@article {pmid31617565,
year = {2019},
author = {Žihala, D and Eliáš, M},
title = {Evolution and unprecedented variants of the mitochondrial genetic code in a lineage of green algae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evz210},
pmid = {31617565},
issn = {1759-6653},
abstract = {Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encode alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.},
}

@article {pmid30076323,
year = {2018},
author = {Duong, NT and Macholdt, E and Ton, ND and Arias, L and Schröder, R and Van Phong, N and Thi Bich Thuy, V and Ha, NH and Thi Thu Hue, H and Thi Xuan, N and Thi Phuong Oanh, K and Hien, LTT and Hoang, NH and Pakendorf, B and Stoneking, M and Van Hai, N},
title = {Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {11651},
pmid = {30076323},
issn = {2045-2322},
mesh = {Asia, Southeastern ; Asian Continental Ancestry Group/genetics ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/*genetics ; Ethnic Groups/genetics ; *Genetics, Population ; Haplotypes ; Humans ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Taiwan ; Whole Genome Sequencing ; },
abstract = {Vietnam is an important crossroads within Mainland Southeast Asia (MSEA) and a gateway to Island Southeast Asia, and as such exhibits high levels of ethnolinguistic diversity. However, comparatively few studies have been undertaken of the genetic diversity of Vietnamese populations. In order to gain comprehensive insights into MSEA mtDNA phylogeography, we sequenced 609 complete mtDNA genomes from individuals belonging to five language families (Austroasiatic, Tai-Kadai, Hmong-Mien, Sino-Tibetan and Austronesian) and analyzed them in comparison with sequences from other MSEA countries and Taiwan. Within Vietnam, we identified 399 haplotypes belonging to 135 haplogroups; among the five language families, the sequences from Austronesian groups differ the most from the other groups. Phylogenetic analysis revealed 111 novel Vietnamese mtDNA lineages. Bayesian estimates of coalescence times and associated 95% HPD for these show a peak of mtDNA diversification around 2.5-3 kya, which coincides with the Dong Son culture, and thus may be associated with the agriculturally-driven expansion of this culture. Networks of major MSEA haplogroups emphasize the overall distinctiveness of sequences from Taiwan, in keeping with previous studies that suggested at most a minor impact of the Austronesian expansion from Taiwan on MSEA. We also see evidence for population expansions across MSEA geographic regions and language families.},
}

Asia, Southeastern
Asian Continental Ancestry Group/genetics
Chromosomes, Human, Y/genetics
DNA, Mitochondrial/*genetics
Ethnic Groups/genetics
*Genetics, Population
Haplotypes
Humans
Mitochondria/genetics
Phylogeny
*Phylogeography
Taiwan
Whole Genome Sequencing

@article {pmid29942045,
year = {2018},
author = {Li, D and Waite, DW and Fan, QH and George, S and Semeraro, L and Blacket, MJ},
title = {Molecular detection of small hive beetle Aethina tumida Murray (Coleoptera: Nitidulidae): DNA barcoding and development of a real-time PCR assay.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {9623},
pmid = {29942045},
issn = {2045-2322},
mesh = {Animals ; *Bees ; Coleoptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology ; Phylogeny ; *Real-Time Polymerase Chain Reaction ; },
abstract = {Small hive beetle (SHB), Aethina tumida can feed on honey, pollen and brood in honey bee colonies. It was endemic to Africa, but since 1996 has been detected in a number of countries worldwide, including Australia, Brazil, Canada, Italy, Mexico, South Korea, Philippines and the USA where it has had economic effects on local apiculture. To improve SHB identification, we obtained the first reference sequences from the DNA barcoding 5' COI gene region for SHB and some species of the family Nitidulidae associated with beehives. Phylogenetic analysis of SHB COI sequences (3' COI) revealed two divergent lineages, with those from Australia and USA being genetically different from the recent detection in Italy. Many countries, including New Zealand, are currently free from SHB, and require a rapid detection method for biosecurity. Here we present the development and validation of a real-time PCR assay for detection of SHB. The assay showed high specificity and sensitivity for detecting SHB, with no cross-reaction observed with closely related species, such as A. concolor. The real-time PCR is sensitive, detecting the target sequences up to 100 copies/µL. This assay should prove a useful biosecurity tool for rapid detection of SHB worldwide.},
}

Animals
*Bees
Coleoptera/*classification/*genetics
*DNA Barcoding, Taxonomic
Electron Transport Complex IV/genetics
Mitochondria/enzymology
Phylogeny
*Real-Time Polymerase Chain Reaction

@article {pmid31611421,
year = {2019},
author = {Khoshravesh, R and Stata, M and Busch, FA and Saladie, M and Castelli, JM and Dakin, N and Hattersley, PW and Macfarlane, TD and Sage, RF and Ludwig, M and Sage, TL},
title = {The Evolutionary Origin of C4 photosynthesis in the Grass Subtribe Neurachninae.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1104/pp.19.00925},
pmid = {31611421},
issn = {1532-2548},
abstract = {The Australian grass subtribe Neurachninae contains closely related species that use C3, C4 and C2 photosynthesis. To gain insight into the evolution of C4 photosynthesis in grasses, we examined leaf gas exchange, anatomy and ultrastructure, and tissue localization of glycine decarboxylase subunit P (GLDP) in nine Neurachninae species. We identified previously unrecognized variation in leaf structure and physiology within Neurachne that represents varying degrees of C3-C4 intermediacy in the Neurachninae. These include inverse correlations between the apparent photosynthetic CO2 compensation point in the absence of day respiration (C*) and a) chloroplast and mitochondrial investment in the mestome sheath (MS), where CO2 is concentrated in C2 and C4 Neurachne species; b) width of the MS cells; c) frequency of plasmodesmata in the MS cell walls adjoining the parenchymatous bundle sheath; and d) the proportion of leaf GLDP invested in the MS tissue. Less than 12% of the leaf GLDP was allocated to the MS of completely C3 Neurachninae species with C* values of 56-61 µmol mol-1, whereas two-thirds of leaf GLDP was in the MS of Neurachne lanigera, which exhibits a newly-identified, partial C2 phenotype with C* of 44 µmol mol-1. Increased investment of GLDP in MS tissue of the C2 species was attributed to more MS mitochondria and less GLDP in mesophyll mitochondria. These results are consistent with a model where C4 evolution in Neurachninae initially occurred via an increase in organelle and GLDP content in MS cells, which generated a sink for photorespired CO2 in MS tissues.},
}

@article {pmid30185526,
year = {2018},
author = {Abbasi, F and Miyata, H and Shimada, K and Morohoshi, A and Nozawa, K and Matsumura, T and Xu, Z and Pratiwi, P and Ikawa, M},
title = {RSPH6A is required for sperm flagellum formation and male fertility in mice.},
journal = {Journal of cell science},
volume = {131},
number = {19},
pages = {},
pmid = {30185526},
issn = {1477-9137},
support = {P01 HD087157/HD/NICHD NIH HHS/United States ; R01 HD088412/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; CRISPR-Cas Systems/genetics ; Conserved Sequence ; Evolution, Molecular ; *Fertility ; Flagella/*metabolism/ultrastructure ; HEK293 Cells ; Humans ; Male ; Mice ; Mice, Mutant Strains ; Mitochondria/metabolism ; Organ Specificity ; Phenotype ; Protein Binding ; Protein Transport ; Proteins/*metabolism ; Sperm Injections, Intracytoplasmic ; Sperm Tail/metabolism ; Spermatozoa/*metabolism/ultrastructure ; Testis/metabolism ; Tubulin/metabolism ; },
abstract = {The flagellum is an evolutionarily conserved appendage used for sensing and locomotion. Its backbone is the axoneme and a component of the axoneme is the radial spoke (RS), a protein complex implicated in flagellar motility regulation. Numerous diseases occur if the axoneme is improperly formed, such as primary ciliary dyskinesia (PCD) and infertility. Radial spoke head 6 homolog A (RSPH6A) is an ortholog of Chlamydomonas RSP6 in the RS head and is evolutionarily conserved. While some RS head proteins have been linked to PCD, little is known about RSPH6A. Here, we show that mouse RSPH6A is testis-enriched and localized in the flagellum. Rsph6a knockout (KO) male mice are infertile as a result of their short immotile spermatozoa. Observation of the KO testis indicates that the axoneme can elongate but is disrupted before accessory structures are formed. Manchette removal is also impaired in the KO testis. Further, RSPH9, another radial spoke protein, disappeared in the Rsph6a KO flagella. These data indicate that RSPH6A is essential for sperm flagellar assembly and male fertility in mice.This article has an associated First Person interview with the first author of the paper.},
}

Animals
Base Sequence
CRISPR-Cas Systems/genetics
Conserved Sequence
Evolution, Molecular
*Fertility
Flagella/*metabolism/ultrastructure
HEK293 Cells
Humans
Male
Mice
Mice, Mutant Strains
Mitochondria/metabolism
Organ Specificity
Phenotype
Protein Binding
Protein Transport
Proteins/*metabolism
Sperm Injections, Intracytoplasmic
Sperm Tail/metabolism
Spermatozoa/*metabolism/ultrastructure
Testis/metabolism
Tubulin/metabolism

@article {pmid31599941,
year = {2019},
author = {Liu, Q and Lin, D and Li, M and Gu, Z and Zhao, Y},
title = {Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evz214},
pmid = {31599941},
issn = {1759-6653},
abstract = {Many studies have suggested that mitochondria and mitochondrial DNA (mtDNA) might be functionally associated with tumor genesis and development. Although the heterogeneity of tumors is well known, most studies were based on the analysis of a single tumor sample. The extent of mtDNA diversity in the same tumor is unclear, as is whether the diversity is influenced by selection pressure. Here, we analyzed the whole exon data from one non-tumor sample and 23 tumor samples from different locations of one single tumor tissue from a hepatocellular carcinoma (HCC) patient. Among 18 heteroplasmic sites identified in the tumor, only two heteroplasmies were shared among all tumor samples. By investigating the correlations between the occurrence and frequency of heteroplasmy (Het) and sampling locations (Coordinate), relative mitochondrial copy numbers (mtCN), and single nucleotide variants (SNV) in the nuclear genome, we found that the Coordinate was significantly correlated with Het, suggesting no strong purifying selection or positive selection acted on the mtDNA in HCC. By further investigating the allele frequency and proportion of nonsynonymous mutations in the tumor mtDNA, we found that mtDNA in HCC did not undergo extra selection compared with mtDNA in the adjacent non-tumor tissue, and they both likely evolved under neutral selection.},
}

@article {pmid31591397,
year = {2019},
author = {Smith, SR and Dupont, CL and McCarthy, JK and Broddrick, JT and Oborník, M and Horák, A and Füssy, Z and Cihlář, J and Kleessen, S and Zheng, H and McCrow, JP and Hixson, KK and Araújo, WL and Nunes-Nesi, A and Fernie, A and Nikoloski, Z and Palsson, BO and Allen, AE},
title = {Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4552},
doi = {10.1038/s41467-019-12407-y},
pmid = {31591397},
issn = {2041-1723},
abstract = {Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.},
}

@article {pmid31587636,
year = {2019},
author = {Wideman, JG and Lax, G and Leonard, G and Milner, DS and Rodríguez-Martínez, R and Simpson, AGB and Richards, TA},
title = {A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1786},
pages = {20190100},
doi = {10.1098/rstb.2019.0100},
pmid = {31587636},
issn = {1471-2970},
abstract = {Euglenozoa comprises euglenids, kinetoplastids, and diplonemids, with each group exhibiting different and highly unusual mitochondrial genome organizations. Although they are sister groups, kinetoplastids and diplonemids have very distinct mitochondrial genome architectures, requiring widespread insertion/deletion RNA editing and extensive trans-splicing, respectively, in order to generate functional transcripts. The evolutionary history by which these differing processes arose remains unclear. Using single-cell genomics, followed by small sub unit ribosomal DNA and multigene phylogenies, we identified an isolated marine cell that branches on phylogenetic trees as a sister to known kinetoplastids. Analysis of single-cell amplified genomic material identified multiple mitochondrial genome contigs. These revealed a gene architecture resembling that of diplonemid mitochondria, with small fragments of genes encoded out of order and or on different contigs, indicating that these genes require extensive trans-splicing. Conversely, no requirement for kinetoplastid-like insertion/deletion RNA-editing was detected. Additionally, while we identified some proteins so far only found in kinetoplastids, we could not unequivocally identify mitochondrial RNA editing proteins. These data invite the hypothesis that extensive genome fragmentation and trans-splicing were the ancestral states for the kinetoplastid-diplonemid clade but were lost during the kinetoplastid radiation. This study demonstrates that single-cell approaches can successfully retrieve lineages that represent important new branches on the tree of life, and thus can illuminate major evolutionary and functional transitions in eukaryotes. This article is part of a discussion meeting issue 'Single cell ecology'.},
}

@article {pmid30350319,
year = {2018},
author = {Temereva, EN and Kuzmina, TV},
title = {Spermatogenesis in the deep-sea brachiopod Pelagodiscus atlanticus and the phylogenetic significance of spermatozoon structure.},
journal = {Journal of morphology},
volume = {279},
number = {11},
pages = {1579-1589},
doi = {10.1002/jmor.20887},
pmid = {30350319},
issn = {1097-4687},
support = {17-04-00586//Russian Foundation for Basic Research/International ; #14-50-00034//Russian Science Foundation/International ; #18-14-00082//Russian Science Foundation/International ; },
mesh = {Animals ; Invertebrates/*classification/*physiology ; Male ; Models, Biological ; *Phylogeny ; *Spermatogenesis ; Spermatogonia/cytology/ultrastructure ; Spermatozoa/cytology/*ultrastructure ; },
abstract = {Details of spermatogenesis and sperm organization are often useful for reconstructing the phylogeny of closely related groups of invertebrates. Development in general and gametogenesis in particular usually differ in shallow water and deep-sea invertebrates. Here, the spermatogenesis and ultrastructure of sperm were studied in the deep-sea brachiopod Pelagodiscus atlanticus. The testes of P. atlanticus are voluminous sacs located along the lateral sides of the body. Germ cells develop around the blood capillaries, contact the basal lamina, and contain germ plasm, numerous mitochondria, Golgi apparatus, lipid droplets, and centrioles of the rudimentary cilium. During spermatogenesis, several proacrosomal vesicles appear at the posterior pole of the cell; these vesicles then fuse and migrate to the anterior pole. The spermatozoon has a head with an acrosome, nucleus, eight mitochondria, proximal and distal centrioles orthogonally arranged, and a long tail. Comparative analysis suggests that the spermatozoon of P. atlanticus can be considered the most ancestral among all brachiopods. Such an organization indicates that fertilization is external in this deep-sea species. Spermatozoa of other brachiopods should be regarded as derived from this ancestral type. The transformation of brachiopod spermatozoa might have occurred in three different ways that correspond to the three main clades of recent brachiopods: Linguliformea, Craniiformea, and Rhynchonelliformea.},
}

Animals
Invertebrates/*classification/*physiology
Male
Models, Biological
*Phylogeny
*Spermatogenesis
Spermatogonia/cytology/ultrastructure
Spermatozoa/cytology/*ultrastructure

@article {pmid30194707,
year = {2018},
author = {Grandi, G and Astolfi, G and Chicca, M and Pezzi, M},
title = {Ultrastructural investigations on spermatogenesis and spermatozoan morphology in the endangered Adriatic sturgeon, Acipenser naccarii (Chondrostei, Acipenseriformes).},
journal = {Journal of morphology},
volume = {279},
number = {10},
pages = {1376-1396},
doi = {10.1002/jmor.20847},
pmid = {30194707},
issn = {1097-4687},
support = {16-01-14404//Italian Ministry of University and Research (MIUR)/International ; },
mesh = {Acrosome/ultrastructure ; Animals ; *Endangered Species ; Fishes/*anatomy & histology ; Male ; Phylogeny ; Principal Component Analysis ; Spermatids/cytology/ultrastructure ; *Spermatogenesis ; Spermatogonia/ultrastructure ; Spermatozoa/cytology/*ultrastructure ; Testis/ultrastructure ; },
abstract = {Spermatogenesis was investigated in the Adriatic sturgeon, Acipenser naccarii, by light and electron microscopy. The testis of the unrestricted type had a germinal compartment composed of lobules containing germ cells and Sertoli cells, and separated by a basal lamina from the interstitial compartment, in which Leydig and myoid cells were detected for the first time in Acipenseridae. Spermatogenesis occurred in spermatocysts produced when Sertoli cells became associated with type A spermatogonia of subsequent generations, which produced a clone of synchronized aligned spermatogonia. In primary spermatocytes at zygo-pachytene stage, the large spherical nucleus contained synaptonemal complexes. The smaller secondary spermatocytes were ovoid with a central round nucleus and scarce cytoplasm. Spermatids were interconnected by cytoplasmic bridges until early spermiogenesis. Chromatin initially condensed as long, twisted, and nonhomogeneous fibers and finally as a compact structure made of thick filaments. Early spermatids showed the flagellum, the primordia of centriole complex and of "implantation fossa," followed by the acrosomal vesicle formed by Golgi complexes and a fibrous body associated to centriole complex. The spermatozoan head had 10 postero-lateral projections and a trapezoidal nucleus, a cylindrical midpiece with six to eight mitochondria, the centriole complex, and a "9 + 2" flagellum with a pair of lateral fins. Three helical endonuclear canals crossed the nucleus from the acrosome base to the implantation fossa; their spiralization and that of chromatin fibers suggest a spiral twisting of the nucleus during spermiogenesis. The Sertoli cells performed phagocytosis of degenerating spermatids and spermatozoa. Significant interindividual differences were detected in most morphological parameters of spermatozoa. Data on spermatogenesis in A. naccarii and morphometric measurements on mature spermatozoa provide information about the reproductive biology of the species useful not only for phylogenetic studies but also for evaluation of sperm quality for artificial reproduction projects and restocking of this and other critically endangered sturgeon species.},
}

Acrosome/ultrastructure
Animals
*Endangered Species
Fishes/*anatomy & histology
Male
Phylogeny
Principal Component Analysis
Spermatids/cytology/ultrastructure
*Spermatogenesis
Spermatogonia/ultrastructure
Spermatozoa/cytology/*ultrastructure
Testis/ultrastructure

@article {pmid29689215,
year = {2018},
author = {McBride, HM},
title = {Mitochondria and endomembrane origins.},
journal = {Current biology : CB},
volume = {28},
number = {8},
pages = {R367-R372},
doi = {10.1016/j.cub.2018.03.052},
pmid = {29689215},
issn = {1879-0445},
mesh = {Animals ; Biological Evolution ; Eukaryota ; Evolution, Molecular ; Humans ; Intracellular Membranes/*physiology ; Mitochondria/*metabolism/*physiology ; Mitochondrial Membranes/metabolism/physiology ; },
abstract = {In this Guest Editorial, Heidi McBride introduces our special issue on membranes with a discussion of the contribution of mitochondria to the emergence of the endomembrane system.},
}

Animals
Biological Evolution
Eukaryota
Evolution, Molecular
Humans
Intracellular Membranes/*physiology
Mitochondria/*metabolism/*physiology
Mitochondrial Membranes/metabolism/physiology

@article {pmid29330875,
year = {2018},
author = {Wai, KT and Barash, M and Gunn, P},
title = {Performance of the Early Access AmpliSeq™ Mitochondrial Panel with degraded DNA samples using the Ion Torrent™ platform.},
journal = {Electrophoresis},
volume = {39},
number = {21},
pages = {2776-2784},
doi = {10.1002/elps.201700371},
pmid = {29330875},
issn = {1522-2683},
mesh = {DNA, Mitochondrial/*genetics ; Female ; Forensic Genetics/*methods ; Heating ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Mitochondria/genetics ; Nucleic Acid Denaturation ; Phylogeny ; },
abstract = {The Early Access AmpliSeq™ Mitochondrial Panel amplifies whole mitochondrial genomes for phylogenetic and kinship identifications, using Ion Torrent™ technology. There is currently limited information on its performance with degraded DNA, a common occurrence in forensic samples. This study evaluated the performance of the Panel with DNA samples degraded in vitro, to mimic conditions commonly found in forensic investigations. Purified DNA from five individuals was heat-treated at five time points each (125°C for 0, 30, 60, 120, and 240 min; total n = 25). The quality of DNA was assessed via a real-time DNA assay of genomic DNA and prepared for massively parallel sequencing on the Ion Torrent™ platform. Mitochondrial sequences were obtained for all samples and had an amplicon coverage averaging between 66X to 2803X. Most amplicons (157/162) displayed high coverages (452 ± 333X), while reads with less than 100X coverage were recorded in five amplicons only (90 ± 5X). Amplicon coverage was decreased with prolonged heating. At 72% strand balance, reads were well balanced between forward and reverse strands. Using a coverage threshold of ten reads per SNP, complete sequences were recovered in all samples and resolved kinship and, haplogroup relations. Additionally, the HV1 and HV2 regions of the reference and 240-min heat-treated samples (n = 10) were Sanger-sequenced for concordance. Overall, this study demonstrates the efficacy of a novel forensic Panel that recovers high quality mitochondrial sequences from degraded DNA samples.},
}

DNA, Mitochondrial/*genetics
Female
Forensic Genetics/*methods
Heating
High-Throughput Nucleotide Sequencing/*methods
Humans
Male
Mitochondria/genetics
Nucleic Acid Denaturation
Phylogeny

@article {pmid31581628,
year = {2019},
author = {Mazzocca, A},
title = {The Systemic-Evolutionary Theory of the Origin of Cancer (SETOC): A New Interpretative Model of Cancer as a Complex Biological System.},
journal = {International journal of molecular sciences},
volume = {20},
number = {19},
pages = {},
doi = {10.3390/ijms20194885},
pmid = {31581628},
issn = {1422-0067},
abstract = {The Systemic-Evolutionary Theory of Cancer (SETOC) is a recently proposed theory based on two important concepts: (i) Evolution, understood as a process of cooperation and symbiosis (Margulian-like), and (ii) The system, in terms of the integration of the various cellular components, so that the whole is greater than the sum of the parts, as in any complex system. The SETOC posits that cancer is generated by the de-emergence of the "eukaryotic cell system" and by the re-emergence of cellular subsystems such as archaea-like (genetic information) and/or prokaryotic-like (mitochondria) subsystems, featuring uncoordinated behaviors. One of the consequences is a sort of "cellular regression" towards ancestral or atavistic biological functions or behaviors similar to those of protists or unicellular organisms in general. This de-emergence is caused by the progressive breakdown of the endosymbiotic cellular subsystem integration (mainly, information = nucleus and energy = mitochondria) as a consequence of long-term injuries. Known cancer-promoting factors, including inflammation, chronic fibrosis, and chronic degenerative processes, cause prolonged damage that leads to the breakdown or failure of this form of integration/endosymbiosis. In normal cells, the cellular "subsystems" must be fully integrated in order to maintain the differentiated state, and this integration is ensured by a constant energy intake. In contrast, when organ or tissue damage occurs, the constant energy intake declines, leading, over time, to energy shortage, failure of endosymbiosis, and the de-differentiated state observed in dysplasia and cancer.},
}

@article {pmid29675831,
year = {2018},
author = {Kauko, A and Lehto, K},
title = {Eukaryote specific folds: Part of the whole.},
journal = {Proteins},
volume = {86},
number = {8},
pages = {868-881},
doi = {10.1002/prot.25517},
pmid = {29675831},
issn = {1097-0134},
mesh = {Archaea/genetics ; Bacteria/classification ; Biological Evolution ; Databases, Protein ; Eukaryota/*classification ; Eukaryotic Cells/classification ; Evolution, Molecular ; Genes, Bacterial ; Genes, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Proteins/genetics ; Symbiosis/*genetics ; },
abstract = {The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor. Despite of this, there exists a large number of protein families and folds found only in eukaryotes. In this study, we have analyzed structural superfamilies and folds that probably appeared during eukaryogenesis. These folds typically represent relatively small binding domains of larger multidomain proteins. They are commonly involved in biological processes that are particularly complex in eukaryotes, such as signaling, trafficking/cytoskeleton, ubiquitination, transcription and RNA processing, but according to recent studies, these processes also have prokaryotic roots. Thus the folds originating from an eukaryotic stem seem to represent accessory parts that have contributed in the expansion of several prokaryotic processes to a new level of complexity. This might have taken place as a co-evolutionary process where increasing complexity and fold innovations have supported each other.},
}

Archaea/genetics
Bacteria/classification
Biological Evolution
Databases, Protein
Eukaryota/*classification
Eukaryotic Cells/classification
Evolution, Molecular
Genes, Bacterial
Genes, Mitochondrial
Mitochondria/genetics
Phylogeny
Proteins/genetics
Symbiosis/*genetics

@article {pmid31154527,
year = {2019},
author = {Suleman, and Khan, MS and Heneberg, P and Zhou, CY and Muhammad, N and Zhu, XQ and Ma, J},
title = {Characterization of the complete mitochondrial genome of Uvitellina sp., representative of the family Cyclocoelidae and phylogenetic implications.},
journal = {Parasitology research},
volume = {118},
number = {7},
pages = {2203-2211},
doi = {10.1007/s00436-019-06358-y},
pmid = {31154527},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Birds/parasitology ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Echinostomatidae/classification/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Mitochondrial (mt) DNA has been useful in revealing the phylogenetic relationship of eukaryotic organisms including flatworms. Therefore, the use of mitogenomic data for the comparative and phylogenetic purposes is needed for those families of digenetic trematodes for which the mitogenomic data are still missing. Molecular data with sufficiently rich informative characters that can better resolve species identification, discrimination, and membership in different genera is also required for members of some morphologically difficult families of trematodes bearing few autapomorphic characters among its members. Here, the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and the complete mt genome of the trematode Uvitellina sp. (Cyclocoelidae: Haematotrephinae) was determined and annotated. The mt genome of this avian trematode is 14,217 bp in length, containing 36 genes plus a single non-coding region. The ITS rDNA sequences were used for the pairwise sequence comparison of Uvitellina sp. with European cyclocoelid species, and the mitochondrial 12 protein-coding genes (PCGs) and two ribosomal RNA genes were used to evaluate the position of the family within selected trematodes. The ITS rDNA analysis of Uvitellina sp. showed less nucleotide differences with Hyptiasmus oculeus (16.77%) than with other European cyclocoelids (18.63-23.58%). The Bayesian inference (BI) analysis using the 12 mt PCGs and two rRNA genes supported the placement of the family Cyclocoelidae within the superfamily Echinostomatoidea (Plagiorchiida: Echinostmata). The availability of the mt genome sequences of Uvitellina sp. provides a novel resource of molecular markers for phylogenetic studies of Cyclocoelidae and other trematodes.},
}

Animals
Base Sequence
Bayes Theorem
Birds/parasitology
DNA, Mitochondrial/*genetics
DNA, Ribosomal/genetics
DNA, Ribosomal Spacer/genetics
Echinostomatidae/classification/*genetics
Genome, Mitochondrial/*genetics
Mitochondria/*genetics
Phylogeny
Sequence Analysis, DNA

@article {pmid30190598,
year = {2018},
author = {Hillen, HS and Temiakov, D and Cramer, P},
title = {Structural basis of mitochondrial transcription.},
journal = {Nature structural & molecular biology},
volume = {25},
number = {9},
pages = {754-765},
doi = {10.1038/s41594-018-0122-9},
pmid = {30190598},
issn = {1545-9985},
support = {R01 GM104231/GM/NIGMS NIH HHS/United States ; R01 GM118941/GM/NIGMS NIH HHS/United States ; },
mesh = {Evolution, Molecular ; Humans ; Mitochondria/enzymology/*metabolism ; Mitochondrial Proteins/*chemistry/*genetics ; Protein Conformation ; Terminator Regions, Genetic ; *Transcription, Genetic ; Transcriptional Elongation Factors/metabolism ; },
abstract = {The mitochondrial genome is transcribed by a single-subunit DNA-dependent RNA polymerase (mtRNAP) and its auxiliary factors. Structural studies have elucidated how mtRNAP cooperates with its dedicated transcription factors to direct RNA synthesis: initiation factors TFAM and TFB2M assist in promoter-DNA binding and opening by mtRNAP while the elongation factor TEFM increases polymerase processivity to the levels required for synthesis of long polycistronic mtRNA transcripts. Here, we review the emerging body of structural and functional studies of human mitochondrial transcription, provide a molecular movie that can be used for teaching purposes and discuss the open questions to guide future directions of investigation.},
}

Evolution, Molecular
Humans
Mitochondria/enzymology/*metabolism
Mitochondrial Proteins/*chemistry/*genetics
Protein Conformation
Terminator Regions, Genetic
*Transcription, Genetic
Transcriptional Elongation Factors/metabolism

@article {pmid29910126,
year = {2018},
author = {Zambelli, F and Mertens, J and Dziedzicka, D and Sterckx, J and Markouli, C and Keller, A and Tropel, P and Jung, L and Viville, S and Van de Velde, H and Geens, M and Seneca, S and Sermon, K and Spits, C},
title = {Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the mtDNA Variant Type and Load in Human Pluripotent Stem Cells.},
journal = {Stem cell reports},
volume = {11},
number = {1},
pages = {102-114},
pmid = {29910126},
issn = {2213-6711},
mesh = {Alleles ; Cell Culture Techniques ; Cell Differentiation/*genetics ; Chromosome Aberrations ; Clonal Evolution/*genetics ; *DNA, Mitochondrial ; Fibroblasts/metabolism ; Gene Expression Profiling ; Genetic Heterogeneity ; Genetic Variation ; Genomic Instability ; Genotype ; Humans ; Mosaicism ; *Mutagenesis ; Pluripotent Stem Cells/*metabolism ; },
abstract = {In this study, we deep-sequenced the mtDNA of human embryonic and induced pluripotent stem cells (hESCs and hiPSCs) and their source cells and found that the majority of variants pre-existed in the cells used to establish the lines. Early-passage hESCs carried few and low-load heteroplasmic variants, similar to those identified in oocytes and inner cell masses. The number and heteroplasmic loads of these variants increased with prolonged cell culture. The study of 120 individual cells of early- and late-passage hESCs revealed a significant diversity in mtDNA heteroplasmic variants at the single-cell level and that the variants that increase during time in culture are always passenger to the appearance of chromosomal abnormalities. We found that early-passage hiPSCs carry much higher loads of mtDNA variants than hESCs, which single-fibroblast sequencing proved pre-existed in the source cells. Finally, we show that these variants are stably transmitted during short-term differentiation.},
}

Alleles
Cell Culture Techniques
Cell Differentiation/*genetics
Chromosome Aberrations
Clonal Evolution/*genetics
*DNA, Mitochondrial
Fibroblasts/metabolism
Gene Expression Profiling
Genetic Heterogeneity
Genetic Variation
Genomic Instability
Genotype
Humans
Mosaicism
*Mutagenesis
Pluripotent Stem Cells/*metabolism

@article {pmid29154466,
year = {2018},
author = {Wei, X and Li, H and Zhao, G and Yang, J and Li, L and Huang, Y and Lan, X and Ma, Y and Hu, L and Zheng, H and Chen, H},
title = {ΔFosB regulates rosiglitazone-induced milk fat synthesis and cell survival.},
journal = {Journal of cellular physiology},
volume = {233},
number = {12},
pages = {9284-9298},
doi = {10.1002/jcp.26218},
pmid = {29154466},
issn = {1097-4652},
mesh = {Animals ; Apoptosis/drug effects/genetics ; Calcium/metabolism ; Cell Proliferation/drug effects ; Cell Survival/drug effects/genetics ; Cells, Cultured ; Cytoprotection/drug effects/genetics ; Epithelial Cells/drug effects/metabolism ; Female ; Gene Expression Regulation/drug effects ; Goats ; Lipid Droplets/drug effects/metabolism ; Lipid Metabolism/genetics ; Lipids/*biosynthesis ; Mammary Glands, Animal/*cytology ; Matrix Metalloproteinase 9/metabolism ; Milk/*chemistry ; Mitochondria/drug effects/metabolism ; PPAR gamma/metabolism ; Proto-Oncogene Proteins c-bcl-2 ; Proto-Oncogene Proteins c-fos/*metabolism ; Rosiglitazone/*pharmacology ; Triglycerides/biosynthesis ; },
abstract = {Rosiglitazone induces adipogenesis in adipocyte and regulates cell survival and differentiation in number of cell types. However, whether PPARγ regulates the synthesis of milk fat and cell survival in goat mammary gland remains unknown. Rosiglitazone strongly enhanced cellular triacylglycerol content and accumulation of lipid droplet in goat mammary epithelial cells (GMEC). Furthermore, ΔFosB decreased the expression of PPARγ at both mRNA and protein levels, and rosiglitazone-induced milk fat synthesis was abolished by ΔFosB overexpression. ΔFosB reduced milk fat synthesis and enhanced saturated fatty acid concentration. Rosiglitazone increased the number of GMEC in G0/G1 phase and inhibited cell proliferation, and these effects were improved by overexpression of ΔFosB. ΔFosB was found to promote the expression of Bcl-2 and suppress the expression of Bax, and protected GMEC from apoptosis induced by rosiglitazone. Intracellular calcium trafficking assay revealed that rosiglitazone markedly increased intracellular calcium concentration. ΔFosB protected GMEC from apoptosis induced by intracellular Ca2+ overload. ΔFosB increased MMP-9 gelatinolytic activity. SB-3CT, an MMP-9 inhibitor, suppressed the expression of Bcl-2, and increased intracellular calcium levels, and this effect was abolished by ΔFosB overexpression. SB-3CT induced GMEC apoptosis and this effect was inhibited by ΔFosB overexpression. These findings suggest that ΔFosB regulates rosiglitazone-induced milk fat synthesis and cell survival. Therefore, ΔFosB may be an important checkpoint to control milk fat synthesis and cell apoptosis.},
}

Animals
Apoptosis/drug effects/genetics
Calcium/metabolism
Cell Proliferation/drug effects
Cell Survival/drug effects/genetics
Cells, Cultured
Cytoprotection/drug effects/genetics
Epithelial Cells/drug effects/metabolism
Female
Gene Expression Regulation/drug effects
Goats
Lipid Droplets/drug effects/metabolism
Lipid Metabolism/genetics
Lipids/*biosynthesis
Mammary Glands, Animal/*cytology
Matrix Metalloproteinase 9/metabolism
Milk/*chemistry
Mitochondria/drug effects/metabolism
PPAR gamma/metabolism
Proto-Oncogene Proteins c-bcl-2
Proto-Oncogene Proteins c-fos/*metabolism
Rosiglitazone/*pharmacology
Triglycerides/biosynthesis

@article {pmid31559328,
year = {2019},
author = {Patita, M and Nunes, G and Alves de Matos, A and Coelho, H and Fonseca, C and Fonseca, J},
title = {Mauriac Syndrome: A Rare Hepatic Glycogenosis in Poorly Controlled Type 1 Diabetes.},
journal = {GE Portuguese journal of gastroenterology},
volume = {26},
number = {5},
pages = {370-374},
doi = {10.1159/000496094},
pmid = {31559328},
issn = {2341-4545},
abstract = {Background: Hepatic glycogenosis (HG) is a complication of poorly controlled type 1 diabetes mellitus (T1DM), characterized by glycogen accumulation in hepatocytes. Mauriac syndrome (MS) is a glycogenic hepatopathy, initially described in 1930, characterized by growth failure, delayed puberty, cushingoid appearance, hepatomegaly with abnormal liver enzymes, and hypercholesterolemia. HG is a condition with good prognosis and fast resolution after adequate glycemic control (although it has potential for relapse), with no case of evolution to end-stage liver disease described.

Case: We describe a 26-year-old female, with T1DM complicated by severe retinopathy. The patient maintained poor glycemic control since childhood, presenting glycated hemoglobin persistently higher than 10% and recurrent episodes of ketoacidosis. In adolescence, she developed hepatomegaly and fluctuating elevation of aminotransferases and triglycerides. A small, nonrepresentative hepatic biopsy suggested macrovacuolar steatosis and mild fibrosis. After 15 years of diabetes, the patient was referred for gastroenterology clinic due to chronic diarrhea and exuberant hepatomegaly. Laboratory showed persistent elevation of aminotransferases and triglycerides. Bilirubin, iron metabolism, and coagulation were normal; viral serologies and autoimmune study were negative. Upper endoscopy, ileocolonoscopy, and enteroscopy presented no lesions. Abdominal magnetic resonance imaging displayed massive hepatomegaly. Liver biopsy was repeated showing marked nuclear glycogenization, mild steatosis, and no fibrosis; electron microscopy revealed very large deposits of glycogen and pleomorphic mitochondria with an unusually dense matrix, described for the first time in this entity. The diagnosis of MS variant and diarrhea due to autonomic neuropathy were assumed.

Conclusion: Currently, HG is a well-recognized disease that occurs at any age and can be present without the full spectrum of features initially described for MS. In the era of insulin therapy, this entity represents a rare complication, caused by low therapeutic compliance.},
}

@article {pmid31311504,
year = {2019},
author = {Wang, L and Zhuang, H and Zhang, Y and Wei, W},
title = {Diversity of the Bosmina (Cladocera: Bosminidae) in China, revealed by analysis of two genetic markers (mtDNA 16S and a nuclear ITS).},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {145},
doi = {10.1186/s12862-019-1474-4},
pmid = {31311504},
issn = {1471-2148},
mesh = {Animals ; Cell Nucleus/genetics ; China ; Cladocera/*genetics ; DNA, Intergenic/*genetics ; DNA, Mitochondrial/*genetics ; Ecosystem ; Genetic Markers ; *Genetic Variation ; Geography ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Zooplankton/genetics ; },
abstract = {BACKGROUND: China is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distribution. Therefore, many biogeographical studies have focused on the organisms of the region, especially zooplankton, which is essential in the formation of biogeographical principles. Moreover, the generality of endemism also reinforces the need for detailed regional studies of zooplankton. Bosmina, a group of cosmopolitan zooplankton, is difficult to identify by morphology, and no genetic data are available to date to assess this species complex in China. In this study, 48 waterbodies were sampled covering a large geographical and ecological range in China, the goal of this research is to explore the species distribution of Bosmina across China and to reveal the genetic information of this species complex, based on two genetic markers (a mtDNA 16S and a nuclear ITS). The diversity of taxa in the Bosmina across China was investigated using molecular tools for the first time.

RESULTS: Two main species were detected in 35 waterbodies: an endemic east Asia B. fatalis, and the B. longirostris that has a Holarctic distribution. B. fatalis had lower genetic polymorphism and population differentiation than B. longirostris. B. fatalis was preponderant in central and eastern China, whereas B. longirostris was dominated in western China. The third lineage (B. hagmanni) was only detected in a reservoir (CJR) of eastern China (Guangdong province). Bosmina had limited distribution on the Tibetan plateau.

CONCLUSIONS: This study revealed that the biogeography of Bosmina appear to be affected by historical events (Pleistocene glaciations) and contemporary environment (such as altitude, eutrophication and isolated habitat).},
}

Animals
Cell Nucleus/genetics
China
Cladocera/*genetics
DNA, Intergenic/*genetics
DNA, Mitochondrial/*genetics
Ecosystem
Genetic Markers
*Genetic Variation
Geography
Haplotypes/genetics
Likelihood Functions
Mitochondria/genetics
Phylogeny
Polymorphism, Genetic
Zooplankton/genetics

@article {pmid30019754,
year = {2018},
author = {Xiao, H and Zhang, Q and Qin, X and Xu, Y and Ni, C and Huang, J and Zhu, L and Zhong, F and Liu, W and Yao, G and Zhu, Y and Hu, J},
title = {Rice PPS1 encodes a DYW motif-containing pentatricopeptide repeat protein required for five consecutive RNA-editing sites of nad3 in mitochondria.},
journal = {The New phytologist},
volume = {220},
number = {3},
pages = {878-892},
doi = {10.1111/nph.15347},
pmid = {30019754},
issn = {1469-8137},
support = {2016YFD0100804//National Key Research and Development Program of China/International ; 31371698//National Natural Science Foundation of China/International ; 31670310//National Natural Science Foundation of China/International ; SNG2017061//Suzhou science and technology project/International ; },
mesh = {Amino Acid Motifs ; Base Sequence ; Cell Nucleus/metabolism ; Conserved Sequence ; Electron Transport ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/chemistry/metabolism ; Oryza/*genetics/ultrastructure ; Phenotype ; Plant Proteins/*chemistry/*metabolism ; Pollen/metabolism/ultrastructure ; Protein Binding ; RNA Editing/*genetics ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Time Factors ; },
abstract = {The pentatricopeptide repeat (PPR) protein family is a large family characterized by tandem arrays of a degenerate 35-amino-acid motif whose members function as important regulators of organelle gene expression at the post-transcriptional level. Despite the roles of PPRs in RNA editing in organelles, their editing activities and the underlying mechanism remain obscure. Here, we show that a novel DYW motif-containing PPR protein, PPS1, is associated with five conserved RNA-editing sites of nad3 located in close proximity to each other in mitochondria, all of which involve conversion from proline to leucine in rice. Both pps1 RNAi and heterozygous plants are characterized by delayed development and partial pollen sterility at vegetative stages and reproductive stage. RNA electrophoresis mobility shift assays (REMSAs) and reciprocal competition assays using different versions of nad3 probes confirm that PPS1 can bind to cis-elements near the five affected sites, which is distinct from the existing mode of PPR-RNA binding because of the continuity of the editing sites. Loss of editing at nad3 in pps1 reduces the activity of several complexes in the mitochondrial electron transport chain and affects mitochondrial morphology. Taken together, our results indicate that PPS1 is required for specific editing sites in nad3 in rice.},
}

Amino Acid Motifs
Base Sequence
Cell Nucleus/metabolism
Conserved Sequence
Electron Transport
Evolution, Molecular
Gene Expression Regulation, Plant
Mitochondria/*metabolism/ultrastructure
Mitochondrial Proteins/chemistry/metabolism
Oryza/*genetics/ultrastructure
Phenotype
Plant Proteins/*chemistry/*metabolism
Pollen/metabolism/ultrastructure
Protein Binding
RNA Editing/*genetics
RNA Interference
RNA, Messenger/genetics/metabolism
Time Factors

@article {pmid30385240,
year = {2018},
author = {Palozzi, JM and Jeedigunta, SP and Hurd, TR},
title = {Mitochondrial DNA Purifying Selection in Mammals and Invertebrates.},
journal = {Journal of molecular biology},
volume = {430},
number = {24},
pages = {4834-4848},
doi = {10.1016/j.jmb.2018.10.019},
pmid = {30385240},
issn = {1089-8638},
support = {FRN 159510//CIHR/Canada ; },
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; Humans ; Invertebrates/*genetics/growth & development ; Mammals/*genetics/growth & development ; Maternal Inheritance ; Mitochondria/*genetics ; Ovum/chemistry/*cytology ; Quality Control ; Selection, Genetic ; },
abstract = {Numerous mitochondrial quality control mechanisms exist within cells, but none have been shown to effectively assess and control the quality of mitochondrial DNA (mtDNA). One reason such mechanisms have yet to be elucidated is that they do not appear to be particularly active in most somatic cells, where many studies are conducted. The female germline, the cell lineage that gives rise to eggs, appears to be an exception. In the germline, strong purifying selection pathways act to eliminate deleterious mtDNA. These pathways have apparently evolved to prevent pathogenic mtDNA mutations from accumulating over successive generations and causing a decline of species via Muller's ratchet. Despite their fundamental biological importance, the mechanisms underlying purifying selection remain poorly understood, with no genes involved in this process yet identified. In this review, we discuss recent studies exploring mechanisms of germline mtDNA purifying selection in both mammalian and invertebrate systems. We also discuss the challenges to future major advances. Understanding the molecular basis of purifying selection is not only a fundamental outstanding question in biology, but may also pave the way to controlling selection in somatic tissues, potentially leading to treatments for people suffering from mitochondrial diseases.},
}

Animals
DNA, Mitochondrial/*genetics
Evolution, Molecular
Female
Humans
Invertebrates/*genetics/growth & development
Mammals/*genetics/growth & development
Maternal Inheritance
Mitochondria/*genetics
Ovum/chemistry/*cytology
Quality Control
Selection, Genetic

@article {pmid30292820,
year = {2018},
author = {Cogliati, S and Lorenzi, I and Rigoni, G and Caicci, F and Soriano, ME},
title = {Regulation of Mitochondrial Electron Transport Chain Assembly.},
journal = {Journal of molecular biology},
volume = {430},
number = {24},
pages = {4849-4873},
doi = {10.1016/j.jmb.2018.09.016},
pmid = {30292820},
issn = {1089-8638},
mesh = {Animals ; *Electron Transport ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Multienzyme Complexes/chemistry/metabolism ; Oxidative Phosphorylation ; Phylogeny ; },
abstract = {Mitochondrial function depends on the correct synthesis, transport, and assembly of proteins and cofactors of the electron transport chain. The initial idea that the respiratory chain protein complexes (RCCs) were independent structures in the inner mitochondrial membrane evolved after the identification of higher quaternary structures called supercomplexes (SCs), whose formation is dynamically regulated in order to accommodate cellular metabolic demands. Due to the dual genetic origin of the mitochondrial proteome, electron transport chain and SCs formation must be tightly regulated to coordinate the expression and assembly of components encoded by both genomes. This regulation occurs at different levels from gene transcription to protein, complex or SCs assembly, and might involve the participation of factors that contribute to the formation and stability of the RCCs and SCs. Here we review the cellular pathways and assembly factors that regulate RCCs and SCs formation.},
}

Animals
*Electron Transport
Evolution, Molecular
Gene Expression Regulation
Humans
Mitochondria/*genetics/metabolism
Mitochondrial Membranes/metabolism
Mitochondrial Proteins/chemistry/genetics/*metabolism
Multienzyme Complexes/chemistry/metabolism
Oxidative Phosphorylation
Phylogeny

@article {pmid31551356,
year = {2019},
author = {Al-Faresi, RAZ and Lightowlers, RN and Chrzanowska-Lightowlers, ZMA},
title = {Mammalian mitochondrial translation - revealing consequences of divergent evolution.},
journal = {Biochemical Society transactions},
volume = {},
number = {},
pages = {},
doi = {10.1042/BST20190265},
pmid = {31551356},
issn = {1470-8752},
abstract = {Mitochondria are ubiquitous organelles present in the cytoplasm of all nucleated eukaryotic cells. These organelles are described as arising from a common ancestor but a comparison of numerous aspects of mitochondria between different organisms provides remarkable examples of divergent evolution. In humans, these organelles are of dual genetic origin, comprising ∼1500 nuclear-encoded proteins and thirteen that are encoded by the mitochondrial genome. Of the various functions that these organelles perform, it is only oxidative phosphorylation, which provides ATP as a source of chemical energy, that is dependent on synthesis of these thirteen mitochondrially encoded proteins. A prerequisite for this process of translation are the mitoribosomes. The recent revolution in cryo-electron microscopy has generated high-resolution mitoribosome structures and has undoubtedly revealed some of the most distinctive molecular aspects of the mitoribosomes from different organisms. However, we still lack a complete understanding of the mechanistic aspects of this process and many of the factors involved in post-transcriptional gene expression in mitochondria. This review reflects on the current knowledge and illustrates some of the striking differences that have been identified between mitochondria from a range of organisms.},
}

@article {pmid31550514,
year = {2019},
author = {Cali, C and Agus, M and Kare, K and Boges, DJ and Lehvaslaiho, H and Hadwiger, M and Magistretti, PJ},
title = {3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat.},
journal = {Progress in neurobiology},
volume = {},
number = {},
pages = {101696},
doi = {10.1016/j.pneurobio.2019.101696},
pmid = {31550514},
issn = {1873-5118},
abstract = {With the rapid evolution in the automation of serial electron microscopy in life sciences, the acquisition of terabyte-sized datasets is becoming increasingly common. High resolution serial block-face imaging (SBEM) of biological tissues offers the opportunity to segment and reconstruct nanoscale structures to reveal spatial features previously inaccessible with simple, single section, two-dimensional images, with a particular focus on glial cells, whose reconstruction efforts in literature are still limited, compared to neurons. Here, we imaged a 750000 cubic micron volume of the somatosensory cortex from a juvenile P14 rat, with 20 nm accuracy. We recognized a total of 186 cells using their nuclei, and classified them as neuronal or glial based on features of the soma and the processes. We reconstructed for the first time 4 almost complete astrocytes and neurons, 4 complete microglia and 4 complete pericytes, including their intracellular mitochondria, 186 nuclei and 213 myelinated axons. We then performed quantitative analysis on the three-dimensional models. Out of the data that we generated, we observed that neurons have larger nuclei, which correlated with their lesser density, and that astrocytes and pericytes have a higher surface to volume ratio, compared to other cell types. All reconstructed morphologies represent an important resource for computational neuroscientists, as morphological quantitative information can be inferred, to tune simulations that take into account the spatial compartmentalization of the different cell types.},
}

@article {pmid30117257,
year = {2018},
author = {Wang, L and Zhang, S and Li, JH and Zhang, YJ},
title = {Mitochondrial genome, comparative analysis and evolutionary insights into the entomopathogenic fungus Hirsutella thompsonii.},
journal = {Environmental microbiology},
volume = {20},
number = {9},
pages = {3393-3405},
doi = {10.1111/1462-2920.14379},
pmid = {30117257},
issn = {1462-2920},
support = {201601D011065//Natural Science Foundation of Shanxi Province/International ; },
mesh = {Acari/*microbiology ; Animals ; Evolution, Molecular ; Fungal Proteins/genetics ; Genome, Fungal ; *Genome, Mitochondrial ; Hypocreales/classification/*genetics/isolation & purification ; Introns ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; },
abstract = {Nuclear genomes of two isolates of Hirsutella thompsonii, a pathogen causing epizootics among mites, have been reported; in contrast, its mitochondrial genome (mitogenome) has remained unknown, limiting our understanding of its evolution. Herein, we annotated the first complete mitogenome of H. thompsonii, which encoded all standard fungal mitochondrial genes plus three free-standing ORFs. Transcriptional analyses validated the expression of most conserved genes and revealed some interesting transcription patterns of mitochondrial genes. Phylogenetic analyses confirmed its placement in Ophiocordycipitaceae. Comparison of five different isolates originally collected from different locations revealed mitogenome size variations (60.3-66.4 kb) mainly due to different numbers of introns. A total of 15 intron loci were identified, with 11 existing in all 5 isolates and 4 showing presence/absence dynamics. These introns were most likely obtained through horizontal transfer from other fungal organisms. Those common introns might have been in H. thompsonii mitogenomes since the divergence of the fungus from its putative sister species H. minnesotensis, whereas those dynamic introns might have experienced 1-2 gain or loss events. We also detected evidence of degeneration for some introns. Overall, our study shed new insights into the mitochondrial evolution of the acaropathogenic fungus H. thompsonii.},
}

Acari/*microbiology
Animals
Evolution, Molecular
Fungal Proteins/genetics
Genome, Fungal
*Genome, Mitochondrial
Hypocreales/classification/*genetics/isolation & purification
Introns
Mitochondria/genetics
Open Reading Frames
Phylogeny

@article {pmid31536728,
year = {2019},
author = {Buonvicino, D and Ranieri, G and Pratesi, S and Guasti, D and Chiarugi, A},
title = {Neuroimmunological characterization of a mouse model of primary progressive experimental autoimmune encephalomyelitis and effects of immunosuppressive or neuroprotective strategies on disease evolution.},
journal = {Experimental neurology},
volume = {},
number = {},
pages = {113065},
doi = {10.1016/j.expneurol.2019.113065},
pmid = {31536728},
issn = {1090-2430},
abstract = {Progressive multiple sclerosis (PMS) is a devastating disorder sustained by neuroimmune interactions still wait to be identified. Recently, immune-independent, neural bioenergetic derangements have been hypothesized as causative of neurodegeneration in PMS patients. To gather information on the immune and neurodegenerative components during PMS, in the present study we investigated the molecular and cellular events occurring in a Non-obese diabetic (NOD) mouse model of experimental autoimmune encephalomyelitis (EAE). In these mice, we also evaluated the effects of clinically-relevant immunosuppressive (dexamethasone) or bioenergetic drugs (bezafibrate and biotin) on functional, immune and neuropathological parameters. We found that immunized NOD mice progressively accumulated disability and severe neurodegeneration in the spinal cord. Unexpectedly, although CD4 and CD8 lymphocytes but not B or NK cells infiltrate the spinal cord linearly with time, their suppression by different dexamethasone treatment schedules did not affect disease progression. Also, the spreading of the autoimmune response towards additional immunogenic myelin antigen occurred neither in the periphery nor in the CNS of EAE mice. Conversely, we found that altered mitochondrial morphology, reduced contents of mtDNA and decreased transcript levels for respiratory complex subunits occurred at early disease stages and preceded axonal degeneration within spinal cord columns. However, the mitochondria boosting drugs, bezafibrate and biotin, were unable to reduce disability progression. Data suggest that EAE NOD mice recapitulate some features of PMS. Also, by showing that bezafibrate or biotin do not affect progression in NOD mice, our study suggests that this model can be harnessed to anticipate experimental information of relevance to innovative treatments of PMS.},
}

@article {pmid31536521,
year = {2019},
author = {Yang, M and Gong, L and Sui, J and Li, X},
title = {The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids.},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0217952},
doi = {10.1371/journal.pone.0217952},
pmid = {31536521},
issn = {1932-6203},
abstract = {The deep-sea chemosynthetic environment is one of the most extreme environments on the Earth, with low oxygen, high hydrostatic pressure and high levels of toxic substances. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, "G(A)nT" motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea chemosynthetic environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea chemosynthetic environment.},
}

@article {pmid30629584,
year = {2019},
author = {Chiovitti, A and Thorpe, F and Gorman, C and Cuxson, JL and Robevska, G and Szwed, C and Duncan, JC and Vanyai, HK and Cross, J and Siemering, KR and Sumner, J},
title = {A citizen science model for implementing statewide educational DNA barcoding.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0208604},
doi = {10.1371/journal.pone.0208604},
pmid = {30629584},
issn = {1932-6203},
mesh = {Animals ; Australia ; Base Sequence ; *DNA Barcoding, Taxonomic ; Feedback ; Genetic Variation ; Mitochondria/genetics ; *Models, Educational ; Phylogeny ; Reptiles/classification/genetics ; *Science ; Species Specificity ; Students ; },
abstract = {Our aim was to develop a widely available educational program in which students conducted authentic research that met the expectations of both the scientific and educational communities. This paper describes the development and implementation of a citizen science project based on DNA barcoding of reptile specimens obtained from the Museums Victoria frozen tissue collection. The student program was run by the Gene Technology Access Centre (GTAC) and was delivered as a "one day plus one lesson" format incorporating a one-day wet laboratory workshop followed by a single lesson at school utilising online bioinformatics tools. The project leveraged the complementary resources and expertise of the research and educational partners to generate robust scientific data that could be analysed with confidence, meet the requirements of the Victorian state education curriculum, and provide participating students with an enhanced learning experience. During two 1-week stints in 2013 and 2014, 406 students mentored by 44 postgraduate university students participated in the project. Students worked mainly in pairs to process ~200 tissue samples cut from 53 curated reptile specimens representing 17 species. A total of 27 novel Cytochrome Oxidase subunit 1 (CO1) sequences were ultimately generated for 8 south-east Australian reptile species of the families Scincidae and Agamidae.},
}

Animals
Australia
Base Sequence
*DNA Barcoding, Taxonomic
Feedback
Genetic Variation
Mitochondria/genetics
*Models, Educational
Phylogeny
Reptiles/classification/genetics
*Science
Species Specificity
Students

@article {pmid31525456,
year = {2019},
author = {Corrêa da Silva, F and Favero de Aguiar, C and Pereira, JAS and de Brito Monteiro, L and Davanzo, GG and Codo, AC and Pimentel de Freitas, L and Berti, AS and Ferruci, D and Castelucci, BG and Consonni, SR and Carvalho, HF and Moraes-Vieira, PMM},
title = {Ghrelin effects on mitochondrial fitness modulates macrophage function.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2019.09.012},
pmid = {31525456},
issn = {1873-4596},
abstract = {Over the past years, systemic derived cues that regulate cellular metabolism have been implicated in the regulation of immune responses. Ghrelin is an orexigenic hormone produced by enteroendocrine cells in the gastric mucosa with known immunoregulatory roles. The mechanism behind the function of ghrelin in immune cells, such as macrophages, is still poorly understood. Here, we explored the hypothesis that ghrelin leads to alterations in macrophage metabolism thus modulating macrophage function. We demonstrated that ghrelin exerts an immunomodulatory effect over LPS-activated peritoneal macrophages, as evidenced by inhibition of TNF-α and IL-1β secretion and increased IL-12 production. Concomitantly, ghrelin increased mitochondrial membrane potential and increased respiratory rate. In agreement, ghrelin prevented LPS-induced ultrastructural damage in the mitochondria. Ghrelin also blunted LPS-induced glycolysis. In LPS-activated macrophages, glucose deprivation did not affect ghrelin-induced IL-12 secretion, whereas the inhibition of pyruvate transport and mitochondria-derived ATP abolished ghrelin-induced IL-12 secretion, indicating a dependence on mitochondrial function. Ghrelin pre-treatment of metabolic activated macrophages inhibited the secretion of TNF-α and enhanced IL-12 levels. Moreover, ghrelin effects on IL-12 are and not on TNF-α are dependent on mitochondria elongation, since ghrelin did not enhance IL-12 secretion in metabolic activated mitofusin-2 deficient macrophages. Thus, ghrelin affects macrophage mitochondrial metabolism and the subsequent macrophage function.},
}

@article {pmid29562168,
year = {2018},
author = {Haroon, S and Li, A and Weinert, JL and Fritsch, C and Ericson, NG and Alexander-Floyd, J and Braeckman, BP and Haynes, CM and Bielas, JH and Gidalevitz, T and Vermulst, M},
title = {Multiple Molecular Mechanisms Rescue mtDNA Disease in C. elegans.},
journal = {Cell reports},
volume = {22},
number = {12},
pages = {3115-3125},
pmid = {29562168},
issn = {2211-1247},
support = {R01 CA204894/CA/NCI NIH HHS/United States ; R01 AG047182/AG/NIA NIH HHS/United States ; T32 ES019851/ES/NIEHS NIH HHS/United States ; R01 GM124532/GM/NIGMS NIH HHS/United States ; R01 ES026222/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; Caenorhabditis elegans/*metabolism ; DNA, Mitochondrial/*genetics ; Disease Progression ; Mice ; Mitochondria/*metabolism ; Models, Animal ; },
abstract = {Genetic instability of the mitochondrial genome (mtDNA) plays an important role in human aging and disease. Thus far, it has proven difficult to develop successful treatment strategies for diseases that are caused by mtDNA instability. To address this issue, we developed a model of mtDNA disease in the nematode C. elegans, an animal model that can rapidly be screened for genes and biological pathways that reduce mitochondrial pathology. These worms recapitulate all the major hallmarks of mtDNA disease in humans, including increased mtDNA instability, loss of respiration, reduced neuromuscular function, and a shortened lifespan. We found that these phenotypes could be rescued by intervening in numerous biological pathways, including IGF-1/insulin signaling, mitophagy, and the mitochondrial unfolded protein response, suggesting that it may be possible to ameliorate mtDNA disease through multiple molecular mechanisms.},
}

Animals
Caenorhabditis elegans/*metabolism
DNA, Mitochondrial/*genetics
Disease Progression
Mice
Mitochondria/*metabolism
Models, Animal

@article {pmid31519789,
year = {2019},
author = {Loiacono, FV and Thiele, W and Schöttler, MA and Tillich, M and Bock, R},
title = {Establishment of a Heterologous RNA Editing Event in Chloroplasts.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1104/pp.19.00922},
pmid = {31519789},
issn = {1532-2548},
abstract = {In chloroplasts and plant mitochondria, specific cytidines in mRNAs are post-transcriptionally converted to uridines by RNA editing. Editing sites are recognized by nucleus-encoded RNA-binding proteins of the pentatricopeptide repeat (PPR) family, which bind upstream of the editing site in a sequence-specific manner and direct the editing activity to the target position. Editing sites have been lost many times during evolution by C-to-T mutations. Loss of an editing site is thought to be accompanied by loss or degeneration of its cognate PPR protein. Consequently, foreign editing sites are usually not recognized when introduced into species lacking the site. Previously, the spinach (Spinacia oleracea) psbF-26 editing site was introduced into the tobacco (Nicotiana tabacum) plastid genome. Tobacco lacks the psbF-26 site and cannot edit it. Expression of the "unedited" PsbF protein resulted in impaired photosystem II function. In Arabidopsis (Arabidopsis thaliana), the PPR protein LPA66 is required for editing at psbF-26. Here, we show that introduction of the Arabidopsis LPA66 reconstitutes editing of the spinach psbF-26 site in tobacco and restores a wild-type-like phenotype. Our findings define the minimum requirements for establishing novel RNA editing sites and suggest that the evolutionary dynamics of editing patterns is largely explained by co-evolution of editing sites and PPR proteins.},
}

@article {pmid31502197,
year = {2019},
author = {Rappocciolo, E and Stiban, J},
title = {Prokaryotic and Mitochondrial Lipids: A Survey of Evolutionary Origins.},
journal = {Advances in experimental medicine and biology},
volume = {1159},
number = {},
pages = {5-31},
doi = {10.1007/978-3-030-21162-2_2},
pmid = {31502197},
issn = {0065-2598},
abstract = {Mitochondria and bacteria share a myriad of properties since it is believed that the powerhouses of the eukaryotic cell have evolved from a prokaryotic origin. Ribosomal RNA sequences, DNA architecture and metabolism are strikingly similar in these two entities. Proteins and nucleic acids have been a hallmark for comparison between mitochondria and prokaryotes. In this chapter, similarities (and differences) between mitochondrial and prokaryotic membranes are addressed with a focus on structure-function relationship of different lipid classes. In order to be suitable for the theme of the book, a special emphasis is reserved to the effects of bioactive sphingolipids, mainly ceramide, on mitochondrial membranes and their roles in initiating programmed cell death.},
}

@article {pmid31068124,
year = {2019},
author = {Wu, Z and Hu, K and Yan, M and Song, L and Wen, J and Ma, C and Shen, J and Fu, T and Yi, B and Tu, J},
title = {Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {348},
doi = {10.1186/s12864-019-5721-2},
pmid = {31068124},
issn = {1471-2164},
support = {31571746//National Natural Science Foundation of China/ ; 2016YFD0100804//National Key Research and Development Program of China/ ; 2662016PY063//the Fundamental Research Funds for the Central Universities/ ; 2016ABA084//Hubei Key Technological Innovation Project/ ; },
mesh = {Cytoplasm/*genetics ; Gene Expression Regulation, Plant ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mustard Plant/*genetics/physiology ; Open Reading Frames ; Phylogeny ; *Plant Infertility ; Plant Proteins/*genetics ; },
abstract = {BACKGROUND: Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea.

RESULTS: The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes.

CONCLUSIONS: On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene.},
}

Cytoplasm/*genetics
Gene Expression Regulation, Plant
*Genome, Mitochondrial
Mitochondria/*genetics
Mustard Plant/*genetics/physiology
Open Reading Frames
Phylogeny
*Plant Infertility
Plant Proteins/*genetics

@article {pmid30318512,
year = {2018},
author = {Ananieva, EA and Bostic, JN and Torres, AA and Glanz, HR and McNitt, SM and Brenner, MK and Boyer, MP and Addington, AK and Hutson, SM},
title = {Mice deficient in the mitochondrial branched-chain aminotransferase (BCATm) respond with delayed tumour growth to a challenge with EL-4 lymphoma.},
journal = {British journal of cancer},
volume = {119},
number = {8},
pages = {1009-1017},
doi = {10.1038/s41416-018-0283-7},
pmid = {30318512},
issn = {1532-1827},
mesh = {AMP-Activated Protein Kinases/metabolism ; Amino Acids, Branched-Chain/blood ; Animals ; Disease Progression ; Female ; Lymphoma/*pathology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondria/genetics/*metabolism ; Neoplasm Transplantation ; Phosphorylation ; Transaminases/*genetics/*metabolism ; },
abstract = {BACKGROUND: The mitochondrial branched-chain aminotransferase (BCATm) is a recently discovered cancer marker with a poorly defined role in tumour progression.

METHODS: To understand how a loss of function of BCATm affects cancer, the global knockout mouse BCATmKO was challenged with EL-4 lymphoma under different diet compositions with varying amounts of branched-chain amino acids (BCAAs). Next, the growth and metabolism of EL-4 cells were studied in the presence of different leucine concentrations in the growth medium.

RESULTS: BCATmKO mice experienced delayed tumour growth when fed standard rodent chow or a normal BCAA diet. Tumour suppression correlated with 37.6- and 18.9-fold increases in plasma and tumour BCAAs, 37.5% and 30.4% decreases in tumour glutamine and alanine, and a 3.5-fold increase in the phosphorylation of tumour AMPK in BCATmKO mice on standard rodent chow. Similar results were obtained with a normal but not with a choice BCAA diet.

CONCLUSIONS: Global deletion of BCATm caused a dramatic build-up of BCAAs, which could not be utilised for energy or amino acid synthesis, ultimately delaying the growth of lymphoma tumours. Furthermore, physiological, but not high, leucine concentrations promoted the growth of EL-4 cells. BCATm and BCAA metabolism were identified as attractive targets for anti-lymphoma therapy.},
}

AMP-Activated Protein Kinases/metabolism
Amino Acids, Branched-Chain/blood
Animals
Disease Progression
Female
Lymphoma/*pathology
Male
Mice
Mice, Inbred C57BL
Mice, Knockout
Mitochondria/genetics/*metabolism
Neoplasm Transplantation
Phosphorylation
Transaminases/*genetics/*metabolism

@article {pmid30063873,
year = {2019},
author = {Kumar Jadav, K and Pratap Singh, A and Srivastav, AB and Sarkhel, BC},
title = {Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus).},
journal = {Animal biotechnology},
volume = {30},
number = {2},
pages = {186-191},
doi = {10.1080/10495398.2018.1469506},
pmid = {30063873},
issn = {1532-2378},
mesh = {Animals ; Breeding ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/veterinary ; Male ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Sus scrofa/*genetics ; },
abstract = {The Indian wild pig is a sub-species (Sus scrofa cristatus) which is different from the other pig breeds and is protected under Schedule-III of the Indian Wildlife (Protection) Act, 1972. In this study, complete mitogenome of two Indian wild pigs was sequenced and characterized by shotgun sequencing and de novo assembly, which revealed sequence size of 16,738 and 16,251 bp, respectively, (Accession no. MG725630 and MG725631). The mitogenome sequence in this study displayed 98% homology with previously reported mitogenome of pigs from different parts of the world. Mitogenome analysis by MITOS Web server revealed similarity of gene organization with the other vertebrates (13 protein-coding, 22 tRNAs, 2 rRNAs genes, and a control region). The mitogenomic sequences of Indian wild pig maintained a separate clade in the phylogenetic tree constructed by using 62 whole mitogenome sequences across the world. The phylogeny derived from mitogenomic sequences revealed distinct separate European-American and Asiatic pig clades. It was concluded that whole mitogenome sequencing using NGS without designing mitogenome-specific primer for amplification, is possible thereby reducing the cost and labor. This study is the first report of complete sequence of mitogenome of Indian wild pig.},
}

Animals
Breeding
Genome, Mitochondrial/*genetics
High-Throughput Nucleotide Sequencing/veterinary
Male
Mitochondria/genetics
Phylogeny
Sequence Analysis, DNA/veterinary
Sus scrofa/*genetics

@article {pmid31495025,
year = {2019},
author = {Zeh, JA and Zawlodzki, MA and Bonilla, MM and Su-Keene, EJ and Padua, MV and Zeh, DW},
title = {Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jeb.13536},
pmid = {31495025},
issn = {1420-9101},
abstract = {Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups (A and B2) in a Neotropical arachnid to investigate the role of mitochondria in sperm competition. DNA profiling demonstrated that B2-carrying males sired more than three times as many offspring in sperm competition experiments than A males, and this B2 competitive advantage cannot be explained by female mitochondrial haplogroup or male nuclear genetic background. RNA-Seq of testicular tissues implicates differential expression of mitochondrial oxidative phosphorylation (OXPHOS) genes in the B2 competitive advantage, including a 22-fold upregulation of atp8 in B2 males. Previous comparative genomic analyses have revealed functionally significant amino acid substitutions in differentially expressed genes, indicating that the mitochondrial haplogroups differ not only in expression but also in DNA sequence and protein functioning. However, mitochondrial haplogroup had no effect on sperm number or sperm viability, and, when females were mated to a single male, neither male haplogroup, female haplogroup nor the interaction between male/female haplogroup significantly affected female reproductive success. Our findings therefore suggest that mitochondrial effects on male reproduction may often go undetected in noncompetitive contexts and may prove more important in nature than is currently appreciated.},
}

@article {pmid31494084,
year = {2019},
author = {Supinski, GS and Schroder, EA and Callahan, LA},
title = {Contemporary Review in Critical Care Medicine:Mitochondria and Critical Illness.},
journal = {Chest},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chest.2019.08.2182},
pmid = {31494084},
issn = {1931-3543},
abstract = {Classically, mitochondria have largely been thought to influence the development of illness by modulating cell metabolism and determining the rate of production of high energy phosphate compounds (e.g. ATP). It is now recognized that this is a simplistic view and that mitochondria play key roles in many other processes, including cell signaling, regulating gene expression, modulating cellular calcium levels and influencing the activation of cell death pathways (e.g. caspase activation). Moreover, these multiple mitochondrial functional characteristics are now known to influence the evolution of cellular and organ function in many disease states, including sepsis, ICU acquired skeletal muscle dysfunction, acute lung injury, acute renal failure, and critical illness related immune function dysregulation. In addition, diseased mitochondria generate toxic compounds, most notably released mitochondrial DNA, which can act as Danger Associated Molecular Patterns (DAMPS) to induce systemic toxicity and damage multiple organs throughout the body. This paper will review these evolving concepts relating mitochondrial function and acute illness and will organize this discussion into four sections: (I) basics of mitochondrial physiology, (II) cellular mechanisms of mitochondrial pathophysiology, (III) critical care disease processes whose initiation and evolution are shaped by mitochondrial pathophysiology, and (IV) emerging treatments for mitochondrial dysfunction in critical illness.},
}

@article {pmid31477008,
year = {2019},
author = {Mossman, JA and Biancani, LM and Rand, DM},
title = {Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {691},
doi = {10.1186/s12864-019-6061-y},
pmid = {31477008},
issn = {1471-2164},
support = {2R01GM067862/GM/NIGMS NIH HHS/United States ; 1R01AG027849/AG/NIA NIH HHS/United States ; },
abstract = {BACKGROUND: Mitochondria perform many key roles in their eukaryotic hosts, from integrating signaling pathways through to modulating whole organism phenotypes. The > 1 billion years of nuclear and mitochondrial gene co-evolution has necessitated coordinated expression of gene products from both genomes that maintain mitochondrial, and more generally, eukaryotic cellular function. How mitochondrial DNA (mtDNA) variation modifies host fitness has proved a challenging question but has profound implications for evolutionary and medical genetics. In Drosophila, we have previously shown that recently diverged mtDNA haplotypes within-species can have more impact on organismal phenotypes than older, deeply diverged haplotypes from different species. Here, we tested the effects of mtDNA haplotype variation on gene expression in Drosophila under standardized conditions. Using the Drosophila Genetic Reference Panel (DGRP), we constructed a panel of mitonuclear genotypes that consists of factorial variation in nuclear and mtDNA genomes, with mtDNAs originating in D. melanogaster (2x haplotypes) and D. simulans (2x haplotypes).

RESULTS: We show that mtDNA haplotype variation unequivocally alters nuclear gene expression in both females and males, and mitonuclear interactions are pervasive modifying factors for gene expression. There was appreciable overlap between the sexes for mtDNA-sensitive genes, and considerable transcriptional variation attributed to particular mtDNA contrasts. These genes are generally found in low-connectivity gene co-expression networks, occur in gene clusters along chromosomes, are often flanked by non-coding RNA, and are under-represented among housekeeping genes. Finally, we identify the giant (gt) transcription factor motif as a putative regulatory sequence associated with mtDNA-sensitive genes.

CONCLUSIONS: There are predictive conditions for nuclear genes that are influenced by mtDNA variation.},
}

@article {pmid31474649,
year = {2019},
author = {Takeda, A and Saitoh, S and Ohkura, H and Sawin, KE and Goshima, G},
title = {Identification of 15 new bypassable essential genes of fission yeast.},
journal = {Cell structure and function},
volume = {},
number = {},
pages = {},
doi = {10.1247/csf.19025},
pmid = {31474649},
issn = {1347-3700},
abstract = {Every organism has a different set of genes essential for its viability. This indicates that an organism can become tolerant to the loss of an essential gene under certain circumstances during evolution, via the manifestation of ‛masked' alternative mechanisms. In our quest to systematically uncover masked mechanisms in eukaryotic cells, we developed an extragenic suppressor screening method using haploid spores deleted of an essential gene in the fission yeast Schizosaccharomyces pombe. We screened for the ‛bypass' suppressors of lethality of 92 randomly selected genes that are essential for viability in standard laboratory culture conditions. Remarkably, extragenic mutations bypassed the essentiality of as many as 20 genes (22%), 15 of which have not been previously reported. Half of the bypass-suppressible genes were involved in mitochondria function; we also identified multiple genes regulating RNA processing. 18 suppressible genes were conserved in the budding yeast Saccharomyces cerevisiae, but 13 of them were non-essential in that species. These trends suggest that essentiality bypass is not a rare event and that each organism may be endowed with secondary or backup mechanisms that can substitute for primary mechanisms in various biological processes. Furthermore, the robustness of our simple spore-based methodology paves the way for genome-scale screening. Keywords: Schizosaccharomyces pombe, essential gene, extragenic suppressor screening.},
}

@article {pmid31473860,
year = {2019},
author = {Yorimitsu, Y and Kadosono, A and Hatakeyama, Y and Yabiku, T and Ueno, O},
title = {Transition from C3 to proto-Kranz to C3-C4 intermediate type in the genus Chenopodium (Chenopodiaceae).},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10265-019-01135-5},
pmid = {31473860},
issn = {1618-0860},
support = {JP15K14638//Japan Society for the promotion of Science KAKENHI/ ; },
abstract = {The Chenopodiaceae is one of the families including C4 species among eudicots. In this family, the genus Chenopodium is considered to include only C3 species. However, we report here a transition from C3 photosynthesis to proto-Kranz to C3-C4 intermediate type in Chenopodium. We investigated leaf anatomical and photosynthetic traits of 15 species, of which 8 species showed non-Kranz anatomy and a CO2 compensation point (Γ) typical of C3 plants. However, 5 species showed proto-Kranz anatomy and a C3-like Γ, whereas C. strictum showed leaf anatomy and a Γ typical of C3-C4 intermediates. Chenopodium album accessions examined included both proto-Kranz and C3-C4 intermediate types, depending on locality. Glycine decarboxylase, a key photorespiratory enzyme that is involved in the decarboxylation of glycine, was located predominantly in the mesophyll (M) cells of C3 species, in both M and bundle-sheath (BS) cells in proto-Kranz species, and exclusively in BS cells in C3-C4 intermediate species. The M/BS tissue area ratio, number of chloroplasts and mitochondria per BS cell, distribution of these organelles to the centripetal region of BS cells, the degree of inner positioning (vacuolar side of chloroplasts) of mitochondria in M cells, and the size of BS mitochondria also changed with the change in glycine decarboxylase localization. All Chenopodium species examined were C3-like regarding activities and amounts of C3 and C4 photosynthetic enzymes and δ13C values, suggesting that these species perform photosynthesis without contribution of the C4 cycle. This study demonstrates that Chenopodium is not a C3 genus and is valuable for studying evolution of C3-C4 intermediates.},
}

@article {pmid31466038,
year = {2019},
author = {Maciszewski, K and Karnkowska, A},
title = {Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles.},
journal = {Current opinion in genetics & development},
volume = {58-59},
number = {},
pages = {33-39},
doi = {10.1016/j.gde.2019.07.013},
pmid = {31466038},
issn = {1879-0380},
abstract = {Our knowledge on the variability of the reduced forms of endosymbiotic organelles - mitochondria and plastids - is expanding rapidly, thanks to growing interest in peculiar microbial eukaryotes, along with the availability of the methods used in modern genomics and transcriptomics. The aim of this work is to highlight the most recent advances in understanding these organelles' diversity, physiology and evolution. We also outline the known mechanisms behind the convergence of traits between organelles which have undergone reduction independently, the importance of the earliest evolutionary events in determining the vestigial organelles' eventual fate, and a proposed classification of nonphotosynthetic plastids.},
}

@article {pmid31452134,
year = {2019},
author = {Soggiu, A and Roncada, P and Bonizzi, L and Piras, C},
title = {Role of Mitochondria in Host-Pathogen Interaction.},
journal = {Advances in experimental medicine and biology},
volume = {1158},
number = {},
pages = {45-57},
doi = {10.1007/978-981-13-8367-0_3},
pmid = {31452134},
issn = {0065-2598},
abstract = {The centrality of the mitochondrion in the evolution and control of the cellare now supported by many experimental studies. Not only with regard to the energy metabolism but also and especially with regard to the other functions indispensable for the cell such as apoptosis and the control of innate immunity through different complex cell signaling pathways. All this makes them one of the main targets during infections supported by pathogenic microorganisms. The interaction and control of these organelles by pathogens results, from the latest experimental evidence, of fundamental importance in the fate of the host cell and in the progression of infectious diseases.},
}

@article {pmid31445096,
year = {2019},
author = {Trasviña-Arenas, CH and Hoyos-Gonzalez, N and Castro-Lara, AY and Rodriguez-Hernandez, A and Sanchez-Sandoval, ME and Jimenez-Sandoval, P and Ayala-García, VM and Díaz-Quezada, C and Lodi, T and Baruffini, E and Brieba, LG},
title = {Amino and carboxy-terminal extensions of yeast mitochondrial DNA polymerase assemble both the polymerization and exonuclease active sites.},
journal = {Mitochondrion},
volume = {49},
number = {},
pages = {166-177},
doi = {10.1016/j.mito.2019.08.005},
pmid = {31445096},
issn = {1872-8278},
abstract = {Human and yeast mitochondrial DNA polymerases (DNAPs), POLG and Mip1, are related by evolution to bacteriophage DNAPs. However, mitochondrial DNAPs contain unique amino and carboxyl-terminal extensions that physically interact. Here we describe that N-terminal deletions in Mip1 polymerases abolish polymerization and decrease exonucleolytic degradation, whereas moderate C-terminal deletions reduce polymerization. Similarly, to the N-terminal deletions, an extended C-terminal deletion of 298 amino acids is deficient in nucleotide addition and exonucleolytic degradation of double and single-stranded DNA. The latter observation suggests that the physical interaction between the amino and carboxyl-terminal regions of Mip1 may be related to the spread of pathogenic POLG mutant along its primary sequence.},
}

@article {pmid31434740,
year = {2019},
author = {Barcenilla, BB and Shippen, DE},
title = {Back to the future: the intimate and evolving connection between telomere-related factors and genotoxic stress.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.AW119.008145},
pmid = {31434740},
issn = {1083-351X},
abstract = {The conversion of circular genomes to linear chromosomes during molecular evolution required the invention of telomeres. This entailed the acquisition of factors necessary to fulfill two new requirements: the need to fully replicate terminal DNA sequences and the ability to distinguish chromosome ends from damaged DNA. Here we consider the multifaceted functions of factors recruited to perpetuate and stabilize telomeres. We discuss recent theories for how telomere factors evolved from existing cellular machineries, and examine their engagement in non-telomeric functions such as DNA repair, replication and transcriptional regulation. We highlight the remarkable versatility of protection of telomeres 1 (POT1) proteins that was fueled by gene duplication and divergence events that occurred independently across several eukaryotic lineages. Finally, we consider the relationship between oxidative stress and telomeres and the enigmatic role of telomere-associated proteins in mitochondria. These findings point to an evolving and intimate connection between telomeres and cellular physiology and the strong drive to maintain chromosome integrity.},
}

@article {pmid31431166,
year = {2019},
author = {Gould, SB and Garg, SG and Handrich, M and Nelson-Sathi, S and Gruenheit, N and Tielens, AGM and Martin, WF},
title = {Adaptation to life on land at high O2 via transition from ferredoxin-to NADH-dependent redox balance.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1909},
pages = {20191491},
doi = {10.1098/rspb.2019.1491},
pmid = {31431166},
issn = {1471-2954},
abstract = {Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H2 as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function-redox balance-served by two electron-transfers in the NADH- and O2-dependent respiratory chains of mitochondria. Although they possess O2-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O2. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O2 levels (21% v/v), Chlamydomonas reinhardtii expresses them with diurnal regulation. High O2 environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O2 environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O2-insensitive two-electron carrier NADH.},
}

@article {pmid31419116,
year = {2019},
author = {Mehta, AP and Ko, Y and Supekova, L and Pestonjamasp, K and Li, J and Schultz, PG},
title = {Toward a Synthetic Yeast Endosymbiont with a Minimal Genome.},
journal = {Journal of the American Chemical Society},
volume = {141},
number = {35},
pages = {13799-13802},
doi = {10.1021/jacs.9b08290},
pmid = {31419116},
issn = {1520-5126},
abstract = {Based on the endosymbiotic theory, one of the key events that occurred during mitochondrial evolution was an extensive loss of nonessential genes from the protomitochondrial endosymbiont genome and transfer of some of the essential endosymbiont genes to the host nucleus. We have developed an approach to recapitulate various aspects of endosymbiont genome minimization using a synthetic system consisting of Escherichia coli endosymbionts within host yeast cells. As a first step, we identified a number of E. coli auxotrophs of central metabolites that can form viable endosymbionts within yeast cells. These studies provide a platform to identify nonessential biosynthetic pathways that can be deleted in the E. coli endosymbionts to investigate the evolutionary adaptations in the host and endosymbiont during the evolution of mitochondria.},
}

@article {pmid31416937,
year = {2019},
author = {Youle, RJ},
title = {Mitochondria-Striking a balance between host and endosymbiont.},
journal = {Science (New York, N.Y.)},
volume = {365},
number = {6454},
pages = {},
doi = {10.1126/science.aaw9855},
pmid = {31416937},
issn = {1095-9203},
abstract = {Mitochondria are organelles with their own genome that arose from α-proteobacteria living within single-celled Archaea more than a billion years ago. This step of endosymbiosis offered tremendous opportunities for energy production and metabolism and allowed the evolution of fungi, plants, and animals. However, less appreciated are the downsides of this endosymbiosis. Coordinating gene expression between the mitochondrial genomes and the nuclear genome is imprecise and can lead to proteotoxic stress. The clonal reproduction of mitochondrial DNA requires workarounds to avoid mutational meltdown. In metazoans that developed innate immune pathways to thwart bacterial and viral infections, mitochondrial components can cross-react with pathogen sensors and invoke inflammation. Here, I focus on the numerous and elegant quality control processes that compensate for or mitigate these challenges of endosymbiosis.},
}

@article {pmid31412712,
year = {2019},
author = {Aimo, A and Castiglione, V and Borrelli, C and Saccaro, LF and Franzini, M and Masi, S and Emdin, M and Giannoni, A},
title = {Oxidative stress and inflammation in the evolution of heart failure: From pathophysiology to therapeutic strategies.},
journal = {European journal of preventive cardiology},
volume = {},
number = {},
pages = {2047487319870344},
doi = {10.1177/2047487319870344},
pmid = {31412712},
issn = {2047-4881},
abstract = {Both oxidative stress and inflammation are enhanced in chronic heart failure. Dysfunction of cardiac mitochondria is a hallmark of heart failure and a leading cause of oxidative stress, which in turn exerts detrimental effects on cellular components, including mitochondria themselves, thus generating a vicious circle. Oxidative stress also causes myocardial tissue damage and inflammation, contributing to heart failure progression. Furthermore, a subclinical inflammatory state may be caused by heart failure comorbidities such as obesity, diabetes mellitus or sleep apnoeas. Some markers of both oxidative stress and inflammation are enhanced in chronic heart failure and hold prognostic significance. For all these reasons, antioxidants or anti-inflammatory drugs may represent interesting additional therapies for subjects either at high risk or with established heart failure. Nonetheless, only a few clinical trials on antioxidants have been carried out so far, with several disappointing results except for vitamin C, elamipretide and coenzyme Q10. With regard to anti-inflammatory drugs, only preliminary data on the interleukin-1 antagonist anakinra are currently available. Therefore, a comprehensive, deep understanding of our current knowledge on oxidative stress and inflammation in chronic heart failure is key to providing some suggestions for future research on this topic.},
}

@article {pmid31407247,
year = {2019},
author = {Wang, H and Kim, H and Lim, WA and Ki, JS},
title = {Molecular cloning and oxidative-stress responses of a novel manganese superoxide dismutase (MnSOD) gene in the dinoflagellate Prorocentrum minimum.},
journal = {Molecular biology reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11033-019-05029-6},
pmid = {31407247},
issn = {1573-4978},
abstract = {Dinoflagellate algae are microeukaryotes that have distinct genomes and gene regulation systems, making them an interesting model for studying protist evolution and genomics. In the present study, we discovered a novel manganese superoxide dismutase (PmMnSOD) gene from the marine dinoflagellate Prorocentrum minimum, examined its molecular characteristics, and evaluated its transcriptional responses to the oxidative stress-inducing contaminants, CuSO4 and NaOCl. Its cDNA was 1238 bp and contained a dinoflagellate spliced leader sequence, a 906 bp open reading frame (301 amino acids), and a poly (A) tail. The gene was coded on the nuclear genome with one 174 bp intron; signal peptide analysis showed that it might be localized to the mitochondria. Real-time PCR analysis revealed an increase in gene expression of MnSOD and SOD activity when P. minimum cells were separately exposed to CuSO4 and NaOCl. In addition, both contaminants considerably decreased chlorophyll autofluorescence, and increased intracellular reactive oxygen species. These results suggest that dinoflagellate MnSOD may be involved in protecting cells against oxidative damage.},
}

@article {pmid31402920,
year = {2019},
author = {Lee, GR and Shaefi, S and Otterbein, LE},
title = {HO-1 and CD39: It Takes Two to Protect the Realm.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {1765},
doi = {10.3389/fimmu.2019.01765},
pmid = {31402920},
issn = {1664-3224},
abstract = {Cellular protective mechanisms exist to ensure survival of the cells and are a fundamental feature of all cells that is necessary for adapting to changes in the environment. Indeed, evolution has ensured that each cell is equipped with multiple overlapping families of genes that safeguard against pathogens, injury, stress, and dysfunctional metabolic processes. Two of the better-known enzymatic systems, conserved through all species, include the heme oxygenases (HO-1/HO-2), and the ectonucleotidases (CD39/73). Each of these systems generates critical bioactive products that regulate the cellular response to a stressor. Absence of these molecules results in the cell being extremely predisposed to collapse and, in most cases, results in the death of the cell. Recent reports have begun to link these two metabolic pathways, and what were once exclusively stand-alone are now being found to be intimately interrelated and do so through their innate ability to generate bioactive products including adenosine, carbon monoxide, and bilirubin. These simple small molecules elicit profound cellular physiologic responses that impact a number of innate immune responses, and participate in the regulation of inflammation and tissue repair. Collectively these enzymes are linked not only because of the mitochondria being the source of their substrates, but perhaps more importantly, because of the impact of their products on specific cellular responses. This review will provide a synopsis of the current state of the field regarding how these systems are linked and how they are now being leveraged as therapeutic modalities in the clinic.},
}

@article {pmid31396441,
year = {2019},
author = {Rodriguez, C and Prieto, GI and Vega, IA and Castro-Vazquez, A},
title = {Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7342},
doi = {10.7717/peerj.7342},
pmid = {31396441},
issn = {2167-8359},
abstract = {Ampullariids are freshwater gastropods bearing a gill and a lung, thus showing different degrees of amphibiousness. In particular, Pomacea canaliculata (Caenogastropoda, Ampullariidae) is an obligate air-breather that relies mainly or solely on the lung for dwelling in poorly oxygenated water, for avoiding predators, while burying in the mud during aestivation, and for oviposition above water level. In this paper, we studied the morphological peculiarities of the gill in this species. We found (1) the gill and lung vasculature and innervation are intimately related, allowing alternation between water and air respiration; (2) the gill epithelium has features typical of a transporting rather than a respiratory epithelium; and (3) the gill has resident granulocytes within intraepithelial spaces that may serve a role for immune defence. Thus, the role in oxygen uptake may be less significant than the roles in ionic/osmotic regulation and immunity. Also, our results provide a morphological background to understand the dependence on aerial respiration of Pomacea canaliculata. Finally, we consider these findings from a functional perspective in the light of the evolution of amphibiousness in the Ampullariidae, and discuss that master regulators may explain the phenotypic convergence of gill structures amongst this molluscan species and those in other phyla.},
}

@article {pmid31387118,
year = {2019},
author = {Karnkowska, A and Treitli, SC and Brzoň, O and Novák, L and Vacek, V and Soukal, P and Barlow, LD and Herman, EK and Pipaliya, SV and Pánek, T and Žihala, D and Petrželková, R and Butenko, A and Eme, L and Stairs, CW and Roger, AJ and Eliáš, M and Dacks, JB and Hampl, V},
title = {The oxymonad genome displays canonical eukaryotic complexity in the absence of a mitochondrion.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz147},
pmid = {31387118},
issn = {1537-1719},
abstract = {The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less 'reduced' than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organisation of endomembrane systems and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent pre-adaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe-S cluster assembly. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.},
}

@article {pmid31380018,
year = {2019},
author = {Ngatia, JN and Lan, TM and Dinh, TD and Zhang, L and Ahmed, AK and Xu, YC},
title = {Signals of positive selection in mitochondrial protein-coding genes of woolly mammoth: Adaptation to extreme environments?.},
journal = {Ecology and evolution},
volume = {9},
number = {12},
pages = {6821-6832},
doi = {10.1002/ece3.5250},
pmid = {31380018},
issn = {2045-7758},
abstract = {The mammoths originated in warm and equatorial Africa and later colonized cold and high-latitude environments. Studies on nuclear genes suggest that woolly mammoth had evolved genetic variations involved in processes relevant to cold tolerance, including lipid metabolism and thermogenesis, and adaptation to extremely varied light and darkness cycles. The mitochondria is a major regulator of cellular energy metabolism, thus the mitogenome of mammoths may also exhibit adaptive evolution. However, little is yet known in this regard. In this study, we analyzed mitochondrial protein-coding genes (MPCGs) sequences of 75 broadly distributed woolly mammoths (Mammuthus primigenius) to test for signatures of positive selection. Results showed that a total of eleven amino acid sites in six genes, namely ND1, ND4, ND5, ND6, CYTB, and ATP6, displayed strong evidence of positive selection. Two sites were located in close proximity to proton-translocation channels in mitochondrial complex I. Biochemical and homology protein structure modeling analyses demonstrated that five amino acid substitutions in ND1, ND5, and ND6 might have influenced the performance of protein-protein interaction among subunits of complex I, and three substitutions in CYTB and ATP6 might have influenced the performance of metabolic regulatory chain. These findings suggest metabolic adaptations in the mitogenome of woolly mammoths in relation to extreme environments and provide a basis for further tests on the significance of the variations on other systems.},
}

@article {pmid31370303,
year = {2019},
author = {Sharaf, A and Gruber, A and Jiroutová, K and Oborník, M},
title = {Characterization of Aminoacyl-tRNA Synthetases in Chromerids.},
journal = {Genes},
volume = {10},
number = {8},
pages = {},
doi = {10.3390/genes10080582},
pmid = {31370303},
issn = {2073-4425},
abstract = {Aminoacyl-tRNA synthetases (AaRSs) are enzymes that catalyze the ligation of tRNAs to amino acids. There are AaRSs specific for each amino acid in the cell. Each cellular compartment in which translation takes place (the cytosol, mitochondria, and plastids in most cases), needs the full set of AaRSs; however, individual AaRSs can function in multiple compartments due to dual (or even multiple) targeting of nuclear-encoded proteins to various destinations in the cell. We searched the genomes of the chromerids, Chromera velia and Vitrella brassicaformis, for AaRS genes: 48 genes encoding AaRSs were identified in C. velia, while only 39 AaRS genes were found in V. brassicaformis. In the latter alga, ArgRS and GluRS were each encoded by a single gene occurring in a single copy; only PheRS was found in three genes, while the remaining AaRSs were encoded by two genes. In contrast, there were nine cases for which C. velia contained three genes of a given AaRS (45% of the AaRSs), all of them representing duplicated genes, except AsnRS and PheRS, which are more likely pseudoparalogs (acquired via horizontal or endosymbiotic gene transfer). Targeting predictions indicated that AaRSs are not (or not exclusively), in most cases, used in the cellular compartment from which their gene originates. The molecular phylogenies of the AaRSs are variable between the specific types, and similar between the two investigated chromerids. While genes with eukaryotic origin are more frequently retained, there is no clear pattern of orthologous pairs between C. velia and V. brassicaformis.},
}

@article {pmid31328352,
year = {2019},
author = {Khemaissia, H and Jelassi, R and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K},
title = {Effects of trace metal elements on ultrastructural features of hepatopancreas of Armadillidium granulatum Brandt, 1833 (Crustacea, Isopoda).},
journal = {Microscopy research and technique},
volume = {},
number = {},
pages = {},
doi = {10.1002/jemt.23349},
pmid = {31328352},
issn = {1097-0029},
support = {LR18ES06//Laboratory of Diversity, Management and Conservation of Biological Systems/ ; },
abstract = {This study was conducted to compare metals bioaccumulation in the terrestrial isopod Armadillidium granulatum collected from Ghar El Melh lagoon. We focused on recognizing the effects of trace elements on hepatopancreas functional role. To this end, isopod specimens were exposed for 3 weeks to sediments contaminated with cadmium, copper, zinc, mercury, and nickel. Three concentrations were used in duplicate for each experimental condition. At the end of the experiment, metal body burdens were determined using flame atomic absorption spectrometry. Results of the bioaccumulation factor (BAF) showed that the species A. granulatum was classified as a Cu macroconcentrator (BAF > 2) and a Zn deconcentrator (BAF < 2). Dose dependent morphological and histological changes were observed in the hepatopancreas cells using transmission electron microscopy. The predominant features were: microvillus border disruption, condensation of the cytoplasm with increasing endoplasmic reticulum, mitochondria, lysosomes and granules that accumulated metals in B and S cells. The number of lipid droplets decreased especially after Cd, Zn, Hg, and Ni treatments. This study demonstrated that the terrestrial isopod A. gramulatum could be a good indicator of soil metal contamination.},
}

@article {pmid31325209,
year = {2019},
author = {Rosenberg, E and Zilber-Rosenberg, I},
title = {The hologenome concept of evolution: do mothers matter most?.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.15882},
pmid = {31325209},
issn = {1471-0528},
abstract = {The hologenome concept of evolution is discussed, with special emphasis placed upon the microbiome of women. The microbiome is dynamic, changing under different conditions, and differs between women and men. Genetic variation occurs not only in the host, but also in the microbiome by the acquisition of novel microbes, the amplification of specific microbes, and horizontal gene transfer. The majority of unique genes in human holobionts are found in microbiomes, and mothers are responsible for transferring most of these to their offspring during birth, breastfeeding, and physical contact. Thus, mothers are likely to be the primary providers of the majority of genetic information to offspring via mitochondria and the microbiome. TWEETABLE ABSTRACT: Microbiomes differ between women and men. Most genes in humans are in the microbiome. Mothers transfer most of these genes to offspring.},
}

@article {pmid31318312,
year = {2019},
author = {Rubalcava-Gracia, D and García-Rincón, J and Pérez-Montfort, R and Hamel, PP and González-Halphen, D},
title = {Key within-membrane residues and precursor dosage impact the allotopic expression of yeast subunit II of cytochrome c oxidase.},
journal = {Molecular biology of the cell},
volume = {30},
number = {18},
pages = {2358-2366},
doi = {10.1091/mbc.E18-12-0788},
pmid = {31318312},
issn = {1939-4586},
abstract = {Experimentally relocating mitochondrial genes to the nucleus for functional expression (allotopic expression) is a challenging process. The high hydrophobicity of mitochondria-encoded proteins seems to be one of the main factors preventing this allotopic expression. We focused on subunit II of cytochrome c oxidase (Cox2) to study which modifications may enable or improve its allotopic expression in yeast. Cox2 can be imported from the cytosol into mitochondria in the presence of the W56R substitution, which decreases the protein hydrophobicity and allows partial respiratory rescue of a cox2-null strain. We show that the inclusion of a positive charge is more favorable than substitutions that only decrease the hydrophobicity. We also searched for other determinants enabling allotopic expression in yeast by examining the COX2 gene in organisms where it was transferred to the nucleus during evolution. We found that naturally occurring variations at within-membrane residues in the legume Glycine max Cox2 could enable yeast COX2 allotopic expression. We also evidence that directing high doses of allotopically synthesized Cox2 to mitochondria seems to be counterproductive because the subunit aggregates at the mitochondrial surface. Our findings are relevant to the design of allotopic expression strategies and contribute to the understanding of gene retention in organellar genomes.},
}

@article {pmid31289699,
year = {2019},
author = {Brian, JI and Davy, SK and Wilkinson, SP},
title = {Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7178},
doi = {10.7717/peerj.7178},
pmid = {31289699},
issn = {2167-8359},
abstract = {Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.},
}

@article {pmid31286324,
year = {2019},
author = {Condori-Apfata, JA and Batista-Silva, W and Medeiros, DB and Vargas, JR and Valente, LML and Heyneke, E and Pérez-Diaz, JL and Fernie, AR and Araújo, WL and Nunes-Nesi, A},
title = {The Arabidopsis E1 subunit of the 2-oxoglutarate dehydrogenase complex modulates plant growth and seed production.},
journal = {Plant molecular biology},
volume = {101},
number = {1-2},
pages = {183-202},
doi = {10.1007/s11103-019-00900-3},
pmid = {31286324},
issn = {1573-5028},
support = {306818/2016-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 402511/2016-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CEX - APQ-02985-14//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
mesh = {Arabidopsis/*enzymology/genetics/growth & development ; Arabidopsis Proteins/genetics/metabolism ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Chlorophyll/metabolism ; Ketoglutarate Dehydrogenase Complex/genetics/*metabolism ; Mitochondria/enzymology ; Mutagenesis, Insertional ; Nitrates/metabolism ; Nitrogen/*metabolism ; Phenotype ; Phylogeny ; Plant Leaves/enzymology/genetics/growth & development ; Protein Isoforms ; Protein Subunits ; Seedlings/enzymology/genetics/growth & development ; Seeds/enzymology/genetics/growth & development ; },
abstract = {KEY MESSAGE: Isoforms of 2-OGDH E1 subunit are not functionally redundant in plant growth and development of A. thaliana. The tricarboxylic acid cycle enzyme 2-oxoglutarate dehydrogenase (2-OGDH) converts 2-oxoglutarate (2-OG) to succinyl-CoA concomitant with the reduction of NAD+. 2-OGDH has an essential role in plant metabolism, being both a limiting step during mitochondrial respiration as well as a key player in carbon-nitrogen interactions. In Arabidopsis thaliana two genes encode for E1 subunit of 2-OGDH but the physiological roles of each isoform remain unknown. Thus, in the present study we isolated Arabidopsis T-DNA insertion knockout mutant lines for each of the genes encoding the E1 subunit of 2-OGDH enzyme. All mutant plants exhibited substantial reduction in both respiration and CO2 assimilation rates. Furthermore, mutant lines exhibited reduced levels of chlorophylls and nitrate, increased levels of sucrose, malate and fumarate and minor changes in total protein and starch levels in leaves. Despite the similar metabolic phenotypes for the two E1 isoforms the reduction in the expression of each gene culminated in different responses in terms of plant growth and seed production indicating distinct roles for each isoform. Collectively, our results demonstrated the importance of the E1 subunit of 2-OGDH in both autotrophic and heterotrophic tissues and suggest that the two E1 isoforms are not functionally redundant in terms of plant growth in A. thaliana.},
}

Arabidopsis/*enzymology/genetics/growth & development
Arabidopsis Proteins/genetics/metabolism
Carbon/*metabolism
Carbon Dioxide/metabolism
Chlorophyll/metabolism
Ketoglutarate Dehydrogenase Complex/genetics/*metabolism
Mitochondria/enzymology
Mutagenesis, Insertional
Nitrates/metabolism
Nitrogen/*metabolism
Phenotype
Phylogeny
Plant Leaves/enzymology/genetics/growth & development
Protein Isoforms
Protein Subunits
Seedlings/enzymology/genetics/growth & development
Seeds/enzymology/genetics/growth & development

@article {pmid31282937,
year = {2019},
author = {Forsythe, ES and Sharbrough, J and Havird, JC and Warren, JM and Sloan, DB},
title = {CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis.},
journal = {Genome biology and evolution},
volume = {11},
number = {8},
pages = {2194-2202},
doi = {10.1093/gbe/evz144},
pmid = {31282937},
issn = {1759-6653},
abstract = {The function and evolution of eukaryotic cells depend upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins. However, the field lacks a consistent classification scheme for mitochondrial- and plastid-targeted proteins based on their molecular interactions with cytoplasmic genomes and gene products, which hinders efforts to standardize and compare results across studies. Here, we take advantage of detailed knowledge about the model angiosperm Arabidopsis thaliana to provide a curated database of plant cytonuclear interactions at the molecular level. CyMIRA (Cytonuclear Molecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/ and https://github.com/dbsloan/cymira and will serve as a resource to aid researchers in partitioning evolutionary genomic data into functional gene classes based on organelle targeting and direct molecular interaction with cytoplasmic genomes and gene products. It includes 11 categories (and 27 subcategories) of different cytonuclear complexes and types of molecular interactions, and it reports residue-level information for cytonuclear contact sites. We hope that this framework will make it easier to standardize, interpret, and compare studies testing the functional and evolutionary consequences of cytonuclear interactions.},
}

@article {pmid31282925,
year = {2019},
author = {McKenzie, JL and Chung, DJ and Healy, TM and Brennan, RS and Bryant, HJ and Whitehead, A and Schulte, PM},
title = {Mitochondrial ecophysiology: assessing the evolutionary forces that shape mitochondrial variation.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icz124},
pmid = {31282925},
issn = {1557-7023},
abstract = {The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.},
}

@article {pmid31279710,
year = {2019},
author = {Parhi, J and Tripathy, PS and Priyadarshi, H and Mandal, SC and Pandey, PK},
title = {Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group.},
journal = {Gene},
volume = {713},
number = {},
pages = {143967},
doi = {10.1016/j.gene.2019.143967},
pmid = {31279710},
issn = {1879-0038},
mesh = {Animals ; Cypriniformes/*genetics ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Phylogenetic tree using mitochondrial genes and nuclear genes have long been used for augmenting biological classification and understanding evolutionary processes in different lineage of life. But a basic question still exists for finding the most suitable gene for constructing robust phylogenetic tree. Much of the controversy appears due to monophyletic, paraphyletic and polyphyletic clade making deviations from original taxonomy. In the present study we report the first complete mitochondrial genome (mitogenome) of queen loach, generated through next-generation sequencing methods. The assembled mitogenome is a 16,492 bp circular DNA, comprising of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. Further in this study we also investigated the suitability of different mitochondrial region for phylogenetic analysis in Cyprinidae and loach group. For this genetic tree were constructed on COI, COII, COIII, 16S rRNA, 12S rRNA, Cyt b, ATPase 6, D-loop, ND1, ND2, ND3, ND4, ND5, and ND6 along with complete mitogenome. The complete mitogenome based phylogenetic tree got inclusive support from available classical taxonomy for these groups. On individual gene basis Cyt b, 12S rRNA, ND2 and ND3 also produced perfect clade at family and subfamily level. For rest of the genes polyphyly were observed for the fishes belonging to same family or subfamily which makes their use questionable for phylogenetic tree construction.},
}

Animals
Cypriniformes/*genetics
*Genes, Mitochondrial
*Genome, Mitochondrial
Mitochondria/*genetics
*Phylogeny
Sequence Analysis, DNA

@article {pmid31253641,
year = {2019},
author = {Aryaman, J and Bowles, C and Jones, NS and Johnston, IG},
title = {Mitochondrial Network State Scales mDNA Genetic Dynamics.},
journal = {Genetics},
volume = {212},
number = {4},
pages = {1429-1443},
doi = {10.1534/genetics.119.302423},
pmid = {31253641},
issn = {1943-2631},
support = {BB/J014575/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UP_1501/2/MRC_/Medical Research Council/United Kingdom ; RE/13/2/30182/BHF_/British Heart Foundation/United Kingdom ; },
abstract = {Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. mtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The role of the resulting mitochondrial networks in the time evolution of the cellular proportion of mutated mtDNA molecules (heteroplasmy), and cell-to-cell variability in heteroplasmy (heteroplasmy variance), remains incompletely understood. Heteroplasmy variance is particularly important since it modulates the number of pathological cells in a tissue. Here, we provide the first wide-reaching theoretical framework which bridges mitochondrial network and genetic states. We show that, under a range of conditions, the (genetic) rate of increase in heteroplasmy variance and de novo mutation are proportionally modulated by the (physical) fraction of unfused mitochondria, independently of the absolute fission-fusion rate. In the context of selective fusion, we show that intermediate fusion:fission ratios are optimal for the clearance of mtDNA mutants. Our findings imply that modulating network state, mitophagy rate, and copy number to slow down heteroplasmy dynamics when mean heteroplasmy is low could have therapeutic advantages for mitochondrial disease and healthy aging.},
}

@article {pmid31248014,
year = {2019},
author = {Levitskii, S and Baleva, MV and Chicherin, I and Krasheninnikov, IA and Kamenski, P},
title = {S. cerevisiae Strain Lacking Mitochondrial IF3 Shows Increased Levels of Tma19p during Adaptation to Respiratory Growth.},
journal = {Cells},
volume = {8},
number = {7},
pages = {},
doi = {10.3390/cells8070645},
pmid = {31248014},
issn = {2073-4409},
abstract = {After billions of years of evolution, mitochondrion retains its own genome, which gets expressed in mitochondrial matrix. Mitochondrial translation machinery rather differs from modern bacterial and eukaryotic cytosolic systems. Any disturbance in mitochondrial translation drastically impairs mitochondrial function. In budding yeast Saccharomyces cerevisiae, deletion of the gene coding for mitochondrial translation initiation factor 3 - AIM23, leads to an imbalance in mitochondrial protein synthesis and significantly delays growth after shifting from fermentable to non-fermentable carbon sources. Molecular mechanism underlying this adaptation to respiratory growth was unknown. Here, we demonstrate that slow adaptation from glycolysis to respiration in the absence of Aim23p is accompanied by a gradual increase of cytochrome c oxidase activity and by increased levels of Tma19p protein, which protects mitochondria from oxidative stress.},
}

@article {pmid31247505,
year = {2019},
author = {Breda, CNS and Davanzo, GG and Basso, PJ and Saraiva Câmara, NO and Moraes-Vieira, PMM},
title = {Mitochondria as central hub of the immune system.},
journal = {Redox biology},
volume = {26},
number = {},
pages = {101255},
doi = {10.1016/j.redox.2019.101255},
pmid = {31247505},
issn = {2213-2317},
abstract = {Nearly 130 years after the first insights into the existence of mitochondria, new rolesassociated with these organelles continue to emerge. As essential hubs that dictate cell fate, mitochondria integrate cell physiology, signaling pathways and metabolism. Thus, recent research has focused on understanding how these multifaceted functions can be used to improve inflammatory responses and prevent cellular dysfunction. Here, we describe the role of mitochondria on the development and function of immune cells, highlighting metabolic aspects and pointing out some metabolic- independent features of mitochondria that sustain cell function.},
}

@article {pmid31239554,
year = {2019},
author = {Ågren, JA and Davies, NG and Foster, KR},
title = {Enforcement is central to the evolution of cooperation.},
journal = {Nature ecology & evolution},
volume = {3},
number = {7},
pages = {1018-1029},
doi = {10.1038/s41559-019-0907-1},
pmid = {31239554},
issn = {2397-334X},
abstract = {Cooperation occurs at all levels of life, from genomes, complex cells and multicellular organisms to societies and mutualisms between species. A major question for evolutionary biology is what these diverse systems have in common. Here, we review the full breadth of cooperative systems and find that they frequently rely on enforcement mechanisms that suppress selfish behaviour. We discuss many examples, including the suppression of transposable elements, uniparental inheritance of mitochondria and plastids, anti-cancer mechanisms, reciprocation and punishment in humans and other vertebrates, policing in eusocial insects and partner choice in mutualisms between species. To address a lack of accompanying theory, we develop a series of evolutionary models that show that the enforcement of cooperation is widely predicted. We argue that enforcement is an underappreciated, and often critical, ingredient for cooperation across all scales of biological organization.},
}

@article {pmid31239372,
year = {2019},
author = {Sun, N and Parrish, RS and Calderone, RA and Fonzi, WA},
title = {Unique, Diverged, and Conserved Mitochondrial Functions Influencing Candida albicans Respiration.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
doi = {10.1128/mBio.00300-19},
pmid = {31239372},
issn = {2150-7511},
abstract = {Candida albicans is an opportunistic fungal pathogen of major clinical concern. The virulence of this pathogen is intimately intertwined with its metabolism. Mitochondria, which have a central metabolic role, have undergone many lineage-specific adaptations in association with their eukaryotic host. A screen for lineage-specific genes identified seven such genes specific to the CTG clade of fungi, of which C. albicans is a member. Each is required for respiratory growth and is integral to expression of complex I, III, or IV of the electron transport chain. Two genes, NUO3 and NUO4, encode supernumerary subunits of complex I, whereas NUE1 and NUE2 have nonstructural roles in expression of complex I. Similarly, the other three genes have nonstructural roles in expression of complex III (QCE1) or complex IV (COE1 and COE2). In addition to these novel additions, an alternative functional assignment was found for the mitochondrial protein encoded by MNE1MNE1 was required for complex I expression in C. albicans, whereas the distantly related Saccharomyces cerevisiae ortholog participates in expression of complex III. Phenotypic analysis of deletion mutants showed that fermentative metabolism is unable to support optimal growth rates or yields of C. albicans However, yeast-hypha morphogenesis, an important virulence attribute, did not require respiratory metabolism under hypoxic conditions. The inability to respire also resulted in hypersensitivity to the antifungal fluconazole and in attenuated virulence in a Galleria mellonella infection model. The results show that lineage-specific adaptations have occurred in C. albicans mitochondria and highlight the significance of respiratory metabolism in the pathobiology of C. albicansIMPORTANCECandida albicans is an opportunistic fungal pathogen of major clinical concern. The virulence of this pathogen is intimately intertwined with its metabolic behavior, and mitochondria have a central role in that metabolism. Mitochondria have undergone many evolutionary changes, which include lineage-specific adaptations in association with their eukaryotic host. Seven lineage-specific genes required for electron transport chain function were identified in the CTG clade of fungi, of which C. albicans is a member. Additionally, examination of several highly diverged orthologs encoding mitochondrial proteins demonstrated functional reassignment for one of these. Deficits imparted by deletion of these genes revealed the critical role of respiration in virulence attributes of the fungus and highlight important evolutionary adaptations in C. albicans metabolism.},
}

@article {pmid31234402,
year = {2019},
author = {Emelyantsev, S and Prazdnova, E and Chistyakov, V and Alperovich, I},
title = {Biological Effects of C60 Fullerene Revealed with Bacterial Biosensor-Toxic or Rather Antioxidant?.},
journal = {Biosensors},
volume = {9},
number = {2},
pages = {},
doi = {10.3390/bios9020081},
pmid = {31234402},
issn = {2079-6374},
support = {16-32-60077 mol_а_dk//Russian Foundation for Basic Research/ ; },
abstract = {Nanoparticles have been attracting growing interest for both their antioxidant and toxic effects. Their exact action on cells strongly depends on many factors, including experimental conditions, preparation, and solvents used, which have contributed to the confusion regarding their safety and possible health benefits. In order to clarify the biological effects of the most abundant fullerene C60, its impact on the Escherichia coli model has been studied. The main question was if C60 would have any antioxidant influence on the cell and, if yes, whether and to which extent it would be concentration-dependent. An oxidative stress induced by adding hydrogen peroxide was measured with an E. coli MG1655 pKatG-lux strain sensor, with its time evolution being recorded in the presence of fullerene C60 suspensions of different concentrations. Optimal conditions for the fullerene C60 solubilization in TWEEN 80 2% aqueous solution, together with resulting aggregate sizes, were determined. Results obtained for the bacterial model can be extrapolated on eukaryote mitochondria. The ability of C60 to penetrate through biological membranes, conduct protons, and interact with free radicals is likely responsible for its protective effect detected for E. coli. Thus, fullerene can be considered as a mitochondria-targeted antioxidant, worth further researching as a prospective component of novel medications.},
}

@article {pmid31229574,
year = {2019},
author = {Havird, JC and Noe, GR and Link, L and Torres, A and Logan, DC and Sloan, DB and Chicco, AJ},
title = {Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function?.},
journal = {Mitochondrion},
volume = {49},
number = {},
pages = {1-11},
doi = {10.1016/j.mito.2019.06.005},
pmid = {31229574},
issn = {1872-8278},
abstract = {Angiosperm mitochondrial (mt) genes are generally slow-evolving, but multiple lineages have undergone dramatic accelerations in rates of nucleotide substitution and extreme changes in mt genome structure. While molecular evolution in these lineages has been investigated, very little is known about their mt function. Some studies have suggested altered respiration in individual taxa, although there are several reasons why mt variation might be neutral in others. Here, we develop a new protocol to characterize respiration in isolated plant mitochondria and apply it to species of Silene with mt genomes that are rapidly evolving, highly fragmented, and exceptionally large (~11 Mbp). This protocol, complemented with traditional measures of plant fitness, cytochrome c oxidase activity assays, and fluorescence microscopy, was also used to characterize inter- and intraspecific variation in mt function. Contributions of the individual "classic" OXPHOS complexes, the alternative oxidase, and external NADH dehydrogenases to overall mt respiratory flux were found to be similar to previously studied angiosperms with more typical mt genomes. Some differences in mt function could be explained by inter- and intraspecific variation. This study suggests that Silene species with peculiar mt genomes still show relatively normal mt respiration. This may be due to strong purifying selection on mt variants, coevolutionary responses in the nucleus, or a combination of both. Future experiments should explore such questions using a comparative framework and investigating other lineages with unusual mitogenomes.},
}

@article {pmid31227544,
year = {2019},
author = {Cooper, BS and Vanderpool, D and Conner, WR and Matute, DR and Turelli, M},
title = {Wolbachia Acquisition by Drosophila yakuba-Clade Hosts and Transfer of Incompatibility Loci Between Distantly Related Wolbachia.},
journal = {Genetics},
volume = {212},
number = {4},
pages = {1399-1419},
doi = {10.1534/genetics.119.302349},
pmid = {31227544},
issn = {1943-2631},
support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; R01 GM121750/GM/NIGMS NIH HHS/United States ; R01 GM104325/GM/NIGMS NIH HHS/United States ; },
abstract = {Maternally transmitted Wolbachia infect about half of insect species, yet the predominant mode(s) of Wolbachia acquisition remains uncertain. Species-specific associations could be old, with Wolbachia and hosts codiversifying (i.e., cladogenic acquisition), or relatively young and acquired by horizontal transfer or introgression. The three Drosophila yakuba-clade hosts [(D. santomea, D. yakuba) D. teissieri] diverged ∼3 MYA and currently hybridize on the West African islands Bioko and São Tomé. Each species is polymorphic for nearly identical Wolbachia that cause weak cytoplasmic incompatibility (CI)-reduced egg hatch when uninfected females mate with infected males. D. yakuba-clade Wolbachia are closely related to wMel, globally polymorphic in D. melanogaster We use draft Wolbachia and mitochondrial genomes to demonstrate that D. yakuba-clade phylogenies for Wolbachia and mitochondria tend to follow host nuclear phylogenies. However, roughly half of D. santomea individuals, sampled both inside and outside of the São Tomé hybrid zone, have introgressed D. yakuba mitochondria. Both mitochondria and Wolbachia possess far more recent common ancestors than the bulk of the host nuclear genomes, precluding cladogenic Wolbachia acquisition. General concordance of Wolbachia and mitochondrial phylogenies suggests that horizontal transmission is rare, but varying relative rates of molecular divergence complicate chronogram-based statistical tests. Loci that cause CI in wMel are disrupted in D. yakuba-clade Wolbachia; but a second set of loci predicted to cause CI are located in the same WO prophage region. These alternative CI loci seem to have been acquired horizontally from distantly related Wolbachia, with transfer mediated by flanking Wolbachia-specific ISWpi1 transposons.},
}

@article {pmid31218630,
year = {2019},
author = {Gerlach, L and Gholami, O and Schürmann, N and Kleinschmidt, JH},
title = {Folding of β-Barrel Membrane Proteins into Lipid Membranes by Site-Directed Fluorescence Spectroscopy.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2003},
number = {},
pages = {465-492},
doi = {10.1007/978-1-4939-9512-7_20},
pmid = {31218630},
issn = {1940-6029},
abstract = {Protein-lipid interactions are important for folding and membrane insertion of integral membrane proteins that are composed either of α-helical or of β-barrel structure in their transmembrane domains. While α-helical transmembrane proteins fold co-translationally while they are synthesized by a ribosome, β-barrel transmembrane proteins (β-TMPs) fold and insert posttranslationally-in bacteria after translocation across the cytoplasmic membrane, in cell organelles of eukaryotes after import across the outer membrane of the organelle. β-TMPs can be unfolded in aqueous solutions of chaotropic denaturants like urea and spontaneously refold upon denaturant dilution in the presence of preformed lipid bilayers. This facilitates studies on lipid interactions during folding into lipid bilayers. For several β-TMPs, the kinetics of folding has been reported as strongly dependent on protein-lipid interactions. The kinetics of adsorption/insertion and folding of β-TMPs can be monitored by fluorescence spectroscopy. These fluorescence methods are even more powerful when combined with site-directed mutagenesis for the preparation of mutants of a β-TMP that are site-specifically labeled with a fluorophore or a fluorophore and fluorescence quencher or fluorescence resonance energy acceptor. Single tryptophan or single cysteine mutants of the β-TMP allow for the investigation of local protein-lipid interactions, at specific regions within the protein. To examine the structure formation of β-TMPs in a lipid environment, fluorescence spectroscopy has been used for double mutants of β-TMPs that contain a fluorescent tryptophan and a spin-label, covalently attached to a cysteine as a fluorescence quencher. The sites of mutation are selected so that the tryptophan is in close proximity to the quencher at the cysteine only when the β-TMP is folded. In a folding experiment, the evolution of fluorescence quenching as a function of time at specific sites within the protein can provide important information on the folding mechanism of the β-TMP. Here, we report protocols to examine membrane protein folding for two β-TMPs in a lipid environment, the outer membrane protein A from Escherichia coli, OmpA, and the voltage-dependent anion-selective channel, human isoform 1, hVDAC1, from mitochondria.},
}

@article {pmid31218358,
year = {2019},
author = {Krasovec, M and Sanchez-Brosseau, S and Piganeau, G},
title = {First Estimation of the Spontaneous Mutation Rate in Diatoms.},
journal = {Genome biology and evolution},
volume = {11},
number = {7},
pages = {1829-1837},
doi = {10.1093/gbe/evz130},
pmid = {31218358},
issn = {1759-6653},
abstract = {Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation-accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10-10 and the insertion-deletion mutation rate is μid = 1.58 × 10-11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.},
}

@article {pmid31209489,
year = {2019},
author = {Nieuwenhuis, M and van de Peppel, LJJ and Bakker, FT and Zwaan, BJ and Aanen, DK},
title = {Enrichment of G4DNA and a Large Inverted Repeat Coincide in the Mitochondrial Genomes of Termitomyces.},
journal = {Genome biology and evolution},
volume = {11},
number = {7},
pages = {1857-1869},
doi = {10.1093/gbe/evz122},
pmid = {31209489},
issn = {1759-6653},
abstract = {Mitochondria retain their own genome, a hallmark of their bacterial ancestry. Mitochondrial genomes (mtDNA) are highly diverse in size, shape, and structure, despite their conserved function across most eukaryotes. Exploring extreme cases of mtDNA architecture can yield important information on fundamental aspects of genome biology. We discovered that the mitochondrial genomes of a basidiomycete fungus (Termitomyces spp.) contain an inverted repeat (IR), a duplicated region half the size of the complete genome. In addition, we found an abundance of sequences capable of forming G-quadruplexes (G4DNA); structures that can disrupt the double helical formation of DNA. G4DNA is implicated in replication fork stalling, double-stranded breaks, altered gene expression, recombination, and other effects. To determine whether this occurrence of IR and G4DNA was correlated within the genus Termitomyces, we reconstructed the mitochondrial genomes of 11 additional species including representatives of several closely related genera. We show that the mtDNA of all sampled species of Termitomyces and its sister group, represented by the species Tephrocybe rancida and Blastosporella zonata, are characterized by a large IR and enrichment of G4DNA. To determine whether high mitochondrial G4DNA content is common in fungi, we conducted the first broad survey of G4DNA content in fungal mtDNA, revealing it to be a highly variable trait. The results of this study provide important direction for future research on the function and evolution of G4DNA and organellar IRs.},
}

@article {pmid31207496,
year = {2019},
author = {Farooq, MA and Niazi, AK and Akhtar, J and Saifullah, and Farooq, M and Souri, Z and Karimi, N and Rengel, Z},
title = {Acquiring control: The evolution of ROS-Induced oxidative stress and redox signaling pathways in plant stress responses.},
journal = {Plant physiology and biochemistry : PPB},
volume = {141},
number = {},
pages = {353-369},
doi = {10.1016/j.plaphy.2019.04.039},
pmid = {31207496},
issn = {1873-2690},
mesh = {Acclimatization ; Antioxidants/metabolism ; Arabidopsis/metabolism ; Cell Nucleus/metabolism ; Chloroplasts/metabolism ; Cytosol/metabolism ; Gene Expression Regulation ; Genes, Plant ; Mitochondria/metabolism ; Oryza/metabolism ; *Oxidation-Reduction ; *Oxidative Stress ; Oxygen/metabolism ; Peroxisomes/metabolism ; Photosynthesis ; *Plant Physiological Phenomena ; Populus/metabolism ; Reactive Oxygen Species/*metabolism ; *Signal Transduction ; *Stress, Physiological ; },
abstract = {Reactive oxygen species (ROS) - the byproducts of aerobic metabolism - influence numerous aspects of the plant life cycle and environmental response mechanisms. In plants, ROS act like a double-edged sword; they play multiple beneficial roles at low concentrations, whereas at high concentrations ROS and related redox-active compounds cause cellular damage through oxidative stress. To examine the dual role of ROS as harmful oxidants and/or crucial cellular signals, this review elaborates that (i) how plants sense and respond to ROS in various subcellular organelles and (ii) the dynamics of subsequent ROS-induced signaling processes. The recent understanding of crosstalk between various cellular compartments in mediating their redox state spatially and temporally is discussed. Emphasis on the beneficial effects of ROS in maintaining cellular energy homeostasis, regulating diverse cellular functions, and activating acclimation responses in plants exposed to abiotic and biotic stresses are described. The comprehensive view of cellular ROS dynamics covering the breadth and versatility of ROS will contribute to understanding the complexity of apparently contradictory ROS roles in plant physiological responses in less than optimum environments.},
}

Acclimatization
Antioxidants/metabolism
Arabidopsis/metabolism
Cell Nucleus/metabolism
Chloroplasts/metabolism
Cytosol/metabolism
Gene Expression Regulation
Genes, Plant
Mitochondria/metabolism
Oryza/metabolism
*Oxidation-Reduction
*Oxidative Stress
Oxygen/metabolism
Peroxisomes/metabolism
Photosynthesis
*Plant Physiological Phenomena
Populus/metabolism
Reactive Oxygen Species/*metabolism
*Signal Transduction
*Stress, Physiological

@article {pmid31204914,
year = {2019},
author = {Wang, J and Zhou, YA and Su, LP and Li, FM and Chen, M},
title = {[Instability of Mitochondrial DNA D-loop Region Genes in Patients with Leukemia].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {27},
number = {3},
pages = {657-663},
doi = {10.19746/j.cnki.issn.1009-2137.2019.03.005},
pmid = {31204914},
issn = {1009-2137},
mesh = {*DNA, Mitochondrial ; Humans ; *Leukemia ; Mitochondria ; Mutation ; Mutation Rate ; },
abstract = {OBJECTIVE: To study the instability of mitochondrial DNA（mt DNA） D-loop region genes in patients with Leukemia.

METHODS: The HV-1 and HV-2 regions of D-loop region in 24 patients with leukemia were amplificated and sequenced, then their results were compared with revised Cambridge reference sequence (rCRS) and Databank mtDB. The mutation rate was detected by SPSS 22.0 statistics software.

RESULTS: The total mutation rate in patients was 95.83% (23/24), the detection showed 82 mutated genes, out of which 47 (57.32%) mutated genes located in HV-1 region, 35 (42.68%) mutated genes in HV-2 region. The comparison showed that the mutation rate in untreated (UT) group and treated (T) group of AML patients was (2.37±0.82)×10-3 and (4.76±2.45)×10-3 respectively(P＜0.01), the mutation rate in PR and CR groups of treated AML patients was (5.10±2.56)×10-3 and (4.51±2.51)×10-3 respectively (P＜0.05), the comparison among M3 group showed that the mutation rates in UT, PR and CR groups were (2.55±0.63)×10-3, (5.37±3.41)×10-3 and (3.71±1.65)×10-3 respectively (P＞0.05).

CONCLUSION: The more high mutation rate and many kinds of mutation types exist in D-loop region, suggesting that the genes in D-loop region display the more strong instability, the chemotherapy may aggravate the instability of genes in D-loop region.},
}

*DNA, Mitochondrial
Humans
*Leukemia
Mitochondria
Mutation
Mutation Rate

@article {pmid31203379,
year = {2019},
author = {Bloomfield, G},
title = {The molecular foundations of zygosis.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-019-03187-1},
pmid = {31203379},
issn = {1420-9071},
abstract = {Zygosis is the generation of new biological individuals by the sexual fusion of gamete cells. Our current understanding of eukaryotic phylogeny indicates that sex is ancestral to all extant eukaryotes. Although sexual development is extremely diverse, common molecular elements have been retained. HAP2-GCS1, a protein that promotes the fusion of gamete cell membranes that is related in structure to certain viral fusogens, is conserved in many eukaryotic lineages, even though gametes vary considerably in form and behaviour between species. Similarly, although zygotes have dramatically different forms and fates in different organisms, diverse eukaryotes share a common developmental programme in which homeodomain-containing transcription factors play a central role. These common mechanistic elements suggest possible common evolutionary histories that, if correct, would have profound implications for our understanding of eukaryogenesis.},
}

@article {pmid31196888,
year = {2019},
author = {Pan, Z and Ren, X and Zhao, H and Liu, L and Tan, Z and Qiu, F},
title = {A Mitochondrial Transcription Termination Factor, ZmSmk3, Is Required for nad1 Intron4 and nad4 Intron1 Splicing and Kernel Development in Maize.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {8},
pages = {2677-2686},
doi = {10.1534/g3.119.400265},
pmid = {31196888},
issn = {2160-1836},
abstract = {The expression systems of the mitochondrial genes are derived from their bacterial ancestors, but have evolved many new features in their eukaryotic hosts. Mitochondrial RNA splicing is a complex process regulated by families of nucleus-encoded RNA-binding proteins, few of which have been characterized in maize (Zea mays L.). Here, we identified the Zea mays small kernel 3 (Zmsmk3) candidate gene, which encodes a mitochondrial transcription termination factor (mTERF) containing two mTERF motifs, which is conserved in monocotyledon; and the target introns were also quite conserved during evolution between monocotyledons and dicotyledons. The mutations of Zmsmk3 led to arrested embryo and endosperm development, resulting in small kernels. A transcriptome of 12 days after pollination endosperm analysis revealed that the starch biosynthetic pathway and the zein gene family were down-regulated in the Zmsmk3 mutant kernels. ZmSMK3 is localized in mitochondria. The reduced expression of ZmSmk3 in the mutant resulted in the splicing deficiency of mitochondrial nad4 intron1 and nad1 intron4, causing a reduction in complex I assembly and activity, impairing mitochondria structure and activating the alternative respiratory pathway. So, the results suggest that ZmSMK3 is required for the splicing of nad4 intron 1 and nad1 intron 4, complex I assembly and kernel development in maize.},
}

@article {pmid31196150,
year = {2018},
author = {Gerlitz, M and Knopp, M and Kapust, N and Xavier, JC and Martin, WF},
title = {Elusive data underlying debate at the prokaryote-eukaryote divide.},
journal = {Biology direct},
volume = {13},
number = {1},
pages = {21},
doi = {10.1186/s13062-018-0221-x},
pmid = {31196150},
issn = {1745-6150},
abstract = {BACKGROUND: The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature.

RESULTS: We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure.

CONCLUSION: The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution.

REVIEWERS: This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.},
}

@article {pmid31179502,
year = {2019},
author = {Schober, AF and Rï O Bï Rtulos, C and Bischoff, A and Lepetit, B and Gruber, A and Kroth, PG},
title = {Organelle Studies and Proteome Analyses of Mitochondria and Plastids Fractions from the Diatom Thalassiosira pseudonana.},
journal = {Plant & cell physiology},
volume = {60},
number = {8},
pages = {1811-1828},
doi = {10.1093/pcp/pcz097},
pmid = {31179502},
issn = {1471-9053},
mesh = {Diatoms/*metabolism ; Mitochondria/*metabolism ; Plastids/*metabolism ; Proteome/*metabolism ; Thylakoids/metabolism ; },
abstract = {Diatoms are unicellular algae and evolved by secondary endosymbiosis, a process in which a red alga-like eukaryote was engulfed by a heterotrophic eukaryotic cell. This gave rise to plastids of remarkable complex architecture and ultrastructure that require elaborate protein importing, trafficking, signaling and intracellular cross-talk pathways. Studying both plastids and mitochondria and their distinctive physiological pathways in organello may greatly contribute to our understanding of photosynthesis, mitochondrial respiration and diatom evolution. The isolation of such complex organelles, however, is still demanding, and existing protocols are either limited to a few species (for plastids) or have not been reported for diatoms so far (for mitochondria). In this work, we present the first isolation protocol for mitochondria from the model diatom Thalassiosira pseudonana. Apart from that, we extended the protocol so that it is also applicable for the purification of a high-quality plastids fraction, and provide detailed structural and physiological characterizations of the resulting organelles. Isolated mitochondria were structurally intact, showed clear evidence of mitochondrial respiration, but the fractions still contained residual cell fragments. In contrast, plastid isolates were virtually free of cellular contaminants, featured structurally preserved thylakoids performing electron transport, but lost most of their stromal components as concluded from Western blots and mass spectrometry. Liquid chromatography electrospray-ionization mass spectrometry studies on mitochondria and thylakoids, moreover, allowed detailed proteome analyses which resulted in extensive proteome maps for both plastids and mitochondria thus helping us to broaden our understanding of organelle metabolism and functionality in diatoms.},
}

Diatoms/*metabolism
Mitochondria/*metabolism
Plastids/*metabolism
Proteome/*metabolism
Thylakoids/metabolism

@article {pmid31170405,
year = {2019},
author = {Edgar, JA},
title = {L-ascorbic acid and the evolution of multicellular eukaryotes.},
journal = {Journal of theoretical biology},
volume = {476},
number = {},
pages = {62-73},
doi = {10.1016/j.jtbi.2019.06.001},
pmid = {31170405},
issn = {1095-8541},
abstract = {The lifeless earth was formed around 4.5 billion years ago and the first anaerobic unicellular "organisms" may have appeared half a billion years later. Despite subsequent prokaryotes (bacteria and archaea) evolving quite complex biochemistry and some eukaryote characteristics, the transition from unicellular prokaryotes to multicellular, aerobic eukaryotes took a further 2.5 billion years to begin. The key factor or factors that eventually caused this long-delayed transition is a question that has been a focus of considerable research and a topic of discussion over many years. On the basis of the extensive literature available and consideration of some of the characteristics that distinguish multicellular eukaryotes from prokaryotes, it is proposed that, as well as the development of oxygenic photosynthesis producing high levels of environmental oxygen and the formation of vital organelles such as aerobic adenosine triphosphate-generating mitochondria, the concurrent evolution of the L-ascorbic acid redox system should be considered as a key factor that led to the evolution of multicellular eukaryotes and it remains vitally involved in the maintenance of multicellularity and many other eukaryote characteristics.},
}

@article {pmid31163164,
year = {2019},
author = {Havird, JC and Forsythe, ES and Williams, AM and Werren, JH and Dowling, DK and Sloan, DB},
title = {Selfish Mitonuclear Conflict.},
journal = {Current biology : CB},
volume = {29},
number = {11},
pages = {R496-R511},
doi = {10.1016/j.cub.2019.03.020},
pmid = {31163164},
issn = {1879-0445},
support = {F32 GM116361/GM/NIGMS NIH HHS/United States ; },
abstract = {Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.},
}

@article {pmid31153884,
year = {2019},
author = {Wu, Q and Lan, Y and Cao, X and Yao, H and Qiao, D and Xu, H and Cao, Y},
title = {Characterization and diverse evolution patterns of glycerol-3-phosphate dehydrogenase family genes in Dunaliella salina.},
journal = {Gene},
volume = {710},
number = {},
pages = {161-169},
doi = {10.1016/j.gene.2019.05.056},
pmid = {31153884},
issn = {1879-0038},
mesh = {Algal Proteins/chemistry/genetics ; Amino Acid Motifs ; Chlorophyceae/*enzymology/genetics ; Chloroplasts/enzymology ; Data Mining/*methods ; Evolution, Molecular ; Glycerolphosphate Dehydrogenase/*chemistry/*genetics ; Mitochondria/enzymology ; Multigene Family ; Phylogeny ; Protein Domains ; Sequence Analysis, DNA ; },
abstract = {The glycerol-3-phosphate dehydrogenase (GPD) gene family plays a major role in glycerol synthesis and adaptation to abiotic stresses. Few studies on GPD family genes from the halotolerant algae Dunaliella salina are available. In this study, seven DsaGPD genes were identified by mining D. salina sequencing data. Among them, DsaGPD5 contained the canonical NAD+-GPD protein domain, called si-GPD. In comparison, DsaGPD1-4 not only contained the canonical NAD+-GPD domain but also a unique domain, the haloacid dehalogenase (HAD)-like superfamily domain, in their N-terminal region, called bi-GPD. DsaGPD6, 7 contained the FAD+-GPD domain. In the transient expression system, DsaGPD1, 3, 4 were found in the cytosol of Arabidopsis thaliana protoplast, DsaGPD2, 5 in the chloroplast, and DsaGPD6, 7 in the mitochondria. MEME analysis showed that six conserved motifs were present in both si-GPDs and bi-GPDs, whereas seven highly conserved motifs were only present in bi-GPDs. The quantitative real-time PCR results showed significant induction of the DsaGPD genes under abiotic stresses, indicating their tolerance-related role in D. salina. DsaGPD2 and DsaGPD5 may be the osmoregulator form and glyceride form in the chloroplast, respectively. The evolutionary forces acting on si-GPDs and bi-GPDs were different in the same organism: bi-GPDs were under purifying selection, while si-GPDs were mainly under positive selection. Furthermore, evolution of the N_HAD domain and C_GPD domain in bi-GPDs is highly correlated. In summary, this study characterizes DsaGPD gene family members and provides useful information for elucidating the salt tolerance mechanism in D. salina.},
}

Algal Proteins/chemistry/genetics
Amino Acid Motifs
Chlorophyceae/*enzymology/genetics
Chloroplasts/enzymology
Data Mining/*methods
Evolution, Molecular
Glycerolphosphate Dehydrogenase/*chemistry/*genetics
Mitochondria/enzymology
Multigene Family
Phylogeny
Protein Domains
Sequence Analysis, DNA

@article {pmid31152352,
year = {2019},
author = {Lassance, JM and Svensson, GP and Kozlov, MV and Francke, W and Löfstedt, C},
title = {Pheromones and Barcoding Delimit Boundaries between Cryptic Species in the Primitive Moth Genus Eriocrania (Lepidoptera: Eriocraniidae).},
journal = {Journal of chemical ecology},
volume = {45},
number = {5-6},
pages = {429-439},
doi = {10.1007/s10886-019-01076-2},
pmid = {31152352},
issn = {1573-1561},
mesh = {Animals ; DNA/isolation & purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Female ; Genetic Variation ; Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/classification/genetics ; Male ; Mitochondria/genetics ; Moths/*genetics ; Phylogeny ; Sex Attractants/*chemistry/metabolism ; },
abstract = {Animal classification is primarily based on morphological characters, even though these may not be the first to diverge during speciation. In many cases, closely related taxa are actually difficult to distinguish based on morphological characters alone, especially when there is no substantial niche separation. As a consequence, the diversity of certain groups is likely to be underestimated. Lepidoptera -moths and butterflies- represent the largest group of herbivorous insects. The extensive diversification in the group is generally assumed to have its origin in the spectacular radiation of flowering plants and the resulting abundance of ecological niches. However, speciation can also occur without strong ecological divergence. For example, reproductive isolation can evolve as the result of divergence in mate preference and the associated pheromone communication system. We combined pheromone trapping and genetic analysis to elucidate the evolutionary relationships within a complex of primitive moth species (Lepidoptera: Eriocraniidae). Mitochondrial and nuclear DNA markers provided evidence that Eriocrania semipurpurella, as currently defined by morphological characters, includes three cryptic species in Northern and Western Europe. Male moths of these cryptic species, as well as of the closely related E. sangii, exhibited relative specificity in terms of their attraction to specific ratios of two major pheromone components, (2S,6Z)-nonen-2-ol and (2R,6Z)-nonen-2-ol. Our data suggest strong assortative mating in these species in the absence of apparent niche separation, indicating that Eriocrania moths may represent an example of non-ecological speciation. Finally, our study argues in favour of combining pheromone investigations and DNA barcoding as powerful tools for identifying and delimitating species boundaries.},
}

Animals
DNA/isolation & purification/metabolism
Electron Transport Complex IV/classification/genetics
Female
Genetic Variation
Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/classification/genetics
Male
Mitochondria/genetics
Moths/*genetics
Phylogeny
Sex Attractants/*chemistry/metabolism

@article {pmid31151779,
year = {2019},
author = {Sihali-Beloui, O and Aroune, D and Benazouz, F and Hadji, A and El-Aoufi, S and Marco, S},
title = {A hypercaloric diet induces hepatic oxidative stress, infiltration of lymphocytes, and mitochondrial reshuffle in Psammomys obesus, a murine model of insulin resistance.},
journal = {Comptes rendus biologies},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.crvi.2019.04.003},
pmid = {31151779},
issn = {1768-3238},
abstract = {The aim of this study was to show, for the first time, the effect of a hypercaloric diet on the mitochondrial reshuffle of hepatocytes during the progression from steatosis to steatohepatitis to cirrhosis in Psammomys obesus, a typical animal model of the metabolic syndrome. Metabolic and oxidative stresses were induced by feeding the animal through a standard laboratory diet (SD) for nine months. Metabolic parameters, liver malondialdehyde (MDA) and glutathione (GSH), were evaluated. The pathological evolution was examined by histopathology and immunohistochemistry, using CD3 and CD20 antibodies. The dynamics of the mitochondrial structure was followed by transmission electron microscopy. SD induced a steatosis in this animal that evolved under the effect of oxidative and metabolic stress by the appearance of adaptive inflammation and fibrosis leading the animal to the cirrhosis stage with serious hepatocyte damage by the triggering, at first the mitochondrial fusion-fission cycles, which attempted to maintain the mitochondria intact and functional, but the hepatocellular oxidative damage was increased inducing a vicious circle of mitochondrial alteration and dysfunction and their elimination by mitophagy. P. obesus is an excellent animal model of therapeutic research that targets mitochondrial dysfunction in the progression of steatosis.},
}

@article {pmid31150090,
year = {2019},
author = {Yin, HZ and Wang, HL and Ji, SG and Medvedeva, YV and Tian, G and Bazrafkan, AK and Maki, NZ and Akbari, Y and Weiss, JH},
title = {Rapid Intramitochondrial Zn2+ Accumulation in CA1 Hippocampal Pyramidal Neurons After Transient Global Ischemia: A Possible Contributor to Mitochondrial Disruption and Cell Death.},
journal = {Journal of neuropathology and experimental neurology},
volume = {78},
number = {7},
pages = {655-664},
doi = {10.1093/jnen/nlz042},
pmid = {31150090},
issn = {1554-6578},
abstract = {Mitochondrial Zn2+ accumulation, particularly in CA1 neurons, occurs after ischemia and likely contributes to mitochondrial dysfunction and subsequent neurodegeneration. However, the relationship between mitochondrial Zn2+ accumulation and their disruption has not been examined at the ultrastructural level in vivo. We employed a cardiac arrest model of transient global ischemia (TGI), combined with Timm's sulfide silver labeling, which inserts electron dense metallic silver granules at sites of labile Zn2+ accumulation, and used transmission electron microscopy (TEM) to examine subcellular loci of the Zn2+ accumulation. In line with prior studies, TGI-induced damage to CA1 was far greater than to CA3 pyramidal neurons, and was substantially progressive in the hours after reperfusion (being significantly greater after 4- than 1-hour recovery). Intriguingly, TEM examination of Timm's-stained sections revealed substantial Zn2+ accumulation in many postischemic CA1 mitochondria, which was strongly correlated with their swelling and disruption. Furthermore, paralleling the evolution of neuronal injury, both the number of mitochondria containing Zn2+ and the degree of their disruption were far greater at 4- than 1-hour recovery. These data provide the first direct characterization of Zn2+ accumulation in CA1 mitochondria after in vivo TGI, and support the idea that targeting these events could yield therapeutic benefits.},
}

@article {pmid31141182,
year = {2019},
author = {de Oliveira Boldrini, V and Dos Santos Farias, A and Degasperi, GR},
title = {Deciphering targets of Th17 cells fate: From metabolism to nuclear receptors.},
journal = {Scandinavian journal of immunology},
volume = {},
number = {},
pages = {e12793},
doi = {10.1111/sji.12793},
pmid = {31141182},
issn = {1365-3083},
support = {//CNPq-INCT (Conselho Nacional de Desenvolvimento Científico e Tecnológico-Instituto Nacional de Ciência e Tecnologia em Neuroimunomodulação)/ ; //CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior)/ ; 17/21363-5//FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo)/ ; },
abstract = {Evidence indicates that reprogramming of metabolism is critically important for the differentiation of CD4 + T lymphocytes, and the manipulation of metabolic pathways in these cells may shape their fate and function. Distinct subgroups from T lymphocytes, such as Th17, adopt specific metabolic programmes to support their needs. Some important metabolic reactions, such as glycolysis, oxidative phosphorylation, are considered important for the differentiation of these lymphocytes. Since their discovery nearly a decade ago, Th17 lymphocytes have received significant attention because of their role in the pathology of several immune-mediated inflammatory diseases such as multiple sclerosis. In this review, it will be discussed as the involvement of T cell metabolism and as metabolic reprogramming in activated T cells dictates fate decisions to Th17. The involvement of nuclear receptors such as RORyt e PPARs in the induction of Th17 cells was also discussed. Understanding the metabolic pathways involved in the differentiation of the distinct subgroups of T lymphocytes helps in the design of promising therapeutic proposals.},
}

@article {pmid31139952,
year = {2019},
author = {Ghadery, C and Best, LA and Pavese, N and Tai, YF and Strafella, AP},
title = {PET Evaluation of Microglial Activation in Non-neurodegenerative Brain Diseases.},
journal = {Current neurology and neuroscience reports},
volume = {19},
number = {7},
pages = {38},
doi = {10.1007/s11910-019-0951-x},
pmid = {31139952},
issn = {1534-6293},
abstract = {PURPOSE OF THE REVIEW: Microglial cell activation is an important component of neuroinflammation, and it is generally well accepted that chronic microglial activation is indicative of accumulating tissue damage in neurodegenerative conditions, particularly in the earlier stages of disease. Until recently, there has been less focus on the role of neuroinflammation in other forms of neurological and neuropsychiatric conditions. Through this review, we hope to demonstrate the important role TSPO PET imaging has played in illuminating the pivotal role of neuroinflammation and microglial activation underpinning these conditions.

RECENT FINDINGS: TSPO is an 18 kDa protein found on the outer membrane of mitochondria and can act as a marker of microglial activation using nuclear imaging. Through the development of radiopharmaceuticals targeting TSPO, researchers have been able to better characterise the spatial-temporal evolution of chronic neurological conditions, ranging from the focal autoimmune reactions seen in multiple sclerosis to the Wallerian degeneration at remote parts of the brain months following acute cerebral infarction. Development of novel techniques to investigate neuroinflammation within the central nervous system, for the purposes of diagnosis and therapeutics, has flourished over the past few decades. TSPO has proven itself a robust and sensitive biomarker of microglial activation and neuroimaging affords a minimally invasive technique to characterise neuroinflammatory processes in vivo.},
}

@article {pmid31138949,
year = {2019},
author = {Storz, JF and Cheviron, ZA and McClelland, GB and Scott, GR},
title = {Evolution of physiological performance capacities and environmental adaptation: insights from high-elevation deer mice (Peromyscus maniculatus).},
journal = {Journal of mammalogy},
volume = {100},
number = {3},
pages = {910-922},
doi = {10.1093/jmammal/gyy173},
pmid = {31138949},
issn = {0022-2372},
support = {R01 HL087216/HL/NHLBI NIH HHS/United States ; },
abstract = {Analysis of variation in whole-animal performance can shed light on causal connections between specific traits, integrated physiological capacities, and Darwinian fitness. Here, we review and synthesize information on naturally occurring variation in physiological performance capacities and how it relates to environmental adaptation in deer mice (Peromyscus maniculatus). We discuss how evolved changes in aerobic exercise capacity and thermogenic capacity have contributed to adaptation to high elevations. Comparative work on deer mice at high and low elevations has revealed evolved differences in aerobic performance capacities in hypoxia. Highland deer mice have consistently higher aerobic performance capacities under hypoxia relative to lowland natives, consistent with the idea that it is beneficial to have a higher maximal metabolic rate (as measured by the maximal rate of O2 consumption, VO2max) in an environment characterized by lower air temperatures and lower O2 availability. Observed differences in aerobic performance capacities between highland and lowland deer mice stem from changes in numerous subordinate traits that alter the flux capacity of the O2-transport system, the oxidative capacity of tissue mitochondria, and the relationship between O2 consumption and ATP synthesis. Many such changes in physiological phenotype are associated with hypoxia-induced changes in gene expression. Research on natural variation in whole-animal performance forms a nexus between physiological ecology and evolutionary biology that requires insight into the natural history of the study species.},
}

@article {pmid31126471,
year = {2019},
author = {Mascolo, C and Ceruso, M and Sordino, P and Palma, G and Anastasio, A and Pepe, T},
title = {Comparison of mitochondrial DNA enrichment and sequencing methods from fish tissue.},
journal = {Food chemistry},
volume = {294},
number = {},
pages = {333-338},
doi = {10.1016/j.foodchem.2019.05.026},
pmid = {31126471},
issn = {1873-7072},
mesh = {Animals ; DNA, Mitochondrial/chemistry/*metabolism ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/genetics ; Perciformes/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; },
abstract = {Sparid fish species have different commercial values related to their organoleptic features. Mitochondrial (mt) DNA provides a potential tool to distinguish species, but the enrichment of high-quality mtDNA from total genomic DNA is critical to obtain entire mtDNA sequences. Conventional mtDNA isolation is relatively low-cost and proficient. However, high numbers of PCR cycles can lead to artefacts (10-6 mutations/bp). We describe a rapid protocol for mtDNA extraction and enrichment from fish tissues, based on conventional miniprep columns and paramagnetic bead-based purification, without the need to employ PCR amplification. This newly described method generates a substrate for next-generation sequencing (NGS) analysis and is likely to have wider applications for mitochondrial studies in other fish families to help ensure traceability and differentiation of fish with high commercial values.},
}

Animals
DNA, Mitochondrial/chemistry/*metabolism
High-Throughput Nucleotide Sequencing/*methods
Mitochondria/genetics
Perciformes/*genetics
Polymerase Chain Reaction
Sequence Analysis, DNA/*methods

@article {pmid31105043,
year = {2019},
author = {Dumesic, PA and Egan, DF and Gut, P and Tran, MT and Parisi, A and Chatterjee, N and Jedrychowski, M and Paschini, M and Kazak, L and Wilensky, SE and Dou, F and Bogoslavski, D and Cartier, JA and Perrimon, N and Kajimura, S and Parikh, SM and Spiegelman, BM},
title = {An Evolutionarily Conserved uORF Regulates PGC1α and Oxidative Metabolism in Mice, Flies, and Bluefin Tuna.},
journal = {Cell metabolism},
volume = {30},
number = {1},
pages = {190-200.e6},
doi = {10.1016/j.cmet.2019.04.013},
pmid = {31105043},
issn = {1932-7420},
support = {F32 DK112638/DK/NIDDK NIH HHS/United States ; R01 DK054477/DK/NIDDK NIH HHS/United States ; R01 DK061562/DK/NIDDK NIH HHS/United States ; },
abstract = {Mitochondrial abundance and function are tightly controlled during metabolic adaptation but dysregulated in pathological states such as diabetes, neurodegeneration, cancer, and kidney disease. We show here that translation of PGC1α, a key governor of mitochondrial biogenesis and oxidative metabolism, is negatively regulated by an upstream open reading frame (uORF) in the 5' untranslated region of its gene (PPARGC1A). We find that uORF-mediated translational repression is a feature of PPARGC1A orthologs from human to fly. Strikingly, whereas multiple inhibitory uORFs are broadly present in fish PPARGC1A orthologs, they are completely absent in the Atlantic bluefin tuna, an animal with exceptionally high mitochondrial content. In mice, an engineered mutation disrupting the PPARGC1A uORF increases PGC1α protein levels and oxidative metabolism and confers protection from acute kidney injury. These studies identify a translational regulatory element governing oxidative metabolism and highlight its potential contribution to the evolution of organismal mitochondrial function.},
}

@article {pmid31092607,
year = {2019},
author = {Tian, R and Seim, I and Ren, W and Xu, S and Yang, G},
title = {Contraction of the ROS Scavenging Enzyme Glutathione S-Transferase Gene Family in Cetaceans.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {7},
pages = {2303-2315},
doi = {10.1534/g3.119.400224},
pmid = {31092607},
issn = {2160-1836},
abstract = {Cetaceans are a group of marine mammals whose ancestors were adaptated for life on land. Life in an aquatic environment poses many challenges for air-breathing mammals. Diving marine mammals have adapted to rapid reoxygenation and reactive oxygen species (ROS)-mediated reperfusion injury. Here, we considered the evolution of the glutathione transferase (GST) gene family which has important roles in the detoxification of endogenously-derived ROS and environmental pollutants. We characterized the cytosolic GST gene family in 21 mammalian species; cetaceans, sirenians, pinnipeds, and their terrestrial relatives. All seven GST classes were identified, showing that GSTs are ubiquitous in mammals. Some GST genes are the product of lineage-specific duplications and losses, in line with a birth-and-death evolutionary model. We detected sites with signatures of positive selection that possibly influence GST structure and function, suggesting that adaptive evolution of GST genes is important for defending mammals from various types of noxious environmental compounds. We also found evidence for loss of alpha and mu GST subclass genes in cetacean lineages. Notably, cetaceans have retained a homolog of at least one of the genes GSTA1, GSTA4, and GSTM1; GSTs that are present in both the cytosol and mitochondria. The observed variation in number and selection pressure on GST genes suggest that the gene family structure is dynamic within cetaceans.},
}

@article {pmid31088635,
year = {2019},
author = {Tan, DX},
title = {Aging: An evolutionary competition between host cells and mitochondria.},
journal = {Medical hypotheses},
volume = {127},
number = {},
pages = {120-128},
doi = {10.1016/j.mehy.2019.04.007},
pmid = {31088635},
issn = {1532-2777},
abstract = {Here, a new theory of aging is proposed. This new theory is referred as the Host-Mitochondria Intracellular Innate Immune Theory of Aging (HMIIITA). The main point of this theory is that the aging is rooted from an evolutionary competition, that is, a never ending coevolutionary race between host cells and mitochondria. Mitochondria are the descendants of bacteria. The host cells will inevitably sense their bacterial origin, particularly their circular mtDNA. The host intracellular innate immune pressure (HIIIP) aims to eliminate mtDNA as more as possible while mitochondria have to adapt the HIIIP for survival. Co-evolution is required for both of them. From biological point of view, the larger, the mtDNA, the higher, the chance, it becomes the target of HIIIP. As a result, mitochondria have to reduce their mtDNA size via deletion. This process has last for 1.5-2 billion yeas and the result is that mitochondria have lost excessive 95% of their DNA. This mtDNA deletion is not associated with free radical attack but a unique trait acquired during evolution. In the postmitotic cells, the deletion is passively selected by the mitochondrial fission-fusion cycles. Eventually, the accumulation of deletion will significantly jeopardize the mitochondrial function. The dysfunctional mitochondria no longer provide sufficient ATP to support host cells' continuous demanding for growth. At this stage, the cell or the organism aging is inevitable.},
}

@article {pmid31088494,
year = {2019},
author = {Shah, A and Hoffman, JI and Schielzeth, H},
title = {Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {370},
doi = {10.1186/s12864-019-5756-4},
pmid = {31088494},
issn = {1471-2164},
support = {SCHI 1188/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Contig Mapping ; Female ; Gene Expression Profiling/*methods ; Genetic Association Studies ; Genome Size ; Grasshoppers/*genetics ; High-Throughput Nucleotide Sequencing ; Male ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Sequence Analysis, RNA/*methods ; },
abstract = {BACKGROUND: The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. However, limited molecular resources are available for this species. Here, we present a de novo transcriptome assembly as reference resource for gene expression studies. We used high-throughput Illumina sequencing to generate 5,070,036 paired-end reads after quality filtering. We then combined the best-assembled contigs from three different de novo transcriptome assemblers (Trinity, SOAPdenovo-trans and Oases/Velvet) into a single assembly.

RESULTS: This resulted in 82,251 contigs with a N50 of 1357 and a TransRate assembly score of 0.325, which compares favourably with other orthopteran transcriptome assemblies. Around 87% of the transcripts could be annotated using InterProScan 5, BLASTx and the dammit! annotation pipeline. We identified a number of genes involved in pigmentation and green pigment metabolism pathways. Furthermore, we identified 76,221 putative single nucleotide polymorphisms residing in 8400 contigs. We also assembled the mitochondrial genome and investigated levels of sequence divergence with other species from the genus Gomphocerus. Finally, we detected and assembled Wolbachia sequences, which revealed close sequence similarity to the strain pel wPip.

CONCLUSIONS: Our study has generated a significant resource for uncovering genotype-phenotype associations in a species with an extraordinarily large genome, while also providing mitochondrial and Wolbachia sequences that will be useful for comparative studies.},
}

Animals
Contig Mapping
Female
Gene Expression Profiling/*methods
Genetic Association Studies
Genome Size
Grasshoppers/*genetics
High-Throughput Nucleotide Sequencing
Male
Mitochondria/*genetics
Molecular Sequence Annotation
Sequence Analysis, RNA/*methods

@article {pmid31077734,
year = {2019},
author = {Karagozlu, MZ and An, HE and Park, SH and Shin, SE and Kim, CB},
title = {Comparative analyses of the three complete mitochondrial genomes from forensic important beetle genus Dermestes with phylogenetic relationships.},
journal = {Gene},
volume = {706},
number = {},
pages = {146-153},
doi = {10.1016/j.gene.2019.05.020},
pmid = {31077734},
issn = {1879-0038},
mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Coleoptera/*genetics ; Forensic Sciences/methods ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; },
abstract = {Necrophagous Dermestes species have high forensic importance in relation to the estimation of elapsed time since death or death season. To further supplement the genome-level features for related species, the complete mitochondrial genome (mitogenome) of Dermestes species D. essellatocollis, D. frischii and D. coarctatus are amplified, sequenced, annotated, analyzed, and compared with other twelve species of the infraorder Bostrichoidea. The mitochondrial genomes were typical circular molecules with 16,218, 15,873 and 15,873 bp in length, respectively. They included 13 protein coding genes, two rRNAs, and 22 tRNAs, as well as the putative control region. The gene orders and orientations are identical to those of other recorded bostrichiformian species and had the ancestral insect gene composition. Furthermore, phylogenetic analyses based on all the mitochondrial protein coding genes for 13 Bostrichoidea and 16 outgroup taxa were performed using Bayesian and Maximum Likelihood analyses. The inferred trees indicate that the genus Dermestes is monophyletic. The monophyly of infraorder Bostrichiformia is not supported. This study provides genomic data for mitochondrial genome library of the genus Dermestes to investigate evolutionary and systematic studies.},
}

Animals
Base Composition/genetics
Base Sequence
Coleoptera/*genetics
Forensic Sciences/methods
Gene Order/genetics
Genome, Mitochondrial/*genetics
Mitochondria/*genetics
Phylogeny
RNA, Ribosomal/genetics
RNA, Transfer/genetics

@article {pmid31076245,
year = {2019},
author = {Brunk, CF and Martin, WF},
title = {Archaeal Histone Contributions to the Origin of Eukaryotes.},
journal = {Trends in microbiology},
volume = {27},
number = {8},
pages = {703-714},
doi = {10.1016/j.tim.2019.04.002},
pmid = {31076245},
issn = {1878-4380},
abstract = {The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.},
}

@article {pmid31073215,
year = {2019},
author = {Castelli, M and Sabaneyeva, E and Lanzoni, O and Lebedeva, N and Floriano, AM and Gaiarsa, S and Benken, K and Modeo, L and Bandi, C and Potekhin, A and Sassera, D and Petroni, G},
title = {Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales.},
journal = {The ISME journal},
volume = {13},
number = {9},
pages = {2280-2294},
doi = {10.1038/s41396-019-0433-9},
pmid = {31073215},
issn = {1751-7370},
support = {FP7-PEOPLE-2009-IRSES grant 247658//European Commission (EC)/ ; 16-14-10157//Russian Science Foundation (RSF)/ ; RGY0075/2017//Human Frontier Science Program (HFSP)/ ; },
abstract = {Rickettsiales are a lineage of obligate intracellular Alphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novel Rickettsiales bacterium associated with Paramecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesise amino acids, compared to all investigated Rickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction of Rickettsiales bacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity in Rickettsiales. According to our reconstruction, the Rickettsiales ancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity would have evolved later, in parallel and independently, in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria within Alphaproteobacteria.},
}

@article {pmid31064825,
year = {2019},
author = {Bertolini, MS and Chiurillo, MA and Lander, N and Vercesi, AE and Docampo, R},
title = {MICU1 and MICU2 Play an Essential Role in Mitochondrial Ca2+ Uptake, Growth, and Infectivity of the Human Pathogen Trypanosoma cruzi.},
journal = {mBio},
volume = {10},
number = {3},
pages = {},
doi = {10.1128/mBio.00348-19},
pmid = {31064825},
issn = {2150-7511},
support = {R01 AI107663/AI/NIAID NIH HHS/United States ; R56 AI107663/AI/NIAID NIH HHS/United States ; },
mesh = {Adaptation, Physiological ; Biological Transport ; CRISPR-Cas Systems ; Calcium/*metabolism ; Calcium-Binding Proteins/genetics/*metabolism ; Cation Transport Proteins ; Cytosol/chemistry/metabolism ; Gene Knockout Techniques ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Protozoan Proteins/genetics/*metabolism ; Trypanosoma cruzi/*genetics/pathogenicity ; },
abstract = {The mitochondrial Ca2+ uptake in trypanosomatids, which belong to the eukaryotic supergroup Excavata, shares biochemical characteristics with that of animals, which, together with fungi, belong to the supergroup Opisthokonta. However, the composition of the mitochondrial calcium uniporter (MCU) complex in trypanosomatids is quite peculiar, suggesting lineage-specific adaptations. In this work, we used Trypanosoma cruzi to study the role of orthologs for mitochondrial calcium uptake 1 (MICU1) and MICU2 in mitochondrial Ca2+ uptake. T. cruzi MICU1 (TcMICU1) and TcMICU2 have mitochondrial targeting signals, two canonical EF-hand calcium-binding domains, and localize to the mitochondria. Using the CRISPR/Cas9 system (i.e., clustered regularly interspaced short palindromic repeats with Cas9), we generated TcMICU1 and TcMICU2 knockout (-KO) cell lines. Ablation of either TcMICU1 or TcMICU2 showed a significantly reduced mitochondrial Ca2+ uptake in permeabilized epimastigotes without dissipation of the mitochondrial membrane potential or effects on the AMP/ATP ratio or citrate synthase activity. However, none of these proteins had a gatekeeper function at low cytosolic Ca2+ concentrations ([Ca2+]cyt), as occurs with their mammalian orthologs. TcMICU1-KO and TcMICU2-KO epimastigotes had a lower growth rate and impaired oxidative metabolism, while infective trypomastigotes have a reduced capacity to invade host cells and to replicate within them as amastigotes. The findings of this work, which is the first to study the role of MICU1 and MICU2 in organisms evolutionarily distant from animals, suggest that, although these components were probably present in the last eukaryotic common ancestor (LECA), they developed different roles during evolution of different eukaryotic supergroups. The work also provides new insights into the adaptations of trypanosomatids to their particular life styles.IMPORTANCETrypanosoma cruzi is the etiologic agent of Chagas disease and belongs to the early-branching eukaryotic supergroup Excavata. Its mitochondrial calcium uniporter (MCU) subunit shares similarity with the animal ortholog that was important to discover its encoding gene. In animal cells, the MICU1 and MICU2 proteins act as Ca2+ sensors and gatekeepers of the MCU, preventing Ca2+ uptake under resting conditions and favoring it at high cytosolic Ca2+ concentrations ([Ca2+]cyt). Using the CRISPR/Cas9 technique, we generated TcMICU1 and TcMICU2 knockout cell lines and showed that MICU1 and -2 do not act as gatekeepers at low [Ca2+]cyt but are essential for normal growth, host cell invasion, and intracellular replication, revealing lineage-specific adaptations.},
}

Adaptation, Physiological
Biological Transport
CRISPR-Cas Systems
Calcium/*metabolism
Calcium-Binding Proteins/genetics/*metabolism
Cation Transport Proteins
Cytosol/chemistry/metabolism
Gene Knockout Techniques
Humans
Mitochondria/*metabolism
Mitochondrial Membrane Transport Proteins/genetics/*metabolism
Protozoan Proteins/genetics/*metabolism
Trypanosoma cruzi/*genetics/pathogenicity

@article {pmid31057485,
year = {2019},
author = {Zhao, D and Yu, Y and Shen, Y and Liu, Q and Zhao, Z and Sharma, R and Reiter, RJ},
title = {Melatonin Synthesis and Function: Evolutionary History in Animals and Plants.},
journal = {Frontiers in endocrinology},
volume = {10},
number = {},
pages = {249},
doi = {10.3389/fendo.2019.00249},
pmid = {31057485},
issn = {1664-2392},
abstract = {Melatonin is an ancient molecule that can be traced back to the origin of life. Melatonin's initial function was likely that as a free radical scavenger. Melatonin presumably evolved in bacteria; it has been measured in both α-proteobacteria and in photosynthetic cyanobacteria. In early evolution, bacteria were phagocytosed by primitive eukaryotes for their nutrient value. According to the endosymbiotic theory, the ingested bacteria eventually developed a symbiotic association with their host eukaryotes. The ingested α-proteobacteria evolved into mitochondria while cyanobacteria became chloroplasts and both organelles retained their ability to produce melatonin. Since these organelles have persisted to the present day, all species that ever existed or currently exist may have or may continue to synthesize melatonin in their mitochondria (animals and plants) and chloroplasts (plants) where it functions as an antioxidant. Melatonin's other functions, including its multiple receptors, developed later in evolution. In present day animals, via receptor-mediated means, melatonin functions in the regulation of sleep, modulation of circadian rhythms, enhancement of immunity, as a multifunctional oncostatic agent, etc., while retaining its ability to reduce oxidative stress by processes that are, in part, receptor-independent. In plants, melatonin continues to function in reducing oxidative stress as well as in promoting seed germination and growth, improving stress resistance, stimulating the immune system and modulating circadian rhythms; a single melatonin receptor has been identified in land plants where it controls stomatal closure on leaves. The melatonin synthetic pathway varies somewhat between plants and animals. The amino acid, tryptophan, is the necessary precursor of melatonin in all taxa. In animals, tryptophan is initially hydroxylated to 5-hydroxytryptophan which is then decarboxylated with the formation of serotonin. Serotonin is either acetylated to N-acetylserotonin or it is methylated to form 5-methoxytryptamine; these products are either methylated or acetylated, respectively, to produce melatonin. In plants, tryptophan is first decarboxylated to tryptamine which is then hydroxylated to form serotonin.},
}

@article {pmid31044222,
year = {2019},
author = {Nagarajan-Radha, V and Rapkin, J and Hunt, J and Dowling, DK},
title = {Interactions between mitochondrial haplotype and dietary macronutrient ratios confer sex-specific effects on longevity in Drosophila melanogaster.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1093/gerona/glz104},
pmid = {31044222},
issn = {1758-535X},
abstract = {Recent studies have demonstrated that modifications to the ratio of dietary macronutrients affect longevity in a diverse range of species. However, the degree to which levels of natural genotypic variation shape these dietary effects on longevity remains unclear. The mitochondria have long been linked to the ageing process. The mitochondria possess their own genome, and previous studies have shown that mitochondrial genetic variation affects longevity in insects. Furthermore, the mitochondria are the sites in which dietary nutrients are oxidized to produce adenosine triphosphate, suggesting a capacity for dietary quality to mediate the link between mitochondrial genotype and longevity. Here, we measured longevity of male and female fruit flies, across a panel of genetic strains of Drosophila melanogaster, which vary only in their mitochondrial haplotype, when fed one of two isocaloric diets that differed in their protein-to-carbohydrate ratio. The mitochondrial haplotype affected the longevity of flies, but the pattern of these effects differed across the two diets in males, but not in females. We discuss the implications of these results in relation to an evolutionary theory linking maternal inheritance of mitochondria to the accumulation of male-harming mitochondrial mutations, and to the theory exploring the evolution of phenotypic plasticity to novel environments.},
}