@article {pmid30738095,
year = {2019},
author = {Gong, L and Jiang, H and Zhu, K and Lu, X and Liu, L and Liu, B and Jiang, L and Ye, Y and Lü, Z},
title = {Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura.},
journal = {Gene},
volume = {695},
number = {},
pages = {75-83},
doi = {10.1016/j.gene.2019.01.035},
pmid = {30738095},
issn = {1879-0038},
mesh = {Animals ; Anomura/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Rearrangement/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; *Phylogeny ; },
abstract = {Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few Paguridae mitogenomes have been reported. Herein, we described the complete mitogenome of hermit crab Pagurus nigrofascia. The total length was 15,423 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNA genes, as well as an AT-rich region. The genome composition was highly A + T biased (71.4%), and exhibited a negative AT-skew (-0.006) and GC-skew (-0.138). Eight tRNA genes, two PCGs and an AT-rich region found to be rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination model were adopted to explain the large-scale gene rearrangement events. Two phylogenetic trees of Anomura involving 12 families were constructed. The results showed that all Paguridae species were clustered into one clade except Pagurus longicarpus, which for the first time imposed raises doubt about the morphological taxonomy of this species. Furthermore, the present study found that higher- level phylogenetic relationships within Anomura were controversial, compared with the previous studies. Our results help to better understand gene rearrangements and the evolutionary status of P. nigrofascia and lay foundation for further phylogenetic study of Anomura.},
}

Animals
Anomura/*genetics
DNA, Mitochondrial/genetics
*Evolution, Molecular
Gene Rearrangement/genetics
Genome, Mitochondrial/*genetics
Mitochondria/genetics
*Phylogeny

@article {pmid30208106,
year = {2018},
author = {Viret, A and Tsaparis, D and Tsigenopoulos, CS and Berrebi, P and Sabatini, A and Arculeo, M and Fassatoui, C and Magoulas, A and Marengo, M and Morales-Nin, B and Caill-Milly, N and Durieux, EDH},
title = {Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0203866},
pmid = {30208106},
issn = {1932-6203},
mesh = {Alleles ; Animals ; Atlantic Ocean ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/analysis/genetics ; Gene Flow ; Gene Frequency/genetics ; Genetic Variation ; Genetics, Population/methods ; Mediterranean Sea ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; },
abstract = {The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well.},
}

Alleles
Animals
Atlantic Ocean
Bayes Theorem
Cell Nucleus/*genetics
DNA, Mitochondrial/analysis/genetics
Gene Flow
Gene Frequency/genetics
Genetic Variation
Genetics, Population/methods
Mediterranean Sea
Microsatellite Repeats/genetics
Mitochondria/*genetics
Perciformes/*genetics
Phylogeny

@article {pmid30753430,
year = {2019},
author = {Hein, A and Brenner, S and Knoop, V},
title = {Multifarious Evolutionary Pathways of a Nuclear RNA Editing Factor: Disjunctions in Coevolution of DOT4 and Its Chloroplast Target rpoC1eU488SL.},
journal = {Genome biology and evolution},
volume = {11},
number = {3},
pages = {798-813},
doi = {10.1093/gbe/evz032},
pmid = {30753430},
issn = {1759-6653},
abstract = {Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 targeting ancient chloroplast editing sites in flowering plants. Here, we report on alternative evolutionary pathways for DOT4 addressing rpoC1eU488SL, a chloroplast editing site in the RNA polymerase β' subunit mRNA. Upon loss of rpoC1eU488SL by C-to-T conversion, DOT4 got lost multiple times independently in angiosperm evolution with intermediate states of DOT4 orthologs in various stages of degeneration. Surprisingly, we now also observe degeneration and loss of DOT4 despite retention of a C in the editing position (in Carica, Coffea, Vicia, and Spirodela). We find that the cytidine remains unedited, proving that DOT4 was not replaced by another editing factor. Yet another pathway of DOT4 evolution is observed among the Poaceae. Although the rpoC1eU488SL edit has been lost through C-to-T conversion, DOT4 orthologs not only remain conserved but also have their array of PPRs extended by six additional repeats. Here, the loss of the ancient target has likely allowed DOT4 to adapt for a new function. We suggest rps3 antisense transcripts as previously demonstrated in barley (Hordeum vulgare) arising from promotor sequences newly emerging in the rpl16 intron of Poaceae as a new candidate target for the extended PPR stretch of DOT4. Altogether, DOT4 and its target show more flexible pathways for evolution than the previously explored editing factors CLB19, CRR28, and RARE1. Certain plant clades (e.g., Amaranthus, Vaccinium, Carica, the Poaceae, Fabales, and Caryophyllales) show pronounced dynamics in the evolution of editing sites and corresponding factors.},
}

@article {pmid30486780,
year = {2018},
author = {Fletcher, K and Klosterman, SJ and Derevnina, L and Martin, F and Bertier, LD and Koike, S and Reyes-Chin-Wo, S and Mou, B and Michelmore, R},
title = {Comparative genomics of downy mildews reveals potential adaptations to biotrophy.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {851},
pmid = {30486780},
issn = {1471-2164},
support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD018223/OD/NIH HHS/United States ; S10 RR026825/RR/NCRR NIH HHS/United States ; Endowed Chair in Genomics//Novozymes Inc./ ; C06 RR012088/RR/NCRR NIH HHS/United States ; },
mesh = {Adaptation, Physiological/*genetics ; *Genomics ; Heterozygote ; Likelihood Functions ; Mitochondria/genetics ; Molecular Sequence Annotation ; Peronospora/*genetics/pathogenicity ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, RNA ; Terminal Repeat Sequences/genetics ; },
abstract = {BACKGROUND: Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years.

RESULTS: We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp.

CONCLUSIONS: We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.},
}

Adaptation, Physiological/*genetics
*Genomics
Heterozygote
Likelihood Functions
Mitochondria/genetics
Molecular Sequence Annotation
Peronospora/*genetics/pathogenicity
Phylogeny
Plant Diseases/*microbiology
Sequence Analysis, RNA
Terminal Repeat Sequences/genetics

@article {pmid30474737,
year = {2019},
author = {Guo, J and Miao, X and He, P and Li, M and Wang, S and Cui, J and Huang, C and He, L and Zhao, J},
title = {Babesia gibsoni endemic to Wuhan, China: mitochondrial genome sequencing, annotation, and comparison with apicomplexan parasites.},
journal = {Parasitology research},
volume = {118},
number = {1},
pages = {235-243},
doi = {10.1007/s00436-018-6158-2},
pmid = {30474737},
issn = {1432-1955},
support = {2017YFD0500402//National Key Research and Development Program of China/ ; 2015CB150300//National Basic Science Research Program (973 program) of China/ ; 31772729//National Natural Science Foundation of China/ ; 2017CFA020//Natural Science Foundation of Hubei Province/ ; },
mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/classification/genetics/isolation & purification ; Babesia/classification/genetics/*isolation & purification ; Babesiosis/*parasitology ; China/epidemiology ; Cytochromes b/genetics ; DNA Primers/genetics ; Dog Diseases/*parasitology ; Dogs ; *Genome, Mitochondrial ; Molecular Sequence Annotation ; Phylogeny ; Protozoan Infections, Animal/epidemiology/*parasitology ; Sequence Analysis, DNA ; },
abstract = {Babesia gibsoni (B. gibsoni), an intracellular apicomplexan protozoan, poses great threat to canine health. Currently, little information is available about the B. gibsoni (WH58) endemic to Wuhan, China. Here, the mitochondrial (mt) genome of B. gibsoni (WH58) was amplified by five pairs of primers and sequenced and annotated by alignment with the reported mt genome sequences of Babesia canis (B. canis, KC207822), Babesia orientalis (KF218819), Babesia bovis (AB499088), and Theileria equi (AB499091). The evolutionary relationships were analyzed with the amino acid sequences of cytochrome c oxidase I (cox1) and cytochrome b (cob) genes in apicomplexan parasite species. Additionally, the mt genomes of Babesia, Theileria, and Plasmodium spp. were compared in size, host infection, form, distribution, and direction of the protein-coding genes. The full size of the mt genome of B. gibsoni (WH58) was 5865 bp with a linear form, containing terminal-inverted repeats on both ends, six large subunit ribosomal RNA fragments, and three protein-coding genes: cox1, cob, and cytochrome c oxidase III (cox3). Babesia, Theileria, and Plasmodium spp. had a similar mt genome size of about 6000 bp. The mt genomes of parasites that cause canine babesiosis showed a slightly smaller size than the other species. Moreover, Babesia microti (R1 strain) was about 11,100 bp in size, which was twice larger than that of the other species. The mt form was linear for Babesia and Theileria spp. but circular for Plasmodium falciparum and Plasmodium knowlesi. Additionally, all the species contained the three protein-coding genes of cox1, cox3, and cob except Toxoplasma gondii (RH strain) which only contained the cox1 and cob genes. The phylogenetic analysis indicated that B. gibsoni (WH58) was more identical to B. gibsoni (AB499087), B. canis (KC207822), and Babesia rossi (KC207823) and most divergent from Babesia conradae in Babesia spp. Despite the highest similarity to B. gibsoni (AB499087) reported in Japan, B. gibsoni (WH58) showed notable differences in the sequence of nucleotides and amino acids and the property in virulence to host and in vitro cultivation. This study compared the mt genomes of the two B. gibsoni isolates and other parasites in the phylum Apicomplexa and provided new insights into their differences and evolutionary relationships.},
}

Amino Acid Sequence
Animals
Apicomplexa/classification/genetics/isolation & purification
Babesia/classification/genetics/*isolation & purification
Babesiosis/*parasitology
China/epidemiology
Cytochromes b/genetics
DNA Primers/genetics
Dog Diseases/*parasitology
Dogs
*Genome, Mitochondrial
Molecular Sequence Annotation
Phylogeny
Protozoan Infections, Animal/epidemiology/*parasitology
Sequence Analysis, DNA

@article {pmid29986214,
year = {2018},
author = {Angers, B and Chapdelaine, V and Deremiens, L and Vergilino, R and Leung, C and Doucet, SL and Glémet, H and Angers, A},
title = {Gene flow prevents mitonuclear co-adaptation: A comparative portrait of sympatric wild types and cybrids in the fish Chrosomus eos.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {27},
number = {},
pages = {77-84},
doi = {10.1016/j.cbd.2018.06.007},
pmid = {29986214},
issn = {1878-0407},
mesh = {Animals ; Cell Nucleus/genetics ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; Epigenesis, Genetic ; Female ; *Gene Flow ; Genetic Speciation ; Male ; Mitochondria/genetics ; Sympatry ; },
abstract = {Allospecific mtDNA can occasionally be beneficial for the fitness of populations. It is, however, difficult to assess the effect of mtDNA in natural conditions due to genetic and/or environmental interactions. In the fish Chrosomus eos, the transfer of C. neogaeus mitochondria occurs in a single generation and results in natural cybrids. For a few lakes in Quebec, C. eos can harbor either a C. eos mtDNA (wild types) or a C. neogaeus mtDNA (cybrids). Moreover, mtDNA of cybrids originated either from Mississippian or Atlantic glacial refuges. Such diversity provides a useful system for in situ assessment of allospecific mtDNA effects. We determined genetic, epigenetic and transcriptomic variation as well as mitochondrial enzymatic activity (complex IV) changes among wild types and cybrids either in sympatry or allopatry. Wild types and cybrids did not segregate spatially within a lake. Moreover, no significant genetic differentiation was detected among wild types and cybrids indicating sustained gene flow. Mitochondrial complex IV activity was higher for cybrids in both sympatry and allopatry while no difference was detected among cybrid haplotypes. Epigenetic and transcriptomic analyses revealed only subtle differences between sympatric wild types and cybrids compared to differences between sites. Altogether, these results indicate a limited influence of allospecific mtDNA in nuclear gene expression when controlling for genetic and environmental effects. The absence of a reproductive barrier between wild types and cybrids results in random association of either C. eos or C. neogaeus mtDNA with C. eos nDNA at each generation, and prevents mitonuclear co-adaptation in sympatry.},
}

Animals
Cell Nucleus/genetics
Cyprinidae/*genetics
DNA, Mitochondrial/*genetics
Epigenesis, Genetic
Female
*Gene Flow
Genetic Speciation
Male
Mitochondria/genetics
Sympatry

@article {pmid30201278,
year = {2018},
author = {Santos, HJ and Makiuchi, T and Nozaki, T},
title = {Reinventing an Organelle: The Reduced Mitochondrion in Parasitic Protists.},
journal = {Trends in parasitology},
volume = {34},
number = {12},
pages = {1038-1055},
doi = {10.1016/j.pt.2018.08.008},
pmid = {30201278},
issn = {1471-5007},
mesh = {Animals ; Biodiversity ; Biological Evolution ; Eukaryota/classification/cytology/*physiology ; Mitochondria/*physiology ; Parasites/classification/cytology/*physiology ; },
abstract = {Mitochondria originated from the endosymbiotic event commencing from the engulfment of an ancestral α-proteobacterium by the first eukaryotic ancestor. Establishment of niches has led to various adaptations among eukaryotes. In anaerobic parasitic protists, the mitochondria have undergone modifications by combining features shared from the aerobic mitochondria with lineage-specific components and mechanisms; a diversified class of organelles emerged and are generally called mitochondrion-related organelles (MROs). In this review we summarize and discuss the recent advances in the knowledge of MROs from parasitic protists, particularly the themes such as metabolic functions, contribution to parasitism, dynamics, protein targeting, and novel lineage- specific proteins, with emphasis on the diversity among these organelles.},
}

Animals
Biodiversity
Biological Evolution
Eukaryota/classification/cytology/*physiology
Mitochondria/*physiology
Parasites/classification/cytology/*physiology

@article {pmid30138782,
year = {2018},
author = {Treitli, SC and Kotyk, M and Yubuki, N and Jirounková, E and Vlasáková, J and Smejkalová, P and Šípek, P and Čepička, I and Hampl, V},
title = {Molecular and Morphological Diversity of the Oxymonad Genera Monocercomonoides and Blattamonas gen. nov.},
journal = {Protist},
volume = {169},
number = {5},
pages = {744-783},
doi = {10.1016/j.protis.2018.06.005},
pmid = {30138782},
issn = {1618-0941},
mesh = {Genetic Variation ; Microscopy, Electron ; Oxymonadida/*genetics/*growth & development/ultrastructure ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Oxymonads are a group of flagellates living as gut symbionts of insects or vertebrates. They have several unique features, one of them being the absence of mitochondria. Diversity of this group is seriously understudied, which is particularly true for small species from the family Polymastigidae. We isolated 34 strains of oxymonads with Polymastigidae-like morphology from 24 host species and unused cesspits and sequenced the SSU rRNA gene. Our strains formed two clades in the phylogenetic tree with Streblomastix strix branching between them. This topology was also supported by a three-gene phylogenetic analysis. Despite considerable genetic differences between the clades, light and electron microscopy revealed only subtle differences. The larger clade is considered genus Monocercomonoides and the isolates belonging here were classified into three new species (including the first potentially free-living species), two previously described species, and three unclassified lineages. The smaller clade, here described as Blattamonas gen. nov., consists of three newly described species. Concomitantly with the description of Blattamonas, we elevate the Monocercomonoides subgenus Brachymonas to the genus level. Our study shows that, despite their conserved morphology, the molecular diversity of Polymastigidae-like oxymonads is broad and represents a substantial part of the diversity of oxymonads.},
}

Genetic Variation
Microscopy, Electron
Oxymonadida/*genetics/*growth & development/ultrastructure
Phylogeny
Sequence Analysis, DNA

@article {pmid30075756,
year = {2018},
author = {Burke, SV and Ungerer, MC and Duvall, MR},
title = {Investigation of mitochondrial-derived plastome sequences in the Paspalum lineage (Panicoideae; Poaceae).},
journal = {BMC plant biology},
volume = {18},
number = {1},
pages = {152},
pmid = {30075756},
issn = {1471-2229},
support = {DEB-1120856//National Science Foundation/ ; DEB-1120761//National Science Foundation/ ; },
mesh = {DNA, Intergenic/genetics ; DNA, Plant/genetics ; Mitochondria/*genetics ; Paspalum/*genetics ; Phylogeny ; Plastids/*genetics ; Poaceae/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; },
abstract = {BACKGROUND: The grass family (Poaceae), ca. 12,075 species, is a focal point of many recent studies that aim to use complete plastomes to reveal and strengthen relationships within the family. The use of Next Generation Sequencing technology has revealed intricate details in many Poaceae plastomes; specifically the trnI - trnL intergenic spacer region. This study investigates this region and the putative mitochondrial inserts within it in complete plastomes of Paspalum and other Poaceae.

RESULTS: Nine newly sequenced plastomes, seven of which contain an insert within the trnI - trnL intergenic spacer, were combined into plastome phylogenomic and divergence date analyses with 52 other species. A robust Paspalum topology was recovered, originating at 10.6 Ma, with the insert arising at 8.7 Ma. The alignment of the insert across Paspalum reveals 21 subregions with pairwise homology in 19. In an analysis of emergent self-organizing maps of tetranucleotide frequencies, the Paspalum insert grouped with mitochondrial DNA.

CONCLUSIONS: A hypothetical ancestral insert, 17,685 bp in size, was found in the trnI - trnL intergenic spacer for the Paspalum lineage. A different insert, 2808 bp, was found in the same region for Paraneurachne muelleri. Seven different intrastrand deletion events were found within the Paspalum lineage, suggesting selective pressures to remove large portions of noncoding DNA. Finally, a tetranucleotide frequency analysis was used to determine that the origin of the insert in the Paspalum lineage is mitochondrial DNA.},
}

DNA, Intergenic/genetics
DNA, Plant/genetics
Mitochondria/*genetics
Paspalum/*genetics
Phylogeny
Plastids/*genetics
Poaceae/genetics
Sequence Alignment
Sequence Homology, Nucleic Acid

@article {pmid30300424,
year = {2018},
author = {Kobayashi, G and Araya, JF},
title = {Southernmost records of Escarpia spicata and Lamellibrachia barhami (Annelida: Siboglinidae) confirmed with DNA obtained from dried tubes collected from undiscovered reducing environments in northern Chile.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0204959},
pmid = {30300424},
issn = {1932-6203},
mesh = {Animals ; Annelida/classification/*genetics/microbiology ; Bacteria/genetics/isolation & purification ; Chile ; DNA/*chemistry/isolation & purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Hemoglobins/classification/genetics ; Mitochondria/genetics ; Phylogeny ; Protein Subunits/classification/genetics ; RNA, Ribosomal, 16S/chemistry/isolation & purification/metabolism ; Sequence Analysis, DNA ; Symbiosis ; },
abstract = {Deep-sea fishing bycatch enables collection of samples of rare species that are not easily accessible, for research purposes. However, these specimens are often degraded, losing diagnostic morphological characteristics. Several tubes of vestimentiferans, conspicuous annelids endemic to chemosynthetic environments, were obtained from a single batch of deep-sea fishing bycatch at depths of around 1,500 m off Huasco, northern Chile, as part of an ongoing study examining bycatch species. DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and an intron region within the hemoglobin subunit B2 (hbB2i) were successfully determined using vestimentiferans' dried-up tubes and their degraded inner tissue. Molecular phylogenetic analyses based on DNA sequence identified the samples as Escarpia spicata Jones, 1985, and Lamellibrachia barhami Webb, 1969. These are the southernmost records, vastly extending the geographical ranges of both species from Santa Catalina Island, California to northern Chile for E. spicata (over 8,000 km), and from Vancouver Island Margin to northern Chile for L. barhami (over 10,000 km). We also determined a 16S rRNA sequence of symbiotic bacteria of L. barhami. The sequence of the bacteria is the same as that of E. laminata, Lamellibrachia sp. 1, and Lamellibrachia sp.2 known from the Gulf of Mexico. The present study provides sound evidence forthe presence of reducing environments along the continental margin of northern Chile.},
}

Animals
Annelida/classification/*genetics/microbiology
Bacteria/genetics/isolation & purification
Chile
DNA/*chemistry/isolation & purification/metabolism
Electron Transport Complex IV/classification/genetics
Hemoglobins/classification/genetics
Mitochondria/genetics
Phylogeny
Protein Subunits/classification/genetics
RNA, Ribosomal, 16S/chemistry/isolation & purification/metabolism
Sequence Analysis, DNA
Symbiosis

@article {pmid29754387,
year = {2018},
author = {Zhu, C and Chen, P and Han, Y and Ruan, L},
title = {Low Genetic Diversity and Low Gene Flow Corresponded to a Weak Genetic Structure of Ruddy-Breasted Crake (Porzana fusca) in China.},
journal = {Biochemical genetics},
volume = {56},
number = {6},
pages = {586-617},
doi = {10.1007/s10528-018-9862-9},
pmid = {29754387},
issn = {1573-4927},
support = {NSFC no. 30960052//National Science Foundation of China/ ; no. 31260510//National Science Foundation of China/ ; no. KT201537//Water - resource Department of Jiangxi Province Science and Technological Project/ ; },
mesh = {Animals ; Birds/*genetics ; DNA, Mitochondrial ; *Gene Flow ; *Genetic Structures ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The Ruddy-breasted Crake (Porzana fusca) is an extremely poorly known species. Although it is not listed as globally endangered, in recent years, with the interference of climate change and human activities, its habitat is rapidly disappearing and its populations have been shrinking. There are two different life history traits for Ruddy-breasted Crake in China, i.e., non-migratory population in the south and migratory population in the north of China. In this study, mitochondrial control sequences and microsatellite datasets of 88 individuals sampled from 8 sites were applied to analyze their genetic diversity, genetic differentiation, and genetic structure. Our results indicated that low genetic diversity and genetic differentiation exit in most populations. The neutrality test suggested significantly negative Fu's Fs value, which, in combination with detection of the mismatch distribution, indicated that population expansion occurred in the interglacier approximately 98,000 years ago, and the time of the most recent common ancestor (TMRCA) was estimated to about 202,705 years ago. Gene flow analysis implied that the gene flow was low, but gene exchange was frequent among adjacent populations. Both phylogenetic and STRUCTURE analyses implied weak genetic structure. In general, the genetic diversity, gene flow, and genetic structure of Ruddy-breasted Crake were low.},
}

Animals
Birds/*genetics
DNA, Mitochondrial
*Gene Flow
*Genetic Structures
*Genetic Variation
*Genetics, Population
Haplotypes
Microsatellite Repeats
Mitochondria/genetics
Phylogeny

@article {pmid30876291,
year = {2019},
author = {Liu, W and Liu, Q and Zhang, Z and Han, Y and Kuang, C and Xu, L and Yang, H and Liu, X},
title = {Three-dimensional super-resolution imaging of live whole cells using galvanometer-based structured illumination microscopy.},
journal = {Optics express},
volume = {27},
number = {5},
pages = {7237-7248},
doi = {10.1364/OE.27.007237},
pmid = {30876291},
issn = {1094-4087},
abstract = {Imaging and tracking three-dimensional (3D) nanoscale organizations and functions of live cells is essential for biological research but it remains challenging. Among different 3D super-resolution techniques, 3D structured illumination microscopy (SIM) has the intrinsic advantages for live-cell studies; it is based on wide-field imaging and does not require high light intensities or special fluorescent dyes to double 3D resolution. However, the 3D SIM system has developed relatively slowly, especially in live imaging. Here, we report a more flexible 3D SIM system based on two galvanometer sets conveniently controlling the structured illumination pattern's period and orientation, which is able to study dynamics of live whole cells with high speed. We demonstrate our microscope's capabilities with strong optical sectioning and lateral, axial, and volume temporal resolution of 104 nm, 320 nm and 4 s, respectively. We do this by imaging nanoparticle and microtubule organizations and mitochondria evolution. These characteristics enable our galvanometer-based 3D SIM system to broaden the accessible imaging content of SIM-family microscopes and further facilitate their applications in life sciences.},
}

@article {pmid30872488,
year = {2019},
author = {Dorrell, RG and Azuma, T and Nomura, M and Audren de Kerdrel, G and Paoli, L and Yang, S and Bowler, C and Ishii, KI and Miyashita, H and Gile, GH and Kamikawa, R},
title = {Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1819976116},
pmid = {30872488},
issn = {1091-6490},
abstract = {The division of life into producers and consumers is blurred by evolution. For example, eukaryotic phototrophs can lose the capacity to photosynthesize, although they may retain vestigial plastids that perform other essential cellular functions. Chrysophyte algae have undergone a particularly large number of photosynthesis losses. Here, we present a plastid genome sequence from a nonphotosynthetic chrysophyte, "Spumella" sp. NIES-1846, and show that it has retained a nearly identical set of plastid-encoded functions as apicomplexan parasites. Our transcriptomic analysis of 12 different photosynthetic and nonphotosynthetic chrysophyte lineages reveals remarkable convergence in the functions of these nonphotosynthetic plastids, along with informative lineage-specific retentions and losses. At one extreme, Cornospumella fuschlensis retains many photosynthesis-associated proteins, although it appears to have lost the reductive pentose phosphate pathway and most plastid amino acid metabolism pathways. At the other extreme, Paraphysomonas lacks plastid-targeted proteins associated with gene expression and all metabolic pathways that require plastid-encoded partners, indicating a complete loss of plastid DNA in this genus. Intriguingly, some of the nucleus-encoded proteins that once functioned in the expression of the Paraphysomonas plastid genome have been retained. These proteins were likely to have been dual targeted to the plastid and mitochondria of the chrysophyte ancestor, and are uniquely targeted to the mitochondria in Paraphysomonas Our comparative analyses provide insights into the process of functional reduction in nonphotosynthetic plastids.},
}

@article {pmid29427777,
year = {2019},
author = {Prager, M},
title = {Unweaving a taxon tangle: Comments on De Silva et al. (2017).},
journal = {Molecular phylogenetics and evolution},
volume = {131},
number = {},
pages = {229-232},
doi = {10.1016/j.ympev.2018.02.005},
pmid = {29427777},
issn = {1095-9513},
mesh = {Animals ; Biomarkers ; *Birds ; Cell Nucleus ; *Mitochondria ; Phylogeny ; },
}

Animals
Biomarkers
*Birds
Cell Nucleus
*Mitochondria
Phylogeny

@article {pmid29883862,
year = {2018},
author = {Tyagi, A and Pramanik, R and Vishnubhatla, S and Ali, S and Bakhshi, R and Chopra, A and Singh, A and Bakhshi, S},
title = {Pattern of mitochondrial D-loop variations and their relation with mitochondrial encoded genes in pediatric acute myeloid leukemia.},
journal = {Mutation research},
volume = {810},
number = {},
pages = {13-18},
doi = {10.1016/j.mrfmmm.2018.05.002},
pmid = {29883862},
issn = {1873-135X},
mesh = {Adolescent ; Base Sequence ; Child ; Child, Preschool ; Cyclooxygenase 1/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex I/*genetics ; Humans ; Infant ; Leukemia, Myeloid, Acute/*genetics ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; *Mutation Rate ; Prospective Studies ; Sequence Analysis, DNA ; },
abstract = {Role of mitochondrial DNA variations, particularly in D loop region, remains investigational in acute myeloid leukaemia (AML). Consecutive 151 pediatric AML patients were prospectively enrolled from June 2013 to August 2016, for evaluating pattern of variations in mitochondrial D-loop region and to determine their association, if any, with expression of mitochondrial-encoded genes. For each patient, D-loop region was sequenced on baseline bone marrow, buccal swab and mother's blood sample. Real time PCR was used for relative gene expression of four mitochondrial DNA encoded genes viz. Nicotinamide-adenine-dineucleotide-dehydrogenase subunit 3 (ND3), Cytochrome-B (Cyt-B), Cytochrome c oxidase-I (COX1) and ATP-synthetase F0 subunit-6 (ATP6). Total 1490 variations were found at 237 positions in D-Loop; 1206 (80.9%) were germline and 284 (19.1%) were somatic. Positions 73-263 were identified as a probable hotspot region. G bases appeared to be most stable nucleotide (least number of single base substitutions) whereas T appeared to be most susceptible to variations with germline T-C being the commonest. Gene expression of Cyt-B was found to be significantly higher for any variation (somatic or germline) at positions 16,192 and 16,327 while it was significantly lower for variations at positions 16,051 and 207. Any variation at positions 152, 207 and 513 significantly decreased COX1 expression while those at positions 16,051 and 152 attenuated ATP6 expression. This first study evaluated type and overall pattern of D-loop variations in AML, and also showed that some of these variations in D loop region might have an effect on the mitochondrial-encoded genes which is new and valuable information in AML genomics.},
}

Adolescent
Base Sequence
Child
Child, Preschool
Cyclooxygenase 1/*genetics
Cytochromes b/*genetics
DNA, Mitochondrial/*genetics
Electron Transport Complex I/*genetics
Humans
Infant
Leukemia, Myeloid, Acute/*genetics
Mitochondria/*genetics
Mitochondrial Proton-Translocating ATPases/*genetics
*Mutation Rate
Prospective Studies
Sequence Analysis, DNA

@article {pmid30862038,
year = {2019},
author = {Le Vasseur, M and Chen, VC and Huang, K and Vogl, WA and Naus, CC},
title = {Pannexin 2 Localizes at ER-Mitochondria Contact Sites.},
journal = {Cancers},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/cancers11030343},
pmid = {30862038},
issn = {2072-6694},
support = {RGPIN-2016-05471//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Endomembrane specialization allows functional compartmentalization but imposes physical constraints to information flow within the cell. However, the evolution of an endomembrane system was associated with the emergence of contact sites facilitating communication between membrane-bound organelles. Contact sites between the endoplasmic reticulum (ER) and mitochondria are highly conserved in terms of their morphological features but show surprising molecular diversity within and across eukaryote species. ER-mitochondria contact sites are thought to regulate key processes in oncogenesis but their molecular composition remains poorly characterized in mammalian cells. In this study, we investigate the localization of pannexin 2 (Panx2), a membrane channel protein showing tumor-suppressing properties in cancer cells. Using a combination of subcellular fractionation, particle tracking in live-cell, and immunogold electron microscopy, we show that Panx2 localizes at ER-mitochondria contact sites in mammalian cells and sensitizes cells to apoptotic stimuli.},
}

@article {pmid30286121,
year = {2018},
author = {Ashrafzadeh, MR and Djan, M and Szendrei, L and Paulauskas, A and Scandura, M and Bagi, Z and Ilie, DE and Kerdikoshvili, N and Marek, P and Soós, N and Kusza, S},
title = {Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778).},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0204653},
pmid = {30286121},
issn = {1932-6203},
mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Europe ; Haplotypes/genetics ; Hares/*genetics ; Hybridization, Genetic/genetics ; Mitochondria/*genetics ; Phylogeny ; Phylogeography/methods ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {European brown hare, Lepus europaeus, from Central and Eastern European countries (Hungary, Poland, Serbia, Lithuania, Romania, Georgia and Italy) were sampled, and phylogenetic analyses were carried out on two datasets: 1.) 137 sequences (358 bp) of control region mtDNA; and 2.) 105 sequences of a concatenated fragment (916 bp), including the cytochrome b, tRNA-Thr, tRNA-Pro and control region mitochondrial DNA. Our sequences were aligned with additional brown hare sequences from GenBank. A total of 52 and 51 haplotypes were detected within the two datasets, respectively, and assigned to two previously described major lineages: Anatolian/Middle Eastern (AME) and European (EUR). Furthermore, the European lineage was divided into two subclades including South Eastern European (SEE) and Central European (CE). Sympatric distribution of the lineages of the brown hare in South-Eastern and Eastern Europe revealed contact zones there. BAPS analysis assigned sequences from L. europaeus to five genetic clusters, whereas CE individuals were assigned to only one cluster, and AME and SEE sequences were each assigned to two clusters. Our findings uncover numerous novel haplotypes of Anatolian/Middle Eastern brown hare outside their main range, as evidence for the combined influence of Late Pleistocene climatic fluctuations and anthropogenic activities in shaping the phylogeographic structure of the species. Our results support the hypothesis of a postglacial brown hare expansion from Anatolia and the Balkan Peninsula to Central and Eastern Europe, and suggest some slight introgression of individual haplotypes from L. timidus to L. europaeus.},
}

Animals
Cytochromes b/genetics
DNA, Mitochondrial/*genetics
Europe
Haplotypes/genetics
Hares/*genetics
Hybridization, Genetic/genetics
Mitochondria/*genetics
Phylogeny
Phylogeography/methods
RNA, Transfer/genetics
Sequence Analysis, DNA/methods

@article {pmid30854477,
year = {2019},
author = {Oldenkott, B and Yang, Y and Lesch, E and Knoop, V and Schallenberg-Rüdinger, M},
title = {Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in Escherichia coli.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {85},
doi = {10.1038/s42003-019-0328-3},
pmid = {30854477},
issn = {2399-3642},
abstract = {RNA editing converting cytidines into uridines is a hallmark of gene expression in land plant chloroplasts and mitochondria. Pentatricopeptide repeat (PPR) proteins have a key role in target recognition, but the functional editosome in the plant organelles has remained elusive. Here we show that individual Physcomitrella patens DYW-type PPR proteins alone can perform efficient C-to-U editing in Escherichia coli reproducing the moss mitochondrial editing. Single amino acid exchanges in the DYW domain abolish RNA editing, confirming it as the functional cytidine deaminase. The modification of RNA targets and the identification of numerous off-targets in the E. coli transcriptome reveal nucleotide identities critical for RNA recognition and cytidine conversion. The straightforward amenability of the new E. coli setup will accelerate future studies on RNA target recognition through PPRs, on the C-to-U editing deamination machinery and towards future establishment of transcript editing in other genetic systems.},
}

@article {pmid30853974,
year = {2019},
author = {Telschow, A and Gadau, J and Werren, JH and Kobayashi, Y},
title = {Genetic Incompatibilities Between Mitochondria and Nuclear Genes: Effect on Gene Flow and Speciation.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {62},
doi = {10.3389/fgene.2019.00062},
pmid = {30853974},
issn = {1664-8021},
abstract = {The process of speciation is, according to the biological species concept, the reduction in gene flow between genetically diverging populations. Most of the previous theoretical studies analyzed the effect of nuclear genetic incompatibilities on gene flow. There is, however, an increasing number of empirical examples suggesting that cytoplasmically inherited genetic elements play an important role in speciation. Here, we present a theoretical analysis of mitochondrial driven speciation, in which genetic incompatibilities occur between mitochondrial haplotypes and nuclear alleles. Four population genetic models with mainland-island structure were analyzed that differ with respect to the type of incompatibility and the underlying genetics. Gene flow reduction was measured on selectively neutral alleles of an unlinked locus and quantified by the effective migration rate. Analytical formulae for the different scenarios were derived using the fitness graph method. For the models with haploid genetics, we found that mito-nuclear incompatibilities (MtNI) are as strong as nuclear-nuclear incompatibilities (NNI) in reducing gene flow at the unlinked locus, but only if males and females migrate in equal number. For models with diploid genetics, we found that MtNI reduce gene flow stronger than NNI when incompatibilities are recessive, but weaker when they are dominant. For both haploid and diploid MtNI, we found that gene flow reduction is stronger if females are the migrating sex, but weaker than NNI when males are the migrating sex. These results encourage further examination on the role of mitochondria on genetic divergence and speciation and point toward specific factors (e.g., migrating sex) that could be the focus of an empirical test.},
}

@article {pmid30239783,
year = {2018},
author = {Hood, WR and Austad, SN and Bize, P and Jimenez, AG and Montooth, KL and Schulte, PM and Scott, GR and Sokolova, I and Treberg, JR and Salin, K},
title = {The Mitochondrial Contribution to Animal Performance, Adaptation, and Life-History Variation.},
journal = {Integrative and comparative biology},
volume = {58},
number = {3},
pages = {480-485},
doi = {10.1093/icb/icy089},
pmid = {30239783},
issn = {1557-7023},
mesh = {*Acclimatization ; Animals ; *Energy Metabolism ; *Life History Traits ; Mitochondria/*physiology ; },
abstract = {Animals display tremendous variation in their rates of growth, reproductive output, and longevity. While the physiological and molecular mechanisms that underlie this variation remain poorly understood, the performance of the mitochondrion has emerged as a key player. Mitochondria not only impact the performance of eukaryotes via their capacity to produce ATP, but they also play a role in producing heat and reactive oxygen species and function as a major signaling hub for the cell. The papers included in this special issue emerged from a symposium titled "Inside the Black Box: The Mitochondrial Basis of Life-history Variation and Animal Performance." Based on studies of diverse animal taxa, three distinct themes emerged from these papers. (1) When linking mitochondrial function to components of fitness, it is crucial that mitochondrial assays are performed in conditions as close as the intracellular conditions experienced by the mitochondria in vivo. (2) Functional plasticity allows mitochondria to retain their performance, as well as that of their host, over a range of exogenous conditions, and selection on mitochondrial and nuclear-derived proteins can optimize the match between the environment and the bioenergetic capacity of the mitochondrion. Finally, (3) studies of wild and wild-derived animals suggest that mitochondria play a central role in animal performance and life history strategy. Taken as a whole, we hope that these papers will foster discussion and inspire new hypotheses and innovations that will further our understanding of the mitochondrial processes that underlie variation in life history traits and animal performance.},
}

*Acclimatization
Animals
*Energy Metabolism
*Life History Traits
Mitochondria/*physiology

@article {pmid30011013,
year = {2018},
author = {Hood, WR and Zhang, Y and Mowry, AV and Hyatt, HW and Kavazis, AN},
title = {Life History Trade-offs within the Context of Mitochondrial Hormesis.},
journal = {Integrative and comparative biology},
volume = {58},
number = {3},
pages = {567-577},
pmid = {30011013},
issn = {1557-7023},
support = {R03 HD083654/HD/NICHD NIH HHS/United States ; },
mesh = {Biological Evolution ; Hormesis/*physiology ; *Life History Traits ; Longevity/*physiology ; Mitochondria/*physiology ; Oxidative Stress/physiology ; Reactive Oxygen Species/metabolism ; Reproduction/*physiology ; },
abstract = {Evolutionary biologists have been interested in the negative interactions among life history traits for nearly a century, but the mechanisms that would create this negative interaction remain poorly understood. One variable that has emerged as a likely link between reproductive effort and longevity is oxidative stress. Specifically, it has been proposed that reproduction generates free radicals that cause oxidative stress and, in turn, oxidative stress damages cellular components and accelerates senescence. We propose that there is limited support for the hypothesis because reactive oxygen species (ROS), the free radicals implicated in oxidative damage, are not consistently harmful. With this review, we define the hormetic response of mitochondria to ROS, termed mitochondrial hormesis, and describe how to test for a mitohormetic response. We interpret existing data using our model and propose that experimental manipulations will further improve our knowledge of this response. Finally, we postulate how the mitohormetic response curve applies to variation in animal performance and longevity.},
}

Biological Evolution
Hormesis/*physiology
*Life History Traits
Longevity/*physiology
Mitochondria/*physiology
Oxidative Stress/physiology
Reactive Oxygen Species/metabolism
Reproduction/*physiology

@article {pmid29945242,
year = {2018},
author = {Buchanan, JL and Meiklejohn, CD and Montooth, KL},
title = {Mitochondrial Dysfunction and Infection Generate Immunity-Fecundity Tradeoffs in Drosophila.},
journal = {Integrative and comparative biology},
volume = {58},
number = {3},
pages = {591-603},
pmid = {29945242},
issn = {1557-7023},
support = {R01 GM067862/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Drosophila melanogaster/genetics/*physiology ; Drosophila simulans/genetics/*physiology ; Female ; Fertility ; *Genotype ; Hybridization, Genetic ; Immunity, Innate ; *Life History Traits ; Male ; Mitochondria/*physiology ; Nutritional Status ; Oxidative Phosphorylation ; Stress, Physiological ; },
abstract = {Physiological responses to short-term environmental stressors, such as infection, can have long-term consequences for fitness, particularly if the responses are inappropriate or nutrient resources are limited. Genetic variation affecting energy acquisition, storage, and usage can limit cellular energy availability and may influence resource-allocation tradeoffs even when environmental nutrients are plentiful. Here, we utilized Drosophila mitochondrial-nuclear genotypes to test whether disrupted mitochondrial function interferes with nutrient-sensing pathways, and whether this disruption has consequences for tradeoffs between immunity and fecundity. We found that an energetically-compromised genotype was relatively resistant to rapamycin-a drug that targets nutrient-sensing pathways and mimics resource limitation. Dietary resource limitation decreased survival of energetically-compromised flies. Furthermore, survival of infection with a natural pathogen was decreased in this genotype, and females of this genotype experienced immunity-fecundity tradeoffs that were not evident in genotypic controls with normal energy metabolism. Together, these results suggest that this genotype may have little excess energetic capacity and fewer cellular nutrients, even when environmental nutrients are not limiting. Genetic variation in energy metabolism may therefore act to limit the resources available for allocation to life-history traits in ways that generate tradeoffs even when environmental resources are not limiting.},
}

Animals
Drosophila melanogaster/genetics/*physiology
Drosophila simulans/genetics/*physiology
Female
Fertility
*Genotype
Hybridization, Genetic
Immunity, Innate
*Life History Traits
Male
Mitochondria/*physiology
Nutritional Status
Oxidative Phosphorylation
Stress, Physiological

@article {pmid30848125,
year = {2019},
author = {Han, Y and Branon, TC and Martell, JD and Boassa, D and Shechner, D and Ellisman, MH and Ting, A},
title = {Directed Evolution of Split APEX2 Peroxidase.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.8b00919},
pmid = {30848125},
issn = {1554-8937},
abstract = {APEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). A total of 20 rounds of fluorescence activated cell sorting (FACS)-based selections from yeast-displayed fragment libraries, using 3 different surface display configurations, produced a 200-amino-acid N-terminal fragment (with 9 mutations relative to APEX2) called "AP" and a 50-amino-acid C-terminal fragment called "EX". AP and EX fragments were each inactive on their own but were reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within a non-coding RNA scaffold, and at mitochondria-endoplasmic reticulum contact sites.},
}

@article {pmid30844054,
year = {2019},
author = {Thairu, MW and Hansen, AK},
title = {It's a small, small world: Unravelling the role and evolution of small RNAs in organelle and endosymbiont genomes.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnz049},
pmid = {30844054},
issn = {1574-6968},
abstract = {Organelles and host-restricted bacterial symbionts are characterized by having highly reduced genomes that lack many key regulatory genes and elements. Thus, it has been hypothesized that the eukaryotic nuclear genome is primarily responsible for regulating these symbioses. However, with the discovery of organelle and symbiont expressed small RNAs (sRNAs) there is emerging evidence that these sRNAs may play a role in gene regulation as well. Here, we compare the diversity of organelle and bacterial symbiont sRNAs recently identified using genome-enabled '-omic' technologies and discuss their potential role in gene regulation. We also discuss how the genome architecture of small genomes may influence the evolution of these sRNAs and their potential function. Additionally, these new studies suggest that some sRNAs are conserved within organelle and symbiont taxa and respond to changes in the environment and/or their hosts. In summary, these results suggest that organelle and symbiont sRNAs may play a role in gene regulation in addition to nuclear-encoded host mechanisms.},
}

@article {pmid30842567,
year = {2019},
author = {Matos, I and Machado, MP and Schartl, M and Coelho, MM},
title = {Allele-specific expression variation at different ploidy levels in Squalius alburnoides.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {3688},
doi = {10.1038/s41598-019-40210-8},
pmid = {30842567},
issn = {2045-2322},
support = {SFRH/BD/61217/2009//Ministério da Educação e Ciência (Ministry of Education and Science)/ ; UID/BIA/00329/2013//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; },
abstract = {Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides.},
}

@article {pmid30838029,
year = {2019},
author = {Dixit, S and Henderson, JC and Alfonzo, JD},
title = {Multi-Substrate Specificity and the Evolutionary Basis for Interdependence in tRNA Editing and Methylation Enzymes.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {104},
doi = {10.3389/fgene.2019.00104},
pmid = {30838029},
issn = {1664-8021},
support = {R56 AI131248/AI/NIAID NIH HHS/United States ; },
abstract = {Among tRNA modification enzymes there is a correlation between specificity for multiple tRNA substrates and heteromultimerization. In general, enzymes that modify a conserved residue in different tRNA sequences adopt a heterodimeric structure. Presumably, such changes in the oligomeric state of enzymes, to gain multi-substrate recognition, are driven by the need to accommodate and catalyze a particular reaction in different substrates while maintaining high specificity. This review focuses on two classes of enzymes where the case for multimerization as a way to diversify molecular recognition can be made. We will highlight several new themes with tRNA methyltransferases and will also discuss recent findings with tRNA editing deaminases. These topics will be discussed in the context of several mechanisms by which heterodimerization may have been achieved during evolution and how these mechanisms might impact modifications in different systems.},
}

@article {pmid30824066,
year = {2019},
author = {Forgione, I and Bonavita, S and Regina, TMR},
title = {Mitochondria of Cedrus atlantica and allied species: A new chapter in the horizontal gene transfer history.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {281},
number = {},
pages = {93-101},
doi = {10.1016/j.plantsci.2019.01.013},
pmid = {30824066},
issn = {1873-2259},
abstract = {The extraordinary incidence of Horizontal Gene Transfer (HGT) mostly in mitochondrial genomes of flowering plants is well known. Here, we report another episode of HGT affecting a large mitochondrial gene region in the evergreen conifer Atlas cedar (Cedrus atlantica). Mitochondria of this Pinaceae species possess an rps3 gene that harbours two introns and shares the same genomic context with a downstream overlapping rpl16 gene, like in the major groups of gymnosperms and angiosperms analyzed so far. Interestingly, C. atlantica contains additional copies of the rps3 and rpl16 sequences that are more closely related to angiosperm counterparts than to those from gymnosperms, as also confirmed by phylogenetic analyses. This suggests that a lateral transfer from a flowering plant donor is the most likely mechanism for the origin of the Atlas cedar extra sequences. Quantitative PCR and reverse-transcription (RT)-PCR analyses demonstrate, respectively, mitochondrial location and lack of expression for the rps3 and rpl16 additional sequences in C. atlantica. Furthermore, our study provides evidence that a similar HGT event takes place in two other Cedrus species, which occurr in Cyprus and North Africa. Only the West Himalayan C. deodara lacks the transferred genes. The potential donor and the molecular mechanism underlying this lateral DNA transfer remain still unclear.},
}

@article {pmid30813887,
year = {2019},
author = {Kuzminkova, AA and Sokol, AD and Ushakova, KE and Popadin, KY and Gunbin, KV},
title = {mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.},
journal = {BMC evolutionary biology},
volume = {19},
number = {Suppl 1},
pages = {47},
doi = {10.1186/s12862-019-1371-x},
pmid = {30813887},
issn = {1471-2148},
abstract = {BACKGROUND: Heterotachy is the variation in the evolutionary rate of aligned sites in different parts of the phylogenetic tree. It occurs mainly due to epistatic interactions among the substitutions, which are highly complex and make it difficult to study protein evolution. The vast majority of computational evolutionary approaches for studying these epistatic interactions or their evolutionary consequences in proteins require high computational time. However, recently, it has been shown that the evolution of residue solvent accessibility (RSA) is tightly linked with changes in protein fitness and intra-protein epistatic interactions. This provides a computationally fast alternative, based on comparison of evolutionary rates of amino acid replacements with the rates of RSA evolutionary changes in order to recognize any shifts in epistatic interaction.

RESULTS: Based on RSA information, data randomization and phylogenetic approaches, we constructed a software pipeline, which can be used to analyze the evolutionary consequences of intra-protein epistatic interactions with relatively low computational time. We analyzed the evolution of 512 protein families tightly linked to mitochondrial function in Vertebrates and created "mtProtEvol", the web resource with data on protein evolution. In strict agreement with lifespan and metabolic rate data, we demonstrated that different functional categories of mitochondria-related proteins subjected to selection on accelerated and decelerated RSA rates in rodents and primates. For example, accelerated RSA evolution in rodents has been shown for Krebs cycle enzymes, respiratory chain and reactive oxygen species metabolism, while in primates these functions are stress-response, translation and mtDNA integrity. Decelerated RSA evolution in rodents has been demonstrated for translational machinery and oxidative stress response components.

CONCLUSIONS: mtProtEvol is an interactive resource focused on evolutionary analysis of epistatic interactions in protein families involved in Vertebrata mitochondria function and available at http://bioinfodbs.kantiana.ru/mtProtEvol /. This resource and the devised software pipeline may be useful tool for researchers in area of protein evolution.},
}

@article {pmid30809302,
year = {2019},
author = {Tan, Y and Zhu, Y and Wen, L and Yang, X and Liu, X and Meng, T and Dai, S and Ping, Y and Yuan, H and Hu, F},
title = {Mitochondria-Responsive Drug Release along with Heat Shock Mediated by Multifunctional Glycolipid Micelles for Precise Cancer Chemo-Phototherapy.},
journal = {Theranostics},
volume = {9},
number = {3},
pages = {691-707},
doi = {10.7150/thno.31022},
pmid = {30809302},
issn = {1838-7640},
abstract = {Responsive drug release in tumor mitochondria is a pre-requisite for mitochondria-targeted drug delivery systems to improve the efficacy of this promising therapeutic modality. To this end, a photothermal stimulation strategy for mitochondria-responsive drug release along with heat shock is developed to maximize the antitumor effects with minimal side effects. Methods: This strategy relies on mitochondrial-targeted delivery of doxorubicin (DOX) through a photothermal and lipophilic agent IR-780 iodide (IR780)-modified glycolipid conjugates (CSOSA), which can synergistically triggers high-level reactive oxygen species (ROS) to kill tumor cells. Results: Specifically, upon laser irradiation, the photothermal conversion by IR780-CSOSA can not only weaken the hydrophobic interaction between the core of micelles and DOX and trigger unexpected micelle swelling to release DOX in mitochondria for the amplification of ROS, but also induce mitochondria-specific heat shock to promote the fast evolution of ROS at the same locus to eradicate cancer cells in a more effective way. Furthermore, IR780-CSOSA micelles may independently realize the real-time diagnosis and imaging on multiple tumor models. Deep penetration into tumors by IR780-CSOSA/DOX micelles can be manipulated under laser irradiation. Conclusion: Such multifunctional IR780-CSOSA/DOX micelles with integration of mitochondria-responsive drug release and heat shock are demonstrated to be superior to the non-mitochondria-responsive therapy. This study opens up new avenues for the future cancer diagnosis and treatment.},
}

@article {pmid30809252,
year = {2019},
author = {Hirata, A},
title = {Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {103},
doi = {10.3389/fgene.2019.00103},
pmid = {30809252},
issn = {1664-8021},
abstract = {RNA-splicing endonuclease (EndA) cleaves out introns from archaeal and eukaryotic precursor (pre)-tRNA and is essential for tRNA maturation. In archaeal EndA, the molecular mechanisms underlying complex assembly, substrate recognition, and catalysis have been well understood. Recently, certain studies have reported novel findings including the identification of new subunit types in archaeal EndA structures, providing insights into the mechanism underlying broad substrate specificity. Further, metagenomics analyses have enabled the acquisition of numerous DNA sequences of EndAs and intron-containing pre-tRNAs from various species, providing information regarding the co-evolution of substrate specificity of archaeal EndAs and tRNA genetic diversity, and the evolutionary pathway of archaeal and eukaryotic EndAs. Although the complex structure of the heterothermic form of eukaryotic EndAs is unknown, previous reports regarding their functions indicated that mutations in human EndA cause neurological disorders including pontocerebellar hypoplasia and progressive microcephaly, and yeast EndA significantly cleaves mitochondria-localized mRNA encoding cytochrome b mRNA processing 1 (Cpb1) for mRNA maturation. This mini-review summarizes the aforementioned results, discusses their implications, and offers my personal opinion regarding future directions for the analysis of the structure and function of EndAs.},
}

@article {pmid30804878,
year = {2019},
author = {Festoff, BW and Citron, BA},
title = {Thrombin and the Coag-Inflammatory Nexus in Neurotrauma, ALS, and Other Neurodegenerative Disorders.},
journal = {Frontiers in neurology},
volume = {10},
number = {},
pages = {59},
doi = {10.3389/fneur.2019.00059},
pmid = {30804878},
issn = {1664-2295},
abstract = {This review details our current understanding of thrombin signaling in neurodegeneration, with a focus on amyotrophic lateral sclerosis (ALS, Lou Gehrig's disease) as well as future directions to be pursued. The key factors are multifunctional and involved in regulatory pathways, namely innate immune and the coagulation cascade activation, that are essential for normal nervous system function and health. These two major host defense systems have a long history in evolution and include elements and regulators of the coagulation pathway that have significant impacts on both the peripheral and central nervous system in health and disease. The clotting cascade responds to a variety of insults to the CNS including injury and infection. The blood brain barrier is affected by these responses and its compromise also contributes to these detrimental effects. Important molecules in signaling that contribute to or protect against neurodegeneration include thrombin, thrombomodulin (TM), protease activated receptor 1 (PAR1), damage associated molecular patterns (DAMPs), such as high mobility group box protein 1 (HMGB1) and those released from mitochondria (mtDAMPs). Each of these molecules are entangled in choices dependent upon specific signaling pathways in play. For example, the particular cleavage of PAR1 by thrombin vs. activated protein C (APC) will have downstream effects through coupled factors to result in toxicity or neuroprotection. Furthermore, numerous interactions influence these choices such as the interplay between HMGB1, thrombin, and TM. Our hope is that improved understanding of the ways that components of the coagulation cascade affect innate immune inflammatory responses and influence the course of neurodegeneration, especially after injury, will lead to effective therapeutic approaches for ALS, traumatic brain injury, and other neurodegenerative disorders.},
}

@article {pmid30804213,
year = {2019},
author = {Tang, K and Li, Y and Yu, C and Wei, Z},
title = {Structural mechanism for versatile cargo recognition by the yeast class V myosin Myo2.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA119.007550},
pmid = {30804213},
issn = {1083-351X},
abstract = {Class V myosins are actin-dependent motors, which recognize numerous cellular cargos mainly via the C-terminal globular tail domain (GTD). Myo2, a yeast class V myosin, can transport a broad range of organelles. However, little is known about the capacity of Myo2-GTD to recognize such a diverse array of cargos specifically at the molecular level. Here, we solved crystal structures of Myo2-GTD (at 1.9-3.1 Å resolutions) in complex with three cargo adaptor proteins: Smy1 (for polarization of secretory vesicles), Inp2 (for peroxisome transport), and Mmr1 (for mitochondria transport). The structures of Smy1- and Inp2-bound Myo2-GTD, along with site-directed mutagenesis experiments, revealed a binding site in the subdomain-I having a hydrophobic groove with high flexibility enabling Myo2-GTD to accommodate different protein sequence. The Myo2-GTD-Mmr1 complex structure confirmed and complemented a previously identified mitochondrion/vacuole-specific binding region. Moreover, differences between the conformations and locations of cargo-binding sites identified here for Myo2 and those reported for mammalian MyoVA (MyoVA) suggest that class V myosins potentially have co-evolved with their specific cargos. Our structural and biochemical analysis not only uncovers a molecular mechanism that explains the diverse cargo recognition by Myo2-GTD, but also provides structural information useful for future functional studies of class V myosins in cargo transport.},
}

@article {pmid30785203,
year = {2019},
author = {Yan, Z and Ye, G and Werren, JH},
title = {Evolutionary rate correlation between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins in insects.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz036},
pmid = {30785203},
issn = {1537-1719},
abstract = {The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear and mitochondrial encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which is likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase (MCM) complex.},
}

@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 = {42},
number = {2},
pages = {113-127},
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 {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.

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.

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 {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 = {95},
number = {},
pages = {118-128},
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 Q-PCR 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 "changes" 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 "organelles", 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 "host/symbiont" and "eukaryote/organelle" 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 "sexual symbiont integration". 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 "host"; 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 {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.},
}

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

@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 = {116},
number = {6},
pages = {2187-2192},
doi = {10.1073/pnas.1814425116},
pmid = {30670662},
issn = {1091-6490},
support = {MC_U105115237//Medical Research Council/United Kingdom ; },
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 {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 {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 = {30},
number = {5},
pages = {691-702},
doi = {10.1091/mbc.E18-07-0466},
pmid = {30649994},
issn = {1939-4586},
support = {R01 GM120303/GM/NIGMS NIH HHS/United States ; },
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 Schizosaccharomyces pombe Num1 homologue. In addition to its function in dynein anchoring, we find that S. pombe Num1, also known as Mcp5, interacts with and tethers mitochondria to the plasma membrane in S. pombe and Saccharomyces cerevisiae. Thus, the mitochondria and plasma membrane-binding domains of the Num1 homologues, 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 {pmid30630097,
year = {2019},
author = {Li, W and Freudenberg, J and Freudenberg, J},
title = {Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome.},
journal = {Gene},
volume = {691},
number = {},
pages = {141-152},
doi = {10.1016/j.gene.2018.12.040},
pmid = {30630097},
issn = {1879-0038},
mesh = {Algorithms ; Cell Nucleus/*genetics ; Evolution, Molecular ; Genome, Human ; Humans ; Mitochondria/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; },
abstract = {The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.},
}

Algorithms
Cell Nucleus/*genetics
Evolution, Molecular
Genome, Human
Humans
Mitochondria/*genetics
Phylogeny
Sequence Alignment
Sequence Analysis, DNA/*methods

@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},
support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; },
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 {pmid30612859,
year = {2019},
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 = {27},
number = {3},
pages = {464-475.e6},
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 {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 = {26},
number = {6},
pages = {5577-5587},
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 {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},
support = {FT130101338//ARC Australian Future Fellow/ ; //Faculty of Natural Sciences/Leibniz Universität Hannover/ ; CE140100008//Australian Research Council/ ; },
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 because of its accessory subunits (SDH5-SDH8), in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1-SDH4). Here, we review compositional and phylogenetic analysis and biochemical dissection studies to both clarify the presence and propose a role for 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 defense response and reactive oxygen species-dependent stress responses. Signaling molecules such as salicyclic acid (SA) and nitric oxide (NO) are also reported to interact with the ubiquinone (UQ) binding site of SDH, influencing signaling 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 the succinate-dependent production of reactive oxygen species in plants and new avenues to explore the evolution of plant mitochondrial complex II and its utility.},
}

@article {pmid30598556,
year = {2019},
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 & molecular biology},
volume = {26},
number = {1},
pages = {50-57},
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 = {2019},
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 = {211},
number = {3},
pages = {963-976},
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. It also predicts 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 {pmid30590568,
year = {2019},
author = {Łukasik, P and Chong, RA and Nazario, K and Matsuura, Y and Bublitz, AC and Campbell, MA and Meyer, MC and Van Leuven, JT and Pessacq, P and Veloso, C and Simon, C and McCutcheon, JP},
title = {One Hundred Mitochondrial Genomes of Cicadas.},
journal = {The Journal of heredity},
volume = {110},
number = {2},
pages = {247-256},
doi = {10.1093/jhered/esy068},
pmid = {30590568},
issn = {1465-7333},
abstract = {Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.},
}

@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 {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},
support = {DGE-1321845//National Science Foundation (NSF) Graduate Research Fellowship/ ; MCB-1733227//National Science Foundation (NSF) Graduate Research Fellowship/ ; MCB-1614629//National Science Foundation (NSF) Graduate Research Fellowship/ ; //Department of Education GAANN Fellowship/ ; },
abstract = {Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi-subunit 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. TheclpP1 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 ofclpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA-editing sites) within seed plants. AlthoughclpP1 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 genusSilene, which has highly elevated and heterogeneous rates ofclpP1 evolution. We confirmed thatclpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergentSilene species. Additionally, there is a tight correlation between amino acid substitution rates inclpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.},
}

@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 = {2019},
author = {Wynn, EL and Christensen, AC},
title = {Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {2},
pages = {549-559},
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.

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.

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 {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.},
}

Biological Evolution
DNA, Mitochondrial/*genetics
*Genetic Variation
*Genome, Mitochondrial
*Interspersed Repetitive Sequences
Mitochondria/*genetics
Phycomyces/*genetics
Phylogeny
*Selection, Genetic
Sequence Homology

@article {pmid30545443,
year = {2019},
author = {Son, JM and Lee, C},
title = {Mitochondria: multifaceted regulators of aging.},
journal = {BMB reports},
volume = {52},
number = {1},
pages = {13-23},
pmid = {30545443},
issn = {1976-670X},
support = {R01 AG052558/AG/NIA NIH HHS/United States ; },
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 mechanisms 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. [BMB Reports 2019; 52(1): 13-23].},
}

@article {pmid30523084,
year = {2018},
author = {Antonova-Koch, Y and Meister, S and Abraham, M and Luth, MR and Ottilie, S and Lukens, AK and Sakata-Kato, T and Vanaerschot, M and Owen, E and Jado, JC and Maher, SP and Calla, J and Plouffe, D and Zhong, Y and Chen, K and Chaumeau, V and Conway, AJ and McNamara, CW and Ibanez, M and Gagaring, K and Serrano, FN and Eribez, K and Taggard, CM and Cheung, AL and Lincoln, C and Ambachew, B and Rouillier, M and Siegel, D and Nosten, F and Kyle, DE and Gamo, FJ and Zhou, Y and Llinás, M and Fidock, DA and Wirth, DF and Burrows, J and Campo, B and Winzeler, EA},
title = {Open-source discovery of chemical leads for next-generation chemoprotective antimalarials.},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6419},
pages = {},
doi = {10.1126/science.aat9446},
pmid = {30523084},
issn = {1095-9203},
support = {R01 AI103058/AI/NIAID NIH HHS/United States ; R01 AI090141/AI/NIAID NIH HHS/United States ; P50 GM085764/GM/NIGMS NIH HHS/United States ; R01 AI093716/AI/NIAID NIH HHS/United States ; },
mesh = {Antimalarials/chemistry/isolation & purification/*pharmacology/therapeutic use ; *Chemoprevention ; *Drug Discovery ; Drug Evaluation, Preclinical ; Humans ; Malaria/*prevention & control ; Mitochondria/drug effects ; Plasmodium/*drug effects/growth & development ; },
abstract = {To discover leads for next-generation chemoprotective antimalarial drugs, we tested more than 500,000 compounds for their ability to inhibit liver-stage development of luciferase-expressing Plasmodium spp. parasites (681 compounds showed a half-maximal inhibitory concentration of less than 1 micromolar). Cluster analysis identified potent and previously unreported scaffold families as well as other series previously associated with chemoprophylaxis. Further testing through multiple phenotypic assays that predict stage-specific and multispecies antimalarial activity distinguished compound classes that are likely to provide symptomatic relief by reducing asexual blood-stage parasitemia from those which are likely to only prevent malaria. Target identification by using functional assays, in vitro evolution, or metabolic profiling revealed 58 mitochondrial inhibitors but also many chemotypes possibly with previously unidentified mechanisms of action.},
}

Antimalarials/chemistry/isolation & purification/*pharmacology/therapeutic use
*Chemoprevention
*Drug Discovery
Drug Evaluation, Preclinical
Humans
Malaria/*prevention & control
Mitochondria/drug effects
Plasmodium/*drug effects/growth & development

@article {pmid30535838,
year = {2019},
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 = {24},
number = {2},
pages = {255-267},
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).

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&E sections and the tumor cell content was quantified by digital pathology analyses.

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).

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 {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 + "1" 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.},
}

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

@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 "adaptors" that accommodate the translation factor of bacterial origin to the evolutionary changed protein biosynthesis system in mitochondria.},
}

@article {pmid30517740,
year = {2019},
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 = {36},
number = {2},
pages = {207-219},
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 "patched" 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 {pmid30517696,
year = {2019},
author = {Ilhan, J and Kupczok, A and Woehle, C and Wein, T and Hülter, NF and Rosenstiel, P and Landan, G and Mizrahi, I and Dagan, T},
title = {Segregational Drift and the Interplay between Plasmid Copy Number and Evolvability.},
journal = {Molecular biology and evolution},
volume = {36},
number = {3},
pages = {472-486},
doi = {10.1093/molbev/msy225},
pmid = {30517696},
issn = {1537-1719},
abstract = {The ubiquity of plasmids in all prokaryotic phyla and habitats and their ability to transfer between cells marks them as prominent constituents of prokaryotic genomes. Many plasmids are found in their host cell in multiple copies. This leads to an increased mutational supply of plasmid-encoded genes and genetically heterogeneous plasmid genomes. Nonetheless, the segregation of plasmid copies into daughter cells during cell division is considered to occur in the absence of selection on the plasmid alleles. We investigate the implications of random genetic drift of multicopy plasmids during cell division-termed here "segregational drift"-to plasmid evolution. Performing experimental evolution of low- and high-copy non-mobile plasmids in Escherichia coli, we find that the evolutionary rate of multicopy plasmids does not reflect the increased mutational supply expected according to their copy number. In addition, simulated evolution of multicopy plasmid alleles demonstrates that segregational drift leads to increased loss frequency and extended fixation time of plasmid mutations in comparison to haploid chromosomes. Furthermore, an examination of the experimentally evolved hosts reveals a significant impact of the plasmid type on the host chromosome evolution. Our study demonstrates that segregational drift of multicopy plasmids interferes with the retention and fixation of novel plasmid variants. Depending on the selection pressure on newly emerging variants, plasmid genomes may evolve slower than haploid chromosomes, regardless of their higher mutational supply. We suggest that plasmid copy number is an important determinant of plasmid evolvability due to the manifestation of segregational drift.},
}

@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},
doi = {10.11646/zootaxa.4524.5.1},
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.},
}

Animals
*Color
India
*Lizards
Mitochondria
Myanmar
Phylogeny

@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 ("niches"), 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 "induced pluripotent stem" cells, challenges to the origin of these "iPS" 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 "iPS" 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 {pmid30481564,
year = {2019},
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 = {443},
number = {},
pages = {56-66},
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 {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},
pmid = {30466434},
issn = {1741-7007},
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.

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.

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 = {564},
number = {7734},
pages = {125-129},
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 {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.},
}

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

@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 {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},
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, "who dies" 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 {pmid30421421,
year = {2019},
author = {Patten, MM},
title = {The X chromosome favors males under sexually antagonistic selection.},
journal = {Evolution; international journal of organic evolution},
volume = {73},
number = {1},
pages = {84-91},
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.},
}

@article {pmid30419142,
year = {2018},
author = {Muthye, V and Lavrov, DV},
title = {Characterization of mitochondrial proteomes of nonbilaterian animals.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1289-1301},
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, 70(12):1289-1301, 2018.},
}

@article {pmid30417348,
year = {2019},
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 = {73},
number = {2},
pages = {262-277},
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 multigeneration crossing scheme, using two cline-end populations of Drosophila melanogaster, to estimate the relative contributions of the X chromosome, autosomes, and mitochondrial genome to divergence in four traits involved in local adaptation (wing size, 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.},
}

@article {pmid30395972,
year = {2019},
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 & medicine},
volume = {130},
number = {},
pages = {436-445},
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 = {70},
number = {12},
pages = {1275-1288},
pmid = {30394643},
issn = {1521-6551},
support = {2R01GM067862/GF/NIH HHS/United States ; //Brown University/ ; R01 GM067862/GM/NIGMS NIH HHS/United States ; NIA grant 1R01AG027849NIH grant 2R01GM067862/GF/NIH HHS/United States ; R01 AG027849/AG/NIA NIH HHS/United States ; 1R01AG027849/GF/NIH HHS/United States ; },
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 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1275-1288, 2018.},
}

@article {pmid30391331,
year = {2019},
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 = {1862},
number = {1},
pages = {47-57},
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},
pmid = {30390623},
issn = {1471-2148},
mesh = {Base Sequence ; Cell Nucleus/*genetics ; DNA End-Joining Repair/*genetics ; DNA, Mitochondrial/genetics ; *Genome, Plant ; Homologous Recombination/*genetics ; Mitochondria/*genetics ; *Mosaicism ; Mutagenesis, Insertional/*genetics ; Plastids/*genetics ; },
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.

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.

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.},
}

Base Sequence
Cell Nucleus/*genetics
DNA End-Joining Repair/*genetics
DNA, Mitochondrial/genetics
*Genome, Plant
Homologous Recombination/*genetics
Mitochondria/*genetics
*Mosaicism
Mutagenesis, Insertional/*genetics
Plastids/*genetics

@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 = {115},
number = {46},
pages = {11778-11783},
pmid = {30385634},
issn = {1091-6490},
support = {80NSSC18K0093/ImNASA/Intramural NASA/United States ; DP2 OD006478/OD/NIH HHS/United States ; },
mesh = {Computer Simulation ; Databases, Protein ; Evolution, Molecular ; Humans ; Hydrogen-Ion Concentration ; Isoelectric Point ; Lysosomes/metabolism ; Protein Folding ; Protein Stability ; Proteome/*chemistry/metabolism ; Proteomics/*methods ; Subcellular Fractions/chemistry/metabolism ; },
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.},
}

Computer Simulation
Databases, Protein
Evolution, Molecular
Humans
Hydrogen-Ion Concentration
Isoelectric Point
Lysosomes/metabolism
Protein Folding
Protein Stability
Proteome/*chemistry/metabolism
Proteomics/*methods
Subcellular Fractions/chemistry/metabolism

@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 = {146},
number = {6},
pages = {529-540},
pmid = {30377874},
issn = {1573-6857},
support = {18ZR1417400//Shanghai Natural Science Fund/ ; 41576163//National Natural Science Foundation of China/ ; 2016YFC1402105//National Key R&D Program of China/ ; MATHAB2017010//Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, S.O.A./ ; },
mesh = {Codon/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Microsatellite Repeats ; Open Reading Frames ; RNA, Transfer/genetics ; Sequence Homology, Nucleic Acid ; Ulva/classification/*genetics ; },
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.},
}

Codon/genetics
Evolution, Molecular
*Genome, Mitochondrial
Microsatellite Repeats
Open Reading Frames
RNA, Transfer/genetics
Sequence Homology, Nucleic Acid
Ulva/classification/*genetics

@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 = {115},
number = {46},
pages = {11796-11801},
pmid = {30373839},
issn = {1091-6490},
support = {P41 GM103445/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Bioengineering/*methods ; Biological Evolution ; Escherichia coli/genetics/metabolism ; Mitochondria/*genetics/metabolism ; Models, Biological ; Saccharomyces cerevisiae/genetics/metabolism ; Symbiosis/*genetics ; Thiamine/metabolism ; },
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.},
}

Adenosine Triphosphate/metabolism
Amino Acid Sequence
Bioengineering/*methods
Biological Evolution
Escherichia coli/genetics/metabolism
Mitochondria/*genetics/metabolism
Models, Biological
Saccharomyces cerevisiae/genetics/metabolism
Symbiosis/*genetics
Thiamine/metabolism

@article {pmid30368957,
year = {2018},
author = {Olsson, M and Friesen, CR and Rollings, N and Sudyka, J and Lindsay, W and Whittington, CM and Wilson, M},
title = {Long-term effects of superoxide and DNA repair on lizard telomeres.},
journal = {Molecular ecology},
volume = {27},
number = {24},
pages = {5154-5164},
doi = {10.1111/mec.14913},
pmid = {30368957},
issn = {1365-294X},
support = {//Swedish Science Council/ ; //Australian Research Council/ ; },
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.},
}

@article {pmid30364957,
year = {2018},
author = {Lee, JM and Song, HJ and Park, SI and Lee, YM and Jeong, SY and Cho, TO and Kim, JH and Choi, HG and Choi, CG and Nelson, WA and Fredericq, S and Bhattacharya, D and Yoon, HS},
title = {Mitochondrial and Plastid Genomes from Coralline Red Algae Provide Insights into the Incongruent Evolutionary Histories of Organelles.},
journal = {Genome biology and evolution},
volume = {10},
number = {11},
pages = {2961-2972},
pmid = {30364957},
issn = {1759-6653},
mesh = {*Biological Evolution ; *Genome, Mitochondrial ; *Genome, Plastid ; Rhodophyta/*genetics ; },
abstract = {Mitochondria and plastids are generally uniparentally inherited and have a conserved gene content over hundreds of millions of years, which makes them potentially useful phylogenetic markers. Organelle single gene-based trees have long been the basis for elucidating interspecies relationships that inform taxonomy. More recently, high-throughput genome sequencing has enabled the construction of massive organelle genome databases from diverse eukaryotes, and these have been used to infer species relationships in deep evolutionary time. Here, we test the idea that despite their expected utility, conflicting phylogenetic signal may exist in mitochondrial and plastid genomes from the anciently diverged coralline red algae (Rhodophyta). We generated complete organelle genome data from five coralline red algae (Lithothamnion sp., Neogoniolithon spectabile, Renouxia sp., Rhodogorgon sp., and Synarthrophyton chejuensis) for comparative analysis with existing organelle genome data from two other species (Calliarthron tuberculosum and Sporolithon durum). We find strong evidence for incongruent phylogenetic signal from both organelle genomes that may be explained by incomplete lineage sorting that has maintained anciently derived gene copies or other molecular evolutionary processes such as hybridization or gene flow during the evolutionary history of coralline red algae.},
}

*Biological Evolution
*Genome, Mitochondrial
*Genome, Plastid
Rhodophyta/*genetics

@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 = {18},
number = {23},
pages = {e1800136},
doi = {10.1002/pmic.201800136},
pmid = {30358111},
issn = {1615-9861},
support = {2016YFA0500100//National Key R&D Program of China/ ; XDA12040218//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB13030600//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; U1402225//National Natural Science Foundation of China/ ; U1702288//National Natural Science Foundation of China/ ; U1702287//National Natural Science Foundation of China/ ; 31571388//National Natural Science Foundation of China/ ; 31671402//National Natural Science Foundation of China/ ; 31671233//National Natural Science Foundation of China/ ; 31671230//National Natural Science Foundation of China/ ; 31701018//National Natural Science Foundation of China/ ; 81700520,//National Natural Science Foundation of China/ ; 81471082//National Natural Science Foundation of China/ ; CAS16SC01//CAS-Croucher Joint Laboratory Project/ ; 2017FA007//Yunnan Applied Basic Research Projects/ ; 2018FB117//Yunnan Applied Basic Research Projects/ ; 2015HA039//Yunnan Oversea High-level Talents Program/ ; 2015HA040//Yunnan Oversea High-level Talents Program/ ; },
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 are 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 demonstrate that HSD3B2 is localized on LDs. Furthermore, in vitro experiments confirm that the isolated LDs from HeLa cell stably expressing HSD3B2 or from rat adrenal glands have 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.},
}

@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 = {70},
number = {12},
pages = {1207-1213},
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, 70(12):1207-1213, 2018.},
}

@article {pmid30358047,
year = {2018},
author = {Gabaldón, T},
title = {Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1188-1196},
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 "pre-mitochondrial symbioses" hypothesis that provides a framework for eukaryogenesis scenarios involving alternative symbiotic interactions that predate the acquisition of mitochondria. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1188-1196, 2018.},
}

@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 & 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 & 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.},
}

Animals
Caenorhabditis elegans/cytology/enzymology/metabolism
Carboxy-Lyases/antagonists & 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 & control
Rats
Sirtuins/metabolism

@article {pmid30347487,
year = {2019},
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 = {97},
number = {3},
pages = {447-459},
doi = {10.1111/tpj.14133},
pmid = {30347487},
issn = {1365-313X},
support = {//Centre National pour la Recherche Scientifique/ ; //Max Planck Society/ ; PIRG256398//Marie Curie International Reintegration Grant/ ; },
abstract = {All present-day mitochondria originate from a single endosymbiotic event that gave rise to the last eukaryotic common ancestor 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 for 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 in 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 proteomics approach called complexome profiling, we have resolved the different steps in the assembly process in plants. We propose a model for the stepwise assembly of complex I, including every subunit. We then compare this pathway with the corresponding pathway in humans and find that complex I assembly in plants follows a different, and likely ancestral, pathway compared with 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.},
}

@article {pmid30343708,
year = {2018},
author = {Tanaka, A and Leung, PSC and Gershwin, ME},
title = {Evolution of our understanding of PBC.},
journal = {Best practice & 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.},
}

Animals
Autoantibodies/blood
Autoantigens/immunology
Epitopes
Humans
Liver Cirrhosis, Biliary/*immunology/*pathology
Mitochondria/immunology

@article {pmid30341492,
year = {2019},
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 = {132},
number = {1},
pages = {227-240},
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},
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 "Systems Biology" 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.},
}