@article {pmid32230306,
year = {2020},
author = {Ceríaco, LMP and Agarwal, I and Marques, MP and Bauer, AM},
title = {A review of the genus Hemidactylus Goldfuss, 1820 (Squamata: Gekkonidae) from Angola, with the description of two new species.},
journal = {Zootaxa},
volume = {4746},
number = {1},
pages = {zootaxa.4746.1.1},
doi = {10.11646/zootaxa.4746.1.1},
pmid = {32230306},
issn = {1175-5334},
mesh = {Angola ; Animals ; *Lizards ; Mitochondria ; Phylogeny ; },
abstract = {The genus Hemidactylus in Angola is represented by six species, all of them part of taxonomically and nomenclaturally challenging species complexes. We present a detailed taxonomic revision of the group in the region and describe two new species, Hemidactylus nzingae sp. nov. and Hemidactylus paivae sp. nov., both occuring in and potentially endemic to the highlands of Angola. Phylogenetic analysis using a combination of mitochondrial (ND2) and nuclear (MXRA5, PDC, RAG1) markers, as well as morphological and scalation data support the recognition of the new species. In addition, data support the revalidation of Hemidactylus bayonii Bocage, 1893, and Hemidactylus benguellensis Bocage, 1893. We also provide a redefinition of Hemidactylus longicephalus Bocage, 1873 with which we synonymize Hemidactylus mabouia molleri Bedriaga, 1892, from São Tomé in the Gulf of Guinea. Given that the type material of H. bayonii, H. benguellensis, H. longicephalus and H. mabouia molleri have all been lost or destroyed, we designate neotypes for all of these nomina for purposes of nomenclatural stability. The description of the new species and the revision and revalidation of the Angolan species already described contributes to a better understanding of the taxonomy and biogeography of West and Central African Hemidactylus, as well as to the general biogeographic and evolutionary patterns of Angolan fauna. A key to the Angolan species is also presented.},
}

Angola
Animals
*Lizards
Mitochondria
Phylogeny

@article {pmid31767817,
year = {2019},
author = {Abou-Shaara, HF},
title = {Utilizing bioinformatics to detect genetic similarities between African honey bee subspecies.},
journal = {Journal of genetics},
volume = {98},
number = {},
pages = {},
pmid = {31767817},
issn = {0973-7731},
mesh = {Africa ; Animals ; Base Sequence ; Bees/*classification/*genetics ; *Computational Biology ; DNA Primers ; DNA, Mitochondrial/genetics ; Mitochondria/*genetics ; Multigene Family ; Open Reading Frames ; Phylogeny ; Sequence Analysis ; },
abstract = {Various honey bees, especially subspecies Apis mellifera, occur in Africa and are distribute across the continent. The genetic relationships and identical genetic characteristics between honey bee subspecies in Africa (African bee subspecies) have not been widely investigated using sequence analysis. On the other hand, bioinformatics are developed rapidly and have diverse applications. It is anticipated that bioinformatics can show the genetic relationships and similarities among subspecies. These points have high importance, especially subspecies with identical genetic characteristics can be infected with the same group of pathogens, which have implications on honey bee health. In this study, the mitochondrial DNA sequences of four African subspecies and Africanized bees were subjected to the analyses of base composition, phylogeny, shared gene clusters, enzymatic digestion, and open reading frames. High identical base composition was detected in the studied subspecies, and high identical results from all tests were found between A. m. scutellata and A. m. capensis followed by A. m. intermissa and A. m. monticola. The least genetic relationships were found between A. m. lamarckii and the other subspecies. This study presents insights into the genetic aspects of African bee subspecies and highlights similarity and dissimilarity aspects. Also, Africanized honey bees derived from A. m. scutellata showed high genetic similarities to other African bees, especially A. m. capensis. Additionally, specific primers to identify these subspecies were designed and tested.},
}

Africa
Animals
Base Sequence
Bees/*classification/*genetics
*Computational Biology
DNA Primers
DNA, Mitochondrial/genetics
Mitochondria/*genetics
Multigene Family
Open Reading Frames
Phylogeny
Sequence Analysis

@article {pmid31767814,
year = {2019},
author = {Kumar De, A and Ponraj, P and Malakar, D and Muthiyan, R and Kundu, A and Bhattacharya, D},
title = {Complete mitogenome sequencing of Andaman buffalo: an endangered germplasm of Andaman and Nicobar Islands, India.},
journal = {Journal of genetics},
volume = {98},
number = {},
pages = {},
pmid = {31767814},
issn = {0973-7731},
mesh = {Animals ; Base Composition ; Buffaloes/*genetics ; China ; Codon, Initiator ; Codon, Terminator ; Genes, Mitochondrial/*genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; India ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Andaman buffalo is an indigenous buffalo of Andaman and Nicobar Islands, India. Over the last decade, it has witnessed a rapid decline in population, necessitating its immediate characterization and conservation. The present study reports the complete mitogenome profile of Andaman buffalo which is 16,359 bp in length and comprised of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs. In addition, one A + T rich region (D-loop) was also present. A biasness towards A and T base was observed in all the genes. All the PCGs except ND6 were present on heavy strand. Start codons for all the 13 PCGs were ATN codon and abbreviated/truncated stop codons were observed in ND1, ND2, COX3, ND3 and ND4. The phylogenetic analysis revealed that the Andaman buffalo is closely related to buffalo from India and China. The results from this study will help in sketching the conservation plan of the threatened breed.},
}

Animals
Base Composition
Buffaloes/*genetics
China
Codon, Initiator
Codon, Terminator
Genes, Mitochondrial/*genetics
Genes, rRNA/genetics
Genome, Mitochondrial/*genetics
High-Throughput Nucleotide Sequencing
India
Mitochondria/*genetics
Nucleic Acid Conformation
Phylogeny
RNA, Ribosomal/genetics
RNA, Transfer/genetics
Sequence Alignment
Sequence Analysis, DNA

@article {pmid31670613,
year = {2019},
author = {Achatz, TJ and Dmytrieva, I and Kuzmin, Y and Tkach, VV},
title = {Phylogenetic Position of Codonocephalus Diesing, 1850 (Digenea, Diplostomoidea), an Unusual Diplostomid with Progenetic Metacercariae.},
journal = {The Journal of parasitology},
volume = {105},
number = {5},
pages = {821-826},
pmid = {31670613},
issn = {1937-2345},
mesh = {Animals ; Bayes Theorem ; DNA, Helminth/chemistry/isolation & purification ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/chemistry/genetics ; Life Cycle Stages ; Metacercariae/classification/genetics ; Microscopy, Electron, Scanning/veterinary ; Mitochondria/enzymology ; *Phylogeny ; RNA, Helminth/genetics ; RNA, Nuclear/genetics ; RNA, Ribosomal, 28S/genetics ; Ranidae/*parasitology ; Trematoda/*classification/genetics/ultrastructure ; Trematode Infections/parasitology/*veterinary ; },
abstract = {Codonocephalus is a monotypic genus of diplostomid digeneans and is the only genus in the sub-family Codonocephalinae. The type-species Codonocephalus urniger has an unusual progenetic metacercaria that uses frogs as intermediate hosts and can use snakes as paratenic hosts. Adult C. urniger parasitize ardeid wading birds in the Palearctic. Despite the broad distribution of Codonocephalus, no DNA sequence data are currently available for the genus. In this study, we generated sequence data for nuclear ribosomal and mitochondrial DNA from progenetic metacercaria of the type-species C. urniger from marsh frog, Pelophylax ridibundus, collected in Ukraine. We used partial sequences of the nuclear ribosomal 28S gene to examine for the first time the phylogenetic position of Codonocephalus among the Diplostomoidea.},
}

Animals
Bayes Theorem
DNA, Helminth/chemistry/isolation & purification
DNA, Ribosomal/chemistry
Electron Transport Complex IV/chemistry/genetics
Life Cycle Stages
Metacercariae/classification/genetics
Microscopy, Electron, Scanning/veterinary
Mitochondria/enzymology
*Phylogeny
RNA, Helminth/genetics
RNA, Nuclear/genetics
RNA, Ribosomal, 28S/genetics
Ranidae/*parasitology
Trematoda/*classification/genetics/ultrastructure
Trematode Infections/parasitology/*veterinary

@article {pmid31633437,
year = {2019},
author = {de Oliveira Simões, R and Fraga-Neto, S and Vilar, EM and Maldonado, A and do Val Vilela, R},
title = {A New Species of Bidigiticauda (Nematoda: Strongylida) from the Bat Artibeus Planirostris (Chiroptera: Phyllostomidae) in the Atlantic Forest and a Molecular Phylogeny of the Molineid Bat Parasites.},
journal = {The Journal of parasitology},
volume = {105},
number = {5},
pages = {783-792},
pmid = {31633437},
issn = {1937-2345},
mesh = {Animals ; Bayes Theorem ; Brazil ; Chiroptera/*parasitology ; DNA Barcoding, Taxonomic/veterinary ; DNA, Helminth/chemistry/isolation & purification ; Electron Transport Complex IV/genetics ; Female ; Forests ; Male ; Mitochondria/enzymology ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Trichostrongyloidea/anatomy & histology/*classification/genetics/isolation & purification ; Trichostrongyloidiasis/parasitology/*veterinary ; },
abstract = {The nematode genus Bidigiticauda has 2 species (Bidigiticauda vivipara and Bidigiticauda embryophilum), which are parasites of bats from the Neotropical region. The present paper describes a new species of Bidigiticauda from a male Artibeus planirostris specimen collected in the Pratigi Environmental Protection Area in Bahia state, Brazil. The new species, Bidigiticauda serrafreirei n. sp., differs from B. embryophilum by having longer spicules, rays 5 and 6 arising from a common trunk and bifurcating in its first third, rays 3 and 4 emerging slightly separated from each other, and dorsal rays reaching the margin of the caudal bursa. The new species also differs from B. vivipara by the dorsal ray bifurcating at the extremity of the trunk. A molecular phylogenetic analysis was conducted to determine the evolutionary affinities of Bidigiticauda serrafreirei n. sp. within the Strongylida, which identified a clade that grouped Bidigiticauda with the other members of the Anoplostrongylinae. However, the molineid subfamilies did not group together, indicating that the family Molineidae is polyphyletic. Further analyses, which include additional taxa and genetic markers, should elucidate the complex relationships within the Molineidae, in particular its subfamilies and the evolution of the traits that define these groups.},
}

Animals
Bayes Theorem
Brazil
Chiroptera/*parasitology
DNA Barcoding, Taxonomic/veterinary
DNA, Helminth/chemistry/isolation & purification
Electron Transport Complex IV/genetics
Female
Forests
Male
Mitochondria/enzymology
*Phylogeny
RNA, Ribosomal, 28S/genetics
Trichostrongyloidea/anatomy & histology/*classification/genetics/isolation & purification
Trichostrongyloidiasis/parasitology/*veterinary

@article {pmid31580787,
year = {2019},
author = {Velázquez-Urrieta, Y and Oceguera-Figueroa, A and León-Règagnon, V},
title = {Two New Species of Haematoloechus (Digenea: Plagiorchidae) Parasitizing Rana brownorum (Amphibia: Ranidae) from Southeast Mexico.},
journal = {The Journal of parasitology},
volume = {105},
number = {5},
pages = {724-732},
pmid = {31580787},
issn = {1937-2345},
mesh = {Animals ; Base Sequence ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Lung/parasitology ; Mexico ; Mitochondria/enzymology ; Phylogeny ; Prevalence ; RNA, Ribosomal, 28S/genetics ; Ranidae/*parasitology ; Sequence Alignment/veterinary ; Trematoda/anatomy & histology/*classification/genetics/isolation & purification ; Trematode Infections/epidemiology/parasitology/*veterinary ; },
abstract = {In an ongoing investigation on the helminths of amphibians in southeastern Mexico, specimens of 2 undescribed species of Haematoloechus were collected from Rana brownorum. Haematoloechus ceciliae n. sp. is morphologically most similar to Haematoloechus meridionalis, but differs in the shape of the oral sucker, in the nature of the acetabulum, and in the distribution of the glandular cells in the pharyngeal region; Haematoloechus celestunensis n. sp. closely resembles Haematoloechus floedae, but differs in the form and size of the testes and measurements of acetabulum. COI and 28S DNA sequences of both new species show high divergence compared to other species of the genus. In the phylogenetic trees, H. ceciliae appears most closely related to Haematoloechus danbrooksi and H. celestunensis to Haematoloechus veracruzanus.},
}

Animals
Base Sequence
DNA, Ribosomal/chemistry
Electron Transport Complex IV/genetics
Lung/parasitology
Mexico
Mitochondria/enzymology
Phylogeny
Prevalence
RNA, Ribosomal, 28S/genetics
Ranidae/*parasitology
Sequence Alignment/veterinary
Trematoda/anatomy & histology/*classification/genetics/isolation & purification
Trematode Infections/epidemiology/parasitology/*veterinary

@article {pmid31580785,
year = {2019},
author = {Achatz, TJ and Curran, SS and Patitucci, KF and Fecchio, A and Tkach, VV},
title = {Phylogenetic Affinities of Uvulifer Spp. (Digenea: Diplostomidae) in the Americas with Description of Two New Species from Peruvian Amazon.},
journal = {The Journal of parasitology},
volume = {105},
number = {5},
pages = {704-717},
pmid = {31580785},
issn = {1937-2345},
support = {R15 AI092622/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Bayes Theorem ; Bird Diseases/*parasitology ; Birds ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Intestine, Small/parasitology ; Mitochondria/enzymology ; Peru ; *Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 28S/genetics ; Rivers ; Sequence Alignment/veterinary ; Trematoda/anatomy & histology/*classification/genetics ; Trematode Infections/parasitology/*veterinary ; },
abstract = {Uvulifer Yamaguti, 1934, is a genus of diplostomoidean digeneans that parasitizes kingfishers worldwide. Species have a Neascus-type metacercaria that encysts in or on fish intermediate hosts, often causing black spot disease. Only 3 prior studies published DNA sequence data for Uvulifer species with only 1 including a single named species (Uvulifer spinatus López-Jiménez, Pérez-Ponce de León, & García-Varela, 2018). Herein we describe 2 new species of Uvulifer from the green-and-rufous kingfisher, Chloroceryle inda (Linnaeus), collected in Peru (Uvulifer batesi n. sp. and Uvulifer pequenae n. sp.). Both new species are readily differentiated from their New World congeners by a combination of morphological characters including distribution of vitelline follicles and prosoma:opisthosoma length ratios. In addition, we used newly generated nuclear 28S rRNA and mitochondrial COI gene sequence data to differentiate among species and examine phylogenetic affinities of Uvulifer. This includes the 2 new species and Uvulifer ambloplitis (Hughes, 1927), as well as Uvulifer elongatus Dubois, 1988 , Uvulifer prosocotyle (Lutz, 1928), and Uvulifer weberi Dubois, 1985 , none of which have been part of prior molecular phylogenetic studies. Our data on Uvulifer revealed 0.1-2.2% interspecific divergence in 28S sequences and 9.3-15.3% in COI sequences. Our 28S phylogeny revealed at least 6 well-supported clades within the genus. In contrast, the branch topology in the COI phylogenetic tree was overall less supported, indicating that although COI sequences are a great tool for species differentiation, they should be used with caution for phylogenetic inference at higher taxonomic levels. Our 28S phylogeny did not reveal any clear patterns of host association between Uvulifer and particular species of kingfishers; however, it identified 2 well-supported clades uniting Uvulifer species from distant geographical locations and more than 1 biogeographic realm, indicating at least 2 independent dispersal events in the evolutionary history of the New World Uvulifer. Our results clearly demonstrate that the diversity of Uvulifer in the New World has been underestimated.},
}

Animals
Bayes Theorem
Bird Diseases/*parasitology
Birds
DNA, Mitochondrial/genetics
DNA, Ribosomal/genetics
Electron Transport Complex IV/genetics
Genetic Variation
Intestine, Small/parasitology
Mitochondria/enzymology
Peru
*Phylogeny
Polymerase Chain Reaction/veterinary
RNA, Ribosomal, 28S/genetics
Rivers
Sequence Alignment/veterinary
Trematoda/anatomy & histology/*classification/genetics
Trematode Infections/parasitology/*veterinary

@article {pmid31257025,
year = {2019},
author = {Cui, R and Medeiros, T and Willemsen, D and Iasi, LNM and Collier, GE and Graef, M and Reichard, M and Valenzano, DR},
title = {Relaxed Selection Limits Lifespan by Increasing Mutation Load.},
journal = {Cell},
volume = {178},
number = {2},
pages = {385-399.e20},
doi = {10.1016/j.cell.2019.06.004},
pmid = {31257025},
issn = {1097-4172},
mesh = {Aging ; Animals ; DNA Replication ; Evolution, Molecular ; Gene Frequency ; Genome, Mitochondrial ; Killifishes/classification/genetics ; *Longevity ; Mitochondria/genetics/metabolism ; Mutation ; Phylogeny ; Phylogeography ; *Selection, Genetic ; },
abstract = {To uncover the selective forces shaping life-history trait evolution across species, we investigate the genomic basis underlying adaptations to seasonal habitat desiccation in African killifishes, identifying the genetic variants associated with positive and relaxed purifying selection in 45 killifish species and 231 wild individuals distributed throughout sub-Saharan Africa. In annual species, genetic drift led to the expansion of nuclear and mitochondrial genomes and caused the accumulation of deleterious genetic variants in key life-history modulating genes such as mtor, insr, ampk, foxo3, and polg. Relaxation of purifying selection is also significantly associated with mitochondrial function and aging in human populations. We find that relaxation of purifying selection prominently shapes genomes and is a prime candidate force molding the evolution of lifespan and the distribution of genetic variants associated with late-onset diseases in different species. VIDEO ABSTRACT.},
}

Aging
Animals
DNA Replication
Evolution, Molecular
Gene Frequency
Genome, Mitochondrial
Killifishes/classification/genetics
*Longevity
Mitochondria/genetics/metabolism
Mutation
Phylogeny
Phylogeography
*Selection, Genetic

@article {pmid32251374,
year = {2020},
author = {Waltz, F and Soufari, H and Bochler, A and Giegé, P and Hashem, Y},
title = {Cryo-EM structure of the RNA-rich plant mitochondrial ribosome.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41477-020-0631-5},
pmid = {32251374},
issn = {2055-0278},
support = {ANR-16-CE11-0024-02//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-14-ACHN-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-CE11-0024-02//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-CE11-0024-02//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-14-ACHN-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-LABX-0057_MITOCROSS//Agence Nationale de la Recherche (French National Research Agency)/ ; 759120//European Commission (EC)/ ; 759120//European Commission (EC)/ ; },
abstract = {The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs1. These organelles have a bacterial origin and were acquired during an early endosymbiosis event2. Mitochondria possess specialized gene expression systems composed of various molecular machines, including the mitochondrial ribosomes (mitoribosomes). Mitoribosomes are in charge of translating the few essential mRNAs still encoded by mitochondrial genomes3. While chloroplast ribosomes strongly resemble those of bacteria4,5, mitoribosomes have diverged significantly during evolution and present strikingly different structures across eukaryotic species6-10. In contrast to animals and trypanosomatids, plant mitoribosomes have unusually expanded ribosomal RNAs and have conserved the short 5S rRNA, which is usually missing in mitoribosomes11. We have previously characterized the composition of the plant mitoribosome6, revealing a dozen plant-specific proteins in addition to the common conserved mitoribosomal proteins. In spite of the tremendous recent advances in the field, plant mitoribosomes remained elusive to high-resolution structural investigations and the plant-specific ribosomal features of unknown structures. Here, we present a cryo-electron microscopy study of the plant 78S mitoribosome from cauliflower at near-atomic resolution. We show that most of the plant-specific ribosomal proteins are pentatricopeptide repeat proteins (PPRs) that deeply interact with the plant-specific rRNA expansion segments. These additional rRNA segments and proteins reshape the overall structure of the plant mitochondrial ribosome, and we discuss their involvement in the membrane association and mRNA recruitment prior to translation initiation. Finally, our structure unveils an rRNA-constructive phase of mitoribosome evolution across eukaryotes.},
}

@article {pmid32246837,
year = {2020},
author = {Rank, NE and Mardulyn, P and Heidl, SJ and Roberts, KT and Zavala, NA and Smiley, JT and Dahlhoff, EP},
title = {Mitonuclear mismatch alters performance and reproductive success in naturally-introgressed populations of a montane leaf beetle.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1111/evo.13962},
pmid = {32246837},
issn = {1558-5646},
abstract = {Coordination between nuclear and mitochondrial genomes is critical to metabolic processes underlying animals' ability to adapt to local environments, yet consequences of mitonuclear interactions have rarely been investigated in populations where individuals with divergent mitochondrial and nuclear genomes naturally interbreed. Genetic variation in the leaf beetle Chrysomela aeneicollis was assessed along a latitudinal thermal gradient in California's Sierra Nevada. Variation at mitochondrial cytochrome oxidase II (COII) and the nuclear gene phosphoglucose isomerase (PGI) shows concordance and was significantly greater along a 65 km transect than 10 other loci. STRUCTURE analyses using neutral loci identified a southern and northern subpopulation, which interbreed in the central drainage Bishop Creek. COII and PGI were used as indicators of mitochondrial and nuclear genetic variation in field and laboratory experiments conducted on beetles from this admixed population. Fecundity, larval development rate, running speed and male mating frequency were higher for beetles with geographically 'matched' than 'mismatched' mitonuclear genotypes. Effects of mitonuclear mismatch were largest for individuals with northern nuclear genotypes possessing southern mitochondria and were most pronounced after heat treatment or at high elevation. These findings suggest that mitonuclear incompatibility diminishes performance and reproductive success in nature, effects that could intensify at environmental extremes. This article is protected by copyright. All rights reserved.},
}

@article {pmid32245791,
year = {2020},
author = {Guan, X and Okazaki, Y and Zhang, R and Saito, K and Nikolau, BJ},
title = {Dual-localized enzymatic components constitute the fatty acid synthase systems in mitochondria and plastids.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1104/pp.19.01564},
pmid = {32245791},
issn = {1532-2548},
abstract = {Plant fatty acid biosynthesis occurs in both plastids and mitochondria. Here, we report the identification and characterization of Arabidopsis (Arabidopsis thaliana) genes encoding three enzymes shared between the mitochondria- and plastid-localized Type II fatty acid synthase systems (mtFAS and ptFAS, respectively). Two of these enzymes, β-ketoacyl-acyl carrier protein (ACP) reductase (pt/mtKR) and enoyl-ACP reductase (pt/mtER) catalyze two of the reactions that constitute the core four-reaction cycle of the FAS system, which iteratively elongates the acyl-chain by two carbon atoms per cycle. The third enzyme, malonyl-CoA:ACP transacylase (pt/mtMCAT) catalyzes the reaction that loads the mtFAS system with substrate by malonylating the phosphopantetheinyl cofactor of ACP. Green fluorescent protein (GFP) fusion experiments revealed that the these enzymes localize to both chloroplasts and mitochondria. This localization was validated by characterization of mutant alleles, which were rescued by transgenes expressing enzyme variants that were retargeted only to plastids or only mitochondria. The singular retargeting of these proteins to plastids rescued the embryo-lethality associated with disruption of the essential ptFAS system, but these rescued plants displayed phenotypes typical of the lack of mtFAS function, including reduced lipoylation of the H subunit of the glycine decarboxylase complex, hyperaccumulation of glycine, and reduced growth. However, these latter traits were reversible in an elevated CO2 atmosphere, which suppresses mtFAS-associated photorespiration-dependent chemotypes. Sharing enzymatic components between mtFAS and ptFAS systems constrains the evolution of these non-redundant fatty acid biosynthetic machineries.},
}

@article {pmid32244644,
year = {2020},
author = {Harada, R and Hirakawa, Y and Yabuki, A and Kashiyama, Y and Maruyama, M and Onuma, R and Soukal, P and Miyagishima, S and Hampl, V and Tanifuji, G and Inagaki, Y},
title = {Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa.},
journal = {Pathogens (Basel, Switzerland)},
volume = {9},
number = {4},
pages = {},
doi = {10.3390/pathogens9040257},
pmid = {32244644},
issn = {2076-0817},
support = {18KK0203 and 19H03280, YI; 17H03723 and 26840123, GT; 17K19434, AY//Japan Society for the Promotion of Science/ ; 16-25280S, VH//the Czech Science foundation/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for research of pathogenicity and virulence of parasites/ ; },
abstract = {The order Trypanosomatida has been well studied due to its pathogenicity and the unique biology of the mitochondrion. In Trypanosoma brucei, four DNA polymerases, namely PolIA, PolIB, PolIC, and PolID, related to bacterial DNA polymerase I (PolI), were shown to be localized in mitochondria experimentally. These mitochondrion-localized DNA polymerases are phylogenetically distinct from other family A DNA polymerases, such as bacterial PolI, DNA polymerase gamma (Polγ) in human and yeasts, "plant and protist organellar DNA polymerase (POP)" in diverse eukaryotes. However, the diversity of mitochondrion-localized DNA polymerases in Euglenozoa other than Trypanosomatida is poorly understood. In this study, we discovered putative mitochondrion-localized DNA polymerases in broad members of three major classes of Euglenozoa-Kinetoplastea, Diplonemea, and Euglenida-to explore the origin and evolution of trypanosomatid PolIA-D. We unveiled distinct inventories of mitochondrion-localized DNA polymerases in the three classes: (1) PolIA is ubiquitous across the three euglenozoan classes, (2) PolIB, C, and D are restricted in kinetoplastids, (3) new types of mitochondrion-localized DNA polymerases were identified in a prokinetoplastid and diplonemids, and (4) evolutionarily distinct types of POP were found in euglenids. We finally propose scenarios to explain the inventories of mitochondrion-localized DNA polymerases in Kinetoplastea, Diplonemea, and Euglenida.},
}

@article {pmid32244414,
year = {2020},
author = {Hewitt, SK and Duangrattanalert, K and Burgis, T and Zeef, LAH and Naseeb, S and Delneri, D},
title = {Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids.},
journal = {Microorganisms},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/microorganisms8040494},
pmid = {32244414},
issn = {2076-2607},
support = {BB/F017227/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L021471/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Development and Promotion of Science and Technology Talent (DPST)//Royal Government of Thailand/ ; },
abstract = {Mitochondrial DNA (mtDNA) in yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, thus becoming homoplasmic. Therefore, hybrids between the yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Saccharomyces cerevisiae/S.uvarum hybrids preferentially retained S.uvarum mtDNA when formed on rich media at colder temperatures, while S. cerevisiae mtDNA was primarily retained on non-fermentable carbon source, at any temperature. Transcriptome data for hybrids harbouring different mtDNA showed a strong environmentally dependent allele preference, which was more important in respiratory conditions. Co-expression analysis for specific biological functions revealed a clear pattern of concerted allelic transcription within the same allele type, which supports the notion that the hybrid cell works preferentially with one set of parental alleles (or the other) for different cellular functions. Given that the type of mtDNA retained in hybrids affects both nuclear expression and fitness, it might play a role in driving hybrid genome evolution in terms of gene retention and loss.},
}

@article {pmid32229686,
year = {2020},
author = {Khosravi, S and Harner, ME},
title = {The MICOS complex, a structural element of mitochondria with versatile functions.},
journal = {Biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1515/hsz-2020-0103},
pmid = {32229686},
issn = {1437-4315},
abstract = {Mitochondria perform a plethora of functions in various cells of different tissues. Their architecture differs remarkably, for instance in neurons versus steroidogenic cells. Furthermore, aberrant mitochondrial architecture results in mitochondrial dysfunction. This indicates strongly that mitochondrial architecture and function are intimately linked. Therefore, a deep knowledge about the determinants of mitochondrial architecture and their function on a molecular level is of utmost importance. In the past decades, various proteins and protein complexes essential for formation of mitochondrial architecture have been identified. Here we will review the current knowledge of the MICOS complex, one of the major structural elements of mitochondria. MICOS is a multi-subunit complex present in the inner mitochondrial membrane. Multiple interaction partners in the inner and outer mitochondrial membrane point to participation in a multitude of important processes, such as generation of mitochondrial architecture, lipid metabolism, and protein import into mitochondria. Since the MICOS complex is highly conserved in form and function throughout evolution, we will highlight the importance of MICOS for mammals. We will emphasize in particular the current knowledge of the association of MICOS with severe human diseases, including Charcot-Marie-Tooth disease type 2, Alzheimer's disease, Parkinson's disease, Frontotemporal Dementia and Amyotrophic Lateral Sclerosis.},
}

@article {pmid31851687,
year = {2019},
author = {Barbosa, AD and Austen, J and Portas, TJ and Friend, JA and Ahlstrom, LA and Oskam, CL and Ryan, UM and Irwin, PJ},
title = {Sequence analyses at mitochondrial and nuclear loci reveal a novel Theileria sp. and aid in the phylogenetic resolution of piroplasms from Australian marsupials and ticks.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225822},
pmid = {31851687},
issn = {1932-6203},
mesh = {Animals ; Australia ; DNA, Protozoan/genetics ; Genetic Loci ; Marsupialia/*parasitology ; Mitochondria/*genetics ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/*genetics ; *Theileria/classification/genetics/isolation & purification ; Theileriasis/*parasitology ; Ticks/*parasitology ; },
abstract = {The order Piroplasmida encompasses two main families: Babesiidae and Theileriidae, containing tick-borne pathogens of veterinary and medical importance worldwide. While only three genera (Babesia, Cytauxzoon and Theileria) comprising piroplasm parasites are currently recognised, phylogenetic studies at the 18S rRNA (18S) gene suggest that these organisms represent at least ten lineages, one of which comprises the relatively unique and highly diverse Theileria spp. from Australian marsupials and ticks. As an alternative to analysing 18S sequences alone, sequencing of mitochondrial genes has proven to be useful for the elucidation of evolutionary relationships amongst some groups of piroplasms. This research aimed to characterise piroplasms from Australian native mammals and ticks using multiple genetic markers (18S, cytochrome c, oxidase subunit III (cox3) and cytochrome B (cytB)) and microscopy. For this, nearly complete piroplasm-18S sequences were obtained from 32 animals belonging to six marsupial species: eastern bettong (Bettongia gaimardi), eastern quoll (Dasyurus viverrinus), eastern grey kangaroo (Macropus giganteus), swamp wallaby (Wallabia bicolor), quokka (Setonix brachyurus) and Gilbert's potoroo (Potorous gilbertii). The organisms detected represented eight novel Theileria genotypes, which formed five sub-clades within the main marsupial clade containing previously reported Australian marsupial and tick-derived Theileria spp. A selection of both novel and previously described Australian piroplasms at the 18S were also successfully characterised, for the first time, at the cox3 and cytB loci, and corroborated the position of Australian native theilerias in a separate, well-supported clade. Analyses of the cox3 and cytB genes also aided in the taxonomic resolution within the clade of Australian Piroplasmida. Importantly, microscopy and molecular analysis at multiple loci led to the discovery of a unique piroplasm species that clustered with the Australian marsupial theilerias, for which we propose the name Theileria lupei n. sp.},
}

Animals
Australia
DNA, Protozoan/genetics
Genetic Loci
Marsupialia/*parasitology
Mitochondria/*genetics
Phylogeny
RNA, Protozoan/genetics
RNA, Ribosomal, 18S/*genetics
*Theileria/classification/genetics/isolation & purification
Theileriasis/*parasitology
Ticks/*parasitology

@article {pmid32224234,
year = {2020},
author = {Petersen, G and Anderson, B and Braun, HP and Meyer, EH and Max Møller, I},
title = {Mitochondria in parasitic plants.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2020.03.008},
pmid = {32224234},
issn = {1872-8278},
abstract = {Plant mitochondrial genomes are renowned for their structural complexity, extreme variation in size and mutation rates, and ability to incorporate foreign DNA. Parasitic flowering plants are no exception, and the close association between parasite and host may even enhance the likelihood of horizontal gene transfer (HGT) between them. Recent studies on mistletoes (Viscum) have revealed that these parasites have lost an exceptional number of mitochondrial genes, including all complex I genes of the respiratory chain. At the same time, an altered respiratory pathway has been demonstrated. Here we review the current understanding of mitochondrial evolution in parasitic plants with a special emphasis on HGT to and from parasite mitochondrial genomes, as well as the uniquely altered mitochondria in Viscum and related plants.},
}

@article {pmid30789345,
year = {2019},
author = {Muñoz-Gómez, SA and Hess, S and Burger, G and Lang, BF and Susko, E and Slamovits, CH and Roger, AJ},
title = {An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {30789345},
issn = {2050-084X},
support = {HE7560/1-1//Deutsche Forschungsgemeinschaft/International ; RGPIN/05286-2014//Natural Sciences and Engineering Research Council of Canada/International ; RGPIN-2017-05411//Natural Sciences and Engineering Research Council of Canada/International ; RGPIN/05754-2015//Natural Sciences and Engineering Research Council of Canada/International ; 2016-06792//Natural Sciences and Engineering Research Council of Canada/International ; },
mesh = {Alphaproteobacteria/*classification/*genetics ; Computational Biology ; *Evolution, Molecular ; Genes, Bacterial ; Molecular Biology ; *Phylogeny ; },
abstract = {The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.},
}

Alphaproteobacteria/*classification/*genetics
Computational Biology
*Evolution, Molecular
Genes, Bacterial
Molecular Biology
*Phylogeny

@article {pmid30537423,
year = {2019},
author = {Tsakiri, EN and Gumeni, S and Iliaki, KK and Benaki, D and Vougas, K and Sykiotis, GP and Gorgoulis, VG and Mikros, E and Scorrano, L and Trougakos, IP},
title = {Hyperactivation of Nrf2 increases stress tolerance at the cost of aging acceleration due to metabolic deregulation.},
journal = {Aging cell},
volume = {18},
number = {1},
pages = {e12845},
pmid = {30537423},
issn = {1474-9726},
support = {BIOIMAGING-GR (MIS 5002755)//General Secretariat for Research and Technology, Greece/International ; TASCMAR (EU-H2020/634674)//European Union, H2020/International ; },
mesh = {*Adaptation, Physiological ; Aging/*physiology ; Animals ; Cytoprotection ; Drosophila Proteins/metabolism ; Drosophila melanogaster/*metabolism/*physiology ; Energy Metabolism ; Insulin/metabolism ; Metabolic Networks and Pathways ; Mitochondria/metabolism ; Mitochondrial Dynamics ; NF-E2-Related Factor 2/*metabolism ; Phenotype ; Signal Transduction ; Somatomedins/metabolism ; *Stress, Physiological ; },
abstract = {Metazoans viability depends on their ability to regulate metabolic processes and also to respond to harmful challenges by mounting anti-stress responses; these adaptations were fundamental forces during evolution. Central to anti-stress responses are a number of short-lived transcription factors that by functioning as stress sensors mobilize genomic responses aiming to eliminate stressors. We show here that increased expression of nuclear factor erythroid 2-related factor (Nrf2) in Drosophila activated cytoprotective modules and enhanced stress tolerance. However, while mild Nrf2 activation extended lifespan, high Nrf2 expression levels resulted in developmental lethality or, after inducible activation in adult flies, in altered mitochondrial bioenergetics, the appearance of Diabetes Type 1 hallmarks and aging acceleration. Genetic or dietary suppression of Insulin/IGF-like signaling (IIS) titrated Nrf2 activity to lower levels, largely normalized metabolic pathways signaling, and extended flies' lifespan. Thus, prolonged stress signaling by otherwise cytoprotective short-lived stress sensors perturbs IIS resulting in re-allocation of resources from growth and longevity to somatic preservation and stress tolerance. These findings provide a reasonable explanation of why most (if not all) cytoprotective stress sensors are short-lived proteins, and it also explains the build-in negative feedback loops (shown here for Nrf2); the low basal levels of these proteins, and why their suppressors were favored by evolution.},
}

*Adaptation, Physiological
Aging/*physiology
Animals
Cytoprotection
Drosophila Proteins/metabolism
Drosophila melanogaster/*metabolism/*physiology
Energy Metabolism
Insulin/metabolism
Metabolic Networks and Pathways
Mitochondria/metabolism
Mitochondrial Dynamics
NF-E2-Related Factor 2/*metabolism
Phenotype
Signal Transduction
Somatomedins/metabolism
*Stress, Physiological

@article {pmid32208680,
year = {2020},
author = {Yue, J and Shen, Y and Liang, L and Cong, L and Xu, W and Shi, W and Liang, C and Xu, S},
title = {Revealing mitochondrial microenvironmental evolution triggered by photodynamic therapy.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.0c00497},
pmid = {32208680},
issn = {1520-6882},
abstract = {Mitochondrion is one of the most important organelles and becomes a target in many cancer therapeutic strategies. Mitochondrial microenvironments in response to therapeutic methods are the key to understand therapeutic mechanisms. However, they are al-most rarely studied. Herein, the mitochondrial microenvironments, including mitochondrial membrane potential (MMP) and reac-tive oxygen species (ROS) after different photodynamic therapy (PDT) dosages, were monitored by fluorescent imaging and com-pared among three cell lines (HepG2, MCF-7, and LO2). Furthermore, the fluctuations of intra-mitochondrial pHs were revealed via a plasmonic mitochondrion-targeting surface-enhanced Raman scattering (SERS) pH nanosensor. Results indicate that the MMP decreases gradually with the ROS generation and the cancerous cells exhibit less responsive to excess ROS relative to nor-mal cells. On the other hand, the pH value in the mitochondria decreases initially and then increases when the amount of ROS increases. The LO2 cell is preliminarily evidenced to have a higher self-adjustment ability due to its better tolerance to differential intra/extra cellular pHs. This study may provide a basis for an in-depth understanding of the mechanisms of the mitochondrial tar-geting-based PDT therapeutic processes. It is also helpful for more accurate and useful diagnosis according to intra-mitochondrial microenvironments, and improvement on therapy efficiency of cancers.},
}

@article {pmid31809841,
year = {2020},
author = {Ju, Y and Liu, H and He, J and Wang, L and Xu, J and Liu, H and Dong, Y and Zhang, R and Zhao, P and Xing, X},
title = {Genetic diversity of Aoluguya Reindeer based on D-loop region of mtDNA and its conservation implications.},
journal = {Gene},
volume = {733},
number = {},
pages = {144271},
doi = {10.1016/j.gene.2019.144271},
pmid = {31809841},
issn = {1879-0038},
mesh = {Animals ; China ; Conservation of Natural Resources/methods ; DNA, Mitochondrial/*genetics ; Finland ; Genetic Variation/genetics ; Haplotypes ; Introduced Species ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Reindeer/*genetics ; },
abstract = {Aoluguya Reindeer is the only reindeer population in China. In recent years, habitat loss and inbreeding have led to population decline, and population growth has been slow, maintaining a thousand or so. To better protect the Aoluguya Reindeer and improve its fecundity, we have introduced reindeer from Finland, crossbreeding help us to reach this goal. However, it is lacking in the study of genetic diversity of reindeer in China and Finland. Therefore, we used the partial sequences of the D-loop region of mitochondrial DNA to analyze the genetic diversity of Chinese reindeer (Aoluguya Reindeer) and the introduced Finnish reindeer, and identified twenty-six haplotypes, including nineteen in China, five in Finland, and two in Russia. There is no shared haplotype among them. The nucleotide diversity of Aoluguya Reindeer is 0.00752, which is significantly lower than that of reindeer in Finland and other countries. The haplotype and phylogenetic analysis show that reindeer from different geographical origins are not clustered completely according to geographical distribution. Aoluguya Reindeer populations and the introduced reindeer herds from Finland are all closely related to the reindeer from Russia. AMOVA analysis showed that there was significant differentiation between reindeer populations in China and Finland, and mismatch analysis showed that both populations had not experienced expansion. In this study, we identified the genetic diversity of Aoluguya Reindeer and the introduced reindeer, and provided a scientific basis for the conservation and breeding of Aoluguya Reindeer resources.},
}

Animals
China
Conservation of Natural Resources/methods
DNA, Mitochondrial/*genetics
Finland
Genetic Variation/genetics
Haplotypes
Introduced Species
Mitochondria/genetics
Phylogeny
Polymorphism, Genetic
Reindeer/*genetics

@article {pmid31687086,
year = {2019},
author = {Poljsak, B and Kovac, V and Dahmane, R and Levec, T and Starc, A},
title = {Cancer Etiology: A Metabolic Disease Originating from Life's Major Evolutionary Transition?.},
journal = {Oxidative medicine and cellular longevity},
volume = {2019},
number = {},
pages = {7831952},
pmid = {31687086},
issn = {1942-0994},
mesh = {Animals ; *Biological Evolution ; Drug Resistance, Neoplasm ; Energy Metabolism ; Humans ; Metabolic Diseases/*etiology ; Mitochondria/metabolism ; Neoplasms/*etiology ; },
abstract = {A clear understanding of the origins of cancer is the basis of successful strategies for effective cancer prevention and management. The origin of cancer at the molecular and cellular levels is not well understood. Is the primary cause of the origin of cancer the genomic instability or impaired energy metabolism? An attempt was made to present cancer etiology originating from life's major evolutionary transition. The first evolutionary transition went from simple to complex cells when eukaryotic cells with glycolytic energy production merged with the oxidative mitochondrion (The Endosymbiosis Theory first proposed by Lynn Margulis in the 1960s). The second transition went from single-celled to multicellular organisms once the cells obtained mitochondria, which enabled them to obtain a higher amount of energy. Evidence will be presented that these two transitions, as well as the decline of NAD+ and ATP levels, are the root of cancer diseases. Restoring redox homeostasis and reactivation of mitochondrial oxidative metabolism are important factors in cancer prevention.},
}

Animals
*Biological Evolution
Drug Resistance, Neoplasm
Energy Metabolism
Humans
Metabolic Diseases/*etiology
Mitochondria/metabolism
Neoplasms/*etiology

@article {pmid32206790,
year = {2020},
author = {Orton, LM and Fitzek, E and Feng, X and Grayburn, WS and Mower, JP and Liu, K and Zhang, C and Duvall, MR and Yin, Y},
title = {Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraa149},
pmid = {32206790},
issn = {1460-2431},
abstract = {The complete chloroplast and mitochondrial genomes of Charophyta have shed new light on the land plant terrestrialization. Here, we reported the organellar genomes of the Zygnema circumcarinatum strain UTEX 1559, and a comparative genomics investigation of 33 plastomes and 18 mitogenomes of Chlorophyta, Charophyta (including UTEX 1559 and its conspecific relative SAG 698-1a), and Embryophyta. Gene presence/absence was determined across these plastomes and mitogenomes. A comparison between the plastomes of UTEX 1559 (157,548 bp) and SAG 698-1a (165,372 bp) revealed very similar gene contents, but substantial genome rearrangements. Surprisingly, the two plastomes share only 85.69% nucleotide sequence identity. The UTEX 1559 mitogenome size is 215,954 bp, the largest among all sequenced Charophyta. Interestingly, this large mitogenome contains a 50 kb region without homology to any other organellar genomes, which is flanked by two 86 bp direct repeats and contains 15 open reading frames (ORFs). These ORFs have significant homology to proteins from bacteria and plants with functions such as primase, RNA polymerase and DNA polymerase. We conclude that (i) the previously published SAG 698-1a plastome is likely from a different Zygnema species, and (ii) the 50 kb region in the UTEX 1559 mitogenome might be recently acquired as a mobile element.},
}

@article {pmid32201093,
year = {2020},
author = {de Brito Monteiro, L and Davanzo, GG and de Aguiar, CF and Corrêa da Silva, F and Andrade, JR and Campos Codo, A and Silva Pereira, JAD and Freitas, LP and Moraes-Vieira, PM},
title = {M-CSF- and L929-derived macrophages present distinct metabolic profiles with similar inflammatory outcomes.},
journal = {Immunobiology},
volume = {},
number = {},
pages = {151935},
doi = {10.1016/j.imbio.2020.151935},
pmid = {32201093},
issn = {1878-3279},
abstract = {Macrophages are essential components of the immune system. Macrophages can be derived from the bone marrow of mice with either recombinant M-CSF or L929 supernatant. Recent literature considers recombinant M-CSF- and L929-derived macrophages as equals, even though L929-derived macrophages are exposed to other substances secreted in the L929 supernatant, and not only M-CSF. Thus, we decided to perform a comparative analysis of both inflammatory and metabolic profiles of macrophages differentiated under the aforementioned conditions, which is relevant for standardization and interpretation of in vitro studies. We observed that, when treated with LPS, L929macs secrete lower levels of proinflammatory cytokines (TNF-α, IL-6, IL12) and present higher glycolysis and oxygen consumption when compared with M-CSFmacs. L929macs also have increased mitochondrial mass, with higher percentage of dysfunctional mitochondria. This sort of information can help direct further studies towards a more specific approach for macrophage generation.},
}

@article {pmid32199599,
year = {2020},
author = {Noguera, R and Burgos-Panadero, R and Lucantoni, F and de la Cruz-Merino, L and Álvaro Naranjo, T},
title = {[An integral view of cancer (III). Evaluation of new biomarkers and treatment strategies].},
journal = {Revista espanola de patologia : publicacion oficial de la Sociedad Espanola de Anatomia Patologica y de la Sociedad Espanola de Citologia},
volume = {53},
number = {2},
pages = {88-99},
doi = {10.1016/j.patol.2019.08.001},
pmid = {32199599},
issn = {1988-561X},
abstract = {We propose a comprehensive approach to oncological disease, based on a systemic consideration of biology, health and disease. Our two previous review articles focused on tumour microenvironment and the discovery of new biomarkers; here we discuss the practical application of these principles to pathology, through the identification, evaluation and quantitative analysis of new prognostic and predictive factors (Immunoscore, TIME). We also consider the clinical use of promising, better tolerated treatments, such as immunotherapy. The integrative pathologist now has access to the latest improved oncology stratification tools designed to identify effective treatment strategies, based on the natural evolution of clinical and scientific knowledge that transcend the gene-centric theory of cancer.},
}

@article {pmid32199028,
year = {2020},
author = {Buonvicino, D and Ranieri, G and Pratesi, S and Gerace, E and Muzzi, M and Guasti, D and Tofani, L and Chiarugi, A},
title = {Neuroprotection Induced by Dexpramipexole Delays Disease Progression in a Mouse Model of Progressive Multiple Sclerosis.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.15058},
pmid = {32199028},
issn = {1476-5381},
abstract = {BACKGROUND AND PURPOSE: Drugs able to counteract progressive multiple sclerosis (PMS) represent a largely unmet therapeutic need. Even though the pathogenesis of disease evolution is still obscure, accumulating evidence indicates that mitochondrial dysfunction plays a causative role in neurodegeneration and axonopathy in PMS patients. Here, we investigated the effects of dexpramipexole, a compound with a good safety profile in humans and able to sustain mitochondria functioning and energy production, in a mouse model of PMS.

EXPERIMENTAL APPROACH: Female Non-obese diabetic (NOD) mice were immunized with MOG35-55 . Functional, immune and neuropathological parameters were analyzed during disease evolution in animals treated or not with dexpramipexole. The compound's effects on bioenergetics and neuroprotection were also evaluated in vitro.

KEY RESULTS: We found that oral treatment with dexpramipexole at a dose consistent with that well tolerated in humans delayed disability progression, extended survival, counteracted reduction of spinal cord mitochondrial DNA content and reduced spinal cord axonal loss of mice. Accordingly, the drug sustained in vitro bioenergetics of mouse optic nerve and dorsal root ganglia, and counteracted neurodegeneration of organotypic mouse cortical cultures exposed to the adenosine triphosphate (ATP)-depleting agents oligomycin or veratridine. Dexpramipexole, however, was unable to affect the adaptive and innate immune responses both in vivo and in vitro.

CONCLUSION AND IMPLICATION: The present findings corroborate the hypothesis that neuroprotective agents may be of relevance to counteract MS progression, and disclose the translational potential of dexpramipexole to treatment of PMS patients as a stand-alone or adjunctive therapy.},
}

@article {pmid32185389,
year = {2020},
author = {Mbadinga Mbadinga, DL and Li, Q and Ranocha, P and Martinez, Y and Dunand, C},
title = {Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraa141},
pmid = {32185389},
issn = {1460-2431},
abstract = {The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce the hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, several advances have provided an understanding into the origin and evolution of this protein family. Here, we report the most comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences centralized in a dedicated database, we have deepened our understanding of the evolutionary process underlying non-animal peroxidases diversification through phylogenetic reconstructions. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlate with the presence or absence of certain organelles or with specific biological processes. Scrutinizing in near 2000 organisms, we confirmed that ascorbate peroxidases (APx) and cytochromes c peroxidases (CcP) were detected respectively in chloroplast and mitochondria containing organisms. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prx) only found in fungi with wood decay abilities and plant degradation and Class III peroxidases (CIII Prx) only detected in both streptophyte algae and land plants, have been subjected to large family expansion in the latter group. Moreover, we demonstrate that biochemical activities (APx, CcP and CIII Prx) assayed with protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of non-animal peroxidase encoding sequences.},
}

@article {pmid32184120,
year = {2020},
author = {Warren, JM and Sloan, DB},
title = {Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2020.03.007},
pmid = {32184120},
issn = {1872-8278},
abstract = {Transfer RNAs (tRNAs) remain one of the very few classes of genes still encoded in the mitochondrial genome. These key components of the protein translation system must interact with a large enzymatic network of nuclear-encoded gene products to maintain mitochondrial function. Plants have an evolutionarily dynamic mitochondrial tRNA population, including ongoing tRNA gene loss and replacement by both horizontal gene transfer from diverse sources and import of nuclear-expressed tRNAs from the cytosol. Thus, plant mitochondria represent an excellent model for understanding how anciently divergent genes can act as "interchangeable parts" during the evolution of complex molecular systems. In particular, understanding the integration of the mitochondrial translation system with elements of the corresponding machinery used in cytosolic protein synthesis is a key area for eukaryotic cellular evolution. Here, we review the increasingly detailed phylogenetic data about the evolutionary history of mitochondrial tRNA gene loss, transfer, and functional replacement that has created extreme variation in mitochondrial tRNA populations across plant species. We describe emerging tRNA-seq methods with promise for refining our understanding of the expression and subcellular localization of tRNAs. Finally, we summarize current evidence and identify open questions related to coevolutionary changes in nuclear-encoded enzymes that have accompanied turnover in mitochondrial tRNA populations.},
}

@article {pmid32180577,
year = {2020},
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 = {91},
number = {},
pages = {122-130},
pmid = {32180577},
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 {pmid31622439,
year = {2019},
author = {Caicedo-Garzón, V and Salgado-Roa, FC and Sánchez-Herrera, M and Hernández, C and Arias-Giraldo, LM and García, L and Vallejo, G and Cantillo, O and Tovar, C and Aristeu da Rosa, J and Carrasco, HJ and Segovia, M and Salazar, C and Ramírez, JD},
title = {Genetic diversification of Panstrongylus geniculatus (Reduviidae: Triatominae) in northern South America.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0223963},
pmid = {31622439},
issn = {1932-6203},
mesh = {Animals ; Cell Nucleus/*genetics ; Colombia ; DNA, Ribosomal/*genetics ; Evolution, Molecular ; Genetics, Population ; Mitochondria/*genetics ; Panstrongylus/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Triatomines are the vectors of Trypanosoma cruzi, the etiological agent of Chagas disease. Although Triatoma and Rhodnius are the most-studied vector genera, other triatomines, such as Panstrongylus, also transmit T. cruzi, creating new epidemiological scenarios. Panstrongylus has at least 13 reported species but there is limited information about its intraspecific genetic variation and patterns of diversification. Here, we begin to fill this gap by studying populations of P. geniculatus from Colombia and Venezuela and including other epidemiologically important species from the region. We examined the pattern of diversification of P. geniculatus in Colombia using mitochondrial and nuclear ribosomal data. Genetic diversity and differentiation were calculated within and among populations of P. geniculatus. Moreover, we constructed maximum likelihood and Bayesian inference phylogenies and haplotype networks using P. geniculatus and other species from the genus (P. megistus, P. lignarius, P. lutzi, P. tupynambai, P. chinai, P. rufotuberculatus and P. howardi). Using a coalescence framework, we also dated the P. geniculatus lineages. The total evidence tree showed that P. geniculatus is a monophyletic species, with four clades that are concordant with its geographic distribution and are partly explained by the Andes orogeny. However, other factors, including anthropogenic and eco-epidemiological effects must be investigated to explain the existence of recent geographic P. geniculatus lineages. The epidemiological dynamics in structured vector populations, such as those found here, warrant further investigation. Extending our knowledge of P. geniculatus is necessary for the accurate development of effective strategies for the control of Chagas disease vectors.},
}

Animals
Cell Nucleus/*genetics
Colombia
DNA, Ribosomal/*genetics
Evolution, Molecular
Genetics, Population
Mitochondria/*genetics
Panstrongylus/*classification/genetics
Phylogeny
Sequence Analysis, DNA

@article {pmid32159766,
year = {2020},
author = {Hammond, MJ and Nenarokova, A and Butenko, A and Zoltner, M and Dobáková, EL and Field, MC and Lukeš, J},
title = {A uniquely complex mitochondrial proteome from Euglena gracilis.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa061},
pmid = {32159766},
issn = {1537-1719},
abstract = {Euglena gracilis is a metabolically flexible, photosynthetic and adaptable free-living protist of considerable environmental importance and biotechnological value. By label-free LC-MSMS, a total of 1,786 proteins were identified from the E. gracilis purified mitochondria, representing one of the largest mitochondrial proteomes so far described. Despite this apparent complexity, protein machinery responsible for the extensive RNA editing, splicing and processing in the sister clades diplonemids and kinetoplastids, is absent. This strongly suggests that the complex mechanisms of mitochondrial gene expression in diplonemids and kinetoplastids occurred late in euglenozoan evolution, arising independently. By contrast, the alternative oxidase pathway and numerous ribosomal subunits presumed to be specific for parasitic trypanosomes are present in E. gracilis. We investigated the evolution of unexplored protein families, including import complexes, cristae formation proteins and translation termination factors, as well as canonical and unique metabolic pathways. We additionally compare this mitoproteome with the transcriptome of Eutreptiella gymnastica, illuminating conserved features of Euglenida mitochondria as well as those exclusive to E. gracilis. This is the first mitochondrial proteome of a free-living protist from the Excavata, and one of few available for protists as a whole. This study alters our views of the evolution of the mitochondrion, and indicates early emergence of complexity within euglenozoan mitochondria, independent of parasitism.},
}

@article {pmid32157725,
year = {2020},
author = {Speijer, D},
title = {Debating Eukaryogenesis: Part 2: How Anachronistic Reasoning Can Lure Us into Inventing Intermediates.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e1900153},
doi = {10.1002/bies.201900153},
pmid = {32157725},
issn = {1521-1878},
abstract = {Eukaryotic origins are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry. However, the nature of the "host" cell and the mode of entry are subject to heavy debate. It is becoming clear that the mutual adaptation of a relatively simple, archaeal host and the endosymbiont has been the defining influence at the beginning of the eukaryotic lineage; however, many still resist such symbiogenic models. In part 1, it is posited that a symbiotic stage before uptake ("pre-symbiosis") seems essential to allow further metabolic integration of the two partners ending in endosymbiosis. Thus, the author argued against phagocytic mechanisms (in which the bacterium is prey or parasite) as the mode of entry. Such positions are still broadly unpopular. Here it is explained why. Evolutionary thinking, especially in the case of eukaryogenesis, is still dominated by anachronistic reasoning, in which highly derived protozoan organisms are seen as in some way representative of intermediate steps during eukaryotic evolution, hence poisoning the debate. This reasoning reflects a mind-set that ignores that Darwinian evolution is a fundamentally historic process. Numerous examples of this kind of erroneous reasoning are given, and some basic precautions against its use are formulated.},
}

@article {pmid32157325,
year = {2020},
author = {Tomáška, Ľ and Nosek, J},
title = {Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00239-020-09935-3},
pmid = {32157325},
issn = {1432-1432},
support = {APVV-15-0022//Agentúra na Podporu Výskumu a Vývoja/ ; APVV-18-0239//Agentúra na Podporu Výskumu a Vývoja/ ; VEGA 1/0061/20//Ministerstvo školstva, vedy, výskumu a športu Slovenskej republiky/ ; VEGA 1/0027/19//Ministerstvo školstva, vedy, výskumu a športu Slovenskej republiky/ ; },
abstract = {Biological entities are multicomponent systems where each part is directly or indirectly dependent on the others. In effect, a change in a single component might have a consequence on the functioning of its partners, thus affecting the fitness of the entire system. In this article, we provide a few examples of such complex biological systems, ranging from ant colonies to a population of amino acids within a single-polypeptide chain. Based on these examples, we discuss one of the central and still challenging questions in biology: how do such multicomponent consortia co-evolve? More specifically, we ask how telomeres, nucleo-protein complexes protecting the integrity of linear DNA chromosomes, originated from the ancestral organisms having circular genomes and thus not dealing with end-replication and end-protection problems. Using the examples of rapidly evolving topologies of mitochondrial genomes in eukaryotic microorganisms, we show what means of co-evolution were employed to accommodate various types of telomere-maintenance mechanisms in mitochondria. We also describe an unprecedented runaway evolution of telomeric repeats in nuclei of ascomycetous yeasts accompanied by co-evolution of telomere-associated proteins. We propose several scenarios derived from research on telomeres and supported by other studies from various fields of biology, while emphasizing that the relevant answers are still not in sight. It is this uncertainty and a lack of a detailed roadmap that makes the journey through the jungle of biological systems still exciting and worth undertaking.},
}

@article {pmid31881988,
year = {2019},
author = {Liu, Y and Qu, J and Zhang, L and Xu, X and Wei, G and Zhao, Z and Ren, M and Cao, M},
title = {Identification and characterization of the TCA cycle genes in maize.},
journal = {BMC plant biology},
volume = {19},
number = {1},
pages = {592},
pmid = {31881988},
issn = {1471-2229},
support = {2016YFD0101206//National Key Research and Development Program of China/ ; NASC2019TI13//Chengdu Agricultural Science and Technology Center local financial special fund project/ ; 19-001-09//Fundamental Research Funds for the Central Institutes/ ; },
mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Citric Acid Cycle/*genetics ; Computational Biology ; *Genes, Plant ; Lycopersicon esculentum/genetics ; Phylogeny ; Plant Proteins/genetics ; Sequence Alignment ; Transcriptome ; Zea mays/*genetics/metabolism ; },
abstract = {BACKGROUND: The tricarboxylic acid (TCA) cycle is crucial for cellular energy metabolism and carbon skeleton supply. However, the detailed functions of the maize TCA cycle genes remain unclear.

RESULTS: In this study, 91 TCA genes were identified in maize by a homology search, and they were distributed on 10 chromosomes and 1 contig. Phylogenetic results showed that almost all maize TCA genes could be classified into eight major clades according to their enzyme families. Sequence alignment revealed that several genes in the same subunit shared high protein sequence similarity. The results of cis-acting element analysis suggested that several TCA genes might be involved in signal transduction and plant growth. Expression profile analysis showed that many maize TCA cycle genes were expressed in specific tissues, and replicate genes always shared similar expression patterns. Moreover, qPCR analysis revealed that some TCA genes were highly expressed in the anthers at the microspore meiosis phase. In addition, we predicted the potential interaction networks among the maize TCA genes. Next, we cloned five TCA genes located on different TCA enzyme complexes, Zm00001d008244 (isocitrate dehydrogenase, IDH), Zm00001d017258 (succinyl-CoA synthetase, SCoAL), Zm00001d025258 (α-ketoglutarate dehydrogenase, αKGDH), Zm00001d027558 (aconitase, ACO) and Zm00001d044042 (malate dehydrogenase, MDH). Confocal observation showed that their protein products were mainly localized to the mitochondria; however, Zm00001d025258 and Zm00001d027558 were also distributed in the nucleus, and Zm00001d017258 and Zm00001d044042 were also located in other unknown positions in the cytoplasm. Through the bimolecular fluorescent complimentary (BiFC) method, it was determined that Zm00001d027558 and Zm00001d044042 could form homologous dimers, and both homologous dimers were mainly distributed in the mitochondria. However, no heterodimers were detected between these five genes. Finally, Arabidopsis lines overexpressing the above five genes were constructed, and those transgenic lines exhibited altered primary root length, salt tolerance, and fertility.

CONCLUSION: Sequence compositions, duplication patterns, phylogenetic relationships, cis-elements, expression patterns, and interaction networks were investigated for all maize TCA cycle genes. Five maize TCA genes were overexpressed in Arabidopsis, and they could alter primary root length, salt tolerance, and fertility. In conclusion, our findings may help to reveal the molecular function of the TCA genes in maize.},
}

Amino Acid Sequence
Arabidopsis/genetics
Citric Acid Cycle/*genetics
Computational Biology
*Genes, Plant
Lycopersicon esculentum/genetics
Phylogeny
Plant Proteins/genetics
Sequence Alignment
Transcriptome
Zea mays/*genetics/metabolism

@article {pmid31827088,
year = {2019},
author = {Shiratori, T and Suzuki, S and Kakizawa, Y and Ishida, KI},
title = {Phagocytosis-like cell engulfment by a planctomycete bacterium.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5529},
pmid = {31827088},
issn = {2041-1723},
mesh = {Alphaproteobacteria/classification/genetics/*physiology/ultrastructure ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Genome, Bacterial ; *Phagocytosis ; Phylogeny ; },
abstract = {Phagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving force behind endosymbiosis, a process by which α-proteobacteria and cyanobacteria evolved into mitochondria and plastids, respectively. Here we describe a planctomycete bacterium, 'Candidatus Uab amorphum', which is able to engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism. Observations via light and electron microscopy suggest that this bacterium digests prey cells in specific compartments. With the possible exception of a gene encoding an actin-like protein, analysis of the 'Ca. Uab amorphum' genomic sequence does not reveal any genes homologous to eukaryotic phagocytosis genes, suggesting that cell engulfment in this microorganism is probably not homologous to eukaryotic phagocytosis. The discovery of this "phagotrophic" bacterium expands our understanding of the cellular complexity of prokaryotes, and may be relevant to the origin of eukaryotic cells.},
}

Alphaproteobacteria/classification/genetics/*physiology/ultrastructure
Bacterial Proteins/genetics/metabolism
Biological Evolution
Genome, Bacterial
*Phagocytosis
Phylogeny

@article {pmid31484671,
year = {2019},
author = {Yang, H and Deng, L and Liu, H and Fan, S and Hua, W and Liu, J},
title = {Overexpression of BnaAOX1b Confers Tolerance to Osmotic and Salt Stress in Rapeseed.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {10},
pages = {3501-3511},
pmid = {31484671},
issn = {2160-1836},
mesh = {Abscisic Acid ; Amino Acid Sequence ; Brassica napus/*physiology ; Computational Biology/methods ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Germination/genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics ; Osmoregulation/*genetics ; Oxidoreductases/chemistry/*genetics ; Phenotype ; Phylogeny ; Plant Proteins/chemistry/*genetics ; Protein Transport ; Salt Tolerance/*genetics ; Seedlings/genetics ; },
abstract = {Alternative oxidases (AOXs) are the terminal oxidase in the cyanide-resistant respiration pathway in plant mitochondria, which play an important role in abiotic stress and are proposed as a functional marker for high tolerant breeding. In this study, ten AOX genes (BnaAOXs) were identified, and CysI and CysII of AOX isoforms were highly conserved in rapeseed. Among them, Bna.AOX1b was mainly expressed in the ovule and displayed varying expression between rapeseed cultivars which showed different salt resistance in seed germination. We identified its mitochondrial localization of this gene. To investigate the function of BnaAOX1b in rapeseed, transgenic rapeseed lines with overexpressed BnaAOX1b were created and seed germination and seedling establishment assays were performed under osmotic, salt, and ABA treatment. The results indicated that overexpression of BnaAOX1b significantly improved seed germination under osmotic and salt stress and weakened ABA sensitivity. In addition, post-germination seedling growth was improved under high salt condition, but showed hypersensitivity to ABA. RNA-sequencing analysis indicated that the genes involved in electron transport or energy pathway were induced and a number of gene responses to salt stress and ABA were regulated in Bna.AOX1b overexpressing seeds. Taken together, our results imply that Bna.AOX1b confers tolerance to osmotic and salt stress in terms of seed germination and seedling establishment by regulating stress responsive genes and the response to ABA, and could be utilized as a candidate gene in transgenic breeding.},
}

Abscisic Acid
Amino Acid Sequence
Brassica napus/*physiology
Computational Biology/methods
Gene Expression Profiling
*Gene Expression Regulation, Plant
Gene Ontology
Germination/genetics
Mitochondria/genetics/metabolism
Mitochondrial Proteins/chemistry/*genetics
Osmoregulation/*genetics
Oxidoreductases/chemistry/*genetics
Phenotype
Phylogeny
Plant Proteins/chemistry/*genetics
Protein Transport
Salt Tolerance/*genetics
Seedlings/genetics

@article {pmid31448547,
year = {2019},
author = {Derkarabetian, S and Benavides, LR and Giribet, G},
title = {Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault.},
journal = {Molecular ecology resources},
volume = {19},
number = {6},
pages = {1531-1544},
doi = {10.1111/1755-0998.13072},
pmid = {31448547},
issn = {1755-0998},
support = {//Harvard Dean's Fund/ ; DEB-1601208//Division of Environmental Biology/ ; DEB-1754278//Division of Environmental Biology/ ; },
mesh = {Animals ; Biodiversity ; Birds/*genetics ; DNA/genetics ; Ethanol/chemistry ; Formaldehyde/chemistry ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Insecta ; Mitochondria/genetics ; Museums ; Phylogeny ; Preservation, Biological/*methods ; Sequence Analysis, DNA/*methods ; Specimen Handling/methods ; },
abstract = {Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics-based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin-fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol-preserved museum specimens. Alongside sequencing of "fresh" specimens preserved in >95% ethanol and stored at -80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%-80% ethanol and stored at room temperature, the standard for such ethanol-preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol-preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off-target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol-preserved museum specimens held in collections worldwide.},
}

Animals
Biodiversity
Birds/*genetics
DNA/genetics
Ethanol/chemistry
Formaldehyde/chemistry
Genomics/methods
High-Throughput Nucleotide Sequencing/methods
Insecta
Mitochondria/genetics
Museums
Phylogeny
Preservation, Biological/*methods
Sequence Analysis, DNA/*methods
Specimen Handling/methods

@article {pmid32152094,
year = {2020},
author = {Vyssokikh, MY and Holtze, S and Averina, OA and Lyamzaev, KG and Panteleeva, AA and Marey, MV and Zinovkin, RA and Severin, FF and Skulachev, MV and Fasel, N and Hildebrandt, TB and Skulachev, VP},
title = {Mild depolarization of the inner mitochondrial membrane is a crucial component of an anti-aging program.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1916414117},
pmid = {32152094},
issn = {1091-6490},
abstract = {The mitochondria of various tissues from mice, naked mole rats (NMRs), and bats possess two mechanistically similar systems to prevent the generation of mitochondrial reactive oxygen species (mROS): hexokinases I and II and creatine kinase bound to mitochondrial membranes. Both systems operate in a manner such that one of the kinase substrates (mitochondrial ATP) is electrophoretically transported by the ATP/ADP antiporter to the catalytic site of bound hexokinase or bound creatine kinase without ATP dilution in the cytosol. One of the kinase reaction products, ADP, is transported back to the mitochondrial matrix via the antiporter, again through an electrophoretic process without cytosol dilution. The system in question continuously supports H+-ATP synthase with ADP until glucose or creatine is available. Under these conditions, the membrane potential, ∆ψ, is maintained at a lower than maximal level (i.e., mild depolarization of mitochondria). This ∆ψ decrease is sufficient to completely inhibit mROS generation. In 2.5-y-old mice, mild depolarization disappears in the skeletal muscles, diaphragm, heart, spleen, and brain and partially in the lung and kidney. This age-dependent decrease in the levels of bound kinases is not observed in NMRs and bats for many years. As a result, ROS-mediated protein damage, which is substantial during the aging of short-lived mice, is stabilized at low levels during the aging of long-lived NMRs and bats. It is suggested that this mitochondrial mild depolarization is a crucial component of the mitochondrial anti-aging system.},
}

@article {pmid31349102,
year = {2019},
author = {Schweizer, M and Warmuth, VM and Alaei Kakhki, N and Aliabadian, M and Förschler, M and Shirihai, H and Ewels, P and Gruselius, J and Olsen, RA and Schielzeth, H and Suh, A and Burri, R},
title = {Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.},
journal = {Molecular phylogenetics and evolution},
volume = {139},
number = {},
pages = {106568},
doi = {10.1016/j.ympev.2019.106568},
pmid = {31349102},
issn = {1095-9513},
mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/classification/genetics ; Ecosystem ; *Genome ; Mitochondria/*genetics ; Passeriformes/classification/*genetics ; Phenotype ; Phylogeny ; },
abstract = {In wheatears and related species ('open-habitat chats'), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species' relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats' plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on ~1'300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.},
}

Animals
Biological Evolution
DNA, Mitochondrial/classification/genetics
Ecosystem
*Genome
Mitochondria/*genetics
Passeriformes/classification/*genetics
Phenotype
Phylogeny

@article {pmid31349101,
year = {2019},
author = {Caro, A and Neiber, MT and Gómez-Moliner, BJ and Madeira, MJ},
title = {Molecular phylogeny and biogeography of the land snail subfamily Leptaxinae (Gastropoda: Hygromiidae).},
journal = {Molecular phylogenetics and evolution},
volume = {139},
number = {},
pages = {106570},
doi = {10.1016/j.ympev.2019.106570},
pmid = {31349101},
issn = {1095-9513},
mesh = {Animals ; Electron Transport Complex IV/chemistry/classification/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal/chemistry/classification/genetics ; Snails/*classification/genetics ; Spain ; },
abstract = {The subfamily Leptaxinae is included within the highly diverse land snail family Hygromiidae. In the absence of clear diagnostic morphological differences, the subfamily status is currently based solely on molecular information and includes three disjunctly distributed tribes, Leptaxini, Cryptosaccini and Metafruticicolini. However, the phylogenetic relationships among these tribes are not fully resolved and the clustering of some of the genera to the tribes is not statistically supported. To resolve the relationships within Leptaxinae and their position within Hygromiidae, we reconstructed their phylogeny using a multi-locus approach with two mitochondrial genes and eight nuclear markers. The phylogeny was further calibrated and an analysis of ancestral area estimation was carried out to infer the biogeographic history of the group. We elevated Metafruticicolini to subfamily level (Metafruticicolinae) and we restricted Leptaxinae to Cryptosaccini and Leptaxini. The Lusitanian genus Portugala was moved to Leptaxini, previously containing only the Macaronesian genus Leptaxis. Within Cryptosaccini, a new genus strictly confined to the Sierra de la Cabrera (Spain) is described, Fractanella gen. nov. According to our results, Leptaxinae originated in the Early Miocene in the Iberian Peninsula, from which the Macaronesian Islands were colonized. Due to the old split recovered for the divergence between Macaronesian and Iberian lineages, we hypothesize that this colonization may have occurred via the once emerged seamounts located between the archipelagos and the European and African continents, although this could also have occurred through the oldest now emerged islands of Macaronesia. In the Iberian Peninsula, the climatic shift that began during the Middle Miocene, changing progressively from subtropical climate towards the present-day Mediterranean climate, was identified as an important factor shaping the subfamily's diversification, along with Pleistocene climatic fluctuations.},
}

Animals
Electron Transport Complex IV/chemistry/classification/genetics
Mitochondria/genetics
Phylogeny
Phylogeography
RNA, Ribosomal/chemistry/classification/genetics
Snails/*classification/genetics
Spain

@article {pmid31326515,
year = {2019},
author = {Zhang, T and Fan, X and Gao, F and Al-Farraj, SA and El-Serehy, HA and Song, W},
title = {Further analyses on the phylogeny of the subclass Scuticociliatia (Protozoa, Ciliophora) based on both nuclear and mitochondrial data.},
journal = {Molecular phylogenetics and evolution},
volume = {139},
number = {},
pages = {106565},
doi = {10.1016/j.ympev.2019.106565},
pmid = {31326515},
issn = {1095-9513},
mesh = {Cell Nucleus/*genetics ; DNA, Ribosomal/chemistry/classification/genetics ; Electron Transport Complex IV/chemistry/classification/genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Oligohymenophorea/*classification/genetics ; Phylogeny ; RNA, Ribosomal/chemistry/classification/genetics ; Sequence Analysis, DNA ; },
abstract = {So far, the phylogenetic studies on ciliated protists have mainly based on single locus, the nuclear ribosomal DNA (rDNA). In order to avoid the limitations of single gene/genome trees and to add more data to systematic analyses, information from mitochondrial DNA sequence has been increasingly used in different lineages of ciliates. The systematic relationships in the subclass Scuticociliatia are extremely confused and largely unresolved based on nuclear genes. In the present study, we have characterized 72 new sequences, including 40 mitochondrial cytochrome oxidase c subunit I (COI) sequences, 29 mitochondrial small subunit ribosomal DNA (mtSSU-rDNA) sequences and three nuclear small subunit ribosomal DNA (nSSU-rDNA) sequences from 47 isolates of 44 morphospecies. Phylogenetic analyses based on single gene as well as concatenated data were performed and revealed: (1) compared to mtSSU-rDNA, COI gene reveals more consistent relationships with those of nSSU-rDNA; (2) the secondary structures of mtSSU-rRNA V4 region are predicted and compared in scuticociliates, which can contribute to discrimination of closely related species; (3) neither nuclear nor mitochondrial data support the monophyly of the order Loxocephalida, which may represent some divergent and intermediate lineages between the subclass Scuticociliatia and Hymenostomatia; (4) the assignments of thigmotrichids to the order Pleuronematida and the confused taxon Sulcigera comosa to the genus Histiobalantium are confirmed by mitochondrial genes; (5) both nuclear and mitochondrial data reveal that the species in the family Peniculistomatidae always group in the genus Pleuronema, suggesting that peniculistomatids are more likely evolved from Pleuronema-like ancestors; (6) mitochondrial genes support the monophyly of the order Philasterida, but the relationships among families of the order Philasterida remain controversial due to the discrepancies between their morphological and molecular data.},
}

Cell Nucleus/*genetics
DNA, Ribosomal/chemistry/classification/genetics
Electron Transport Complex IV/chemistry/classification/genetics
Mitochondria/*genetics
Nucleic Acid Conformation
Oligohymenophorea/*classification/genetics
Phylogeny
RNA, Ribosomal/chemistry/classification/genetics
Sequence Analysis, DNA

@article {pmid31323336,
year = {2019},
author = {Jana, A and Karanth, P},
title = {Multilocus nuclear markers provide new insights into the origin and evolution of the blackbuck (Antilope cervicapra, Bovidae).},
journal = {Molecular phylogenetics and evolution},
volume = {139},
number = {},
pages = {106560},
doi = {10.1016/j.ympev.2019.106560},
pmid = {31323336},
issn = {1095-9513},
mesh = {Animals ; Antelopes/*classification/genetics ; *Biological Evolution ; Cell Nucleus/*genetics ; Fossils ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Evolutionary relationships between members of the Antilopina taxon have been much debated in recent years. The 'true antelope' clade is currently comprised of 4 genera viz., Gazella, Nanger, Eudorcas and the monotypic genus Antilope, that includes A. cervicapra. Most studies have focused on the mitochondrial genome or morphological data to study their relationships. However, signals from mitochondrial data can often be misleading when compared with nuclear markers, as has been shown in multiple taxonomic groups. In this study, we revisit the phylogenetic relationships among members of Antilopina, particularly the phylogenetic position of A. cervicapra, using 12 nuclear markers and compare it with the mitochondrial tree. Furthermore, we explore the implications of the results of this study on the taxonomy and biogeography of Indian antelopes. The nuclear phylogenetic trees built using multiple coalescent and concatenated methods all supported a paraphyletic genus Gazella. Antilope was nested within Gazella as opposed to being sister to it, which was suggested by previous studies and our results based on mitochondrial markers. Our fossil-calibrated larger bovid phylogeny, based on nuclear markers, suggested that the Antilope lineage diverged from its sister species more recently in the Pleistocene, rather than in late Miocene as per previous studies. Our biogeographic analyses suggest that the lineage leading to genus Antilope dispersed into India from the Saharo-Arabian realm around 2 mya, post the expansion of grasslands. We speculate that the adaptations of this savanna-grassland specialist did not allow them to extend their range beyond the Indian subcontinent. Whereas, the only other true antelope in India, G. bennetti, extended its range into India more recently, probably after the establishment of the Thar desert in northwest India.},
}

Animals
Antelopes/*classification/genetics
*Biological Evolution
Cell Nucleus/*genetics
Fossils
Mitochondria/genetics
Phylogeny

@article {pmid31715688,
year = {2019},
author = {Jeon, HK and Eom, KS},
title = {Mitochondrial DNA Sequence Variability of Spirometra Species in Asian Countries.},
journal = {The Korean journal of parasitology},
volume = {57},
number = {5},
pages = {481-487},
pmid = {31715688},
issn = {1738-0006},
support = {2017K1A3A1A09085607//National Research Foundation of Korea/ ; },
mesh = {Animals ; Cestode Infections/*parasitology ; China ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Helminth Proteins/genetics ; Humans ; Japan ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Republic of Korea ; Spirometra/classification/*genetics/isolation & purification ; },
abstract = {Mitochondrial DNA sequence variability of Spirometra erinaceieuropaei in GenBank was observed by reinvestigation of mitochondrial cox1 and cytb sequences. The DNA sequences were analyzed in this study, comprising complete DNA sequences of cox1 (n=239) and cytb (n=213) genes. The 10 complete mitochondrial DNA sequences of Spirometra species were compared with those of Korea, China and Japan. The sequences were analyzed for nucleotide composition, conserved sites, variable sites, singleton sites and parsimony-informative sites. Phylogenetic analyses was done using neighbor joining, maximum parsimony, Bayesian inference and maximum-likelihood on cox1 and cytb sequences of Spirometra species. These polymorphic sites identified 148 (cox1) and 83 (cytb) haplotypes within 239 and 213 isolates from 3 Asian countries. Phylogenetic tree topologies were presented high-level confidence values for the 2 major branches of 2 Spirometra species containing S. erinaceieuropaei and S. decipiens, and S. decipiens sub-clades including all sequences registered as S. erinaceieuropaei in cox1 and cytb genes. These results indicated that mitochondrial haplotypes of S. erinaceieuropaei and S. decipiens were found in the 3 Asian countries.},
}

Animals
Cestode Infections/*parasitology
China
DNA, Helminth/*genetics
DNA, Mitochondrial/*genetics
Genetic Variation
Helminth Proteins/genetics
Humans
Japan
Mitochondria/genetics
Phylogeny
Polymorphism, Genetic
Republic of Korea
Spirometra/classification/*genetics/isolation & purification

@article {pmid32144830,
year = {2020},
author = {Trist, B and Hilton, JB and Crouch, PJ and Hare, DJ and Double, KL},
title = {Superoxide dismutase 1 in health and disease: How a front-line antioxidant becomes neurotoxic.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {},
doi = {10.1002/anie.202000451},
pmid = {32144830},
issn = {1521-3773},
abstract = {Cu/Zn superoxide dismutase (SOD1) is a front-line antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology, with the clearest demonstration provided by cases of amyotrophic lateral sclerosis associated with SOD1 gene mutations. But far from providing a simple demonstration of how disease arises from SOD1 loss-of-function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises contemporary understanding of SOD1 biology from SOD1 genetics through to protein function and stability. Our cumulative knowledge of these processes is advancing efforts to identify and target pathways of neurotoxicity driven by atypical mutant and wild-type SOD1 in multiple incurable neurodegenerative conditions.},
}

@article {pmid32142472,
year = {2019},
author = {Schneider, A},
title = {Evolution of mitochondrial protein import - lessons from trypanosomes.},
journal = {Biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1515/hsz-2019-0444},
pmid = {32142472},
issn = {1437-4315},
abstract = {The evolution of mitochondrial protein import and the systems that mediate it marks the boundary between the endosymbiotic ancestor of mitochondria and a true organelle that is under the control of the nucleus. Protein import has been studied in great detail in Saccharomyces cerevisiae. More recently it has also been extensively investigated in the parasitic protozoan Trypanosoma brucei making it arguably the second best studied system. Here I provide a comparative analysis of the protein import complexes of yeast and trypanosomes. Together with data from other systems, this allows to reconstruct the ancestral features of import complexes that were present in the last eukaryotic common ancestor (LECA) and to identify which subunits were added later in evolution. I discuss how these data can be translated into plausible scenarios providing insights into the evolution of (i) outer membrane protein import receptors, (ii) proteins involved in biogenesis of α-helically anchored outer membrane proteins, and (iii) of the intermembrane space import and assembly system. Finally, I show that the unusual presequence-associated import motor of trypanosomes suggests a scenario of how the two ancestral inner membrane protein translocases present in LECA evolved into the single bifunctional one found in extant trypanosomes.},
}

@article {pmid32133457,
year = {2019},
author = {Mehta, AR and Walters, R and Waldron, FM and Pal, S and Selvaraj, BT and Macleod, MR and Hardingham, GE and Chandran, S and Gregory, JM},
title = {Targeting mitochondrial dysfunction in amyotrophic lateral sclerosis: a systematic review and meta-analysis.},
journal = {Brain communications},
volume = {1},
number = {1},
pages = {fcz009},
doi = {10.1093/braincomms/fcz009},
pmid = {32133457},
issn = {2632-1297},
abstract = {Interventions targeting mitochondrial dysfunction have the potential to extend survival in preclinical models of amyotrophic lateral sclerosis. The aim of this systematic review was to assess the efficacy of targeting mitochondria as a potential therapeutic target in amyotrophic lateral sclerosis. Preclinical studies written in the English language were identified with no restrictions on publication date from PubMed, Medline and EMBASE databases. All studies adopting interventions targeting mitochondria to treat amyotrophic lateral sclerosis in genetic or drug-induced organism models were considered for inclusion. A total of 76 studies were included in the analysis. Survival data were extracted, and the meta-analysis was completed in RevMan 5 software. We show that targeting mitochondrial dysfunction in amyotrophic lateral sclerosis results in a statistically significant improvement in survival (Z = 5.31; P<0.00001). The timing of administration of the intervention appears to affect the improvement in survival, with the greatest benefit occurring for interventions given prior to disease onset. Interventions at other time points were not significant, although this is likely to be secondary to a lack of publications examining these timepoints. The quality score had no impact on efficacy, and publication bias revealed an overestimation of the effect size, owing to one outlier study; excluding this led to the recalculated effect size changing from 5.31 to 3.31 (P<0.00001). The extant preclinical literature indicates that targeting mitochondrial dysfunction may prolong survival in amyotrophic lateral sclerosis, particularly if the intervention is administered early. A limitation of current research is a significant bias towards models based on superoxide dismutase 1, with uncertainty about generalisability to amyotrophic lateral sclerosis with an underlying TAR DNA binding protein 43 proteinopathy. However, further mechanistic research is clearly warranted in this field.},
}

@article {pmid31520778,
year = {2019},
author = {Dufresnes, C and Mazepa, G and Jablonski, D and Oliveira, RC and Wenseleers, T and Shabanov, DA and Auer, M and Ernst, R and Koch, C and Ramírez-Chaves, HE and Mulder, KP and Simonov, E and Tiutenko, A and Kryvokhyzha, D and Wennekes, PL and Zinenko, OI and Korshunov, OV and Al-Johany, AM and Peregontsev, EA and Masroor, R and Betto-Colliard, C and Denoël, M and Borkin, LJ and Skorinov, DV and Pasynkova, RA and Mazanaeva, LF and Rosanov, JM and Dubey, S and Litvinchuk, S},
title = {Fifteen shades of green: The evolution of Bufotes toads revisited.},
journal = {Molecular phylogenetics and evolution},
volume = {141},
number = {},
pages = {106615},
doi = {10.1016/j.ympev.2019.106615},
pmid = {31520778},
issn = {1095-9513},
mesh = {Animals ; *Biological Evolution ; Bufonidae/classification/genetics/*physiology ; DNA, Mitochondrial/genetics ; Genetic Speciation ; Genome Size ; Genome, Mitochondrial ; Genomics ; Hybridization, Genetic ; Mitochondria/genetics ; Phenotype ; Phylogeny ; Phylogeography ; Principal Component Analysis ; Time Factors ; },
abstract = {The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopolyploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (<6My), above which species barely admix and eventually evolve different mating calls (6-10My), or can successfully cross-breed through allopolyploidization (>15My). Finally, we clarified the taxonomy of Bufotes (including genetic analyses of type series) and formally described two new species, B. cypriensis sp. nov. (endemic to Cyprus) and B. perrini sp. nov. (endemic to Central Asia). Embracing the genomic age, our framework marks the advent of a new exciting era for evolutionary research in these iconic amphibians.},
}

Animals
*Biological Evolution
Bufonidae/classification/genetics/*physiology
DNA, Mitochondrial/genetics
Genetic Speciation
Genome Size
Genome, Mitochondrial
Genomics
Hybridization, Genetic
Mitochondria/genetics
Phenotype
Phylogeny
Phylogeography
Principal Component Analysis
Time Factors

@article {pmid31449853,
year = {2019},
author = {Dorchin, N and Harris, KM and Stireman, JO},
title = {Phylogeny of the gall midges (Diptera, Cecidomyiidae, Cecidomyiinae): Systematics, evolution of feeding modes and diversification rates.},
journal = {Molecular phylogenetics and evolution},
volume = {140},
number = {},
pages = {106602},
doi = {10.1016/j.ympev.2019.106602},
pmid = {31449853},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Calibration ; Diptera/*classification/genetics ; *Feeding Behavior ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Predatory Behavior ; },
abstract = {Gall midges (Cecidomyiidae) constitute one of the largest and most diverse families of Diptera, with close to 6600 described species and thousands of undescribed species worldwide. The family is divided into six subfamilies, the five basal ones comprising only fungivorous taxa, whereas the largest, youngest and most diverse subfamily Cecidomyiinae includes fungivorous as well as herbivorous and predatory species. The currently accepted classification of the Cecidomyiinae is morphology-based, and the few phylogenetic inferences that have previously been suggested for it were based on fragmentary or limited datasets. In a first comprehensive phylogenetic analysis of the Cecidomyiinae we sampled 142 species representing 88 genera of 13 tribes from all feeding guilds and zoogeographic regions in order to test the validity of the systematic division of the subfamily and gain insight into patterns of diversification and the evolution of feeding modes. We used sequences from five mitochondrial and nuclear genes to reconstruct maximum likelihood and Bayesian, time-calibrated phylogenies and conducted ancestral state reconstruction of feeding modes. Our results corroborate to a great extent the morphology-based classification of the Cecidomyiinae, with strong support for all supertribes and tribes, all were apparently established in the Upper Cretaceous concordant with the major radiation of angiosperms. We infer that transitions from fungus-feeding to plant-feeding occurred only once or twice in the evolution of the subfamily and that predation evolved only once, contrary to previous hypotheses. All herbivorous clades in the subfamily are very species rich and have diversified at a significantly greater rate than expected, but we found no support for the assertion that herbivorous clades associated with symbiotic fungi in their galls diversify faster than clades that do not have such associations. Currently available data also do not support the hypothesis that symbiotic clades have broader host ranges than non-symbiotic clades.},
}

Animals
Bayes Theorem
*Biodiversity
Calibration
Diptera/*classification/genetics
*Feeding Behavior
Likelihood Functions
Mitochondria/genetics
*Phylogeny
Predatory Behavior

@article {pmid31404610,
year = {2019},
author = {Kanduma, EG and Bishop, RP and Githaka, NW and Skilton, RA and Heyne, H and Mwacharo, JM},
title = {Mitochondrial and nuclear multilocus phylogeny of Rhipicephalus ticks from Kenya.},
journal = {Molecular phylogenetics and evolution},
volume = {140},
number = {},
pages = {106579},
doi = {10.1016/j.ympev.2019.106579},
pmid = {31404610},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; *Genetic Loci ; Haplotypes/genetics ; Kenya ; Mitochondria/*genetics ; *Phylogeny ; Rhipicephalus/anatomy & histology/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {The morphological diversity of African ticks of the genus Rhipicephalus and subgenus Boophilus have been studied in detail. However, their taxonomy remains poorly resolved with limited molecular studies performed to improve inter-species discrimination. Herein, ribosomal cytochrome c oxidase I (COI), 12S ribosomal DNA (12S rDNA) and nuclear ribosomal DNA internal transcriber spacer 2 (ITS2) were analyzed in Rhipicephalus tick populations in Kenya. While the morphological and molecular criteria separated R. e. evertsi, R. pulchellus and R. appendiculatus from other members of the genus, except the morphologically similar sibling species R. zambeziensis, this was not the case for other tick populations. COI sequences of Rhipicephalus ticks from Ruma National Park (RNP) in Southwestern Kenya, that were morphologically similar to R. praetextatus/R. simus, a formed distinct clade and barcode gap group. 12S rDNA haplotypes of this population were 99% identical to a GenBank accession of R. muhsamae which is thought to be endemic in West and Central Africa. However, the ITS2 locus indicated that the RNP samples were genetically closest to ticks identified morphologically as R. praetextatus. The COI and 12S rDNA haplotype sequences of R. praetextatus clustered closely with R. simus reference sequences though the two species occurred in distinct barcode gap groups. Our results suggest that the R. simus/R. praetextatus/R. muhsamae comprise a closely related tick species complex found across sub-Saharan Africa and includes the yet to be described RNP population. More studies on the biology, ecology and genomics of all life stages of tick species in the complex may clarify their taxonomic status. A continent-wide study that combines morphology, DNA marker sequencing and emerging methods, such as mass spectrometry and whole-genome resequencing may reveal the diversity and distribution of taxa within the genus Rhipicephalus in sub-Saharan Africa.},
}

Animals
Base Sequence
Cell Nucleus/*genetics
DNA Barcoding, Taxonomic
DNA, Ribosomal Spacer/genetics
Electron Transport Complex IV/genetics
*Genetic Loci
Haplotypes/genetics
Kenya
Mitochondria/*genetics
*Phylogeny
Rhipicephalus/anatomy & histology/*classification/*genetics
Sequence Analysis, DNA

@article {pmid31278983,
year = {2019},
author = {Taylor, RS and Bolton, M and Beard, A and Birt, T and Deane-Coe, P and Raine, AF and González-Solís, J and Lougheed, SC and Friesen, VL},
title = {Cryptic species and independent origins of allochronic populations within a seabird species complex (Hydrobates spp.).},
journal = {Molecular phylogenetics and evolution},
volume = {139},
number = {},
pages = {106552},
doi = {10.1016/j.ympev.2019.106552},
pmid = {31278983},
issn = {1095-9513},
mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; Biodiversity ; Breeding ; Charadriiformes/*classification/genetics ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetics, Population ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Pacific Ocean ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; },
abstract = {Humans are inherently biased towards naming species based on morphological differences, which can lead to reproductively isolated species being mistakenly classified as one if they are morphologically similar. Recognising cryptic diversity is needed to understand drivers of speciation fully, and for accurate estimates of global biodiversity and assessments for conservation. We investigated cryptic species across the range of band-rumped storm-petrels (Hydrobates spp.): highly pelagic, nocturnal seabirds that breed on tropical and sub-tropical islands in the Atlantic and Pacific Oceans. In many breeding colonies, band-rumped storm-petrels have sympatric but temporally isolated (allochronic) populations; we sampled all breeding locations and allochronic populations. Using mitochondrial control region sequences from 754 birds, cytochrome b sequences from 69 birds, and reduced representation sequencing of the nuclear genomes of 133 birds, we uncovered high levels of genetic structuring. Population genomic analyses revealed up to seven unique clusters, and phylogenomic reconstruction showed that these represent seven monophyletic groups. We uncovered up to six independent breeding season switches across the phylogeny, spanning the continuum from genetically undifferentiated temporal populations to full allochronic species. Thus, band-rumped storm-petrels encompass multiple cryptic species, with non-geographic barriers potentially comprising strong barriers to gene flow.},
}

Animals
Atlantic Ocean
Bayes Theorem
Biodiversity
Breeding
Charadriiformes/*classification/genetics
DNA, Mitochondrial/genetics
Gene Flow
Genetics, Population
Geography
Likelihood Functions
Mitochondria/genetics
Pacific Ocean
*Phylogeny
Principal Component Analysis
Species Specificity

@article {pmid32130873,
year = {2020},
author = {Hornak, I and Rieger, H},
title = {Stochastic Model of T Cell Repolarization during Target Elimination I.},
journal = {Biophysical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bpj.2020.01.045},
pmid = {32130873},
issn = {1542-0086},
abstract = {Cytotoxic T lymphocytes (T) and natural killer cells are the main cytotoxic killer cells of the human body to eliminate pathogen-infected or tumorigenic cells (i.e., target cells). Once a natural killer or T cell has identified a target cell, they form a tight contact zone, the immunological synapse (IS). One then observes a repolarization of the cell involving the rotation of the microtubule (MT) cytoskeleton and a movement of the MT organizing center (MTOC) to a position that is just underneath the plasma membrane at the center of the IS. Concomitantly, a massive relocation of organelles attached to MTs is observed, including the Golgi apparatus, lytic granules, and mitochondria. Because the mechanism of this relocation is still elusive, we devise a theoretical model for the molecular-motor-driven motion of the MT cytoskeleton confined between plasma membrane and nucleus during T cell polarization. We analyze different scenarios currently discussed in the literature, the cortical sliding and capture-shrinkage mechanisms, and compare quantitative predictions about the spatiotemporal evolution of MTOC position and MT cytoskeleton morphology with experimental observations. The model predicts the experimentally observed biphasic nature of the repositioning due to an interplay between MT cytoskeleton geometry and motor forces and confirms the dominance of the capture-shrinkage over the cortical sliding mechanism when the MTOC and IS are initially diametrically opposed. We also find that the two mechanisms act synergistically, thereby reducing the resources necessary for repositioning. Moreover, it turns out that the localization of dyneins in the peripheral supramolecular activation cluster facilitates their interaction with the MTs. Our model also opens a way to infer details of the dynein distribution from the experimentally observed features of the MT cytoskeleton dynamics. In a subsequent publication, we will address the issue of general initial configurations and situations in which the T cell established two ISs.},
}

@article {pmid32122349,
year = {2020},
author = {Gray, MW and Burger, G and Derelle, R and Klimeš, V and Leger, MM and Sarrasin, M and Vlček, Č and Roger, AJ and Eliáš, M and Lang, BF},
title = {The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {22},
doi = {10.1186/s12915-020-0741-6},
pmid = {32122349},
issn = {1741-7007},
support = {RGPIN-2014-05286//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN- 2017-05411//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2016-06792//Natural Sciences and Engineering Research Council of Canada/ ; AFR grant PHD-08-001//Fonds National de la Recherche Luxembourg/ ; 18-13458S//Czech Science Foundation/ ; OPVVV 16_019/0000759//ERD Funds/ ; },
abstract = {BACKGROUND: Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date.

RESULTS: In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids.

CONCLUSIONS: As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.},
}

@article {pmid31888438,
year = {2019},
author = {Lichtblau, D},
title = {Alignment-free genomic sequence comparison using FCGR and signal processing.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {742},
pmid = {31888438},
issn = {1471-2105},
mesh = {Animals ; Genomics/*methods ; Humans ; Influenza A virus/classification ; Mitochondria/classification ; Phylogeny ; *Software ; },
abstract = {BACKGROUND: Alignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes of deducing "nearby" species in a reference data set, or for constructing phylogenetic trees.

RESULTS: We describe one such method that gives quite strong results. We use the Frequency Chaos Game Representation (FCGR) to create images from such sequences, We then reduce dimension, first using a Fourier trig transform, followed by a Singular Values Decomposition (SVD). This gives vectors of modest length. These in turn are used for fast sequence lookup, construction of phylogenetic trees, and classification of virus genomic data. We illustrate the accuracy and scalability of this approach on several benchmark test sets.

CONCLUSIONS: The tandem of FCGR and dimension reductions using Fourier-type transforms and SVD provides a powerful approach for alignment-free genomic comparison. Results compare favorably and often surpass best results reported in prior literature. Good scalability is also observed.},
}

Animals
Genomics/*methods
Humans
Influenza A virus/classification
Mitochondria/classification
Phylogeny
*Software

@article {pmid32117399,
year = {2020},
author = {Lee, DW and Lee, S and Min, CK and Park, C and Kim, JM and Hwang, CS and Park, SK and Cho, NH and Hwang, I},
title = {Cross-Species Functional Conservation and Possible Origin of the N-Terminal Specificity Domain of Mitochondrial Presequences.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {64},
doi = {10.3389/fpls.2020.00064},
pmid = {32117399},
issn = {1664-462X},
abstract = {Plants have two endosymbiotic organelles, chloroplast and mitochondrion. Although they have their own genomes, proteome assembly in these organelles depends on the import of proteins encoded by the nuclear genome. Previously, we elucidated the general design principles of chloroplast and mitochondrial targeting signals, transit peptide, and presequence, respectively, which are highly diverse in primary structure. Both targeting signals are composed of N-terminal specificity domain and C-terminal translocation domain. Especially, the N-terminal specificity domain of mitochondrial presequences contains multiple arginine residues and hydrophobic sequence motif. In this study we investigated whether the design principles of plant mitochondrial presequences can be applied to those in other eukaryotic species. We provide evidence that both presequences and import mechanisms are remarkably conserved throughout the species. In addition, we present evidence that the N-terminal specificity domain of presequence might have evolved from the bacterial TAT (twin-arginine translocation) signal sequence.},
}

@article {pmid31326431,
year = {2019},
author = {Fimmel, E and Strüngmann, L},
title = {Linear codes and the mitochondrial genetic code.},
journal = {Bio Systems},
volume = {184},
number = {},
pages = {103990},
doi = {10.1016/j.biosystems.2019.103990},
pmid = {31326431},
issn = {1872-8324},
mesh = {Algorithms ; Amino Acids/genetics ; Base Sequence ; Codon/*genetics ; Evolution, Molecular ; Genetic Code/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Models, Genetic ; Nucleotides/genetics ; },
abstract = {The origin of the genetic code can certainly be regarded as one of the most challenging problems in the theory of molecular evolution. Thus the known variants of the genetic code and a possible common ancestry of them haven been studied extensively in the literature. Gonzalez et al. (2012) developed the theory of a primeval mitochondrial genetic code composed of four base codons. These were called tesserae and it was shown that the tesserae code has some remarkable error detection capabilities. In our paper we will show that using classical coding theory we can construct the tessera code as a linear coding of the standard genetic code and at the same time it can be deduced from the code of all dinucleotides by Plotkin's construction. It shows that the tessera model of the mitochondrial code does not just have a biological explanation but also has a clear mathematical structure. This underlines the role that the tessera model might have played in evolution.},
}

Algorithms
Amino Acids/genetics
Base Sequence
Codon/*genetics
Evolution, Molecular
Genetic Code/*genetics
Genome, Mitochondrial/*genetics
Mitochondria/*genetics
Models, Genetic
Nucleotides/genetics

@article {pmid32112190,
year = {2020},
author = {Lang, SA and McIlroy, P and Shain, DH},
title = {Structural Evolution of the Glacier Ice Worm Fo ATP Synthase Complex.},
journal = {The protein journal},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10930-020-09889-x},
pmid = {32112190},
issn = {1875-8355},
support = {ARRA NIH R15GM093685//National Institutes of Health (US)/ ; },
abstract = {The segmented annelid worm, Mesenchytraeus solifugus, is a permanent resident of temperate, maritime glaciers in the Pacific northwestern region of North America, displaying atypically high intracellular ATP levels which have been linked to its unusual ability to thrive in hydrated glacier ice. We have shown previously that ice worms contain a highly basic, carboxy terminal extension on their ATP6 regulatory subunit, likely acquired by horizontal gene transfer from a microbial dietary source. Here we examine the full complement of F1F0 ATP synthase structural subunits with attention to non-conservative, ice worm-specific structural modifications. Our genomics analyses and molecular models identify putative proton shuttling domains on either side of the F0 hemichannel, which predictably function to enhance proton flow across the mitochondrial membrane. Other components of the ice worm ATP synthase complex have remained largely unchanged in the context of Metazoan evolution.},
}

@article {pmid32109602,
year = {2020},
author = {Muthye, V and Lavrov, DV},
title = {Causes and consequences of mitochondrial proteome size-variation in animals.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2020.02.007},
pmid = {32109602},
issn = {1872-8278},
abstract = {Despite a conserved set of core mitochondrial functions, animal mitochondrial proteomes show a large variation in size. In this study, we analyzed the putative mechanisms behind and functional significance of this variation by performing comparative analysis of the experimentally-verified mitochondrial proteomes of four bilaterian animals (human, mouse, Caenorhabditis elegans, and Drosophila melanogaster and two non-animal outgroups (Acanthamoeba castellanii and Saccharomyces cerevisiae). We found that, of several factors affecting mitochondrial proteome size, evolution of novel mitochondrial proteins in mammals and loss of ancestral proteins in protostomes were the main contributors. Interestingly, the gain and loss of conventional mitochondrial targeting signals was not a significant factor in the proteome size evolution.},
}

@article {pmid31234016,
year = {2019},
author = {Cobley, JN and Noble, A and Jimenez-Fernandez, E and Valdivia Moya, MT and Guille, M and Husi, H},
title = {Catalyst-free Click PEGylation reveals substantial mitochondrial ATP synthase sub-unit alpha oxidation before and after fertilisation.},
journal = {Redox biology},
volume = {26},
number = {},
pages = {101258},
doi = {10.1016/j.redox.2019.101258},
pmid = {31234016},
issn = {2213-2317},
support = {/WT_/Wellcome Trust/United Kingdom ; 212942/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/R014841/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adenosine Triphosphate/biosynthesis ; Amino Acid Sequence ; Animals ; Click Chemistry/*methods ; Disulfides/chemistry ; Embryo, Nonmammalian ; Female ; Fertilization in Vitro ; Glutathione/metabolism ; Heterocyclic Compounds, 1-Ring/chemistry ; Male ; Mitochondria/*chemistry/enzymology ; Mitochondrial Proton-Translocating ATPases/*chemistry/metabolism ; Ovum/*chemistry/cytology/enzymology ; Oxidation-Reduction ; Phylogeny ; Polyethylene Glycols/*chemistry ; *Protein Processing, Post-Translational ; Protein Subunits/*chemistry/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sulfhydryl Compounds/chemistry/metabolism ; Xenopus laevis/classification/embryology/metabolism ; },
abstract = {Using non-reducing Western blotting to assess protein thiol redox state is challenging because most reduced and oxidised forms migrate at the same molecular weight and are, therefore, indistinguishable. While copper catalysed Click chemistry can be used to ligate a polyethylene glycol (PEG) moiety termed Click PEGylation to mass shift the reduced or oxidised form as desired, the potential for copper catalysed auto-oxidation is problematic. Here we define a catalyst-free trans-cyclooctene-methyltetrazine (TCO-Tz) inverse electron demand Diels Alder chemistry approach that affords rapid (k ~2000 M-1 s-1), selective and bio-orthogonal Click PEGylation. We used TCO-Tz Click PEGylation to investigate how fertilisation impacts reversible mitochondrial ATP synthase F1-Fo sub-unit alpha (ATP-α-F1) oxidation-an established molecular correlate of impaired enzyme activity-in Xenopus laevis. TCO-Tz Click PEGylation studies reveal substantial (~65%) reversible ATP-α-F1 oxidation at evolutionary conserved cysteine residues (i.e., C244 and C294) before and after fertilisation. A single thiol is, however, preferentially oxidised likely due to greater solvent exposure during the catalytic cycle. Selective reduction experiments show that: S-glutathionylation accounts for ~50-60% of the reversible oxidation observed, making it the dominant oxidative modification type. Intermolecular disulphide bonds may also contribute due to their relative stability. Substantial reversible ATP-α-F1 oxidation before and after fertilisation is biologically meaningful because it implies low mitochondrial F1-Fo ATP synthase activity. Catalyst-free TCO-Tz Click PEGylation is a valuable new tool to interrogate protein thiol redox state in health and disease.},
}

Adenosine Triphosphate/biosynthesis
Amino Acid Sequence
Animals
Click Chemistry/*methods
Disulfides/chemistry
Embryo, Nonmammalian
Female
Fertilization in Vitro
Glutathione/metabolism
Heterocyclic Compounds, 1-Ring/chemistry
Male
Mitochondria/*chemistry/enzymology
Mitochondrial Proton-Translocating ATPases/*chemistry/metabolism
Ovum/*chemistry/cytology/enzymology
Oxidation-Reduction
Phylogeny
Polyethylene Glycols/*chemistry
*Protein Processing, Post-Translational
Protein Subunits/*chemistry/metabolism
Sequence Alignment
Sequence Homology, Amino Acid
Sulfhydryl Compounds/chemistry/metabolism
Xenopus laevis/classification/embryology/metabolism

@article {pmid31884104,
year = {2020},
author = {Al-Eitan, L and Saadeh, H and Alnaamneh, A and Darabseh, S and Al-Sarhan, N and Alzihlif, M and Hakooz, N and Ivanova, E and Kelsey, G and Dajani, R},
title = {The genetic landscape of Arab Population, Chechens and Circassians subpopulations from Jordan through HV1 and HV2 regions of mtDNA.},
journal = {Gene},
volume = {729},
number = {},
pages = {144314},
doi = {10.1016/j.gene.2019.144314},
pmid = {31884104},
issn = {1879-0038},
mesh = {Arabs/*genetics ; DNA, Mitochondrial/*genetics ; Ethnic Groups/*genetics ; Female ; Genetic Variation/genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Humans ; Jordan/epidemiology ; Male ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Mitochondrial DNA (mtDNA) is widely used in several fields including medical genetics, forensic science, genetic genealogy, and evolutionary anthropology. In this study, mtDNA haplotype diversity was determined for 293 unrelated subjects from Jordanian population (Circassians, Chechens, and the original inhabitants of Jordan). A total of 102 haplotypes were identified and analyzed among the populations to describe the maternal lineage landscape. Our results revealed that the distribution of mtDNA haplotype frequencies among the three populations showed disparity and significant differences when compared to each other. We also constructed mitochondrial haplotype classification trees for the three populations to determine the phylogenetic relationship of mtDNA haplotype variants, and we observed clear differences in the distribution of maternal genetic ancestries, especially between Arab and the minority ethnic populations. To our knowledge, this study is the first, to date, to characterize mitochondrial haplotypes and haplotype distributions in a population-based sample from the Jordanian population. It provides a powerful reference for future studies investigating the contribution of mtDNA variation to human health and disease and studying population history and evolution by comparing the mtDNA haplotypes to other populations.},
}

Arabs/*genetics
DNA, Mitochondrial/*genetics
Ethnic Groups/*genetics
Female
Genetic Variation/genetics
Genetics, Population/methods
Haplotypes/genetics
Humans
Jordan/epidemiology
Male
Mitochondria/genetics
Phylogeny

@article {pmid30636322,
year = {2019},
author = {Broddrick, JT and Du, N and Smith, SR and Tsuji, Y and Jallet, D and Ware, MA and Peers, G and Matsuda, Y and Dupont, CL and Mitchell, BG and Palsson, BO and Allen, AE},
title = {Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum.},
journal = {The New phytologist},
volume = {222},
number = {3},
pages = {1364-1379},
doi = {10.1111/nph.15685},
pmid = {30636322},
issn = {1469-8137},
support = {GMBF3828//Gordon and Betty Moore Foundation/International ; JP15K16156//Japan Society for the Promotion of Science/International ; JP16H06557//Japan Society for the Promotion of Science/International ; JP17K15326//Japan Society for the Promotion of Science/International ; JP24310015//Japan Society for the Promotion of Science/International ; SP16005//Japan Society for the Promotion of Science/International ; //Edna Bailey Sussman Foundation/International ; NSF-MCB-1024913//National Science Foundation/International ; No. 1614398//National Science Foundation/International ; DE-EE0003373//US Department of Energy/International ; DE-SC0008593//US Department of Energy/International ; DE-SC0008595//US Department of Energy/International ; //Individual Special Research Fund of Kwansei Gakuin University/International ; //Promotion and Mutual Aid Corporation for Private Schools of Japan (PMAC)/International ; },
mesh = {Acclimatization/radiation effects ; Alcohol Oxidoreductases/metabolism ; Biomass ; Cell Respiration/radiation effects ; Circadian Rhythm/radiation effects ; Computer Simulation ; Diatoms/*metabolism/*radiation effects ; Electron Transport/radiation effects ; *Light ; Metabolic Networks and Pathways/radiation effects ; Mitochondria/metabolism/radiation effects ; Models, Biological ; Photosynthesis/radiation effects ; Pyruvic Acid/metabolism ; },
abstract = {Photoacclimation consists of short- and long-term strategies used by photosynthetic organisms to adapt to dynamic light environments. Observable photophysiology changes resulting from these strategies have been used in coarse-grained models to predict light-dependent growth and photosynthetic rates. However, the contribution of the broader metabolic network, relevant to species-specific strategies and fitness, is not accounted for in these simple models. We incorporated photophysiology experimental data with genome-scale modeling to characterize organism-level, light-dependent metabolic changes in the model diatom Phaeodactylum tricornutum. Oxygen evolution and photon absorption rates were combined with condition-specific biomass compositions to predict metabolic pathway usage for cells acclimated to four different light intensities. Photorespiration, an ornithine-glutamine shunt, and branched-chain amino acid metabolism were hypothesized as the primary intercompartment reductant shuttles for mediating excess light energy dissipation. Additionally, simulations suggested that carbon shunted through photorespiration is recycled back to the chloroplast as pyruvate, a mechanism distinct from known strategies in photosynthetic organisms. Our results suggest a flexible metabolic network in P. tricornutum that tunes intercompartment metabolism to optimize energy transport between the organelles, consuming excess energy as needed. Characterization of these intercompartment reductant shuttles broadens our understanding of energy partitioning strategies in this clade of ecologically important primary producers.},
}

Acclimatization/radiation effects
Alcohol Oxidoreductases/metabolism
Biomass
Cell Respiration/radiation effects
Circadian Rhythm/radiation effects
Computer Simulation
Diatoms/*metabolism/*radiation effects
Electron Transport/radiation effects
*Light
Metabolic Networks and Pathways/radiation effects
Mitochondria/metabolism/radiation effects
Models, Biological
Photosynthesis/radiation effects
Pyruvic Acid/metabolism

@article {pmid32097597,
year = {2020},
author = {Camus, MF and Moore, J and Reuter, M},
title = {Nutritional geometry of mitochondrial genetic effects on male fertility.},
journal = {Biology letters},
volume = {16},
number = {2},
pages = {20190891},
doi = {10.1098/rsbl.2019.0891},
pmid = {32097597},
issn = {1744-957X},
abstract = {Organismal fitness is partly determined by how well the nutritional intake matches sex-specific metabolic requirements. Metabolism itself is underpinned by complex genomic interactions involving products from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, used and recycled, processes vital for fuelling reproduction. Given the complicated nature of metabolism, it is not well understood how the functioning of these two genomes is modulated by nutrients. Here we use nutritional geometry techniques on Drosophila lines that only differ in their mtDNA, with the aim to understand if there is nutrient-dependent mitochondrial genetic variance for male reproduction. We first find genetic variance for diet consumption, indicating that flies are consuming different amounts of food to meet new physiological requirements. We then find an interaction between mtDNA and diet for fitness, suggesting that the mtDNA plays a role in modulating diet-dependent fitness. Our results enhance our basic understanding of nutritional health and our chimeric genomes.},
}

@article {pmid32094163,
year = {2020},
author = {Yahalomi, D and Atkinson, SD and Neuhof, M and Chang, ES and Philippe, H and Cartwright, P and Bartholomew, JL and Huchon, D},
title = {A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1909907117},
pmid = {32094163},
issn = {1091-6490},
abstract = {Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria-related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no mitochondrial genome, and thus has lost the ability to perform aerobic cellular respiration. This indicates that these core eukaryotic features are not ubiquitous among animals. Our analyses suggest that H. salminicola lost not only its mitochondrial genome but also nearly all nuclear genes involved in transcription and replication of the mitochondrial genome. In contrast, we identified many genes that encode proteins involved in other mitochondrial pathways and determined that genes involved in aerobic respiration or mitochondrial DNA replication were either absent or present only as pseudogenes. As a control, we used the same sequencing and annotation methods to show that a closely related myxozoan, Myxobolus squamalis, has a mitochondrial genome. The molecular results are supported by fluorescence micrographs, which show the presence of mitochondrial DNA in M. squamalis, but not in H. salminicola. Our discovery confirms that adaptation to an anaerobic environment is not unique to single-celled eukaryotes, but has also evolved in a multicellular, parasitic animal. Hence, H. salminicola provides an opportunity for understanding the evolutionary transition from an aerobic to an exclusive anaerobic metabolism.},
}

@article {pmid32093266,
year = {2020},
author = {Muellner, J and Schmidt, KH},
title = {Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family.},
journal = {Genes},
volume = {11},
number = {2},
pages = {},
doi = {10.3390/genes11020224},
pmid = {32093266},
issn = {2073-4425},
abstract = {The two PIF1 family helicases in Saccharomyces cerevisiae, Rrm3, and ScPif1, associate with thousands of sites throughout the genome where they perform overlapping and distinct roles in telomere length maintenance, replication through non-histone proteins and G4 structures, lagging strand replication, replication fork convergence, the repair of DNA double-strand break ends, and transposable element mobility. ScPif1 and its fission yeast homolog Pfh1 also localize to mitochondria where they protect mitochondrial genome integrity. In addition to yeast serving as a model system for the rapid functional evaluation of human Pif1 variants, yeast cells lacking Rrm3 have proven useful for elucidating the cellular response to replication fork pausing at endogenous sites. Here, we review the increasingly important cellular functions of the yeast PIF1 helicases in maintaining genome integrity, and highlight recent advances in our understanding of their roles in facilitating fork progression through replisome barriers, their functional interactions with DNA repair, and replication stress response pathways.},
}

@article {pmid31561749,
year = {2019},
author = {Lorenz, C and Alves, JMP and Foster, PG and Sallum, MAM and Suesdek, L},
title = {First record of translocation in Culicidae (Diptera) mitogenomes: evidence from the tribe Sabethini.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {721},
pmid = {31561749},
issn = {1471-2164},
support = {311805/2014-0 and 311984/2018-5//CAPES/ ; 2013/05521-9 and 2015/12784-1//FAPESP/ ; 2014/26229-9//FAPESP/ ; 301877/2016-5//CNPq/ ; },
mesh = {Animals ; Culicidae/*classification/genetics ; Evolution, Molecular ; Gene Order ; Gene Rearrangement ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: The tribe Sabethini (Diptera: Culicidae) contains important vectors of the yellow fever virus and presents remarkable morphological and ecological diversity unequalled in other mosquito groups. However, there is limited information about mitochondrial genomes (mitogenomes) from these species. As mitochondrial genetics has been fundamental for posing evolutionary hypotheses and identifying taxonomical markers, in this study we sequenced the first sabethine mitogenomes: Sabethes undosus, Trichoprosopon pallidiventer, Runchomyia reversa, Limatus flavisetosus, and Wyeomyia confusa. In addition, we performed phylogenetic analyses of Sabethini within Culicidae and compared its mitogenomic architecture to that of other insects.

RESULTS: Similar to other insects, the Sabethini mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. However, the gene order is not the same as that in other mosquitoes; the tyrosine (Y) and cysteine (C) tRNA genes have translocated. In general, mitogenome rearrangements within insects are uncommon events; the translocation reported here is unparalleled among Culicidae and can be considered an autapomorphy for the Neotropical sabethines.

CONCLUSIONS: Our study provides clear evidence of gene rearrangements in the mitogenomes of these Neotropical genera in the tribe Sabethini. Gene order can be informative at the taxonomic level of tribe. The translocations found, along with the mitogenomic sequence data and other recently published findings, reinforce the status of Sabethini as a well-supported monophyletic taxon. Furthermore, T. pallidiventer was recovered as sister to R. reversa, and both were placed as sisters of other Sabethini genera (Sabethes, Wyeomyia, and Limatus).},
}

Animals
Culicidae/*classification/genetics
Evolution, Molecular
Gene Order
Gene Rearrangement
Genome Size
Genome, Mitochondrial
Mitochondria/*genetics
Phylogeny
Sequence Analysis, DNA/*methods

@article {pmid31264965,
year = {2019},
author = {Zarin, T and Strome, B and Nguyen Ba, AN and Alberti, S and Forman-Kay, JD and Moses, AM},
title = {Proteome-wide signatures of function in highly diverged intrinsically disordered regions.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
doi = {10.7554/eLife.46883},
pmid = {31264965},
issn = {2050-084X},
support = {Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/International ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/International ; PJT-148532//CIHR/Canada ; FDN-148375//CIHR/Canada ; Postdoctoral Fellowship//Natural Sciences and Engineering Research Council of Canada/International ; Alexander Graham Bell Scholarship//National Sciences and Engineering Research Council/International ; Discovery Grant//National Sciences and Engineering Research Council/International ; },
mesh = {Amino Acid Sequence ; DNA Repair ; Evolution, Molecular ; Gene Ontology ; Intrinsically Disordered Proteins/chemistry/*metabolism ; Mitochondria/metabolism ; Molecular Sequence Annotation ; Protein Sorting Signals ; Proteome/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; },
abstract = {Intrinsically disordered regions make up a large part of the proteome, but the sequence-to-function relationship in these regions is poorly understood, in part because the primary amino acid sequences of these regions are poorly conserved in alignments. Here we use an evolutionary approach to detect molecular features that are preserved in the amino acid sequences of orthologous intrinsically disordered regions. We find that most disordered regions contain multiple molecular features that are preserved, and we define these as 'evolutionary signatures' of disordered regions. We demonstrate that intrinsically disordered regions with similar evolutionary signatures can rescue function in vivo, and that groups of intrinsically disordered regions with similar evolutionary signatures are strongly enriched for functional annotations and phenotypes. We propose that evolutionary signatures can be used to predict function for many disordered regions from their amino acid sequences.},
}

Amino Acid Sequence
DNA Repair
Evolution, Molecular
Gene Ontology
Intrinsically Disordered Proteins/chemistry/*metabolism
Mitochondria/metabolism
Molecular Sequence Annotation
Protein Sorting Signals
Proteome/chemistry/*metabolism
Saccharomyces cerevisiae/metabolism

@article {pmid32084398,
year = {2020},
author = {Schäfer, K and Künzler, P and Klingl, A and Eubel, H and Carrie, C},
title = {The Plant Mitochondrial TAT Pathway Is Essential for Complex III Biogenesis.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2020.01.001},
pmid = {32084398},
issn = {1879-0445},
abstract = {Twin arginine translocation (TAT) pathways have been extensively studied in bacteria and chloroplasts for their role in membrane translocation of folded proteins. However, an increasing number of organisms have been found to contain mitochondria-located TAT subunits, including plant mitochondria, which contain TAT subunits, though in an unusual arrangement with only TatB and TatC subunits. To date, no confirmed function has been attributed to mitochondrial TAT pathways in any organism. Using a truncation mutant approach, we demonstrate that the plant mitochondrial TatB (MTTATB) is required for complex III biogenesis. More specifically, MTTATB performs at a late stage in complex III biogenesis, conveying the translocation of the C terminus of the Rieske FeS subunit back across the inner membrane. This work confirms that plant mitochondria retained a functional TAT pathway for the Rieske FeS translocation, most likely from the original mitochondrial ancestor. It is hypothesized that the original mitochondria contained a bacteria-derived TAT pathway required for at least the Rieske FeS translocation. In several eukaryotic lineages, this mitochondrial TAT pathway was lost and replaced by BCS1. Interestingly, plant mitochondria appear to assemble complex III in the same subunit order as yeast and mammals but in contrast use bacteria-like assembly factors for this process.},
}

@article {pmid32080867,
year = {2020},
author = {Speijer, D},
title = {Debating Eukaryogenesis-Part 1: Does Eukaryogenesis Presuppose Symbiosis Before Uptake?.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e1900157},
doi = {10.1002/bies.201900157},
pmid = {32080867},
issn = {1521-1878},
abstract = {Eukaryotic origins are heavily debated. The author as well as others have proposed that they are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry, in a so-called symbiogenic scenario. The ensuing mutual adaptation of archaeal host and endosymbiont seems to have been a defining influence during the processes leading to the last eukaryotic common ancestor. An unresolved question in this scenario deals with the means by which the bacterium ends up inside. Older hypotheses revolve around the application of known antagonistic interactions, the bacterium being prey or parasite. Here, in reviewing the field, the author argues that such models share flaws, hence making them less likely, and that a "pre-symbiotic stage" would have eased ongoing metabolic integration. Based on this the author will speculate about the nature of the (endo) symbiosis that started eukaryotic evolution-in the context of bacterial entry being a relatively "early" event-and stress the differences between this uptake and subsequent ones. He will also briefly discuss how the mutual adaptation following the merger progressed and how many eukaryotic hallmarks can be understood in light of coadaptation.},
}

@article {pmid32080176,
year = {2020},
author = {Kuhle, B and Chihade, J and Schimmel, P},
title = {Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {969},
doi = {10.1038/s41467-020-14725-y},
pmid = {32080176},
issn = {2041-1723},
support = {1R01GM125908-01A//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R01GM125908-01A//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Metazoan complexity and life-style depend on the bioenergetic potential of mitochondria. However, higher aerobic activity and genetic drift impose strong mutation pressure and risk of irreversible fitness decline in mitochondrial (mt)DNA-encoded genes. Bilaterian mitochondria-encoded tRNA genes, key players in mitochondrial activity, have accumulated mutations at significantly higher rates than their cytoplasmic counterparts, resulting in foreshortened and fragile structures. Here we show that fragility of mt tRNAs coincided with the evolution of bilaterian animals. We demonstrate that bilaterians compensated for this reduced structural complexity in mt tRNAs by sequence-independent induced-fit adaption to the cognate mitochondrial aminoacyl-tRNA synthetase (aaRS). Structural readout by nuclear-encoded aaRS partners relaxed the sequence constraints on mt tRNAs and facilitated accommodation of functionally disruptive mutational insults by cis-acting epistatic compensations. Our results thus suggest that mutational freedom in mt tRNA genes is an adaptation to increased mutation pressure that was associated with the evolution of animal complexity.},
}

@article {pmid31374295,
year = {2019},
author = {Tolomeo, AM and Carraro, A and Bakiu, R and Toppo, S and Garofalo, F and Pellegrino, D and Gerdol, M and Ferro, D and Place, SP and Santovito, G},
title = {Molecular characterization of novel mitochondrial peroxiredoxins from the Antarctic emerald rockcod and their gene expression in response to environmental warming.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {225},
number = {},
pages = {108580},
doi = {10.1016/j.cbpc.2019.108580},
pmid = {31374295},
issn = {1532-0456},
mesh = {Amino Acid Sequence ; Animals ; Antarctic Regions ; Fish Proteins/classification/metabolism ; Gene Expression ; Global Warming ; Mitochondria/*enzymology ; Perciformes/*metabolism ; *Peroxiredoxins/classification/metabolism ; Phylogeny ; Protein Isoforms ; Temperature ; },
abstract = {In the present study we describe the molecular characterization of the two paralogous mitochondrial peroxiredoxins from Trematomus bernacchii, a teleost that plays a pivotal role in the Antarctic food chain. The two putative amino acid sequences were compared with orthologs from other fish, highlighting a high percentage of identity and similarity with the respective variant, in particular for the residues that are essential for the characteristic peroxidase activity of these enzymes. The temporal expression of Prdx3 and Prdx5 mRNAs in response to short-term thermal stress showed a general upregulation of prdx3, suggesting that this isoform is the most affected by temperature increase. These data, together with the peculiar differences between the molecular structures of the two mitochondrial Prdxs in T. bernacchii as well as in the tropical species Stegastes partitus, suggest an adaptation that allowed these poikilothermic aquatic vertebrates to colonize very different environments, characterized by different temperature ranges.},
}

Amino Acid Sequence
Animals
Antarctic Regions
Fish Proteins/classification/metabolism
Gene Expression
Global Warming
Mitochondria/*enzymology
Perciformes/*metabolism
*Peroxiredoxins/classification/metabolism
Phylogeny
Protein Isoforms
Temperature

@article {pmid30040943,
year = {2018},
author = {Gawryluk, RMR},
title = {Evolutionary Biology: A New Home for the Powerhouse?.},
journal = {Current biology : CB},
volume = {28},
number = {14},
pages = {R798-R800},
doi = {10.1016/j.cub.2018.05.073},
pmid = {30040943},
issn = {1879-0445},
mesh = {*Alphaproteobacteria ; Biological Evolution ; Biology ; Oceans and Seas ; Phylogeny ; },
abstract = {Metagenomic assemblies of oceanic datasets have unearthed novel and diverse alphaproteobacterial groups. Sophisticated phylogenetic analyses based on these metagenomes suggest that mitochondria do not descend from within Alphaproteobacteria, as typically thought, but from a still undiscovered sister lineage.},
}

*Alphaproteobacteria
Biological Evolution
Biology
Oceans and Seas
Phylogeny

@article {pmid32074218,
year = {2020},
author = {Báez, AL and Lo Presti, MS and Bazán, PC and Strauss, M and Velázquez López, DA and Miler, N and Rivarola, HW and Paglini-Oliva, PA},
title = {Analysis of mitochondrial enzymatic activity in blood lymphomonocyte fractions during infection with different Trypanosoma cruzi strains.},
journal = {Revista do Instituto de Medicina Tropical de Sao Paulo},
volume = {62},
number = {},
pages = {e15},
doi = {10.1590/S1678-9946202062015},
pmid = {32074218},
issn = {1678-9946},
abstract = {Proinflammatory and inflammatory mediators induced by Trypanosoma cruzi infection increase the oxidative stress, generating toxicity for cells targeting mitochondria of different tissues. We studied the activity of citrate synthase and complexes I-IV of respiratory chain in mitochondria of blood lymphomonocyte fraction, from albino Swiss mice infected with different isolates of T. cruzi , during Chagas disease evolution. Complexes I-IV were modified in infected groups (p<0.05) in all the stages, and an inflammatory process of different magnitudes was detected in the heart and skeletal muscle according to the isolate. The citrate synthase activity presented modifications in the SGO Z12 and the Tulahuen group (p<0.05). Hearts showed fiber fragmentation and fibrosis; skeletal muscle presented inflammatory infiltrates and in the Tulahuen infected group, there were also amastigote nests. The inflammatory processes produced an oxidative stress that induced different alterations of mitochondrial enzymes activities in the lymphomonocyte fraction that can be detected by a simple blood extraction, suggesting that they could be used as disease markers, especially in the indeterminate phase of Chagas disease.},
}

@article {pmid32065920,
year = {2020},
author = {Sunil, B and Rajsheel, P and Aswani, V and Bapatla, RB and Talla, SK and Raghavendra, AS},
title = {Photosynthesis is sensitive to nitric oxide and respiration sensitive to hydrogen peroxide: Studies with pea mesophyll protoplasts.},
journal = {Journal of plant physiology},
volume = {246-247},
number = {},
pages = {153133},
doi = {10.1016/j.jplph.2020.153133},
pmid = {32065920},
issn = {1618-1328},
abstract = {Reports on the effect of nitric oxide (NO) or reactive oxygen species (ROS) on photosynthesis and respiration in leaf tissues are intriguing; therefore, the effects of exogenous addition of sodium nitroprusside (SNP, releases NO) or H2O2 on the photosynthetic O2 evolution and respiratory O2 uptake by mesophyll protoplasts in pea (Pisum sativum) were evaluated in the present study. Low concentrations of SNP or H2O2 were used to minimize nonspecific effects. The effects of NO or H2O2 on respiration and photosynthesis were different. The presence of NO decreased the rate of photosynthesis but caused a marginal stimulation of dark respiration. Conversely, externally administered H2O2 drastically decreased the rate of respiration but only slightly decreased photosynthesis. The PS I activity was more sensitive to NO than PS II. On the other hand, 100 μM H2O2 had no effect on the photochemical reactions of either PS I or PS II. The sensitivity of photosynthesis to antimycin A or SHAM (reflecting the interplay between chloroplasts and mitochondria) was not affected by NO. By contrast, H2O2 markedly decreased the sensitivity of photosynthesis to antimycin A and SHAM. It can be concluded that chloroplasts are the primary targets of NO, while mitochondria are the primary targets of ROS in plant cells. We propose that H2O2 can be an important signal to modulate the crosstalk between chloroplasts and mitochondria.},
}

@article {pmid31504759,
year = {2019},
author = {Mignerot, L and Nagasato, C and Peters, AF and Perrineau, MM and Scornet, D and Pontheaux, F and Djema, W and Badis, Y and Motomura, T and Coelho, SM and Cock, JM},
title = {Unusual Patterns of Mitochondrial Inheritance in the Brown Alga Ectocarpus.},
journal = {Molecular biology and evolution},
volume = {36},
number = {12},
pages = {2778-2789},
doi = {10.1093/molbev/msz186},
pmid = {31504759},
issn = {1537-1719},
mesh = {*Genes, Mitochondrial ; Genome, Mitochondrial ; Life History Traits ; Parthenogenesis/genetics ; Phaeophyta/*genetics ; Recombination, Genetic ; },
abstract = {Most eukaryotes inherit their mitochondria from only one of their parents. When there are different sexes, it is almost always the maternal mitochondria that are transmitted. Indeed, maternal uniparental inheritance has been reported for the brown alga Ectocarpus but we show in this study that different strains of Ectocarpus can exhibit different patterns of inheritance: Ectocarpus siliculosus strains showed maternal uniparental inheritance, as expected, but crosses using different Ectocarpus species 7 strains exhibited either paternal uniparental inheritance or an unusual pattern of transmission where progeny inherited either maternal or paternal mitochondria, but not both. A possible correlation between the pattern of mitochondrial inheritance and male gamete parthenogenesis was investigated. Moreover, in contrast to observations in the green lineage, we did not detect any change in the pattern of mitochondrial inheritance in mutant strains affected in life cycle progression. Finally, an analysis of field-isolated strains provided evidence of mitochondrial genome recombination in both Ectocarpus species.},
}

*Genes, Mitochondrial
Genome, Mitochondrial
Life History Traits
Parthenogenesis/genetics
Phaeophyta/*genetics
Recombination, Genetic

@article {pmid32060025,
year = {2020},
author = {Frank, C and Jendrossek, D},
title = {Acidocalcisomes and Polyphosphate Granules Are Different Subcellular Structures in Agrobacterium tumefaciens.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02759-19},
pmid = {32060025},
issn = {1098-5336},
abstract = {Acidocalcisomes are membrane-enclosed, polyphosphate-containing acidic organelles in lower Eukaryota but have been described likewise for Agrobacterium tumefaciens (Seufferheld, M., Vieira, M., Ruiz, F. A., Rodrigues, C. O., Moreno, S., & Docampo, R. 2003. J. Biol. Chem. 278:29971-29978). This study aimed at the characterization of polyphosphate-containing acidocalcisomes in this α-proteobacterium. Unexpectedly, fluorescence microscopical investigation of A. tumefaciens cells using fluorescent dyes and localization of constructed fusions of polyphosphate kinases (PPKs) and of vacuolar H+-translocating pyrophosphatase (HppA) with enhanced yellow fluorescent protein (eYFP) suggested that acidocalcisomes and polyphosphate are different subcellular structures. Acidocalcisomes and polyphosphate granules were frequently located closely together and both near the cell poles. However, they never shared the same position. Mutant strains of A. tumefaciens with deletions of both ppk genes (Δppk1, Δppk2) were unable to form polyphosphate, but still showed cell pole-located eYFP-HppA-foci and could be stained with MitoTracker. In conclusion, A. tumefaciens forms polyP granules that are free of a surrounding membrane and thus resemble polyP granules of Ralstonia eutropha and other bacteria. The composition, contents and function of the subcellular structures that are stainable with MitoTracker and harbor eYFP-HppA remain unclear.IMPORTANCE The uptake of α-proteobacterial-like cells by ancestors of eukaryotic cells and subsequent conversion of these α-proteobacterial-like cells to mitochondria are thought to be a key step in the evolution of the first eukaryotic cells. The identification of acidocalcisomes in two α-proteobacterial species some years ago and the presence of homologs of the vacuolar proton translocating pyrophosphatase HppA, a marker protein of the acidocalcisome membrane in eukaryotes, in virtually all species within the α-proteobacteria suggests that eukaryotic acidocalcisomes might also origin from related structures in ancestors of α-proteobacterial species. Accordingly, α-proteobacterial acidocalcisomes and eukaryotic acidocalcisomes should have similar features. Since hardly any information is available on bacterial acidocalcisomes this study aimed at the characterization of organelle-like structures in α-proteobacterial cells at the example of A. tumefaciens.},
}

@article {pmid32058540,
year = {2020},
author = {Prakash, NR and Chhabra, R and Zunjare, RU and Muthusamy, V and Hossain, F},
title = {Molecular characterization of teosinte branched1 gene governing branching architecture in cultivated maize and wild relatives.},
journal = {3 Biotech},
volume = {10},
number = {2},
pages = {77},
doi = {10.1007/s13205-020-2052-6},
pmid = {32058540},
issn = {2190-572X},
abstract = {We sequenced the entire tb1 gene in six maize inbreds and its wild relatives (parviglumis, mexicana, perennis and luxurians) to characterize it at molecular level. Hopscotch and Tourist transposable elements were observed in the upstream of tb1 in all maize inbreds, while they were absent in wild relatives. In maize, tb1 consisted of 431-443 bp 5'UTR, 1101 bp coding sequence and 211-219 bp 3'UTR. In promoter region, mutations in the light response element in mexicana (~ 35 bp and ~ 55 bp upstream of TSS) and perennis (at ~ 35 bp upstream of TSS) were found. A 6 bp insertion at 420 bp downstream of the polyA signal site was present among teosinte accessions, while it was not observed in maize. A codominant marker flanking the 6 bp InDel was developed, and it differentiated the teosintes from maize. In Tb1 protein, alanine (12.7-14.6%) was the most abundant amino acid with tryptophan as the rarest (0.5-0.9%). The molecular weight of Tb1 protein was 38757.15 g/mol except 'Palomero Toluqueno' and HKI1128. R and TCP motifs in Tb1 protein were highly conserved across maize, teosinte and orthologues, while TCP domain differed for tb1 paralogue. Tb1 possessed important role in light-, auxin-, stress-response and meristem identity maintenance. Presence of molecular signal suggested its localization in mitochondria, nucleus and nucleolus. Parviglumis and mexicana shared closer relationship with maize than perennis and luxurians. A highly conserved 59-60 amino acids long bHLH region was observed across genotypes. Information generated here assumes significance in evolution of tb1 gene and breeding for enhancement of prolificacy in maize.},
}

@article {pmid31233550,
year = {2019},
author = {Monteiro, KJL and Calegar, DA and Santos, JP and Bacelar, PAA and Coronato-Nunes, B and Reis, ERC and Boia, MN and Carvalho-Costa, FA and Jaeger, LH},
title = {Genetic diversity of Ascaris spp. infecting humans and pigs in distinct Brazilian regions, as revealed by mitochondrial DNA.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0218867},
doi = {10.1371/journal.pone.0218867},
pmid = {31233550},
issn = {1932-6203},
mesh = {Animals ; Ascariasis/parasitology ; Ascaris lumbricoides/*genetics ; Ascaris suum/*genetics ; Brazil ; Cross-Sectional Studies ; DNA, Mitochondrial/*genetics ; Genetic Variation/*genetics ; Haplotypes/genetics ; Humans ; Mitochondria/*genetics ; Phylogeny ; Swine ; Swine Diseases/parasitology ; },
abstract = {In this study, we assessed the genetic diversity of Ascaris lumbricoides / Ascaris suum circulating in humans and pigs, exploring potential zoonotic cycles in endemic areas in Brazil. We carried out cross-sectional surveys in four municipalities: Santa Isabel do Rio Negro (SIRN-AM) (n = 328); Nossa Senhora de Nazaré (NSN-PI) and Teresina (TER-PI) (n = 605 and n = 297, respectively); and Cachoeiras de Macacu (CAM-RJ) (n = 543). We also studied 61 fecal samples/adult worms obtained from pigs (n = 53 in NSN-PI and n = 8 in TER-PI). A ~450 bp fragment of the Ascaris cytochrome c oxidase subunit 1 (cox1) and ~400 bp of the NADH dehydrogenase subunit 1 (nad1) were amplified and sequenced. Maximum-likelihood (ML) tree and Median-joining (MJ) haplotype network analyses were performed. We also performed scanning electron micrographs of adult specimens. Positivity rates were 93/328 (28.4%) in SIRN-AM, 6/297 (2.0%) in TER-PI, 0/605 (0%) in NSN-PI, and 6/543 (1.1%) in CAM-RJ. In NSN-PI it reached 11/53 (20.7%) in pigs. The MJ network based on cox1 locus (383 bp) revealed three main clusters, one centered around haplotypes H01/H28/H32 and the other around H07/H11. The cox1 haplotypes had a heterogeneous distribution, showing no pattern by geographic region, and high haplotype diversity. The ML trees based on cox1 and nad1 loci showed a similar topology with each other, and with the haplotype networks. Three distinct clusters were observed. Sequences of cox1 and nad1 from humans and animals were distributed throughout the tree and it was not possible to differentiate specimens of human and swine origin. Ascaris populations obtained from humans and swine in different Brazilian regions are not discriminable through the genetic markers used, which indicates the potential for zoonotic transmission and the need for better control of these infections in swine herds, mainly when created in a peridomestic environment.},
}

Animals
Ascariasis/parasitology
Ascaris lumbricoides/*genetics
Ascaris suum/*genetics
Brazil
Cross-Sectional Studies
DNA, Mitochondrial/*genetics
Genetic Variation/*genetics
Haplotypes/genetics
Humans
Mitochondria/*genetics
Phylogeny
Swine
Swine Diseases/parasitology

@article {pmid31086122,
year = {2019},
author = {Santos, HJ and Hanadate, Y and Imai, K and Nozaki, T},
title = {An Entamoeba-Specific Mitosomal Membrane Protein with Potential Association to the Golgi Apparatus.},
journal = {Genes},
volume = {10},
number = {5},
pages = {},
doi = {10.3390/genes10050367},
pmid = {31086122},
issn = {2073-4425},
mesh = {Amino Acid Sequence ; Biological Evolution ; Calcium-Transporting ATPases/metabolism ; Computer Simulation ; Entamoeba/*metabolism ; Entamoeba histolytica/genetics/metabolism ; Golgi Apparatus/metabolism ; Membrane Proteins/*metabolism ; Microscopy, Immunoelectron/methods ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Organelles/metabolism ; Protein Transport ; Protozoan Proteins ; },
abstract = {The aerobic mitochondrion had undergone evolutionary diversification, most notable among lineages of anaerobic protists. Entamoeba is one of the genera of parasitic protozoans that lack canonical mitochondria, and instead possess mitochondrion-related organelles (MROs), specifically mitosomes. Entamoeba mitosomes exhibit functional reduction and divergence, most exemplified by the organelle's inability to produce ATP and synthesize iron-sulfur cluster. Instead, this organelle is capable of sulfate activation, which has been linked to amoebic stage conversion. In order to understand other unique features and components of this MRO, we utilized an in silico prediction tool to screen transmembrane domain containing proteins in the mitosome proteome. Here, we characterize a novel lineage-specific mitosomal membrane protein, named Entamoeba transmembrane mitosomal protein of 30 kDa (ETMP30; EHI_172170), predicted to contain five transmembrane domains. Immunofluorescence analysis demonstrated colocalization of hemagglutinin (HA)-tagged ETMP30 with the mitosomal marker, adenosine-5'-phosphosulfate kinase. Mitosomal membrane localization was indicated by immunoelectron microscopy analysis, which was supported by carbonate fractionation assay. Transcriptional gene silencing successfully repressed RNA expression by 60%, and led to a defect in growth and partial elongation of mitosomes. Immunoprecipitation of ETMP30 from ETMP30-HA-expressing transformant using anti-HA antibody pulled down one interacting protein of 126 kDa. Protein sequencing by mass spectrometry revealed this protein as a cation-transporting P-type ATPase, previously reported to localize to vacuolar compartments/Golgi-like structures, hinting at a possible mitosome-vacuole/Golgi contact site.},
}

Amino Acid Sequence
Biological Evolution
Calcium-Transporting ATPases/metabolism
Computer Simulation
Entamoeba/*metabolism
Entamoeba histolytica/genetics/metabolism
Golgi Apparatus/metabolism
Membrane Proteins/*metabolism
Microscopy, Immunoelectron/methods
Mitochondria/metabolism
Mitochondrial Membranes/*metabolism
Organelles/metabolism
Protein Transport
Protozoan Proteins

@article {pmid32049644,
year = {2020},
author = {Kornmann, B},
title = {The endoplasmic reticulum-mitochondria encounter structure: coordinating lipid metabolism across membranes.},
journal = {Biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1515/hsz-2020-0102},
pmid = {32049644},
issn = {1437-4315},
abstract = {Endosymbiosis, the beginning of a collaboration between an Archaeon and a Bacterium and founding step in the evolution of Eukaryotes, owes its success to the establishment of communication routes between the host and the symbiont to allow the exchange of metabolites. As far as lipids are concerned, it is the host that has learnt the symbiont's language, as eukaryote lipids appear to have been borrowed from the bacterial symbiont. Mitochondria exchange lipids with the rest of the cell at membrane contact sites. In fungi, the Endoplasmic Reticulum-Mitochondria Encounter Structure (ERMES) is one of the best understood membrane tethering complexes. Its discovery has yielded crucial insight into the mechanisms of intracellular lipid trafficking. Despite a wealth of data, our understanding of ERMES formation and its exact role(s) remains incomplete. Here, I endeavour to summarize our knowledge on the ERMES complex and to identify lingering gaps.},
}

@article {pmid31561566,
year = {2019},
author = {Varré, JS and D'Agostino, N and Touzet, P and Gallina, S and Tamburino, R and Cantarella, C and Ubrig, E and Cardi, T and Drouard, L and Gualberto, JM and Scotti, N},
title = {Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome.},
journal = {International journal of molecular sciences},
volume = {20},
number = {19},
pages = {},
pmid = {31561566},
issn = {1422-0067},
mesh = {Amino Acid Sequence ; *Gene Expression Profiling ; *Genome, Mitochondrial ; *Genomics/methods ; Open Reading Frames ; Phylogeny ; RNA Editing ; Solanum tuberosum/*genetics ; *Whole Genome Sequencing ; },
abstract = {Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions. Based on the relevance of the potato crop worldwide, herewith we report the complete mtDNA sequence of two S. tuberosum cultivars, namely Cicero and Désirée, and a comprehensive study of its expression, based on high-coverage RNA sequencing data. We found that the potato mitogenome has a multi-partite architecture, divided in at least three independent molecules that according to our data should behave as autonomous chromosomes. Inter-cultivar variability was null, while comparative analyses with other species of the Solanaceae family allowed the investigation of the evolutionary history of their mitogenomes. The RNA-seq data revealed peculiarities in transcriptional and post-transcriptional processing of mRNAs. These included co-transcription of genes with open reading frames that are probably expressed, methylation of an rRNA at a position that should impact translation efficiency and extensive RNA editing, with a high proportion of partial editing implying frequent mis-targeting by the editing machinery.},
}

Amino Acid Sequence
*Gene Expression Profiling
*Genome, Mitochondrial
*Genomics/methods
Open Reading Frames
Phylogeny
RNA Editing
Solanum tuberosum/*genetics
*Whole Genome Sequencing

@article {pmid31282925,
year = {2019},
author = {McKenzie, JL and Chung, DJ and Healy, TM and Brennan, RS and Bryant, HJ and Whitehead, A and Schulte, PM},
title = {Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation.},
journal = {Integrative and comparative biology},
volume = {59},
number = {4},
pages = {925-937},
doi = {10.1093/icb/icz124},
pmid = {31282925},
issn = {1557-7023},
mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*physiology ; Fundulidae/genetics/*physiology ; Genetic Speciation ; *Genome ; Genome, Mitochondrial ; Mitochondria/genetics/*physiology ; },
abstract = {The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.},
}

Animals
*Biological Evolution
Cell Nucleus/*physiology
Fundulidae/genetics/*physiology
Genetic Speciation
*Genome
Genome, Mitochondrial
Mitochondria/genetics/*physiology

@article {pmid31173136,
year = {2019},
author = {Montooth, KL and Dhawanjewar, AS and Meiklejohn, CD},
title = {Temperature-Sensitive Reproduction and the Physiological and Evolutionary Potential for Mother's Curse.},
journal = {Integrative and comparative biology},
volume = {59},
number = {4},
pages = {890-899},
pmid = {31173136},
issn = {1557-7023},
mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/genetics/*physiology ; Female ; Male ; Maternal Inheritance/*genetics ; Mitochondria/*genetics ; Mutation/*genetics ; Reproduction/genetics ; Selection, Genetic ; *Temperature ; },
abstract = {Strict maternal transmission of mitochondrial DNA (mtDNA) is hypothesized to permit the accumulation of mitochondrial variants that are deleterious to males but not females, a phenomenon called mother's curse. However, direct evidence that mtDNA mutations exhibit such sexually antagonistic fitness effects is sparse. Male-specific mutational effects can occur when the physiological requirements of the mitochondria differ between the sexes. Such male-specific effects could potentially occur if sex-specific cell types or tissues have energy requirements that are differentially impacted by mutations affecting energy metabolism. Here we summarize findings from a model mitochondrial-nuclear incompatibility in the fruit fly Drosophila that demonstrates sex-biased effects, but with deleterious effects that are generally larger in females. We present new results showing that the mitochondrial-nuclear incompatibility does negatively affect male fertility, but only when males are developed at high temperatures. The temperature-dependent male sterility can be partially rescued by diet, suggesting an energetic basis. Finally, we discuss fruitful paths forward in understanding the physiological scope for sex-specific effects of mitochondrial mutations in the context of the recent discovery that many aspects of metabolism are sexually dimorphic and downstream of sex-determination pathways in Drosophila. A key parameter of these models that remains to be quantified is the fraction of mitochondrial mutations with truly male-limited fitness effects across extrinsic and intrinsic environments. Given the energy demands of reproduction in females, only a small fraction of the mitochondrial mutational spectrum may have the potential to contribute to mother's curse in natural populations.},
}

Animals
*Biological Evolution
Cell Nucleus/*genetics
DNA, Mitochondrial/genetics
Drosophila melanogaster/genetics/*physiology
Female
Male
Maternal Inheritance/*genetics
Mitochondria/*genetics
Mutation/*genetics
Reproduction/genetics
Selection, Genetic
*Temperature

@article {pmid31168607,
year = {2019},
author = {Hood, WR and Williams, AS and Hill, GE},
title = {An Ecologist's Guide to Mitochondrial DNA Mutations and Senescence.},
journal = {Integrative and comparative biology},
volume = {59},
number = {4},
pages = {970-982},
doi = {10.1093/icb/icz097},
pmid = {31168607},
issn = {1557-7023},
mesh = {Aging/*genetics ; Animals ; DNA, Mitochondrial/*genetics ; *Microsatellite Instability ; Mitochondria/genetics/*physiology ; Mutation/*physiology ; Mutation Rate ; },
abstract = {Longevity plays a key role in the fitness of organisms, so understanding the processes that underlie variance in senescence has long been a focus of ecologists and evolutionary biologists. For decades, the performance and ultimate decline of mitochondria have been implicated in the demise of somatic tissue, but exactly why mitochondrial function declines as individual's age has remained elusive. A possible source of decline that has been of intense debate is mutations to the mitochondrial DNA. There are two primary sources of such mutations: oxidative damage, which is widely discussed by ecologists interested in aging, and mitochondrial replication error, which is less familiar to most ecologists. The goal of this review is to introduce ecologists and evolutionary biologists to the concept of mitochondrial replication error and to review the current status of research on the relative importance of replication error in senescence. We conclude by detailing some of the gaps in our knowledge that currently make it difficult to deduce the relative importance of replication error in wild populations and encourage organismal biologists to consider this variable both when interpreting their results and as viable measure to include in their studies.},
}

Aging/*genetics
Animals
DNA, Mitochondrial/*genetics
*Microsatellite Instability
Mitochondria/genetics/*physiology
Mutation/*physiology
Mutation Rate

@article {pmid31120535,
year = {2019},
author = {Sokolova, IM and Sokolov, EP and Haider, F},
title = {Mitochondrial Mechanisms Underlying Tolerance to Fluctuating Oxygen Conditions: Lessons from Hypoxia-Tolerant Organisms.},
journal = {Integrative and comparative biology},
volume = {59},
number = {4},
pages = {938-952},
doi = {10.1093/icb/icz047},
pmid = {31120535},
issn = {1557-7023},
mesh = {*Adaptation, Biological ; Anaerobiosis ; Animals ; Mitochondria/*physiology ; Oxidation-Reduction ; *Oxidative Stress ; Oxygen/*metabolism ; },
abstract = {Oxygen (O2) is essential for most metazoan life due to its central role in mitochondrial oxidative phosphorylation (OXPHOS), which generates >90% of the cellular adenosine triphosphate. O2 fluctuations are an ultimate mitochondrial stressor resulting in mitochondrial damage, energy deficiency, and cell death. This work provides an overview of the known and putative mechanisms involved in mitochondrial tolerance to fluctuating O2 conditions in hypoxia-tolerant organisms including aquatic and terrestrial vertebrates and invertebrates. Mechanisms of regulation of the mitochondrial OXPHOS and electron transport system (ETS) (including alternative oxidases), sulphide tolerance, regulation of redox status and mitochondrial quality control, and the potential role of hypoxia-inducible factor (HIF) in mitochondrial tolerance to hypoxia are discussed. Mitochondrial phenotypes of distantly related animal species reveal common features including conservation and/or anticipatory upregulation of ETS capacity, suppression of reactive oxygen species (ROS)-producing electron flux through ubiquinone, reversible suppression of OXPHOS activity, and investment into the mitochondrial quality control mechanisms. Despite the putative importance of oxidative stress in adaptations to hypoxia, establishing the link between hypoxia tolerance and mitochondrial redox mechanisms is complicated by the difficulties of establishing the species-specific concentration thresholds above which the damaging effects of ROS outweigh their potentially adaptive signaling function. The key gaps in our knowledge about the potential mechanisms of mitochondrial tolerance to hypoxia include regulation of mitochondrial biogenesis and fusion/fission dynamics, and HIF-dependent metabolic regulation that require further investigation in hypoxia-tolerant species. Future physiological, molecular and genetic studies of mitochondrial responses to hypoxia, and reoxygenation in phylogenetically diverse hypoxia-tolerant species could reveal novel solutions to the ubiquitous and metabolically severe problem of O2 deficiency and would have important implications for understanding the evolution of hypoxia tolerance and the potential mitigation of pathological states caused by O2 fluctuations.},
}

*Adaptation, Biological
Anaerobiosis
Animals
Mitochondria/*physiology
Oxidation-Reduction
*Oxidative Stress
Oxygen/*metabolism

@article {pmid30937430,
year = {2019},
author = {Hill, GE},
title = {Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression.},
journal = {Integrative and comparative biology},
volume = {59},
number = {4},
pages = {912-924},
doi = {10.1093/icb/icz019},
pmid = {30937430},
issn = {1557-7023},
mesh = {*Biological Evolution ; Cell Nucleus/*genetics ; Eukaryota/*genetics ; Genetic Introgression ; Genome, Mitochondrial/*genetics ; Genotype ; },
abstract = {The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.},
}

*Biological Evolution
Cell Nucleus/*genetics
Eukaryota/*genetics
Genetic Introgression
Genome, Mitochondrial/*genetics
Genotype

@article {pmid30790556,
year = {2019},
author = {Léveillé, AN and Baneth, G and Barta, JR},
title = {Next generation sequencing from Hepatozoon canis (Apicomplexa: Coccidia: Adeleorina): Complete apicoplast genome and multiple mitochondrion-associated sequences.},
journal = {International journal for parasitology},
volume = {49},
number = {5},
pages = {375-387},
doi = {10.1016/j.ijpara.2018.12.001},
pmid = {30790556},
issn = {1879-0135},
mesh = {Animals ; Apicomplexa/classification/*genetics/isolation & purification ; Apicoplasts/*genetics ; Cytochromes b/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dog Diseases/parasitology ; Dogs ; Genome, Mitochondrial ; *Genome, Plastid ; Genome, Protozoan ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Protozoan Infections, Animal/parasitology ; },
abstract = {Extrachromosomal genomes of the adeleorinid parasite Hepatozoon canis infecting an Israeli dog were investigated using next-generation and standard sequencing technologies. A complete apicoplast genome and several mitochondrion-associated sequences were generated. The apicoplast genome (31,869 bp) possessed two copies of both large subunit (23S) and small subunit (16S) ribosomal RNA genes (rDNA) within an inverted repeat region, as well as 22 protein-coding sequences, 25 transfer RNA genes (tDNA) and seven open reading frames of unknown function. Although circular-mapping, the apicoplast genome was physically linear according to next-generation data. Unlike other apicoplast genomes, genes encoding ribosomal protein S19 and tDNAs for alanine, aspartic acid, histidine, threonine and valine were not identified. No complete mitochondrial genome was recovered using next-generation data or directed PCR amplifications. Eight mitochondrion-associated (215-3523 bp) contigs assembled from next-generation data encoded a complete cytochrome c oxidase subunit I coding sequence, a complete cytochrome c oxidase subunit III coding sequence, two complete cytochrome B coding sequences, a non-coding, pseudogene for cytochrome B and multiple fragmented mitochondrial rDNA genes (SSUA, SSUB, SSUD, LSUC, LSUG, RNA6, RNA10, RNA14, RNA18). The paucity of NGS reads generating each of the mitochondrion-like sequences suggested that a complete mitochondrial genome at typically high copy number was absent in H. canis. In contrast, the complete nuclear rDNA unit sequence of H. canis (18S rDNA to 28S rDNA, 6977 bp) had >1000-fold next-generation coverage. Multiple divergent (from 93.6% to 99.9% pairwise identities) nuclear 18S rDNA contigs were generated (three types with 10 subtypes total). To our knowledge this is the first apicoplast genome sequenced from any adeleorinid coccidium and the first mitochondrion-associated sequences from this serious pathogen of wild and domestic canids. These newly generated sequences may provide useful genetic loci for high-resolution species-level genotyping that is currently impossible using existing nuclear rDNA targets.},
}

Animals
Apicomplexa/classification/*genetics/isolation & purification
Apicoplasts/*genetics
Cytochromes b/genetics
DNA, Protozoan/genetics
DNA, Ribosomal/genetics
Dog Diseases/parasitology
Dogs
Genome, Mitochondrial
*Genome, Plastid
Genome, Protozoan
High-Throughput Nucleotide Sequencing
Mitochondria/*genetics
Phylogeny
Protozoan Infections, Animal/parasitology

@article {pmid31332387,
year = {2019},
author = {Barandun, J and Hunziker, M and Vossbrinck, CR and Klinge, S},
title = {Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.},
journal = {Nature microbiology},
volume = {4},
number = {11},
pages = {1798-1804},
pmid = {31332387},
issn = {2058-5276},
support = {DP2 GM123459/GM/NIGMS NIH HHS/United States ; },
mesh = {Cryoelectron Microscopy ; Evolution, Molecular ; Fungal Proteins/metabolism ; Genome, Fungal ; Microsporidia/*classification/genetics/metabolism ; RNA, Ribosomal/genetics ; Ribosomal Proteins/*metabolism ; Ribosomes/*chemistry/genetics/metabolism ; },
abstract = {Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance1-3, and are significant opportunistic parasites of humans4. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle5, rudimentary mitochondria and the smallest known eukaryotic genomes5-7. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome8-10. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.},
}

Cryoelectron Microscopy
Evolution, Molecular
Fungal Proteins/metabolism
Genome, Fungal
Microsporidia/*classification/genetics/metabolism
RNA, Ribosomal/genetics
Ribosomal Proteins/*metabolism
Ribosomes/*chemistry/genetics/metabolism

@article {pmid32027368,
year = {2020},
author = {Guo, W and Zhu, A and Fan, W and Adams, RP and Mower, JP},
title = {Extensive shifts from cis to trans splicing of gymnosperm mitochondrial introns.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaa029},
pmid = {32027368},
issn = {1537-1719},
abstract = {Hundreds of plant mitogenomes have been sequenced from angiosperms, but relatively few mitogenomes are available from its sister lineage, gymnosperms. To examine mitogenomic diversity among extant gymnosperms, we generated draft mitogenomes from 11 diverse species and compared them with four previously published mitogenomes. Examined mitogenomes from Pinaceae and cycads retained all 41 protein genes and 26 introns present in the common ancestor of seed plants, whereas gnetophyte and cupressophyte mitogenomes experienced extensive gene and intron loss. In Pinaceae and cupressophyte mitogenomes, an unprecedented number of exons are distantly dispersed, requiring trans splicing of 50-70% of mitochondrial introns to generate mature transcripts. RNAseq data confirms trans splicing of these dispersed exons in Pinus. The prevalence of trans splicing in vascular plant lineages with recombinogenic mitogenomes suggests that genomic rearrangement is the primary cause of shifts from cis to trans splicing in plant mitochondria.},
}

@article {pmid32025511,
year = {2019},
author = {Gao, J and Chau, S and Meneghini, MD},
title = {Viral attenuation by Endonuclease G during yeast gametogenesis: insights into ancestral roles of programmed cell death?.},
journal = {Microbial cell (Graz, Austria)},
volume = {7},
number = {2},
pages = {32-35},
doi = {10.15698/mic2020.02.705},
pmid = {32025511},
issn = {2311-2638},
abstract = {Viruses and other genetic parasites are present in virtually all forms of life. This chronic condition has led to diverse host cell adaptations such as CRISPR and RNAi, whose functions attenuate these parasites. It is hypothesized that programmed cell death (PCD) is an additional adaptation whose origins reside in viral defense. A core event of apoptotic PCD is the regulated release of mitochondrial inter-membrane space proteins into the cytosol, following which these apoptogenic proteins bring about the demise of the cell. The most well studied example of this is found in animals, where the release of mitochondrial cytochrome C nucleates the formation of the apoptosome, which then activates caspase mediated cell death. The release of mitochondrial proteins contributes to PCD in diverse organisms lacking the apoptosome, indicating that regulated mitochondrial release predates the evolution of canonical apoptosis. Using the budding yeast Saccharomyces cerevisiae, we recently confirmed an early study showing that Nuc1, a homolog of the mitochondrial apoptotic driver protein Endonuclease G, attenuates cytosolic double stranded RNA (dsRNA) viruses, which are endemic to yeast and many other organisms. Viral attenuation by Nuc1 occurs most prominently during meiosis and in association with its developmentally programmed relocation from the mitochondria to the cytosol. Intriguingly, meiotic viral attenuation by Nuc1 occurs within the context of meiotic PCD of the superfluous mother cell that we have also discovered. These findings are discussed here.},
}

@article {pmid32025367,
year = {2020},
author = {Schultz, DT and Eizenga, JM and Corbett-Detig, RB and Francis, WR and Christianson, LM and Haddock, SHD},
title = {Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e8356},
doi = {10.7717/peerj.8356},
pmid = {32025367},
issn = {2167-8359},
abstract = {To date, five ctenophore species' mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.},
}

@article {pmid32019493,
year = {2020},
author = {Kurbalija Novičić, Z and Sayadi, A and Jelić, M and Arnqvist, G},
title = {Negative frequency dependent selection contributes to the maintenance of a global polymorphism in mitochondrial DNA.},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {20},
doi = {10.1186/s12862-020-1581-2},
pmid = {32019493},
issn = {1471-2148},
support = {656338//H2020 Marie Skłodowska-Curie Actions/ ; AdG-294333/ERC_/European Research Council/International ; 621-2014-4523//Vetenskapsrådet/ ; },
abstract = {BACKGROUND: Understanding the forces that maintain diversity across a range of scales is at the very heart of biology. Frequency-dependent processes are generally recognized as the most central process for the maintenance of ecological diversity. The same is, however, not generally true for genetic diversity. Negative frequency dependent selection, where rare genotypes have an advantage, is often regarded as a relatively weak force in maintaining genetic variation in life history traits because recombination disassociates alleles across many genes. Yet, many regions of the genome show low rates of recombination and genetic variation in such regions (i.e., supergenes) may in theory be upheld by frequency dependent selection.

RESULTS: We studied what is essentially a ubiquitous life history supergene (i.e., mitochondrial DNA) in the fruit fly Drosophila subobscura, showing sympatric polymorphism with two main mtDNA genotypes co-occurring in populations world-wide. Using an experimental evolution approach involving manipulations of genotype starting frequencies, we show that negative frequency dependent selection indeed acts to maintain genetic variation in this region. Moreover, the strength of selection was affected by food resource conditions.

CONCLUSIONS: Our work provides novel experimental support for the view that balancing selection through negative frequency dependency acts to maintain genetic variation in life history genes. We suggest that the emergence of negative frequency dependent selection on mtDNA is symptomatic of the fundamental link between ecological processes related to resource use and the maintenance of genetic variation.},
}

@article {pmid32013845,
year = {2020},
author = {Kleandrova, VV and Speck-Planche, A},
title = {The QSAR Paradigm in Fragment-Based Drug Discovery: From the Virtual Generation of Target Inhibitors to Multi-Scale Modeling.},
journal = {Mini reviews in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/1389557520666200204123156},
pmid = {32013845},
issn = {1875-5607},
abstract = {BACKGROUND: Fragment-based drug design (FBDD) has established itself as a promising approach in modern drug discovery, accelerating and improving lead optimization, while playing a crucial role in diminishing the high attrition rates at all stages in the drug development process. On the other hand, FBDD has benefited from the application of computational methodologies, where the models derived from the quantitative structure-activity relationships (QSAR) have become consolidated tools.

OBJECTIVE: This mini-review focuses on the evolution and main applications of the QSAR paradigm in the context of FBDD in the last five years.

METHODS AND RESULTS: This report places particular emphasis on the QSAR models focused on fragment-based topological approaches to extract physicochemical and/or structural information, allowing to design potentially novel mono- or multi-target inhibitors from relatively large and heterogeneous databases. Here, we also discuss the need to apply multi-scale modeling, exemplifying how different datasets based on target inhibition can be simultaneously integrated and predicted together with other relevant endpoints such as the biological activity against non-biomolecular targets, as well as in vitro and in vivo toxicity and pharmacokinetic properties. In this context, seminal papers are briefly analyzed.

CONCLUSION: As huge amounts of data continue to accumulate in the domains of the chemical, biological and biomedical sciences, it has become clear that drug discovery must be viewed as a multi-scale optimization process. An ideal multi-scale approach should integrate diverse chemical and biological data and also serve as a knowledge generator, enabling the design of potentially optimal chemicals that may become therapeutic agents.},
}

@article {pmid31511073,
year = {2019},
author = {Honeycutt, RL and Proudfoot, GA and Silvy, NJ},
title = {Mitochondrial DNA variation of the ruffed grouse (Bonasa umbellus).},
journal = {BMC research notes},
volume = {12},
number = {1},
pages = {570},
doi = {10.1186/s13104-019-4607-3},
pmid = {31511073},
issn = {1756-0500},
support = {DEB 9615163//National Science Foundation/ ; },
mesh = {Animals ; Canada ; DNA, Mitochondrial/*genetics ; Galliformes/classification/*genetics ; Gene Frequency ; *Genetic Variation ; Geography ; Haplotypes ; Mitochondria/*genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA/methods ; United States ; },
abstract = {OBJECTIVE: The ruffed grouse, Bonasa umbellus, is broadly distributed across North America and displays considerable taxonomic diversity. Except for a genetic study of some western populations of ruffed grouse, nothing is known about genetic variation in other regions of Canada and the United States. Our objective is to examine patterns of mitochondrial DNA (mtDNA) variation in the ruffed grouse across western, central, and eastern parts of its distribution. We compare patterns of mtDNA variation to those characterized by morphology and ecology. Additionally, we evaluate the demographic history of the species based on mitochondrial haplotype diversity.

RESULTS: Patterns of mtDNA variation revealed geographic subdivision, with populations of ruffed grouse subdivided into 3 to 4 genetically distinct groups. This subdivision partially coincided with the ranges of described subspecies. Behavioral traits prohibiting long-distance movement and barriers to dispersal in response to physiography and unsuitable habitat help explain these patterns of subdivision. Historically, the ruffed grouse probably experienced a population expansion, possibly in response to changes during the Pleistocene.},
}

Animals
Canada
DNA, Mitochondrial/*genetics
Galliformes/classification/*genetics
Gene Frequency
*Genetic Variation
Geography
Haplotypes
Mitochondria/*genetics/metabolism
Phylogeny
Sequence Analysis, DNA/methods
United States

@article {pmid31482589,
year = {2019},
author = {Chen, J and Xia, L and Wang, W and Wang, Z and Hou, S and Xie, C and Cai, J and Lu, Y},
title = {Identification of a mitochondrial-targeting secretory protein from Nocardia seriolae which induces apoptosis in fathead minnow cells.},
journal = {Journal of fish diseases},
volume = {42},
number = {11},
pages = {1493-1507},
doi = {10.1111/jfd.13062},
pmid = {31482589},
issn = {1365-2761},
support = {2017A030313179//Natural Science Foundation of Guangdong Province/ ; 231419017//Research Projects of Guangdong Ocean University's Top-ranking Discipline Construction/ ; JCYJ20170306161613251//Shenzhen Science and Technology Project/ ; KY20160207//Shenzhen Dapeng New District special fund for industry development/ ; PT201901-06//Shenzhen Dapeng New District special fund for industry development/ ; C17377//Natural Science Foundation of Guangdong Ocean University/ ; C13454//Natural Science Foundation of Guangdong Ocean University/ ; },
mesh = {Amino Acid Sequence ; Animals ; *Apoptosis ; Bacterial Proteins/chemistry/genetics/immunology ; Base Sequence ; *Cyprinidae ; Fish Diseases/*immunology/microbiology ; Nocardia/*genetics ; Nocardia Infections/immunology/microbiology/*veterinary ; Phylogeny ; Sequence Alignment/veterinary ; Virulence Factors/*genetics/metabolism ; },
abstract = {Nocardia seriolae is the main pathogen responsible for fish nocardiosis. A mitochondrial-targeting secretory protein (MTSP) 3141 with an N-terminal transit peptide (TP) from N. seriolae was predicted by bioinformatic analysis based on the genomic sequence of the N. seriolae strain ZJ0503. However, the function of the MTSP3141 and its homologs remains totally unknown. In this study, mass spectrometry analysis of the extracellular products from N. seriolae proved that MTSP3141 was a secretory protein, subcellular localization research showed the MTSP3141-GFP fusion protein co-localized with mitochondria in fathead minnow (FHM) cells, the TP played an important role in mitochondria targeting, and only the TP located at N-terminus but not C-terminus can lead to mitochondria directing. Moreover, quantitative assays of mitochondrial membrane potential (ΔΨm) value, caspase-3 activity and apoptosis-related gene (Bcl-2, Bax, Bad, Bid and p53) mRNA expression suggested that cell apoptosis was induced in FHM cells by the overexpression of both MTSP3141 and MTSP3141ΔTP (with the N-terminal TP deleted) proteins. Taken together, the results of this study indicated that the MTSP3141 of N. seriolae was a secretory protein, might target mitochondria, induce apoptosis in host cells and function as a virulence factor.},
}

Amino Acid Sequence
Animals
*Apoptosis
Bacterial Proteins/chemistry/genetics/immunology
Base Sequence
*Cyprinidae
Fish Diseases/*immunology/microbiology
Nocardia/*genetics
Nocardia Infections/immunology/microbiology/*veterinary
Phylogeny
Sequence Alignment/veterinary
Virulence Factors/*genetics/metabolism

@article {pmid30909863,
year = {2019},
author = {Shaari, N'AL and Jaoi-Edward, M and Loo, SS and Salisi, MS and Yusoff, R and Ab Ghani, NI and Saad, MZ and Ahmad, H},
title = {Karyotypic and mtDNA based characterization of Malaysian water buffalo.},
journal = {BMC genetics},
volume = {20},
number = {1},
pages = {37},
doi = {10.1186/s12863-019-0741-0},
pmid = {30909863},
issn = {1471-2156},
mesh = {Animals ; Buffaloes/classification/*genetics ; *DNA, Mitochondrial ; Genetic Variation ; Haplotypes ; Karyotype ; *Karyotyping ; Malaysia ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: In Malaysia, the domestic water buffaloes (Bubalus bubalis) are classified into the swamp and the murrah buffaloes. Identification of these buffaloes is usually made via their phenotypic appearances. This study characterizes the subspecies of water buffaloes using karyotype, molecular and phylogenetic analyses. Blood of 105 buffaloes, phenotypically identified as swamp, murrah and crossbred buffaloes were cultured, terminated and harvested using conventional karyotype protocol to determine the number of chromosomes. Then, the D-loop of mitochondrial DNA of 10 swamp, 6 crossbred and 4 murrah buffaloes which were identified earlier by karyotyping were used to construct a phylogenetic tree was constructed.

RESULTS: Karyotypic analysis confirmed that all 93 animals phenotypically identified as swamp buffaloes with 48 chromosomes, all 7 as crossbreds with 49 chromosomes, and all 5 as murrah buffaloes with 50 chromosomes. The D-loop of mitochondrial DNA analysis showed that 10 haplotypes were observed with haplotype diversity of 0.8000 ± 0.089. Sequence characterization revealed 72 variables sites in which 67 were parsimony informative sites with sequence diversity of 0.01906. The swamp and murrah buffaloes clearly formed 2 different clades in the phylogenetic tree, indicating clear maternal divergence from each other. The crossbreds were grouped within the swamp buffalo clade, indicating the dominant maternal swamp buffalo gene in the crossbreds.

CONCLUSION: Thus, the karyotyping could be used to differentiate the water buffaloes while genotypic analysis could be used to characterize the water buffaloes and their crossbreds.},
}

Animals
Buffaloes/classification/*genetics
*DNA, Mitochondrial
Genetic Variation
Haplotypes
Karyotype
*Karyotyping
Malaysia
Mitochondria/genetics
Phylogeny
Polymerase Chain Reaction

@article {pmid32008087,
year = {2020},
author = {Zachar, I and Boza, G},
title = {Endosymbiosis before eukaryotes: mitochondrial establishment in protoeukaryotes.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-020-03462-6},
pmid = {32008087},
issn = {1420-9071},
support = {NKFI-K124438//National Research, Development, and Innovation Office/ ; GINOP-2.3.2-15-2016-00057//National Research, Development, and Innovation Office/ ; GINOP-2.3.2-15-2016-00057//National Research, Development, and Innovation Office/ ; },
abstract = {Endosymbiosis and organellogenesis are virtually unknown among prokaryotes. The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote-prokaryote endosymbioses as symbiosis is extremely common among prokaryotes, e.g., in biofilms. Therefore, it is even more precarious to draw conclusions about potentially existing (or once existing) prokaryotic endosymbioses based on a single example. It is yet unknown if the bacterial endosymbiont was captured by a prokaryote or by a (proto-)eukaryote, and if the process of internalization was parasitic infection, slow engulfment, or phagocytosis. In this review, we accordingly explore multiple mechanisms and processes that could drive the evolution of unicellular microbial symbioses with a special attention to prokaryote-prokaryote interactions and to the mitochondrion, possibly the single prokaryotic endosymbiosis that turned out to be a major evolutionary transition. We investigate the ecology and evolutionary stability of inter-species microbial interactions based on dependence, physical proximity, cost-benefit budget, and the types of benefits, investments, and controls. We identify challenges that had to be conquered for the mitochondrial host to establish a stable eukaryotic lineage. Any assumption about the initial interaction of the mitochondrial ancestor and its contemporary host based solely on their modern relationship is rather perilous. As a result, we warn against assuming an initial mutually beneficial interaction based on modern mitochondria-host cooperation. This assumption is twice fallacious: (i) endosymbioses are known to evolve from exploitative interactions and (ii) cooperativity does not necessarily lead to stable mutualism. We point out that the lack of evidence so far on the evolution of endosymbiosis from mutual syntrophy supports the idea that mitochondria emerged from an exploitative (parasitic or phagotrophic) interaction rather than from syntrophy.},
}

@article {pmid32003549,
year = {2020},
author = {Wesley, CC and Mishra, S and Levy, DL},
title = {Organelle size scaling over embryonic development.},
journal = {Wiley interdisciplinary reviews. Developmental biology},
volume = {},
number = {},
pages = {e375},
doi = {10.1002/wdev.376},
pmid = {32003549},
issn = {1759-7692},
support = {RSG-15-035-01-DDC//American Cancer Society/ ; P20GM103432/GM/NIGMS NIH HHS/United States ; R01GM113028/GM/NIGMS NIH HHS/United States ; R35GM134885/GM/NIGMS NIH HHS/United States ; },
abstract = {Cell division without growth results in progressive cell size reductions during early embryonic development. How do the sizes of intracellular structures and organelles scale with cell size and what are the functional implications of such scaling relationships? Model organisms, in particular Caenorhabditis elegans worms, Drosophila melanogaster flies, Xenopus laevis frogs, and Mus musculus mice, have provided insights into developmental size scaling of the nucleus, mitotic spindle, and chromosomes. Nuclear size is regulated by nucleocytoplasmic transport, nuclear envelope proteins, and the cytoskeleton. Regulators of microtubule dynamics and chromatin compaction modulate spindle and mitotic chromosome size scaling, respectively. Developmental scaling relationships for membrane-bound organelles, like the endoplasmic reticulum, Golgi, mitochondria, and lysosomes, have been less studied, although new imaging approaches promise to rectify this deficiency. While models that invoke limiting components and dynamic regulation of assembly and disassembly can account for some size scaling relationships in early embryos, it will be exciting to investigate the contribution of newer concepts in cell biology such as phase separation and interorganellar contacts. With a growing understanding of the underlying mechanisms of organelle size scaling, future studies promise to uncover the significance of proper scaling for cell function and embryonic development, as well as how aberrant scaling contributes to disease. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Early Embryonic Development > Fertilization to Gastrulation Comparative Development and Evolution > Model Systems.},
}

@article {pmid31679533,
year = {2019},
author = {Li, Y and Ma, XX and Lv, QB and Hu, Y and Qiu, HY and Chang, QC and Wang, CR},
title = {Characterization of the complete mitochondrial genome sequence of Tracheophilus cymbius (Digenea), the first representative from the family Cyclocoelidae.},
journal = {Journal of helminthology},
volume = {94},
number = {},
pages = {e101},
doi = {10.1017/S0022149X19000932},
pmid = {31679533},
issn = {1475-2697},
mesh = {Animals ; Base Sequence ; Genome, Helminth ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Trematoda/classification/*genetics/isolation & purification ; },
abstract = {Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1-3, nad 1-6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.},
}

Animals
Base Sequence
Genome, Helminth
*Genome, Mitochondrial
Mitochondria/genetics
Phylogeny
Sequence Analysis, DNA
Trematoda/classification/*genetics/isolation & purification

@article {pmid31648074,
year = {2020},
author = {Wu, H and Li, R and Liu, Y and Zhang, X and Zhang, J and Ma, E},
title = {A second intracellular copper/zinc superoxide dismutase and a manganese superoxide dismutase in Oxya chinensis: Molecular and biochemical characteristics and roles in chlorpyrifos stress.},
journal = {Ecotoxicology and environmental safety},
volume = {187},
number = {},
pages = {109830},
doi = {10.1016/j.ecoenv.2019.109830},
pmid = {31648074},
issn = {1090-2414},
mesh = {Animals ; Chlorpyrifos/*metabolism ; Copper/metabolism ; Grasshoppers/classification/*enzymology ; Insect Proteins/chemistry/genetics/metabolism/*physiology ; Manganese/metabolism ; Metals, Heavy/*metabolism ; Phylogeny ; Superoxide Dismutase/chemistry/genetics/metabolism/*physiology ; Zinc/metabolism ; },
abstract = {A second intracellular copper/zinc superoxide dismutase (icCuZnSOD2) and manganese SOD (MnSOD) were cloned and characterized in Oxya chinensis. The open reading frame (ORF) of OcicCuZnSOD2 and OcMnSOD are 462 and 672 bp encoding 153 and 223 amino acids, respectively. OcicCuZnSOD2 contains two signature sequences, one potential N-glycosylation site, and seven copper/zinc binding sites. OcMnSOD includes a mitochondria targeting sequence of 7 amino acids at N-terminal, one signature sequence, two N-glycosylation sites, and four manganese binding sites. The secondary structure and homology model of OcicCuZnSOD2 include nine β sheets, two Greek-key motifs, and one electrostatic loop. OcMnSOD contains nine α-helices and three β-sheets. Phylogenetic analysis shows that OcMnSOD is evolutionarily conserved while OcicCuZnSOD2 may be gene duplication and is paralogous to OcicCuZnSOD1. OcMnSOD expressed widely in all tissues and developmental stages. OcicCuZnSOD2 showed testis-specific expression and expressed highest in the 5th-instar nymph and the adult. The optimum temperatures and pH values of the recombinant OcicCuZnSOD2 and OcMnSOD were 40 °C and 8.0. They were stable at 25-55 °C and at pH 5.0-12.0 and pH 6.0-12.0, respectively. The activity and mRNA expression of each OcSOD were assayed after chlorpyrifos treatments. Total SOD and CuZnSOD activities first increased then declined under chlorpyrifos stress. Chlorpyrifos induced the mRNA expression and activity of OcMnSOD as a dose-dependent manner and inhibited OcicCuZnSOD2 transcription. The role of each OcSOD gene in chlorpyrifos stress was investigated using RNAi and disc diffusion assay with Escherichia coli overexpressing OcSOD proteins. Silencing of OcMnSOD significantly increased ROS content in chlorpyrifos-exposed grasshoppers. Disc diffusion assay showed that the plates with E. coli overexpressing OcMnSOD had the smaller inhibition zones around the chlorpyrifos-soaked filter discs. These results implied that OcMnSOD played a significant role in defense chlorpyrifos-induced oxidative stress.},
}

Animals
Chlorpyrifos/*metabolism
Copper/metabolism
Grasshoppers/classification/*enzymology
Insect Proteins/chemistry/genetics/metabolism/*physiology
Manganese/metabolism
Metals, Heavy/*metabolism
Phylogeny
Superoxide Dismutase/chemistry/genetics/metabolism/*physiology
Zinc/metabolism

@article {pmid30761963,
year = {2019},
author = {Santacruz, A and Ornelas-García, CP and Pérez-Ponce de León, G},
title = {Diversity of Rhabdochona mexicana (Nematoda: Rhabdochonidae), a parasite of Astyanax spp. (Characidae) in Mexico and Guatemala, using mitochondrial and nuclear genes, with the description of a new species.},
journal = {Journal of helminthology},
volume = {94},
number = {},
pages = {e34},
doi = {10.1017/S0022149X19000014},
pmid = {30761963},
issn = {1475-2697},
mesh = {Animals ; Cell Nucleus/*genetics ; Characidae/*parasitology ; Fish Diseases/*parasitology ; Guatemala ; Helminth Proteins/genetics ; Mexico ; Mitochondria/*genetics ; Phylogeny ; Spirurida Infections/parasitology/*veterinary ; Spiruroidea/classification/genetics/growth & development/*isolation & purification ; },
abstract = {Among fish parasitic nematodes Rhabdochona is one of the most speciose genera, with c. 100 species. Twelve congeneric species occur in Mexican freshwater fishes, in a region located between the Nearctic and Neotropical biogeographical regions. Host association and biogeographical history have determined the high species richness of Rhabdochona in Mexico. One of these species, Rhabdochona mexicana, is highly specific to the characid genus Astyanax. Characids are a group of freshwater fish with Neotropical affinity. In this paper, we explore the genetic diversity of R. mexicana through samples obtained from populations of Astyanax spp. across river basins of Mexico and Guatemala. Sequences of one mitochondrial and two ribosomal genes were obtained from 38 individuals and analysed using Maximum Likelihood and Bayesian Inference analysis. Phylogenetic analyses using cox1, and a concatenated alignment of 18S + 28S + cox1 recovered two genetic lineages. One of them corresponded with R. mexicana sensu stricto; this lineage included three reciprocally monophyletic subgroups; the other lineage was highly divergent and represented a putative candidate species. A detailed morphological study was conducted to corroborate the molecular findings. We describe a new species herein and discuss the implications of using molecular tools to increase our knowledge about the diversity of a speciose genus such as Rhabdochona.},
}

Animals
Cell Nucleus/*genetics
Characidae/*parasitology
Fish Diseases/*parasitology
Guatemala
Helminth Proteins/genetics
Mexico
Mitochondria/*genetics
Phylogeny
Spirurida Infections/parasitology/*veterinary
Spiruroidea/classification/genetics/growth & development/*isolation & purification

@article {pmid31486889,
year = {2019},
author = {Wang, J and Gao, X and Zheng, X and Hou, C and Xie, Q and Lou, B and Zhu, J},
title = {Expression and potential functions of KIF3A/3B to promote nuclear reshaping and tail formation during Larimichthys polyactis spermiogenesis.},
journal = {Development genes and evolution},
volume = {229},
number = {5-6},
pages = {161-181},
pmid = {31486889},
issn = {1432-041X},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Nucleus/metabolism ; Cloning, Molecular ; Fish Proteins/chemistry/genetics/*metabolism ; Fishes/*physiology ; Humans ; Kinesin/chemistry/genetics/*metabolism ; Male ; Phylogeny ; Sequence Alignment ; *Spermatogenesis ; Spermatozoa/*cytology/metabolism ; },
abstract = {KIF3A and KIF3B are homologous motor subunits of the Kinesin II protein family. KIF3A, KIF3B, and KAP3 form a heterotrimeric complex and play a significant role in spermatogenesis. Here, we first cloned full-length kif3a/3b cDNAs from Larimichthys polyactis. Lp-kif3a/3b are highly related to their homologs in other animals. The proteins are composed of three domains, an N-terminal head domain, a central stalk domain, and a C-terminus tail domain. Lp-kif3a/3b mRNAs were found to be ubiquitously expressed in the examined tissues, with high expression in the testis. Fluorescence in situ hybridization (FISH) was used to analyze the expression of Lp-kif3a/3b mRNAs during spermiogenesis. The results showed that Lp-kif3a/3b mRNAs had similar expression pattern and were continuously expressed during spermiogenesis. From middle spermatid to mature sperm, Lp-kif3a/3b mRNAs gradually localized to the side of the spermatid where the midpiece and tail form. In addition, we used immunofluorescence (IF) to observe that Lp-KIF3A protein co-localizes with tubulin during spermiogenesis. In early spermatid, Lp-KIF3A protein and microtubule signals were randomly distributed in the cytoplasm. In middle spermatid, however, the protein was detected primarily around the nucleus. In late spermatid, the protein migrated primarily to one side of the nucleus where the tail forms. In mature sperm, Lp-KIF3A and microtubules accumulated in the midpiece. Moreover, Lp-KIF3A co-localized with the mitochondria. In mature sperm, Lp-KIF3A and mitochondria were present in the midpiece. Therefore, Lp-KIF3A/KIF3B may be involved in spermiogenesis in L. polyactis, particularly during nuclear reshaping and tail formation.},
}

Amino Acid Sequence
Animals
Base Sequence
Cell Nucleus/metabolism
Cloning, Molecular
Fish Proteins/chemistry/genetics/*metabolism
Fishes/*physiology
Humans
Kinesin/chemistry/genetics/*metabolism
Male
Phylogeny
Sequence Alignment
*Spermatogenesis
Spermatozoa/*cytology/metabolism

@article {pmid31192351,
year = {2019},
author = {Zhang, D and Zou, H and Hua, CJ and Li, WX and Mahboob, S and Al-Ghanim, KA and Al-Misned, F and Jakovlić, I and Wang, GT},
title = {Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda.},
journal = {Genome biology and evolution},
volume = {11},
number = {7},
pages = {1797-1812},
doi = {10.1093/gbe/evz121},
pmid = {31192351},
issn = {1759-6653},
mesh = {Algorithms ; Animals ; Genome, Mitochondrial/*genetics ; Isopoda/*genetics ; Mitochondria/*genetics ; Mutation/genetics ; Phylogeny ; },
abstract = {The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.},
}

Algorithms
Animals
Genome, Mitochondrial/*genetics
Isopoda/*genetics
Mitochondria/*genetics
Mutation/genetics
Phylogeny