and NIX, as the targets of oxygen sensing HIF-1α, showed higher rates of substitution in fishes than in mammals. Conversely, FUNDC1 and its regulator MARCH5 showed higher rates of substitution in mammals. Thus, we postulate that the structural traces of mitophagy receptors in land vertebrates and fishes may reflect the process of vertebrate transition from water onto land, during which the changes in atmospheric oxygen concentrations acted as a selection force in vertebrate evolution. In conclusion, our study, combined with previous experimental results, shows that hypoxia-induced mitophagy regulated by FUDNC1/MARCH5 might use a different mechanism from the HIF-1α-dependent mitophagy regulated by BNIP3/NIX.}, }
@article {pmid28792749, year = {2017}, author = {Thompson, AD and Bewersdorf, J and Toomre, D and Schepartz, A}, title = {HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution.}, journal = {Biochemistry}, volume = {56}, number = {39}, pages = {5194-5201}, doi = {10.1021/acs.biochem.7b00545}, pmid = {28792749}, issn = {1520-4995}, support = {F31 GM119259/GM/NIGMS NIH HHS/United States ; 095927/A/11/Z//Wellcome Trust/United Kingdom ; R01 GM118486/GM/NIGMS NIH HHS/United States ; P30 DK045735/DK/NIDDK NIH HHS/United States ; R01 GM083257/GM/NIGMS NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {HeLa Cells ; Humans ; Intracellular Membranes/metabolism ; Molecular Imaging/*methods ; Organelles/*metabolism ; Signal-To-Noise Ratio ; Time Factors ; }, abstract = {Living cells are complex and dynamic assemblies that carefully sequester and orchestrate multiple diverse processes that enable growth, division, regulation, movement, and communication. Membrane-bound organelles such as the endoplasmic reticulum, mitochondria, plasma membrane, and others are integral to these processes, and their functions demand dynamic reorganization in both space and time. Visualizing these dynamics in live cells over long time periods demands probes that label discrete organelles specifically, at high density, and withstand long-term irradiation. Here we describe the evolution of our work on the development of a set of high-density environmentally sensitive (HIDE) membrane probes that enable long-term, live-cell nanoscopy of the dynamics of multiple organelles in live cells using single-molecule switching and stimulated emission depletion imaging modalities.}, }
@article {pmid28791889, year = {2018}, author = {Greenberg, EF and Vatolin, S}, title = {Symbiotic Origin of Aging.}, journal = {Rejuvenation research}, volume = {21}, number = {3}, pages = {225-231}, doi = {10.1089/rej.2017.1973}, pmid = {28791889}, issn = {1557-8577}, abstract = {Normally aging cells are characterized by an unbalanced mitochondrial dynamic skewed toward punctate mitochondria. Genetic and pharmacological manipulation of mitochondrial fission/fusion cycles can contribute to both accelerated and decelerated cellular or organismal aging. In this work, we connect these experimental data with the symbiotic theory of mitochondrial origin to generate new insight into the evolutionary origin of aging. Mitochondria originated from autotrophic α-proteobacteria during an ancient endosymbiotic event early in eukaryote evolution. To expand beyond individual host cells, dividing α-proteobacteria initiated host cell lysis; apoptosis is a product of this original symbiont cell lytic exit program. Over the course of evolution, the host eukaryotic cell attenuated the harmful effect of symbiotic proto-mitochondria, and modern mitochondria are now functionally interdependent with eukaryotic cells; they retain their own circular genomes and independent replication timing. In nondividing differentiated or multipotent eukaryotic cells, intracellular mitochondria undergo repeated fission/fusion cycles, favoring fission as organisms age. The discordance between cellular quiescence and mitochondrial proliferation generates intracellular stress, eventually leading to a gradual decline in host cell performance and age-related pathology. Hence, aging evolved from a conflict between maintenance of a quiescent, nonproliferative state and the evolutionarily conserved propagation program driving the life cycle of former symbiotic organisms: mitochondria.}, }
@article {pmid28782594, year = {2017}, author = {Poliseno, A and Feregrino, C and Sartoretto, S and Aurelle, D and Wörheide, G and McFadden, CS and Vargas, S}, title = {Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae).}, journal = {Molecular phylogenetics and evolution}, volume = {115}, number = {}, pages = {181-189}, doi = {10.1016/j.ympev.2017.08.001}, pmid = {28782594}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*classification/genetics ; Biological Evolution ; DNA/chemistry/isolation &amp; purification/metabolism ; Genetic Variation ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/classification/genetics ; Phylogeny ; RNA, Ribosomal/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.}, }
@article {pmid28782202, year = {2017}, author = {Speijer, D}, title = {Evolution of peroxisomes illustrates symbiogenesis.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {9}, pages = {}, doi = {10.1002/bies.201700050}, pmid = {28782202}, issn = {1521-1878}, mesh = {Adaptation, Biological/physiology ; Animals ; Biological Evolution ; Eukaryotic Cells/metabolism/physiology ; Humans ; Mitochondria/metabolism/physiology ; Oxidation-Reduction ; Peroxisomes/*metabolism/*physiology ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/physiology ; }, abstract = {Recently, the group of McBride reported a stunning observation regarding peroxisome biogenesis: newly born peroxisomes are hybrids of mitochondrial and ER-derived pre-peroxisomes. What was stunning? Studies performed with the yeast Saccharomyces cerevisiae had convincingly shown that peroxisomes are ER-derived, without indications for mitochondrial involvement. However, the recent finding using fibroblasts dovetails nicely with a mechanism inferred to be driving the eukaryotic invention of peroxisomes: reduction of mitochondrial reactive oxygen species (ROS) generation associated with fatty acid (FA) oxidation. This not only explains the mitochondrial involvement, but also its apparent absence in yeast. The latest results allow a reconstruction of the evolution of the yeast's highly derived metabolism and its limitations as a model organism in this instance. As I review here, peroxisomes are eukaryotic inventions reflecting mutual host endosymbiont adaptations: this is predicted by symbiogenetic theory, which states that the defining eukaryotic characteristics evolved as a result of mutual adaptations of two merging prokaryotes.}, }
@article {pmid28780151, year = {2017}, author = {Addy, F and Wassermann, M and Kagendo, D and Ebi, D and Zeyhle, E and Elmahdi, IE and Umhang, G and Casulli, A and Harandi, MF and Aschenborn, O and Kern, P and Mackenstedt, U and Romig, T}, title = {Genetic differentiation of the G6/7 cluster of Echinococcus canadensis based on mitochondrial marker genes.}, journal = {International journal for parasitology}, volume = {47}, number = {14}, pages = {923-931}, doi = {10.1016/j.ijpara.2017.06.003}, pmid = {28780151}, issn = {1879-0135}, mesh = {Africa ; Animals ; Camelus ; Cattle ; DNA, Mitochondrial/chemistry ; Deer ; Dogs ; Echinococcus/classification/*genetics ; Europe ; Genetic Markers/*genetics ; Genetic Variation/*genetics ; Goats ; Haplotypes/genetics ; Humans ; Middle East ; Mitochondria/*genetics ; Multigene Family/*genetics ; Phylogeny ; Polymorphism, Genetic ; Swine ; Wolves ; }, abstract = {Among the genotype/species causing cystic echinococcosis, the taxonomic status of Echinococcus canadensis is only partially resolved. Within E. canadensis, four genotypes (G6, G7, G8 and G10) have been described based on short mitochondrial sequences, of which G6 and G7 (the 'camel' and the 'pig' strain, respectively) are closely related and variously regarded as microvariants of a single strain G6/7. Globally, this G6/7 cluster is the second most important agent of human cystic echinococcosis and is the predominant Echinococcus taxon in large parts of sub-Saharan Africa. To add data on the internal structure and the geographical distribution of this cluster, we analysed diversity and population structure of 296 isolates of E. canadensis from sub-Saharan Africa, the Middle East and Europe using the complete mitochondrial cytochrome c oxidase subunit 1 (cox1) (1,608bp) and NADH dehydrogenase subunit 1 (nad1) (894bp) gene sequences. Polymorphism of the mtDNA loci gave 51 (cox1), 33 (nad1) and 73 (cox1-nad1 concatenated) haplotypes. African and Middle Eastern isolates mainly grouped in a star-like structure around a predominant haplotype, while the European isolates produced more diversified networks. Although the cox1 diagnostic sequence for G6 is frequent in the African/Middle Eastern sub-cluster, and that for G7 is common in the European isolates, numerous intermediate variants prevent a clear distinction into 'G6' or 'G7', and the entire taxon is best treated as a common haplotype cluster G6/7. Meanwhile, the G6/7 cluster is clearly distinct from sequences of wildlife isolates of G8 and G10 from the northern hemisphere, and sequences of the latter genotypes were remarkably distant from each other. It is clear from the present study that, based on mitochondrial data, G6/7 is a coherent genotypic entity within E. canadensis that retains substantial intraspecific variance, and sub-populations share common ancestral polymorphisms and haplotypes. This study provides the basis for wider biogeographic comparison and population genetics studies of this taxon.}, }
@article {pmid28779732, year = {2016}, author = {Aziz, NMA and Esa, Y and Arshad, A}, title = {DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene.}, journal = {Journal of environmental biology}, volume = {37}, number = {4 Spec No}, pages = {725-733}, pmid = {28779732}, issn = {0254-8704}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Fishes/*genetics ; Haplotypes ; Mitochondria/*enzymology ; *Phylogeny ; Species Specificity ; }, abstract = {The present study was carried out to examine the species identification and phylogenetic relationships of groupers in Malaysia using mitochondrial Cytochrome c Oxidase I (COI) gene, commonly known as barcoding gene. A total of 63 individuals comprising 10 species from three genera were collected from the coastal areas of Johor, Kelantan, Pahang, Perak, Selangor and Terengganu. All the individuals were morphologically identified and molecular works involved polymerase chain reaction (PCR) and sequencing of COI barcoding fragment (655 base pairs). Results from the BLAST search showed that 55 sequences could be assigned to 10 grouper species with high percentage identity index (≥95% to 100%), while eight grouper individuals showed discrepancies in their taxonomic identification based on the morphology and the COI barcoding results. The histogram of distances showed that there was a clear-cut barcode gap present in the sequences indicating a clear separation between intraspecific and interspecific distances. The pairwise genetic distances showed lowest pairwise distance between P. leopardus and P. maculatus (4.4%), while the highest pairwise distance was between E. bleekeri and P. maculatus (23.5%), supporting their morphological and habitat similarities and differences. Phylogenetic analysis (Neighbor-Joining) showed the presence of two major clades (1) genus Epinephelus vs (2) genus Plectropomus and Cephalopholis). In conclusion, the present study has managed to show the accuracy of DNA barcoding method for species identification, and utilization of COI gene for phylogenetic study among groupers. ?}, }
@article {pmid28778567, year = {2018}, author = {Chen, XJ and Clark-Walker, GD}, title = {Unveiling the mystery of mitochondrial DNA replication in yeasts.}, journal = {Mitochondrion}, volume = {38}, number = {}, pages = {17-22}, doi = {10.1016/j.mito.2017.07.009}, pmid = {28778567}, issn = {1872-8278}, support = {R01 AG023731/AG/NIA NIH HHS/United States ; R21 AG047400/AG/NIA NIH HHS/United States ; }, abstract = {Conventional DNA replication is initiated from specific origins and requires the synthesis of RNA primers for both the leading and lagging strands. In contrast, the replication of yeast mitochondrial DNA is origin-independent. The replication of the leading strand is likely primed by recombinational structures and proceeded by a rolling circle mechanism. The coexistent linear and circular DNA conformers facilitate the recombination-based initiation. The replication of the lagging strand is poorly understood. Re-evaluation of published data suggests that the rolling circle may also provide structures for the synthesis of the lagging-strand by mechanisms such as template switching. Thus, the coupling of recombination with rolling circle replication and possibly, template switching, may have been selected as an economic replication mode to accommodate the reductive evolution of mitochondria. Such a replication mode spares the need for conventional replicative components, including those required for origin recognition/remodelling, RNA primer synthesis and lagging-strand processing.}, }
@article {pmid28766501, year = {2017}, author = {Hu, JJ and Huang, S and Wen, T and Esch, GW and Liang, Y and Li, HL}, title = {Sarcocystis spp. in domestic sheep in Kunming City, China: prevalence, morphology, and molecular characteristics.}, journal = {Parasite (Paris, France)}, volume = {24}, number = {}, pages = {30}, doi = {10.1051/parasite/2017025}, pmid = {28766501}, issn = {1776-1042}, mesh = {Animals ; China/epidemiology ; DNA, Protozoan/chemistry/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Microscopy, Electron, Transmission/veterinary ; Mitochondria/enzymology ; Muscles/parasitology ; Phylogeny ; Prevalence ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sarcocystis/classification/genetics/*isolation &amp; purification/ultrastructure ; Sarcocystosis/epidemiology/parasitology/*veterinary ; Sheep ; Sheep Diseases/epidemiology/*parasitology ; }, abstract = {Sheep (Ovis aries) are intermediate hosts for at least six named species of Sarcocystis: S. tenella, S. arieticanis, S. gigantea, S. medusiformis, S. mihoensis, and S. microps. Here, only two species, S. tenella and S. arieticanis, were found in 79 of 86 sheep (91.9%) in Kunming, China, based on their morphological characteristics. Four genetic markers, i.e., 18S rRNA gene, 28S rRNA gene, mitochondrial cox1 gene, and ITS-1 region, were sequenced and characterized for the two species of Sarcocystis. Sequences of the three former markers for S. tenella shared high identities with those of S. capracanis in goats, i.e., 99.0%, 98.3%, and 93.6%, respectively; the same three marker sequences of S. arieticanis shared high identities with those of S. hircicanis in goats, i.e., 98.5%, 96.5%, and 92.5%, respectively. No sequences in GenBank were found to significantly resemble the ITS-1 regions of S. tenella and S. arieticanis. Identities of the four genetic markers for S. tenella and S. arieticanis were 96.3%, 95.4%, 82.5%, and 66.2%, respectively.}, }
@article {pmid28763510, year = {2017}, author = {Oliveira Da Silva, W and Pieczarka, JC and Ferguson-Smith, MA and O'Brien, PCM and Mendes-Oliveira, AC and Sampaio, I and Carneiro, J and Nagamachi, CY}, title = {Chromosomal diversity and molecular divergence among three undescribed species of Neacomys (Rodentia, Sigmodontinae) separated by Amazonian rivers.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182218}, doi = {10.1371/journal.pone.0182218}, pmid = {28763510}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Brazil ; *Chromosome Mapping ; Chromosome Painting ; Chromosomes/*ultrastructure ; Cytochromes b/metabolism ; Electron Transport Complex IV/metabolism ; Female ; Genetic Variation ; Geography ; Haplotypes ; In Situ Hybridization, Fluorescence ; Karyotyping ; Likelihood Functions ; Male ; Mitochondria/genetics ; Phylogeny ; Rodentia/classification/*genetics ; }, abstract = {The Neacomys genus (Rodentia, Sigmodontinae) is distributed in the Amazon region, with some species limited to a single endemic area, while others may occur more widely. The number of species within the genus and their geographical boundaries are not known accurately, due to their high genetic diversity and difficulties in taxonomic identification. In this work we collected Neacomys specimens from both banks of the Tapajós River in eastern Amazon, and studied them using chromosome painting with whole chromosome probes of Hylaeamys megacephalus (HME; Rodentia, Sigmodontinae), and molecular analysis using haplotypes of mitochondrial genes COI and Cytb. Chromosome painting shows that Neacomys sp. A (NSP-A, 2n = 58/FN = 68) and Neacomys sp. B (NSP-B, 2n = 54/FN = 66) differ by 11 fusion/fission events, one translocation, four pericentric inversions and four heterochromatin amplification events. Using haplotypes of the concatenated mitochondrial genes COI and Cyt b, Neacomys sp. (2n = 58/FN = 64 and 70) shows a mean divergence of 6.2% for Neacomys sp. A and 9.1% for Neacomys sp. B, while Neacomys sp. A and Neacomys sp. B presents a medium nucleotide divergence of 7.4%. Comparisons were made with other published Neacomys data. The Tapajós and Xingu Rivers act as geographic barriers that define the distribution of these Neacomys species. Furthermore, our HME probes reveal four synapomorphies for the Neacomys genus (associations HME 20/[13,22]/4, 6a/21, [9,10]/7b/[9,10] and 12/[16,17]) and demonstrate ancestral traits of the Oryzomyini tribe (HME 8a and 8b, 18 and 25) and Sigmodontinae subfamily (HME 15 and 24), which can be used as taxonomic markers for these groups.}, }
@article {pmid28763193, year = {2017}, author = {Stutz, K and Müller, AT and Hiss, JA and Schneider, P and Blatter, M and Pfeiffer, B and Posselt, G and Kanfer, G and Kornmann, B and Wrede, P and Altmann, KH and Wessler, S and Schneider, G}, title = {Peptide-Membrane Interaction between Targeting and Lysis.}, journal = {ACS chemical biology}, volume = {12}, number = {9}, pages = {2254-2259}, doi = {10.1021/acschembio.7b00504}, pmid = {28763193}, issn = {1554-8937}, mesh = {Amino Acid Sequence ; Anti-Infective Agents/*chemistry/metabolism/*pharmacology ; Antimicrobial Cationic Peptides/*chemistry/metabolism/*pharmacology ; Cell Membrane/drug effects/metabolism ; Cell Membrane Permeability ; HeLa Cells ; Humans ; Liposomes/*metabolism ; Mitochondria/*drug effects/metabolism ; Models, Molecular ; Staphylococcal Infections/drug therapy ; Staphylococcus aureus/*drug effects/growth &amp; development ; }, abstract = {Certain cationic peptides interact with biological membranes. These often-complex interactions can result in peptide targeting to the membrane, or in membrane permeation, rupture, and cell lysis. We investigated the relationship between the structural features of membrane-active peptides and these effects, to better understand these processes. To this end, we employed a computational method for morphing a membranolytic antimicrobial peptide into a nonmembranolytic mitochondrial targeting peptide by &quot;directed simulated evolution.&quot; The results obtained demonstrate that superficially subtle sequence modifications can strongly affect the peptides' membranolytic and membrane-targeting abilities. Spectroscopic and computational analyses suggest that N- and C-terminal structural flexibility plays a crucial role in determining the mode of peptide-membrane interaction.}, }
@article {pmid28755372, year = {2017}, author = {Negroni, L and Zivy, M and Lemaire, C}, title = {Mass Spectrometry of Mitochondrial Membrane Protein Complexes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1635}, number = {}, pages = {233-246}, doi = {10.1007/978-1-4939-7151-0_12}, pmid = {28755372}, issn = {1940-6029}, mesh = {Chromatography, Liquid ; Electrophoresis, Polyacrylamide Gel ; Membrane Proteins/*metabolism ; Mitochondrial Membranes/*metabolism ; Oxidative Phosphorylation ; Protein Subunits/metabolism ; Proteomics ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Tandem Mass Spectrometry ; }, abstract = {The ATP production (oxidative phosphorylation) involves five complexes embedded in the inner membrane of mitochondria. The yeast Saccharomyces cerevisiae is mainly used as a model for the study of oxidative phosphorylation; mutants are easy to produce and are still viable due to their ability to grow using the fermentation pathway. Here, we present a process for analyzing mitochondrial respiratory complexes using native electrophoresis (BN-PAGE) coupled to LC-MS/MS. BN-PAGE (1) permits the separation of functional respiratory complexes, thus allowing in-gel activity detection of most of the respiratory complexes and (2) provides convenient samples for bottom-up proteomics. Combining BN-PAGE and LC-MS/MS leads to the identification of the subunit composition of membrane complexes and offers the possibility of highlighting potential interacting proteins.}, }
@article {pmid28755245, year = {2018}, author = {Díaz, ML and Cuppari, S and Soresi, D and Carrera, A}, title = {In Silico Analysis of Fatty Acid Desaturase Genes and Proteins in Grasses.}, journal = {Applied biochemistry and biotechnology}, volume = {184}, number = {2}, pages = {484-499}, doi = {10.1007/s12010-017-2556-7}, pmid = {28755245}, issn = {1559-0291}, support = {PGI (24/B228)//Universidad Nacional del Sur/ ; PICT 2188//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, mesh = {Amino Acid Motifs ; *Computer Simulation ; Databases, Genetic ; *Fatty Acid Desaturases/biosynthesis/chemistry/genetics ; Gene Expression Regulation, Enzymologic/*physiology ; Gene Expression Regulation, Plant/*physiology ; Genes, Plant/*physiology ; *Plant Proteins/biosynthesis/chemistry/genetics ; *Poaceae/enzymology/genetics ; }, abstract = {Fatty acid desaturases (FADs) catalyze the introduction of a double bond into acyl chains. Two FAD groups have been identified in plants: acyl-acyl carrier proteins (ACPs) and acyl-lipid or membrane-bound FAD. The former catalyze the conversion of 18:0 to 18:1 and to date have only been identified in plants. The latter are found in eukaryotes and bacteria and are responsible for multiple desaturations. In this study, we identified 82 desaturase gene and protein sequences from 10 grass species deposited in GenBank that were analyzed using bioinformatic approaches. Subcellular localization predictions of desaturase family revealed their localization in plasma membranes, chloroplasts, endoplasmic reticula, and mitochondria. The in silico mapping showed multiple chromosomal locations in most species. Furthermore, the presence of the characteristic histidine domains, the predicted motifs, and the finding of transmembrane regions strongly support the protein functionality. The identification of putative regulatory sites in the promotor and the expression profiles revealed the wide range of pathways in which fatty acid desaturases are involved. This study is an updated survey on desaturases of grasses that provides a comprehensive insight into diversity and evolution. This characterization is a necessary first step before considering these genes as candidates for new biotechnological approaches.}, }
@article {pmid28754286, year = {2017}, author = {Harish, A and Kurland, CG}, title = {Mitochondria are not captive bacteria.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {88-98}, doi = {10.1016/j.jtbi.2017.07.011}, pmid = {28754286}, issn = {1095-8541}, mesh = {Biological Coevolution ; *Biological Evolution ; Mitochondria/chemistry/*genetics ; *Phylogeny ; *Proteome ; Symbiosis ; }, abstract = {Lynn Sagan's conjecture (1967) that three of the fundamental organelles observed in eukaryote cells, specifically mitochondria, plastids and flagella were once free-living primitive (prokaryotic) cells was accepted after considerable opposition. Even though the idea was swiftly refuted for the specific case of origins of flagella in eukaryotes, the symbiosis model in general was accepted for decades as a realistic hypothesis to describe the endosymbiotic origins of eukaryotes. However, a systematic analysis of the origins of the mitochondrial proteome based on empirical genome evolution models now indicates that 97% of modern mitochondrial protein domains as well their homologues in bacteria and archaea were present in the universal common ancestor (UCA) of the modern tree of life (ToL). These protein domains are universal modular building blocks of modern genes and genomes, each of which is identified by a unique tertiary structure and a specific biochemical function as well as a characteristic sequence profile. Further, phylogeny reconstructed from genome-scale evolution models reveals that Eukaryotes and Akaryotes (archaea and bacteria) descend independently from UCA. That is to say, Eukaryotes and Akaryotes are both primordial lineages that evolved in parallel. Finally, there is no indication of massive inter-lineage exchange of coding sequences during the descent of the two lineages. Accordingly, we suggest that the evolution of the mitochondrial proteome was autogenic (endogenic) and not endosymbiotic (exogenic).}, }
@article {pmid28749584, year = {2017}, author = {Kopečná, M and Vigouroux, A and Vilím, J and Končitíková, R and Briozzo, P and Hájková, E and Jašková, L and von Schwartzenberg, K and Šebela, M and Moréra, S and Kopečný, D}, title = {The ALDH21 gene found in lower plants and some vascular plants codes for a NADP+ -dependent succinic semialdehyde dehydrogenase.}, journal = {The Plant journal : for cell and molecular biology}, volume = {92}, number = {2}, pages = {229-243}, doi = {10.1111/tpj.13648}, pmid = {28749584}, issn = {1365-313X}, mesh = {Bryophyta/enzymology/*genetics ; Ferns/enzymology/*genetics ; Genes, Plant/*genetics/physiology ; Phylogeny ; Protein Conformation ; Structure-Activity Relationship ; Substrate Specificity ; Succinate-Semialdehyde Dehydrogenase/*genetics/metabolism ; Succinic Acid/metabolism ; gamma-Aminobutyric Acid/analogs &amp; derivatives/metabolism ; }, abstract = {Lower plant species including some green algae, non-vascular plants (bryophytes) as well as the oldest vascular plants (lycopods) and ferns (monilophytes) possess a unique aldehyde dehydrogenase (ALDH) gene named ALDH21, which is upregulated during dehydration. However, the gene is absent in flowering plants. Here, we show that ALDH21 from the moss Physcomitrella patens codes for a tetrameric NADP+ -dependent succinic semialdehyde dehydrogenase (SSALDH), which converts succinic semialdehyde, an intermediate of the γ-aminobutyric acid (GABA) shunt pathway, into succinate in the cytosol. NAD+ is a very poor coenzyme for ALDH21 unlike for mitochondrial SSALDHs (ALDH5), which are the closest related ALDH members. Structural comparison between the apoform and the coenzyme complex reveal that NADP+ binding induces a conformational change of the loop carrying Arg-228, which seals the NADP+ in the coenzyme cavity via its 2'-phosphate and α-phosphate groups. The crystal structure with the bound product succinate shows that its carboxylate group establishes salt bridges with both Arg-121 and Arg-457, and a hydrogen bond with Tyr-296. While both arginine residues are pre-formed for substrate/product binding, Tyr-296 moves by more than 1 Å. Both R121A and R457A variants are almost inactive, demonstrating a key role of each arginine in catalysis. Our study implies that bryophytes but presumably also some green algae, lycopods and ferns, which carry both ALDH21 and ALDH5 genes, can oxidize SSAL to succinate in both cytosol and mitochondria, indicating a more diverse GABA shunt pathway compared with higher plants carrying only the mitochondrial ALDH5.}, }
@article {pmid28742928, year = {2017}, author = {Choo, LQ and Crampton-Platt, A and Vogler, AP}, title = {Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum.}, journal = {Molecular ecology}, volume = {26}, number = {19}, pages = {5086-5098}, doi = {10.1111/mec.14258}, pmid = {28742928}, issn = {1365-294X}, mesh = {Animals ; *Body Size ; Borneo ; Contig Mapping ; DNA, Mitochondrial/genetics ; Diptera/anatomy &amp; histology/*classification ; *Genome, Mitochondrial ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA mixtures of mass-trapped arthropods (&quot;mitochondrial metagenomics&quot;), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small-bodied fraction was the by far most species-rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small-bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log-linear, indicating a uniformly filled abundance spectrum, especially for small-bodied species. Small-bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria.}, }
@article {pmid28742865, year = {2017}, author = {Yan, C and Mou, B and Meng, Y and Tu, F and Fan, Z and Price, M and Yue, B and Zhang, X}, title = {A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0181649}, doi = {10.1371/journal.pone.0181649}, pmid = {28742865}, issn = {1932-6203}, mesh = {Animals ; Asia, Southeastern ; Biological Evolution ; Frameshift Mutation/genetics ; Galliformes/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; }, abstract = {The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.}, }
@article {pmid28741861, year = {2018}, author = {López-Escardó, D and López-García, P and Moreira, D and Ruiz-Trillo, I and Torruella, G}, title = {Parvularia atlantis gen. et sp. nov., a Nucleariid Filose Amoeba (Holomycota, Opisthokonta).}, journal = {The Journal of eukaryotic microbiology}, volume = {65}, number = {2}, pages = {170-179}, doi = {10.1111/jeu.12450}, pmid = {28741861}, issn = {1550-7408}, support = {322669//European Research Council/International ; }, abstract = {The opisthokonts constitute a eukaryotic supergroup divided into two main clades: the holozoans, which include animals and their unicellular relatives, and the holomycotans, which include fungi, opisthosporidians, and nucleariids. Nucleariids are phagotrophic filose amoebae that phenotypically resemble more their distant holozoan cousins than their holomycotan phylogenetic relatives. Despite their evolutionary interest, the diversity and internal phylogenetic relationships within the nucleariids remain poorly studied. Here, we formally describe and characterize by molecular phylogeny and microscopy observations Parvularia atlantis gen. et sp. nov. (formerly Nuclearia sp. ATCC 50694), and compare its features with those of other nucleariid genera. Parvularia is an amoebal genus characterized by radiating knobbed and branching filopodia. It exhibits prominent vacuoles observable under light microscopy, a cyst-like stage, and completely lacks cilia. P. atlantis possesses one or two nuclei with a central nucleolus, and mitochondria with flat or discoid cristae. These morphological features, although typical of nucleariids, represent a combination of characters different to those of any other described Nuclearia species. Likewise, 18S rRNA-based phylogenetic analyses show that P. atlantis represents a distinct lineage within the nucleariids.}, }
@article {pmid28738827, year = {2017}, author = {Lutfullahoğlu-Bal, G and Keskin, A and Seferoğlu, AB and Dunn, CD}, title = {Bacterial tail anchors can target to the mitochondrial outer membrane.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {16}, doi = {10.1186/s13062-017-0187-0}, pmid = {28738827}, issn = {1745-6150}, support = {637649//European Research Council/International ; }, mesh = {Escherichia coli Proteins/chemistry/*metabolism ; Eukaryotic Cells/metabolism/ultrastructure ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Organelle Biogenesis ; Protein Sorting Signals/physiology ; Protein Transport ; Saccharomyces cerevisiae/*metabolism/ultrastructure ; }, abstract = {BACKGROUND: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol.<br><br>RESULTS: Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacterium Escherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeast Saccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM.<br><br>CONCLUSIONS: Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins.<br><br>REVIEWERS: This article was reviewed by Michael Ryan and Thomas Simmen.}, }
@article {pmid28736036, year = {2017}, author = {Campos-Silva, C and Reyes-Torres, I and Rivera, M and Meza-Torres, C and Hernández-Camacho, JD and Rodríguez-Bies, E and Navas, P and López-Lluch, G}, title = {[Regulation of the expression of coenzyme Q-synthesis complex during ageing].}, journal = {Revista espanola de geriatria y gerontologia}, volume = {52}, number = {6}, pages = {307-312}, doi = {10.1016/j.regg.2017.03.003}, pmid = {28736036}, issn = {1578-1747}, mesh = {Aging/genetics/*metabolism ; Animals ; Gene Expression Regulation ; Male ; Mice ; Mice, Inbred C57BL ; Ubiquinone/*biosynthesis/genetics ; }, abstract = {INTRODUCTION: Coenzyme Q is an essential component in the activity of the mitochondrial electron transport chain. Its synthesis involves, at least, a complex of ten different proteins. In this study, an attempt is made to determine the evolution of the expression of the genes involved in coenzyme Q synthesis during mouse ageing.<br><br>MATERIAL AND METHODS: The messenger RNA (mRNA) of different organs, such as brain, liver, kidney and skeletal muscle from young (8 months), mature (18 months), and old (24 months) mice was extracted by using Trizol and was then analysed by real time PCR (qPCR) using specific primers for all the known components of the coenzyme Q-synthesis complex (COQ genes).<br><br>RESULTS: Liver showed the highest age-dependent changes in mRNA levels of the different components of Q-synthesis complex, affecting the extent of the variation as well as the significance of the change. In most of the cases, mRNA levels of the different components were higher in mature animals compared to young and old animals. When mRNAs of young and old animals were compared, only minor reductions of mRNA levels were found. Kidney showed a pattern similar to that found in liver as regards the changes in expression, although with lower increases in mature animals than those observed in the liver. Brain and skeletal muscle showed low variations, with muscle being the tissue with less changes, although a pattern similar to that found in liver and kidney was found, with slight increases in mature animals.<br><br>DISCUSSION: The results of this study indicate that ageing is an important factor affecting COQ gene expression, but its effect depends on the organ, and that mature animals show higher levels of mRNA than young and old animals. Taken into consideration the importance of coenzyme Q in cell metabolism and ageing, a more detailed study is needed to understand the gene regulation of the coenzyme Q-synthesis mechanisms during ageing.}, }
@article {pmid28733390, year = {2017}, author = {Ung, H and Karia, P and Ebine, K and Ueda, T and Yoshioka, K and Moeder, W}, title = {Triphosphate Tunnel Metalloenzyme Function in Senescence Highlights a Biological Diversification of This Protein Superfamily.}, journal = {Plant physiology}, volume = {175}, number = {1}, pages = {473-485}, doi = {10.1104/pp.17.00700}, pmid = {28733390}, issn = {1532-2548}, mesh = {Acid Anhydride Hydrolases/genetics/*metabolism ; Arabidopsis/*enzymology/genetics/physiology/radiation effects ; Arabidopsis Proteins/genetics/*metabolism ; Cell Death ; Darkness ; Gene Knockout Techniques ; Genes, Reporter ; Mitochondria/enzymology ; Mutation ; Organ Specificity ; Phenotype ; Plant Leaves/enzymology/genetics/physiology/radiation effects ; Polyphosphates/metabolism ; Protein Domains ; Pyrophosphatases/genetics/*metabolism ; Tobacco/enzymology/genetics/physiology ; }, abstract = {The triphosphate tunnel metalloenzyme (TTM) superfamily comprises a group of enzymes that hydrolyze organophosphate substrates. They exist in all domains of life, yet the biological role of most family members is unclear. Arabidopsis (Arabidopsis thaliana) encodes three TTM genes. We have previously reported that AtTTM2 displays pyrophosphatase activity and is involved in pathogen resistance. Here, we report the biochemical activity and biological function of AtTTM1 and diversification of the biological roles between AtTTM1 and 2 Biochemical analyses revealed that AtTTM1 displays pyrophosphatase activity similar to AtTTM2, making them the only TTMs characterized so far to act on a diphosphate substrate. However, knockout mutant analysis showed that AtTTM1 is not involved in pathogen resistance but rather in leaf senescence. AtTTM1 is transcriptionally up-regulated during leaf senescence, and knockout mutants of AtTTM1 exhibit delayed dark-induced and natural senescence. The double mutant of AtTTM1 and AtTTM2 did not show synergistic effects, further indicating the diversification of their biological function. However, promoter swap analyses revealed that they functionally can complement each other, and confocal microscopy revealed that both proteins are tail-anchored proteins that localize to the mitochondrial outer membrane. Additionally, transient overexpression of either gene in Nicotiana benthamiana induced senescence-like cell death upon dark treatment. Taken together, we show that two TTMs display the same biochemical properties but distinct biological functions that are governed by their transcriptional regulation. Moreover, this work reveals a possible connection of immunity-related programmed cell death and senescence through novel mitochondrial tail-anchored proteins.}, }
@article {pmid28716740, year = {2017}, author = {Ochoa, LE and Roxo, FF and DoNascimiento, C and Sabaj, MH and Datovo, A and Alfaro, M and Oliveira, C}, title = {Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae.}, journal = {Molecular phylogenetics and evolution}, volume = {115}, number = {}, pages = {71-81}, doi = {10.1016/j.ympev.2017.07.007}, pmid = {28716740}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/genetics ; Cytochromes b/classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Mitochondria/genetics ; Myosin Heavy Chains/classification/genetics ; Nuclear Proteins/classification/genetics ; Phylogeny ; RNA, Ribosomal, 16S/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {Trichomycteridae is the second most diverse family of the order Siluriformes, its members are widely distributed through the freshwaters of Central and South America, exhibiting an exceptional ecological and phenotypic disparity. The most diverse subfamily, Trichomycterinae, represented mainly by the genus Trichomycterus, historically has been recognized as non-monophyletic and various characters used to unite or divide its constituents are repeatedly called into question. No comprehensive molecular phylogenetic hypothesis regarding relationships of trichomycterids has been produced, and the present study is the first extensive phylogeny for the family Trichomycteridae, based on a multilocus dataset of three mitochondrial loci and two nuclear markers (3284bp total). Our analysis has the most comprehensive taxon-sampling of the Trichomycteridae published so far, including members of all subfamilies and a vast representation of Trichomycterus diversity. Analysis of these data showed a phylogenetic hypothesis with broad agreement between the Bayesian (BI) and maximum-likelihood (ML) trees. The results provided overwhelming support for the monophyletic status of Copionodontinae, Stegophilinae, Trichomycterinae, and Vandelliinae, but not Sarcoglanidinae and Glanapteryginae. A major feature of our results is the support to the current conceptualization of Trichomycterinae, which includes Ituglanis and Scleronema and excludes the &quot;Trichomycterus&quot; hasemani group. Divergence time analysis based on DNA substitution rates suggested a Lower Cretaceous origin of the family and the divergence events at subfamilial level shaped by Paleogene events in the geohistory of South America. This hypothesis lays a foundation for an array of future studies of evolution and biogeography of the family.}, }
@article {pmid28711665, year = {2017}, author = {Pérez, T and Rodríguez, F and Fernández, M and Albornoz, J and Domínguez, A}, title = {Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus.}, journal = {Gene}, volume = {628}, number = {}, pages = {63-71}, doi = {10.1016/j.gene.2017.07.035}, pmid = {28711665}, issn = {1879-0038}, mesh = {Animals ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Hybridization, Genetic ; Mitochondria/genetics ; Phylogeny ; *Pseudogenes ; Rupicapra/classification/*genetics ; }, abstract = {Mitochondrial pseudogenes (numts) inserted in the nuclear genome are frequently found in population studies. Its presence is commonly connected with problems and errors when they are confounded with true mitochondrial sequences. In the opposite side, numts can provide valuable phylogenetic information when they are copies of ancient mitochondrial lineages. We show that Rupicapra individuals of different geographic origin from the Cantabrian Mountains to the Apennines and the Caucasus share a nuclear COI fragment. The numt copies are monophyletic, and their pattern of differentiation shows two outstanding features: a long evolution as differentiated true mitochondrial lineage, and a recent integration and spread through the chamois populations. The COI pseudogene is much older than the present day mitochondrial clades of Rupicapra and occupies a basal position within the Rupicapra-Ammotragus-Arabitragus node. Joint analysis of this numt and a cytb pseudogene with a similar pattern of evolution places the source mitochondrial lineage as a sister branch that separated from the Ammotragus-Arabitragus lineage 6millionyearsago (Mya). The occurrence of this sequence in the nucleus of chamois suggests hybridization between highly divergent lineages. The integration event seems to be very recent, more recent than the split of the present day mtDNA lineages of Rupicapra (1.9Mya). This observation invites to think of the spread across the genus by horizontal transfer through recent male-biased dispersal.}, }
@article {pmid28709986, year = {2017}, author = {Barba-Montoya, J and Dos Reis, M and Yang, Z}, title = {Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.}, journal = {Molecular phylogenetics and evolution}, volume = {114}, number = {}, pages = {386-400}, doi = {10.1016/j.ympev.2017.07.005}, pmid = {28709986}, issn = {1095-9513}, support = {BB/N000609/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Calibration ; Cytochromes b/classification/genetics ; Electron Transport Complex IV/classification/genetics ; *Fossils/history ; History, Ancient ; Mitochondria/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; Plants/classification/genetics ; Primates/classification/genetics ; }, abstract = {Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny. We study a simple example that is analytically tractable, and analyze two real datasets (one of 10 primate species and another of 48 seed plant species) using three Bayesian dating programs: MCMCTree, MrBayes and BEAST2. We examine how different calibration strategies, the birth-death process, and automatic truncation (to enforce the constraint that ancestral nodes are older than descendent nodes) interact to determine the time prior. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. Our results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis.}, }
@article {pmid28708996, year = {2017}, author = {Bushell, E and Gomes, AR and Sanderson, T and Anar, B and Girling, G and Herd, C and Metcalf, T and Modrzynska, K and Schwach, F and Martin, RE and Mather, MW and McFadden, GI and Parts, L and Rutledge, GG and Vaidya, AB and Wengelnik, K and Rayner, JC and Billker, O}, title = {Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes.}, journal = {Cell}, volume = {170}, number = {2}, pages = {260-272.e8}, doi = {10.1016/j.cell.2017.06.030}, pmid = {28708996}, issn = {1097-4172}, support = {R01 AI028398/AI/NIAID NIH HHS/United States ; R56 AI028398/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Female ; Gene Knockout Techniques ; Genes, Essential ; *Genome, Protozoan ; Host-Parasite Interactions ; Metabolic Networks and Pathways ; Mice ; Mice, Inbred BALB C ; Plasmodium berghei/*genetics/*growth &amp; development/metabolism ; Saccharomyces cerevisiae/genetics ; Toxoplasma/genetics ; Trypanosoma brucei brucei/genetics ; }, abstract = {The genomes of malaria parasites contain many genes of unknown function. To assist drug development through the identification of essential genes and pathways, we have measured competitive growth rates in mice of 2,578 barcoded Plasmodium berghei knockout mutants, representing >50% of the genome, and created a phenotype database. At a single stage of its complex life cycle, P. berghei requires two-thirds of genes for optimal growth, the highest proportion reported from any organism and a probable consequence of functional optimization necessitated by genomic reductions during the evolution of parasitism. In contrast, extreme functional redundancy has evolved among expanded gene families operating at the parasite-host interface. The level of genetic redundancy in a single-celled organism may thus reflect the degree of environmental variation it experiences. In the case of Plasmodium parasites, this helps rationalize both the relative successes of drugs and the greater difficulty of making an effective vaccine.}, }
@article {pmid28704930, year = {2017}, author = {Lai, YC and Baker, JS and Donti, T and Graham, BH and Craigen, WJ and Anderson, AE}, title = {Mitochondrial Dysfunction Mediated by Poly(ADP-Ribose) Polymerase-1 Activation Contributes to Hippocampal Neuronal Damage Following Status Epilepticus.}, journal = {International journal of molecular sciences}, volume = {18}, number = {7}, pages = {}, doi = {10.3390/ijms18071502}, pmid = {28704930}, issn = {1422-0067}, support = {K08 NS063117/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Blotting, Western ; Electroencephalography ; Hippocampus/*metabolism/*pathology ; Mitochondria/*metabolism/*pathology ; Neurons/*metabolism/*pathology ; Poly (ADP-Ribose) Polymerase-1/*metabolism ; Rats ; Rats, Sprague-Dawley ; Status Epilepticus/*metabolism/*pathology ; }, abstract = {Mitochondrial dysfunction plays a central role in the neuropathology associated with status epilepticus (SE) and is implicated in the development of epilepsy. While excitotoxic mechanisms are well-known mediators affecting mitochondrial health following SE, whether hyperactivation of poly(ADP-ribose) polymerase-1 (PARP-1) also contributes to SE-induced mitochondrial dysfunction remains to be examined. Here we first evaluated the temporal evolution of poly-ADP-ribosylated protein levels in hippocampus following kainic acid-induced SE as a marker for PARP-1 activity, and found that PARP-1 was hyperactive at 24 h following SE. We evaluated oxidative metabolism and found decreased NAD⁺ levels by enzymatic cycling, and impaired NAD⁺-dependent mitochondrial respiration as measured by polarography at 24 h following SE. Stereological estimation showed significant cell loss in the hippocampal CA₁ and CA₃ subregions 72 h following SE. PARP-1 inhibition using N-(6-Oxo-5,6-dihydro-phenanthridin-2-yl)- N,N-dimethylacetamide (PJ-34) in vivo administration was associated with preserved NAD⁺ levels and NAD⁺-dependent mitochondrial respiration, and improved CA₁ neuronal survival. These findings suggest that PARP-1 hyperactivation contributes to SE-associated mitochondrial dysfunction and CA₁ hippocampal damage. The deleterious effects of PARP-1 hyperactivation on mitochondrial respiration are in part mediated through intracellular NAD⁺ depletion. Therefore, modulating PARP-1 activity may represent a potential therapeutic target to preserve intracellular energetics and mitochondrial function following SE.}, }
@article {pmid28703292, year = {2017}, author = {Bonnet, T and Leblois, R and Rousset, F and Crochet, PA}, title = {A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {9}, pages = {2140-2158}, doi = {10.1111/evo.13296}, pmid = {28703292}, issn = {1558-5646}, mesh = {Computer Simulation ; *DNA, Mitochondrial ; *Genome, Mitochondrial ; *Hybridization, Genetic ; Mitochondria ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of sex-biases, drift, negative selection against introgression in the nuclear genome, and spatial expansion. Most of these hypotheses are verbal, and have not been quantitatively evaluated so far. We use individual-based, multilocus, computer simulations of secondary contact under a wide range of demographic and genetic scenarios to evaluate the ability of the different mechanisms to produce discordant introgression. Sex-biases and spatial expansions fail to produce substantial mito-nuclear discordance. Drift and nuclear selection can produce strong discordance, but only under a limited range of conditions. In contrast, selection on the mitochondrial genome produces strong discordance, particularly when dispersal rates are low. However, commonly used statistical tests have little power to detect this selection. Altogether, these results dismiss several popular hypotheses, and provide support for adaptive mitochondrial introgression.}, }
@article {pmid28699890, year = {2017}, author = {Brandt, T and Mourier, A and Tain, LS and Partridge, L and Larsson, NG and Kühlbrandt, W}, title = {Changes of mitochondrial ultrastructure and function during ageing in mice and Drosophila.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, doi = {10.7554/eLife.24662}, pmid = {28699890}, issn = {2050-084X}, mesh = {Aging/*physiology ; Animals ; Cryoelectron Microscopy ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/*physiology ; Energy Metabolism ; Imaging, Three-Dimensional ; Mice ; Mitochondria/metabolism/*ultrastructure ; Organ Specificity ; Tomography ; }, abstract = {Ageing is a progressive decline of intrinsic physiological functions. We examined the impact of ageing on the ultrastructure and function of mitochondria in mouse and fruit flies (Drosophila melanogaster) by electron cryo-tomography and respirometry. We discovered distinct age-related changes in both model organisms. Mitochondrial function and ultrastructure are maintained in mouse heart, whereas subpopulations of mitochondria from mouse liver show age-related changes in membrane morphology. Subpopulations of mitochondria from young and old mouse kidney resemble those described for apoptosis. In aged flies, respiratory activity is compromised and the production of peroxide radicals is increased. In about 50% of mitochondria from old flies, the inner membrane organization breaks down. This establishes a clear link between inner membrane architecture and functional decline. Mitochondria were affected by ageing to very different extents, depending on the organism and possibly on the degree to which tissues within the same organism are protected against mitochondrial damage.}, }
@article {pmid28690821, year = {2017}, author = {Zhang, B and Zhang, YH and Wang, X and Zhang, HX and Lin, Q}, title = {The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment.}, journal = {Ecology and evolution}, volume = {7}, number = {13}, pages = {4951-4962}, doi = {10.1002/ece3.3067}, pmid = {28690821}, issn = {2045-7758}, abstract = {The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep-sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein-coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon-like noncanonical open reading frames (ORFs), and a control region-like (CR-like) element. All of the mitochondrial genes were coded by the same strand (the H-strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep-sea environment.}, }
@article {pmid28690785, year = {2017}, author = {Láruson, ÁJ}, title = {Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora.}, journal = {Ecology and evolution}, volume = {7}, number = {13}, pages = {4543-4551}, doi = {10.1002/ece3.3042}, pmid = {28690785}, issn = {2045-7758}, abstract = {In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently av