@article {pmid31797248,
year = {2019},
author = {Hein, A and Brenner, S and Polsakiewicz, M and Knoop, V},
title = {The dual-targeted RNA editing factor AEF1 is universally conserved among angiosperms and reveals only minor adaptations upon loss of its chloroplast or its mitochondrial target.},
journal = {Plant molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11103-019-00940-9},
pmid = {31797248},
issn = {1573-5028},
abstract = {KEY MESSAGE: Upon loss of either its chloroplast or mitochondrial target, a uniquely dual-targeted factor for C-to-U RNA editing in angiosperms reveals low evidence for improved molecular adaptation to its remaining target. RNA-binding pentatricopeptide repeat (PPR) proteins specifically recognize target sites for C-to-U RNA editing in the transcriptomes of plant chloroplasts and mitochondria. Among more than 80 PPR-type editing factors that have meantime been characterized, AEF1 (or MPR25) is a special case given its dual targeting to both organelles and addressing an essential mitochondrial (nad5eU1580SL) and an essential chloroplast (atpFeU92SL) RNA editing site in parallel in Arabidopsis. Here, we explored the angiosperm-wide conservation of AEF1 and its two organelle targets. Despite numerous independent losses of the chloroplast editing site by C-to-T conversion and at least four such conversions at the mitochondrial target site in other taxa, AEF1 remains consistently conserved in more than 120 sampled angiosperm genomes. Not a single case of simultaneous loss of the chloroplast and mitochondrial editing target or of AEF1 disintegration or loss could be identified, contrasting previous findings for editing factors targeted to only one organelle. Like in most RNA editing factors, the PPR array of AEF1 reveals potential for conceptually "improved fits" to its targets according to the current PPR-RNA binding code. Surprisingly, we observe only minor evidence for adaptation to the mitochondrial target also after deep losses of the chloroplast target among Asterales, Caryophyllales and Poales or, vice versa, for the remaining chloroplast target after a deep loss of the mitochondrial target among Malvales. The evolutionary observations support the notion that PPR-RNA mismatches may be essential for proper function of editing factors.},
}

@article {pmid31794060,
year = {2019},
author = {Kumar, S and Nandi, A and Mahesh, A and Sinha, S and Flores, E and Chakrabarti, R},
title = {Novel function of ∆Np63 in cell polarity and metabolism in pubertal mammary gland development.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.13703},
pmid = {31794060},
issn = {1873-3468},
abstract = {The ∆Np63 isoform of the p53-family transcription factor Trp63 is a key regulator of mammary epithelial stem cells that is involved in breast cancer development. To investigate the role of ∆Np63 at different stages of normal mammary gland development, we generated a ∆Np63 inducible conditional knockout (cKO) mouse model. We demonstrate that deletion of ∆Np63 at puberty results in depletion of mammary stem cell-enriched basal cells, reduces expression of E-cadherin and β-catenin, and leads to a closed ductal lumen. RNA-sequencing analysis reveals reduced expression of oxidative phosphorylation (OXPHOS)-associated proteins and desmosomal polarity proteins. Functional assays show reduced numbers of mitochondria in the mammary epithelial cells of ΔNp63 cKO compared to wildtype, supporting the reduced OXPHOS phenotype. These findings identify a novel role for ∆Np63 in cellular metabolism and mammary epithelial cell polarity.},
}

@article {pmid31787040,
year = {2020},
author = {Bettinazzi, S and Nadarajah, S and Dalpé, A and Milani, L and Blier, PU and Breton, S},
title = {Linking paternally inherited mtDNA variants and sperm performance.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1790},
pages = {20190177},
doi = {10.1098/rstb.2019.0177},
pmid = {31787040},
issn = {1471-2970},
abstract = {Providing robust links between mitochondrial genotype and phenotype is of major importance given that mitochondrial DNA (mtDNA) variants can affect reproductive success. Because of the strict maternal inheritance (SMI) of mitochondria in animals, haplotypes that negatively affect male fertility can become fixed in populations. This phenomenon is known as 'mother's curse'. Doubly uniparental inheritance (DUI) of mitochondria is a stable exception in bivalves, which entails two mtDNA lineages that evolve independently and are transmitted separately through oocytes and sperm. This makes the DUI mitochondrial lineages subject to different sex-specific selective sieves during mtDNA evolution, thus DUI is a unique model to evaluate how direct selection on sperm mitochondria could contribute to male reproductive fitness. In this study, we tested the impact of mtDNA variants on sperm performance and bioenergetics in DUI and SMI species. Analyses also involved measures of sperm performance following inhibition of main energy pathways and sperm response to oocyte presence. Compared to SMI, DUI sperm exhibited (i) low speed and linearity, (ii) a strict OXPHOS-dependent strategy of energy production, and (iii) a partial metabolic shift towards fermentation following egg detection. Discussion embraces the adaptive value of mtDNA variation and suggests a link between male-energetic adaptation, fertilization success and paternal mitochondria preservation. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.},
}

@article {pmid31787038,
year = {2020},
author = {Nagarajan-Radha, V and Aitkenhead, I and Clancy, DJ and Chown, SL and Dowling, DK},
title = {Sex-specific effects of mitochondrial haplotype on metabolic rate in Drosophila melanogaster support predictions of the Mother's Curse hypothesis.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1790},
pages = {20190178},
doi = {10.1098/rstb.2019.0178},
pmid = {31787038},
issn = {1471-2970},
abstract = {Evolutionary theory proposes that maternal inheritance of mitochondria will facilitate the accumulation of mitochondrial DNA (mtDNA) mutations that are harmful to males but benign or beneficial to females. Furthermore, mtDNA haplotypes sampled from across a given species distribution are expected to differ in the number and identity of these 'male-harming' mutations they accumulate. Consequently, it is predicted that the genetic variation which delineates distinct mtDNA haplotypes of a given species should confer larger phenotypic effects on males than females (reflecting mtDNA mutations that are male-harming, but female-benign), or sexually antagonistic effects (reflecting mutations that are male-harming, but female-benefitting). These predictions have received support from recent work examining mitochondrial haplotypic effects on adult life-history traits in Drosophila melanogaster. Here, we explore whether similar signatures of male-bias or sexual antagonism extend to a key physiological trait-metabolic rate. We measured the effects of mitochondrial haplotypes on the amount of carbon dioxide produced by individual flies, controlling for mass and activity, across 13 strains of D. melanogaster that differed only in their mtDNA haplotype. The effects of mtDNA haplotype on metabolic rate were larger in males than females. Furthermore, we observed a negative intersexual correlation across the haplotypes for metabolic rate. Finally, we uncovered a male-specific negative correlation, across haplotypes, between metabolic rate and longevity. These results are consistent with the hypothesis that maternal mitochondrial inheritance has led to the accumulation of a sex-specific genetic load within the mitochondrial genome, which affects metabolic rate and that may have consequences for the evolution of sex differences in life history. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.},
}

@article {pmid31787037,
year = {2020},
author = {Camus, MF and O'Leary, M and Reuter, M and Lane, N},
title = {Impact of mitonuclear interactions on life-history responses to diet.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1790},
pages = {20190416},
doi = {10.1098/rstb.2019.0416},
pmid = {31787037},
issn = {1471-2970},
abstract = {Mitochondria are central to both energy metabolism and biosynthesis. Mitochondrial function could therefore influence resource allocation. Critically, mitochondrial function depends on interactions between proteins encoded by the mitochondrial and nuclear genomes. Severe incompatibilities between these genomes can have pervasive effects on both fitness and longevity. How milder deficits in mitochondrial function affect life-history trade-offs is less well understood. Here, we analyse how mitonuclear interactions affect the trade-off between fecundity and longevity in Drosophila melanogaster. We consider a panel of 10 different mitochondrial DNA haplotypes against two contrasting nuclear backgrounds (w1118 (WE) and Zim53 (ZIM)) in response to high-protein versus standard diet. We report strikingly different responses between the two nuclear backgrounds. WE females have higher fecundity and decreased longevity on high protein. ZIM females have much greater fecundity and shorter lifespan than WE flies on standard diet. High protein doubled their fecundity with no effect on longevity. Mitochondrial haplotype reflected nuclear life-history trade-offs, with a negative correlation between longevity and fecundity in WE flies and no correlation in ZIM flies. Mitonuclear interactions had substantial effects but did not reflect genetic distance between mitochondrial haplotypes. We conclude that mitonuclear interactions can have significant impact on life-history trade-offs, but their effects are not predictable by relatedness. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.},
}

@article {pmid31553224,
year = {2019},
author = {Seligmann, H},
title = {Syntenies Between Cohosted Mitochondrial, Chloroplast, and Phycodnavirus Genomes: Functional Mimicry and/or Common Ancestry?.},
journal = {DNA and cell biology},
volume = {38},
number = {11},
pages = {1257-1268},
doi = {10.1089/dna.2019.4858},
pmid = {31553224},
issn = {1557-7430},
mesh = {Adaptive Immunity/genetics ; Chloroplasts/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions/genetics/immunology ; Immune Evasion/genetics ; Mitochondria/*genetics ; Molecular Mimicry/*physiology ; Organelles/genetics ; Phycodnaviridae/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Synteny/*genetics ; },
abstract = {Recent analyses suggest bacterial and/or mitochondrion-like ancestry for giant viruses (Megavirales sensu latu): amoeban mitochondrial gene arrangements resemble those of their candidate homologs in megaviral genomes. This presumed ancestral synteny decreases with genome size across megaviral families at large and within Poxviridae. In this study, analyses focus on Phycodnaviridae, a polyphyletic group of giant viruses infecting Haplophyta, Stramenopiles, and other algae, using syntenies between algal mitogene arrangements and chloroplast genomes and Rickettsia prowazekii as positive controls. Mitogene alignment qualities with Rickettsia are much higher than with viral genomes. Mitogenome synteny with some viruses is higher, for others lower than with Rickettsia, despite lower alignments qualities. In some algae, syntenies among cohosted chloroplast, virus, and mitochondrion are higher, in others lower than expected. This suggests gene order coevolution in cohosted genomes, different coregulations of organelle metabolisms for different algae, and viral mitogenome mimicry, to hijack organelle-committed cellular resources and/or escape cellular defenses/genetic immunity systems. This principle might explain high synteny between human mitochondria and the pathogenic endocellular alphaproteobacterium R. prowazekii beyond common ancestry. Results indicate that putative bacteria/mitochondrion-like genomic ancestors of Phycodnaviridae originated before or at the mitochondrion-bacteria split, and ulterior functional constraints on gene arrangements of cohosted genomes.},
}

Adaptive Immunity/genetics
Chloroplasts/*genetics
*Evolution, Molecular
Genome, Mitochondrial/genetics
Genome, Viral/genetics
Host-Pathogen Interactions/genetics/immunology
Immune Evasion/genetics
Mitochondria/*genetics
Molecular Mimicry/*physiology
Organelles/genetics
Phycodnaviridae/*genetics
Phylogeny
Sequence Analysis, DNA
Synteny/*genetics

@article {pmid30639162,
year = {2019},
author = {López Rivero, AS and Rossi, MA and Ceccarelli, EA and Catalano-Dupuy, DL},
title = {A bacterial 2[4Fe4S] ferredoxin as redox partner of the plastidic-type ferredoxin-NADP+ reductase from Leptospira interrogans.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {1863},
number = {4},
pages = {651-660},
doi = {10.1016/j.bbagen.2019.01.004},
pmid = {30639162},
issn = {1872-8006},
mesh = {Amino Acid Sequence ; Ferredoxin-NADP Reductase/chemistry/*metabolism ; Ferredoxins/chemistry/*metabolism ; Leptospira interrogans/*enzymology ; Models, Molecular ; Oxidation-Reduction ; Phylogeny ; Protein Conformation ; Sequence Alignment ; },
abstract = {BACKGROUND: Ferredoxins are small iron-sulfur proteins that participate as electron donors in various metabolic pathways. They are recognized substrates of ferredoxin-NADP+ reductases (FNR) in redox metabolisms in mitochondria, plastids, and bacteria. We previously found a plastidic-type FNR in Leptospira interrogans (LepFNR), a parasitic bacterium of animals and humans. Nevertheless, we did not identify plant-type ferredoxins or flavodoxins, the common partners of this kind of FNR.

METHODS: Sequence alignment, phylogenetical analyses and structural modeling were performed for the identification of a 2[4Fe4S] ferredoxin (LepFd2) as a putative redox partner of LepFNR in L. interrogans. The gene encoding LepFd2 was cloned and the protein overexpressed and purified. The functional properties of LepFd2 and LepFNR-LepFd2 complex were analyzed by kinetic and mutagenesis studies.

RESULTS: We succeeded in expressing and purifying LepFd2 with its FeS cluster properly bound. We found that LepFd2 exchanges electrons with LepFNR. Moreover, a unique structural subdomain of LepFNR (loop P75-Y91), was shown to be involved in the recognition and binding of LepFd2. This structural subdomain is not found in other FNR homologs.

CONCLUSIONS: We report for the first time a redox pair in L. interrogans in which a plastidic FNR exchanges electron with a bacterial 2[4Fe4S] ferredoxin. We characterized this reaction and proposed a model for the productive LepFNR-LepFd2 complex.

GENERAL SIGNIFICANCE: Our findings suggest that the interaction of LepFNR with the iron-sulfur protein would be different from the one previously described for the homolog enzymes. This knowledge would be useful for the design of specific LepFNR inhibitors.},
}

Amino Acid Sequence
Ferredoxin-NADP Reductase/chemistry/*metabolism
Ferredoxins/chemistry/*metabolism
Leptospira interrogans/*enzymology
Models, Molecular
Oxidation-Reduction
Phylogeny
Protein Conformation
Sequence Alignment

@article {pmid31786061,
year = {2019},
author = {Chiang, AC and McCartney, E and O'Farrell, PH and Ma, H},
title = {A Genome-wide Screen Reveals that Reducing Mitochondrial DNA Polymerase Can Promote Elimination of Deleterious Mitochondrial Mutations.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2019.10.060},
pmid = {31786061},
issn = {1879-0445},
abstract = {A mutant mitochondrial genome arising amid the pool of mitochondrial genomes within a cell must compete with existing genomes to survive to the next generation. Even weak selective forces can bias transmission of one genome over another to affect the inheritance of mitochondrial diseases and guide the evolution of mitochondrial DNA (mtDNA). Studies in several systems suggested that purifying selection in the female germline reduces transmission of detrimental mitochondrial mutations [1-7]. In contrast, some selfish genomes can take over despite a cost to host fitness [8-13]. Within individuals, the outcome of competition is therefore influenced by multiple selective forces. The nuclear genome, which encodes most proteins within mitochondria, and all external regulators of mitochondrial biogenesis and dynamics can influence the competition between mitochondrial genomes [14-18], yet little is known about how this works. Previously, we established a Drosophila line transmitting two mitochondrial genomes in a stable ratio enforced by purifying selection benefiting one genome and a selfish advantage favoring the other [8]. Here, to find nuclear genes that impact mtDNA competition, we screened heterozygous deletions tiling ∼70% of the euchromatic regions and examined their influence on this ratio. This genome-wide screen detected many nuclear modifiers of this ratio and identified one as the catalytic subunit of mtDNA polymerase gene (POLG), tam. A reduced dose of tam drove elimination of defective mitochondrial genomes. This study suggests that our approach will uncover targets for interventions that would block propagation of pathogenic mitochondrial mutations.},
}

@article {pmid31784872,
year = {2019},
author = {Wang, J and Yang, M and Xiao, H and Huang, GH and Deng, F and Hu, Z},
title = {Genome Analysis of Dasineura jujubifolia Toursvirus 2, A Novel Ascovirus.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12250-019-00177-2},
pmid = {31784872},
issn = {1995-820X},
abstract = {So far, ascoviruses have only been identified from Lepidoptera host insects and their transmission vectors-endoparasitic wasps. Here, we reported the first finding of a complete novel ascovirus genome from a Diptera insect, Dasineura jujubifolia. Initially, sequence fragments with homology to ascoviruses were incidentally identified during metagenomic sequencing of the mitochondria of D. jujubifolia (Cecidomyiidae, Diptera) which is a major pest on Ziziphus jujuba. Then a full circular viral genome was assembled from the metagenomic data, which has an A+T percentage of 74% and contains 142,600 bp with 141 open reading frames (ORFs). Among the 141 ORFs, 37 were conserved in all sequenced ascoviruses (core genes) including proteins predicted to participate in DNA replication, gene transcription, protein modification, virus assembly, lipid metabolism and apoptosis. Multi-gene families including those encode for baculovirus repeated open reading frames (BROs), myristylated membrane proteins, RING/U-box E3 ubiquitin ligases, and ATP-binding cassette (ABC) transporters were found in the virus genome. Phylogenetic analysis showed that the newly identified virus belongs to genus Toursvirus of Ascoviridae, and is therefore named as Dasineura jujubifolia toursvirus 2 (DjTV-2a). The virus becomes the second reported species of the genus after Diadromus pulchellus toursvirus 1 (DpTV-1a). The genome arrangement of DjTV-2a is quite different from that of DpTV-1a, suggesting these two viruses separated in an early time of evolution. The results suggest that the ascoviruses may infect a much broader range of hosts than our previous knowledge, and shed lights on the evolution of ascoviruses and particularly on that of the toursviruses.},
}

@article {pmid31780199,
year = {2019},
author = {Waltz, F and Giegé, P},
title = {Striking Diversity of Mitochondria-Specific Translation Processes across Eukaryotes.},
journal = {Trends in biochemical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibs.2019.10.004},
pmid = {31780199},
issn = {0968-0004},
abstract = {Mitochondria are essential organelles that act as energy conversion powerhouses and metabolic hubs. Their gene expression machineries combine traits inherited from prokaryote ancestors and specific features acquired during eukaryote evolution. Mitochondrial research has wide implications ranging from human health to agronomy. We highlight recent advances in mitochondrial translation. Functional, biochemical, and structural data have revealed an unexpected diversity of mitochondrial translation systems, particularly of their key players, the mitochondrial ribosomes (mitoribosomes). Ribosome assembly and translation mechanisms, such as initiation, are discussed and put in perspective with the prevalence of eukaryote-specific families of mitochondrial translation factors such as pentatricopeptide repeat (PPR) proteins.},
}

@article {pmid31300133,
year = {2019},
author = {Mirbadie, SR and Najafi Nasab, A and Mohaghegh, MA and Norouzi, P and Mirzaii, M and Spotin, A},
title = {Molecular phylodiagnosis of Echinococcus granulosus sensu lato and Taenia hydatigena determined by mitochondrial Cox1 and SSU-rDNA markers in Iranian dogs: Indicating the first record of pig strain (G7) in definitive host in the Middle East.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {65},
number = {},
pages = {88-95},
doi = {10.1016/j.cimid.2019.05.005},
pmid = {31300133},
issn = {1878-1667},
mesh = {Animals ; Cyclooxygenase 1/genetics ; DNA, Ribosomal/genetics ; Dog Diseases/diagnosis/*epidemiology ; Dogs/parasitology ; Echinococcosis/diagnosis/epidemiology/*veterinary ; Echinococcus granulosus/genetics ; Feces/parasitology ; Genotype ; Intestinal Diseases, Parasitic/diagnosis/*veterinary ; Iran/epidemiology ; Middle East/epidemiology ; Mitochondria/genetics ; *Phylogeny ; Prevalence ; Swine/parasitology ; Taenia/genetics ; Taeniasis/diagnosis/epidemiology/*veterinary ; },
abstract = {Unawareness of canine parasitic diseases among at-risk hosts and an uncontrolled program of stray dog population have caused that zoonotic parasites received great attention in endemic regions of the Middle East. A total of 552 faecal samples were collected between December 2016 to January 2018 from stray (n = 408) and domestic (n = 144) dogs of Iran. All specimens were coproscopically observed following concentration and flotation techniques. Subsequently, the DNAs of taeniid eggs were extracted, amplified, and sequenced by targeting of mitochondrial cytochrome oxidase subunit 1 and small-subunit ribosomal DNA markers. The overall prevalence of canine intestinal parasites found 53.6%. The following parasites and their total frequencies were identified: taeniid (10.5%), Dicrocoelium dendriticum (0.7%), Trichuris vulpis (1.2%), Capillaria spp. (2.3%), Blastocystis spp. (5.2%), Ancylostoma spp. (2%), Eimeria spp. (13.2%), Dipylidium caninum (2.3%), Toxocara canis (3.8%), Giardia spp. (8.5%), and Toxascaris leonina (3.6%). Stray dogs were characterized more likely to be poliparasitized and indicated a higher prevalence of taeniid (10.9%), T. canis (4.4%) Giardia spp. (10.1%) than domestic dogs (P > 0.05). Phylogenetic and sequence analysis of Cox1 and SSU-rDNA indicated a low genetic diversity (Haplotype diversity; 0 to 0.495) in E. granulosus sensu lato G1, G3, G7 genotypes, and Taenia hydatigena. The pairwise sequence distances between G7 isolates showed an intra-diversity of 0.7%-1.5% and identity of 98.5%-100%. The first occurrence of pig strain (G7) from Iranian dogs might have substantial implications in the drug treatment of infected dogs due to the shorter maturation time of G7 compared with G1 genotype. Thus, the preventive strategies should be noticed to determine the risk factors, the importance of applying the hygienic practices, and well adjusting deworming programs for the Iranian dogs and at-risk individuals.},
}

Animals
Cyclooxygenase 1/genetics
DNA, Ribosomal/genetics
Dog Diseases/diagnosis/*epidemiology
Dogs/parasitology
Echinococcosis/diagnosis/epidemiology/*veterinary
Echinococcus granulosus/genetics
Feces/parasitology
Genotype
Intestinal Diseases, Parasitic/diagnosis/*veterinary
Iran/epidemiology
Middle East/epidemiology
Mitochondria/genetics
*Phylogeny
Prevalence
Swine/parasitology
Taenia/genetics
Taeniasis/diagnosis/epidemiology/*veterinary

@article {pmid31136801,
year = {2019},
author = {Peres, EA and Benedetti, AR and Hiruma, ST and Sobral-Souza, T and Pinto-da-Rocha, R},
title = {Phylogeography of Sodreaninae harvestmen (Arachnida: Opiliones: Gonyleptidae): Insights into the biogeography of the southern Brazilian Atlantic Forest.},
journal = {Molecular phylogenetics and evolution},
volume = {138},
number = {},
pages = {1-16},
doi = {10.1016/j.ympev.2019.05.028},
pmid = {31136801},
issn = {1095-9513},
mesh = {Animals ; Arachnida/*classification/genetics ; Bayes Theorem ; Brazil ; Cell Nucleus/genetics ; *Forests ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Population Dynamics ; },
abstract = {The Brazilian Atlantic Forest has long been considered a global biodiversity hotspot. In the last decade, the phylogeographic patterns of endemic taxa have been unraveling the biogeographic history of the biome. However, highly diverse invertebrate species have still been poorly studied. Sodreana harvestmen (Gonyleptidae) are distributed in most of the humid coastal forests in the southern portion of the Atlantic Forest, a region that has experienced complex topographic evolution and differing climatic conditions since the Early Cretaceous, which likely affected the geographic distribution and diversification of the group. In this study, we investigated the molecular phylogeny and phylogeography of Sodreana to clarify the species relationships and to make inferences about the historical biogeography of the southern Atlantic Forest. We applied coalescent-based phylogenetic analyses using one mitochondrial and three nuclear markers coupled with an ecological niche modeling approach to verify relationships among species, date the main divergence events in the genus, and make inferences concerning possible changes in the geographical distribution and population dynamics from the past. Our results supported the validity of most Sodreana species and suggested that Paleogene-Neogene geomorphologic processes such as the formation of rivers systems, uplift of mountain ranges and related environmental changes have profoundly affected the evolutionary history of Sodreana. The ecological niche models showed that the areas potentially occupied by the species were greatly reduced during Quaternary glacial periods but no recent lineage divergences or genetic bottlenecks were detected, suggesting that climatically stable micro-habitats could have helped maintain populations during drier periods. Our study highlights the importance of humidity-dependent and poor-dispersal taxa in understanding the effects of ancient geological and climate processes on the Atlantic Forest biota.},
}

Animals
Arachnida/*classification/genetics
Bayes Theorem
Brazil
Cell Nucleus/genetics
*Forests
Genetic Variation
Genetics, Population
Haplotypes/genetics
Mitochondria/genetics
Phylogeny
*Phylogeography
Population Dynamics

@article {pmid31121309,
year = {2019},
author = {Santos, JCMD and Ferreira, ES and Oliveira, C and Oliveira, TB and Costa, ASLD and Queiroz, AKO and Schneider, H and Sampaio, I and Santos, S},
title = {Phylogeny of the genus Hypophthalmus Cuvier, 1829 (Pimelodidae - Siluriformes), based on a multilocus analysis, indicates diversification and introgression in the Amazon basin.},
journal = {Molecular phylogenetics and evolution},
volume = {137},
number = {},
pages = {285-292},
doi = {10.1016/j.ympev.2019.05.017},
pmid = {31121309},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genetic Loci ; *Genetic Variation ; Hybridization, Genetic ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; },
abstract = {The genus Hypophthalmus encompasses four valid South American freshwater catfish species: H. marginatus, H. edentatus, H. fimbriatus, and H. oremaculatus. More recently two new species were proposed Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2. While Hypophthalmus species are a fundamentally important resource for the commercial fisheries that operate in the continental waters of the Amazon basin, their phylogenetic relationships and the true diversity of the genus have yet to be defined conclusively. Given this, the present study analyzed sequences of the mitochondrial COI gene and four nuclear markers (RAG2, Myh6, Plagl2 and Glyt) to evaluate the phylogenetic relationships and the diversity of the species of this genus. All the analyses showed that Hypophthalmus is monophyletic, and the species delimitation tests recovered all the Hypophthalmus taxa as distinct species. The putative new species Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2 presented mean genetic divergence similar to or greater than that observed between valid Hypophthalmus taxa. All the analyses showed that H. oremaculatus is the sister group of H. n. sp. 1, which together group with H. fimbriatus. This clade is the sister group of the clade containing H. edentatus and H. n. sp. 2. One specimen, morphologically identified as H. oremaculatus, presented the nuclear genome of this species and the mitochondrial genome of H. n. sp. 1; while another specimen, morphologically identified as H. n. sp. 2, presented the nuclear Myh6 of H. n. sp. 2 and the mitochondrial and RAG2 genome of H. edentatus. These results indicate that hybridization and introgression has occurred between species in Hypophthalmus. The findings of this study indicate that the diversity of the Hypophthalmus is underestimated, emphasize the need for a taxonomic review of the genus, and a more systematic evaluation of the hybridization patterns found, to understanding the role of hybridization and introgression in the evolution of the genus.},
}

Animals
Bayes Theorem
Catfishes/*classification/*genetics
Cell Nucleus/genetics
DNA, Mitochondrial/genetics
*Genetic Loci
*Genetic Variation
Hybridization, Genetic
Mitochondria/genetics
*Phylogeny
Species Specificity

@article {pmid31112782,
year = {2019},
author = {Gandini, CL and Garcia, LE and Abbona, CC and Sanchez-Puerta, MV},
title = {The complete organelle genomes of Physochlaina orientalis: Insights into short sequence repeats across seed plant mitochondrial genomes.},
journal = {Molecular phylogenetics and evolution},
volume = {137},
number = {},
pages = {274-284},
doi = {10.1016/j.ympev.2019.05.012},
pmid = {31112782},
issn = {1095-9513},
mesh = {Base Sequence ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; *Genome, Plant ; Genome, Plastid ; Introns/genetics ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Seeds/*genetics ; Solanaceae/*genetics ; },
abstract = {Short repeats (SR) play an important role in shaping seed plant mitochondrial genomes (mtDNAs). However, their origin, distribution, and relationships across the different plant lineages remain unresolved. We focus on the angiosperm family Solanaceae that shows great variation in repeat content and extend the study to a wide diversity of seed plants. We determined the complete nucleotide sequences of the organellar genomes of the medicinal plant Physochlaina orientalis (Solanaceae), member of the tribe Hyoscyameae. To understand the evolution of the P. orientalis mtDNA we made comparisons with those of five other Solanaceae. P. orientalis mtDNA presents the largest mitogenome (∼685 kb in size) among the Solanaceae and has an unprecedented 8-copy repeat family of ∼8.2 kb in length and a great number of SR arranged in tandem-like structures. We found that the SR in the Solanaceae share a common origin, but these only expanded in members of the tribe Hyoscyameae. We discuss a mechanism that could explain SR formation and expansion in P. orientalis and Hyoscyamus niger. Finally, the great increase in plant mitochondrial data allowed us to systematically extend our repeat analysis to a total of 136 seed plants to characterize and analyze for the first time families of SR among seed plant mtDNAs.},
}

Base Sequence
DNA, Mitochondrial/genetics
*Genome, Mitochondrial
*Genome, Plant
Genome, Plastid
Introns/genetics
Microsatellite Repeats/*genetics
Mitochondria/genetics
Phylogeny
Seeds/*genetics
Solanaceae/*genetics

@article {pmid31018163,
year = {2019},
author = {Torres-Cambas, Y and Ferreira, S and Cordero-Rivera, A and Lorenzo-Carballa, MO},
title = {Mechanisms of allopatric speciation in an Antillean damselfly genus (Odonata, Zygoptera): Vicariance or long-distance dispersal?.},
journal = {Molecular phylogenetics and evolution},
volume = {137},
number = {},
pages = {14-21},
doi = {10.1016/j.ympev.2019.04.018},
pmid = {31018163},
issn = {1095-9513},
mesh = {Animal Migration/*physiology ; Animals ; Base Sequence ; Cell Nucleus/genetics ; Cuba ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; Genetic Variation ; Mitochondria/genetics ; Odonata/*genetics/*physiology ; Phylogeny ; Species Specificity ; Time Factors ; },
abstract = {We have examined divergence times of the Antillean damselfly genus Hypolestes, to elucidate which mechanism of allopatric speciation, vicariance or long-distance dispersal, could better explain the currently observed disjunct distributions of this genus. Samples of the three extant species of the genus, Hypolestes clara (Jamaica), H. hatuey (Hispaniola) and H. trinitatis (Cuba), were collected. Mitochondrial and nuclear DNA gene fragments were amplified to reconstruct phylogenetic relationships and estimate divergence times in this genus. Hypolestes comprises currently three species, which consist in four geographically and genetically isolated lineages located in Jamaica, Hispaniola, Eastern Cuba and Central Cuba. Results of our analyses suggest that the three species diverged between ∼5.91 and 1.69 mya, and that the separation between the lineages from Central Cuba and Eastern Cuba occurred between ∼2.0 and 0.62 mya. Disjunct distributions in the genus Hypolestes can be better explained by a long-distance dispersal mechanism, since the divergence times of the three species do not coincide with the timeline formation of the geographic barriers between Cuba, Hispaniola and Jamaica. The Cuban lineages of H. trinitatis constitute different molecular operational taxonomic units (MOTU). The elevation of these MOTU to the species category requires the analysis of additional characters.},
}

Animal Migration/*physiology
Animals
Base Sequence
Cell Nucleus/genetics
Cuba
DNA, Mitochondrial/genetics
*Genetic Speciation
Genetic Variation
Mitochondria/genetics
Odonata/*genetics/*physiology
Phylogeny
Species Specificity
Time Factors

@article {pmid30974201,
year = {2019},
author = {Strong, EE and Whelan, NV},
title = {Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda).},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {87-103},
doi = {10.1016/j.ympev.2019.04.009},
pmid = {30974201},
issn = {1095-9513},
mesh = {Algorithms ; Animal Shells/anatomy & histology ; Animals ; Bayes Theorem ; California ; Cell Nucleus/genetics ; Gastropoda/anatomy & histology/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Juga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific levels of genetic diversity, and concluded almost every sampled population to be a distinct OTU. We assembled a multilocus mitochondrial (COI, 16S) and nuclear gene (ITS1) dataset for ∼100 populations collected across the range of the genus. We generated primary species hypotheses using ABGD with best-fit model-corrected distances and further explored our data, both individual gene partitions and concatenated datasets, using a diversity of phylogenetic and species delimitation methods (Bayesian inference, maximum likelihood estimation, StarBEAST2, bGMYC, bPTP, BP&P). Our secondary species delimitation hypotheses, based primarily on the criterion of reciprocal monophyly, and informed by a combination of geography and morphology, support the interpretation that Juga comprises a mixture of geographically widespread species and narrow range endemics. As might be expected in taxa with low vagility and poor dispersal capacities, analysis of molecular variance (AMOVA) revealed highly structured populations with up to 80% of the observed genetic variance explained by variation between populations. Analyses with bGMYC, bPTP, and BP&P appeared sensitive to this genetic structure and returned highly dissected species hypotheses that are likely oversplit. The species diversity of Juga is concluded to be lower than presently recognized, and the systematics to require extensive revision. Features of the teleoconch considered significant in species-level and subgeneric classification were found to be variable within some species, sometimes at a single site. Of a number of potentially new species identified in non-peer reviewed reports and field guides, only one was supported as a distinct OTU.},
}

Algorithms
Animal Shells/anatomy & histology
Animals
Bayes Theorem
California
Cell Nucleus/genetics
Gastropoda/anatomy & histology/*genetics
*Genetic Variation
Genetics, Population
Geography
Haplotypes/genetics
Mitochondria/genetics
Phylogeny
Species Specificity

@article {pmid30954588,
year = {2019},
author = {Sajeela, KA and Gopalakrishnan, A and Basheer, VS and Mandal, A and Bineesh, KK and Grinson, G and Gopakumar, SD},
title = {New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean.},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {53-64},
doi = {10.1016/j.ympev.2019.04.007},
pmid = {30954588},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Indian Ocean ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Penaeidae/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.},
}

Animals
Base Sequence
Bayes Theorem
Cell Nucleus/*genetics
Electron Transport Complex IV/genetics
Genetic Markers
*Genetic Variation
Genetics, Population
Geography
Haplotypes/genetics
Indian Ocean
Microsatellite Repeats/genetics
Mitochondria/*genetics
Penaeidae/*genetics
Phylogeny
Species Specificity

@article {pmid30951923,
year = {2019},
author = {Kinoshita, G and Nunome, M and Kryukov, AP and Kartavtseva, IV and Han, SH and Yamada, F and Suzuki, H},
title = {Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus).},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {65-75},
doi = {10.1016/j.ympev.2019.04.003},
pmid = {30951923},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/genetics ; DNA/genetics ; DNA, Mitochondrial/genetics ; Far East ; Genetic Loci ; Geography ; Hares/classification/*genetics ; *Islands ; Mitochondria/*genetics ; Phylogeny ; *Phylogeography ; },
abstract = {Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.},
}

Animals
Base Sequence
Bayes Theorem
Cell Nucleus/genetics
DNA/genetics
DNA, Mitochondrial/genetics
Far East
Genetic Loci
Geography
Hares/classification/*genetics
*Islands
Mitochondria/*genetics
Phylogeny
*Phylogeography

@article {pmid29938587,
year = {2019},
author = {Gvozdanović, K and Margeta, V and Margeta, P and Djurkin Kušec, I and Galović, D and Dovč, P and Kušec, G},
title = {Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism.},
journal = {Animal biotechnology},
volume = {30},
number = {3},
pages = {242-251},
doi = {10.1080/10495398.2018.1478847},
pmid = {29938587},
issn = {1532-2378},
mesh = {Animals ; Breeding ; DNA, Mitochondrial/genetics ; Female ; Gene Frequency ; *Genetic Variation ; Haplotypes ; Male ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Sus scrofa ; Swine/*genetics ; },
abstract = {The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.},
}

Animals
Breeding
DNA, Mitochondrial/genetics
Female
Gene Frequency
*Genetic Variation
Haplotypes
Male
Microsatellite Repeats/*genetics
Mitochondria/genetics
Phylogeny
Polymorphism, Genetic
Sus scrofa
Swine/*genetics

@article {pmid31216623,
year = {2019},
author = {Myszczyński, K and Ślipiko, M and Sawicki, J},
title = {Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends.},
journal = {International journal of molecular sciences},
volume = {20},
number = {12},
pages = {},
doi = {10.3390/ijms20122963},
pmid = {31216623},
issn = {1422-0067},
support = {Grant No. 2017/01/X/NZ8/01094, Grant No. 2016/21/B/NZ8/03325, Grant No. 2015/19/B/NZ8/03970//Narodowe Centrum Nauki/ ; },
mesh = {Base Composition ; Bryophyta/classification/genetics ; Embryophyta/*classification/*genetics ; Genome Size ; *Genome, Mitochondrial ; Genomics/methods ; Open Reading Frames ; Phylogeny ; *RNA Editing ; RNA, Messenger/*genetics ; *RNA, Plant ; },
abstract = {RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.},
}

Base Composition
Bryophyta/classification/genetics
Embryophyta/*classification/*genetics
Genome Size
*Genome, Mitochondrial
Genomics/methods
Open Reading Frames
Phylogeny
*RNA Editing
RNA, Messenger/*genetics
*RNA, Plant

@article {pmid30395997,
year = {2019},
author = {López-Rubio, A and Suaza-Vasco, JD and Solari, S and Gutiérez-Builes, L and Porter, C and Uribe, SI},
title = {Intraspecific phylogeny of Anopheles (Kerteszia) neivai Howard, Dyar & Knab 1913, based on mitochondrial and nuclear ribosomal genes.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {67},
number = {},
pages = {183-190},
doi = {10.1016/j.meegid.2018.10.013},
pmid = {30395997},
issn = {1567-7257},
mesh = {Animals ; Anopheles/*classification/*genetics ; Central America/epidemiology ; *Genes, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/*genetics ; South America/epidemiology ; },
abstract = {Three mitochondrial regions and a fragment of a large nuclear ribosomal subunit was used to study the evolutionary patterns of An. neivai, a mosquito inhabiting mangroves and tropical forest in the lowland and coastal areas of the Yucatan Peninsula through the Pacific Ecuadorian coast. This species exhibits epidemiological importance regarding Malaria transmission in natural ecosystems, particularly in rural areas of the Pacific Colombian coast. The results based on phylogenetic networks and Bayesian inference showed no robust evidence supporting the existence of previously suggested cryptic species. Diversification patterns in geographically widespread species such as this one, are complex and therefore could impact malaria control strategies. Further studies focused on behavior, morphology, and phylogenomics will improve the understanding of the evolutionary patterns within An. neivai and its role as a disease vector.},
}

Animals
Anopheles/*classification/*genetics
Central America/epidemiology
*Genes, Mitochondrial
Haplotypes
Mitochondria/*genetics
Phylogeny
RNA, Ribosomal/*genetics
South America/epidemiology

@article {pmid31766564,
year = {2019},
author = {Brieba, LG},
title = {Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System.},
journal = {Plants (Basel, Switzerland)},
volume = {8},
number = {12},
pages = {},
doi = {10.3390/plants8120533},
pmid = {31766564},
issn = {2223-7747},
support = {13//SEP-Cinvestav/ ; },
abstract = {Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.},
}

@article {pmid31754022,
year = {2019},
author = {Li, H and Rukina, D and David, FPA and Li, TY and Oh, CM and Gao, AW and Katsyuba, E and Bou Sleiman, M and Komljenovic, A and Huang, Q and Williams, RW and Robinson-Rechavi, M and Schoonjans, K and Morgenthaler, S and Auwerx, J},
title = {Identifying gene function and module connections by the integration of multispecies expression compendia.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.251983.119},
pmid = {31754022},
issn = {1549-5469},
abstract = {The functions of many eukaryotic genes are still poorly understood. Here, we developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First, Gene-Module Association Determination (G-MAD) allows the annotation of gene function. Second, Module-Module Association Determination (M-MAD) allows predicting connectivity among modules. We applied the GeneBridge tools to large-scale multispecies expression compendia-1700 data sets with over 300,000 samples from human, mouse, rat, fly, worm, and yeast-collected in this study. G-MAD identifies novel functions of genes-for example, DDT in mitochondrial respiration and WDFY4 in T cell activation-and also suggests novel components for modules, such as for cholesterol biosynthesis. By applying G-MAD on data sets from respective tissues, tissue-specific functions of genes were identified-for instance, the roles of EHHADH in liver and kidney, as well as SLC6A1 in brain and liver. Using M-MAD, we identified a list of module-module associations, such as those between mitochondria and proteasome, mitochondria and histone demethylation, as well as ribosomes and lipid biosynthesis. The GeneBridge tools together with the expression compendia are available as an open resource, which will facilitate the identification of connections linking genes, modules, phenotypes, and diseases.},
}

@article {pmid31751405,
year = {2019},
author = {Voleman, L and Doležal, P},
title = {Mitochondrial dynamics in parasitic protists.},
journal = {PLoS pathogens},
volume = {15},
number = {11},
pages = {e1008008},
doi = {10.1371/journal.ppat.1008008},
pmid = {31751405},
issn = {1553-7374},
abstract = {The shape and number of mitochondria respond to the metabolic needs during the cell cycle of the eukaryotic cell. In the best-studied model systems of animals and fungi, the cells contain many mitochondria, each carrying its own nucleoid. The organelles, however, mostly exist as a dynamic network, which undergoes constant cycles of division and fusion. These mitochondrial dynamics are driven by intricate protein machineries centered around dynamin-related proteins (DRPs). Here, we review recent advances on the dynamics of mitochondria and mitochondrion-related organelles (MROs) of parasitic protists. In contrast to animals and fungi, many parasitic protists from groups of Apicomplexa or Kinetoplastida carry only a single mitochondrion with a single nucleoid. In these groups, mitochondrial division is strictly coupled to the cell cycle, and the morphology of the organelle responds to the cell differentiation during the parasite life cycle. On the other hand, anaerobic parasitic protists such as Giardia, Entamoeba, and Trichomonas contain multiple MROs that have lost their organellar genomes. We discuss the function of DRPs, the occurrence of mitochondrial fusion, and mitophagy in the parasitic protists from the perspective of eukaryote evolution.},
}

@article {pmid31750917,
year = {2019},
author = {Costello, R and Emms, DM and Kelly, S},
title = {Gene duplication accelerates the pace of protein gain and loss from plant organelles.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz275},
pmid = {31750917},
issn = {1537-1719},
abstract = {Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the plant kingdom arise, in part, as a result of differences in the cohort of nuclear-encoded proteins that are targeted to them. However, neither the rate at which differences in protein targeting accumulate nor the evolutionary consequences of these changes are known. Using phylogenomic approaches coupled to ancestral state estimation we show that the plant organellar proteome has diversified in proportion with molecular sequence evolution such that the proteomes of plant chloroplasts and mitochondria lose or gain on average 3.6 proteins per million years. We further demonstrated that change to organellar targeting is associated with an increase in the rate of molecular sequence evolution and that changes in protein targeting predominantly occurred in genes with regulatory rather than metabolic functions. Finally, we show that gain and loss of protein targeting occurs at a higher rate following gene duplication, revealing that gene and genome duplication are a key facilitator of plant organelle evolution.},
}

@article {pmid31740334,
year = {2019},
author = {Feng, JM and Jiang, CQ and Sun, ZY and Hua, CJ and Wen, JF and Miao, W and Xiong, J},
title = {Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106687},
doi = {10.1016/j.ympev.2019.106687},
pmid = {31740334},
issn = {1095-9513},
abstract = {Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.},
}

@article {pmid31716895,
year = {2019},
author = {Tominaga, A and Matsui, M and Tanabe, S and Nishikawa, K},
title = {A revision of Hynobius stejnegeri, a lotic breeding salamander from western Japan, with a description of three new species (Amphibia, Caudata, Hynobiidae).},
journal = {Zootaxa},
volume = {4651},
number = {3},
pages = {zootaxa.4651.3.1},
doi = {10.11646/zootaxa.4651.3.1},
pmid = {31716895},
issn = {1175-5334},
mesh = {Animals ; Breeding ; Japan ; Mitochondria ; Phylogeny ; Tooth ; *Urodela ; },
abstract = {A lotic-breeding salamander Hynobius stejnegeri, formerly called H. yatsui, from western Japan is revised based on genetic and morphological evidence, and three species are described: H. guttatus sp. nov. from Chubu-Kinki districts of Honshu Island, H. tsurugiensis sp. nov. from east highland of Shikoku Island, and H. kuishiensis sp. nov. from other parts of Shikoku Island. Thus, H. stejnegeri sensu stricto is restricted to Kyushu Island. Of these four species, H. kuishiensis sp. nov. contains two distinct mitochondrial lineages, but this split is not reflected in differentiation of allozyme (nuclear genome) markers. These species are morphologically similar to each other but can be differentiated by several characteristics, especially in combination of dorsal coloration, the number of vomerine, upper, and lower jaw teeth, and depth of vomerine teeth series. In coloration, H. guttatus sp. nov. is brown or dark brown mostly with tiny white to brownish white marking, while H. tsurugiensis sp. nov. is dark brown with bright yellow continuous markings. Hynobius kuishiensis sp. nov. is reddish purple or dark brown with small to continuous brownish white markings, in contrast to reddish purple or dark brown with small to large brownish white markings in H. stejnegeri.},
}

Animals
Breeding
Japan
Mitochondria
Phylogeny
Tooth
*Urodela

@article {pmid31716534,
year = {2019},
author = {Braun, MP and Datzmann, T and Arndt, T and Reinschmidt, M and Schnitker, H and Bahr, N and Sauer-Gürth, H and Wink, M},
title = {A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, †Mascarinus) with taxonomic implications.},
journal = {Zootaxa},
volume = {4563},
number = {3},
pages = {zootaxa.4563.3.8},
doi = {10.11646/zootaxa.4563.3.8},
pmid = {31716534},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; Mitochondria ; *Parrots ; Phylogeny ; *Psittaciformes ; *Psittacula ; },
abstract = {The long-tailed parakeets of the genus Psittacula Cuvier, 1800 have thus far been regarded as a homogeneous and monophyletic group of parrots. We used nucleotide sequences of two genetic markers (mitochondrial CYTB, nuclear RAG-1) to reconstruct the phylogenetic relationships of Psittacula and closely related species. We found that the Asian genus Psittacula is apparently paraphyletic because two genera of short-tailed parrots, Psittinus Blyth, 1842 and Tanygnathus Wagler, 1832, cluster within Psittacula, as does †Mascarinus Lesson, 1830. To create monophyletic genera, we propose recognition of the following genera: Himalayapsitta Braun, 2016 for P. himalayana, P. finschii, P. roseata, and P. cyanocephala; Nicopsitta Braun, 2016 for P. columboides and P. calthrapae; Belocercus S. Müller, 1847 for P. longicauda; Psittacula Cuvier, 1800 for P. alexandri and P. derbiana; Palaeornis Vigors, 1825 for †P. wardi and P. eupatria; and Alexandrinus Braun, 2016 for P. krameri, †P. exsul, and P. (eques) echo. Additionally, Psittacula krameri and P. alexandri are paraphyletic species, which should be split to form monophyletic species.},
}

Animals
Base Sequence
Mitochondria
*Parrots
Phylogeny
*Psittaciformes
*Psittacula

@article {pmid31716329,
year = {2019},
author = {Macià, R and Mally, R and Ylla, J and Gastón, J and Huertas, M},
title = {Integrative revision of the Iberian species of Coscinia Hübner, [1819] sensu lato and Spiris Hübner, [1819], (Lepidoptera: Erebidae, Arctiinae).},
journal = {Zootaxa},
volume = {4615},
number = {3},
pages = {zootaxa.4615.3.1},
doi = {10.11646/zootaxa.4615.3.1},
pmid = {31716329},
issn = {1175-5334},
mesh = {Animals ; Female ; Genitalia ; Male ; Mitochondria ; *Moths ; *Mustelidae ; Phylogeny ; },
abstract = {The Iberian species of the genera Coscinia Hübner, [1819] and Spiris Hübner, [1819], as well as three other species from the Mediterranean area, are revised based on morphological and molecular genetic data. Our results suggest the separation into four morphologically and phylogenetically different genera: Coscinia Hübner, [1819], Lerautia Kemal Koçak, 2006 stat. rev., Sagarriella Macià, Mally, Ylla, Gastón Huertas gen. nov. and Spiris Hübner, [1819]. We conclude that there are eight species of the Coscinia genus group present in the studied area: Coscinia cribraria (Linnaeus, 1758), Coscinia chrysocephala (Hübner, [1810]) stat. rev., Coscinia mariarosae Expósito, 1991, Sagarriella libyssa caligans (Turati, 1907) comb. nov., Sagarriella romei (Sagarra, 1924) (= romeii sensu auctorum) comb. nov., Spiris striata Hübner, [1819], Spiris slovenica (Daniel, 1939) and Lerautia bifasciata (Rambur, 1832) comb. rev. We consider Coscinia cribraria benderi (Marten, 1957) stat. nov., Coscinia c. rippertii (Boisduval, 1834) and Coscinia c. ibicenca Kobes, 1991 stat. rev. to be subspecies of C. cribraria. COI Barcodes of C. cribraria diverge by up to 7.99%, and the investigated specimens group into six different COI Barcode BINs. Both the phylogenetic analysis of mitochondrial and nuclear DNA and the morphological examination of different specimens corroborate the changes in taxonomic status and justify the proposed taxonomic categories. We present images of adults and genitalia of both sexes, the immature stages of some of the species and the subspecies studied, as well as phylogenetic results from the analysis of genetic data. We also include data on life history, foodplants and geographical distribution.},
}

Animals
Female
Genitalia
Male
Mitochondria
*Moths
*Mustelidae
Phylogeny

@article {pmid31716318,
year = {2019},
author = {Hibbitts, TJ and Ryberg, WA and Harvey, JA and Voelker, G and Lawing, AM and Adams, CS and Neuharth, DB and Dittmer, DE and Duran, CM and Wolaver, BD and Pierre, JP and Labay, BJ and Laduc, TJ},
title = {Phylogenetic structure of Holbrookia lacerata (Cope 1880) (Squamata: Phrynosomatidae): one species or two?.},
journal = {Zootaxa},
volume = {4619},
number = {1},
pages = {zootaxa.4619.1.6},
doi = {10.11646/zootaxa.4619.1.6},
pmid = {31716318},
issn = {1175-5334},
mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial ; *Lizards ; Mitochondria ; Phylogeny ; Texas ; },
abstract = {Species delimitation attempts to match species-level taxonomy with actual evolutionary lineages. Such taxonomic conclusions are typically, but not always, based on patterns of congruence across multiple data sources and methods of analyses. Here, we use this pluralistic approach to species delimitation to help resolve uncertainty in species boundaries of phrynosomatid sand lizards of the genus Holbrookia. Specifically, the Spot-tailed Earless Lizard (H. lacerata) was historically divided into a northern (H. l. lacerata) and southern (H. l. subcaudalis) subspecies based on differences in morphology and allopatry, but no research has been conducted evaluating genetic differences between these taxa. In this study, patterns in sequence data derived from two genes, one nuclear and one mitochondrial, for 66 individuals sampled across 18 counties in Texas revealed three strongly supported, reciprocally monophyletic lineages, each comprised of individuals from a single geographic region. Distinct genetic variation evident across two of these regions corresponds with differences in morphology, differences in environmental niche, and lines up with the presumed geographic barrier, the Balcones Escarpment, which is the historical subspecies boundary. The combined evidence from genetics, morphology and environmental niche is sufficient to consider these subspecies as distinct species with the lizards north of the Balcones Escarpment retaining the name Holbrookia lacerata, and those south of the Balcones Escarpment being designated as Holbrookia subcaudalis.},
}

Animals
Biological Evolution
DNA, Mitochondrial
*Lizards
Mitochondria
Phylogeny
Texas

@article {pmid31715832,
year = {2019},
author = {Han, H and Skou, P and Cheng, R},
title = {Neochloroglyphica, a new genus of Geometrinae from China (Lepidoptera, Geometridae), with description of a new species.},
journal = {Zootaxa},
volume = {4571},
number = {1},
pages = {zootaxa.4571.1.6},
doi = {10.11646/zootaxa.4571.1.6},
pmid = {31715832},
issn = {1175-5334},
mesh = {Animals ; China ; Genitalia ; *Lepidoptera ; Mitochondria ; *Moths ; Phylogeny ; },
abstract = {Neochloroglyphica gen. nov. and its type species N. perbella sp. nov. are described from Yunnan, China. Morphological characters and molecular phylogenetic analysis, based on one mitochondrial and three nuclear genes, support the hypothesis that Neochloroglyphica is a member of the tribe Neohipparchini, and that it is a sister genus to Chloroglyphica. Morphological characters, including those of the genitalia, are figured and compared with related genera, especially Chloroglyphica, Neohipparchus and Chlororithra. Diagnoses for the genus and the species are provided and illustrations of external features and genitalia are presented.},
}

Animals
China
Genitalia
*Lepidoptera
Mitochondria
*Moths
Phylogeny

@article {pmid31711195,
year = {2019},
author = {Dourmap, C and Roque, S and Morin, A and Caubrière, D and Kerdiles, M and Béguin, K and Perdoux, R and Reynoud, N and Bourdet, L and Audebert, PA and Moullec, JL and Couée, I},
title = {Stress signalling dynamics of the mitochondrial electron transport chain and oxidative phosphorylation system in higher plants.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcz184},
pmid = {31711195},
issn = {1095-8290},
abstract = {BACKGROUND: Mitochondria play a diversity of physiological and metabolic roles under conditions of abiotic or biotic stress. They may be directly subjected to physico-chemical constraints, and they are also involved in integrative responses to environmental stresses through their central position in cell nutrition, respiration, energy balance and biosyntheses. In plant cells, mitochondria present various biochemical peculiarities, such as cyanide-insensitive alternative respiration, and, besides integration with ubiquitous eukaryotic compartments, their functioning must be coupled with plastid functioning. Moreover, given the sessile lifestyle of plants, their relative lack of protective barriers and present threats of climate change, the plant cell is an attractive model to understand the mechanisms of stress/organelle/cell integration in the context of environmental stress responses.

SCOPE: The involvement of mitochondria in this integration entails a complex network of signalling, which has not been fully elucidated, because of the great diversity of mitochondrial constituents (metabolites, reactive molecular species, structural and regulatory biomolecules) that are linked to stress signalling pathways. The present review analyses the complexity of stress signalling connexions that are related to the mitochondrial electron transport chain and oxidative phosphorylation system, and how they can be involved in stress perception and transduction, signal amplification, or cell stress response modulation.

CONCLUSIONS: Plant mitochondria are endowed with a diversity of multi-directional hubs of stress signalling that lead to regulatory loops and regulatory rheostats, whose functioning can amplify and diversify some signals or, conversely, dampen and reduce other signals. Involvement in a wide range of abiotic and biotic responses also implies that mitochondrial stress signalling could result in synergistic or conflicting outcomes during acclimation to multiple and complex stresses, such as those arising from climate change.},
}

@article {pmid31705651,
year = {2019},
author = {Igloi, GL},
title = {Molecular evidence for the evolution of the eukaryotic mitochondrial arginyl-tRNA synthetase from the prokaryotic suborder Cystobacterineae.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.13665},
pmid = {31705651},
issn = {1873-3468},
abstract = {The evolutionary origin of the family of eukaryotic aminoacyl-tRNA synthetases that are essential to all living organisms is a matter of debate. In order to shed molecular light on the ancient source of arginyl-tRNA synthetase, a total of 1347 eukaryotic arginyl-tRNA synthetase sequences were mined from databases and analyzed. Their multiple sequence alignment reveals a signature sequence that is characteristic of the nuclear-encoded enzyme, which is imported into mitochondria. Using this molecular beacon, the origins of this gene can be traced to modern prokaryotes. In this way, a previous phylogenetic analysis linking Myxococcus to the emergence of the eukaryotic mitochondrial arginyl-tRNA synthetase is supported by the unique existence of the molecular signature within the suborder Cystobacterineae that includes Myxococcus.},
}

@article {pmid31702777,
year = {2019},
author = {Wang, BJ and Xia, JM and Wang, Q and Yu, JL and Song, Z and Zhao, H},
title = {Diet and adaptive evolution of alanine-glyoxylate aminotransferase mitochondrial targeting in birds.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz266},
pmid = {31702777},
issn = {1537-1719},
abstract = {Adaptations to different diets represent a hallmark of animal diversity. The diets of birds are highly variable, making them an excellent model system for studying adaptive evolution driven by dietary changes. To test whether molecular adaptations to diet have occurred during the evolution of birds, we examined a dietary enzyme alanine-glyoxylate aminotransferase (AGT), which tends to target mitochondria in carnivorous mammals, peroxisomes in herbivorous mammals, and both mitochondria and peroxisomes in omnivorous mammals. A total of 31 bird species were examined in this study, which included representatives of most major avian lineages. Of these, 29 have an intact mitochondrial targeting sequence (MTS) of AGT. This finding is in stark contrast to mammals, which showed a number of independent losses of the MTS. Our cell-based functional assays revealed that the efficiency of AGT mitochondrial targeting was greatly reduced in unrelated lineages of granivorous birds, yet it tended to be high in insectivorous and carnivorous lineages. Furthermore, we found that proportions of animal tissue in avian diets were positively correlated with mitochondrial targeting efficiencies that were experimentally determined, but not with those that were computationally predicted. Adaptive evolution of AGT mitochondrial targeting in birds was further supported by the detection of positive selection on MTS regions. Our study contributes to the understanding of how diet drives molecular adaptations in animals, and suggests that caution must be taken when computationally predicting protein subcellular targeting.},
}

@article {pmid31697708,
year = {2019},
author = {Bénit, P and Kahn, A and Chretien, D and Bortoli, S and Huc, L and Schiff, M and Gimenez-Roqueplo, AP and Favier, J and Gressens, P and Rak, M and Rustin, P},
title = {Evolutionarily conserved susceptibility of the mitochondrial respiratory chain to SDHI pesticides and its consequence on the impact of SDHIs on human cultured cells.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224132},
pmid = {31697708},
issn = {1932-6203},
abstract = {Succinate dehydrogenase (SDH) inhibitors (SDHIs) are used worldwide to limit the proliferation of molds on plants and plant products. However, as SDH, also known as respiratory chain (RC) complex II, is a universal component of mitochondria from living organisms, highly conserved through evolution, the specificity of these inhibitors toward fungi warrants investigation. We first establish that the human, honeybee, earthworm and fungal SDHs are all sensitive to the eight SDHIs tested, albeit with varying IC50 values, generally in the micromolar range. In addition to SDH, we observed that five of the SDHIs, mostly from the latest generation, inhibit the activity of RC complex III. Finally, we show that the provision of glucose ad libitum in the cell culture medium, while simultaneously providing sufficient ATP and reducing power for antioxidant enzymes through glycolysis, allows the growth of RC-deficient cells, fully masking the deleterious effect of SDHIs. As a result, when glutamine is the major carbon source, the presence of SDHIs leads to time-dependent cell death. This process is significantly accelerated in fibroblasts derived from patients with neurological or neurodegenerative diseases due to RC impairment (encephalopathy originating from a partial SDH defect) and/or hypersensitivity to oxidative insults (Friedreich ataxia, familial Alzheimer's disease).},
}

@article {pmid31696767,
year = {2019},
author = {Ayyub, SA and Varshney, U},
title = {Translation initiation in mammalian mitochondria- a prokaryotic perspective.},
journal = {RNA biology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/15476286.2019.1690099},
pmid = {31696767},
issn = {1555-8584},
abstract = {ATP is generated in mitochondria of eukaryotic cells by oxidative phosphorylation (OXPHOS). The OXPHOS complex, which is crucial for cellular metabolism, comprises of both nuclear and mitochondrially encoded subunits. Also, the occurrence of several pathologies because of mutations in the mitochondrial translation apparatus indicates the importance of mitochondrial translation and its regulation. The mitochondrial translation apparatus is similar to its prokaryotic counterpart due to a common origin of evolution. However, mitochondrial translation has diverged from prokaryotic translation in many ways by reductive evolution. In this review, we focus on mammalian mitochondrial translation initiation, a highly regulated step of translation, and present a comparison with prokaryotic translation.},
}

@article {pmid31681764,
year = {2019},
author = {Naumann, B and Burkhardt, P},
title = {Spatial Cell Disparity in the Colonial Choanoflagellate Salpingoeca rosetta.},
journal = {Frontiers in cell and developmental biology},
volume = {7},
number = {},
pages = {231},
pmid = {31681764},
issn = {2296-634X},
abstract = {Choanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to the co-existence of specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellate Salpingoeca rosetta that exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity of S. rosetta cells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial, and food vacuole volumes of 40 individual cells from four different S. rosetta rosette colonies and compared our findings to sponge choanocytes. Our analysis shows that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria, and food vacuoles. Furthermore, cell disparity within S. rosetta colonies is slightly higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.},
}

@article {pmid31670447,
year = {2019},
author = {Surana, S and Villarroel-Campos, D and Lazo, OM and Moretto, E and Tosolini, AP and Rhymes, ER and Richter, S and Sleigh, JN and Schiavo, G},
title = {The evolution of the axonal transport toolkit.},
journal = {Traffic (Copenhagen, Denmark)},
volume = {},
number = {},
pages = {},
doi = {10.1111/tra.12710},
pmid = {31670447},
issn = {1600-0854},
abstract = {Neurons are highly polarised cells that critically depend on long-range, bidirectional transport between the cell body and synapse for their function. This continual and highly coordinated trafficking process, which takes place via the axon, has fascinated researchers since the early twentieth century. Ramon y Cajal first proposed the existence of axonal trafficking of biological material after observing that dissociation of the axon from the cell body led to neuronal degeneration. Since these first indirect observations, the field has come a long way in its understanding of this fundamental process. However, these advances in our knowledge have been aided by breakthroughs in other scientific disciplines, as well as the parallel development of novel tools, techniques and model systems. In this review, we summarise the evolution of tools used to study axonal transport and discuss how their deployment has refined our understanding of this process. We also highlight innovative tools currently being developed and how their addition to the available axonal transport toolkit might help to address key outstanding questions. This article is protected by copyright. All rights reserved.},
}

@article {pmid31669617,
year = {2019},
author = {Barros, MH and McStay, GP},
title = {Modular biogenesis of mitochondrial respiratory complexes.},
journal = {Mitochondrion},
volume = {50},
number = {},
pages = {94-114},
doi = {10.1016/j.mito.2019.10.008},
pmid = {31669617},
issn = {1872-8278},
abstract = {Mitochondrial function relies on the activity of oxidative phosphorylation to synthesise ATP and generate an electrochemical gradient across the inner mitochondrial membrane. These coupled processes are mediated by five multi-subunit complexes that reside in this inner membrane. These complexes are the product of both nuclear and mitochondrial gene products. Defects in the function or assembly of these complexes can lead to mitochondrial diseases due to deficits in energy production and mitochondrial functions. Appropriate biogenesis and function are mediated by a complex number of assembly factors that promote maturation of specific complex subunits to form the active oxidative phosphorylation complex. The understanding of the biogenesis of each complex has been informed by studies in both simple eukaryotes such as Saccharomyces cerevisiae and human patients with mitochondrial diseases. These studies reveal each complex assembles through a pathway using specific subunits and assembly factors to form kinetically distinct but related assembly modules. The current understanding of these complexes has embraced the revolutions in genomics and proteomics to further our knowledge on the impact of mitochondrial biology in genetics, medicine, and evolution.},
}

@article {pmid31647561,
year = {2019},
author = {Lewis, WH and Lind, AE and Sendra, KM and Onsbring, H and Williams, TA and Esteban, GF and Hirt, RP and Ettema, TJG and Embley, TM},
title = {Convergent evolution of hydrogenosomes from mitochondria by gene transfer and loss.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msz239},
pmid = {31647561},
issn = {1537-1719},
abstract = {Hydrogenosomes are H2-producing mitochondrial homologues found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition we generated genomic and transcriptomic datasets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.},
}

@article {pmid31640544,
year = {2019},
author = {Wang, G and Lin, J and Shi, Y and Chang, X and Wang, Y and Guo, L and Wang, W and Dou, M and Deng, Y and Ming, R and Zhang, J},
title = {Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {765},
pmid = {31640544},
issn = {1471-2164},
support = {KNJ-153011-1//Agricultural technology extension service system for edible fungus industry in Fujian, China/ ; 2016NZ0001//the Science and Technology Major Project of Fujian Province/ ; 31670021//Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells.

RESULTS: In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene.

CONCLUSIONS: Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.},
}

@article {pmid31632444,
year = {2019},
author = {Shen, X and Pu, Z and Chen, X and Murphy, RW and Shen, Y},
title = {Convergent Evolution of Mitochondrial Genes in Deep-Sea Fishes.},
journal = {Frontiers in genetics},
volume = {10},
number = {},
pages = {925},
pmid = {31632444},
issn = {1664-8021},
abstract = {Deep seas have extremely harsh conditions including high hydrostatic pressure, total darkness, cold, and little food and oxygen. The adaptations of fishes to deep-sea environment apparently have occurred independently many times. The genetic basis of adaptation for obtaining their energy remains unknown. Mitochondria play a central role in aerobic respiration. Analyses of the available 2,161 complete mitochondrial genomes of 1,042 fishes, including 115 deep-sea species, detect signals of positive selection in mitochondrial genes in nine branches of deep-sea fishes. Aerobic metabolism yields much more energy per unit of source material than anaerobic metabolism. The adaptive evolution of the mtDNA may reflect that aerobic metabolism plays a more important role than anaerobic metabolism in deep-sea fishes, whose energy sources (food) are extremely limited. This strategy maximizes the usage of energy sources. Eleven mitochondrial genes have convergent/parallel amino acid changes between branches of deep-sea fishes. Thus, these amino acid sites may be functionally important in the acquisition of energy, and reflect convergent evolution during their independent invasion of the harsh deep-sea ecological niche.},
}

@article {pmid31631459,
year = {2019},
author = {Jelassi, R and Khemaissia, H and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K},
title = {The induced damage in the hepatopancreas of Orchestia species after exposure to a mixture of Cu/Zn-An ultrastructural study.},
journal = {Microscopy research and technique},
volume = {},
number = {},
pages = {},
doi = {10.1002/jemt.23397},
pmid = {31631459},
issn = {1097-0029},
support = {//Research Laboratory of Diversity, Management and Conservation of Biological Systems, Faculty of Science of Tunis, University of Tunis El Manar/ ; //Erasmus Mundus Al Idrisi II Programme of the European Union/ ; },
abstract = {The hepatopancreas of crustaceans species has been recognized as an essential target organ to assess trace elements' effects. Due to its dynamic and capability of detoxifying trace metal, this organ often indicates distinct pathological disturbances. In the present work, we intend to evaluate the bioaccumulation of trace metal in three Orchestia species (Orchestia montagui, Orchestia gammarellus, and Orchestia mediterranea) living in symmetry in the banks of Bizerte lagoon (37°13'8″N 09°55'1″E) after their exposure during 14 days to a mixture of copper and zinc, and to highlight the effect of these metals on their hepatopancreas ultrastructure using transmission electron microscopy. At the end of the experiment, results showed that the mortality and the body mass varied according to the used nominal concentrations. Significant alterations were noted in all the treatment groups. The degree of these alterations depends on the used concentration, and they are represented especially by the cells remoteness and the border lyses, the reduction of the nuclear volume, the increase in the cytoplasm density with the presence of trace metal in the nucleus as well as in the vacuole, the disorganization and the destruction of microvilli, the condensation of the majority of cellular organelles and mitochondria swelling. Through this study, Orchestia genus could be an attractive candidate for the biochemical study of trace metal toxicity in Tunisian wetlands.},
}

@article {pmid31630458,
year = {2019},
author = {Small, ID and Schallenberg-Rüdinger, M and Takenaka, M and Mireau, H and Ostersetzer-Biran, O},
title = {Plant organellar RNA editing: what 30 years of research has revealed.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.14578},
pmid = {31630458},
issn = {1365-313X},
abstract = {The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-to-U base transitions) is highly prevalent within organelles (i.e., mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.},
}

@article {pmid31630139,
year = {2019},
author = {Ozozan, OV and Dinc, T and Vural, V and Ozogul, C and Ozmen, MM and Coskun, F},
title = {An electron microscopy study of liver and kidney damage in an experimental model of obstructive jaundice.},
journal = {Annali italiani di chirurgia},
volume = {8},
number = {},
pages = {},
pmid = {31630139},
issn = {2239-253X},
abstract = {With this experimental study we investigated the consequences of ligation of the common bile duct (CBD) on hepatic cells and on the renal ultrastructure by electron microscopy and also determine the effects after liberation of the ductus joint in order to clarify the mechanisms of renal failure commonly observed in cholestatic liver disease. The study was conducted on 53 Wistar albino rats divided into 4 subgroups. In the comparison group (sham) we proceeded to the simple laparotomy. After preparation of the common bile duct of all the rats of the four groups, and ligation of the duct at the level of the distal third, eight rats in each group were sacrificed on the 3rd, 7th, 10th and 14th day after surgery, taking blood samples to measure the serum levels of ALP and bilirubin, and liver and renal tissue samples for histological evaluation. In four rats of each group the common bile duct was unligated at the same deadlines to obtain free drainage of the bile for a week. At the end of this week, the rats were sacrificed by collecting blood and liver and kidney tissue samples.

RESULTS: after CBD ligation in both groups, the ALP value, total and direct bilurubin levels were proportionally increased. After duct release, bilurubin levels decreased significantly. In group II, while large lipid granules were observed to indicate oxidative damage, mitochondrial swelling and crystals were observed after duct liberation. Areas of glycogen and normal mitochondria were observed in group IV. After duct release in this group, increases in Ito granules, lipid granules and normal mitochondria were observed, which may reflect the evolution of hepatic regeneration. When renal tissue was examined in group II, fusion processes in the feet, thickening of the basement membrane and mesengium were observed, and mitochondrial crystals were observed in renal tissue as well as in the liver after duct release. Damage in group III and group IV was increased parallel to prolongation of jaundice and after loosening persistent damage with mitochondrial crystals.

CONCLUSION: Ultrastructural changes in rat liver tissue in conditions of obstructive jaundice may be reversible after restoration of drainage. On the other hand, ultrastructural changes in renal tissue in cases of prolonged jaundice are irreversible even if the internal drainage is restored.

KEY WORDS: Bile Duct, Liver, Kidney, Obstructive Jaundice.},
}

@article {pmid31617565,
year = {2019},
author = {Žihala, D and Eliáš, M},
title = {Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae.},
journal = {Genome biology and evolution},
volume = {11},
number = {10},
pages = {2992-3007},
pmid = {31617565},
issn = {1759-6653},
abstract = {Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.},
}

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

@article {pmid31599941,
year = {2019},
author = {Liu, Q and Lin, D and Li, M and Gu, Z and Zhao, Y},
title = {Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma.},
journal = {Genome biology and evolution},
volume = {11},
number = {10},
pages = {2909-2916},
pmid = {31599941},
issn = {1759-6653},
abstract = {Many studies have suggested that mitochondria and mitochondrial DNA (mtDNA) might be functionally associated with tumor genesis and development. Although the heterogeneity of tumors is well known, most studies were based on the analysis of a single tumor sample. The extent of mtDNA diversity in the same tumor is unclear, as is whether the diversity is influenced by selection pressure. Here, we analyzed the whole exon data from 1 nontumor sample and 23 tumor samples from different locations of one single tumor tissue from a hepatocellular carcinoma (HCC) patient. Among 18 heteroplasmic sites identified in the tumor, only 2 heteroplasmies were shared among all tumor samples. By investigating the correlations between the occurrence and frequency of heteroplasmy (Het) and sampling locations (Coordinate), relative mitochondrial copy numbers, and single-nucleotide variants in the nuclear genome, we found that the Coordinate was significantly correlated with Het, suggesting no strong purifying selection or positive selection acted on the mtDNA in HCC. By further investigating the allele frequency and proportion of nonsynonymous mutations in the tumor mtDNA, we found that mtDNA in HCC did not undergo extra selection compared with mtDNA in the adjacent nontumor tissue, and they both likely evolved under neutral selection.},
}

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

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

@article {pmid31585116,
year = {2019},
author = {Betgiri, AA and Jadhav, SN and Pawde, M and Shukla, A and Mote, C and Pawar, PD and Shanmugam, D and Kundu, K},
title = {Mitochondrial cytochrome oxidase C subunit III (cox3) gene as a sensitive and specific target for molecular detection of Babesia gibsoni infection in dogs.},
journal = {Experimental parasitology},
volume = {206},
number = {},
pages = {107771},
doi = {10.1016/j.exppara.2019.107771},
pmid = {31585116},
issn = {1090-2449},
mesh = {Animals ; Babesia/classification/genetics/*isolation & purification ; Babesiosis/*diagnosis/parasitology ; Base Sequence ; Cross Reactions ; DNA, Ribosomal Spacer/chemistry ; Dog Diseases/*diagnosis/parasitology ; Dogs ; Electron Transport Complex IV/*genetics ; Erythrocytes/parasitology ; Likelihood Functions ; Mitochondria/*enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Predictive Value of Tests ; RNA, Ribosomal, 18S/analysis ; Sensitivity and Specificity ; Sequence Alignment/veterinary ; },
abstract = {A PCR targeting mitochondrial cytochrome oxidase subunit III (cox3) for molecular detection of Babesia gibsoni infection in dogs has been developed in this study. Fifty blood samples from suspected clinical cases from dogs, brought to the veterinary college clinics, were examined for presence of B. gibsoni using conventional diagnosis by microscopic examination of Giemsa stained thin blood smears. In addition, species specific PCRs targeting ITS-1 region (BgITS-1 PCR) and nested PCR targeting 18S ribosomal RNA gene (Bg18SnPCR) were carried out. A 634 bp PCR fragment of B. gibsoni cox3 gene was amplified in positive samples from three geographical locations of Satara, Wai and Pune in Maharashtra state of India. From analysis of the sequence of the B. gibsoni cox3 gene, we found that the Indian isolate had 96-98% similarity to the isolate from Japan and China. Post sequencing, de-novo diagnostic primer pair for species specific amplification of 164 bp fragment of B. gibsonicox3 was designed and the PCR was standardized. The diagnostic results of de-novo Bgcox3 PCR were compared with BgITS-1 PCR and Bg18S nPCR. Thin blood smears detected 22% (11/50) samples positive for small form of Babesia species. The BgITS-1 PCR detected 25% samples (15/50) as positive and Bg18S nPCR detected 80% (40/50) B. gibsoni positive samples. The de-novo Bgcox3 PCR detected 66% (33/50) samples positive for B. gibsoni (at 95% CI). The analytical sensitivity of cox3 PCR was evaluated as 0.000003% parasitaemia or 09 parasites in 100 μl of blood. The de-novo diagnostic cox3 PCR did not cross react with control positive DNA from other haemoprotozoa and rickettsia like B. vogeli, Hepatozoon canis, Trypanosoma evansi, Ehrlichia canis and Anaplasma platys. Statistically, cox3 PCR had better diagnostic efficiency than ITS-1 PCR in terms of sensitivity (p = 0.0006). No statistically significant difference between results of cox3 PCR and 18S nPCR was observed (p = 0.1760). Kappa values estimated for each test pair showed fair to moderate agreement between the observations. Specificity of Bgcox3 PCR was 100% when compared with microscopy or BgITS-1 PCR. Sensitivity of Bgcox3 PCR was 100% when compared with that of Bg18S nPCR.},
}

Animals
Babesia/classification/genetics/*isolation & purification
Babesiosis/*diagnosis/parasitology
Base Sequence
Cross Reactions
DNA, Ribosomal Spacer/chemistry
Dog Diseases/*diagnosis/parasitology
Dogs
Electron Transport Complex IV/*genetics
Erythrocytes/parasitology
Likelihood Functions
Mitochondria/*enzymology
Phylogeny
Polymerase Chain Reaction/veterinary
Predictive Value of Tests
RNA, Ribosomal, 18S/analysis
Sensitivity and Specificity
Sequence Alignment/veterinary

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

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

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

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

@article {pmid31551356,
year = {2019},
author = {Al-Faresi, RAZ and Lightowlers, RN and Chrzanowska-Lightowlers, ZMA},
title = {Mammalian mitochondrial translation - revealing consequences of divergent evolution.},
journal = {Biochemical Society transactions},
volume = {47},
number = {5},
pages = {1429-1436},
doi = {10.1042/BST20190265},
pmid = {31551356},
issn = {1470-8752},
abstract = {Mitochondria are ubiquitous organelles present in the cytoplasm of all nucleated eukaryotic cells. These organelles are described as arising from a common ancestor but a comparison of numerous aspects of mitochondria between different organisms provides remarkable examples of divergent evolution. In humans, these organelles are of dual genetic origin, comprising ∼1500 nuclear-encoded proteins and thirteen that are encoded by the mitochondrial genome. Of the various functions that these organelles perform, it is only oxidative phosphorylation, which provides ATP as a source of chemical energy, that is dependent on synthesis of these thirteen mitochondrially encoded proteins. A prerequisite for this process of translation are the mitoribosomes. The recent revolution in cryo-electron microscopy has generated high-resolution mitoribosome structures and has undoubtedly revealed some of the most distinctive molecular aspects of the mitoribosomes from different organisms. However, we still lack a complete understanding of the mechanistic aspects of this process and many of the factors involved in post-transcriptional gene expression in mitochondria. This review reflects on the current knowledge and illustrates some of the striking differences that have been identified between mitochondria from a range of organisms.},
}

@article {pmid31550514,
year = {2019},
author = {Calì, C and Agus, M and Kare, K and Boges, DJ and Lehväslaiho, H and Hadwiger, M and Magistretti, PJ},
title = {3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat.},
journal = {Progress in neurobiology},
volume = {},
number = {},
pages = {101696},
doi = {10.1016/j.pneurobio.2019.101696},
pmid = {31550514},
issn = {1873-5118},
abstract = {With the rapid evolution in the automation of serial electron microscopy in life sciences, the acquisition of terabyte-sized datasets is becoming increasingly common. High resolution serial block-face imaging (SBEM) of biological tissues offers the opportunity to segment and reconstruct nanoscale structures to reveal spatial features previously inaccessible with simple, single section, two-dimensional images. In particular, we focussed here on glial cells, whose reconstruction efforts in literature are still limited, compared to neurons. We imaged a 750,000 cubic micron volume of the somatosensory cortex from a juvenile P14 rat, with 20 nm accuracy. We recognized a total of 186 cells using their nuclei, and classified them as neuronal or glial based on features of the soma and the processes. We reconstructed for the first time 4 almost complete astrocytes and neurons, 4 complete microglia and 4 complete pericytes, including their intracellular mitochondria, 186 nuclei and 213 myelinated axons. We then performed quantitative analysis on the three-dimensional models. Out of the data that we generated, we observed that neurons have larger nuclei, which correlated with their lesser density, and that astrocytes and pericytes have a higher surface to volume ratio, compared to other cell types. All reconstructed morphologies represent an important resource for computational neuroscientists, as morphological quantitative information can be inferred, to tune simulations that take into account the spatial compartmentalization of the different cell types.},
}

@article {pmid31536728,
year = {2019},
author = {Buonvicino, D and Ranieri, G and Pratesi, S and Guasti, D and Chiarugi, A},
title = {Neuroimmunological characterization of a mouse model of primary progressive experimental autoimmune encephalomyelitis and effects of immunosuppressive or neuroprotective strategies on disease evolution.},
journal = {Experimental neurology},
volume = {322},
number = {},
pages = {113065},
doi = {10.1016/j.expneurol.2019.113065},
pmid = {31536728},
issn = {1090-2430},
abstract = {Progressive multiple sclerosis (PMS) is a devastating disorder sustained by neuroimmune interactions still wait to be identified. Recently, immune-independent, neural bioenergetic derangements have been hypothesized as causative of neurodegeneration in PMS patients. To gather information on the immune and neurodegenerative components during PMS, in the present study we investigated the molecular and cellular events occurring in a Non-obese diabetic (NOD) mouse model of experimental autoimmune encephalomyelitis (EAE). In these mice, we also evaluated the effects of clinically-relevant immunosuppressive (dexamethasone) or bioenergetic drugs (bezafibrate and biotin) on functional, immune and neuropathological parameters. We found that immunized NOD mice progressively accumulated disability and severe neurodegeneration in the spinal cord. Unexpectedly, although CD4 and CD8 lymphocytes but not B or NK cells infiltrate the spinal cord linearly with time, their suppression by different dexamethasone treatment schedules did not affect disease progression. Also, the spreading of the autoimmune response towards additional immunogenic myelin antigen occurred neither in the periphery nor in the CNS of EAE mice. Conversely, we found that altered mitochondrial morphology, reduced contents of mtDNA and decreased transcript levels for respiratory complex subunits occurred at early disease stages and preceded axonal degeneration within spinal cord columns. However, the mitochondria boosting drugs, bezafibrate and biotin, were unable to reduce disability progression. Data suggest that EAE NOD mice recapitulate some features of PMS. Also, by showing that bezafibrate or biotin do not affect progression in NOD mice, our study suggests that this model can be harnessed to anticipate experimental information of relevance to innovative treatments of PMS.},
}

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

@article {pmid31525456,
year = {2019},
author = {Corrêa da Silva, F and Aguiar, C and Pereira, JAS and de Brito Monteiro, L and Davanzo, GG and Codo, AC and Pimentel de Freitas, L and Berti, AS and Lopes Ferrucci, D and Castelucci, BG and Consonni, SR and Carvalho, HF and Moraes-Vieira, PMM},
title = {Ghrelin effects on mitochondrial fitness modulates macrophage function.},
journal = {Free radical biology & medicine},
volume = {145},
number = {},
pages = {61-66},
doi = {10.1016/j.freeradbiomed.2019.09.012},
pmid = {31525456},
issn = {1873-4596},
abstract = {Over the past years, systemic derived cues that regulate cellular metabolism have been implicated in the regulation of immune responses. Ghrelin is an orexigenic hormone produced by enteroendocrine cells in the gastric mucosa with known immunoregulatory roles. The mechanism behind the function of ghrelin in immune cells, such as macrophages, is still poorly understood. Here, we explored the hypothesis that ghrelin leads to alterations in macrophage metabolism thus modulating macrophage function. We demonstrated that ghrelin exerts an immunomodulatory effect over LPS-activated peritoneal macrophages, as evidenced by inhibition of TNF-α and IL-1β secretion and increased IL-12 production. Concomitantly, ghrelin increased mitochondrial membrane potential and increased respiratory rate. In agreement, ghrelin prevented LPS-induced ultrastructural damage in the mitochondria. Ghrelin also blunted LPS-induced glycolysis. In LPS-activated macrophages, glucose deprivation did not affect ghrelin-induced IL-12 secretion, whereas the inhibition of pyruvate transport and mitochondria-derived ATP abolished ghrelin-induced IL-12 secretion, indicating a dependence on mitochondrial function. Ghrelin pre-treatment of metabolic activated macrophages inhibited the secretion of TNF-α and enhanced IL-12 levels. Moreover, ghrelin effects on IL-12, and not on TNF-α, are dependent on mitochondria elongation, since ghrelin did not enhance IL-12 secretion in metabolic activated mitofusin-2 deficient macrophages. Thus, ghrelin affects macrophage mitochondrial metabolism and the subsequent macrophage function.},
}

@article {pmid31519789,
year = {2019},
author = {Loiacono, FV and Thiele, W and Schöttler, MA and Tillich, M and Bock, R},
title = {Establishment of a Heterologous RNA Editing Event in Chloroplasts.},
journal = {Plant physiology},
volume = {181},
number = {3},
pages = {891-900},
pmid = {31519789},
issn = {1532-2548},
abstract = {In chloroplasts and plant mitochondria, specific cytidines in mRNAs are posttranscriptionally converted to uridines by RNA editing. Editing sites are recognized by nucleus-encoded RNA-binding proteins of the pentatricopeptide repeat (PPR) family, which bind upstream of the editing site in a sequence-specific manner and direct the editing activity to the target position. Editing sites have been lost many times during evolution by C-to-T mutations. Loss of an editing site is thought to be accompanied by loss or degeneration of its cognate PPR protein. Consequently, foreign editing sites are usually not recognized when introduced into species lacking the site. Previously, the spinach (Spinacia oleracea) psbF-26 editing site was introduced into the tobacco (Nicotiana tabacum) plastid genome. Tobacco lacks the psbF-26 site and cannot edit it. Expression of the "unedited" PsbF protein resulted in impaired PSII function. In Arabidopsis (Arabidopsis thaliana), the PPR protein LPA66 is required for editing at psbF-26. Here, we show that introduction of the Arabidopsis LPA66 reconstitutes editing of the spinach psbF-26 site in tobacco and restores a wild-type-like phenotype. Our findings define the minimum requirements for establishing new RNA editing sites and suggest that the evolutionary dynamics of editing patterns is largely explained by coevolution of editing sites and PPR proteins.},
}

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

*Biological Evolution
Cell Membrane/*chemistry
Ceramides
Lipids/*chemistry
Mitochondria/*chemistry
Prokaryotic Cells/*chemistry
Sphingolipids

@article {pmid31495025,
year = {2019},
author = {Zeh, JA and Zawlodzki, MA and Bonilla, MM and Su-Keene, EJ and Padua, MV and Zeh, DW},
title = {Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jeb.13536},
pmid = {31495025},
issn = {1420-9101},
support = {IOS-1656670//National Science Foundation/ ; GM103440/NH/NIH HHS/United States ; },
abstract = {Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups (A and B2) in a Neotropical arachnid to investigate the role of mitochondria in sperm competition. DNA profiling demonstrated that B2-carrying males sired more than three times as many offspring in sperm competition experiments than A males, and this B2 competitive advantage cannot be explained by female mitochondrial haplogroup or male nuclear genetic background. RNA-Seq of testicular tissues implicates differential expression of mitochondrial oxidative phosphorylation (OXPHOS) genes in the B2 competitive advantage, including a 22-fold upregulation of atp8 in B2 males. Previous comparative genomic analyses have revealed functionally significant amino acid substitutions in differentially expressed genes, indicating that the mitochondrial haplogroups differ not only in expression but also in DNA sequence and protein functioning. However, mitochondrial haplogroup had no effect on sperm number or sperm viability, and, when females were mated to a single male, neither male haplogroup, female haplogroup nor the interaction between male/female haplogroup significantly affected female reproductive success. Our findings therefore suggest that mitochondrial effects on male reproduction may often go undetected in noncompetitive contexts and may prove more important in nature than is currently appreciated.},
}

@article {pmid31494084,
year = {2019},
author = {Supinski, GS and Schroder, EA and Callahan, LA},
title = {Mitochondria and Critical Illness.},
journal = {Chest},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chest.2019.08.2182},
pmid = {31494084},
issn = {1931-3543},
abstract = {Classically, mitochondria have largely been believed to influence the development of illness by modulating cell metabolism and determining the rate of production of high-energy phosphate compounds (eg, adenosine triphosphate). It is now recognized that this view is simplistic and that mitochondria play key roles in many other processes, including cell signaling, regulating gene expression, modulating cellular calcium levels, and influencing the activation of cell death pathways (eg, caspase activation). Moreover, these multiple mitochondrial functional characteristics are now known to influence the evolution of cellular and organ function in many disease states, including sepsis, ICU-acquired skeletal muscle dysfunction, acute lung injury, acute renal failure, and critical illness-related immune function dysregulation. In addition, diseased mitochondria generate toxic compounds, most notably released mitochondrial DNA, which can act as danger-associated molecular patterns to induce systemic toxicity and damage multiple organs throughout the body. This article reviews these evolving concepts relating mitochondrial function and acute illness. The discussion is organized into four sections: (1) basics of mitochondrial physiology; (2) cellular mechanisms of mitochondrial pathophysiology; (3) critical care disease processes whose initiation and evolution are shaped by mitochondrial pathophysiology; and (4) emerging treatments for mitochondrial dysfunction in critical illness.},
}

@article {pmid31484504,
year = {2019},
author = {Feng, C and Tang, Y and Liu, S and Tian, F and Zhang, C and Zhao, K},
title = {Multiple convergent events created a nominal widespread species: Triplophysa stoliczkae (Steindachner, 1866) (Cobitoidea: Nemacheilidae).},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {177},
doi = {10.1186/s12862-019-1503-3},
pmid = {31484504},
issn = {1471-2148},
mesh = {Animals ; Biological Evolution ; China ; Cypriniformes/*classification/*genetics ; Genetic Speciation ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Tibet ; },
abstract = {BACKGROUND: Triplophysa stoliczkae is the most widespread species in the genus Triplophysa and may have originated from morphological convergence. To understand the evolutionary history of T. stoliczkae, we employed a multilocus approach to investigate the phylogenetics and the morphological evolution of T. stoliczkae on the Qinghai-Tibetan Plateau.

RESULTS: All phylogenetic analyses (two mitochondrial and five nuclear loci), a genealogical sorting index and species tree inferences suggested that T. stoliczkae consists of distinct lineages that were not closest relatives. The time estimation indicated that the divergence events between "T. stoliczkae" and other Triplophysa species occurred from approximately 0.10 to 4.51 Ma. The ancestral state analyses supported the independent evolution of T. stoliczkae morphology in distinct lineages. The morphometric analysis and convergence estimates demonstrated significant phenotypic convergence among "T. stoliczkae" lineages.

CONCLUSIONS: Triplophysa stoliczkae includes 4 different lineages with similar morphologies. The increasingly harsh environments that have occurred since the Pliocene have driven the occurrences of scrape-feeding fish in the genus Triplophysa. Morphological adaptations associated with scrape-feeding behavior resulted in convergences and the artificial lumping of four different species in the nominal taxon T. stoliczkae. A taxonomic revision for T. stoliczkae is needed.},
}

Animals
Biological Evolution
China
Cypriniformes/*classification/*genetics
Genetic Speciation
Mitochondria/genetics
Phylogeny
Sequence Analysis, DNA
Tibet

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

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

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

@article {pmid31474649,
year = {2019},
author = {Takeda, A and Saitoh, S and Ohkura, H and Sawin, KE and Goshima, G},
title = {Identification of 15 New Bypassable Essential Genes of Fission Yeast.},
journal = {Cell structure and function},
volume = {44},
number = {2},
pages = {113-119},
pmid = {31474649},
issn = {1347-3700},
support = {203149/WT_/Wellcome Trust/United Kingdom ; 098030/WT_/Wellcome Trust/United Kingdom ; 210659/WT_/Wellcome Trust/United Kingdom ; 206315/WT_/Wellcome Trust/United Kingdom ; 094517/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Every organism has a different set of genes essential for its viability. This indicates that an organism can become tolerant to the loss of an essential gene under certain circumstances during evolution, via the manifestation of 'masked' alternative mechanisms. In our quest to systematically uncover masked mechanisms in eukaryotic cells, we developed an extragenic suppressor screening method using haploid spores deleted of an essential gene in the fission yeast Schizosaccharomyces pombe. We screened for the 'bypass' suppressors of lethality of 92 randomly selected genes that are essential for viability in standard laboratory culture conditions. Remarkably, extragenic mutations bypassed the essentiality of as many as 20 genes (22%), 15 of which have not been previously reported. Half of the bypass-suppressible genes were involved in mitochondria function; we also identified multiple genes regulating RNA processing. 18 suppressible genes were conserved in the budding yeast Saccharomyces cerevisiae, but 13 of them were non-essential in that species. These trends suggest that essentiality bypass is not a rare event and that each organism may be endowed with secondary or backup mechanisms that can substitute for primary mechanisms in various biological processes. Furthermore, the robustness of our simple spore-based methodology paves the way for genome-scale screening.Key words: Schizosaccharomyces pombe, extragenic suppressor screening, bypass of essentiality (BOE), cut7 (kinesin-5), hul5 (E3 ubiquitin ligase).},
}

@article {pmid31473860,
year = {2019},
author = {Yorimitsu, Y and Kadosono, A and Hatakeyama, Y and Yabiku, T and Ueno, O},
title = {Transition from C3 to proto-Kranz to C3-C4 intermediate type in the genus Chenopodium (Chenopodiaceae).},
journal = {Journal of plant research},
volume = {132},
number = {6},
pages = {839-855},
pmid = {31473860},
issn = {1618-0860},
support = {JP15K14638//Japan Society for the promotion of Science KAKENHI/ ; },
abstract = {The Chenopodiaceae is one of the families including C4 species among eudicots. In this family, the genus Chenopodium is considered to include only C3 species. However, we report here a transition from C3 photosynthesis to proto-Kranz to C3-C4 intermediate type in Chenopodium. We investigated leaf anatomical and photosynthetic traits of 15 species, of which 8 species showed non-Kranz anatomy and a CO2 compensation point (Γ) typical of C3 plants. However, 5 species showed proto-Kranz anatomy and a C3-like Γ, whereas C. strictum showed leaf anatomy and a Γ typical of C3-C4 intermediates. Chenopodium album accessions examined included both proto-Kranz and C3-C4 intermediate types, depending on locality. Glycine decarboxylase, a key photorespiratory enzyme that is involved in the decarboxylation of glycine, was located predominantly in the mesophyll (M) cells of C3 species, in both M and bundle-sheath (BS) cells in proto-Kranz species, and exclusively in BS cells in C3-C4 intermediate species. The M/BS tissue area ratio, number of chloroplasts and mitochondria per BS cell, distribution of these organelles to the centripetal region of BS cells, the degree of inner positioning (vacuolar side of chloroplasts) of mitochondria in M cells, and the size of BS mitochondria also changed with the change in glycine decarboxylase localization. All Chenopodium species examined were C3-like regarding activities and amounts of C3 and C4 photosynthetic enzymes and δ13C values, suggesting that these species perform photosynthesis without contribution of the C4 cycle. This study demonstrates that Chenopodium is not a C3 genus and is valuable for studying evolution of C3-C4 intermediates.},
}

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

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

Apoptosis
*Host-Pathogen Interactions
Immunity, Innate
*Mitochondria/metabolism
Signal Transduction

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

@article {pmid31434740,
year = {2019},
author = {Barbero Barcenilla, B and Shippen, DE},
title = {Back to the future: The intimate and evolving connection between telomere-related factors and genotoxic stress.},
journal = {The Journal of biological chemistry},
volume = {294},
number = {40},
pages = {14803-14813},
pmid = {31434740},
issn = {1083-351X},
support = {R01 GM065383/GM/NIGMS NIH HHS/United States ; R01 GM127402/GM/NIGMS NIH HHS/United States ; },
abstract = {The conversion of circular genomes to linear chromosomes during molecular evolution required the invention of telomeres. This entailed the acquisition of factors necessary to fulfill two new requirements: the need to fully replicate terminal DNA sequences and the ability to distinguish chromosome ends from damaged DNA. Here we consider the multifaceted functions of factors recruited to perpetuate and stabilize telomeres. We discuss recent theories for how telomere factors evolved from existing cellular machineries and examine their engagement in nontelomeric functions such as DNA repair, replication, and transcriptional regulation. We highlight the remarkable versatility of protection of telomeres 1 (POT1) proteins that was fueled by gene duplication and divergence events that occurred independently across several eukaryotic lineages. Finally, we consider the relationship between oxidative stress and telomeres and the enigmatic role of telomere-associated proteins in mitochondria. These findings point to an evolving and intimate connection between telomeres and cellular physiology and the strong drive to maintain chromosome integrity.},
}

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

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

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

Animals
DNA, Mitochondrial/immunology
Host Microbial Interactions/*immunology
Humans
*Immunity, Innate
Mitochondria/genetics/*immunology
Mitochondrial Degradation/immunology
Symbiosis/*immunology

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

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

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

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

@article {pmid31387118,
year = {2019},
author = {Karnkowska, A and Treitli, SC and Brzoň, O and Novák, L and Vacek, V and Soukal, P and Barlow, LD and Herman, EK and Pipaliya, SV and Pánek, T and Žihala, D and Petrželková, R and Butenko, A and Eme, L and Stairs, CW and Roger, AJ and Eliáš, M and Dacks, JB and Hampl, V},
title = {The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion.},
journal = {Molecular biology and evolution},
volume = {36},
number = {10},
pages = {2292-2312},
pmid = {31387118},
issn = {1537-1719},
abstract = {The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less "reduced" than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe-S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.},
}

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

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

@article {pmid31328352,
year = {2019},
author = {Khemaissia, H and Jelassi, R and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K},
title = {Effects of trace metal elements on ultrastructural features of hepatopancreas of Armadillidium granulatum Brandt, 1833 (Crustacea, Isopoda).},
journal = {Microscopy research and technique},
volume = {82},
number = {10},
pages = {1819-1831},
doi = {10.1002/jemt.23349},
pmid = {31328352},
issn = {1097-0029},
support = {LR18ES06//Laboratory of Diversity, Management and Conservation of Biological Systems/ ; },
abstract = {This study was conducted to compare metals bioaccumulation in the terrestrial isopod Armadillidium granulatum collected from Ghar El Melh lagoon. We focused on recognizing the effects of trace elements on hepatopancreas functional role. To this end, isopod specimens were exposed for 3 weeks to sediments contaminated with cadmium, copper, zinc, mercury, and nickel. Three concentrations were used in duplicate for each experimental condition. At the end of the experiment, metal body burdens were determined using flame atomic absorption spectrometry. Results of the bioaccumulation factor (BAF) showed that the species A. granulatum was classified as a Cu macroconcentrator (BAF > 2) and a Zn deconcentrator (BAF < 2). Dose dependent morphological and histological changes were observed in the hepatopancreas cells using transmission electron microscopy. The predominant features were: microvillus border disruption, condensation of the cytoplasm with increasing endoplasmic reticulum, mitochondria, lysosomes and granules that accumulated metals in B and S cells. The number of lipid droplets decreased especially after Cd, Zn, Hg, and Ni treatments. This study demonstrated that the terrestrial isopod A. gramulatum could be a good indicator of soil metal contamination.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid31239554,
year = {2019},
author = {Ågren, JA and Davies, NG and Foster, KR},
title = {Enforcement is central to the evolution of cooperation.},
journal = {Nature ecology & evolution},
volume = {3},
number = {7},
pages = {1018-1029},
doi = {10.1038/s41559-019-0907-1},
pmid = {31239554},
issn = {2397-334X},
support = {209397/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Biological Evolution ; *Cooperative Behavior ; Humans ; Symbiosis ; },
abstract = {Cooperation occurs at all levels of life, from genomes, complex cells and multicellular organisms to societies and mutualisms between species. A major question for evolutionary biology is what these diverse systems have in common. Here, we review the full breadth of cooperative systems and find that they frequently rely on enforcement mechanisms that suppress selfish behaviour. We discuss many examples, including the suppression of transposable elements, uniparental inheritance of mitochondria and plastids, anti-cancer mechanisms, reciprocation and punishment in humans and other vertebrates, policing in eusocial insects and partner choice in mutualisms between species. To address a lack of accompanying theory, we develop a series of evolutionary models that show that the enforcement of cooperation is widely predicted. We argue that enforcement is an underappreciated, and often critical, ingredient for cooperation across all scales of biological organization.},
}

Animals
*Biological Evolution
*Cooperative Behavior
Humans
Symbiosis

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

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

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

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

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

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

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

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

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