@article {pmid28358800,
year = {2017},
author = {Roberts, RG},
title = {Mitochondria-A billion years of cohabitation.},
journal = {PLoS biology},
volume = {15},
number = {3},
pages = {e2002338},
doi = {10.1371/journal.pbio.2002338},
pmid = {28358800},
issn = {1545-7885},
mesh = {Animals ; Apoptosis ; Archaea/*cytology/*physiology ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Cytophagocytosis ; Endoplasmic Reticulum/physiology ; Energy Metabolism ; Humans ; Mitochondria/genetics/*physiology ; Models, Biological ; *Symbiosis ; },
}

Animals
Apoptosis
Archaea/*cytology/*physiology
*Bacterial Physiological Phenomena
*Biological Evolution
Cytophagocytosis
Endoplasmic Reticulum/physiology
Energy Metabolism
Humans
Mitochondria/genetics/*physiology
Models, Biological
*Symbiosis

@article {pmid30211573,
year = {2018},
author = {Geary, DC},
title = {Efficiency of mitochondrial functioning as the fundamental biological mechanism of general intelligence (g).},
journal = {Psychological review},
volume = {},
number = {},
pages = {},
doi = {10.1037/rev0000124},
pmid = {30211573},
issn = {1939-1471},
abstract = {General intelligence or g is one of the most thoroughly studied concepts in the behavioral sciences. Measures of intelligence are predictive of a wide range of educational, occupational, and life outcomes, including creative productivity and are systematically related to physical health and successful aging. The nexus of relations suggests 1 or several fundamental biological mechanisms underlie g, health, and aging, among other outcomes. Cell-damaging oxidative stress has been proposed as 1 of many potential mechanisms, but the proposal is underdeveloped and does not capture other important mitochondrial functions. I flesh out this proposal and argue that the overall efficiency of mitochondrial functioning is a core component of g; the most fundamental biological mechanism common to all brain and cognitive processes and that contributes to the relations among intelligence, health, and aging. The proposal integrates research on intelligence with models of the centrality of mitochondria to brain development and functioning, neurological diseases, and health more generally. Moreover, the combination of the maternal inheritance of mitochondrial DNA (mtDNA), the evolution of compensatory nuclear DNA, and the inability of evolutionary processes to purge deleterious mtDNA in males may contribute to the sex difference in variability in intelligence and in other cognitive domains. The proposal unifies many now disparate literatures and generates testable predictions for future studies. (PsycINFO Database Record},
}

@article {pmid30209549,
year = {2018},
author = {Sandor, S and Zhang, Y and Xu, J},
title = {Fungal mitochondrial genomes and genetic polymorphisms.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9350-5},
pmid = {30209549},
issn = {1432-0614},
support = {531998//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Mitochondria are the powerhouses of eukaryotic cells, responsible for ATP generation and playing a role in a diversity of cellular and organismal functions. Different from the majority of other intracellular membrane structures, mitochondria contain their own genetic materials that are capable of independent replication and inheritance. In this mini-review, we provide brief summaries of fungal mitochondrial genome structure, size, gene content, inheritance, and genetic variation. We pay special attention to the relative genetic polymorphisms of the mitochondrial vs nuclear genomes at the population level within individual fungal species. Among the 20 species/groups of species reviewed here, there is a range of variation among genes and species in the relative nuclear and mitochondrial genetic polymorphisms. Interestingly, most (15/20) showed a greater genetic diversity for nuclear genes and genomes than for mitochondrial genes and genomes, with the remaining five showing similar or slower nuclear genome genetic variations. This fungal pattern is different from the dominant pattern in animals, but more similar to that in plants. At present, the mechanisms for the variations among fungal species and the overall low level of mitochondrial sequence polymorphisms are not known. The increasing availability of population genomic data should help us reveal the potential genetic and ecological factors responsible for the observed variations.},
}

@article {pmid30021129,
year = {2018},
author = {Sun, S and Sha, Z and Wang, Y},
title = {Complete mitochondrial genome of the first deep-sea spongicolid shrimp Spongiocaris panglao (Decapoda: Stenopodidea): Novel gene arrangement and the phylogenetic position and origin of Stenopodidea.},
journal = {Gene},
volume = {676},
number = {},
pages = {123-138},
doi = {10.1016/j.gene.2018.07.026},
pmid = {30021129},
issn = {1879-0038},
mesh = {Animals ; Base Composition ; Decapoda (Crustacea)/*genetics ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry ; Sequence Analysis, DNA/*methods ; },
abstract = {Stenopodidea Claus, 1872 (Crustacea: Decapoda) is one of the major groups of decapods crustaceans. Hitherto, only one complete mitochondrial genome (mitogenome) from the family Stenopodidae is available for the infraorder Stenopodidea. Here, we determined the complete mitogenome of Spongiocaris panglao de Grave and Saito, 2016 using Illumina sequencing, representing the first species from the family Spongicolidae. The 15,909 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. Although the overall genome organization is typical for metazoans, the mitogenome of S. panglao shows some derived characters. A + T content of 77.42% in S. pamglao mitogenome is second-highest among the dacapods described to date. The trnR gene exhibit modified secondary structure with the TψC loop completely missing, which might be a putative autapomorphy of S. pamglao mitogenome. Compared with the shallow-water stenopodidean species S. hispidus, the control region of S. pamglao exhibits three characteristics: larger size, higher A + T content, and more tandem repeat sequences. The gene order exhibited difference from the ancestral mitogenome pattern of the Pancrustacea, with 5 tRNA genes rearrangement. The result from BI was agreed with most morphological characters and molecular evidences, revealing that Stenopodidea and Reptantia had the closest relationship, as the sister group of Caridea. Still, the alternative hypothesis supported from ML topology cannot be completely rejected based on the current data. Estimated times revealed that the two stenopodideans families Stenopodidae and Spongicolidae diverged from each other around 122 Mya. The divergence time of spongicolid shrimp is in good agreement with the origin of their hexactinellid hosts (78-144 Mya).},
}

Animals
Base Composition
Decapoda (Crustacea)/*genetics
Gene Order
Genome Size
Genome, Mitochondrial
High-Throughput Nucleotide Sequencing/*methods
Mitochondria/*genetics
Nucleic Acid Conformation
Phylogeny
RNA/chemistry
Sequence Analysis, DNA/*methods

@article {pmid30206380,
year = {2018},
author = {Jebb, D and Foley, NM and Whelan, CV and Touzalin, F and Puechmaille, SJ and Teeling, EC},
title = {Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {13634},
doi = {10.1038/s41598-018-31093-2},
pmid = {30206380},
issn = {2045-2322},
support = {ERC-2012-StG311000//EC | European Research Council (ERC)/ ; },
abstract = {Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The "Free Radical Theory of Ageing" (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria deep-sequenced, with a subset sampled over multiple years. The majority of heteroplasmies were at a low frequency and were transitions. Oxidative mutations were present in only a small number of individuals, suggesting local oxidative stress events. Cohort data showed no significant increase in heteroplasmy with age, while longitudinal data from recaptured individuals showed heteroplasmy is dynamic, and does not increase uniformly over time. We show that bats do not suffer from the predicted, inevitable increase in heteroplasmy as posited by the FRTA, instead heteroplasmy was found to be dynamic, questioning its presumed role as a primary driver of ageing.},
}

@article {pmid30195322,
year = {2018},
author = {Verechshagina, NA and Konstantinov, YM and Kamenski, PA and Mazunin, IO},
title = {Import of Proteins and Nucleic Acids into Mitochondria.},
journal = {Biochemistry. Biokhimiia},
volume = {83},
number = {6},
pages = {643-661},
doi = {10.1134/S0006297918060032},
pmid = {30195322},
issn = {1608-3040},
abstract = {Many mitochondrial genes have been transferred to the nucleus in course of evolution. The products of expression of these genes, being still necessary for organelle function, are imported there from the cytosol. Molecular mechanisms of protein import are studied much deeper than those of nucleic acids. The latter, it seems to us, retards the development of mitochondrial genome editing technologies. In this review, we describe mechanisms of DNA, RNA, and protein import into mitochondria of different eukaryotes. The description is given for the natural processes, as well as for artificial targeting of macromolecules into mitochondria for therapy. Also, we discuss different approaches to introduce changes into the mitochondrial DNA sequence.},
}

@article {pmid30179526,
year = {2018},
author = {Haenel, GJ and Del Gaizo Moore, V},
title = {Functional Divergence of Mitochondria and Coevolution of Genomes: Cool Mitochondria in Hot Lizards.},
journal = {Physiological and biochemical zoology : PBZ},
volume = {91},
number = {5},
pages = {1068-1081},
doi = {10.1086/699918},
pmid = {30179526},
issn = {1537-5293},
abstract = {Mitochondria play a key role in the ecology and evolution of species through their influence on aerobic metabolism. Mitochondrial DNA (mtDNA) and nuclear genomes must interact for optimal functioning of oxidative phosphorylation to produce ATP, and breakdown of coadaptation components from each may have important evolutionary consequences for hybridization. Introgression of mitochondria in natural populations through hybridization with unidirectional backcrossing allows the testing of coadaptation of mitochondria to different nuclear backgrounds. We compared the function of mitochondria isolated from two species of Urosaurus lizards and hybrid populations. Due to past introgression, hybrids contain the nuclear genome of the "hot-adapted" species (U. graciosus) but the mtDNA of the less heat-tolerant species (U. ornatus). It was found that the function of the parental forms of mitochondria had significantly diverged with the hot-adapted species. There was significant genotype × genotype × environment interactions for mitochondrial membrane potential and genotype × genotype interactions for ATP production. Membrane potential decreased less at a higher temperature, while ATP production was higher at both temperatures in introgressed mitochondria. Oxygen consumption was lower in U. graciosus than in U. ornatus parental-type mitochondria, indicating a likely response to living in hotter environments. Respiratory control ratio values, which provide an indication of the functional quality of isolated mitochondria, were lower in introgressed mitochondria than in parental U. ornatus types, indicating a negative impact on biological function in introgressed mitochondria.},
}

@article {pmid29410353,
year = {2018},
author = {Rose, JP and Kleist, TJ and Löfstrand, SD and Drew, BT and Schönenberger, J and Sytsma, KJ},
title = {Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections.},
journal = {Molecular phylogenetics and evolution},
volume = {122},
number = {},
pages = {59-79},
doi = {10.1016/j.ympev.2018.01.014},
pmid = {29410353},
issn = {1095-9513},
mesh = {Animals ; *Biodiversity ; Chloroplasts/genetics ; Far East ; Fossils/history ; Genetic Speciation ; History, Ancient ; Magnoliopsida/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Phylogeography/history ; Ribosomes/genetics ; },
abstract = {Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.},
}

Animals
*Biodiversity
Chloroplasts/genetics
Far East
Fossils/history
Genetic Speciation
History, Ancient
Magnoliopsida/*classification/genetics
Mitochondria/genetics
*Phylogeny
Phylogeography/history
Ribosomes/genetics

@article {pmid29408286,
year = {2018},
author = {Yuan, ML and Zhang, QL and Zhang, L and Jia, CL and Li, XP and Yang, XZ and Feng, RQ},
title = {Mitochondrial phylogeny, divergence history and high-altitude adaptation of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) inhabiting the Tibetan Plateau.},
journal = {Molecular phylogenetics and evolution},
volume = {122},
number = {},
pages = {116-124},
doi = {10.1016/j.ympev.2018.01.016},
pmid = {29408286},
issn = {1095-9513},
mesh = {*Adaptation, Physiological/genetics ; *Altitude ; Animals ; Biodiversity ; DNA/chemistry/isolation & purification/metabolism ; Grassland ; Mitochondria/*genetics ; Moths/*classification/genetics ; Open Reading Frames/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Tibet ; },
abstract = {Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most important pests in alpine meadows of the Tibetan Plateau (TP) and have well adapted to high-altitude environments. To further understand the evolutionary history and their adaptation to the TP, we newly determined seven complete TP Gynaephora mitogenomes. Compared to single genes, whole mitogenomes provided the best phylogenetic signals and obtained robust results, supporting the monophyly of the TP Gynaephora species and a phylogeny of Arctiinae + (Aganainae + Lymantriinae). Incongruent phylogenetic signals were found among single mitochondrial genes, none of which recovered the same phylogeny as the whole mitogenome. We identified six best-performing single genes using Shimodaira-Hasegawa tests and found that the combinations of rrnS and either cox1 or cox3 generated the same phylogeny as the whole mitogenome, indicating the phylogenetic potential of these three genes for future evolutionary studies of Gynaephora. The TP Gynaephora species were estimated to radiate on the TP during the Pliocene and Quaternary, supporting an association of the diversification and speciation of the TP Gynaephora species with the TP uplifts and associated climate changes during this time. Selection analyses revealed accelerated evolutionary rates of the mitochondrial protein-coding genes in the TP Gynaephora species, suggesting that they accumulated more nonsynonymous substitutions that may benefit their adaptation to high altitudes. Furthermore, signals of positive selection were detected in nad5 of two Gynaephora species with the highest altitude-distributions, indicating that this gene may contribute to Gynaephora's adaptation to divergent altitudes. This study adds to the understanding of the TP Gynaephora evolutionary relationships and suggests a link between mitogenome evolution and ecological adaptation to high-altitude environments in grassland caterpillars.},
}

*Adaptation, Physiological/genetics
*Altitude
Animals
Biodiversity
DNA/chemistry/isolation & purification/metabolism
Grassland
Mitochondria/*genetics
Moths/*classification/genetics
Open Reading Frames/genetics
*Phylogeny
Sequence Analysis, DNA
Tibet

@article {pmid30176236,
year = {2018},
author = {Virji, AZ and Thekkiniath, J and Ma, W and Lawres, L and Knight, J and Swei, A and Roch, KL and Ben Mamoun, C},
title = {Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2018.05.008},
pmid = {30176236},
issn = {1879-0135},
abstract = {Babesia microti and Babesia duncani are the main causative agents of human babesiosis in the United States. While significant knowledge about B. microti has been gained over the past few years, nothing is known about B. duncani biology, pathogenesis, mode of transmission or sensitivity to currently recommended therapies. Studies in immunocompetent wild type mice and hamsters have shown that unlike B. microti, infection with B. duncani results in severe pathology and ultimately death. The parasite factors involved in B. duncani virulence remain unknown. Here we report the first known completed sequence and annotation of the apicoplast and mitochondrial genomes of B. duncani. We found that the apicoplast genome of this parasite consists of a 34 kb monocistronic circular molecule encoding functions that are important for apicoplast gene transcription as well as translation and maturation of the organelle's proteins. The mitochondrial genome of B. duncani consists of a 5.9 kb monocistronic linear molecule with two inverted repeats of 48 bp at both ends. Using the conserved cytochrome b (Lemieux) and cytochrome c oxidase subunit I (coxI) proteins encoded by the mitochondrial genome, phylogenetic analysis revealed that B. duncani defines a new lineage among apicomplexan parasites distinct from B. microti, Babesia bovis, Theileria spp. and Plasmodium spp. Annotation of the apicoplast and mitochondrial genomes of B. duncani identified targets for development of effective therapies. Our studies set the stage for evaluation of the efficacy of these drugs alone or in combination against B. duncani in culture as well as in animal models.},
}

@article {pmid30154842,
year = {2018},
author = {Berzabá-Evoli, E and Zazueta, C and Cruz Hernández, JH and Gómez-Crisóstomo, NP and Juárez-Rojop, IE and De la Cruz-Hernández, EN and Martínez-Abundis, E},
title = {Leptin Modifies the Rat Heart Performance Associated with Mitochondrial Dysfunction Independently of Its Prohypertrophic Effects.},
journal = {International journal of endocrinology},
volume = {2018},
number = {},
pages = {6081415},
doi = {10.1155/2018/6081415},
pmid = {30154842},
issn = {1687-8337},
abstract = {Background: Functional receptors for leptin were described on the surface of cardiomyocytes, and there was a prohypertrophic effect with high concentrations of the cytokine. Therefore, leptin could be a link between obesity and the prevalence of cardiovascular diseases. On the other hand, a deleterious effect of leptin on mitochondrial performance was described, which was also associated with the evolution of cardiac hypertrophy to heart failure. The goal of our study was to analyze the effect of the exposure of rat hearts to a high concentration of leptin on cardiac and mitochondrial function.

Methods: Rat hearts were perfused continuously with or without 3.1 nM leptin for 1, 2, 3, or 4 hours. Homogenates and mitochondria were prepared by centrifugation and analyzed for cardiac actin, STAT3, and pSTAT3 by Western blotting, as well as for mitochondrial oxidative phosphorylation, membrane potential, swelling, calcium transport, and content of oxidized lipids.

Results: In our results, leptin induced an increased rate-pressure product as a result of increased heart rate and contraction force, as well oxidative stress. In addition, mitochondrial dysfunction expressed as a loss of membrane potential, decreased ability for calcium transport and retention, faster swelling, and less respiratory control was observed.

Conclusions: Our results support the role of leptin as a deleterious factor for cardiac function and indicates that mitochondrial dysfunction could be a trigger for cardiac hypertrophy and failure.},
}

@article {pmid29495437,
year = {2018},
author = {Mansilla, N and Racca, S and Gras, DE and Gonzalez, DH and Welchen, E},
title = {The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants.},
journal = {International journal of molecular sciences},
volume = {19},
number = {3},
pages = {},
doi = {10.3390/ijms19030662},
pmid = {29495437},
issn = {1422-0067},
mesh = {Animals ; Catalytic Domain ; Electron Transport Complex IV/chemistry/genetics/*metabolism ; *Energy Metabolism ; Enzyme Activation ; Gene Expression Regulation, Plant ; Humans ; Mammals/genetics/metabolism ; Mitochondria/genetics/*metabolism ; Mutation ; Plant Development ; Plant Physiological Phenomena ; Plants/genetics/*metabolism ; Protein Subunits ; Yeasts/genetics/metabolism ; },
abstract = {Mitochondrial respiration is an energy producing process that involves the coordinated action of several protein complexes embedded in the inner membrane to finally produce ATP. Complex IV or Cytochrome c Oxidase (COX) is the last electron acceptor of the respiratory chain, involved in the reduction of O₂ to H₂O. COX is a multimeric complex formed by multiple structural subunits encoded in two different genomes, prosthetic groups (heme a and heme a₃), and metallic centers (CuA and CuB). Tens of accessory proteins are required for mitochondrial RNA processing, synthesis and delivery of prosthetic groups and metallic centers, and for the final assembly of subunits to build a functional complex. In this review, we perform a comparative analysis of COX composition and biogenesis factors in yeast, mammals and plants. We also describe possible external and internal factors controlling the expression of structural proteins and assembly factors at the transcriptional and post-translational levels, and the effect of deficiencies in different steps of COX biogenesis to infer the role of COX in different aspects of plant development. We conclude that COX assembly in plants has conserved and specific features, probably due to the incorporation of a different set of subunits during evolution.},
}

Animals
Catalytic Domain
Electron Transport Complex IV/chemistry/genetics/*metabolism
*Energy Metabolism
Enzyme Activation
Gene Expression Regulation, Plant
Humans
Mammals/genetics/metabolism
Mitochondria/genetics/*metabolism
Mutation
Plant Development
Plant Physiological Phenomena
Plants/genetics/*metabolism
Protein Subunits
Yeasts/genetics/metabolism

@article {pmid29463212,
year = {2018},
author = {Wagner, JT and Singh, PP and Romney, AL and Riggs, CL and Minx, P and Woll, SC and Roush, J and Warren, WC and Brunet, A and Podrabsky, JE},
title = {The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {155},
doi = {10.1186/s12864-018-4539-7},
pmid = {29463212},
issn = {1471-2164},
support = {IOS-1354549//National Science Foundation/International ; CEHG Fellowship//Stanford University/International ; },
mesh = {Adaptation, Biological/*genetics ; Animals ; Base Composition ; Biological Evolution ; Chickens ; Embryo, Nonmammalian ; Embryonic Development/*genetics ; Gene Expression Regulation ; *Genome ; Genome Size ; Genomics/methods ; Killifishes/*embryology/genetics/*physiology ; Mitochondria/genetics/metabolism ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Stress, Physiological/*genetics ; Vertebrates ; Zebrafish ; },
abstract = {BACKGROUND: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system.

RESULTS: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection.

CONCLUSION: The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution.},
}

Adaptation, Biological/*genetics
Animals
Base Composition
Biological Evolution
Chickens
Embryo, Nonmammalian
Embryonic Development/*genetics
Gene Expression Regulation
*Genome
Genome Size
Genomics/methods
Killifishes/*embryology/genetics/*physiology
Mitochondria/genetics/metabolism
Phylogeny
Repetitive Sequences, Nucleic Acid
Stress, Physiological/*genetics
Vertebrates
Zebrafish

@article {pmid29337274,
year = {2018},
author = {Ballesteros, JA and Hormiga, G},
title = {Species delimitation of the North American orchard-spider Leucauge venusta (Walckenaer, 1841) (Araneae, Tetragnathidae).},
journal = {Molecular phylogenetics and evolution},
volume = {121},
number = {},
pages = {183-197},
doi = {10.1016/j.ympev.2018.01.002},
pmid = {29337274},
issn = {1095-9513},
mesh = {Animals ; Brazil ; Calibration ; Canada ; Ecosystem ; Florida ; Geography ; Male ; Mexico ; Mitochondria/genetics ; North America ; *Phylogeny ; Probability ; Species Specificity ; Spiders/classification/*genetics ; Time Factors ; United States ; },
abstract = {The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through the southeastern USA to investigate the observed genetic divide. The dataset, complemented with additional samples from Mexico, and Brazil was analyzed for species delimitation using STACEY and bGMYC based on sequences from one nuclear (ITS2) and one mitochondrial marker (COI). The analyses clearly separate USA samples into two deeply divergent and geographically structured groups (north-south) which we interpret as two different species. We generated ecological niche models for these two groups rejecting a niche equivalence hypothesis for these lineages. Taxonomic changes are proposed based on these findings, Leucauge venusta is restricted to denote the northern clade, and its known distribution restricted to the USA. Leucauge argyrobapta (White, 1841) is removed from synonymy to denote the populations in Florida, Mexico and Brazil. Although the delimitation analyses suggest each of these geographic clusters within the L. argyrobapta samples represent different species, more specimens from Central and South America are needed to properly test the cohesion of L. argyrobapta populations.},
}

Animals
Brazil
Calibration
Canada
Ecosystem
Florida
Geography
Male
Mexico
Mitochondria/genetics
North America
*Phylogeny
Probability
Species Specificity
Spiders/classification/*genetics
Time Factors
United States

@article {pmid30144423,
year = {2018},
author = {Pustylnikov, S and Costabile, F and Beghi, S and Faccibene, A},
title = {Targeting mitochondria in cancer: current concepts and immunotherapy approaches.},
journal = {Translational research : the journal of laboratory and clinical medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.trsl.2018.07.013},
pmid = {30144423},
issn = {1878-1810},
abstract = {An essential advantage during eukaryotic cell evolution was the acquisition of a network of mitochondria as a source of energy for cell metabolism and contrary to conventional wisdom, functional mitochondria are essential for the cancer cell. Multiple aspects of mitochondrial biology beyond bioenergetics support transformation including mitochondrial biogenesis, fission and fusion dynamics, cell death susceptibility, oxidative stress regulation, metabolism, and signaling. In cancer, the metabolism of cells is reprogrammed for energy generation from oxidative phosphorylation to aerobic glycolysis and impacts cancer mitochondrial function. Furthermore cancer cells can also modulate energy metabolism within the cancer microenvironment including immune cells and induce "metabolic anergy" of antitumor immune response. Classical approaches targeting the mitochondria of cancer cells usually aim at inducing changing energy metabolism or directly affecting functions of mitochondrial antiapoptotic proteins but most of such approaches miss the required specificity of action and carry important side effects. Several types of cancers harbor somatic mitochondrial DNA mutations and specific immune response to mutated mitochondrial proteins has been observed. An attractive alternative way to target the mitochondria in cancer cells is the induction of an adaptive immune response against mutated mitochondrial proteins. Here, we review the cancer cell-intrinsic and cell-extrinsic mechanisms through which mitochondria influence all steps of oncogenesis, with a focus on the therapeutic potential of targeting mitochondrial DNA mutations or Tumor Associated Mitochondria Antigens using the immune system.},
}

@article {pmid30141728,
year = {2018},
author = {Boratyński, JS and Szafrańska, PA},
title = {Does Basal Metabolism Set the Limit for Metabolic Downregulation during Torpor?.},
journal = {Physiological and biochemical zoology : PBZ},
volume = {91},
number = {5},
pages = {1057-1067},
doi = {10.1086/699917},
pmid = {30141728},
issn = {1537-5293},
abstract = {The evolution of endothermic thermoregulation is rooted in the processes involving high metabolism, which allows the maintenance of high and stable body temperatures (Tb). In turn, selection for high endothermic metabolism correlates with increased size of metabolically active organs and thus with high basal metabolic rate (BMR). Endothermic animals are characterized by an MR several times that of similar-sized ectotherms. However, many small mammals are temporally heterothermic and are able to temporally decrease Tb and MR by entering daily torpor or hibernation. Both BMR and minimum MR during torpor (TMRmin) likely result from oxidative respiration in mitochondria of the same tissues. It should be expected that these two MRs are positively correlated, suggesting that the evolution of endothermy and higher BMR set the limit for the ability to reduce MR while entering torpor. Using published data for 96 mammal species, we tested the hypothesis that, among heterothermic mammals, the processes leading to the evolution of higher BMR limit the ability to downregulate metabolism during torpor. We found that body mass (mb)-adjusted BMR was positively correlated with mb- and Tb-adjusted TMRmin, in a phylogenetically corrected analysis. Phylogenetic path modeling indicated that the mechanisms underlying the evolutionary increase of BMR in endotherms most likely constrain their ability to reduce MR during torpor. Given that heterothermy is considered an ancestral state in mammals, these results suggest an increase in BMR during the evolution of endothermy in homeothermic animals, which leads to the loss of their ability to enter torpor.},
}

@article {pmid30139961,
year = {2018},
author = {Liu, J and Kim, SY and Shin, S and Jung, SH and Yim, SH and Lee, JY and Lee, SH and Chung, YJ},
title = {Overexpression of TFF3 is involved in prostate carcinogenesis via blocking mitochondria-mediated apoptosis.},
journal = {Experimental & molecular medicine},
volume = {50},
number = {8},
pages = {110},
doi = {10.1038/s12276-018-0137-7},
pmid = {30139961},
issn = {2092-6413},
support = {2012R1A5A2047939//National Research Foundation of Korea (NRF)/ ; 2012R1A1A3002027//National Research Foundation of Korea (NRF)/ ; },
abstract = {The overexpression of trefoil factor family 3 (TFF3) is observed in a variety of cancers, including prostate cancer (PCa), and its potential role in carcinogenesis, such as activating the PI3K/AKT pathway, is suggested. However, its role and its related mechanisms in prostate tumorigenesis remain unknown. To elucidate the role of TFF3 overexpression in PCa, we silenced TFF3 in two PCa cell lines that overexpressed TFF3 and explored the molecular mechanism behind its antiapoptotic role. We also examined TFF3 expression in 108 Korean PCa specimens and 106 normal prostate tissues by immunohistochemistry (IHC) analysis. The mean TFF3 IHC score in the tumor tissues was significantly higher than that in the normal tissues (4.702 vs. 0.311, P = 2.52 × 10-24). TFF3-silenced cells showed suppressed tumor cell growth and migration. TFF3 silencing decreased BCL2 and increased BAX expression. The translocation of BAX to the mitochondria was also confirmed. After TFF3 silencing, the expression of the mitochondrial proapoptotic proteins, cytochrome C and Smac/DIABLO, was elevated, and these proteins were released from the mitochondria to the cytosol. Downstream mediators of mitochondrial apoptosis, including cleaved caspase-3, caspase-9, and PARP, were also elevated. Accordingly, the proportion of apoptotic cells was significantly higher among TFF3-silenced cells. There was no difference in extrinsic apoptosis-related molecules after TFF3 silencing. All the results support that TFF3 silencing induces the downstream signaling pathway of mitochondria-mediated apoptosis. This study provides a better understanding of the mechanism of prostate tumorigenesis, suggesting TFF3 as a potential biomarker and therapeutic target of PCa.},
}

@article {pmid29950419,
year = {2018},
author = {Bilz, NC and Jahn, K and Lorenz, M and Lüdtke, A and Hübschen, JM and Geyer, H and Mankertz, A and Hübner, D and Liebert, UG and Claus, C},
title = {Rubella Viruses Shift Cellular Bioenergetics to a More Oxidative and Glycolytic Phenotype with a Strain-Specific Requirement for Glutamine.},
journal = {Journal of virology},
volume = {92},
number = {17},
pages = {},
doi = {10.1128/JVI.00934-18},
pmid = {29950419},
issn = {1098-5514},
mesh = {A549 Cells ; Endothelial Cells/metabolism/virology ; *Energy Metabolism ; Glucose/metabolism/pharmacology ; Glutamine/*metabolism/pharmacology ; Glycolysis/*drug effects ; Homeostasis ; Humans ; Kynurenine/metabolism ; Metabolic Networks and Pathways/drug effects ; Mitochondria/metabolism ; Nucleotides/biosynthesis ; Oxidation-Reduction ; Oxidative Stress ; Oxygen Consumption/drug effects/*physiology ; Phenotype ; Pyruvic Acid/metabolism/pharmacology ; Rubella virus/*metabolism ; Virus Replication/drug effects ; },
abstract = {The flexible regulation of cellular metabolic pathways enables cellular adaptation to changes in energy demand under conditions of stress such as posed by a virus infection. To analyze such an impact on cellular metabolism, rubella virus (RV) was used in this study. RV replication under selected substrate supplementation with glucose, pyruvate, and glutamine as essential nutrients for mammalian cells revealed its requirement for glutamine. The assessment of the mitochondrial respiratory (based on the oxygen consumption rate) and glycolytic (based on the extracellular acidification rate) rate and capacity by respective stress tests through Seahorse technology enabled determination of the bioenergetic phenotype of RV-infected cells. Irrespective of the cellular metabolic background, RV infection induced a shift of the bioenergetic state of epithelial cells (Vero and A549) and human umbilical vein endothelial cells to a higher oxidative and glycolytic level. Interestingly there was a RV strain-specific, but genotype-independent demand for glutamine to induce a significant increase in metabolic activity. While glutaminolysis appeared to be rather negligible for RV replication, glutamine could serve as donor of its amide nitrogen in biosynthesis pathways for important metabolites. This study suggests that the capacity of RVs to induce metabolic alterations could evolve differently during natural infection. Thus, changes in cellular bioenergetics represent an important component of virus-host interactions and could complement our understanding of the viral preference for a distinct host cell population.IMPORTANCE RV pathologies, especially during embryonal development, could be connected with its impact on mitochondrial metabolism. With bioenergetic phenotyping we pursued a rather novel approach in virology. For the first time it was shown that a virus infection could shift the bioenergetics of its infected host cell to a higher energetic state. Notably, the capacity to induce such alterations varied among different RV isolates. Thus, our data add viral adaptation of cellular metabolic activity to its specific needs as a novel aspect to virus-host evolution. In addition, this study emphasizes the implementation of different viral strains in the study of virus-host interactions and the use of bioenergetic phenotyping of infected cells as a biomarker for virus-induced pathological alterations.},
}

A549 Cells
Endothelial Cells/metabolism/virology
*Energy Metabolism
Glucose/metabolism/pharmacology
Glutamine/*metabolism/pharmacology
Glycolysis/*drug effects
Homeostasis
Humans
Kynurenine/metabolism
Metabolic Networks and Pathways/drug effects
Mitochondria/metabolism
Nucleotides/biosynthesis
Oxidation-Reduction
Oxidative Stress
Oxygen Consumption/drug effects/*physiology
Phenotype
Pyruvic Acid/metabolism/pharmacology
Rubella virus/*metabolism
Virus Replication/drug effects

@article {pmid27876802,
year = {2016},
author = {Mottawea, W and Chiang, CK and Mühlbauer, M and Starr, AE and Butcher, J and Abujamel, T and Deeke, SA and Brandel, A and Zhou, H and Shokralla, S and Hajibabaei, M and Singleton, R and Benchimol, EI and Jobin, C and Mack, DR and Figeys, D and Stintzi, A},
title = {Altered intestinal microbiota-host mitochondria crosstalk in new onset Crohn's disease.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {13419},
doi = {10.1038/ncomms13419},
pmid = {27876802},
issn = {2041-1723},
support = {R01 DK073338/DK/NIDDK NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; R01 DK047700/DK/NIDDK NIH HHS/United States ; R21 CA195226/CA/NCI NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; },
mesh = {Adolescent ; Animals ; Bacteria/classification/*genetics/isolation & purification ; Child ; Child, Preschool ; Crohn Disease/*microbiology ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Interleukin-10/genetics/metabolism ; Male ; Mice ; Mice, Knockout ; Phylogeny ; },
abstract = {Intestinal microbial dysbiosis is associated with Crohn's disease (CD). However, the mechanisms leading to the chronic mucosal inflammation that characterizes this disease remain unclear. In this report, we use systems-level approaches to study the interactions between the gut microbiota and host in new-onset paediatric patients to evaluate causality and mechanisms of disease. We report an altered host proteome in CD patients indicative of impaired mitochondrial functions. In particular, mitochondrial proteins implicated in H2S detoxification are downregulated, while the relative abundance of H2S microbial producers is increased. Network correlation analysis reveals that Atopobium parvulum controls the central hub of H2S producers. A. parvulum induces pancolitis in colitis-susceptible interleukin-10-deficient mice and this phenotype requires the presence of the intestinal microbiota. Administrating the H2S scavenger bismuth mitigates A. parvulum-induced colitis in vivo. This study reveals that host-microbiota interactions are disturbed in CD and thus provides mechanistic insights into CD pathogenesis.},
}

Adolescent
Animals
Bacteria/classification/*genetics/isolation & purification
Child
Child, Preschool
Crohn Disease/*microbiology
Female
*Gastrointestinal Microbiome
Germ-Free Life
Humans
Interleukin-10/genetics/metabolism
Male
Mice
Mice, Knockout
Phylogeny

@article {pmid30137656,
year = {2018},
author = {Kagda, M and Vu, AL and Ah-Fong, AMV and Judelson, HS},
title = {Phosphagen kinase function in flagellated spores of the oomycete Phytophthora infestans integrates transcriptional regulation, metabolic dynamics, and protein retargeting.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.14108},
pmid = {30137656},
issn = {1365-2958},
abstract = {Flagellated spores play important roles in the infection of plants and animals by many eukaryotic microbes. The oomycete Phytophthora infestans, which causes potato blight, expresses two phosphagen kinases (PKs). These enzymes store energy in taurocyamine, and are hypothesized to resolve spatial and temporal imbalances between rates of ATP creation and use in zoospores. A dimeric PK is found at low levels in vegetative mycelia, but high levels in ungerminated sporangia and zoospores. In contrast, a monomeric PK protein is at similar levels in all tissues, although is transcribed primarily in mycelia. Subcellular localization studies indicate that the monomeric PK is mitochondrial. In contrast, the dimeric PK is cytoplasmic in mycelia and sporangia but is retargeted to flagellar axonemes during zoosporogenesis. This supports a model in which PKs shuttle energy from mitochondria to and through flagella. Metabolite analysis indicates that deployment of the flagellar PK is coordinated with a large increase in taurocyamine, synthesized by sporulation-induced enzymes that were lost during the evolution of zoospore-lacking oomycetes. Thus, PK function is enabled by coordination of the transcriptional, metabolic, and protein targeting machinery during the life cycle. Since plants lack PKs, the enzymes may be useful targets for inhibitors of oomycete plant pathogens. This article is protected by copyright. All rights reserved.},
}

@article {pmid29247559,
year = {2018},
author = {Lee, K and Lee, HY and Back, K},
title = {Rice histone deacetylase 10 and Arabidopsis histone deacetylase 14 genes encode N-acetylserotonin deacetylase, which catalyzes conversion of N-acetylserotonin into serotonin, a reverse reaction for melatonin biosynthesis in plants.},
journal = {Journal of pineal research},
volume = {64},
number = {2},
pages = {},
doi = {10.1111/jpi.12460},
pmid = {29247559},
issn = {1600-079X},
mesh = {Arabidopsis/*metabolism ; Arylalkylamine N-Acetyltransferase/metabolism ; Histone Deacetylases/*metabolism ; Melatonin/*biosynthesis ; Oryza/*metabolism ; Phylogeny ; Plant Proteins/*metabolism ; Serotonin/analogs & derivatives/metabolism ; },
abstract = {In plants, melatonin production is strictly regulated, unlike the production of its precursor, serotonin, which is highly inducible in response to stimuli, such as senescence and pathogen exposure. Exogenous serotonin treatment does not greatly induce the production of N-acetylserotonin (NAS) and melatonin in plants, which suggests the possible existence of one or more regulatory genes in the pathway for the biosynthesis of melatonin from serotonin. In this report, we found that NAS was rapidly and abundantly converted into serotonin in rice seedlings, indicating the presence of an N-acetylserotonin deacetylase (ASDAC). To clone the putative ASDAC gene, we screened 4 genes that were known as histone deacetylase (HDAC) genes, but encoded proteins targeted into chloroplasts or mitochondria rather than nuclei. Of 4 recombinant Escherichia coli strains expressing these genes, one E. coli strain expressing the rice HDAC10 gene was found to be capable of producing serotonin in response to treatment with NAS. The recombinant purified rice HDAC10 (OsHDAC10) protein exhibited ASDAC enzyme activity toward NAS, N-acetyltyramine (NAT), N-acetyltryptamine, and melatonin, with the highest ASDAC activity for NAT. In addition, its Arabidopsis ortholog, AtHDAC14, showed similar ASDAC activity to that of OsHDAC10. Both OsHDAC10 and AtHDAC14 were found to be expressed in chloroplasts. Phylogenetic analysis indicated that ASDAC homologs were present in archaea, but not in cyanobacteria, which differs from the distribution of serotonin N-acetyltransferase (SNAT). This suggests that SNAT and ASDAC may have evolved differently from ancestral eukaryotic cells.},
}

Arabidopsis/*metabolism
Arylalkylamine N-Acetyltransferase/metabolism
Histone Deacetylases/*metabolism
Melatonin/*biosynthesis
Oryza/*metabolism
Phylogeny
Plant Proteins/*metabolism
Serotonin/analogs & derivatives/metabolism

@article {pmid30127539,
year = {2018},
author = {Betts, HC and Puttick, MN and Clark, JW and Williams, TA and Donoghue, PCJ and Pisani, D},
title = {Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-018-0644-x},
pmid = {30127539},
issn = {2397-334X},
abstract = {Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth's history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053-1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.},
}

@article {pmid29433421,
year = {2018},
author = {Li, Q and Dong, K and Xu, L and Jia, X and Wu, J and Sun, W and Zhang, X and Fu, S},
title = {The distribution of three candidate cold-resistant SNPs in six minorities in North China.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {134},
doi = {10.1186/s12864-018-4524-1},
pmid = {29433421},
issn = {1471-2164},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Adaptation, Physiological/*genetics ; Asian Continental Ancestry Group/genetics ; Carnitine O-Palmitoyltransferase/genetics ; China ; *Cold Temperature ; Ethnic Groups/classification/*genetics ; Fatty Acid Desaturases/genetics ; Gene Frequency ; Genotype ; Humans ; Linkage Disequilibrium ; Phylogeny ; *Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Heilongjiang Province located in northeast China is a multi-ethnic region with people who have lived in cold conditions for several generations. Fatty acids are important to people with cold resistance. CPT1A encodes a protein that imports long-chain fatty acids into the mitochondria for fatty-acid oxidation. FADS is an essential enzyme for the synthesis of long-chain polyunsaturated fatty acids.

RESULTS: In the present study, we investigated the distributions of three cold resistance-related SNPs (rs80356779 G > A in CPT1A, rs7115739 T > G in FADS3 and rs174570 C > T in FADS2) from six populations that included 1093 individuals who have lived in Heilongjiang Province for at least three generations. The frequencies of rs174570 and rs7115739 were different in our six north minorities compared to the Chinese Dai in Xishuangbanna (CDX) in southern China. All the SNPs in Hezhen were significantly different from other five studied populations. In addition, the genetic distribution of rs174570 in Daur was significantly different from Manchu and Korea, and the frequency of rs7115739 in Ewenki was significantly different from the other populations. The results also showed that the frequencies of the three SNPs in the six minorities were different from those of Greenlandic Inuit and Siberian population.

CONCLUSIONS: Our results showed the distributions of the three cold resistance-related SNPs from six populations that included 1093 individuals in northern China. Distributions of the allele frequencies for the cold resistance-related SNPs in northern China were statistically different from those in southern China. These data help to establish the DNA genome database for the six populations and fully preserve existing minority genetic information.},
}

Adaptation, Physiological/*genetics
Asian Continental Ancestry Group/genetics
Carnitine O-Palmitoyltransferase/genetics
China
*Cold Temperature
Ethnic Groups/classification/*genetics
Fatty Acid Desaturases/genetics
Gene Frequency
Genotype
Humans
Linkage Disequilibrium
Phylogeny
*Polymorphism, Single Nucleotide

@article {pmid30121730,
year = {2018},
author = {Radzinski, M and Reichmann, D},
title = {Variety is the spice of life: how to explore a redox-dependent heterogeneity in genomically identical cellular populations.},
journal = {Current genetics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00294-018-0878-9},
pmid = {30121730},
issn = {1432-0983},
support = {1765/13//Israel Science Foundation/ ; 1649/16//legacy Heritage Biomedical Science Partnership/ ; CDA00064/2014//Human Frontier Science Program/ ; 2015056//United States - Israel Binational Science Foundation/ ; },
abstract = {Cellular heterogeneity is a widespread phenomenon, existing across organisms and serving a crucial role in evolution and cell survival. Genetically identical cells may as a result present in a variety of forms with different gene and protein expressions, as well as oxidation level. As a result, a wide range of methodologies and techniques for dissecting different types of genetic, proteomic, and phenotypic heterogeneous traits have emerged in recent years in an effort to better understand how diversity exists within a single population and its effects therein. A key area of interest seeks to establish the ways in which cellular heterogeneity and aging processes interact with each other. Here, we discuss recent developments in defining cellular heterogeneity, specifically focusing on redox-dependent heterogeneity, its characterization, quantification, and behavior. We further expand on potential applications of a cell sorting-based methodology for distinguishing between cells harboring different redox statuses. As an example, we use organelle-specific fluorescence protein-based probes to examine the crosstalk between cytosol and mitochondria in a yeast strain lacking glutathione reductase. Together, these may have wide-reaching implications for future research into redox-associated factors, as well as mechanisms of redox-dependent heterogeneity and its influence on organelles and the cell at large.},
}

@article {pmid29294404,
year = {2018},
author = {Qu, M and Tang, W and Liu, Q and Wang, D and Ding, S},
title = {Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker.},
journal = {Molecular phylogenetics and evolution},
volume = {121},
number = {},
pages = {46-51},
doi = {10.1016/j.ympev.2017.12.031},
pmid = {29294404},
issn = {1095-9513},
mesh = {Animals ; Biomarkers/*metabolism ; Cell Nucleus/genetics ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; *Genetic Variation ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Oceans and Seas ; Phylogeny ; Ryanodine Receptor Calcium Release Channel/*genetics ; Species Specificity ; },
abstract = {Groupers (family Epinephelidae) are an assemblage of coral reef fishes comprising more than 160 species in 16 genera, many of which are both environmentally and economically valuable. Because of their similar morphology, variable color patterns, and tendency for interspecies hybridization, morphological identification of groupers usually leads to taxonomic confusion. To find an effective method for identifying different grouper species and hybrids, evaluate genetic diversity and uncover any synonymous or cryptic species, we sampled a total of 221 specimens representing 57 species in 9 genera in the China Seas. Both mitochondrial (mt) cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) were found to be effective barcoding genes. We also developed an efficient protocol for identifying hybrid groupers using mt markers and the nuclear RYR3 gene and found the first record of wide interspecies hybridization in genus Epinephelus. This barcoding study revealed high genetic divergence in many widespread species and possible synonyms. In addition to providing a molecular method for identifying grouper species, this study offers important resources for the further study of grouper conservation genetics, speciation, hybridization and other evolutionary traits.},
}

Animals
Biomarkers/*metabolism
Cell Nucleus/genetics
China
DNA Barcoding, Taxonomic/*methods
Electron Transport Complex IV/genetics
Fishes/*genetics
*Genetic Variation
Geography
*Hybridization, Genetic
Mitochondria/genetics
Oceans and Seas
Phylogeny
Ryanodine Receptor Calcium Release Channel/*genetics
Species Specificity

@article {pmid30110634,
year = {2018},
author = {Vazquez, JM and Sulak, M and Chigurupati, S and Lynch, VJ},
title = {A Zombie LIF Gene in Elephants Is Upregulated by TP53 to Induce Apoptosis in Response to DNA Damage.},
journal = {Cell reports},
volume = {24},
number = {7},
pages = {1765-1776},
doi = {10.1016/j.celrep.2018.07.042},
pmid = {30110634},
issn = {2211-1247},
abstract = {Large-bodied organisms have more cells that can potentially turn cancerous than small-bodied organisms, imposing an increased risk of developing cancer. This expectation predicts a positive correlation between body size and cancer risk; however, there is no correlation between body size and cancer risk across species ("Peto's paradox"). Here, we show that elephants and their extinct relatives (proboscideans) may have resolved Peto's paradox in part through refunctionalizing a leukemia inhibitory factor pseudogene (LIF6) with pro-apoptotic functions. LIF6 is transcriptionally upregulated by TP53 in response to DNA damage and translocates to the mitochondria where it induces apoptosis. Phylogenetic analyses of living and extinct proboscidean LIF6 genes indicates that its TP53 response element evolved coincident with the evolution of large body sizes in the proboscidean stem lineage. These results suggest that refunctionalizing of a pro-apoptotic LIF pseudogene may have been permissive (although not sufficient) for the evolution of large body sizes in proboscideans.},
}

@article {pmid30109028,
year = {2018},
author = {Wideman, JG and Balacco, DL and Fieblinger, T and Richards, TA},
title = {PDZD8 is not the 'functional ortholog' of Mmm1, it is a paralog.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {1088},
doi = {10.12688/f1000research.15523.1},
pmid = {30109028},
issn = {2046-1402},
abstract = {Authors of a recent paper demonstrate that, like ERMES (ER-mitochondria encounter structure) in fungal cells, PDZD8 (PDZ domain containing 8) tethers mitochondria to the ER in mammalian cells. However, identifying PDZD8 as a "functional ortholog" of yeast Mmm1 (maintenance of mitochondrial morphology protein 1) is at odds with the phylogenetic data. PDZD8 and Mmm1 are paralogs, not orthologs, which affects the interpretation of the data with respect to the evolution of ER-mitochondria tethering. Our phylogenetic analyses show that PDZD8 co-occurs with ERMES components in lineages closely related to animals solidifying its identity as a paralog of Mmm1. Additionally, we identify two related paralogs, one specific to flagellated fungi, and one present only in unicellular relatives of animals. These results point to a complex evolutionary history of ER-mitochondria tethering involving multiple gene gains and losses in the lineage leading to animals and fungi.},
}

@article {pmid30107780,
year = {2018},
author = {Dong, S and Zhao, C and Chen, F and Liu, Y and Zhang, S and Wu, H and Zhang, L and Liu, Y},
title = {The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {614},
doi = {10.1186/s12864-018-4991-4},
pmid = {30107780},
issn = {1471-2164},
support = {31470314//National Natural Science Foundation of China/ ; 31600171//National Natural Science Foundation of China/ ; FLSF2017-03//National Natural Science Foundation of China/ ; 201520//Shenzhen Urban Management Bureau Fund/ ; DEB-1240045//National Science Foundation/ ; JCYJ20150529150409546//Shenzhen Municipal Government of China/ ; },
abstract = {BACKGROUND: Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms.

RESULTS: Assembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195 bp with an average depth of 601×. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome.

CONCLUSIONS: The Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.},
}

@article {pmid29976842,
year = {2018},
author = {He, K and Chen, X and Chen, P and He, SW and Cheng, F and Jiang, XL and Campbell, K},
title = {A new genus of Asiatic short-tailed shrew (Soricidae, Eulipotyphla) based on molecular and morphological comparisons.},
journal = {Zoological research},
volume = {39},
number = {5},
pages = {321-334},
doi = {10.24272/j.issn.2095-8137.2018.058},
pmid = {29976842},
issn = {2095-8137},
mesh = {Animals ; Biological Evolution ; China ; Mitochondria/genetics ; North America ; Sequence Analysis, DNA ; Shrews/*anatomy & histology/classification/genetics ; Skull/anatomy & histology ; },
abstract = {Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiatic short-tailed shrew genus Blarinella currently persist (mostly in southwestern China and adjacent areas). Only three forms of Blarinella have been recognized as either species or subspecies. However, recent molecular studies indicated a strikingly deep divergence within the genus, implying the existence of a distinct genus-level lineage. We sequenced the complete mitochondrial genomes and one nuclear gene of three Asiatic short-tailed and two North American shrews and analyzed them morphometrically and morphologically. Our molecular analyses revealed that specimens ascribed to B. griselda formed two deeply diverged lineages, one a close relative to B. quadraticauda, whereas the other - comprised of topotype specimens from southern Gansu - diverged from other Blarinella in the middle Miocene (ca. 18.2 million years ago (Ma), 95% confidence interval=13.4-23.6 Ma). Although the skulls were similarly shaped in both lineages, we observed several diagnostic characteristics, including the shape of the upper P4. In consideration of the molecular and morphological evidence, we recognize B. griselda as the sole species of a new genus, namely, Pantherina gen. nov. Interestingly, some characteristics of Pantherina griselda are more similar to fossil genera, suggesting it represents an evolutionarily more primitive form than Blarinella. Recognition of this new genus sheds light on the systematics and evolutionary history of the tribe Blarinellini throughout Eurasia and North America.},
}

Animals
Biological Evolution
China
Mitochondria/genetics
North America
Sequence Analysis, DNA
Shrews/*anatomy & histology/classification/genetics
Skull/anatomy & histology

@article {pmid29955026,
year = {2018},
author = {Liu, SY and He, K and Chen, SD and Jin, W and Murphy, RW and Tang, MK and Liao, R and Li, FJ},
title = {How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses.},
journal = {Zoological research},
volume = {39},
number = {5},
pages = {309-320},
doi = {10.24272/j.issn.2095-8137.2018.053},
pmid = {29955026},
issn = {2095-8137},
mesh = {Animals ; China ; Cytochromes b/*genetics ; Mitochondria/*genetics ; Murinae/anatomy & histology/*genetics ; Phylogeny ; Rats/anatomy & histology/*genetics ; Skull/anatomy & histology ; Surveys and Questionnaires ; Tooth/anatomy & histology ; },
abstract = {Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.},
}

Animals
China
Cytochromes b/*genetics
Mitochondria/*genetics
Murinae/anatomy & histology/*genetics
Phylogeny
Rats/anatomy & histology/*genetics
Skull/anatomy & histology
Surveys and Questionnaires
Tooth/anatomy & histology

@article {pmid29897900,
year = {2018},
author = {Chadha, S and Vijayan, R and Gupta, S and Munde, M and Gourinath, S and Madhubala, R},
title = {Genetic manipulation of Leishmania donovani threonyl tRNA synthetase facilitates its exploration as a potential therapeutic target.},
journal = {PLoS neglected tropical diseases},
volume = {12},
number = {6},
pages = {e0006575},
doi = {10.1371/journal.pntd.0006575},
pmid = {29897900},
issn = {1935-2735},
mesh = {Drug Delivery Systems ; Escherichia coli/enzymology/genetics ; Fatty Alcohols/pharmacology ; Gene Expression ; Humans ; Leishmania donovani/drug effects/*enzymology/genetics/pathogenicity ; Leishmaniasis, Visceral/*parasitology ; Organisms, Genetically Modified ; Phylogeny ; Protein Domains ; Protein Transport ; Protozoan Proteins/antagonists & inhibitors/genetics/isolation & purification/metabolism ; Recombinant Proteins ; Sequence Deletion ; Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/isolation & purification/metabolism ; },
abstract = {BACKGROUND: Aminoacyl tRNA synthetases are central enzymes required for protein synthesis. These enzymes are the known drug targets in bacteria and fungi. Here, we for the first time report the functional characterization of threonyl tRNA synthetase (LdThrRS) of Leishmania donovani, a protozoan parasite, the primary causative agent of visceral leishmaniasis.

METHODOLOGY: Recombinant LdThrRS (rLdThrRS) was expressed in E. coli and purified. The kinetic parameters for rLdThrRS were determined. The subcellular localization of LdThrRS was done by immunofluorescence analysis. Heterozygous mutants of LdThrRS were generated in Leishmania promastigotes. These genetically manipulated parasites were checked for their proliferation, virulence, aminoacylation activity and sensitivity to the known ThrRS inhibitor, borrelidin. An in silico generated structural model of L. donovani ThrRS was compared to that of human.

CONCLUSIONS: Recombinant LdThrRS displayed aminoacylation activity, and the protein is possibly localized to both the cytosol and mitochondria. The comparison of the 3D-model of LdThrRS to human ThrRS displayed considerable similarity. Heterozygous parasites showed restrictive growth phenotype and had attenuated infectivity. These heterozygous parasites were more susceptible to inhibition by borrelidin. Several attempts to obtain ThrRS homozygous null mutants were not successful, indicating its essentiality for the Leishmania parasite. Borrelidin showed a strong affinity for LdThrRS (KD: 0.04 μM) and was effective in inhibiting the aminoacylation activity of the rLdThrRS (IC50: 0.06 μM). Borrelidin inhibited the promastigotes (IC50: 21 μM) stage of parasites. Our data shows that LdThrRS is essential for L. donovani survival and is likely to bind with small drug-like molecules with strong affinity, thus making it a potential target for drug discovery efforts.},
}

Drug Delivery Systems
Escherichia coli/enzymology/genetics
Fatty Alcohols/pharmacology
Gene Expression
Humans
Leishmania donovani/drug effects/*enzymology/genetics/pathogenicity
Leishmaniasis, Visceral/*parasitology
Organisms, Genetically Modified
Phylogeny
Protein Domains
Protein Transport
Protozoan Proteins/antagonists & inhibitors/genetics/isolation & purification/metabolism
Recombinant Proteins
Sequence Deletion
Threonine-tRNA Ligase/antagonists & inhibitors/*genetics/isolation & purification/metabolism

@article {pmid29724860,
year = {2018},
author = {Garg, SG and Martin, WF},
title = {Asking endosymbionts to do an enzyme's job.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {20},
pages = {E4543-E4544},
doi = {10.1073/pnas.1804397115},
pmid = {29724860},
issn = {1091-6490},
mesh = {*Biological Evolution ; Enzymes/*metabolism ; Mitochondria ; *Symbiosis ; },
}

*Biological Evolution
Enzymes/*metabolism
Mitochondria
*Symbiosis

@article {pmid29718949,
year = {2018},
author = {Lv, C and Li, Q and Kong, L},
title = {Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae.},
journal = {PloS one},
volume = {13},
number = {5},
pages = {e0196466},
doi = {10.1371/journal.pone.0196466},
pmid = {29718949},
issn = {1932-6203},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Bayes Theorem ; Bivalvia/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.},
}

Animals
Base Composition/genetics
Base Sequence/genetics
Bayes Theorem
Bivalvia/*genetics
Genome, Mitochondrial/*genetics
Mitochondria/*genetics
Phylogeny
RNA, Ribosomal/genetics
RNA, Transfer/genetics
Sequence Analysis, DNA

@article {pmid29616678,
year = {2018},
author = {Nie, WH and Wang, JH and Su, WT and Hu, Y and He, SW and Jiang, XL and He, K},
title = {Species identification of crested gibbons (Nomascus) in captivity in China using karyotyping- and PCR-based approaches.},
journal = {Zoological research},
volume = {39},
number = {5},
pages = {356-363},
doi = {10.24272/j.issn.2095-8137.2018.036},
pmid = {29616678},
issn = {2095-8137},
mesh = {Animals ; Animals, Zoo ; Cell Nucleus/genetics ; China ; Endangered Species ; Genes/genetics ; Hylobates/classification/*genetics ; In Situ Hybridization, Fluorescence ; Karyotype ; Karyotyping ; Mitochondria/genetics ; Polymerase Chain Reaction ; },
abstract = {Gibbons and siamangs (Hylobatidae) are well-known for their rapid chromosomal evolution, which has resulted in high speciation rate within the family. On the other hand, distinct karyotypes do not prevent speciation, allowing interbreeding between individuals in captivity, and the unwanted hybrids are ethically problematic as all gibbon species are endangered or critically endangered. Thus, accurate species identification is crucial for captive breeding, particularly in China where studbooks are unavailable. Identification based on external morphology is difficult, especially for hybrids, because species are usually similar in appearance. In this study, we employed G-banding karyotyping and fluorescence in situ hybridization (FISH) as well as a PCR-based approach to examine karyotypic characteristics and identify crested gibbons of the genus Nomascus from zoos and nature reserves in China. We characterized and identified five karyotypes from 21 individuals of Nomascus. Using karyotypes and mitochondrial and nuclear genes, we identified three purebred species and three hybrids, including one F2 hybrid between N. gabriellae and N. siki. Our results also supported that N. leucogenys and N. siki shared the same inversion on chromosome 7, which resolves arguments from previous studies. Our results demonstrated that both karyotyping and DNA-based approaches were suitable for identifying purebred species, though neither was ideal for hybrid identification. The advantages and disadvantages of both approaches are discussed. Our results further highlight the importance of animal ethics and welfare, which are critical for endangered species in captivity.},
}

Animals
Animals, Zoo
Cell Nucleus/genetics
China
Endangered Species
Genes/genetics
Hylobates/classification/*genetics
In Situ Hybridization, Fluorescence
Karyotype
Karyotyping
Mitochondria/genetics
Polymerase Chain Reaction

@article {pmid29551757,
year = {2018},
author = {McLean, BS and Nyamsuren, B and Tchabovsky, A and Cook, JA},
title = {Impacts of late Quaternary environmental change on the long-tailed ground squirrel (Urocitellus undulatus) in Mongolia.},
journal = {Zoological research},
volume = {39},
number = {5},
pages = {364-372},
doi = {10.24272/j.issn.2095-8137.2018.042},
pmid = {29551757},
issn = {2095-8137},
mesh = {Animals ; Climate Change ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Environment ; Genotyping Techniques ; Mitochondria/genetics ; Mongolia ; Phylogeny ; Phylogeography ; Sciuridae/classification/*genetics ; },
abstract = {Impacts of Quaternary environmental changes on mammal faunas of central Asia remain poorly understood due to a lack of geographically comprehensive phylogeographic sampling for most species. To help address this knowledge gap, we conducted the most extensive molecular analysis to date of the long-tailed ground squirrel (Urocitellus undulatus Pallas 1778) in Mongolia, a country that comprises the southern core of this species' range. Drawing on material from recent collaborative field expeditions, we genotyped 128 individuals at 2 mitochondrial genes (cytochrome b and cytochrome oxidase I; 1 797 bp total). Phylogenetic inference supports the existence of two deeply divergent infraspecific lineages (corresponding to subspecies U. u. undulatus and U. u. eversmanni), a result in agreement with previous molecular investigations but discordant with patterns of range-wide craniometric and external phenotypic variation. In the widespread westerneversmanni lineage, we recovered geographically-associated clades from the: (a) Khangai, (b) Mongolian Altai, and (c) Govi Altai mountain ranges. Phylogeographic structure in U. u. eversmanni is consistent with an isolation-by-distance model; however, genetic distances are significantly lower than among subspecies, and intra-clade relationships are largely unresolved. The latter patterns, as well as the relatively higher nucleotide polymorphism of populations from the Great Lakes Depression of northwestern Mongolia, suggest a history of range shifts into these lowland areas in response to Pleistocene glaciation and environmental change, followed by upslope movements and mitochondrial lineage sorting with Holocene aridification. Our study illuminates possible historical mechanisms responsible for U. undulatus genetic structure and contributes to a framework for ongoing exploration of mammalian response to past and present climate change in central Asia.},
}

Animals
Climate Change
Cytochromes b/genetics
Electron Transport Complex IV/genetics
Environment
Genotyping Techniques
Mitochondria/genetics
Mongolia
Phylogeny
Phylogeography
Sciuridae/classification/*genetics

@article {pmid29191733,
year = {2018},
author = {Chatterjee, K and Nostramo, RT and Wan, Y and Hopper, AK},
title = {tRNA dynamics between the nucleus, cytoplasm and mitochondrial surface: Location, location, location.},
journal = {Biochimica et biophysica acta},
volume = {1861},
number = {4},
pages = {373-386},
doi = {10.1016/j.bbagrm.2017.11.007},
pmid = {29191733},
issn = {0006-3002},
support = {R01 GM027930/GM/NIGMS NIH HHS/United States ; R01 GM122884/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Biological Transport ; Cell Nucleus/*metabolism ; Cytoplasm/*metabolism ; Endoribonucleases/metabolism ; Evolution, Molecular ; Fungal Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondrial Membranes/*metabolism ; Nuclear Pore Complex Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/*metabolism ; Plant Proteins/metabolism ; RNA Precursors/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Transfer/*metabolism ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription, Genetic ; Vertebrates/metabolism ; Yeasts/metabolism ; },
abstract = {Although tRNAs participate in the essential function of protein translation in the cytoplasm, tRNA transcription and numerous processing steps occur in the nucleus. This subcellular separation between tRNA biogenesis and function requires that tRNAs be efficiently delivered to the cytoplasm in a step termed "primary tRNA nuclear export". Surprisingly, tRNA nuclear-cytoplasmic traffic is not unidirectional, but, rather, movement is bidirectional. Cytoplasmic tRNAs are imported back to the nucleus by the "tRNA retrograde nuclear import" step which is conserved from budding yeast to vertebrate cells and has been hijacked by viruses, such as HIV, for nuclear import of the viral reverse transcription complex in human cells. Under appropriate environmental conditions cytoplasmic tRNAs that have been imported into the nucleus return to the cytoplasm via the 3rd nuclear-cytoplasmic shuttling step termed "tRNA nuclear re-export", that again is conserved from budding yeast to vertebrate cells. We describe the 3 steps of tRNA nuclear-cytoplasmic movements and their regulation. There are multiple tRNA nuclear export and import pathways. The different tRNA nuclear exporters appear to possess substrate specificity leading to the tantalizing possibility that the cellular proteome may be regulated at the level of tRNA nuclear export. Moreover, in some organisms, such as budding yeast, the pre-tRNA splicing heterotetrameric endonuclease (SEN), which removes introns from pre-tRNAs, resides on the cytoplasmic surface of the mitochondria. Therefore, we also describe the localization of the SEN complex to mitochondria and splicing of pre-tRNA on mitochondria, which occurs prior to the participation of tRNAs in protein translation. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.},
}

Animals
Biological Transport
Cell Nucleus/*metabolism
Cytoplasm/*metabolism
Endoribonucleases/metabolism
Evolution, Molecular
Fungal Proteins/metabolism
HSP70 Heat-Shock Proteins/metabolism
Mitochondrial Membranes/*metabolism
Nuclear Pore Complex Proteins/metabolism
Nucleocytoplasmic Transport Proteins/*metabolism
Plant Proteins/metabolism
RNA Precursors/metabolism
RNA Processing, Post-Transcriptional
RNA, Transfer/*metabolism
RNA-Binding Proteins/metabolism
Saccharomyces cerevisiae Proteins/metabolism
Transcription, Genetic
Vertebrates/metabolism
Yeasts/metabolism

@article {pmid29770661,
year = {2018},
author = {Cang-Lin, Z and Jia, P and Zhen, R and Jin-Rong, Z and Ya-Ming, Y},
title = {[Genotyping and polymorphism analysis of cytochrome c oxidase subunit Ⅰ gene of Pomacea canaliculata from Lincang City in Yunnan Province].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {30},
number = {2},
pages = {179-183},
pmid = {29770661},
issn = {1005-6661},
mesh = {Angiostrongylus cantonensis ; Animals ; China ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Gastropoda/enzymology/*genetics ; Genotype ; Haplotypes ; Phylogeny ; },
abstract = {OBJECTIVE: To analyze the genetic diversity of Pomacea canaliculata based on the mitochondria DNA cytochrome c oxidase subunit Ⅰ (mtDNA COⅠ) gene as a molecular marker in Lincang City of Yunnan Province, so as to provide the scientific data for monitoring Angiostrongylus cantonensis in local areas.

METHODS: The genotypes and polymorphisms of 38 specimens of P. canaliculata collected from Mengding Town of Lincang City were analyzed by sequencing COⅠ gene. The phylogenetic tree and genetic distances were produced based on the haplotypes from GenBank and the present study by using the neighbourjoining method with the software MEGA version 6.06.

RESULTS: Totally 31 sequences were acquired in the present study and they produced 3 unique haplotypes. Haplotype 1 showed a higher frequency compared to the others and it accounted for 83.9 % (26/31). The data showed that the least genetic distances ranged from 0 to 0.052 between P. canaliculata and 3 haplotypes, as well as the largest genetic distances ranged from 0.021 to 0.239 between Pila conica and 3 haplotypes. Otherwise, the analysis of the phylogenetic trees based on COⅠ gene sequences of P. canaliculata indicated that all of 3 haplotypes clustered into one big clade with that from Japan (GenBank accession number: AB433769), China (GenBank accession number: KT313034) and USA (GenBank accession number: EU523129), which owned the closet relationship amongst them. Their genetic relationships were distantly related to the GenBank's reference sequences of P. insularum (GenBank accession number: EF514942), P. camena (GenBank accession number: EF515059) and so on.

CONCLUSIONS: There is a P. canaliculata species in Lincang City of Yunnan Province as well as a high genetic diversity amongst the acquired 3 haplotypes in this study.},
}

Angiostrongylus cantonensis
Animals
China
DNA, Mitochondrial/genetics
Electron Transport Complex IV/*genetics
Gastropoda/enzymology/*genetics
Genotype
Haplotypes
Phylogeny

@article {pmid29112874,
year = {2017},
author = {Roger, AJ and Muñoz-Gómez, SA and Kamikawa, R},
title = {The Origin and Diversification of Mitochondria.},
journal = {Current biology : CB},
volume = {27},
number = {21},
pages = {R1177-R1192},
doi = {10.1016/j.cub.2017.09.015},
pmid = {29112874},
issn = {1879-0445},
mesh = {Adenosine Triphosphate/biosynthesis/metabolism ; Alphaproteobacteria/*genetics/growth & development ; *Biological Evolution ; Eukaryotic Cells/*metabolism ; Genome, Mitochondrial/genetics ; Membrane Transport Proteins/genetics ; *Mitochondria/genetics/metabolism/physiology ; Protein Transport/genetics/physiology ; Symbiosis/genetics/physiology ; },
abstract = {Mitochondria are best known for their role in the generation of ATP by aerobic respiration. Yet, research in the past half century has shown that they perform a much larger suite of functions and that these functions can vary substantially among diverse eukaryotic lineages. Despite this diversity, all mitochondria derive from a common ancestral organelle that originated from the integration of an endosymbiotic alphaproteobacterium into a host cell related to Asgard Archaea. The transition from endosymbiotic bacterium to permanent organelle entailed a massive number of evolutionary changes including the origins of hundreds of new genes and a protein import system, insertion of membrane transporters, integration of metabolism and reproduction, genome reduction, endosymbiotic gene transfer, lateral gene transfer and the retargeting of proteins. These changes occurred incrementally as the endosymbiont and the host became integrated. Although many insights into this transition have been gained, controversy persists regarding the nature of the original endosymbiont, its initial interactions with the host and the timing of its integration relative to the origin of other features of eukaryote cells. Since the establishment of the organelle, proteins have been gained, lost, transferred and retargeted as mitochondria have specialized into the spectrum of functional types seen across the eukaryotic tree of life.},
}

Adenosine Triphosphate/biosynthesis/metabolism
Alphaproteobacteria/*genetics/growth & development
*Biological Evolution
Eukaryotic Cells/*metabolism
Genome, Mitochondrial/genetics
Membrane Transport Proteins/genetics
*Mitochondria/genetics/metabolism/physiology
Protein Transport/genetics/physiology
Symbiosis/genetics/physiology

@article {pmid29056456,
year = {2017},
author = {Wang, P and Khoshravesh, R and Karki, S and Tapia, R and Balahadia, CP and Bandyopadhyay, A and Quick, WP and Furbank, R and Sage, TL and Langdale, JA},
title = {Re-creation of a Key Step in the Evolutionary Switch from C3 to C4 Leaf Anatomy.},
journal = {Current biology : CB},
volume = {27},
number = {21},
pages = {3278-3287.e6},
doi = {10.1016/j.cub.2017.09.040},
pmid = {29056456},
issn = {1879-0445},
mesh = {Biological Evolution ; Chloroplasts/*genetics/physiology ; Mitochondria/genetics ; Oryza/*genetics ; Photosynthesis/*genetics ; Plant Leaves/anatomy & histology/genetics/*metabolism ; Plant Proteins/*genetics ; Transcription Factors/*genetics ; Zea mays/*genetics ; },
abstract = {The C4 photosynthetic pathway accounts for ∼25% of primary productivity on the planet despite being used by only 3% of species. Because C4 plants are higher yielding than C3 plants, efforts are underway to introduce the C4 pathway into the C3 crop rice. This is an ambitious endeavor; however, the C4 pathway evolved from C3 on multiple independent occasions over the last 30 million years, and steps along the trajectory are evident in extant species. One approach toward engineering C4 rice is to recapitulate this trajectory, one of the first steps of which was a change in leaf anatomy. The transition from C3 to so-called "proto-Kranz" anatomy requires an increase in organelle volume in sheath cells surrounding leaf veins. Here we induced chloroplast and mitochondrial development in rice vascular sheath cells through constitutive expression of maize GOLDEN2-LIKE genes. Increased organelle volume was accompanied by the accumulation of photosynthetic enzymes and by increased intercellular connections. This suite of traits reflects that seen in "proto-Kranz" species, and, as such, a key step toward engineering C4 rice has been achieved.},
}

Biological Evolution
Chloroplasts/*genetics/physiology
Mitochondria/genetics
Oryza/*genetics
Photosynthesis/*genetics
Plant Leaves/anatomy & histology/genetics/*metabolism
Plant Proteins/*genetics
Transcription Factors/*genetics
Zea mays/*genetics

@article {pmid29061908,
year = {2017},
author = {Yang, Y and Zhu, G and Li, R and Yan, S and Fu, D and Zhu, B and Tian, H and Luo, Y and Zhu, H},
title = {The RNA Editing Factor SlORRM4 Is Required for Normal Fruit Ripening in Tomato.},
journal = {Plant physiology},
volume = {175},
number = {4},
pages = {1690-1702},
doi = {10.1104/pp.17.01265},
pmid = {29061908},
issn = {1532-2548},
mesh = {CRISPR-Cas Systems ; Fruit/*physiology ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/*physiology ; Gene Silencing ; Lycopersicon esculentum/genetics/*physiology ; Mitochondria ; Mutation ; Phylogeny ; Plant Development/genetics/physiology ; Plant Proteins/genetics/*metabolism ; RNA Editing/genetics/*physiology ; },
abstract = {RNA editing plays a key posttranscriptional role in gene expression. Existing studies on cytidine-to-uridine RNA editing in plants have focused on maize (Zea mays), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana). However, the importance and regulation of RNA editing in several critical agronomic processes are not well understood, a notable example of which is fruit ripening. Here, we analyzed the expression profile of 33 RNA editing factors and identified 11 putative tomato (Solanum lycopersicum) fruit ripening-related factors. A rapid virus-induced gene silencing assay indicated that the organelle RNA recognition motif-containing protein SlORRM4 affected tomato fruit ripening. Knocking out SlORRM4 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy delayed tomato fruit ripening by lowering respiratory rate and ethylene production. Additionally, the expression of numerous genes associated with fruit ripening and mitochondrial functions changed significantly when SlORRM4 was knocked out. Moreover, the loss of SlORRM4 function significantly reduced RNA editing of many mitochondrial transcripts, leading to low-level expression of some core subunits that are critical for mitochondrial complex assembly (i.e. Nad3, Cytc1, and COX II). Taken together, these results indicate that SlORRM4 is involved in RNA editing of transcripts in ripening fruit that influence mitochondrial function and key aspects of fruit ripening.},
}

CRISPR-Cas Systems
Fruit/*physiology
Gene Expression Regulation, Developmental/physiology
Gene Expression Regulation, Plant/*physiology
Gene Silencing
Lycopersicon esculentum/genetics/*physiology
Mitochondria
Mutation
Phylogeny
Plant Development/genetics/physiology
Plant Proteins/genetics/*metabolism
RNA Editing/genetics/*physiology

@article {pmid29698456,
year = {2018},
author = {Peña-Diaz, P and Mach, J and Kriegová, E and Poliak, P and Tachezy, J and Lukeš, J},
title = {Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase.},
journal = {PloS one},
volume = {13},
number = {4},
pages = {e0196474},
doi = {10.1371/journal.pone.0196474},
pmid = {29698456},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Down-Regulation ; Electron Transport Complex IV/metabolism ; Metalloendopeptidases/antagonists & inhibitors/classification/genetics/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*enzymology ; Phylogeny ; Protein Subunits/antagonists & inhibitors/genetics/metabolism ; RNA Interference ; RNA, Small Interfering/metabolism ; Substrate Specificity ; Trypanosoma brucei brucei/*metabolism ; },
abstract = {Upon their translocation into the mitochondrial matrix, the N-terminal pre-sequence of nuclear-encoded proteins undergoes cleavage by mitochondrial processing peptidases. Some proteins require more than a single processing step, which involves several peptidases. Down-regulation of the putative Trypanosoma brucei mitochondrial intermediate peptidase (MIP) homolog by RNAi renders the cells unable to grow after 48 hours of induction. Ablation of MIP results in the accumulation of the precursor of the trypanosomatid-specific trCOIV protein, the largest nuclear-encoded subunit of the cytochrome c oxidase complex in this flagellate. However, the trCOIV precursor of the same size accumulates also in trypanosomes in which either alpha or beta subunits of the mitochondrial processing peptidase (MPP) have been depleted. Using a chimeric protein that consists of the N-terminal sequence of a putative subunit of respiratory complex I fused to a yellow fluorescent protein, we assessed the accumulation of the precursor protein in trypanosomes, in which RNAi was induced against the alpha or beta subunits of MPP or MIP. The observed accumulation of precursors indicates MIP depletion affects the activity of the cannonical MPP, or at least one of its subunits.},
}

Amino Acid Sequence
Down-Regulation
Electron Transport Complex IV/metabolism
Metalloendopeptidases/antagonists & inhibitors/classification/genetics/*metabolism
Microscopy, Fluorescence
Mitochondria/*enzymology
Phylogeny
Protein Subunits/antagonists & inhibitors/genetics/metabolism
RNA Interference
RNA, Small Interfering/metabolism
Substrate Specificity
Trypanosoma brucei brucei/*metabolism

@article {pmid29196205,
year = {2018},
author = {Medina, CD and Avila, LJ and Sites, JW and Santos, J and Morando, M},
title = {Alternative methods of phylogenetic inference for the Patagonian lizard group Liolaemus elongatus-kriegi (Iguania: Liolaemini) based on mitochondrial and nuclear markers.},
journal = {Molecular phylogenetics and evolution},
volume = {120},
number = {},
pages = {158-169},
doi = {10.1016/j.ympev.2017.11.017},
pmid = {29196205},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; Cytochromes b/classification/genetics/metabolism ; DNA/chemistry/isolation & purification/metabolism ; Databases, Genetic ; Lizards/*classification/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/chemistry/classification/genetics ; Sequence Analysis, DNA ; },
abstract = {We present different approaches to a multi-locus phylogeny for the Liolaemus elongatus-kriegi group, including almost all species and recognized lineages. We sequenced two mitochondrial and five nuclear gene regions for 123 individuals from 35 taxa, and compared relationships resolved from concatenated and species tree methods. The L. elongatus-kriegi group was inferred as monophyletic in three of the five analyses (concatenated mitochondrial, concatenated mitochondrial + nuclear gene trees, and SVD quartet species tree). The mitochondrial gene tree resolved four haploclades, three corresponding to the previously recognized complexes: L. elongatus, L. kriegi and L. petrophilus complexes, and the L. punmahuida group. The BEAST species tree approach included the L. punmahuida group within the L. kriegi complex, but the SVD quartet method placed it as sister to the L. elongatus-kriegi group. BEAST inferred species of the L. elongatus and L. petrophilus complexes as one clade, while SVDquartet inferred these two complexes as monophyletic (although with no statistical support for the L. petrophilus complex). The species tree approach also included the L. punmahuida group as part of the L. elongatus-kriegi group. Our study provides detailed multilocus phylogenetic hypotheses for the L. elongatus-kriegi group, and we discuss possible reasons for differences in the concatenation and species tree methods.},
}

Animals
Bayes Theorem
Cell Nucleus/*genetics
Cytochromes b/classification/genetics/metabolism
DNA/chemistry/isolation & purification/metabolism
Databases, Genetic
Lizards/*classification/genetics
Mitochondria/*genetics
Phylogeny
RNA, Ribosomal/chemistry/classification/genetics
Sequence Analysis, DNA

@article {pmid29075935,
year = {2017},
author = {Glasgow, RIC and Thompson, K and Barbosa, IA and He, L and Alston, CL and Deshpande, C and Simpson, MA and Morris, AAM and Neu, A and Löbel, U and Hall, J and Prokisch, H and Haack, TB and Hempel, M and McFarland, R and Taylor, RW},
title = {Novel GFM2 variants associated with early-onset neurological presentations of mitochondrial disease and impaired expression of OXPHOS subunits.},
journal = {Neurogenetics},
volume = {18},
number = {4},
pages = {227-235},
doi = {10.1007/s10048-017-0526-4},
pmid = {29075935},
issn = {1364-6753},
support = {FKZ 01ZX1405C//German Federal Ministry of Education and Research (BMBF)/ ; 01GM1603, 01GM1207//German Bundesministerium für Bildung und Forschung (BMBF) and Horizon2020/ ; 203105/Z/16/Z//Wellcome Centre for Mitochondrial Research/ ; 633974//EU Horizon2020 Collaborative Research Project SOUND/ ; G0800674//Mitochondrial Disease Patient Cohort (UK)/ ; NIHR-HCS-D12-03-04//NIHR/CSO Healthcare Science Research Fellowship/ ; NIHR-HCS-D12-03-04//Department of Health/United Kingdom ; },
mesh = {Child ; Exome/genetics ; Female ; Homozygote ; Humans ; Male ; Mitochondria/*genetics/metabolism ; Mitochondrial Diseases/*genetics ; Mitochondrial Proteins/genetics/*metabolism ; Mutation/genetics ; Pedigree ; Peptide Elongation Factor G/*genetics ; Phenotype ; },
abstract = {Mitochondrial diseases are characterised by clinical, molecular and functional heterogeneity, reflecting their bi-genomic control. The nuclear gene GFM2 encodes mtEFG2, a protein with an essential role during the termination stage of mitochondrial translation. We present here two unrelated patients harbouring different and previously unreported compound heterozygous (c.569G>A, p.(Arg190Gln); c.636delA, p.(Glu213Argfs*3)) and homozygous (c.275A>C, p.(Tyr92Ser)) recessive variants in GFM2 identified by whole exome sequencing (WES) together with histochemical and biochemical findings to support the diagnoses of pathological GFM2 variants in each case. Both patients presented similarly in early childhood with global developmental delay, raised CSF lactate and abnormalities on cranial MRI. Sanger sequencing of familial samples confirmed the segregation of bi-allelic GFM2 variants with disease, while investigations into steady-state mitochondrial protein levels revealed respiratory chain subunit defects and loss of mtEFG2 protein in muscle. These data demonstrate the effects of defective mtEFG2 function, caused by previously unreported variants, confirming pathogenicity and expanding the clinical phenotypes associated with GFM2 variants.},
}

Child
Exome/genetics
Female
Homozygote
Humans
Male
Mitochondria/*genetics/metabolism
Mitochondrial Diseases/*genetics
Mitochondrial Proteins/genetics/*metabolism
Mutation/genetics
Pedigree
Peptide Elongation Factor G/*genetics
Phenotype

@article {pmid30060640,
year = {1983},
author = {Ruppert, EE and Travis, PB},
title = {Hemoglobin-containing cells of Neodasys (Gastrotricha, Chaetonotida). I. Morphology and ultrastructure.},
journal = {Journal of morphology},
volume = {175},
number = {1},
pages = {57-64},
doi = {10.1002/jmor.1051750106},
pmid = {30060640},
issn = {1097-4687},
abstract = {The overall anatomy of Neodasys as well as data for hemoglobin-containing cells are described. Hemoglobin-containing cells are shown to be mesodermal specializations constituting approximately 14% of the animal's total body volume (4.87 ± 104 μl). These globular cells (10-14 μm) are situated in two longitudinal rows, each dorsolateral to the straight gut. Branches from the cells enwrap perikarya of muscle and nerve cells whose mitochondria are found just below their respective plasmalemmata in intimate association with the hemoglobin-containing cells. The ground substance of the cytoplasm and nucleoplasm of these nearly organelle-free cells is extremely electron-dense and is presumed to represent the hemoglobin molecules. Locomotion analyses indicate that the cells can undergo a threefold change in linear dimension in 0.25 seconds, raising the possibility of convective mixing in these cells. Structural and ultrastructural comparisons with similar cells in adults of other species of Gastrotricha indicate that the hemoglobin-containing cells of Neodasys may be homologous to the socalled Y cells of other species, some of which contain myofilaments. A muscle-cell origin is considered for the evolution of hemoglobin-containing cells of Neodasys.},
}

@article {pmid30055249,
year = {2018},
author = {Torrezan-Nitao, E and Figueiredo, RCBQ and Marques-Santos, LF},
title = {Mitochondrial permeability transition pore in sea urchin female gametes.},
journal = {Mechanisms of development},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mod.2018.07.008},
pmid = {30055249},
issn = {1872-6356},
abstract = {Mitochondrial permeability transition pore (MPTP) has been associated to calcium homeostasis and reactive oxygen species (ROS) generation in several cell types. While extensively investigated in somatic cells, there are few data regarding MPTP phenomenon in gametes. The aim of the present work was to investigate MPTP occurrence in sea urchin female gametes. The protonophores CCCP and FCCP, and the Ca2+ ionophore ionomycin, were used as pore inductors. Pore opening was monitored by mitochondrial potential sensitive probes and cobalt-quenched calcein assay. The pore desensitizer cyclosporin A (CsA) prevented the loss of mitochondrial inner membrane potential (ΔΨm) and pore opening induced by MPTP activators. The disruption of ΔΨm led to an increase in ROS generation, which was completely prevented by CsA. Our data also demonstrated that the increase in ROS production induced by MPTP opening requires extracellular Ca2+. In summary, the current study provides evidence about the occurrence of MPTP in sea urchin eggs in a similar manner as described in vertebrate somatic cells - CsA-sensitive, voltage- and Ca2+-triggered - and shows MPTP as a highly conserved physiological event through the evolution.},
}

@article {pmid29199107,
year = {2018},
author = {Solano-Zavaleta, I and Nieto-Montes de Oca, A},
title = {Species limits in the Morelet's Alligator lizard (Anguidae: Gerrhonotinae).},
journal = {Molecular phylogenetics and evolution},
volume = {120},
number = {},
pages = {16-27},
doi = {10.1016/j.ympev.2017.11.011},
pmid = {29199107},
issn = {1095-9513},
mesh = {Alligators and Crocodiles/*physiology ; Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Central America ; DNA, Mitochondrial/genetics ; Lizards/genetics/*physiology ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Species Specificity ; Time Factors ; },
abstract = {The widely distributed, Central American anguid lizard Mesaspis moreletii is currently recognized as a polytypic species with five subspecies (M. m. fulvus, M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis). We reevaluated the species limits within Mesaspis moreletii using DNA sequences of one mitochondrial and three nuclear genes. The multi-locus data set included samples of all of the subspecies of M. moreletii, the other species of Mesaspis in Central America (M. cuchumatanus and M. monticola), and some populations assignable to M. moreletii but of uncertain subspecific identity from Honduras and Nicaragua. We first used a tree-based method for delimiting species based on mtDNA data to identify potential evolutionary independent lineages, and then analized the multilocus dataset with two species delimitation methods that use the multispecies coalescent model to evaluate different competing species delimitation models: the Bayes factors species delimitation method (BFD) implemented in ∗BEAST, and the Bayesian Phylogenetics and Phylogeography (BP&P) method. Our results suggest that M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis represent distinct evolutionary independent lineages, and that the populations of uncertain status from Honduras and Nicaragua may represent additional undescribed species. Our results also suggest that M. m. fulvus is a synonym of M. m. moreletii. The biogeography of the Central American lineages of Mesaspis is discussed.},
}

Alligators and Crocodiles/*physiology
Animals
Bayes Theorem
Cell Nucleus/genetics
Central America
DNA, Mitochondrial/genetics
Lizards/genetics/*physiology
Mitochondria/genetics
Phylogeny
Phylogeography
Species Specificity
Time Factors

@article {pmid29137957,
year = {2018},
author = {Saunders, GW and Jackson, C and Salomaki, ED},
title = {Phylogenetic analyses of transcriptome data resolve familial assignments for genera of the red-algal Acrochaetiales-Palmariales Complex (Nemaliophycidae).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {151-159},
doi = {10.1016/j.ympev.2017.11.002},
pmid = {29137957},
issn = {1095-9513},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Rhodophyta/*classification/*genetics ; Transcriptome/*genetics ; },
abstract = {Phylogenetic analyses of transcriptome data for representatives of the red algal Acrochaetiales-Palmariales Complex provided robust support for the assignment of genera to the constituent families. In the Acrochaetiales, the genera Acrochaetium, Grania, and an unnamed genus-level lineage (Acrochaetiac sp._1Aus) were assigned to the Acrochaetiaceae, while Audouinella is placed in a resurrected Audouinellaceae and Rhodochorton and Rhododrewia constitute the resurrected Rhodochortonaceae. For the Palmariales, transcriptome data solidly support the inclusion of Camontagnea and Rhodothamniella in the Rhodothamniellaceae, Meiodiscus and Rubrointrusa in the Meiodiscaceae, Rhodonematella and Rhodophysema in the Rhodophysemataceae, while Devaleraea and Palmaria remained in the Palmariaceae. These analyses, however, questioned the monophyly of Palmaria, which prompted a second round of analyses using eight common red algal phylogenetic markers and including a broader sampling of red algal genera in our analyses. These results supported transfer of Palmaria callophylloides and P. mollis to the genus Devaleraea necessitating new combinations, and further added the genus Halosaccion to the Palmariaceae and the genera Kallymenicola and Rhodophysemopsis to the Meiodiscaceae. Finally, DNA barcode (mitochondrial COI-5P) and ITS data were explored and supported the continued recognition of Palmaria palmata as a single species in the North Atlantic.},
}

Base Sequence
DNA Barcoding, Taxonomic
DNA, Intergenic/genetics
Likelihood Functions
Mitochondria/genetics
*Phylogeny
Rhodophyta/*classification/*genetics
Transcriptome/*genetics

@article {pmid29107618,
year = {2018},
author = {da Cruz, MOR and Weksler, M},
title = {Impact of tree priors in species delimitation and phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {1-12},
doi = {10.1016/j.ympev.2017.10.021},
pmid = {29107618},
issn = {1095-9513},
mesh = {Animals ; Arvicolinae/*classification ; Bayes Theorem ; Mitochondria/metabolism ; *Phylogeny ; Probability ; Species Specificity ; Time Factors ; },
abstract = {The use of genetic data and tree-based algorithms to delimit evolutionary lineages is becoming an important practice in taxonomic identification, especially in morphologically cryptic groups. The effects of different phylogenetic and/or coalescent models in the analyses of species delimitation, however, are not clear. In this paper, we assess the impact of different evolutionary priors in phylogenetic estimation, species delimitation, and molecular dating of the genus Oligoryzomys (Mammalia: Rodentia), a group with complex taxonomy and morphological cryptic species. Phylogenetic and coalescent analyses included 20 of the 24 recognized species of the genus, comprising of 416 Cytochrome b sequences, 26 Cytochrome c oxidase I sequences, and 27 Beta-Fibrinogen Intron 7 sequences. For species delimitation, we employed the General Mixed Yule Coalescent (GMYC) and Bayesian Poisson tree processes (bPTP) analyses, and contrasted 4 genealogical and phylogenetic models: Pure-birth (Yule), Constant Population Size Coalescent, Multiple Species Coalescent, and a mixed Yule-Coalescent model. GMYC analyses of trees from different genealogical models resulted in similar species delimitation and phylogenetic relationships, with incongruence restricted to areas of poor nodal support. bPTP results, however, significantly differed from GMYC for 5 taxa. Oligoryzomys early diversification was estimated to have occurred in the Early Pleistocene, between 0.7 and 2.6 MYA. The mixed Yule-Coalescent model, however, recovered younger dating estimates for Oligoryzomys diversification, and for the threshold for the speciation-coalescent horizon in GMYC. Eight of the 20 included Oligoryzomys species were identified as having two or more independent evolutionary units, indicating that current taxonomy of Oligoryzomys is still unsettled.},
}

Animals
Arvicolinae/*classification
Bayes Theorem
Mitochondria/metabolism
*Phylogeny
Probability
Species Specificity
Time Factors

@article {pmid29104141,
year = {2018},
author = {Lüddecke, T and Krehenwinkel, H and Canning, G and Glaw, F and Longhorn, SJ and Tänzler, R and Wendt, I and Vences, M},
title = {Discovering the silk road: Nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies.},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {63-70},
doi = {10.1016/j.ympev.2017.10.015},
pmid = {29104141},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Silk/*genetics ; Spiders/*classification/*genetics ; },
abstract = {The mygalomorph spiders in the family Theraphosidae, also known as "tarantulas", are one of the most popular and diverse groups of arachnids, but their evolutionary history remains poorly understood because morphological analyses have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of the Theraphosidae and of most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of the previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.},
}

Animals
Bayes Theorem
Cell Nucleus/*genetics
DNA, Mitochondrial/*genetics
Mitochondria/genetics
*Phylogeny
Sequence Analysis, DNA
Silk/*genetics
Spiders/*classification/*genetics

@article {pmid29079378,
year = {2018},
author = {Yoshizawa, K and Johnson, KP and Sweet, AD and Yao, I and Ferreira, RL and Cameron, SL},
title = {Mitochondrial phylogenomics and genome rearrangements in the barklice (Insecta: Psocodea).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {118-127},
doi = {10.1016/j.ympev.2017.10.014},
pmid = {29079378},
issn = {1095-9513},
mesh = {Animals ; Evolution, Molecular ; *Gene Order ; *Genome, Mitochondrial ; Insecta/*classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial genome arrangement in the insect order Psocodea (booklice, barklice, and parasitic lice) is extremely variable. Genome organization ranges from the rearrangement of a few tRNAs and protein coding genes, through extensive tRNA and protein coding gene rearrangements, to subdivision into multiple mini-chromosomes. Evolution of the extremely modified mitochondrial genome in parasitic lice (Phthiraptera) has been the subject of several studies, but limited information is available regarding the mitochondrial genome organization of the more plesiomorphic, free-living Psocodea (formerly known as the "Psocoptera"). In particular, the ancestral state of the psocodean mitochondrial genome arrangement and the evolutionary pathway to the rearranged conditions are still unknown. In this study, we addressed mitochondrial evolutionary questions within the Psocodea by using mitochondrial genome sequences obtained from a wide range of Psocoptera, covering all three suborders. We identified seven types of mitochondrial genome arrangements in Psocoptera, including the first example in Psocodea of retention of the ancestral pancrustacean condition in Prionoglaris (Prionoglarididae). Two methods (condition-based parsimony reconstruction and common-interval genome distances) were applied to estimate the ancestral mitochondrial arrangement in Psocodea, and both provided concordant results. Specifically, the common ancestor of Psocodea retained the ancestral pancrustacean condition, and most of the gene arrangement types have originated independently from this ancestral condition. We also utilized the genomic data for phylogenetic estimation. The tree estimated from the mitochondrial genomic data was well resolved, strongly supported, and in agreement with previously estimated phylogenies. It also provided the first robust support for the family Prionoglarididae, as its monophyly was uncertain in previous morphological and molecular studies.},
}

Animals
Evolution, Molecular
*Gene Order
*Genome, Mitochondrial
Insecta/*classification/*genetics
Mitochondria/*genetics
Molecular Sequence Annotation
*Phylogeny
Sequence Analysis, DNA

@article {pmid29074460,
year = {2018},
author = {Smith, CH and Johnson, NA and Pfeiffer, JM and Gangloff, MM},
title = {Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {50-62},
doi = {10.1016/j.ympev.2017.10.018},
pmid = {29074460},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Bivalvia/*anatomy & histology/*genetics ; Florida ; *Fresh Water ; *Genetic Speciation ; Geography ; Haplotypes/genetics ; Louisiana ; Mitochondria/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent 'Strophitus' connasaugaensis and 'Strophitus' subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.},
}

Animals
Bayes Theorem
Bivalvia/*anatomy & histology/*genetics
Florida
*Fresh Water
*Genetic Speciation
Geography
Haplotypes/genetics
Louisiana
Mitochondria/metabolism
*Phylogeny
Sequence Analysis, DNA
Species Specificity

@article {pmid28947489,
year = {2017},
author = {Majsec, K and Bhuiyan, NH and Sun, Q and Kumari, S and Kumar, V and Ware, D and van Wijk, KJ},
title = {The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis.},
journal = {The Plant cell},
volume = {29},
number = {11},
pages = {2687-2710},
doi = {10.1105/tpc.17.00481},
pmid = {28947489},
issn = {1532-298X},
mesh = {Arabidopsis Proteins/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Gene Regulatory Networks/genetics ; Mitochondria/*enzymology/genetics ; Peptide Hydrolases/classification/genetics/*metabolism ; Phylogeny ; Plastids/*enzymology/genetics ; Proteome/genetics/metabolism ; Proteostasis/genetics ; },
abstract = {Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.},
}

Arabidopsis Proteins/genetics/*metabolism
Gene Expression Regulation, Enzymologic
Gene Expression Regulation, Plant
Gene Regulatory Networks/genetics
Mitochondria/*enzymology/genetics
Peptide Hydrolases/classification/genetics/*metabolism
Phylogeny
Plastids/*enzymology/genetics
Proteome/genetics/metabolism
Proteostasis/genetics

@article {pmid30046113,
year = {2018},
author = {Dhir, A and Dhir, S and Borowski, LS and Jimenez, L and Teitell, M and Rötig, A and Crow, YJ and Rice, GI and Duffy, D and Tamby, C and Nojima, T and Munnich, A and Schiff, M and de Almeida, CR and Rehwinkel, J and Dziembowski, A and Szczesny, RJ and Proudfoot, NJ},
title = {Mitochondrial double-stranded RNA triggers antiviral signalling in humans.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-018-0363-0},
pmid = {30046113},
issn = {1476-4687},
abstract = {Mitochondria are descendants of endosymbiotic bacteria and retain essential prokaryotic features such as a compact circular genome. Consequently, in mammals, mitochondrial DNA is subjected to bidirectional transcription that generates overlapping transcripts, which are capable of forming long double-stranded RNA structures1,2. However, to our knowledge, mitochondrial double-stranded RNA has not been previously characterized in vivo. Here we describe the presence of a highly unstable native mitochondrial double-stranded RNA species at single-cell level and identify key roles for the degradosome components mitochondrial RNA helicase SUV3 and polynucleotide phosphorylase PNPase in restricting the levels of mitochondrial double-stranded RNA. Loss of either enzyme results in massive accumulation of mitochondrial double-stranded RNA that escapes into the cytoplasm in a PNPase-dependent manner. This process engages an MDA5-driven antiviral signalling pathway that triggers a type I interferon response. Consistent with these data, patients carrying hypomorphic mutations in the gene PNPT1, which encodes PNPase, display mitochondrial double-stranded RNA accumulation coupled with upregulation of interferon-stimulated genes and other markers of immune activation. The localization of PNPase to the mitochondrial inter-membrane space and matrix suggests that it has a dual role in preventing the formation and release of mitochondrial double-stranded RNA into the cytoplasm. This in turn prevents the activation of potent innate immune defence mechanisms that have evolved to protect vertebrates against microbial and viral attack.},
}

@article {pmid30042786,
year = {2018},
author = {Riggs, CL and Summers, A and Warren, DE and Nilsson, GE and Lefevre, S and Dowd, WW and Milton, S and Podrabsky, JE},
title = {Small Non-coding RNA Expression and Vertebrate Anoxia Tolerance.},
journal = {Frontiers in genetics},
volume = {9},
number = {},
pages = {230},
doi = {10.3389/fgene.2018.00230},
pmid = {30042786},
issn = {1664-8021},
abstract = {Background: Extreme anoxia tolerance requires a metabolic depression whose modulation could involve small non-coding RNAs (small ncRNAs), which are specific, rapid, and reversible regulators of gene expression. A previous study of small ncRNA expression in embryos of the annual killifish Austrofundulus limnaeus, the most anoxia-tolerant vertebrate known, revealed a specific expression pattern of small ncRNAs that could play important roles in anoxia tolerance. Here, we conduct a comparative study on the presence and expression of small ncRNAs in the most anoxia-tolerant representatives of several major vertebrate lineages, to investigate the evolution of and mechanisms supporting extreme anoxia tolerance. The epaulette shark (Hemiscyllium ocellatum), crucian carp (Carassius carassius), western painted turtle (Chrysemys picta bellii), and leopard frog (Rana pipiens) were exposed to anoxia and recovery, and small ncRNAs were sequenced from the brain (one of the most anoxia-sensitive tissues) prior to, during, and following exposure to anoxia. Results: Small ncRNA profiles were broadly conserved among species under normoxic conditions, and these expression patterns were largely conserved during exposure to anoxia. In contrast, differentially expressed genes are mostly unique to each species, suggesting that each species may have evolved distinct small ncRNA expression patterns in response to anoxia. Mitochondria-derived small ncRNAs (mitosRNAs) which have a robust response to anoxia in A. limnaeus embryos, were identified in the other anoxia tolerant vertebrates here but did not display a similarly robust response to anoxia. Conclusion: These findings support an overall stabilization of the small ncRNA transcriptome during exposure to anoxic insults, but also suggest that multiple small ncRNA expression pathways may support anoxia tolerance, as no conserved small ncRNA response was identified among the anoxia-tolerant vertebrates studied. This may reflect divergent strategies to achieve the same endpoint: anoxia tolerance. However, it may also indicate that there are multiple cellular pathways that can trigger the same cellular and physiological survival processes, including hypometabolism.},
}

@article {pmid29100916,
year = {2018},
author = {Krishnan, R and Girish Babu, P and Jeena, K and Tripathi, G and Pani Prasad, K},
title = {Molecular characterization, ontogeny and expression profiling of mitochondrial antiviral signaling adapter, MAVS from Asian seabass Lates calcarifer, Bloch (1790).},
journal = {Developmental and comparative immunology},
volume = {79},
number = {},
pages = {175-185},
doi = {10.1016/j.dci.2017.10.019},
pmid = {29100916},
issn = {1879-0089},
mesh = {Adaptor Proteins, Signal Transducing/*genetics ; Animals ; Bass/*immunology ; Cloning, Molecular ; Fish Diseases/*immunology ; Fish Proteins ; Gene Expression Profiling ; Immunity, Innate ; Mitochondria/*metabolism ; Nodaviridae/*physiology ; Phylogeny ; RNA Virus Infections/*immunology ; Signal Transduction ; Spleen/*metabolism ; Zebrafish Proteins/genetics ; },
abstract = {Mitochondrial antiviral signaling protein (MAVS), an innate immune signaling adapter coordinates the signals received from two independent cytosolic pathogen recognition receptors (RIG-1 and MDA5) to induce antiviral genes. In the present study the MAVS gene of Lates calcarifer (LcMAVS) was cloned and characterized. The complete cDNA sequence of LcMAVS was 3160 bp and encodes a poly peptide of 577 amino acids. Structural analysis of LcMAVS revealed an N-terminal CARD-like domain, central proline-rich domain and a C-terminal transmembrane domain. Phylogenetic analysis indicated that LcMAVS exhibited the closest relationship to P. olivaceous MAVS. LcMAVS was ubiquitously expressed in all tested tissues of healthy fish viz., brain, gill, heart, liver, spleen, kidney and intestine, with highest transcript level in spleen. The mRNA transcript level of LcMAVS in different developmental stages showed constitutive expression in all the stages tested suggesting the maternal transfer of the gene. Significant up regulation in MAVS expression was observed post nervous necrosis virus (NNV) challenge in vivo in all the selected tissues. Further, time course analysis showed that LcMAVS transcripts significantly increased in the brain and spleen tissues after NNV infection. These findings provide useful information for further elucidating the function of LcMAVS in antiviral innate immune response against NNV in Asian seabass.},
}

Adaptor Proteins, Signal Transducing/*genetics
Animals
Bass/*immunology
Cloning, Molecular
Fish Diseases/*immunology
Fish Proteins
Gene Expression Profiling
Immunity, Innate
Mitochondria/*metabolism
Nodaviridae/*physiology
Phylogeny
RNA Virus Infections/*immunology
Signal Transduction
Spleen/*metabolism
Zebrafish Proteins/genetics

@article {pmid30022808,
year = {2018},
author = {Lang, SA and Shain, DH},
title = {Atypical Evolution of the F1Fo Adenosine Triphosphate Synthase Regulatory ATP6 subunit in Glacier Ice Worms (Annelida: Clitellata: Mesenchytraeus).},
journal = {Evolutionary bioinformatics online},
volume = {14},
number = {},
pages = {1176934318788076},
doi = {10.1177/1176934318788076},
pmid = {30022808},
issn = {1176-9343},
abstract = {The glacier ice worm, Mesenchytraeus solifugus, is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction. Furthermore, sequence analysis suggests that this insertion is not of metazoan origin, but rather is a product of horizontal gene transfer from a microbial dietary source, and may act as a proton shuttle to accelerate the rate of ATP synthesis.},
}

@article {pmid30003876,
year = {2018},
author = {Katane, M and Ariyoshi, M and Tateishi, S and Koiwai, S and Takaku, K and Nagai, K and Nakayama, K and Saitoh, Y and Miyamoto, T and Sekine, M and Mita, M and Hamase, K and Matoba, S and Homma, H},
title = {Structural and enzymatic properties of mammalian d-glutamate cyclase.},
journal = {Archives of biochemistry and biophysics},
volume = {654},
number = {},
pages = {10-18},
doi = {10.1016/j.abb.2018.07.005},
pmid = {30003876},
issn = {1096-0384},
abstract = {d-Glutamate cyclase (DGLUCY) is a unique enzyme that reversibly converts free d-glutamate to 5-oxo-d-proline and H2O. Mammalian DGLUCY is highly expressed in the mitochondrial matrix in the heart, and its downregulation disrupts d-glutamate and/or 5-oxo-d-proline levels, contributing to the onset and/or exacerbation of heart failure. However, detailed characterisation of DGLUCY has not yet been performed. Herein, the structural and enzymatic properties of purified recombinant mouse DGLUCY were examined. The results revealed a dimeric oligomerisation state, and both d-glutamate-to-5-oxo-d-proline and 5-oxo-d-proline-to-d-glutamate reactions were catalysed in a stereospecific manner. Catalytic activity is modulated by divalent cations and nucleotides including ATP and ADP. Interestingly, the presence of Mn2+ completely abolished the 5-oxo-d-proline-to-d-glutamate reaction but stimulated the d-glutamate-to-5-oxo-d-proline reaction. The optimum pH is ∼8.0, similar to that in the mitochondrial matrix, and the catalytic efficiency for d-glutamate is markedly higher than that for 5-oxo-d-proline. These findings suggest that DGLUCY functions as a metalloenzyme that degrades d-glutamate in the mitochondrial matrix in mammalian cells. The results also provide insight into the correlation between DGLUCY enzyme activity and the physiological and pathological roles of d-glutamate and 5-oxo-d-proline in cardiac function, which is of relevance to the risk of onset of heart failure.},
}

@article {pmid29992378,
year = {2018},
author = {Kasperski, A and Kasperska, R},
title = {Bioenergetics of life, disease and death phenomena.},
journal = {Theory in biosciences = Theorie in den Biowissenschaften},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12064-018-0266-5},
pmid = {29992378},
issn = {1611-7530},
abstract = {In this article, some new aspects of unified cell bioenergetics are presented. From the perspective of unified cell bioenergetics certain subsequent stages of cancer development, from initiation stage, through transformation to metastasis, are analyzed. Here we show that after transformation, cancer cells are permanently exposed to reactive oxygen species, that causes continual random DNA mutations and as a result genome and chromosomal destabilizations. The modern cancer attractor hypothesis has been extended in explaining cancer development. Discussion is conducted in light of current cancerogenesis research, including bioenergetic cancer initiation, the somatic mutation theory and the tissue organization field theory. In the article reasons complicating the discovery of patterns of cancer genome changes and cancer evolution are presented. In addition certain cancer therapeutic aspects are given attention to.},
}

@article {pmid29989670,
year = {2018},
author = {Iha, C and Grassa, CJ and de M Lyra, G and Davis, CC and Verbruggen, H and Oliveira, MC},
title = {Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta).},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.12765},
pmid = {29989670},
issn = {1529-8817},
abstract = {Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from ten species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny, Melanthalia intermedia is sister to a monophyletic clade including Gracilaria and Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes cob and trnL, and trnA and trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between psdD and rrs genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial leuC/leuD operon was found in chloroplast genomes of Gracilaria tenuistipitata, G. chilensis, and M. intermedia, and in extrachromosomal plasmid of G. vermiculophylla. Phylogenetic trees show two different origins of leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria. This article is protected by copyright. All rights reserved.},
}

@article {pmid29987715,
year = {2018},
author = {Rolland, N and Bouchnak, I and Moyet, L and Salvi, D and Kuntz, M},
title = {The Main Functions of Plastids.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1829},
number = {},
pages = {73-85},
doi = {10.1007/978-1-4939-8654-5_5},
pmid = {29987715},
issn = {1940-6029},
abstract = {Plastids are semiautonomous organelles like mitochondria, and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.},
}

@article {pmid29987711,
year = {2018},
author = {Maréchal, E},
title = {Primary Endosymbiosis: Emergence of the Primary Chloroplast and the Chromatophore, Two Independent Events.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1829},
number = {},
pages = {3-16},
doi = {10.1007/978-1-4939-8654-5_1},
pmid = {29987711},
issn = {1940-6029},
abstract = {The emergence of semiautonomous organelles, such as the mitochondrion, the chloroplast, and more recently, the chromatophore, are critical steps in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and finally the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter describes our current understanding of primary endosymbiosis, with a specific focus on primary chloroplasts considered to have emerged more than one billion years ago, and on the chromatophore, having emerged about one hundred million years ago.},
}

@article {pmid29984192,
year = {2018},
author = {MacDonald, JA and Fowle, WH and Shin, E and Woods, DC},
title = {A method for freeze-fracture and scanning electron microscopy of isolated mitochondria.},
journal = {MethodsX},
volume = {5},
number = {},
pages = {593-598},
doi = {10.1016/j.mex.2018.05.006},
pmid = {29984192},
issn = {2215-0161},
abstract = {Electron microscopy as a methodology for the study of mitochondria based on morphological features is a standard technique that has experienced little evolution over the course of several decades. This technology has identified heterogeneity of mitochondria populations across both whole tissues, as well between individual cells, using primarily ultrathin sections for transmission electron microscopy (TEM). However, this technique constrains the evaluation of a sample to a single two-dimensional plane. To overcome this limitation, scanning electron microscopy (SEM) has been successfully utilized to observe three-dimensional mitochondria structures within the complex microenvironment containing total cellular components. In response to these dual technical caveats of existing electron microscopy protocols, we developed a methodology to evaluate the three-dimensional ultrastructure of isolated mitochondria, utilizing a freeze-fracture step and rigorous preservation of sample morphology. This protocol allows for a more high-throughput analysis of mitochondria populations from a specimen of interest, as the sample has been previously purified, as well as a finer resolution of complex intra-mitochondrial structures, using the depth of field created by SEM. •Protocol designed for SEM of isolated mitochondria samples.•SEM visualizes mitochondria ultrastructure in 3-D.•Freeze-fracture creates cross-sectional plane for view of interior organelle structures.},
}

@article {pmid29970001,
year = {2018},
author = {Lenz, H and Hein, A and Knoop, V},
title = {Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {255},
doi = {10.1186/s12859-018-2244-9},
pmid = {29970001},
issn = {1471-2105},
abstract = {BACKGROUND: Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encoded in the organelle genomes. Predicting and analyzing RNA editing, which ranges from only few sites in some species to thousands in other taxa, is bioinformatically demanding.

RESULTS: Here, we present major enhancements and extensions of PREPACT, a WWW-based service for analysing, predicting and cataloguing plant-type RNA editing. New features in PREPACT's core include direct GenBank accession query input and options to restrict searches to candidate U-to-C editing or to sites where editing has been documented previously in the references. The reference database has been extended by 20 new organelle editomes. PREPACT 3.0 features new modules "EdiFacts" and "TargetScan". EdiFacts integrates information on pentatricopeptide repeat (PPR) proteins characterized as site-specific RNA editing factors. PREPACT's editome references connect into EdiFacts, linking editing events to specific co-factors where known. TargetScan allows position-weighted querying for sequence motifs in the organelle references, optionally restricted to coding regions or sequences around editing sites, or in queries uploaded by the user. TargetScan is mainly intended to evaluate and further refine the proposed PPR-RNA recognition code but may be handy for other tasks as well. We present an analysis for the immediate sequence environment of more than 15,000 documented editing sites finding strong and different bias in the editome data sets.

CONCLUSIONS: We exemplarily present the novel features of PREPACT 3.0 aimed to enhance the analyses of plant-type RNA editing, including its new modules EdiFacts integrating information on characterized editing factors and TargetScan aimed to analyse RNA editing site recognition specificities.},
}

@article {pmid29953866,
year = {2018},
author = {Woodling, NS and Partridge, L},
title = {Parkinson's Disease: Mitochondria Parked at the ER Hit the Snooze Button.},
journal = {Neuron},
volume = {98},
number = {6},
pages = {1059-1061},
doi = {10.1016/j.neuron.2018.06.025},
pmid = {29953866},
issn = {1097-4199},
abstract = {Parkinson's disease patients report sleep disturbances well ahead of motor symptoms. In this issue of Neuron, Valadas et al. (2018) report that the disease genes pink1 and parkin exert novel, cell-type-specific effects to modulate ER-mitochondria contacts, neuropeptidergic transmission, and sleep patterns.},
}

@article {pmid29948488,
year = {2018},
author = {Yoshida, Y},
title = {The cellular machineries responsible for the division of endosymbiotic organelles.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10265-018-1050-9},
pmid = {29948488},
issn = {1618-0860},
support = {Career Development Award/CDA00049/2018-C//Human Frontier Science Program/ ; KAKENHI/JP18K06325//Japan Society for the Promotion of Science/ ; },
abstract = {Chloroplasts (plastids) and mitochondria evolved from endosymbiotic bacteria. These organelles perform vital functions in photosynthetic eukaryotes, such as harvesting and converting energy for use in biological processes. Consistent with their evolutionary origins, plastids and mitochondria proliferate by the binary fission of pre-existing organelles. Here, I review the structures and functions of the supramolecular machineries driving plastid and mitochondrial division, which were discovered and first studied in the primitive red alga Cyanidioschyzon merolae. In the past decade, intact division machineries have been isolated from plastids and mitochondria and examined to investigate their underlying structure and molecular mechanisms. A series of studies has elucidated how these division machineries assemble and transform during the fission of these organelles, and which of the component proteins generate the motive force for their contraction. Plastid- and mitochondrial-division machineries have important similarities in their structures and mechanisms despite sharing no component proteins, implying that these division machineries evolved in parallel. The establishment of these division machineries might have enabled the host eukaryotic ancestor to permanently retain these endosymbiotic organelles by regulating their binary fission and the equal distribution of resources to daughter cells. These findings provide key insights into the establishment of endosymbiotic organelles and have opened new avenues of research into their evolution and mechanisms of proliferation.},
}

@article {pmid29946965,
year = {2018},
author = {Sharma, M and Bennewitz, B and Klösgen, RB},
title = {Rather rule than exception? How to evaluate the relevance of dual protein targeting to mitochondria and chloroplasts.},
journal = {Photosynthesis research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11120-018-0543-7},
pmid = {29946965},
issn = {1573-5079},
abstract = {Dual targeting of a nuclearly encoded protein into two different cell organelles is an exceptional event in eukaryotic cells. Yet, the frequency of such dual targeting is remarkably high in case of mitochondria and chloroplasts, the two endosymbiotic organelles of plant cells. In most instances, it is mediated by "ambiguous" transit peptides, which recognize both organelles as the target. A number of different approaches including in silico, in organello as well as both transient and stable in vivo assays are established to determine the targeting specificity of such transit peptides. In this review, we will describe and compare these approaches and discuss the potential role of this unusual targeting process. Furthermore, we will present a hypothetical scenario how dual targeting might have arisen during evolution.},
}

@article {pmid29945721,
year = {2018},
author = {Barshad, G and Marom, S and Cohen, T and Mishmar, D},
title = {Mitochondrial DNA Transcription and Its Regulation: An Evolutionary Perspective.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2018.05.009},
pmid = {29945721},
issn = {0168-9525},
abstract = {The bacterial heritage of mitochondria, as well as its independent genome [mitochondrial DNA (mtDNA)] and polycistronic transcripts, led to the view that mitochondrial transcriptional regulation relies on an evolutionarily conserved, prokaryotic-like system that is separated from the rest of the cell. Indeed, mtDNA transcription was previously thought to be governed by a few dedicated direct regulators, namely, the mitochondrial RNA polymerase (POLRMT), two transcription factors (TFAM and TF2BM), one transcription elongation (TEFM), and one known transcription termination factor (mTERF1). Recent findings have, however, revealed that known nuclear gene expression regulators are also involved in mtDNA transcription and have identified novel transcriptional features consistent with adaptation of the mitochondria to the regulatory environment of the precursor of the eukaryotic cell. Finally, whereas mammals follow the human mtDNA transcription pattern, other organisms notably diverge in terms of mtDNA transcriptional regulation. Hence, mtDNA transcriptional regulation is likely more evolutionary diverse than once thought.},
}

@article {pmid29945248,
year = {2018},
author = {Bize, P and Lowe, I and Lehto Hürlimann, M and Heckel, G},
title = {Effects of the mitochondrial and nuclear genomes on nonshivering thermogenesis in a wild derived rodent.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icy072},
pmid = {29945248},
issn = {1557-7023},
abstract = {A key adaptation of mammals to their environment is their ability to maintain a constant high body temperature, even at rest, under a wide range of ambient temperatures. In cold climates, this is achieved by an adaptive production of endogenous heat, known as nonshivering thermogenesis (NST), in the brown adipose tissue (BAT). This organ, unique to mammals, contains a very high density of mitochondria, and BAT correct functioning relies on the correct functioning of its mitochondria. Mitochondria enclose proteins encoded both in the maternally inherited mitochondrial genome and in the biparentally inherited nuclear genome, and one overlooked hypothesis is that both genomes and their interaction may shape NST. By housing under standardised conditions wild-derived common voles (Microtus arvalis) from two distinct evolutionary lineages (Western and Central), we show that Western voles had greater NST than Central voles. By introgressing those two lineages over at least 9 generations, we then experimentally tested the influence of the nuclear and mitochondrial genomes on NST and related phenotypic traits. We found that between-lineage variation in NST and BAT size were significantly influenced by the mitochondrial and nuclear genomes, respectively, with the Western mitochondrial genotype being associated with higher NST and the Western nuclear genotype with a larger BAT. There were significant mito-nuclear interactions on whole animal body weight and resting metabolic rate. Hybrid voles were lighter and had higher resting metabolic rate. Overall, our findings turn new light on the influence of the mitochondrial and nuclear genomes on thermogenesis and building adaptation to the environment in mammals.},
}

@article {pmid29944924,
year = {2018},
author = {Chakrabarty, S and Kabekkodu, SP and Singh, RP and Thangaraj, K and Singh, KK and Satyamoorthy, K},
title = {Mitochondria in health and disease.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2018.06.006},
pmid = {29944924},
issn = {1872-8278},
abstract = {Mitochondrial biology has become an area of intense research owing to the unique physiology of the organelle and its role in several types of cancers and other disorders. It has been found that mitochondria-encoded proteins, mitochondrial DNA and even RNA influence the functioning of the cell in more ways than were previously imagined. This may contribute to disease phenotypes which require detailed investigation and communication to the community health care providers. Additionally, this provides several novel avenues in drug designing against various cancers, neurodegenerative diseases and other metabolic disorders. The sixth annual conference of the Society for Mitochondrial Research and Medicine - India (SMRM) titled, 'Mitochondria in Health and Disease' was organized by Rana P. Singh at the School of Life Sciences, Jawaharlal Nehru University in New Delhi, India from 10th to 11th February 2017. The underlying objective of the conference was to provide a platform to discuss the recent advances in basic and translational research in mitochondrial biology and diseases. The conference aimed to translate academic research into clinical practice by providing a forum for basic researchers and clinicians to share their knowledge and build collaborations towards development of advanced therapeutic in mitochondrial diseases. To facilitate the knowledge-sharing, six major themes for the scientific sessions were (1) understanding of mitochondrial biology in disease progression, (2) advances in basic and translational mitochondrial research, (3) mitochondria in evolution and development, (4) targeting mitochondria for cancer prevention and treatment, (5) mitochondria in metabolic and neurological disorders and (6) mitochondria in stem cell and regeneration biology. This report summarizes the major outcomes of the discussions at the conference.},
}

@article {pmid29940392,
year = {2018},
author = {Wang, Q and Lu, W and Yang, J and Jiang, L and Zhang, Q and Kan, X and Yang, X},
title = {Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {28},
number = {},
pages = {27-36},
doi = {10.1016/j.cbd.2018.06.002},
pmid = {29940392},
issn = {1878-0407},
abstract = {Recent studies have shown that mitochondria play a crucial role in cellular energy production through the oxidative phosphorylation (OXPHOS) system. Complex I (NADH:ubiquinone oxidoreductase), the first and largest enzyme complex of the OXPHOS system, includes both nuclear- and mitochondrial-encoded proteins. However, the patterns of natural selection and phylogenetic implications of complex I in birds still remain unclear. In this study, we combined transcriptomic and phylogenetic analyses to comprehensively determine the evolution of avian complex I. The transcriptomes of three Passerida species (Leiothrix lutea, Spodiopsar sericeus, and Passer montanus) were obtained using the Illumina HiSeq™ 2500 system. More than 192,000,000 clean reads were assembled in a total of 828,267 transcripts. Evolutionary selection analysis suggested that six genes of the core subunits in avian complex I may have undergone putative positive selection. Notably, we found that the mean dN/dS (ω) ratio for mitochondrial genes of core subunits was significantly lower than that for nuclear genes of non-core subunits within complex I. The constructed maximum-parsimony, maximum-likelihood, and Bayesian inference phylogenetic trees were based on 44 complex I genes. We verified that the family Paridae (represented by Parus major and Pseudopodoces humilis) was clustered with Musicicapoidea. Our results provide new insights into the evolution of avian mitochondrial complex I.},
}

@article {pmid29934612,
year = {2018},
author = {Lajbner, Z and Pnini, R and Camus, MF and Miller, J and Dowling, DK},
title = {Experimental evidence that thermal selection shapes mitochondrial genome evolution.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {9500},
doi = {10.1038/s41598-018-27805-3},
pmid = {29934612},
issn = {2045-2322},
abstract = {Mitochondria are essential organelles, found within eukaryotic cells, which contain their own DNA. Mitochondrial DNA (mtDNA) has traditionally been used in population genetic and biogeographic studies as a maternally-inherited and evolutionary-neutral genetic marker. However, it is now clear that polymorphisms within the mtDNA sequence are routinely non-neutral, and furthermore several studies have suggested that such mtDNA polymorphisms are also sensitive to thermal selection. These observations led to the formulation of the "mitochondrial climatic adaptation" hypothesis, for which all published evidence to date is correlational. Here, we use laboratory-based experimental evolution in the fruit fly, Drosophila melanogaster, to test whether thermal selection can shift population frequencies of two mtDNA haplogroups whose natural frequencies exhibit clinal associations with latitude along the Australian east-coast. We present experimental evidence that the thermal regime in which the laboratory populations were maintained drove changes in haplogroup frequencies across generations. Our results strengthen the emerging view that intra-specific mtDNA variants are sensitive to selection, and suggest spatial distributions of mtDNA variants in natural populations of metazoans might reflect adaptation to climatic environments rather than within-population coalescence and diffusion of selectively-neutral haplotypes across populations.},
}

@article {pmid29923829,
year = {2018},
author = {Vitali, DG and Käser, S and Kolb, A and Dimmer, KS and Schneider, A and Rapaport, D},
title = {Independent evolution of functionally exchangeable mitochondrial outer membrane import complexes.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.34488},
pmid = {29923829},
issn = {2050-084X},
support = {ITN TAMPting, 607072//H2020 Marie Skłodowska-Curie Actions/ ; 138355//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; RA 1028/7-1,RA 1028/10-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Assembly and/or insertion of a subset of mitochondrial outer membrane (MOM) proteins, including subunits of the main MOM translocase, require the fungi-specific Mim1/Mim2 complex. So far it was unclear which proteins accomplish this task in other eukaryotes. Here, we show by reciprocal complementation that the MOM protein pATOM36 of trypanosomes is a functional analogue of yeast Mim1/Mim2 complex, even though these proteins show neither sequence nor topological similarity. Expression of pATOM36 rescues almost all growth, mitochondrial biogenesis, and morphology defects in yeast cells lacking Mim1 and/or Mim2. Conversely, co-expression of Mim1 and Mim2 restores the assembly and/or insertion defects of MOM proteins in trypanosomes ablated for pATOM36. Mim1/Mim2 and pATOM36 form native-like complexes when heterologously expressed, indicating that additional proteins are not part of these structures. Our findings indicate that Mim1/Mim2 and pATOM36 are the products of convergent evolution and arose only after the ancestors of fungi and trypanosomatids diverged.},
}

@article {pmid29923828,
year = {2018},
author = {Tokatlidis, K},
title = {Shaping the import system of mitochondria.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.38209},
pmid = {29923828},
issn = {2050-084X},
abstract = {Evidence is accumulating that unrelated species have independently evolved the same way of importing proteins in their mitochondria.},
}

@article {pmid29879897,
year = {2018},
author = {Hein, A and Knoop, V},
title = {Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {85},
doi = {10.1186/s12862-018-1203-4},
pmid = {29879897},
issn = {1471-2148},
abstract = {BACKGROUND: C-to-U RNA editing in mitochondria and chloroplasts and the nuclear-encoded, RNA-binding PPR proteins acting as editing factors present a wide field of co-evolution between the different genetic systems in a plant cell. Recent studies on chloroplast editing factors RARE1 and CRR28 addressing one or two chloroplast editing sites, respectively, found them strictly conserved among 65 flowering plants as long as one of their RNA editing targets remained present.

RESULTS: Extending the earlier sampling to 117 angiosperms with high-quality genome or transcriptome data, we find more evidence confirming previous conclusions but now also identify cases for expected evolutionary transition states such as retention of RARE1 despite loss of its editing target or the degeneration of CRR28 truncating its carboxyterminal DYW domain. The extended angiosperm set was now used to explore CLB19, an "E+"-type PPR editing factor targeting two chloroplast editing sites, rpoAeU200SF and clpPeU559HY, in Arabidopsis thaliana. We found CLB19 consistently conserved if one of the two targets was retained and three independent losses of CLB19 after elimination of both targets. The Ericales show independent regains of the ancestrally lost clpPeU559HY editing, further explaining why multiple-target editing factors are lost much more rarely than single target factors like RARE1. The retention of CLB19 despite loss of both editing targets in some Ericaceae, Apocynaceae and in Camptotheca (Nyssaceae) likely represents evolutionary transitions. However, the retention of CLB19 after a phylogenetic deep loss in the Poaceae rather suggests a yet unrecognized further editing target, for which we suggest editing event ndhAeU473SL.

CONCLUSION: Extending the scope of studies on plant organelle RNA editing to further taxa and additional nuclear cofactors reveals expected evolutionary transitions, strikingly different evolutionary dynamics for multiple-target editing factors like CLB19 and CRR28 and suggests additional functions for editing factor CLB19 among the Poaceae.},
}

@article {pmid29873740,
year = {2018},
author = {Scott, GR and Guo, KH and Dawson, NJ},
title = {The Mitochondrial Basis for Adaptive Variation in Aerobic Performance in High-Altitude Deer Mice.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icy056},
pmid = {29873740},
issn = {1557-7023},
abstract = {SYNOPSIS: Mitochondria play a central role in aerobic performance. Studies aimed at elucidating how evolved variation in mitochondrial physiology contributes to adaptive variation in aerobic performance can therefore provide a unique and powerful lens to understanding the evolution of complex physiological traits. Here, we review our ongoing work on the importance of changes in mitochondrial quantity and quality to adaptive variation in aerobic performance in high-altitude deer mice. Whole-organism aerobic capacity in hypoxia (VO2max) increases in response to hypoxia acclimation in this species, but high-altitude populations have evolved consistently greater VO2max than populations from low altitude. The evolved increase in VO2max in highlanders is associated with an evolved increase in the respiratory capacity of the gastrocnemius muscle. This appears to result from highlanders having more mitochondria in this tissue, attributed to a higher proportional abundance of oxidative fibre-types and a greater mitochondrial volume density within oxidative fibres. The latter is primarily caused by an over-abundance of subsarcolemmal mitochondria in high-altitude mice, which is likely advantageous for mitochondrial O2 supply because more mitochondria are situated adjacent to the cell membrane and close to capillaries. Evolved changes in gastrocnemius phenotype appear to be underpinned by population differences in the expression of genes involved in energy metabolism, muscle development, and vascular development. Hypoxia acclimation has relatively little effect on respiratory capacity of the gastrocnemius, but it increases respiratory capacity of the diaphragm. However, the mechanisms responsible for this increase differ between populations: lowlanders appear to adjust mitochondrial quantity and quality (i.e., increases in citrate synthase [CS] activity, and mitochondrial respiration relative to CS activity) and they exhibit higher rates of mitochondrial release of reactive oxygen species (ROS), whereas highlanders only increase mitochondrial quantity in response to hypoxia acclimation. In contrast to the variation in skeletal muscles, the respiratory capacity of cardiac muscle does not appear to be affected by hypoxia acclimation and varies little between populations. Therefore, evolved changes in mitochondrial quantity and quality make important tissue-specific contributions to adaptive variation in aerobic performance in high-altitude deer mice.},
}

@article {pmid29857468,
year = {2018},
author = {Avelange-Macherel, MH and Candat, A and Neveu, M and Tolleter, D and Macherel, D},
title = {Decoding the Divergent Subcellular Location of Two Highly Similar Paralogous LEA Proteins.},
journal = {International journal of molecular sciences},
volume = {19},
number = {6},
pages = {},
doi = {10.3390/ijms19061620},
pmid = {29857468},
issn = {1422-0067},
abstract = {Many mitochondrial proteins are synthesized as precursors in the cytosol with an N-terminal mitochondrial targeting sequence (MTS) which is cleaved off upon import. Although much is known about import mechanisms and MTS structural features, the variability of MTS still hampers robust sub-cellular software predictions. Here, we took advantage of two paralogous late embryogenesis abundant proteins (LEA) from Arabidopsis with different subcellular locations to investigate structural determinants of mitochondrial import and gain insight into the evolution of the LEA genes. LEA38 and LEA2 are short proteins of the LEA_3 family, which are very similar along their whole sequence, but LEA38 is targeted to mitochondria while LEA2 is cytosolic. Differences in the N-terminal protein sequences were used to generate a series of mutated LEA2 which were expressed as GFP-fusion proteins in leaf protoplasts. By combining three types of mutation (substitution, charge inversion, and segment replacement), we were able to redirect the mutated LEA2 to mitochondria. Analysis of the effect of the mutations and determination of the LEA38 MTS cleavage site highlighted important structural features within and beyond the MTS. Overall, these results provide an explanation for the likely loss of mitochondrial location after duplication of the ancestral gene.},
}

@article {pmid29852202,
year = {2018},
author = {Wang, M and Teng, Y},
title = {Genome-wide identification and analysis of MICU genes in land plants and their potential role in calcium stress.},
journal = {Gene},
volume = {670},
number = {},
pages = {174-181},
doi = {10.1016/j.gene.2018.05.102},
pmid = {29852202},
issn = {1879-0038},
mesh = {Calcium/metabolism ; Calcium-Binding Proteins/chemistry/*genetics/metabolism ; Down-Regulation ; Embryophyta/classification/genetics/*metabolism ; Evolution, Molecular ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Domains ; Signal Transduction ; *Stress, Physiological ; },
abstract = {Mitochondrial calcium uptake (MICU) plays a vital role in the regulation of mitochondrial calcium homeostasis, and, consequently, influences calcium signaling transduction. Although genes involved in mitochondrial calcium uptake have been well studied in animals, less is known about their ubiquity and function in plants. In this study, we identified 96 MICU genes in land plants. On the basis of phylogenetic analysis of MICU proteins, they were classified into three clades: MICU from eudicots (Clade I), from monocots (Clade II), and from a basal angiosperm, a bryophyte, and a lycophyte (Clade III). Pairwise identity analysis across all MICU proteins showed that they are highly conserved among land plants at the protein level. Conserved motif analysis showed that most MICU proteins contained three EF-hands, and an additional EF-hand motif first identified in the MICU of Arabidopsis thaliana but not mammals was found in all 96 putative MICU proteins. This suggests that a cellular pathway of calcium uptake and signaling that requires three EF-hand motifs is evolutionarily conserved in plants. In addition, we discovered that MICU-defective mutants of Arabidopsis thaliana exhibited longer roots than wild-type under high calcium stress. Concurrently, the mRNA transcription levels of MICU were decreased under high calcium conditions. These results suggest that loss-of-function mutations of MICU may have potential roles in helping plants resist high calcium stress. This study provides clues to the possible role of plant MICU in mitochondrial calcium uptake, as well as useful information to support further studies on MICU function in plants.},
}

Calcium/metabolism
Calcium-Binding Proteins/chemistry/*genetics/metabolism
Down-Regulation
Embryophyta/classification/genetics/*metabolism
Evolution, Molecular
Phylogeny
Plant Proteins/chemistry/genetics/metabolism
Protein Domains
Signal Transduction
*Stress, Physiological

@article {pmid29848286,
year = {2018},
author = {Darbani, B and Kell, DB and Borodina, I},
title = {Energetic evolution of cellular Transportomes.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {418},
doi = {10.1186/s12864-018-4816-5},
pmid = {29848286},
issn = {1471-2164},
support = {NNF10CC1016517//The Novo Nordisk Foundation Center for Biosustainability/ ; BB/M006891/1, BB/M017702/1 and BB/P009042/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 757384//H2020 European Research Council/ ; },
abstract = {BACKGROUND: Transporter proteins mediate the translocation of substances across the membranes of living cells. Many transport processes are energetically expensive and the cells use 20 to 60% of their energy to power the transportomes. We hypothesized that there may be an evolutionary selection pressure for lower energy transporters.

RESULTS: We performed a genome-wide analysis of the compositional reshaping of the transportomes across the kingdoms of bacteria, archaea, and eukarya. We found that the share of ABC transporters is much higher in bacteria and archaea (ca. 27% of the transportome) than in primitive eukaryotes (13%), algae and plants (10%) and in fungi and animals (5-6%). This decrease is compensated by an increased occurrence of secondary transporters and ion channels. The share of ion channels is particularly high in animals (ca. 30% of the transportome) and algae and plants with (ca. 13%), when compared to bacteria and archaea with only 6-7%. Therefore, our results show a move to a preference for the low-energy-demanding transporters (ion channels and carriers) over the more energy-costly transporter classes (ATP-dependent families, and ABCs in particular) as part of the transition from prokaryotes to eukaryotes. The transportome analysis also indicated seven bacterial species, including Neorickettsia risticii and Neorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, based on the phylogenetically restricted presence therein of clear homologues of modern mitochondrial solute carriers.

CONCLUSIONS: The results indicate that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. These changes have likely been important in the development of tissues performing energetically costly cellular functions.},
}

@article {pmid29843612,
year = {2018},
author = {Hartmann, T and Bernt, M and Middendorf, M},
title = {EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements.},
journal = {BMC bioinformatics},
volume = {19},
number = {1},
pages = {192},
doi = {10.1186/s12859-018-2170-x},
pmid = {29843612},
issn = {1471-2105},
support = {PhD student fellowship//Universit?t Leipzig/ ; },
abstract = {BACKGROUND: To study the differences between two unichromosomal circular genomes, e.g., mitochondrial genomes, under the tandem duplication random loss (TDRL) rearrangement it is important to consider the whole set of potential TDRL rearrangement events that could have taken place. The reason is that for two given circular gene orders there can exist different TDRL rearrangements that transform one of the gene orders into the other. Hence, a TDRL event cannot always be reconstructed only from the knowledge of the circular gene order before a TDRL event and the circular gene order after it.

RESULTS: We present the program EqualTDRL that computes and illustrates the complete set of TDRLs for pairs of circular gene orders that differ by only one TDRL. EqualTDRL considers the circularity of the given genomes and certain restrictions on the TDRL rearrangements. Examples for the latter are sequences of genes that have to be conserved during a TDRL or pairs of genes that frame intergenic regions which might represent remnants of duplicated genes. Additionally, EqualTDRL allows to determine the set of TDRLs that are minimum with respect to the number of duplicated genes.

CONCLUSION: EqualTDRL supports scientists to study the complete set of TDRLs that possibly could have taken place in the evolution of mitochondrial genomes. EqualTDRL is implemented in C++ using the ggplot2 package of the open source programming language R and is freely available from http://pacosy.informatik.uni-leipzig.de/equaltdrl .},
}

@article {pmid29808012,
year = {2018},
author = {Yuan, L and Zhai, L and Qian, L and Huang, and Ding, Y and Xiang, H and Liu, X and Thompson, JW and Liu, J and He, YH and Chen, XQ and Hu, J and Kong, QP and Tan, M and Wang, XF},
title = {Switching off IMMP2L signaling drives senescence via simultaneous metabolic alteration and blockage of cell death.},
journal = {Cell research},
volume = {28},
number = {6},
pages = {625-643},
doi = {10.1038/s41422-018-0043-5},
pmid = {29808012},
issn = {1748-7838},
support = {R01 CA154586/CA/NCI NIH HHS/United States ; UL1 TR001117/TR/NCATS NIH HHS/United States ; },
abstract = {Cellular senescence is a fundamental cell fate playing a significant role throughout the natural aging process. However, the molecular determinants distinguishing senescence from other cell-cycle arrest states such as quiescence and post-mitotic state, and the specified mechanisms underlying cell-fate decisions towards senescence versus cell death in response to cellular stress stimuli remain less understood. Employing multi-omics approaches, we revealed that switching off the specific mitochondrial processing machinery involving the peptidase IMMP2L serves as the foundation of the senescence program, which was also observed during the mammalian aging process. Mechanistically, we demonstrate that IMMP2L processes and thus activates at least two substrates, mitochondrial metabolic enzyme glycerol-3-phosphate dehydrogenase (GPD2) and cell death regulator apoptosis-inducing factor (AIF). For cells destined to senesce, concerted shutdown of the IMMP2L-GPD2 and IMMP2L-AIF signaling axes collaboratively drives the senescent process by reprogramming mitochondria-associated redox status, phospholipid metabolism and signaling network, and simultaneously blocking cell death under oxidative stress conditions.},
}

@article {pmid29806019,
year = {2018},
author = {Taborsky, M and Schütz, D and Goffinet, O and van Doorn, GS},
title = {Alternative male morphs solve sperm performance/longevity trade-off in opposite directions.},
journal = {Science advances},
volume = {4},
number = {5},
pages = {eaap8563},
doi = {10.1126/sciadv.aap8563},
pmid = {29806019},
issn = {2375-2548},
abstract = {Males pursuing alternative reproductive tactics have been predicted to face a trade-off between maximizing either swimming performance or endurance of their sperm. However, empirical evidence for this trade-off is equivocal, which may be due to simplistic assumptions. In the shell-brooding cichlid fish Lamprologus callipterus, two Mendelian male morphs compete for fertilization by divergent means: Bourgeois nest males ejaculate sperm, on average, about six times farther from the unfertilized ova than do parasitic dwarf males. This asymmetry is opposite to the usual situation, in which bourgeois males typically benefit from superior fertilization opportunities, suggesting that nest males' sperm should persist longer than dwarf male sperm. The assumed trade-off between sperm swimming performance and longevity predicts that, in turn, sperm of dwarf males should outperform that of nest males in swimming efficiency. Measurement of sperm performance and endurance reveals that dwarf male spermatozoa swim straighter initially than those of nest males, but their motility declines earlier and their velocity slows down more abruptly. Nest male sperm survives longer, which relates to a larger sperm head plus midpiece, implying more mitochondria. Thus, the trade-off between sperm performance and endurance is optimized in opposite directions by alternative male morphs. We argue that the relative success of alternative sperm performance strategies can be influenced strongly by environmental factors such as the time window between gamete release and fertilization, and the position of gamete release. This is an important yet little understood aspect of gametic adaptations to sperm competition.},
}

@article {pmid29802659,
year = {2018},
author = {Tilquin, A and Christie, JR and Kokko, H},
title = {Mitochondrial complementation: a possible neglected factor behind early eukaryotic sex.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jeb.13293},
pmid = {29802659},
issn = {1420-9101},
abstract = {Sex is ancestral in eukaryotes. Meiotic sex differs from bacterial ways of exchanging genetic material by involving the fusion of two cells. We examine the hypothesis that fusion evolved in early eukaryotes because it was directly beneficial, rather than a passive side effect of meiotic sex. We assume that the uptake of (proto)mitochondria into eukaryotes preceded the evolution of cell fusion and that Muller's ratchet operating within symbiont lineages led to the accumulation of lineage-specific sets of mutations in asexual host cells. We examine whether cell fusion, and the consequent biparental inheritance of symbionts, helps to mitigate the effects of this mutational meltdown of mitochondria. In our model, host cell fitness improves when two independently evolved mitochondrial strains co-inhabit a single cytoplasm, mirroring mitochondrial complementation found in modern eukaryotes. If fusion incurs no cost, we find that an allele coding for fusion can invade a population of nonfusers. If fusion is costly, there are two thresholds. The first describes a maximal fusing rate (probability of fusion per round of cell division) that is able to fix. An allele that codes for a rate above this threshold can reach a polymorphic equilibrium with nonfusers, as long as the rate is below the second threshold, above which the fusion allele is counter-selected. Whenever it evolves, fusion increases the population-wide level of heteroplasmy, which allows mitochondrial complementation and increases population fitness. We conclude that beneficial interactions between mitochondria are a potential factor that selected for cell fusion in early eukaryotes.},
}

@article {pmid29799088,
year = {2018},
author = {Li, Q and Chen, C and Xiong, C and Jin, X and Chen, Z and Huang, W},
title = {Comparative mitogenomics reveals large-scale gene rearrangements in the mitochondrial genome of two Pleurotus species.},
journal = {Applied microbiology and biotechnology},
volume = {102},
number = {14},
pages = {6143-6153},
doi = {10.1007/s00253-018-9082-6},
pmid = {29799088},
issn = {1432-0614},
support = {2016NZ0042//The National Science & Technology Pillar Program of Sichuan/ ; 2016NZ0103//the Crop Molecular Breeding Platform in Sichuan/ ; },
abstract = {In the present study, we assembled the mitogenomes of Pleurotus citrinopileatus and Pleurotus platypus. The circular mitogenome of the two Pleurotus species comprises a set of 14 conserved protein-encoding genes (PEGs), 2 RNA genes (small subunit ribosomal RNA and large subunit ribosomal RNA), and 24 tRNAs, with sizes of 60,694 and 73,807 bp, respectively. They contain 4 and 10 introns with 3 and 10 intronic open reading frames (ORFs), respectively. Thirteen position classes (Pcls) of introns were found in the cox1 gene of four Pleurotus species. The number and class of Pcl varied among different Pleurotus species, indicating that numerous events of loss and gain occurred during evolution of Pleurotus. Comparative mitogenomic and collinearity analyses reveal that large-scale gene rearrangements may have occurred during the evolution of Pleurotus citrinopileatus and Pleurotus platypus, including gene rearrangements and inversions, which may be related to the observed high amounts of repetitive DNA elements (5.62 and 5.45%, respectively). Phylogenetic analysis based on concatenated mitochondrial protein sequences reveals that concatenated mitochondrial genes are suitable as molecular markers for phylogenetic analysis. This serves as the first report on large-scale rearrangements in the mitochondria of the genus Pleurotus, thereby improving our understanding of the evolution of the Pleurotus genus and other macrofungi.},
}

@article {pmid29794041,
year = {2018},
author = {Camus, MF and Dowling, DK},
title = {Mitochondrial genetic effects on reproductive success: signatures of positive intrasexual, but negative intersexual pleiotropy.},
journal = {Proceedings. Biological sciences},
volume = {285},
number = {1879},
pages = {},
doi = {10.1098/rspb.2018.0187},
pmid = {29794041},
issn = {1471-2954},
abstract = {Theory predicts that maternal inheritance of mitochondria will facilitate the accumulation of mtDNA mutations that are male biased, or even sexually antagonistic, in effect. While there are many reported cases of mtDNA mutations conferring cytoplasmic male sterility in plants, historically it was assumed such mutations would not persist in the streamlined mitochondrial genomes of bilaterian metazoans. Intriguingly, recent cases of mitochondrial variants exerting male biases in effect have come to light in bilaterians. These cases aside, it remains unknown whether the mitochondrial genetic variation affecting phenotypic expression, and in particular reproductive performance, in bilaterians is routinely composed of sex-biased or sex-specific variation. If selection consistently favours mtDNA variants that augment female fitness, but at cost to males, this could shape patterns of pleiotropy and lead to negative intersexual correlations across mtDNA haplotypes. Here, we show that genetic variation across naturally occurring mitochondrial haplotypes affects components of reproductive success in both sexes, in the fruit fly Drosophila melanogaster We find that intrasexual correlations across mitochondrial haplotypes, for components of reproductive success, are generally positive, while intersexual correlations are negative. These results accord with theoretical predictions, suggesting that maternal inheritance has led to the fixation of numerous mutations of sexually antagonistic effect.},
}

@article {pmid29792772,
year = {2018},
author = {Xia, C and Wang, M and Yin, C and Cornejo, OE and Hulbert, S and Chen, X},
title = {Genome sequence resources for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei).},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-04-18-0107-A},
pmid = {29792772},
issn = {0894-0282},
abstract = {Puccinia striiformis f. sp. tritici (Pst) causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei (Psh) causes stripe rust on barley. Several Pst genomes are available, but no Psh genome is available. More genomes of Pst and Psh are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced Pst isolate 93-210 and Psh isolate 93TX-2 using PacBio and Illumina technologies, and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interaction.},
}

@article {pmid29787825,
year = {2018},
author = {Long, Z and Li, H and Du, Y and Han, B},
title = {Congenital sideroblastic anemia: Advances in gene mutations and pathophysiology.},
journal = {Gene},
volume = {668},
number = {},
pages = {182-189},
doi = {10.1016/j.gene.2018.05.074},
pmid = {29787825},
issn = {1879-0038},
mesh = {Anemia, Sideroblastic/congenital/*genetics/metabolism ; Heme/biosynthesis ; Humans ; Iron/metabolism ; Mitochondrial Proteins/biosynthesis ; *Mutation ; },
abstract = {Congenital sideroblastic anemia (CSA) is a series of rare, heterogeneous disorders, characterized by iron overload in the mitochondria of erythroblasts and ringed sideroblasts in bone marrow. In recent years, rapid development of next-generation sequencing technology brings great advance in understanding of genetic and pathophysiologic features of CSA. Based on the pathophysiology of mitochondrial iron metabolism, causative genes of CSA can be divided into three subtypes: heme biosynthesis related; iron‑sulfur cluster biosynthesis and transportation related; and mitochondrial respiratory chain synthesis related. Patients with CSA present various clinical manifestation due to relevant mutation gene and require different treatment strategies. The recognition of the causative genes and evolution of pathogenicity is critical. In this review, we summarize the recent progress in mutation genes of CSA, and its potential role in the pathogenesis, diagnosis and treatment.},
}

Anemia, Sideroblastic/congenital/*genetics/metabolism
Heme/biosynthesis
Humans
Iron/metabolism
Mitochondrial Proteins/biosynthesis
*Mutation

@article {pmid29779502,
year = {2018},
author = {Buysse, M and Duron, O},
title = {Multi-locus phylogenetics of the Midichloria endosymbionts reveals variable specificity of association with ticks.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-10},
doi = {10.1017/S0031182018000793},
pmid = {29779502},
issn = {1469-8161},
abstract = {Candidatus Midichloria mitochondrii is a maternally inherited bacterium of ticks with a unique intra-mitochondrial lifestyle. Here, we investigate on the evolutionary history of these associations and the degree of Midichloria-tick specificity. While previous surveys used the 16S rRNA gene as an exclusive molecular marker, we rather developed a multi-locus typing method based on four more variable housekeeping genes (groEL, rpoB, dnaK and ftsZ) and on one flagellum gene (fliC) present in Midichloria genomes. Using this method, multi-locus phylogenetic analyses revealed the structuring of a wide Midichloria genetic diversity into three distinct lineages associated with ticks. Overall, two distinct evolutionary strategies are obvious depending on lineage: two Midichloria lineages are generalists with infections acquired through horizontal transfers between distantly related tick species but one other Midichloria lineage rather show a high specificity degree to the Ixodes tick genus. This pattern suggests a capacity of certain Midichloria strains to maintain infections in only limited range of related tick species. These different infection strategies of Midichloria highlight an unexpected variability in their dependency to their tick hosts. We further conjecture that this pattern is also likely to indicate variability in their effects on ticks.},
}

@article {pmid29769322,
year = {2018},
author = {Krah, A and Zarco-Zavala, M and McMillan, DGG},
title = {Insights into the regulatory function of the ɛ subunit from bacterial F-type ATP synthases: a comparison of structural, biochemical and biophysical data.},
journal = {Open biology},
volume = {8},
number = {5},
pages = {},
doi = {10.1098/rsob.170275},
pmid = {29769322},
issn = {2046-2441},
abstract = {ATP synthases catalyse the formation of ATP, the most common chemical energy storage unit found in living cells. These enzymes are driven by an electrochemical ion gradient, which allows the catalytic evolution of ATP by a binding change mechanism. Most ATP synthases are capable of catalysing ATP hydrolysis to varying degrees, and to prevent wasteful ATP hydrolysis, bacteria and mitochondria have regulatory mechanisms such as ADP inhibition. Additionally, ɛ subunit inhibition has also been described in three bacterial systems, Escherichia coli, Bacillus PS3 and Caldalkalibacillus thermarum TA2.A1. Previous studies suggest that the ɛ subunit is capable of undergoing an ATP-dependent conformational change from the ATP hydrolytic inhibitory 'extended' conformation to the ATP-induced non-inhibitory 'hairpin' conformation. A recently published crystal structure of the F1 domain of the C. thermarum TA2.A1 F1Fo ATP synthase revealed a mutant ɛ subunit lacking the ability to bind ATP in a hairpin conformation. This is a surprising observation considering it is an organism that performs no ATP hydrolysis in vivo, and appears to challenge the current dogma on the regulatory role of the ɛ subunit. This has prompted a re-examination of present knowledge of the ɛ subunits role in different organisms. Here, we compare published biochemical, biophysical and structural data involving ɛ subunit-mediated ATP hydrolysis regulation in a variety of organisms, concluding that the ɛ subunit from the bacterial F-type ATP synthases is indeed capable of regulating ATP hydrolysis activity in a wide variety of bacteria, making it a potentially valuable drug target, but its exact role is still under debate.},
}

@article {pmid29761268,
year = {2018},
author = {Edera, AA and Gandini, CL and Sanchez-Puerta, MV},
title = {Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria.},
journal = {Plant molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11103-018-0734-9},
pmid = {29761268},
issn = {1573-5028},
abstract = {KEY MESSAGE: Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites. By means of publicly available RNA-seq data, this study identified 10,217 editing sites in mitochondrial protein-coding genes of 17 diverse angiosperms. Even though other types of mismatches were also identified, we did not find evidence of non-canonical editing processes. The results showed an uneven distribution of editing sites among species, genes, and codon positions. The analyses revealed that editing sites were conserved across angiosperms but there were some species-specific sites. Non-synonymous editing sites were particularly highly conserved (~ 80%) across the plant species and were efficiently edited (80% editing extent). In contrast, editing sites at third codon positions were poorly conserved (~ 30%) and only partially edited (~ 40% editing extent). We found that the loss of editing sites along angiosperm evolution is mainly occurring by replacing editing sites with thymidines, instead of a degradation of the editing recognition motif around editing sites. Consecutive and highly conserved editing sites had been replaced by thymidines as result of retroprocessing, by which edited transcripts are reverse transcribed to cDNA and then integrated into the genome by homologous recombination. This phenomenon was more pronounced in eudicots, and in the gene cox1. These results suggest that retroprocessing is a widespread driving force underlying the loss of editing sites in angiosperm mitochondria.},
}

@article {pmid29760081,
year = {2018},
author = {Sharp, NP and Sandell, L and James, CG and Otto, SP},
title = {The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {22},
pages = {E5046-E5055},
doi = {10.1073/pnas.1801040115},
pmid = {29760081},
issn = {1091-6490},
abstract = {By altering the dynamics of DNA replication and repair, alternative ploidy states may experience different rates and types of new mutations, leading to divergent evolutionary outcomes. We report a direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploids and diploids following a mutation-accumulation experiment in the budding yeast Saccharomyces cerevisiae Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide mutations (SNMs) and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that mutations would have weaker effects, due to masking, in diploids. Haploidy is expected to reduce the opportunity for conservative DNA repair involving homologous chromosomes, increasing the insertion-deletion rate, but we found little support for this idea. Instead, haploids were more susceptible to SNMs in late-replicating genomic regions, resulting in a ploidy difference in the spectrum of substitutions. In diploids, we detect mutation rate variation among chromosomes in association with centromere location, a finding that is supported by published polymorphism data. Diploids are not simply doubled haploids; instead, our results predict that the spectrum of spontaneous mutations will substantially shape the dynamics of genome evolution in haploid and diploid populations.},
}

@article {pmid29747566,
year = {2018},
author = {Oetjens, MT and Martin, A and Veeramah, KR and Kidd, JM},
title = {Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {350},
doi = {10.1186/s12864-018-4749-z},
pmid = {29747566},
issn = {1471-2164},
support = {R01 GM103961/GM/NIGMS NIH HHS/United States ; R01GM103961//National Institute of General Medical Sciences/ ; },
abstract = {BACKGROUND: Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs.

RESULTS: We identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700-7000 years old) belong to distinct clades.

CONCLUSIONS: We estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68-151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs.},
}

@article {pmid29743632,
year = {2018},
author = {Sinha, S and Bheemsetty, VA and Inamdar, MS},
title = {A double helical motif in OCIAD2 is essential for its localization, interactions and STAT3 activation.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {7362},
doi = {10.1038/s41598-018-25667-3},
pmid = {29743632},
issn = {2045-2322},
abstract = {The Ovarian Carcinoma Immunoreactive Antigen domain (OCIAD) - containing proteins OCIAD1/Asrij and OCIAD2, are implicated in several cancers and neurodegenerative diseases. While Asrij has a conserved role in facilitating STAT3 activation for JAK/STAT signaling, the expression and function of OCIAD2 in non-cancerous contexts remains unknown. Here, we report that ociad2 neighbors ociad1/asrij in most vertebrate genomes, and the two genes likely arose by tandem gene duplication, probably somewhere between the Ordovician and Silurian eras. We show that ociad2 expression is higher in the mouse kidney, liver and brain relative to other tissues. OCIAD2 localizes to early endosomes and mitochondria, and interacts with Asrij and STAT3. Knockdown and overexpression studies showed that OCIAD2 is essential for STAT3 activation and cell migration, which could contribute to its role in tumor metastasis. Structure prediction programs, protein disruption studies, biochemical and functional assays revealed a double helical motif in the OCIA domain that is necessary and sufficient for its localization, interactions and STAT3 activation. Given the importance of JAK/STAT signaling in development and disease, our studies shed light on the evolution and conserved function of the OCIA domain in regulating this pathway and will be critical for understanding this clinically important protein family.},
}

@article {pmid29731304,
year = {2018},
author = {Maclean, AE and Hertle, AP and Ligas, J and Bock, R and Balk, J and Meyer, EH},
title = {Absence of Complex I Is Associated with Diminished Respiratory Chain Function in European Mistletoe.},
journal = {Current biology : CB},
volume = {28},
number = {10},
pages = {1614-1619.e3},
doi = {10.1016/j.cub.2018.03.036},
pmid = {29731304},
issn = {1879-0445},
abstract = {Parasitism is a life history strategy found across all domains of life whereby nutrition is obtained from a host. It is often associated with reductive evolution of the genome, including loss of genes from the organellar genomes [1, 2]. In some unicellular parasites, the mitochondrial genome (mitogenome) has been lost entirely, with far-reaching consequences for the physiology of the organism [3, 4]. Recently, mitogenome sequences of several species of the hemiparasitic plant mistletoe (Viscum sp.) have been reported [5, 6], revealing a striking loss of genes not seen in any other multicellular eukaryotes. In particular, the nad genes encoding subunits of respiratory complex I are all absent and other protein-coding genes are also lost or highly diverged in sequence, raising the question what remains of the respiratory complexes and mitochondrial functions. Here we show that oxidative phosphorylation (OXPHOS) in European mistletoe, Viscum album, is highly diminished. Complex I activity and protein subunits of complex I could not be detected. The levels of complex IV and ATP synthase were at least 5-fold lower than in the non-parasitic model plant Arabidopsis thaliana, whereas alternative dehydrogenases and oxidases were higher in abundance. Carbon flux analysis indicates that cytosolic reactions including glycolysis are greater contributors to ATP synthesis than the mitochondrial tricarboxylic acid (TCA) cycle. Our results describe the extreme adjustments in mitochondrial functions of the first reported multicellular eukaryote without complex I.},
}

@article {pmid29730527,
year = {2018},
author = {van der Hoek, MD and Madsen, O and Keijer, J and van der Leij, FR},
title = {Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of CPT2 versus CPT1 and related variants.},
journal = {Biochimica et biophysica acta},
volume = {1863},
number = {8},
pages = {909-918},
doi = {10.1016/j.bbalip.2018.05.001},
pmid = {29730527},
issn = {0006-3002},
abstract = {Carnitine/choline acyltransferases play diverse roles in energy metabolism and neuronal signalling. Our knowledge of their evolutionary relationships, important for functional understanding, is incomplete. Therefore, we aimed to determine the evolutionary relationships of these eukaryotic transferases. We performed extensive phylogenetic and intron position analyses. We found that mammalian intramitochondrial CPT2 is most closely related to cytosolic yeast carnitine transferases (Sc-YAT1 and 2), whereas the other members of the family are related to intraorganellar yeast Sc-CAT2. Therefore, the cytosolically active CPT1 more closely resembles intramitochondrial ancestors than CPT2. The choline acetyltransferase is closely related to carnitine acetyltransferase and shows lower evolutionary rates than long chain acyltransferases. In the CPT1 family several duplications occurred during animal radiation, leading to the isoforms CPT1A, CPT1B and CPT1C. In addition, we found five CPT1-like genes in Caenorhabditis elegans that strongly group to the CPT1 family. The long branch leading to mammalian brain isoform CPT1C suggests that either strong positive or relaxed evolution has taken place on this node. The presented evolutionary delineation of carnitine/choline acyltransferases adds to current knowledge on their functions and provides tangible leads for further experimental research.},
}

@article {pmid29728774,
year = {2018},
author = {Gong, S and Vamberger, M and Auer, M and Praschag, P and Fritz, U},
title = {Millennium-old farm breeding of Chinese softshell turtles (Pelodiscus spp.) results in massive erosion of biodiversity.},
journal = {Die Naturwissenschaften},
volume = {105},
number = {5-6},
pages = {34},
doi = {10.1007/s00114-018-1558-9},
pmid = {29728774},
issn = {1432-1904},
support = {31471966//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Biodiversity ; *Breeding ; China ; DNA, Mitochondrial/genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Turtles/*classification/*genetics ; },
abstract = {Chinese softshell turtles (Pelodiscus spp.) are widely distributed, ranging from the Amur and Ussuri Rivers in the Russian Far East through the Korean Peninsula, Japan, and eastern, central, and southern China to southern Vietnam. In East and Southeast Asia, Chinese softshell turtles are traditionally exploited for food and have been farm-bred in China since the Spring and Autumn Period, more than 2400 years ago. Currently, the annual production of Pelodiscus amounts to 340,000 t in China alone. Using mitochondrial DNA (2428 bp) and five nuclear loci (3704 bp), we examined broad sampling of wild and farm-bred Pelodiscus to infer genetic and taxonomic differentiation. We discovered four previously unknown mitochondrial lineages, all from China. One lineage from Jiangxi is deeply divergent and sister to the mitochondrial lineage of Pelodiscus axenaria. The nuclear loci supported species status for P. axenaria and the new lineage from Jiangxi. Pelodiscus maackii and P. parviformis, both harboring distinct mitochondrial lineages, were not differentiated from P. sinensis in the studied nuclear markers. The same is true for two new mitochondrial lineages from Zhejiang, China, represented by only one individual each, and another new lineage from Anhui, Guangdong, Jiangxi and Zhejiang, China. However, Vietnamese turtles yielding a mitochondrial lineage clustering within P. sinensis were distinct in nuclear markers, suggesting that these populations could represent another unknown species with introgressed mitochondria. Its species status is also supported by the syntopic occurrence with P. sinensis in northern Vietnam and by morphology. In addition, we confirmed sympatry of P. axenaria and P. parviformis in Guangxi, China, and found evidence for sympatry of P. sinensis and the new putative species from Jiangxi, China. We also discovered evidence for hybridization in turtle farms and for the occurrence of alien lineages in the wild (Zhejiang, China), highlighting the risk of genetic pollution of native stock. In the face of the large-scale breeding of Pelodiscus, we claim that the long-term survival of distinct genetic lineages and species can only be assured when an upscale market segment for pure-bred softshell turtles is established, making the breeding of pure lineages lucrative for turtle farms. Our findings underline that the diversity of Pelodiscus is currently underestimated and threatened by anthropogenic admixture. We recommend mass screening of genetic and morphological variation of Chinese softshell turtles as a first step to understand and preserve their diversity.},
}

Animals
*Biodiversity
*Breeding
China
DNA, Mitochondrial/genetics
Microsatellite Repeats/genetics
Phylogeny
Turtles/*classification/*genetics

@article {pmid29723685,
year = {2018},
author = {Samuilov, VD and Kiselevsky, DB and Oleskin, AV},
title = {Mitochondria-targeted quinones suppress the generation of reactive oxygen species, programmed cell death and senescence in plants.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2018.04.008},
pmid = {29723685},
issn = {1872-8278},
abstract = {This work focuses on the effect of mitochondria-targeted quinones (SkQs) on plants. SkQs with antioxidant properties are accumulated in the mitochondria of pea cells and suppress the generation of reactive oxygen species. At nanomolar concentrations, SkQs prevented the death of pea leaf epidermal or guard cells caused by chitosan, bacterial lipopolysaccharide or KCN. The protective effect of SkQs was removed by a protonophoric uncoupler. SkQs at micromolar concentrations inhibited the O2 evolution by illuminated chloroplasts and stimulated the respiration of mitochondria. SkQs slowed down the senescence and the death of Arabidopsis thaliana leaves and improved the wheat crop structure.},
}

@article {pmid29706933,
year = {2018},
author = {Goetzman, ES and Prochownik, EV},
title = {The Role for Myc in Coordinating Glycolysis, Oxidative Phosphorylation, Glutaminolysis, and Fatty Acid Metabolism in Normal and Neoplastic Tissues.},
journal = {Frontiers in endocrinology},
volume = {9},
number = {},
pages = {129},
doi = {10.3389/fendo.2018.00129},
pmid = {29706933},
issn = {1664-2392},
support = {R01 CA174713/CA/NCI NIH HHS/United States ; R01 DK090242/DK/NIDDK NIH HHS/United States ; },
abstract = {That cancer cells show patterns of metabolism different from normal cells has been known for over 50 years. Yet, it is only in the past decade or so that an appreciation of the benefits of these changes has begun to emerge. Altered cancer cell metabolism was initially attributed to defective mitochondria. However, we now realize that most cancers do not have mitochondrial mutations and that normal cells can transiently adopt cancer-like metabolism during periods of rapid proliferation. Indeed, an encompassing, albeit somewhat simplified, conceptual framework to explain both normal and cancer cell metabolism rests on several simple premises. First, the metabolic pathways used by cancer cells and their normal counterparts are the same. Second, normal quiescent cells use their metabolic pathways and the energy they generate largely to maintain cellular health and organelle turnover and, in some cases, to provide secreted products necessary for the survival of the intact organism. By contrast, undifferentiated cancer cells minimize the latter functions and devote their energy to producing the anabolic substrates necessary to maintain high rates of unremitting cellular proliferation. Third, as a result of the uncontrolled proliferation of cancer cells, a larger fraction of the metabolic intermediates normally used by quiescent cells purely as a source of energy are instead channeled into competing proliferation-focused and energy-consuming anabolic pathways. Fourth, cancer cell clones with the most plastic and rapidly adaptable metabolism will eventually outcompete their less well-adapted brethren during tumor progression and evolution. This attribute becomes increasingly important as tumors grow and as their individual cells compete in a constantly changing and inimical environment marked by nutrient, oxygen, and growth factor deficits. Here, we review some of the metabolic pathways whose importance has gained center stage for tumor growth, particularly those under the control of the c-Myc (Myc) oncoprotein. We discuss how these pathways differ functionally between quiescent and proliferating normal cells, how they are kidnapped and corrupted during the course of transformation, and consider potential therapeutic strategies that take advantage of common features of neoplastic and metabolic disorders.},
}

@article {pmid29697049,
year = {2018},
author = {Stairs, CW and Eme, L and Muñoz-Gómez, SA and Cohen, A and Dellaire, G and Shepherd, JN and Fawcett, JP and Roger, AJ},
title = {Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.34292},
pmid = {29697049},
issn = {2050-084X},
support = {MOP 341174//Canadian Institutes of Health Research/Canada ; MOP 142349//Canadian Institutes of Health Research/Canada ; R15 GM096398/GM/NIGMS NIH HHS/United States ; 1R15GM096398-01//National Institutes of Health/ ; NSERC-CGS-D//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN 05616//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Under hypoxic conditions, some organisms use an electron transport chain consisting of only complex I and II (CII) to generate the proton gradient essential for ATP production. In these cases, CII functions as a fumarate reductase that accepts electrons from a low electron potential quinol, rhodoquinol (RQ). To clarify the origins of RQ-mediated fumarate reduction in eukaryotes, we investigated the origin and function of rquA, a gene encoding an RQ biosynthetic enzyme. RquA is very patchily distributed across eukaryotes and bacteria adapted to hypoxia. Phylogenetic analyses suggest lateral gene transfer (LGT) of rquA from bacteria to eukaryotes occurred at least twice and the gene was transferred multiple times amongst protists. We demonstrate that RquA functions in the mitochondrion-related organelles of the anaerobic protist Pygsuia and is correlated with the presence of RQ. These analyses reveal the role of gene transfer in the evolutionary remodeling of mitochondria in adaptation to hypoxia.},
}

@article {pmid29695865,
year = {2018},
author = {Martijn, J and Vosseberg, J and Guy, L and Offre, P and Ettema, TJG},
title = {Deep mitochondrial origin outside the sampled alphaproteobacteria.},
journal = {Nature},
volume = {557},
number = {7703},
pages = {101-105},
doi = {10.1038/s41586-018-0059-5},
pmid = {29695865},
issn = {1476-4687},
abstract = {Mitochondria are ATP-generating organelles, the endosymbiotic origin of which was a key event in the evolution of eukaryotic cells 1 . Despite strong phylogenetic evidence that mitochondria had an alphaproteobacterial ancestry 2 , efforts to pinpoint their closest relatives among sampled alphaproteobacteria have generated conflicting results, complicating detailed inferences about the identity and nature of the mitochondrial ancestor. While most studies support the idea that mitochondria evolved from an ancestor related to Rickettsiales3-9, an order that includes several host-associated pathogenic and endosymbiotic lineages10,11, others have suggested that mitochondria evolved from a free-living group12-14. Here we re-evaluate the phylogenetic placement of mitochondria. We used genome-resolved binning of oceanic metagenome datasets and increased the genomic sampling of Alphaproteobacteria with twelve divergent clades, and one clade representing a sister group to all Alphaproteobacteria. Subsequent phylogenomic analyses that specifically address long branch attraction and compositional bias artefacts suggest that mitochondria did not evolve from Rickettsiales or any other currently recognized alphaproteobacterial lineage. Rather, our analyses indicate that mitochondria evolved from a proteobacterial lineage that branched off before the divergence of all sampled alphaproteobacteria. In light of this new result, previous hypotheses on the nature of the mitochondrial ancestor6,15,16 should be re-evaluated.},
}

@article {pmid29689791,
year = {2018},
author = {Sadasivan, K and Ramesh, MB and Palot, MJ and Ambekar, M and Mirza, ZA},
title = {A new species of fan-throated lizard of the genus Sitana Cuvier, 1829 from coastal Kerala, southern India.},
journal = {Zootaxa},
volume = {4374},
number = {4},
pages = {545-564},
pmid = {29689791},
issn = {1175-5334},
mesh = {Animals ; India ; *Lizards ; Mitochondria ; Phylogeny ; },
abstract = {We here describe Sitana attenboroughii sp. nov., a new species of fan-throated lizard of the genus Sitana Cuvier, 1829 from coastal Kerala in southern India. The new species morphologically is closer to Sitana visiri Deepak, 2016 (in Deepak et al. 2016a), however, differs in having higher numbers of ventral scales and a comparatively short but richly colored dewlap. Genetically the new species shows affinity to Sitana marudhamneydhal Deepak, Khandekar, Varma Chaitanya, 2016 from which it differs in an uncorrected pairwise sequence divergence of 2.2% for a fragment of mitochondrial Nicotinamide adenine dinucleotide dehydrogenase (NADH) subunit 2 gene.},
}

Animals
India
*Lizards
Mitochondria
Phylogeny