@article {pmid32615754,
year = {2020},
author = {Zhu, X and Liu, G and Bu, Y and Zhang, J and Wang, L and Tian, Y and Yu, J and Wu, Z and Zhou, H},
title = {In-situ Monitoring of Mitochondria Regulating Cell Viability by the RNA-specific Fluorescent Photosensitizer.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.0c02298},
pmid = {32615754},
issn = {1520-6882},
abstract = {Cell viability is greatly affected by external stimulus eliciting correlated dynamical physiological processes for cells to choose survival or death. A few fluorescent probes have been designed to detect whether the cell is in survival state or apoptotic state, but monitoring the regulation process of the cell undergoing survival to death remains a long-standing challenge. Herein, we highlight the in-situ monitor of mitochondria regulating the cell viability by the RNA-specific fluorescent photosensitizer L. At normal conditions, L anchored mitochondria and interacted with mito-RNA to light up the mitochondria with red fluorescence. With external light stimulus, L generated reactive oxide species (ROS) and cause damage to mitochondria, which activated mitochondrial autophagy to prevent death, during which the red fluorescence of L witnessed dynamical distribution in accordance with the evolution of vacuole structures containing damaged mitochondria into autophagosomes. However, with ROS continuously increasing, the mitochondrial apoptosis was eventually commenced and L with red fluorescent was gradually accumulated in the nucleoli, indicating the programmed cell death. This work demonstrated how the delicate balance between survival and death are regulated by mitochondria.},
}

@article {pmid32612534,
year = {2020},
author = {Noiret, A and Puch, L and Riffaud, C and Costantini, D and Riou, JF and Aujard, F and Terrien, J},
title = {Sex-Specific Response to Caloric Restriction After Reproductive Investment in Microcebus murinus: An Integrative Approach.},
journal = {Frontiers in physiology},
volume = {11},
number = {},
pages = {506},
doi = {10.3389/fphys.2020.00506},
pmid = {32612534},
issn = {1664-042X},
abstract = {In seasonal environments, males and females usually maintain high metabolic activity during the whole summer season, exhausting their energy reserves. In the global warming context, unpredictability of food availability during summer could dramatically challenge the energy budget of individuals. Therefore, one can predict that resilience to environmental stress would be dramatically endangered during summer. Here, we hypothesized that females could have greater capacity to survive harsh conditions than males, considering the temporal shift in their respective reproductive energy investment, which can challenge them differently, as well as enhanced flexibility in females' physiological regulation. We tackled this question on the gray mouse lemur (Microcebus murinus), focusing on the late summer period, after the reproductive effort. We monitored six males and six females before and after a 2-weeks 60% caloric restriction (CR), measuring different physiological and cellular parameters in an integrative and comparative multiscale approach. Before CR, females were heavier than males and mostly characterized by high levels of energy expenditure, a more energetic mitochondrial profile and a downregulation of blood antioxidants. We observed a similar energy balance between sexes due to CR, with a decrease in metabolic activity over time only in males. Oxidative damage to DNA was also reduced by different pathways between sexes, which may reflect variability in their physiological status and life-history traits at the end of summer. Finally, females' mitochondria seemed to exhibit greater flexibility and greater metabolic potential than males in response to CR. Our results showed strong differences between males and females in response to food shortage during late summer, underlining the necessity to consider sex as a factor for population dynamics in climate change models.},
}

@article {pmid32605521,
year = {2020},
author = {Keaney, TA and Wong, HWS and Dowling, DK and Jones, TM and Holman, L},
title = {Sibling rivalry versus mother's curse: can kin competition facilitate a response to selection on male mitochondria?.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1930},
pages = {20200575},
doi = {10.1098/rspb.2020.0575},
pmid = {32605521},
issn = {1471-2954},
abstract = {Assuming that fathers never transmit mitochondrial DNA (mtDNA) to their offspring, mitochondrial mutations that affect male fitness are invisible to direct selection on males, leading to an accumulation of male-harming alleles in the mitochondrial genome (mother's curse). However, male phenotypes encoded by mtDNA can still undergo adaptation via kin selection provided that males interact with females carrying related mtDNA, such as their sisters. Here, using experiments with Drosophila melanogaster carrying standardized nuclear DNA but distinct mitochondrial DNA, we test whether the mitochondrial haplotype carried by interacting pairs of larvae affects survival to adulthood, as well as the fitness of the adults. Although mtDNA had no detectable direct or indirect genetic effect on larva-to-adult survival, the fitness of male and female adults was significantly affected by their own mtDNA and the mtDNA carried by their social partner in the larval stage. Thus, mtDNA mutations that alter the effect of male larvae on nearby female larvae (which often carry the same mutation, due to kinship) could theoretically respond to kin selection. We discuss the implications of our findings for the evolution of mitochondria and other maternally inherited endosymbionts.},
}

@article {pmid32601224,
year = {2020},
author = {Wu, Z and Waneka, G and Broz, AK and King, CR and Sloan, DB},
title = {MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.2001998117},
pmid = {32601224},
issn = {1091-6490},
abstract = {Mitochondrial and plastid genomes in land plants exhibit some of the slowest rates of sequence evolution observed in any eukaryotic genome, suggesting an exceptional ability to prevent or correct mutations. However, the mechanisms responsible for this extreme fidelity remain unclear. We tested seven candidate genes involved in cytoplasmic DNA replication, recombination, and repair (POLIA, POLIB, MSH1, RECA3, UNG, FPG, and OGG1) for effects on mutation rates in the model angiosperm Arabidopsis thaliana by applying a highly accurate DNA sequencing technique (duplex sequencing) that can detect newly arisen mitochondrial and plastid mutations even at low heteroplasmic frequencies. We find that disrupting MSH1 (but not the other candidate genes) leads to massive increases in the frequency of point mutations and small indels and changes to the mutation spectrum in mitochondrial and plastid DNA. We also used droplet digital PCR to show transmission of de novo heteroplasmies across generations in msh1 mutants, confirming a contribution to heritable mutation rates. This dual-targeted gene is part of an enigmatic lineage within the mutS mismatch repair family that we find is also present outside of green plants in multiple eukaryotic groups (stramenopiles, alveolates, haptophytes, and cryptomonads), as well as certain bacteria and viruses. MSH1 has previously been shown to limit ectopic recombination in plant cytoplasmic genomes. Our results point to a broader role in recognition and correction of errors in plant mitochondrial and plastid DNA sequence, leading to greatly suppressed mutation rates perhaps via initiation of double-stranded breaks and repair pathways based on faithful homologous recombination.},
}

@article {pmid31978488,
year = {2020},
author = {Souza, DS and Marinoni, L and Monné, ML and Gómez-Zurita, J},
title = {Molecular phylogenetic assessment of the tribal classification of Lamiinae (Coleoptera: Cerambycidae).},
journal = {Molecular phylogenetics and evolution},
volume = {145},
number = {},
pages = {106736},
doi = {10.1016/j.ympev.2020.106736},
pmid = {31978488},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Coleoptera/*classification ; Electron Transport Complex IV/genetics ; Insect Proteins/chemistry/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Ribosome Subunits, Large/genetics ; },
abstract = {Lamiinae is the most diverse subfamily of longhorned beetles, with about 20,000 described species classified into 80 tribes. Most of the tribes of Lamiinae were proposed during the 19th century and the suprageneric classification of the subfamily has never been assessed under phylogenetic criteria. In this study, we present the first tribal-level phylogeny of Lamiinae, inferred from 130 terminals (representing 46 tribes, prioritizing generic type species of the tribes) and fragments of two mitochondrial and three nuclear markers (cox1, rrnL, Wg, CPS and LSU; 5,024 aligned positions in total). Analyses were performed under Maximum Likelihood and Bayesian methods based on two datasets: a dataset including all taxa available for the study, and a reduced dataset with 111 terminals where taxa only contributing with mitochondrial markers were excluded from the matrix. The monophyly of Lamiinae was corroborated in three of the four analyses and 11 of the 35 tribes with more than one species represented in the analyses were consistently recovered as monophyletic. However, 15 tribes were not retrieved as monophyletic, requiring a revision of their boundaries: Acanthocinini, Acanthoderini, Agapanthiini, Apomecynini, Desmiphorini, Dorcaschematini, Enicodini, Hemilophini, Monochamini, Onciderini, Parmenini, Phytoeciini, Pogonocherini, Pteropliini and Saperdini. Based on these results, when strong support values for paraphyly were recovered, we argue a number of tribe synonymies, including Moneilemini as synonym of Acanthocinini; Onocephalini of Onciderini; Dorcadionini, Gnomini, Monochamini and Rhodopinini of Lamiini; and Obereini and Phytoeciini of Saperdini. Other taxonomic changes proposed in this study based on the criterion of monophyly and supported by morphological characters include the transfer of Tricondyloides and Stenellipsis to Enicodini, and of Dylobolus stat. rest., which is removed as subgenus of Mecas and restituted as genus, to Hemilophini. Furthermore, our analyses suggest that Ostedes and Neohoplonotus should be removed from Acanthocinini and Parmenini, respectively, and Colobotheini should be redefined to encompass several genera currently placed in Acanthocinini.},
}

Animals
Bayes Theorem
Coleoptera/*classification
Electron Transport Complex IV/genetics
Insect Proteins/chemistry/genetics
Likelihood Functions
Mitochondria/genetics
Phylogeny
Ribosome Subunits, Large/genetics

@article {pmid31972240,
year = {2020},
author = {Chang, H and Qiu, Z and Yuan, H and Wang, X and Li, X and Sun, H and Guo, X and Lu, Y and Feng, X and Majid, M and Huang, Y},
title = {Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types.},
journal = {Molecular phylogenetics and evolution},
volume = {145},
number = {},
pages = {106734},
doi = {10.1016/j.ympev.2020.106734},
pmid = {31972240},
issn = {1095-9513},
mesh = {Animals ; Biodiversity ; *Biological Evolution ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Orthoptera/anatomy & histology/*classification/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Wings, Animal/anatomy & histology ; },
abstract = {Orthoptera is the most diverse order of polyneopterans, and the forewing and hindwing of its members exhibit extremely variability from full length to complete loss in many groups; thus, this order provides a good model for studying the effects of insect flight ability on the evolutionary constraints on and evolutionary rate of the mitochondrial genome. Based on a data set of mitochondrial genomes from 171 species, including 43 newly determined, we reconstructed Orthoptera phylogenetic relationships and estimated the divergence times of this group. The results supported Caelifera and Ensifera as two monophyletic groups, and revealed that Orthoptera originated in the Carboniferous (298.997 Mya). The date of divergence between the suborders Caelifera and Ensifera was 255.705 Mya, in the late Permian. The major lineages of Acrididae seemed to have radiated in the Cenozoic, and the six patterns of rearrangement of 171 Orthoptera mitogenomes mostly occurred in the Cretaceous and Cenozoic. Based on phylogenetic relationships and ancestral state reconstruction, we analysed the evolutionary selection pressure on and evolutionary rate of mitochondrial protein-coding genes (mPCGs). The results indicated that during approximately 300 Mya of evolution, these genes experienced purifying selection to maintain their function. Flightless orthopteran insects accumulated more non-synonymous mutations than flying species and experienced more relaxed evolutionary constraints. The different wing types had different evolutionary rates, and the mean evolutionary rate of Orthoptera mitochondrial mPCGs was 13.554 × 10-9 subs/s/y. The differences in selection pressures and evolutionary rates observed between the mitochondrial genomes suggested that functional constraints due to locomotion play an important role in the evolution of mitochondrial DNA in orthopteran insects with different wing types.},
}

Animals
Biodiversity
*Biological Evolution
Mitochondria/*genetics
Open Reading Frames/genetics
Orthoptera/anatomy & histology/*classification/genetics
Phylogeny
RNA, Ribosomal/genetics
Wings, Animal/anatomy & histology

@article {pmid31931136,
year = {2020},
author = {Gautério, TB and Machado, S and Loreto, ELDS and Gottschalk, MS and Robe, LJ},
title = {Phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica (Diptera, Drosophilidae), with insights into the evolution of breeding sites usage.},
journal = {Molecular phylogenetics and evolution},
volume = {145},
number = {},
pages = {106733},
doi = {10.1016/j.ympev.2020.106733},
pmid = {31931136},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Breeding ; Cell Nucleus/genetics ; Dopa Decarboxylase/classification/genetics ; Drosophila/genetics ; Drosophilidae/*classification/genetics/growth & development ; Electron Transport Complex IV/classification/genetics ; Fungi/*physiology ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The Neotropical region harbors an astonishing diversity of species, but still encompasses the least studied biogeographic region of the world. These properties apply for different taxonomic groups, and can be exemplified by drosophilids. In fact, high levels of cryptic diversity have recently been discovered for Neotropical species of the Zygothrica genus group, but relationships among these species, or them and other Drosophilidae species still remains to be addressed. Therefore, the aim of this study was to evaluate the phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica, which together with Paramycodrosophila and Paraliodrosophila compose the Zygothrica genus group. For this, fragments of the mitochondrial cytochrome oxidase subunits I (COI) and II (COII) genes, and the nuclear alpha methyldopa (Amd) and dopa decarboxylase (Ddc) genes were newly characterized for 43 Neotropical specimens of fungus-associated drosophilids, and analyzed in the context of 51 additional Drosophilinae sequences plus one Steganinae outgroup. Based on the resulting phylogeny, the evolution of breeding sites usage was also evaluated through ancestral character reconstructions. Our results revealed the Zygothrica genus group as a monophyletic lineage of Drosophila that branches after the subgenera Sophophora and Drosophila. Within this lineage, Mycodrosophila species seem to encompass the early offshoot, followed by a grade of Hirtodrosophila species, with derived branches mostly occupied by representatives of Zygothrica. This genus, in particular, was subdivided into five major clades, two of which include species of Hirtodrosophila, whose generic status needs to be reevatuated. According to our results, the use of fungi as breeding sites encompasses a symplesiomorphy for the Zygothrica genus group, since one of the recovered clades is currently specialized in using flowers as breeding sites whereas a sole species presents a reversal to the use of fruits of a plant of Gentianales. So, in general, this study supports the paraphyly of Drosophila in relation to fungus-associated Neotropical species of Drosophilidae, providing the first molecular insights into the phylogenetic patterns related to the evolution of this diverse group of species and some of its characteristic traits.},
}

Animals
Bayes Theorem
Biological Evolution
Breeding
Cell Nucleus/genetics
Dopa Decarboxylase/classification/genetics
Drosophila/genetics
Drosophilidae/*classification/genetics/growth & development
Electron Transport Complex IV/classification/genetics
Fungi/*physiology
Mitochondria/genetics
Phylogeny

@article {pmid31904510,
year = {2020},
author = {Kaczmarek, Ł and Roszkowska, M and Poprawa, I and Janelt, K and Kmita, H and Gawlak, M and Fiałkowska, E and Mioduchowska, M},
title = {Integrative description of bisexual Paramacrobiotus experimentalis sp. nov. (Macrobiotidae) from republic of Madagascar (Africa) with microbiome analysis.},
journal = {Molecular phylogenetics and evolution},
volume = {145},
number = {},
pages = {106730},
doi = {10.1016/j.ympev.2019.106730},
pmid = {31904510},
issn = {1095-9513},
mesh = {Animals ; Bacteroides/genetics/isolation & purification ; DNA, Bacterial/chemistry/metabolism ; Electron Transport Complex IV/classification/genetics ; Female ; Madagascar ; Male ; *Microbiota ; Mitochondria/genetics ; Phylogeny ; Proteobacteria/genetics/isolation & purification ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 18S/classification/genetics ; Symbiosis ; Tardigrada/*classification/genetics/microbiology ; },
abstract = {In a moss samples collected on Madagascar two populations of Paramacrobiotus experimentalis sp. nov. were found. Paramacrobiotus experimentalis sp. nov. with the presence of a microplacoid and areolatus type of eggs is similar to Pam. danielae, Pam. garynahi, Pam. hapukuensis, Pam. peteri, Pam. rioplatensis and Pam. savai, but it differs from them by some morphological and morphometric characters of the eggs. The p-distance between two COI haplotypes of Pam. experimentalis sp. nov. was 0.17%. In turn, the ranges of uncorrected genetic p-distances of all Paramacrobiotus species available in GenBank was from 18.27% (for Pam. lachowskae) to 25.26% (for Pam. arduus) with an average distance of 20.67%. We also found that Pam. experimentalis sp. nov. is bisexual. This observation was congruent on three levels: (i) morphological - specimen size dimorphism; (ii) structural (primary sexual characteristics) - females have an unpaired ovary while males have an unpaired testis and (iii) molecular - heterozygous and homozygous strains of the ITS-2 marker. Although symbiotic associations of hosts with bacteria (including endosymbiotic bacteria) are common in nature and these interactions exert various effects on the evolution, biology and reproductive ecology of hosts, there is still very little information on the bacterial community associated with tardigrades. To fill this gap and characterise the bacterial community of Pam. experimentalis sp. nov. populations and microbiome of its microhabitat, high throughput sequencing of the V3-V4 hypervariable regions in the bacterial 16S rRNA gene fragment was performed. The obtained 16S rRNA gene sequences ranged from 92,665 to 131,163. In total, 135 operational taxonomic units (OTUs) were identified across the rarefied dataset. Overall, both Pam. experimentalis sp. nov. populations were dominated by OTUs ascribed to the phylum Proteobacteria (89-92%) and Firmicutes (6-7%). In the case of samples from tardigrades' laboratory habitat, the most abundant bacterial phylum was Proteobacteria (51-90%) and Bacteroides (9-48%). In all compared microbiome profiles, only 16 of 137 OTUs were shared. We found also significant differences in beta diversity between the partly species-specific microbiome of Pam. experimentalis sp. nov. and its culturing environment. Two OTUs belonging to a putative bacterial endosymbiont were identified - Rickettsiales and Polynucleobacter. We also demonstrated that each bacterial community was rich in genes involved in membrane transport, amino acid metabolism, and carbohydrate metabolism.},
}

Animals
Bacteroides/genetics/isolation & purification
DNA, Bacterial/chemistry/metabolism
Electron Transport Complex IV/classification/genetics
Female
Madagascar
Male
*Microbiota
Mitochondria/genetics
Phylogeny
Proteobacteria/genetics/isolation & purification
RNA, Ribosomal, 16S/chemistry/genetics
RNA, Ribosomal, 18S/classification/genetics
Symbiosis
Tardigrada/*classification/genetics/microbiology

@article {pmid31857199,
year = {2020},
author = {Jardim de Queiroz, L and Cardoso, Y and Jacot-des-Combes, C and Bahechar, IA and Lucena, CA and Rapp Py-Daniel, L and Sarmento Soares, LM and Nylinder, S and Oliveira, C and Parente, TE and Torrente-Vilara, G and Covain, R and Buckup, P and Montoya-Burgos, JI},
title = {Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus.},
journal = {Molecular phylogenetics and evolution},
volume = {145},
number = {},
pages = {106711},
doi = {10.1016/j.ympev.2019.106711},
pmid = {31857199},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Membrane Proteins/genetics ; Mitochondria/genetics ; Nerve Tissue Proteins/genetics ; Phylogeny ; Species Specificity ; },
abstract = {With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.},
}

Animals
Bayes Theorem
Catfishes/*classification/genetics
DNA Barcoding, Taxonomic
Electron Transport Complex IV/genetics
*Evolution, Molecular
Membrane Proteins/genetics
Mitochondria/genetics
Nerve Tissue Proteins/genetics
Phylogeny
Species Specificity

@article {pmid32581834,
year = {2020},
author = {Mannella, CA},
title = {Consequences of Folding the Mitochondrial Inner Membrane.},
journal = {Frontiers in physiology},
volume = {11},
number = {},
pages = {536},
doi = {10.3389/fphys.2020.00536},
pmid = {32581834},
issn = {1664-042X},
abstract = {A fundamental first step in the evolution of eukaryotes was infolding of the chemiosmotic membrane of the endosymbiont. This allowed the proto-eukaryote to amplify ATP generation while constraining the volume dedicated to energy production. In mitochondria, folding of the inner membrane has evolved into a highly regulated process that creates specialized compartments (cristae) tuned to optimize function. Internalizing the inner membrane also presents complications in terms of generating the folds and maintaining mitochondrial integrity in response to stresses. This review describes mechanisms that have evolved to regulate inner membrane topology and either preserve or (when appropriate) rupture the outer membrane.},
}

@article {pmid32580582,
year = {2020},
author = {Nesci, S and Pagliarani, A and Algieri, C and Trombetti, F},
title = {Mitochondrial F-type ATP synthase: multiple enzyme functions revealed by the membrane-embedded FO structure.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/10409238.2020.1784084},
pmid = {32580582},
issn = {1549-7798},
abstract = {Of the two main sectors of the F-type ATP synthase, the membrane-intrinsic FO domain is the one which, during evolution, has undergone the highest structural variations and changes in subunit composition. The FO complexity in mitochondria is apparently related to additional enzyme functions that lack in bacterial and thylakoid complexes. Indeed, the F-type ATP synthase has the main bioenergetic role to synthesize ATP by exploiting the electrochemical gradient built by respiratory complexes. The FO membrane domain, essential in the enzyme machinery, also participates in the bioenergetic cost of synthesizing ATP and in the formation of the cristae, thus contributing to mitochondrial morphology. The recent enzyme involvement in a high-conductance channel, which forms in the inner mitochondrial membrane and promotes the mitochondrial permeability transition, highlights a new F-type ATP synthase role. Point mutations which cause amino acid substitutions in FO subunits produce mitochondrial dysfunctions and lead to severe pathologies. The FO variability in different species, pointed out by cryo-EM analysis, mirrors the multiple enzyme functions and opens a new scenario in mitochondrial biology.},
}

@article {pmid32039475,
year = {2020},
author = {Donin, LM and Ferrer, J and Carvalho, TP},
title = {Taxonomical study of Trichomycterus (Siluriformes: Trichomycteridae) from the Ribeira de Iguape River basin reveals a new species recorded in the early 20th century.},
journal = {Journal of fish biology},
volume = {96},
number = {4},
pages = {886-904},
doi = {10.1111/jfb.14278},
pmid = {32039475},
issn = {1095-8649},
support = {//CNPq/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Animals ; Brazil ; Catfishes/anatomy & histology/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Rivers ; Species Specificity ; },
abstract = {A new species of Trichomycterus endemic to the Ribeira de Iguape River basin, southeastern Brazil, was studied based on morphological and molecular evidence. This species had an outer layer of coloration composed of scattered, round, black or dark-brown spots smaller or equivalent in size to the circumference of the eye; eight pectoral-fin rays; 28-29 opercular odontodes; 54-56 interopercular odontodes; and supraorbital line of the laterosensory system not interrupted, with pores s2 absent. Two other species of Trichomycterus from the Ribeira de Iguape River basin are recorded, and their taxonomic status is discussed: Trichomycterus alternatus and Trichomycterus jacupiranga were not differentiated using molecular analysis but may be consistently distinguished based on morphology. The phylogenetic relationships of the co-occurring species, T. alternatus and Cambeva zonata, were inferred using mitochondrial data, reinforcing the taxonomic status of these recently revised species that have a complex taxonomy. In addition, a new combination for Trichomycterus taroba with its inclusion in the genus Cambeva is recommended.},
}

Animals
Brazil
Catfishes/anatomy & histology/*classification/genetics
Mitochondria/genetics
*Phylogeny
Rivers
Species Specificity

@article {pmid31758495,
year = {2020},
author = {Magallón-Gayón, E and Del Río-Portilla, MÁ and de Los Angeles Barriga-Sosa, I},
title = {The complete mitochondrial genomes of two octopods of the eastern Pacific Ocean: Octopus mimus and 'Octopus' fitchi (Cephalopoda: Octopodidae) and their phylogenetic position within Octopoda.},
journal = {Molecular biology reports},
volume = {47},
number = {2},
pages = {943-952},
pmid = {31758495},
issn = {1573-4978},
support = {UAM-147.09.01//Universidad Autónoma Metropolitana (MX)/ ; 04//Universidad Autónoma Metropolitana (MX)/ ; 07//Universidad Autónoma Metropolitana (MX)/ ; 14713349//SEP-PRODEP/ ; },
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/*genetics ; Gene Order ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Octopodiformes/*genetics ; Open Reading Frames ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; },
abstract = {The complete mitochondrial genomes of two important octopus species from the eastern Pacific were sequenced, obtaining their complete nucleotide sequences. Octopus mimus is the most important commercially catched species along the eastern Pacific, from Mexico to Chile, whereas 'Octopus' fitchi is a pigmy species with uncertain taxonomic genus. The mitogenomes of Octopus mimus and 'Octopus' fitchi were 15,696 and 15,780 base pairs (bp) in length with an A + T composition of 75.5% and 75.8%, respectively. Each genome contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, as well as a control region. Gene order is maintained as reported for other species of the Octopodidae. The phylogenetic analysis based on the concatenated thirteen protein-coding genes confirms that O. mimus belongs to the genus Octopus, which is supported by the genetic distance (11-16%) whereas the position of 'O'. fitchi within this group it is not supported. The analysis also indicated that the phylogenetic position of 'O'. fitchi is closer to Callistoctopus than to the Cistopus or the Amphioctopus clades. Based on the tree topology and the high genetic distance observed (24-25%), we suggest that 'O'. fitchi might represent a different genus.},
}

Animals
Base Composition/genetics
Base Sequence/genetics
DNA, Mitochondrial/*genetics
Gene Order
Genome, Mitochondrial/*genetics
Mitochondria/genetics
Octopodiformes/*genetics
Open Reading Frames
Pacific Ocean
Phylogeny
RNA, Ribosomal/genetics
RNA, Transfer/genetics

@article {pmid31299243,
year = {2020},
author = {Montava-Garriga, L and Ganley, IG},
title = {Outstanding Questions in Mitophagy: What We Do and Do Not Know.},
journal = {Journal of molecular biology},
volume = {432},
number = {1},
pages = {206-230},
doi = {10.1016/j.jmb.2019.06.032},
pmid = {31299243},
issn = {1089-8638},
support = {MC_UU_00018/2/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Autophagy/genetics ; *Biological Evolution ; Homeostasis/genetics ; Humans ; Mitochondria/*genetics ; Mitophagy/*genetics ; Signal Transduction/genetics ; },
abstract = {The elimination of mitochondria via autophagy, termed mitophagy, is an evolutionarily conserved mechanism for mitochondrial quality control and homeostasis. Mitophagy, therefore, has an important contribution to cell function and integrity, which extends to the whole organism for development and survival. Research in mitophagy has boomed in recent years, and it is becoming clear that mitophagy is a complex and multi-factorial cellular response that depends on tissue, energetic, stress and signaling contexts. However, we know very little of its physiological regulation and the direct contribution of mitophagy to pathologies like neurodegenerative diseases. In this review, we aim to discuss the outstanding questions (and questions outstanding) in the field and reflect on our current understanding of mitophagy, the current challenges and the future directions to take.},
}

Animals
Autophagy/genetics
*Biological Evolution
Homeostasis/genetics
Humans
Mitochondria/*genetics
Mitophagy/*genetics
Signal Transduction/genetics

@article {pmid32564730,
year = {2020},
author = {Levitskii, SA and Baleva, MV and Chicherin, IV and Krasheninnikov, IA and Kamenski, PA},
title = {Protein Biosynthesis in Mitochondria: Past Simple, Present Perfect, Future Indefinite.},
journal = {Biochemistry. Biokhimiia},
volume = {85},
number = {3},
pages = {257-263},
doi = {10.1134/S0006297920030013},
pmid = {32564730},
issn = {1608-3040},
abstract = {Mitochondria are obligate organelles of most eukaryotic cells that perform many different functions important for cellular homeostasis. The main role of mitochondria is supplying cells with energy in a form of ATP, which is synthesized in a chain of oxidative phosphorylation reactions on the organelle inner membrane. It is commonly believed now that mitochondria have the endosymbiotic origin. In the course of evolution, they have lost most of their genetic material as a result of genome reduction and gene transfer to the nucleus. The majority of mitochondrial proteins are synthesized in the cytosol and then imported to the mitochondria. However, almost all known mitochondria still contain genomes that are maintained and expressed. The processes of protein biosynthesis in the mitochondria - mitochondrial translation - substantially differs from the analogous processes in bacteria and the cytosol of eukaryotic cells. Mitochondrial translation is characterized by a high degree of specialization and specific regulatory mechanisms. In this review, we analyze available information on the common principles of mitochondrial translation with emphasis on the molecular mechanisms of translation initiation in the mitochondria of yeast and mammalian cells.},
}

@article {pmid31701178,
year = {2019},
author = {Aguirre-Dugua, X and Castellanos-Morales, G and Paredes-Torres, LM and Hernández-Rosales, HS and Barrera-Redondo, J and Sánchez-de la Vega, G and Tapia-Aguirre, F and Ruiz-Mondragón, KY and Scheinvar, E and Hernández, P and Aguirre-Planter, E and Montes-Hernández, S and Lira-Saade, R and Eguiarte, LE},
title = {Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita.},
journal = {Journal of molecular evolution},
volume = {87},
number = {9-10},
pages = {327-342},
pmid = {31701178},
issn = {1432-1432},
mesh = {Biological Evolution ; Cucurbita/*genetics ; Evolution, Molecular ; Genes, Plant/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/genetics ; Mitochondria/genetics ; Phylogeny ; Plastids/*genetics ; Sequence Analysis, DNA ; },
abstract = {Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20-rps12 and trnL-trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL-trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL-trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.},
}

Biological Evolution
Cucurbita/*genetics
Evolution, Molecular
Genes, Plant/genetics
Genome, Mitochondrial/*genetics
Genome, Plant/genetics
Mitochondria/genetics
Phylogeny
Plastids/*genetics
Sequence Analysis, DNA

@article {pmid31542425,
year = {2019},
author = {Zheng, F and Colasante, C and Voncken, F},
title = {Characterisation of a mitochondrial iron transporter of the pathogen Trypanosoma brucei.},
journal = {Molecular and biochemical parasitology},
volume = {233},
number = {},
pages = {111221},
doi = {10.1016/j.molbiopara.2019.111221},
pmid = {31542425},
issn = {1872-9428},
support = {BB/G00448X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Cation Transport Proteins/chemistry/genetics/metabolism ; Genes, Fungal ; Genes, Protozoan ; Iron/*metabolism ; Iron-Binding Proteins/chemistry/genetics/metabolism ; Mitochondria/metabolism ; *Mitochondrial Membrane Transport Proteins/chemistry/genetics/metabolism ; Phylogeny ; Protozoan Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Trypanosoma brucei brucei/*metabolism ; },
abstract = {Similar to higher eukaryotes, the protist parasite T. brucei harbours several iron-containing proteins that regulate DNA and protein processing, oxidative stress defence and mitochondrial respiration. The synthesis of these proteins occurs either in the cytoplasm or within the mitochondrion. For mitochondrial iron cluster protein synthesis, iron needs to be transported across the solute impermeable mitochondrial membrane. In T. brucei we previously identified 24 mitochondrial carrier proteins (TbMCPs) sharing conserved structural and functional features with those from higher eukaryotes. One of these carriers (TbMCP17) displayed high similarity with the iron carriers MRS3, MRS4 from yeast and mitoferrin from mammals, insects and plants. In the present study we demonstrated that TbMCP17 functions as an iron carrier by complementation studies using MRS3/4-deficient yeast. Depletion of TbMCP17 in procyclic form T. brucei resulted in growth deficiency, increased sensitivity to iron deprivation, and lowered mitochondrial iron content. Taken together our results suggest that TbMCP17 functions as a mitochondrial iron transporter in the parasite T. brucei.},
}

Cation Transport Proteins/chemistry/genetics/metabolism
Genes, Fungal
Genes, Protozoan
Iron/*metabolism
Iron-Binding Proteins/chemistry/genetics/metabolism
Mitochondria/metabolism
*Mitochondrial Membrane Transport Proteins/chemistry/genetics/metabolism
Phylogeny
Protozoan Proteins/chemistry/genetics/metabolism
Saccharomyces cerevisiae/genetics/metabolism
Saccharomyces cerevisiae Proteins/genetics/metabolism
Trypanosoma brucei brucei/*metabolism

@article {pmid32553108,
year = {2020},
author = {Tobiasson, V and Amunts, A},
title = {Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
doi = {10.7554/eLife.59264},
pmid = {32553108},
issn = {2050-084X},
support = {M44/16//Ragnar Söderbergs stiftelse/ ; 2017/1041//Cancerfonden/ ; ERC-2018-StG- 805230//H2020 European Research Council/ ; 2018.0080//Knut och Alice Wallenbergs Stiftelse/ ; EMBO Young Investigator Program//European Molecular Biology Organization/ ; },
abstract = {To reveal steps in the evolution of translation, we identified ciliates as a model with high coding capacity of the mitochondrial genome and characterized its mitoribosomes by cryo-EM. It revealed a 94-protein and 4-rRNA assembly with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. The structure shows that the small subunit head is constrained, tRNA binding sites are formed by mitochondria-specific protein elements, conserved protein bS1 is excluded, and bacterial RNA polymerase binding site is blocked. We provide evidence for intrinsic protein targeting system through visualization of mitochondria-specific mL105 by the exit tunnel that would facilitate recruitment of a nascent polypeptide. Functional protein uS3m is encoded by three complementary genes from the nucleus and mitochondrion, establishing a link between genetic drift and mitochondrial translation. Finally, we reannotated nine open reading frames in the mitochondrial genome that code for mitoribosomal proteins.},
}

@article {pmid32551463,
year = {2020},
author = {Timón-Gómez, A and Barrientos, A},
title = {Mitochondrial respiratory chain composition and organization in response to changing oxygen levels.},
journal = {Journal of life sciences (Westlake Village, Calif.)},
volume = {2},
number = {2},
pages = {},
doi = {10.36069/JoLS/20200601},
pmid = {32551463},
issn = {2688-1020},
abstract = {Mitochondria are the major consumer of oxygen in eukaryotic cells, owing to the requirement of oxygen to generate ATP through the mitochondrial respiratory chain (MRC) and the oxidative phosphorylation system (OXPHOS). This aerobic energy transduction is more efficient than anaerobic processes such as glycolysis. Hypoxia, a condition in which environmental or intracellular oxygen levels are below the standard range, triggers an adaptive signaling pathway within the cell. When oxygen concentrations are low, hypoxia-inducible factors (HIFs) become stabilized and activated to mount a transcriptional response that triggers modulation of cellular metabolism to adjust to hypoxic conditions. Mitochondrial aerobic metabolism is one of the main targets of the hypoxic response to regulate its functioning and efficiency in the presence of decreased oxygen levels. During evolution, eukaryotic cells and tissues have increased the plasticity of their mitochondrial OXPHOS system to cope with metabolic needs in different oxygen contexts. In mammalian mitochondria, two factors contribute to this plasticity. First, several subunits of the multimeric MRC complexes I and IV exist in multiple tissue-specific and condition-specific isoforms. Second, the MRC enzymes can coexist organized as individual entities or forming supramolecular structures known as supercomplexes, perhaps in a dynamic manner to respond to environmental conditions and cellular metabolic demands. In this review, we will summarize the information currently available on oxygen-related changes in MRC composition and organization and will discuss gaps of knowledge and research opportunities in the field.},
}

@article {pmid32551241,
year = {2020},
author = {Monteiro, LB and Davanzo, GG and de Aguiar, CF and Moraes-Vieira, PMM},
title = {Using flow cytometry for mitochondrial assays.},
journal = {MethodsX},
volume = {7},
number = {},
pages = {100938},
doi = {10.1016/j.mex.2020.100938},
pmid = {32551241},
issn = {2215-0161},
abstract = {The understanding of how different cell types adapt their metabolism in the face of challenges has been attracting the attention of researchers for many years. Recently, immunologists also started to focus on how the metabolism of immune cells can impact the way that immunity drives its responses. The presence of a pathogen or damage in a tissue changes severely the way that the immune cells need to respond. When activated, immune cells usually shift their metabolism from a high energy demanding status using mitochondria respiration to a glycolytic based rapid ATP production. The diminished amount of respiration leads to changes in the mitochondrial membrane potential and, consequently, generation of reactive oxygen species. Here, we show how flow cytometry can be used to track changes in mitochondrial mass, membrane potential and superoxide (ROS) production in live immune cells. ● This protocol suggests a quick way of evaluating mitochondrial fitness using flow cytometry. We propose using the probes MitoTraker Green and MitoTracker Red/ MitoSOX at the same time. This way, it is possible to evaluate different parameters of mitochondrial biology in living cells. ● Flow cytometry is a highly used tool by immunologists. With the advances of studies focusing on the metabolism of immune cells, a simplified application of flow cytometry for mitochondrial studies and screenings is a helpful clarifying method for immunology.},
}

@article {pmid31596994,
year = {2019},
author = {McGaughran, A and Terauds, A and Convey, P and Fraser, CI},
title = {Genome-wide SNP data reveal improved evidence for Antarctic glacial refugia and dispersal of terrestrial invertebrates.},
journal = {Molecular ecology},
volume = {28},
number = {22},
pages = {4941-4957},
doi = {10.1111/mec.15269},
pmid = {31596994},
issn = {1365-294X},
mesh = {Animals ; Antarctic Regions ; Biodiversity ; Evolution, Molecular ; Genetic Variation/*genetics ; Genome-Wide Association Study/methods ; Geography ; Ice Cover ; Invertebrates/*genetics ; Islands ; Mitochondria/genetics ; Polymorphism, Single Nucleotide/*genetics ; Refugium ; },
abstract = {Antarctica is isolated, surrounded by the Southern Ocean and has experienced extreme environmental conditions for millions of years, including during recent Pleistocene glacial maxima. How Antarctic terrestrial species might have survived these glaciations has been a topic of intense interest, yet many questions remain unanswered, particularly for Antarctica's invertebrate fauna. We examine whether genetic data from a widespread group of terrestrial invertebrates, springtails (Collembola, Isotomidae) of the genus Cryptopygus, show evidence for long-term survival in glacial refugia along the Antarctic Peninsula. We use genome-wide SNP analyses (via genotyping-by-sequencing, GBS) and mitochondrial data to examine population diversity and differentiation across more than 20 sites spanning >950 km on the Peninsula, and from islands both close to the Peninsula and up to ~1,900 km away. Population structure analysis indicates the presence of strong local clusters of diversity, and we infer that patterns represent a complex interplay of isolation in local refugia coupled with occasional successful long-distance dispersal events. We identified wind and degree days as significant environmental drivers of genetic diversity, with windier and warmer sites hosting higher diversity. Thus, we infer that refugial areas along the Antarctic Peninsula have allowed populations of indigenous springtails to survive in situ throughout glacial periods. Despite the difficulties of dispersal in cold, desiccating conditions, Cryptopygus springtails on the Peninsula appear to have achieved multiple long-distance colonization events, most likely through wind-related dispersal events.},
}

Animals
Antarctic Regions
Biodiversity
Evolution, Molecular
Genetic Variation/*genetics
Genome-Wide Association Study/methods
Geography
Ice Cover
Invertebrates/*genetics
Islands
Mitochondria/genetics
Polymorphism, Single Nucleotide/*genetics
Refugium

@article {pmid32546620,
year = {2020},
author = {Valero, C and Colabardini, AC and Chiaratto, J and Pardeshi, L and de Castro, PA and Ferreira Filho, JA and Silva, LP and Rocha, MC and Malavazi, I and Costa, JH and Fill, T and Barros, MH and Wong, SSW and Aimanianda, V and Wong, KH and Goldman, GH},
title = {Aspergillus fumigatus Transcription Factors Involved in the Caspofungin Paradoxical Effect.},
journal = {mBio},
volume = {11},
number = {3},
pages = {},
doi = {10.1128/mBio.00816-20},
pmid = {32546620},
issn = {2150-7511},
abstract = {Aspergillus fumigatus is the leading cause of pulmonary fungal diseases. Azoles have been used for many years as the main antifungal agents to treat and prevent invasive aspergillosis. However, in the last 10 years there have been several reports of azole resistance in A. fumigatus and new strategies are needed to combat invasive aspergillosis. Caspofungin is effective against other human-pathogenic fungal species, but it is fungistatic only against A. fumigatus Resistance to caspofungin in A. fumigatus has been linked to mutations in the fksA gene that encodes the target enzyme of the drug β-1,3-glucan synthase. However, tolerance of high caspofungin concentrations, a phenomenon known as the caspofungin paradoxical effect (CPE), is also important for subsequent adaptation and drug resistance evolution. Here, we identified and characterized the transcription factors involved in the response to CPE by screening an A. fumigatus library of 484 null transcription factors (TFs) in CPE drug concentrations. We identified 11 TFs that had reduced CPE and that encoded proteins involved in the basal modulation of the RNA polymerase II initiation sites, calcium metabolism, and cell wall remodeling. One of these TFs, FhdA, was important for mitochondrial respiratory function and iron metabolism. The ΔfhdA mutant showed decreased growth when exposed to Congo red or to high temperature. Transcriptome sequencing (RNA-seq) analysis and further experimental validation indicated that the ΔfhdA mutant showed diminished respiratory capacity, probably affecting several pathways related to the caspofungin tolerance and resistance. Our results provide the foundation to understand signaling pathways that are important for caspofungin tolerance and resistance.IMPORTANCEAspergillus fumigatus, one of the most important human-pathogenic fungal species, is able to cause aspergillosis, a heterogeneous group of diseases that presents a wide range of clinical manifestations. Invasive pulmonary aspergillosis is the most serious pathology in terms of patient outcome and treatment, with a high mortality rate ranging from 50% to 95% primarily affecting immunocompromised patients. Azoles have been used for many years as the main antifungal agents to treat and prevent invasive aspergillosis. However, there were several reports of evolution of clinical azole resistance in the last decade. Caspofungin, a noncompetitive β-1,3-glucan synthase inhibitor, has been used against A. fumigatus, but it is fungistatic and is recommended as second-line therapy for invasive aspergillosis. More information about caspofungin tolerance and resistance is necessary in order to refine antifungal strategies that target the fungal cell wall. Here, we screened a transcription factor (TF) deletion library for TFs that can mediate caspofungin tolerance and resistance. We have identified 11 TFs that are important for caspofungin sensitivity and/or for the caspofungin paradoxical effect (CPE). These TFs encode proteins involved in the basal modulation of the RNA polymerase II initiation sites, calcium metabolism or cell wall remodeling, and mitochondrial respiratory function. The study of those genes regulated by TFs identified in this work will provide a better understanding of the signaling pathways that are important for caspofungin tolerance and resistance.},
}

@article {pmid32538150,
year = {2020},
author = {Li, Y and Nourbakhsh, N and Pham, H and Tham, R and Zuckerman, JE and Singh, P},
title = {Evolution of Altered Tubular Metabolism and Mitochondrial Function in Sepsis Associated Acute Kidney Injury.},
journal = {American journal of physiology. Renal physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajprenal.00390.2019},
pmid = {32538150},
issn = {1522-1466},
support = {R01 DK107852//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; BX002175//Center for Integrated Healthcare, U.S. Department of Veterans Affairs (VISN 2 Center for Integrated Healthcare)/ ; P30-DK 079337//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {Sepsis-associated acute kidney injury (s-AKI) has a staggering impact in patients and lacks any treatment. Incomplete understanding of the pathogenesis of s-AKI is a major barrier to the development of effective therapies. We address the gaps in knowledge regarding renal oxygenation, tubular metabolism, and mitochondrial function in the pathogenesis of s-AKI, utilizing the cecal ligation and puncture (CLP) model in mice. At 24 hours after CLP, renal oxygen delivery was reduced, however, fractional oxygen extraction was unchanged, suggesting inefficient renal oxygen utilization despite decreased GFR and filtered load. To investigate underlying mechanisms, we examined temporal changes in mitochondrial function and metabolism at 4 and 24 hours after CLP. At 4 hours after CLP, markers of mitochondrial content and biogenesis were increased in CLP kidneys, but mitochondrial oxygen consumption rates (OCR) were suppressed in proximal tubules. Interestingly, at 24 hours, proximal tubular mitochondria displayed high respiratory capacity, but with decreased mitochondrial content, biogenesis, fusion and ATP levels in the CLP kidneys, suggesting decreased ATP synthesis efficiency. We further investigated metabolic reprogramming after CLP and observed reduced expression of fatty acid oxidation enzymes, but increased expression of glycolytic enzymes at 24 hours. However, assessment of functional glycolysis revealed lower glycolytic capacity, glycolytic reserve and compensatory glycolysis in CLP proximal tubules, which may explain their susceptibility of injury. In conclusion, we demonstrate significant alterations in renal oxygenation, tubular mitochondrial function and metabolic reprogramming in s-AKI which may play an important role in the progression of injury and recovery from AKI in sepsis.},
}

@article {pmid32148763,
year = {2019},
author = {Pichon, J and Luscombe, NM and Plessy, C},
title = {Widespread use of the "ascidian" mitochondrial genetic code in tunicates.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {2072},
pmid = {32148763},
issn = {2046-1402},
mesh = {Animals ; Base Sequence ; *Genetic Code ; Mitochondria ; *Phylogeny ; *Urochordata/genetics ; },
abstract = {Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.},
}

Animals
Base Sequence
*Genetic Code
Mitochondria
*Phylogeny
*Urochordata/genetics

@article {pmid31665278,
year = {2019},
author = {Kortsinoglou, AM and Korovesi, AG and Theelen, B and Hagen, F and Boekhout, T and Kouvelis, VN},
title = {The mitochondrial intergenic regions nad1-cob and cob-rps3 as molecular identification tools for pathogenic members of the genus Cryptococcus.},
journal = {FEMS yeast research},
volume = {19},
number = {8},
pages = {},
doi = {10.1093/femsyr/foz077},
pmid = {31665278},
issn = {1567-1364},
mesh = {Cryptococcosis/microbiology ; Cryptococcus/*genetics/*pathogenicity ; DNA, Fungal/*genetics ; *DNA, Intergenic ; DNA, Ribosomal/genetics ; *Genes, Mitochondrial ; Humans ; Membrane Glycoproteins/genetics ; Mitochondria/genetics ; Mycological Typing Techniques ; NADH Dehydrogenase/genetics ; Phylogeny ; Ribosomal Proteins/genetics ; },
abstract = {Cryptococcus spp. are fungal species belonging to Tremellomycetes, Agaricomycotina, Basidiomycota, and several members are responsible for cryptococcosis, one of the most ubiquitous human mycoses. Affecting mainly immunosuppressed patients, but also immunocompetent ones, the members of this genus present a high level of genetic diversity. In this study, two mitochondrial intergenic regions, i.e. nad1-cob and cob-rps3, were tested for the intra- or interspecies discrimination and identification of strains and species of the genus Cryptococcus. Phylogenetic trees were constructed based on individual and concatenated sequences from representative pathogenic strains of the Cryptococcus neoformans/Cryptococcus gattii complex, representing serotypes and AFLP genotypes of all newly introduced species of this complex. Using both intergenic regions, as well as the concatenated dataset, the strains clustered in accordance with the new taxonomy. These results suggest that identification of Cryptococcus strains is possible by employing these mitochondrial intergenic regions using PCR amplification as a quick and effective method to elucidate genotypic and taxonomic differences. Thus, these regions may be applicable to a broad range of clinical studies, leading to a rapid recognition of the clinical profiles of patients.},
}

Cryptococcosis/microbiology
Cryptococcus/*genetics/*pathogenicity
DNA, Fungal/*genetics
*DNA, Intergenic
DNA, Ribosomal/genetics
*Genes, Mitochondrial
Humans
Membrane Glycoproteins/genetics
Mitochondria/genetics
Mycological Typing Techniques
NADH Dehydrogenase/genetics
Phylogeny
Ribosomal Proteins/genetics

@article {pmid30467693,
year = {2019},
author = {Aw, WC and Garvin, MR and Ballard, JWO},
title = {Exogenous Factors May Differentially Influence the Selective Costs of mtDNA Mutations.},
journal = {Advances in anatomy, embryology, and cell biology},
volume = {231},
number = {},
pages = {51-74},
doi = {10.1007/102_2018_2},
pmid = {30467693},
issn = {0301-5556},
mesh = {Cell Nucleus/*metabolism ; DNA, Mitochondrial/*genetics ; Diet ; Electron Transport Complex I/*metabolism ; Energy Metabolism/*genetics/physiology ; Evolution, Molecular ; Genetic Fitness ; Humans ; Mitochondria/genetics/*metabolism ; Mutation ; Nutrients/*metabolism ; Signal Transduction/genetics ; Stress, Physiological ; Temperature ; },
abstract = {In this review, we provide evidence to suggest that the cost of specific mtDNA mutations can be influenced by exogenous factors. We focus on macronutrient-mitochondrial DNA interactions as factors that may differentially influence the consequences of a change as mitochondria must be flexible in its utilization of dietary proteins, carbohydrates, and fats. To understand this fundamental dynamic, we briefly discuss the energy processing pathways in mitochondria. Next, we explore the mitochondrial functions that are initiated during energy deficiency or when cells encounter cellular stress. We consider the anterograde response (nuclear control of mitochondrial function) and the retrograde response (nuclear changes in response to mitochondrial signaling) and how this mito-nuclear crosstalk may be influenced by exogenous factors such as temperature and diet. Finally, we employ Complex I of the mitochondrial electron transport system as a case study and discuss the potential role of the dietary macronutrient ratio as a strong selective force that may shape the frequencies of mitotypes in populations and species. We conclude that this underexplored field likely has implications in the fundamental disciplines of evolutionary biology and quantitative genetics and the more biomedical fields of nutrigenomics and pharmacogenomics.},
}

Cell Nucleus/*metabolism
DNA, Mitochondrial/*genetics
Diet
Electron Transport Complex I/*metabolism
Energy Metabolism/*genetics/physiology
Evolution, Molecular
Genetic Fitness
Humans
Mitochondria/genetics/*metabolism
Mutation
Nutrients/*metabolism
Signal Transduction/genetics
Stress, Physiological
Temperature

@article {pmid30456441,
year = {2019},
author = {Serrano-Solís, V and Toscano Soares, PE and de Farías, ST},
title = {Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution.},
journal = {Journal of molecular evolution},
volume = {87},
number = {1},
pages = {7-15},
pmid = {30456441},
issn = {1432-1432},
mesh = {Acanthamoeba/*genetics ; Amoeba/genetics ; Animals ; Bacteria/genetics ; Biological Coevolution/*genetics ; Codon/genetics ; Evolution, Molecular ; Genome, Viral ; Genomics ; Mimiviridae/*genetics ; Mitochondria/genetics ; Parasites/genetics ; Viral Proteins/genetics ; Virophages/genetics ; },
abstract = {The definition of a genomic signature (GS) is "the total net response to selective pressure". Recent isolation and sequencing of naturally occurring organisms, hereby named entoorganisms, within Acanthamoeba polyphaga, raised the hypothesis of a common genomic signature despite their diverse and unrelated evolutionary origin. Widely accepted and implemented tests for GS detection are oligonucleotide relative frequencies (OnRF) and relative codon usage (RCU) surveys. A common pattern and strong correlations were unveiled from OnRFs among A. polyphaga's Mimivirus and virophage Sputnik. RCU showed a common A-T bias at third codon position. We expanded tests to the amoebal mitochondrial genome and amoeba-resistant bacteria, achieving strikingly coherent results to the aforementioned viral analyses. The GSs in these entoorganisms of diverse evolutionary origin are coevolutionarily conserved within an intracellular environment that provides sanctuary for species of ecological and biomedical relevance.},
}

Acanthamoeba/*genetics
Amoeba/genetics
Animals
Bacteria/genetics
Biological Coevolution/*genetics
Codon/genetics
Evolution, Molecular
Genome, Viral
Genomics
Mimiviridae/*genetics
Mitochondria/genetics
Parasites/genetics
Viral Proteins/genetics
Virophages/genetics

@article {pmid32534048,
year = {2020},
author = {Vertika, S and Singh, KK and Rajender, S},
title = {Mitochondria, spermatogenesis, and male infertility - an update.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2020.06.003},
pmid = {32534048},
issn = {1872-8278},
abstract = {The incorporation of mitochondria in the eukaryotic cell is one of the most enigmatic events in the course of evolution. This important organelle was thought to be only the powerhouse of the cell, but was later learnt to perform many other indispensable functions in the cell. Two major contributions of mitochondria in spermatogenesis concern energy production and apoptosis. Apart from this, mitochondria also participate in a number of other processes affecting spermatogenesis and fertility. Mitochondria in sperm are arranged in the periphery of the tail microtubules to serve to energy demand for motility. Apart from this, the role of mitochondria in germ cell proliferation, mitotic regulation, and the elimination of germ cells by apoptosis are now well recognized. Eventually, mutations in the mitochondrial genome have been reported in male infertility, particularly in sluggish sperm (asthenozoospermia); however, heteroplasmy in the mtDNA and a complex interplay between the nucleus and mitochondria affect their penetrance. In this article, we have provided an update on the role of mitochondria in various events of spermatogenesis and male fertility and on the correlation of mitochondrial DNA mutations with male infertility.},
}

@article {pmid31515862,
year = {2019},
author = {Després, L},
title = {One, two or more species? Mitonuclear discordance and species delimitation.},
journal = {Molecular ecology},
volume = {28},
number = {17},
pages = {3845-3847},
doi = {10.1111/mec.15211},
pmid = {31515862},
issn = {1365-294X},
mesh = {Animals ; Butterflies/genetics ; Cell Nucleus/*genetics ; Climate ; DNA, Mitochondrial/genetics ; Gene Flow ; Geography ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; },
abstract = {Delimiting species boundaries is central to understand ecological and evolutionary processes, and to monitor biodiversity patterns over time and space. Yet, most of our current knowledge on animal diversity and phylogeny relies on morphological and mitochondrial (mt) DNA variation, a popular molecular marker also used as a barcode to assign samples to species. For morphologically undistinguishable sympatric species (cryptic species), the congruence of several independent markers is necessary to define separate species. Nuclear markers are becoming more accessible, and have confirmed that cryptic species are widespread in all animal phyla (Fišer, Robinson, & Malard, 2018). However, striking differences between the mitochondrial and nuclear variation patterns are also commonly found within single species. Mitonuclear discordance can result from incomplete lineage sorting, sex-biased dispersal, asymmetrical introgression, natural selection or Wolbachia-mediated genetic sweeps. But more generally, the distinct mode of transmission of these two types of markers (maternal vs. biparental) is sufficient to explain their distinct sensitivity to purely demographic events such as spatial range and population size fluctuations over time. In a From the Cover manuscript in this issue of Molecular Ecology, Hijonosa et al. (2019) show that highly divergent mtDNA lineages coexist in a widespread European butterfly (Figure 1). None of the hundreds of nuclear markers analyzed was associated with mt lineages, nor was Wolbachia variation. These findings rule out the presence of cryptic species but shed light on complex demographic history of lineage divergence/fusion during the Pleistocene climatic fluctuations, and pave the way to a better integration of both mt and nuclear information in demographic models.},
}

Animals
Butterflies/genetics
Cell Nucleus/*genetics
Climate
DNA, Mitochondrial/genetics
Gene Flow
Geography
High-Throughput Nucleotide Sequencing
Mitochondria/*genetics
*Phylogeny
Polymorphism, Single Nucleotide/genetics
Species Specificity

@article {pmid31392804,
year = {2019},
author = {Guo, B and Fang, B and Shikano, T and Momigliano, P and Wang, C and Kravchenko, A and Merilä, J},
title = {A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius.},
journal = {Molecular ecology},
volume = {28},
number = {17},
pages = {4046-4064},
doi = {10.1111/mec.15204},
pmid = {31392804},
issn = {1365-294X},
mesh = {Animals ; Cell Nucleus/genetics ; Female ; Gene Flow ; *Genetic Variation ; Geography ; *Hybridization, Genetic ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Smegmamorpha/*classification/*genetics ; Species Specificity ; Time Factors ; },
abstract = {Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both data sets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.},
}

Animals
Cell Nucleus/genetics
Female
Gene Flow
*Genetic Variation
Geography
*Hybridization, Genetic
Likelihood Functions
Mitochondria/genetics
*Phylogeny
Smegmamorpha/*classification/*genetics
Species Specificity
Time Factors

@article {pmid31233646,
year = {2019},
author = {Hinojosa, JC and Koubínová, D and Szenteczki, MA and Pitteloud, C and Dincă, V and Alvarez, N and Vila, R},
title = {A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris.},
journal = {Molecular ecology},
volume = {28},
number = {17},
pages = {3857-3868},
doi = {10.1111/mec.15153},
pmid = {31233646},
issn = {1365-294X},
mesh = {Animals ; Bayes Theorem ; Butterflies/*genetics ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Loci ; *Genomics ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; },
abstract = {Mitochondrial DNA (mtDNA) sequencing has led to an unprecedented rise in the identification of cryptic species. However, it is widely acknowledged that nuclear DNA (nuDNA) sequence data are also necessary to properly define species boundaries. Next generation sequencing techniques provide a wealth of nuclear genomic data, which can be used to ascertain both the evolutionary history and taxonomic status of putative cryptic species. Here, we focus on the intriguing case of the butterfly Thymelicus sylvestris (Lepidoptera: Hesperiidae). We identified six deeply diverged mitochondrial lineages; three distributed all across Europe and found in sympatry, suggesting a potential case of cryptic species. We then sequenced these six lineages using double-digest restriction-site associated DNA sequencing (ddRADseq). Nuclear genomic loci contradicted mtDNA patterns and genotypes generally clustered according to geography, i.e., a pattern expected under the assumption of postglacial recolonization from different refugia. Further analyses indicated that this strong mtDNA/nuDNA discrepancy cannot be explained by incomplete lineage sorting, sex-biased asymmetries, NUMTs, natural selection, introgression or Wolbachia-mediated genetic sweeps. We suggest that this mitonuclear discordance was caused by long periods of geographic isolation followed by range expansions, homogenizing the nuclear but not the mitochondrial genome. These results highlight T. sylvestris as a potential case of multiple despeciation and/or lineage fusion events. We finally argue, since mtDNA and nuDNA do not necessarily follow the same mechanisms of evolution, their respective evolutionary history reflects complementary aspects of past demographic and biogeographic events.},
}

Animals
Bayes Theorem
Butterflies/*genetics
Cell Nucleus/*genetics
Electron Transport Complex IV/genetics
Genetic Loci
*Genomics
Likelihood Functions
Mitochondria/*genetics
Phylogeny
Polymorphism, Single Nucleotide/genetics
Species Specificity

@article {pmid32520982,
year = {2020},
author = {Enomoto, H and Mittal, N and Inomata, T and Arimura, T and Izumi, T and Kimura, A and Fukuda, K and Makino, S},
title = {Dilated Cardiomyopathy (DCM)-linked Heat shock protein Family D Member 1 (HSPD1) mutations cause upregulation of ROS and autophagy through mitochondrial dysfunction.},
journal = {Cardiovascular research},
volume = {},
number = {},
pages = {},
doi = {10.1093/cvr/cvaa158},
pmid = {32520982},
issn = {1755-3245},
abstract = {BACKGROUND: During heart failure, the levels of circulatory HSPD1 (HSP60) increase. However, its underlying mechanism is still unknown. The apical domain of HSPD1 is conserved throughout evolution. We found a point mutation in HSPD1 in a familial dilated cardiomyopathy (DCM) patient. A similar point mutation in HSPD1 in the zebrafish mutant, nbl, led to loss of its regenerative capacity and development of pericardial edema under heat stress condition. In this study, we aimed to determine the direct involvement of HSPD1 in the development of DCM.

METHODS AND RESULTS: By Sanger method, we found a point mutation (Thr320Ala) in the apical domain of HSPD1, in one familial DCM patient, which was four amino acids away from the point mutation (Val324Glu) in the nbl mutant zebrafish. The nbl mutants showed atrioventricular block and sudden death at eight months post-fertilization. Histological and microscopic analysis of the nbl mutant hearts showed decreased ventricular wall thickness, elevated level of reactive oxygen species (ROS), increased fibrosis, mitochondrial damage, and increased autophagosomes. mRNA and protein expression of autophagy-related genes significantly increased in nbl mutants. We established HEK293 stable cell lines of WT, nbl-type, and DCM-type HSPD1, with tetracycline-dependent expression. Compared to WT, both nbl- and DCM-type cells showed decreased cell growth, increased expression of ROS and autophagy-related genes, inhibition of the activity of mitochondrial electron transport chain complexes III and IV, and decreased mitochondrial fission and fusion.

CONCLUSIONS: Mutations in HSPD1 caused mitochondrial dysfunction and induced mitophagy. Mitochondrial dysfunction caused increased ROS and cardiac atrophy.

TRANSLATIONAL PERSPECTIVE: The aged heart is more susceptible to stress despite the increased compensatory chaperones/co-chaperones activity. Here, we identified a point mutation in HSPD1 in a human DCM family. Using zebrafish, we demonstrated that functional inactivation of HSPD1 resulted in increased ROS level and mitophagy, thereby resulting in heart failure at a relatively early age. Inhibition of ROS activity by antioxidants decreased cell death and mitophagy. This work identifies the key role of HSPD1 in cardiac muscle protection and suggests the supplementation of antioxidants may improve the cardiac function through the mitochondrial ROS pathway in patients with chronic heart failure.},
}

@article {pmid31747540,
year = {2020},
author = {Anderson, K and Braoudakis, G and Kvist, S},
title = {Genetic variation, pseudocryptic diversity, and phylogeny of Erpobdella (Annelida: Hirudinida: Erpobdelliformes), with emphasis on Canadian species.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106688},
doi = {10.1016/j.ympev.2019.106688},
pmid = {31747540},
issn = {1095-9513},
mesh = {Animals ; Annelida/classification/*genetics ; Biodiversity ; Canada ; Electron Transport Complex IV/classification/genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/classification/genetics ; },
abstract = {Leeches of the family Erpobdellidae are important members of benthic freshwater environments, where they are voracious predators of other invertebrates and an important source of nutrition for several species of vertebrates. Beset by a lack of reliable diagnostic morphological characters and destructive identification processes, molecular approaches have, in recent years, been employed to illuminate the relationships within this family, and DNA barcoding has been employed for identification purposes. However, an understanding of the levels of genetic variation across the geographic distributions of members of the genus is still lacking. Herein, we sequence the mitochondrial COI locus for 249 newly collected North American individuals, representing 5 species, as well as mitochondrial 12S rDNA, nuclear 18S rDNA, and nuclear 28S rDNA for a select subset of these. Our COI dataset was leveraged to detect potential cryptic species, and to calculate genetic distances as a proxy for the degree of gene flow between populations. Augmented by numerous sequences from GenBank, the multilocus dataset was used to reconstruct a phylogenetic hypothesis for worldwide members of the genus. Beyond corroborating previous overarching phylogenetic frameworks, our results show that an undescribed species that is morphologically and genetically similar to Erpobdella punctata exists in sympatry with this species - the new species has likely been overlooked in previous studies due to its morphological similarity with Erpobdella punctata. Erpobdella bucera is reported from Canada for the first time; and Erpobdella microstoma is newly reported from Saskatchewan and placed in a phylogeny for the first time. Finally, we find evidence for genetic structure in both E. cf. punctata and Erpobdella obscura that is correlated with major river drainage basin boundaries in North America.},
}

Animals
Annelida/classification/*genetics
Biodiversity
Canada
Electron Transport Complex IV/classification/genetics
*Genetic Variation
Haplotypes
Mitochondria/genetics
Phylogeny
RNA, Ribosomal/classification/genetics

@article {pmid32502904,
year = {2020},
author = {Shah, SI and Ong, HL and Demuro, A and Ullah, G},
title = {PunctaSpecks: A tool for automated detection, tracking, and analysis of multiple types of fluorescently labeled biomolecules.},
journal = {Cell calcium},
volume = {89},
number = {},
pages = {102224},
doi = {10.1016/j.ceca.2020.102224},
pmid = {32502904},
issn = {1532-1991},
abstract = {Recent advances in imaging technology and fluorescent probes have made it possible to gain information about the dynamics of subcellular processes at unprecedented spatiotemporal scales. Unfortunately, a lack of automated tools to efficiently process the resulting imaging data encoding fine details of the biological processes remains a major bottleneck in utilizing the full potential of these powerful experimental techniques. Here we present a computational tool, called PunctaSpecks, that can characterize fluorescence signals arising from a wide range of biological molecules under normal and pathological conditions. Among other things, the program can calculate the number, areas, life-times, and amplitudes of fluorescence signals arising from multiple sources, track diffusing fluorescence sources like moving mitochondria, and determine the overlap probability of two processes or organelles imaged using indicator dyes of different colors. We have tested PunctaSpecks on synthetic time-lapse movies containing mobile fluorescence objects of various sizes, mimicking the activity of biomolecules. The robustness of the software is tested by varying the level of noise along with random but known pattern of appearing, disappearing, and movement of these objects. Next, we use PunctaSpecks to characterize protein-protein interaction involved in store-operated Ca2+ entry through the formation and activation of plasma membrane-bound ORAI1 channel and endoplasmic reticulum membrane-bound stromal interaction molecule (STIM), the evolution of inositol 1,4,5-trisphosphate (IP3)-induced Ca2+ signals from sub-micrometer size local events into global waves in human cortical neurons, and the activity of Alzheimer's disease-associated β amyloid pores in the plasma membrane. The tool can also be used to study other dynamical processes imaged through fluorescence molecules. The open source algorithm allows for extending the program to analyze more than two types of biomolecules visualized using markers of different colors.},
}

@article {pmid32499047,
year = {2020},
author = {Diederich, NJ and Uchihara, T and Grillner, S and Goetz, CG},
title = {The Evolution-Driven Signature of Parkinson's Disease.},
journal = {Trends in neurosciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tins.2020.05.001},
pmid = {32499047},
issn = {1878-108X},
abstract = {In this review, we approach Parkinson's disease (PD) in the context of an evolutionary mismatch of central nervous system functions. The neurons at risk have hyperbranched axons, extensive transmitter release sites, display spontaneous spiking, and elevated mitochondrial stress. They function in networks largely unchanged throughout vertebrate evolution, but now connecting to the expanded human cortex. Their breakdown is favoured by longevity. At the cellular level, mitochondrial dysfunction starts at the synapses, then involves axons and cell bodies. At the behavioural level, network dysfunctions provoke the core motor syndrome of parkinsonism including freezing and failed gait automatization, and non-motor deficits including inactive blindsight and autonomic dysregulation. The proposed evolutionary re-interpretation of PD-prone cellular phenotypes and of prototypical clinical symptoms allows a new conceptual framework for future research.},
}

@article {pmid32295425,
year = {2020},
author = {Rodríguez, M and Valez, V and Cimarra, C and Blasina, F and Radi, R},
title = {Hypoxic-Ischemic Encephalopathy and Mitochondrial Dysfunction: Facts, Unknowns, and Challenges.},
journal = {Antioxidants & redox signaling},
volume = {},
number = {},
pages = {},
doi = {10.1089/ars.2020.8093},
pmid = {32295425},
issn = {1557-7716},
abstract = {Significance: Hypoxic-ischemic events due to intrapartum complications represent the second cause of neonatal mortality and initiate an acute brain disorder known as hypoxic-ischemic encephalopathy (HIE). In HIE, the brain undergoes primary and secondary energy failure phases separated by a latent phase in which partial neuronal recovery is observed. A hypoxic-ischemic event leads to oxygen restriction causing ATP depletion, neuronal oxidative stress, and cell death. Mitochondrial dysfunction and enhanced oxidant formation in brain cells are characteristic phenomena associated with energy failure. Recent Advances: Mitochondrial sources of oxidants in neurons include complex I of the mitochondrial respiratory chain, as a key contributor to O2•- production via succinate by a reverse electron transport mechanism. The reaction of O2•- with nitric oxide (•NO) yields peroxynitrite, a mitochondrial and cellular toxin. Quantitation of the redox state of cytochrome c oxidase, through broadband near-infrared spectroscopy, represents a promising monitoring approach to evaluate mitochondrial dysfunction in vivo in humans, in conjunction with the determination of cerebral oxygenation and their correlation with the severity of brain injury. Critical Issues: The energetic failure being a key phenomenon in HIE connected with the severity of the encephalopathy, measurement of mitochondrial dysfunction in vivo provides an approach to assess evolution, prognosis, and adequate therapies. Restoration of mitochondrial redox homeostasis constitutes a key therapeutic goal. Future Directions: While hypothermia is the only currently accepted therapy in clinical management to preserve mitochondrial function, other mitochondria-targeted and/or redox-based treatments are likely to synergize to ensure further efficacy.},
}

@article {pmid31785298,
year = {2020},
author = {Shi, W and Gong, L and Yu, H},
title = {Double control regions of some flatfish mitogenomes evolve in a concerted manner.},
journal = {International journal of biological macromolecules},
volume = {142},
number = {},
pages = {11-17},
doi = {10.1016/j.ijbiomac.2019.11.204},
pmid = {31785298},
issn = {1879-0003},
mesh = {Animals ; DNA Repair/physiology ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Flatfishes/classification/*genetics ; Gene Order ; Genes, rRNA/genetics ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; RNA, Transfer/genetics ; Recombination, Genetic ; Sequence Analysis ; },
abstract = {Mitochondrial genomes (mitogenomes) typically contain 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a single control region (CR). Flatfish mitochondrial genomes (mitogenomes) from three different genera in Bothidae (bothids) contain double CRs that evolved in a concerted manner. How these double CRs maintained identical sequences throughout the evolutionary process is an interesting issue. In the present study, over four hundred arrays of the double CRs of mitogenomes from three bothids (Arnoglossus tenuis, Lophonectes gallus and Psettina iijimae) were performed. Interesting variations between double CRs were observed in P. iijimae mitogenomes, and the networks of CR sequences from P. iijimae indicated a high possibility of genetic information exchange between CRs. No recombination product was detected in our results, indicating that the mechanism of the concerted evolution between the double CRs of P. iijimae was not recombination. We speculate that mismatch repair, a mitochondrial DNA repair mechanism, is a potential explanation for the concerted evolution between these double CRs.},
}

Animals
DNA Repair/physiology
DNA, Mitochondrial/genetics
Evolution, Molecular
Flatfishes/classification/*genetics
Gene Order
Genes, rRNA/genetics
Genetic Variation
Genome, Mitochondrial/*genetics
Mitochondria/*genetics
RNA, Transfer/genetics
Recombination, Genetic
Sequence Analysis

@article {pmid32486081,
year = {2020},
author = {Tan, M and Tol, HTAV and Rosenkranz, D and Roovers, EF and Damen, MJ and Stout, TAE and Wu, W and Roelen, BAJ},
title = {PIWIL3 Forms a Complex with TDRKH in Mammalian Oocytes.},
journal = {Cells},
volume = {9},
number = {6},
pages = {},
doi = {10.3390/cells9061356},
pmid = {32486081},
issn = {2073-4409},
abstract = {P-element induced wimpy testis (PIWIs) are crucial guardians of genome integrity, particularly in germ cells. While mammalian PIWIs have been primarily studied in mouse and rat, a homologue for the human PIWIL3 gene is absent in the Muridae family, and hence the unique function of PIWIL3 in germ cells cannot be effectively modeled by mouse knockouts. Herein, we investigated the expression, distribution, and interaction of PIWIL3 in bovine oocytes. We localized PIWIL3 to mitochondria, and demonstrated that PIWIL3 expression is stringently controlled both spatially and temporally before and after fertilization. Moreover, we identified PIWIL3 in a mitochondrial-recruited three-membered complex with Tudor and KH domain-containing protein (TDRKH) and poly(A)-specific ribonuclease-like domain containing 1 (PNLDC1), and demonstrated by mutagenesis that PIWIL3 N-terminal arginines are required for complex assembly. Finally, we sequenced the piRNAs bound to PIWIL3-TDRKH-PNLDC1 and report here that about 50% of these piRNAs map to transposable elements, recapitulating the important role of PIWIL3 in maintaining genome integrity in mammalian oocytes.},
}

@article {pmid32485941,
year = {2020},
author = {Mendoza, H and Perlin, MH and Schirawski, J},
title = {Mitochondrial Inheritance in Phytopathogenic Fungi-Everything Is Known, or Is It?.},
journal = {International journal of molecular sciences},
volume = {21},
number = {11},
pages = {},
doi = {10.3390/ijms21113883},
pmid = {32485941},
issn = {1422-0067},
support = {GMB180621//National Science Foundation/ ; SCHI 1114/3-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Mitochondria are important organelles in eukaryotes that provide energy for cellular processes. Their function is highly conserved and depends on the expression of nuclear encoded genes and genes encoded in the organellar genome. Mitochondrial DNA replication is independent of the replication control of nuclear DNA and as such, mitochondria may behave as selfish elements, so they need to be controlled, maintained and reliably inherited to progeny. Phytopathogenic fungi meet with special environmental challenges within the plant host that might depend on and influence mitochondrial functions and services. We find that this topic is basically unexplored in the literature, so this review largely depends on work published in other systems. In trying to answer elemental questions on mitochondrial functioning, we aim to introduce the aspect of mitochondrial functions and services to the study of plant-microbe-interactions and stimulate phytopathologists to consider research on this important organelle in their future projects.},
}

@article {pmid32481110,
year = {2013},
author = {Gaff, DF and Oliver, M},
title = {The evolution of desiccation tolerance in angiosperm plants: a rare yet common phenomenon.},
journal = {Functional plant biology : FPB},
volume = {40},
number = {4},
pages = {315-328},
doi = {10.1071/FP12321},
pmid = {32481110},
issn = {1445-4416},
abstract = {In a minute proportion of angiosperm species, rehydrating foliage can revive from airdryness or even from equilibration with air of ~0% RH. Such desiccation tolerance is known from vegetative cells of some species of algae and of major groups close to the evolutionary path of the angiosperms. It is also found in the reproductive structures of some algae, moss spores and probably the aerial spores of other terrestrial cryptogamic taxa. The occurrence of desiccation tolerance in the seed plants is overwhelmingly in the aerial reproductive structures; the pollen and seed embryos. Spatially and temporally, pollen and embryos are close ontogenetic derivatives of the angiosperm microspores and megaspores respectively. This suggests that the desiccation tolerance of pollen and embryos derives from the desiccation tolerance of the spores of antecedent taxa and that the basic pollen/embryo mechanism of desiccation tolerance has eventually become expressed also in the vegetative tissue of certain angiosperm species whose drought avoidance is inadequate in micro-habitats that suffer extremely xeric episodes. The protective compounds and processes that contribute to desiccation tolerance in angiosperms are found in the modern groups related to the evolutionary path leading to the angiosperms and are also present in the algae and in the cyanobacteria. The mechanism of desiccation tolerance in the angiosperms thus appears to have its origins in algal ancestors and possibly in the endosymbiotic cyanobacteria-related progenitor of chloroplasts and the bacteria-related progenitor of mitochondria. The mechanism may involve the regulation and timing of the accumulation of protective compounds and of other contributing substances and processes.},
}

@article {pmid31940908,
year = {2020},
author = {Liu, W and Cai, Y and Zhang, Q and Shu, F and Chen, L and Ma, X and Bian, Y},
title = {Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes.},
journal = {International journal of molecular sciences},
volume = {21},
number = {2},
pages = {},
pmid = {31940908},
issn = {1422-0067},
mesh = {Ascomycota/genetics/*growth & development ; Chromosome Mapping/*methods ; Gene Expression Regulation, Fungal ; Genome Size ; Genome, Fungal ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phylogeny ; Whole Genome Sequencing/*methods ; },
abstract = {Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.},
}

Ascomycota/genetics/*growth & development
Chromosome Mapping/*methods
Gene Expression Regulation, Fungal
Genome Size
Genome, Fungal
Genome, Mitochondrial
High-Throughput Nucleotide Sequencing
Molecular Sequence Annotation
Phylogeny
Whole Genome Sequencing/*methods

@article {pmid32475470,
year = {2020},
author = {Gibellini, L and De Gaetano, A and Mandrioli, M and Van Tongeren, E and Bortolotti, CA and Cossarizza, A and Pinti, M},
title = {The biology of Lonp1: More than a mitochondrial protease.},
journal = {International review of cell and molecular biology},
volume = {354},
number = {},
pages = {1-61},
doi = {10.1016/bs.ircmb.2020.02.005},
pmid = {32475470},
issn = {1937-6448},
abstract = {Initially discovered as a protease responsible for degradation of misfolded or damaged proteins, the mitochondrial Lon protease (Lonp1) turned out to be a multifaceted enzyme, that displays at least three different functions (proteolysis, chaperone activity, binding of mtDNA) and that finely regulates several cellular processes, within and without mitochondria. Indeed, LONP1 in humans is ubiquitously expressed, and is involved in regulation of response to oxidative stress and, heat shock, in the maintenance of mtDNA, in the regulation of mitophagy. Furthermore, its proteolytic activity can regulate several biochemical pathways occurring totally or partially within mitochondria, such as TCA cycle, oxidative phosphorylation, steroid and heme biosynthesis and glutamine production. Because of these multiple activities, Lon protease is highly conserved throughout evolution, and mutations occurring in its gene determines severe diseases in humans, including a rare syndrome characterized by Cerebral, Ocular, Dental, Auricular and Skeletal anomalies (CODAS). Finally, alterations of LONP1 regulation in humans can favor tumor progression and aggressiveness, further highlighting the crucial role of this enzyme in mitochondrial and cellular homeostasis.},
}

@article {pmid31183910,
year = {2019},
author = {Sun, JT and Duan, XZ and Hoffmann, AA and Liu, Y and Garvin, MR and Chen, L and Hu, G and Zhou, JC and Huang, HJ and Xue, XF and Hong, XY},
title = {Mitochondrial variation in small brown planthoppers linked to multiple traits and probably reflecting a complex evolutionary trajectory.},
journal = {Molecular ecology},
volume = {28},
number = {14},
pages = {3306-3323},
doi = {10.1111/mec.15148},
pmid = {31183910},
issn = {1365-294X},
mesh = {Adaptation, Physiological/genetics ; Animals ; Body Size/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Female ; Fertility/genetics ; Gene Amplification ; Genetics, Population ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; Hemiptera/*genetics ; Male ; Mitochondria/*genetics ; Phylogeny ; *Quantitative Trait, Heritable ; Structural Homology, Protein ; Temperature ; },
abstract = {While it has been proposed in several taxa that the mitochondrial genome is associated with adaptive evolution to different climatic conditions, making links between mitochondrial haplotypes and organismal phenotypes remains a challenge. Mitonuclear discordance occurs in the small brown planthopper (SBPH), Laodelphax striatellus, with one mitochondrial haplogroup (HGI) more common in the cold climate region of China relative to another form (HGII) despite strong nuclear gene flow, providing a promising model to investigate climatic adaptation of mitochondrial genomes. We hypothesized that cold adaptation through HGI may be involved, and considered mitogenome evolution, population genetic analyses, and bioassays to test this hypothesis. In contrast to our hypothesis, chill-coma recovery tests and population genetic tests of selection both pointed to HGII being involved in cold adaptation. Phylogenetic analyses revealed that HGII is nested within HGI, and has three nonsynonymous changes in ND2, ND5 and CYTB in comparison to HGI. These molecular changes likely increased mtDNA copy number, cold tolerance and fecundity of SBPH, particularly through a function-altering amino acid change involving M114T in ND2. Nuclear background also influenced fecundity and chill recovery (i.e., mitonuclear epistasis) and protein modelling indicates possible nuclear interactions for the two nonsynonymous changes in ND2 and CYTB. The high occurrence frequency of HGI in the cold climate region of China remains unexplained, but several possible reasons are discussed. Overall, our study points to a link between mtDNA variation and organismal-level evolution and suggests a possible role of mitonuclear interactions in maintaining mtDNA diversity.},
}

Adaptation, Physiological/genetics
Animals
Body Size/genetics
DNA, Mitochondrial/genetics
*Evolution, Molecular
Female
Fertility/genetics
Gene Amplification
Genetics, Population
Genome, Mitochondrial
Geography
Haplotypes/genetics
Hemiptera/*genetics
Male
Mitochondria/*genetics
Phylogeny
*Quantitative Trait, Heritable
Structural Homology, Protein
Temperature

@article {pmid31543463,
year = {2019},
author = {Guièze, R and Liu, VM and Rosebrock, D and Jourdain, AA and Hernández-Sánchez, M and Martinez Zurita, A and Sun, J and Ten Hacken, E and Baranowski, K and Thompson, PA and Heo, JM and Cartun, Z and Aygün, O and Iorgulescu, JB and Zhang, W and Notarangelo, G and Livitz, D and Li, S and Davids, MS and Biran, A and Fernandes, SM and Brown, JR and Lako, A and Ciantra, ZB and Lawlor, MA and Keskin, DB and Udeshi, ND and Wierda, WG and Livak, KJ and Letai, AG and Neuberg, D and Harper, JW and Carr, SA and Piccioni, F and Ott, CJ and Leshchiner, I and Johannessen, CM and Doench, J and Mootha, VK and Getz, G and Wu, CJ},
title = {Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies.},
journal = {Cancer cell},
volume = {36},
number = {4},
pages = {369-384.e13},
doi = {10.1016/j.ccell.2019.08.005},
pmid = {31543463},
issn = {1878-3686},
support = {U10 CA180861/CA/NCI NIH HHS/United States ; T32 HL007627/HL/NHLBI NIH HHS/United States ; U24 CA210986/CA/NCI NIH HHS/United States ; R35 GM122455/GM/NIGMS NIH HHS/United States ; R21 CA216772/CA/NCI NIH HHS/United States ; R01 CA155010/CA/NCI NIH HHS/United States ; UG1 CA233338/CA/NCI NIH HHS/United States ; U01 CA214125/CA/NCI NIH HHS/United States ; R00 CA190861/CA/NCI NIH HHS/United States ; R01 CA216273/CA/NCI NIH HHS/United States ; R37 NS083524/NS/NINDS NIH HHS/United States ; P01 CA206978/CA/NCI NIH HHS/United States ; R01 CA213442/CA/NCI NIH HHS/United States ; R01 GM095567/GM/NIGMS NIH HHS/United States ; P01 CA081534/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Aged ; Aged, 80 and over ; Animals ; Antineoplastic Combined Chemotherapy Protocols/*pharmacology/therapeutic use ; Apoptosis/drug effects/genetics ; Bridged Bicyclo Compounds, Heterocyclic/*pharmacology/therapeutic use ; Cell Line, Tumor ; Clonal Evolution/drug effects ; Disease Progression ; Drug Resistance, Neoplasm/drug effects/genetics ; Energy Metabolism/drug effects/genetics ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/*drug therapy/pathology ; Male ; Mice ; Middle Aged ; Mitochondria/drug effects/*pathology ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism ; Oxidative Phosphorylation/drug effects ; Proto-Oncogene Proteins c-bcl-2/*antagonists & inhibitors/metabolism ; Sulfonamides/*pharmacology/therapeutic use ; Treatment Outcome ; Xenograft Model Antitumor Assays ; },
abstract = {Mitochondrial apoptosis can be effectively targeted in lymphoid malignancies with the FDA-approved B cell lymphoma 2 (BCL-2) inhibitor venetoclax, but resistance to this agent is emerging. We show that venetoclax resistance in chronic lymphocytic leukemia is associated with complex clonal shifts. To identify determinants of resistance, we conducted parallel genome-scale screens of the BCL-2-driven OCI-Ly1 lymphoma cell line after venetoclax exposure along with integrated expression profiling and functional characterization of drug-resistant and engineered cell lines. We identified regulators of lymphoid transcription and cellular energy metabolism as drivers of venetoclax resistance in addition to the known involvement by BCL-2 family members, which were confirmed in patient samples. Our data support the implementation of combinatorial therapy with metabolic modulators to address venetoclax resistance.},
}

Adult
Aged
Aged, 80 and over
Animals
Antineoplastic Combined Chemotherapy Protocols/*pharmacology/therapeutic use
Apoptosis/drug effects/genetics
Bridged Bicyclo Compounds, Heterocyclic/*pharmacology/therapeutic use
Cell Line, Tumor
Clonal Evolution/drug effects
Disease Progression
Drug Resistance, Neoplasm/drug effects/genetics
Energy Metabolism/drug effects/genetics
Female
Gene Expression Regulation, Neoplastic
Humans
Leukemia, Lymphocytic, Chronic, B-Cell/*drug therapy/pathology
Male
Mice
Middle Aged
Mitochondria/drug effects/*pathology
Myeloid Cell Leukemia Sequence 1 Protein/metabolism
Oxidative Phosphorylation/drug effects
Proto-Oncogene Proteins c-bcl-2/*antagonists & inhibitors/metabolism
Sulfonamides/*pharmacology/therapeutic use
Treatment Outcome
Xenograft Model Antitumor Assays

@article {pmid30833746,
year = {2019},
author = {Bernardo, PH and Sánchez-Ramírez, S and Sánchez-Pacheco, SJ and Álvarez-Castañeda, ST and Aguilera-Miller, EF and Mendez-de la Cruz, FR and Murphy, RW},
title = {Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate.},
journal = {Heredity},
volume = {123},
number = {3},
pages = {359-370},
doi = {10.1038/s41437-019-0204-4},
pmid = {30833746},
issn = {1365-2540},
support = {PGSD3 NSERC, 442235-2013//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/International ; A3148//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/International ; },
mesh = {Animal Migration ; Animals ; California ; Cell Nucleus/genetics ; Female ; *Gene Flow ; *Genetic Drift ; Genetic Variation ; *Genome, Mitochondrial ; *Inheritance Patterns ; Lizards/*genetics ; Male ; Mexico ; Mitochondria/*genetics ; Polymorphism, Single Nucleotide ; Reproductive Isolation ; Selection, Genetic ; },
abstract = {Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.},
}

Animal Migration
Animals
California
Cell Nucleus/genetics
Female
*Gene Flow
*Genetic Drift
Genetic Variation
*Genome, Mitochondrial
*Inheritance Patterns
Lizards/*genetics
Male
Mexico
Mitochondria/*genetics
Polymorphism, Single Nucleotide
Reproductive Isolation
Selection, Genetic

@article {pmid32442459,
year = {2020},
author = {Neveu, E and Khalifeh, D and Salamin, N and Fasshauer, D},
title = {Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota, Potentially Bridging the Gap between the Prokaryotes and Eukaryotes.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2020.04.060},
pmid = {32442459},
issn = {1879-0445},
abstract = {A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.},
}

@article {pmid32440763,
year = {2020},
author = {Roulet, ME and Garcia, LE and Gandini, CL and Sato, H and Ponce, G and Sanchez-Puerta, MV},
title = {Multichromosomal structure and foreign tracts in the Ombrophytum subterraneum (Balanophoraceae) mitochondrial genome.},
journal = {Plant molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11103-020-01014-x},
pmid = {32440763},
issn = {1573-5028},
support = {PICT-0691//Agencia Nacional de Promoción Científica y Tecnológica/ ; 06/A724//Universidad Nacional de Cuyo/ ; 1062432//National Science Foundation/ ; },
abstract = {Horizontal gene transfer (HGT) is frequent in parasitic plant mitochondria as a result of vascular connections established in host-parasite relationships. Recent studies of the holoparasitic plant Lophophytum mirabile (Balanophoraceae) revealed the unprecedented acquisition of a large amount of mitochondrial sequences from its legume host. We focused on a close relative, the generalist holoparasite Ombrophytum subterraneum, to examine the incidence of HGT events in the mitochondrial genome (mtDNA). The mtDNA of O. subterraneum assembles into 54 circular chromosomes, only 34 of which contain the 51 full-length coding regions. Numerous foreign tracts (totaling almost 100 kb, ~ 14% of the mtDNA), including 12 intact genes, were acquired by HGT from the Asteraceae hosts. Nine chromosomes concentrate most of those regions and eight are almost entirely foreign. Native homologs of each foreign gene coexist in the mtDNA and are potentially functional. A large proportion of shorter regions were related to the Fabaceae (a total of ~ 110 kb, 15.4%), some of which were shared with L. mirabile. We also found evidence of foreign sequences donated by angiosperm lineages not reported as hosts (Apocynaceae, Euphorbiaceae, Lamiaceae, and Malvales). We propose an evolutionary hypothesis that involves ancient transfers from legume hosts in the common ancestor of Ombrophytum and Lophophytum followed by more recent transfer events in L. mirabile. Besides, the O. subterraneum mtDNA was also subjected to additional HGT events from diverse angiosperm lineages, including large and recent transfers from the Asteraceae, and also from Lamiaceae.},
}

@article {pmid32430475,
year = {2020},
author = {Speijer, D and Hammond, M and Lukeš, J},
title = {Comparing Early Eukaryotic Integration of Mitochondria and Chloroplasts in the Light of Internal ROS Challenges: Timing is of the Essence.},
journal = {mBio},
volume = {11},
number = {3},
pages = {},
doi = {10.1128/mBio.00955-20},
pmid = {32430475},
issn = {2150-7511},
abstract = {When trying to reconstruct the evolutionary trajectories during early eukaryogenesis, one is struck by clear differences in the developments of two organelles of endosymbiotic origin: the mitochondrion and the chloroplast. From a symbiogenic perspective, eukaryotic development can be interpreted as a process in which many of the defining eukaryotic characteristics arose as a result of mutual adaptions of both prokaryotes (an archaeon and a bacterium) involved. This implies that many steps during the bacterium-to-mitochondrion transition trajectory occurred in an intense period of dramatic and rapid changes. In contrast, the subsequent cyanobacterium-to-chloroplast development in a specific eukaryotic subgroup, leading to the photosynthetic lineages, occurred in a full-fledged eukaryote. The commonalities and differences in the two trajectories shed an interesting light on early, and ongoing, eukaryotic evolutionary driving forces, especially endogenous reactive oxygen species (ROS) formation. Differences between organellar ribosomes, changes to the electron transport chain (ETC) components, and mitochondrial codon reassignments in nonplant mitochondria can be understood when mitochondrial ROS formation, e.g., during high energy consumption in heterotrophs, is taken into account.IMPORTANCE The early eukaryotic evolution was deeply influenced by the acquisition of two endosymbiotic organelles - the mitochondrion and the chloroplast. Here we discuss the possibly important role of reactive oxygen species in these processes.},
}

@article {pmid32428499,
year = {2020},
author = {Pánek, T and Eliáš, M and Vancová, M and Lukeš, J and Hashimi, H},
title = {Returning to the Fold for Lessons in Mitochondrial Crista Diversity and Evolution.},
journal = {Current biology : CB},
volume = {30},
number = {10},
pages = {R575-R588},
doi = {10.1016/j.cub.2020.02.053},
pmid = {32428499},
issn = {1879-0445},
abstract = {Cristae are infoldings of the mitochondrial inner membrane jutting into the organelle's innermost compartment from narrow stems at their base called crista junctions. They are emblematic of aerobic mitochondria, being the fabric for the molecular machinery driving cellular respiration. Electron microscopy revealed that diverse eukaryotes possess cristae of different shapes. Yet, crista diversity has not been systematically examined in light of our current knowledge about eukaryotic evolution. Since crista form and function are intricately linked, we take a holistic view of factors that may underlie both crista diversity and the adherence of cristae to a recognizable form. Based on electron micrographs of 226 species from all major lineages, we propose a rational crista classification system that postulates cristae as variations of two general morphotypes: flat and tubulo-vesicular. The latter is most prevalent and likely ancestral, but both morphotypes are found interspersed throughout the eukaryotic tree. In contrast, crista junctions are remarkably conserved, supporting their proposed role as diffusion barriers that sequester cristae contents. Since cardiolipin, ATP synthase dimers, the MICOS complex, and dynamin-like Opa1/Mgm1 are known to be involved in shaping cristae, we examined their variation in the context of crista diversity. Moreover, we have identified both commonalities and differences that may collectively be manifested as diverse variations of crista form and function.},
}

@article {pmid32428484,
year = {2020},
author = {Lane, N},
title = {How energy flow shapes cell evolution.},
journal = {Current biology : CB},
volume = {30},
number = {10},
pages = {R471-R476},
doi = {10.1016/j.cub.2020.03.055},
pmid = {32428484},
issn = {1879-0445},
abstract = {How mitochondria shaped the evolution of eukaryotic complexity has been controversial for decades. The discovery of the Asgard archaea, which harbor close phylogenetic ties to the eukaryotes, supports the idea that a critical endosymbiosis between an archaeal host and a bacterial endosymbiont transformed the selective constraints present at the origin of eukaryotes. Cultured Asgard archaea are typically prokaryotic in both size and internal morphology, albeit featuring extensive protrusions. The acquisition of the mitochondrial predecessor by an archaeal host cell fundamentally altered the topology of genes in relation to bioenergetic membranes. Mitochondria internalised not only the bioenergetic membranes but also the genetic machinery needed for local control of oxidative phosphorylation. Gene loss from mitochondria enabled expansion of the nuclear genome, giving rise to an extreme genomic asymmetry that is ancestral to all extant eukaryotes. This genomic restructuring gave eukaryotes thousands of fold more energy availability per gene. In principle, that difference can support more and larger genes, far more non-coding DNA, greater regulatory complexity, and thousands of fold more protein synthesis per gene. These changes released eukaryotes from the bioenergetic constraints on prokaryotes, facilitating the evolution of morphological complexity.},
}

@article {pmid32428446,
year = {2020},
author = {He, Q and Luo, J and Xu, JZ and Meng, XZ and Pan, GQ and Li, T and Zhou, ZY},
title = {Characterization of Hsp70 gene family provides insight into its functions related to microsporidian proliferation.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {107394},
doi = {10.1016/j.jip.2020.107394},
pmid = {32428446},
issn = {1096-0805},
abstract = {Heat shock protein 70 (Hsp70), a highly conserved protein family, is widely distributed in organisms and plays fundamental roles in biotic and abiotic stress responses. However, reports on Hsp70 genes are scarce in microsporidia, a very large group of obligate intracellular parasites that can infect nearly all animals, including humans. In this study, we identified 37 Hsp70 proteins from eight microsporidian genomes and classified them into four subfamilies (A-D). The number of Hsp70 genes in these microsporidia was significantly fewer than in Rozella allomycis and yeast. All microsporidian species contained genes from each subfamily and similar subcellular locations (mitochondria, endoplasmic reticulum, cytosol, and cytosol and/or nucleus), indicating that each Hsp70 member may fulfil distinct functions. The conserved structures and motifs of the Hsp70 proteins in the same subfamily were highly similar. Expression analysis indicated that the subfamily C cytosol (cyto)-associated Hsp70s is functional during microsporidia development. Immunofluorescence assays revealed that Cyto-NbHsp70 was cytoplasmically located in the proliferation-stage of Nosema bombycis. Cyto-NbHsp70 antiserum also labeled Encephalitozoon hellem within infected cells, suggesting that this antiserum is a potential molecular marker for labeling the proliferative phases of different microsporidian species. The propagation of N. bombycis was significantly inhibited following RNAi of Cyto-NbHsp70, indicating that Cyto-NbHsp70 is important for pathogen proliferation. Our phylogenetic data suggest that Hsp70 proteins evolved during microsporidia adaption to intracellular parasitism, and they play important roles in pathogen development.},
}

@article {pmid31801053,
year = {2019},
author = {Moraes, CT},
title = {Sorting mtDNA Species-the Role of nDNA-mtDNA Co-evolution.},
journal = {Cell metabolism},
volume = {30},
number = {6},
pages = {1002-1004},
doi = {10.1016/j.cmet.2019.11.005},
pmid = {31801053},
issn = {1932-7420},
support = {R01 EY010804/EY/NEI NIH HHS/United States ; R33 ES025673/ES/NIEHS NIH HHS/United States ; R01 AG036871/AG/NIA NIH HHS/United States ; R01 NS079965/NS/NINDS NIH HHS/United States ; },
mesh = {*DNA, Mitochondrial ; Female ; Humans ; Mitochondria ; *Mothers ; },
abstract = {The segregation of heteroplasmic mtDNA species was thought to be mostly stochastic. However, recent findings, including a study by Latorre-Pellicer et al. (2019) published in this issue of Cell Metabolism, provide evidence that nuclear DNA and mitochondrial DNA interactions play an important role in the sorting process.},
}

*DNA, Mitochondrial
Female
Humans
Mitochondria
*Mothers

@article {pmid31728830,
year = {2020},
author = {Wang, S and Jiao, N and Zhao, L and Zhang, M and Zhou, P and Huang, X and Hu, F and Yang, C and Shu, Y and Li, W and Zhang, C and Tao, M and Chen, B and Ma, M and Liu, S},
title = {Evidence for the paternal mitochondrial DNA in the crucian carp-like fish lineage with hybrid origin.},
journal = {Science China. Life sciences},
volume = {63},
number = {1},
pages = {102-115},
doi = {10.1007/s11427-019-9528-1},
pmid = {31728830},
issn = {1869-1889},
mesh = {Animals ; Base Sequence ; Carps/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Gene Expression ; Goldfish/*classification/*genetics ; Hybridization, Genetic ; Male ; Mitochondria/genetics ; Ploidies ; },
abstract = {In terms of taxonomic status, common carp (Cyprinus carpio, Cyprininae) and crucian carp (Carassius auratus, Cyprininae) are different species; however, in this study, a newborn homodiploid crucian carp-like fish (2n=100) (2nNCRC) lineage (F1-F3) was established from the interspecific hybridization of female common carp (2n=100)×male blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n=48). The phenotypes and genotypes of 2nNCRC differed from those of its parents but were closely related to those of the existing diploid crucian carp. We further sequenced the whole mitochondrial (mt) genomes of the 2nNCRC lineage from F1 to F3. The paternal mtDNA fragments were stably embedded in the mt-genomes of F1-F3 generations of 2nNCRC to form chimeric DNA fragments. Along with this chimeric process, numerous base sites of F1-F3 generations of 2nNCRC underwent mutations. Most of these mutation sites were consistent with the existing diploid crucian carp. Moreover, the mtDNA organization and nucleotide composition of 2nNCRC were more similar to those of the existing diploid crucian carp than those of the parents. The inheritable chimeric DNA fragments and mutant loci in the mt-genomes of different generations of 2nNCRC provided important evidence of the mtDNA change process in the newborn lineage derived from hybridization of different species. Our findings demonstrated for the first time that the paternal mtDNA were transmitted into the mt-genomes of homodiploid lineage, which provided new insights into the existence of paternal mtDNA in the mtDNA inheritance.},
}

Animals
Base Sequence
Carps/*classification/*genetics
DNA, Mitochondrial/*genetics
Female
Gene Expression
Goldfish/*classification/*genetics
Hybridization, Genetic
Male
Mitochondria/genetics
Ploidies

@article {pmid32413571,
year = {2020},
author = {Arad, M and Waldman, M and Abraham, NG and Hochhauser, E},
title = {Therapeutic approaches to diabetic cardiomyopathy: Targeting the antioxidant pathway.},
journal = {Prostaglandins & other lipid mediators},
volume = {},
number = {},
pages = {106454},
doi = {10.1016/j.prostaglandins.2020.106454},
pmid = {32413571},
issn = {1098-8823},
abstract = {The global epidemic of cardiovascular disease continues unabated and remains the leading cause of death both in the US and worldwide. In the current review we summarize the available therapies for diabetes and cardiovascular disease in diabetics. Clearly, the current approaches to diabetic heart disease often target the manifestations and certain mediators but not the specific pathways leading to myocardial injury, remodeling and dysfunction. Better understanding of the molecular events determining the evolution of diabetic cardiomyopathy will provide insight into the development of specific and targeted therapies. This review reflects a dramatic increase in understanding the role of enhanced inflammatory response, ROS production, fibrosis in diabetic heart, as well as the contribution of Cyp-P450-epoxygenase-derived epoxyeicosatrienoic acid (EET), Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1α (PGC-1α), Heme Oxygenase (HO)-1 and 20-HETE in pathophysiology and therapy of cardiovascular disease. PGC-1α increases production of the HO-1 which has a major role in protecting the heart against oxidative stress, microcirculation and mitochondrial dysfunction. This review focuses on potential drugs and their downstream targets, PGC-1α and HO-1, as major loci for developing therapeutic approaches beside diet and lifestyle modification for the treatment and prevention of heart disease associated with obesity and diabetes.},
}

@article {pmid32411111,
year = {2020},
author = {Fonseca, PLC and Badotti, F and De-Paula, RB and Araújo, DS and Bortolini, DE and Del-Bem, LE and Azevedo, VA and Brenig, B and Aguiar, ERGR and Góes-Neto, A},
title = {Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {765},
doi = {10.3389/fmicb.2020.00765},
pmid = {32411111},
issn = {1664-302X},
abstract = {The order Hypocreales (Ascomycota) is composed of ubiquitous and ecologically diverse fungi such as saprobes, biotrophs, and pathogens. Despite their phylogenetic relationship, these species exhibit high variability in biomolecules production, lifestyle, and fitness. The mitochondria play an important role in the fungal biology, providing energy to the cells and regulating diverse processes, such as immune response. In spite of its importance, the mechanisms that shape fungal mitogenomes are still poorly understood. Herein, we investigated the variability and evolution of mitogenomes and its relationship with the divergence time using the order Hypocreales as a study model. We sequenced and annotated for the first time Trichoderma harzianum mitochondrial genome (mtDNA), which was compared to other 34 mtDNAs species that were publicly available. Comparative analysis revealed a substantial structural and size variation on non-coding mtDNA regions, despite the conservation of copy number, length, and structure of protein-coding elements. Interestingly, we observed a highly significant correlation between mitogenome length, and the number and size of non-coding sequences in mitochondrial genome. Among the non-coding elements, group I and II introns and homing endonucleases genes (HEGs) were the main contributors to discrepancies in mitogenomes structure and length. Several intronic sequences displayed sequence similarity among species, and some of them are conserved even at gene position, and were present in the majority of mitogenomes, indicating its origin in a common ancestor. On the other hand, we also identified species-specific introns that advocate for the origin by different mechanisms. Investigation of mitochondrial gene transfer to the nuclear genome revealed that nuclear copies of the nad5 are the most frequent while atp8, atp9, and cox3 could not be identified in any of the nuclear genomes analyzed. Moreover, we also estimated the divergence time of each species and investigated its relationship with coding and non-coding elements as well as with the length of mitogenomes. Altogether, our results demonstrated that introns and HEGs are key elements on mitogenome shaping and its presence on fast-evolving mtDNAs could be mostly explained by its divergence time, although the intron sharing profile suggests the involvement of other mechanisms on the mitochondrial genome evolution, such as horizontal transference.},
}

@article {pmid30861107,
year = {2019},
author = {Sinha, S and Manoj, N},
title = {Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics.},
journal = {FEBS letters},
volume = {593},
number = {7},
pages = {703-718},
doi = {10.1002/1873-3468.13356},
pmid = {30861107},
issn = {1873-3468},
support = {//Indian Institute of Technology Madras/International ; },
mesh = {Animals ; Dynamins/*genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Fungi/genetics ; Mitochondria/genetics ; Mitochondrial Dynamics/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; },
abstract = {Eukaryotes employ a subset of dynamins to mediate mitochondrial fusion and fission dynamics. Here we report the molecular evolution and diversification of the dynamin-related mitochondrial proteins that drive the fission (Drp1) and the fusion processes (mitofusin and OPA1). We demonstrate that the three paralogs emerged concurrently in an early mitochondriate eukaryotic ancestor. Furthermore, multiple independent duplication events from an ancestral bifunctional fission protein gave rise to specialized fission proteins. The evolutionary history of these proteins is marked by transformations that include independent gain and loss events occurring at the levels of entire genes, specific functional domains, and intronic regions. The domain level variations primarily comprise loss-gain of lineage specific domains that are present in the terminal regions of the sequences.},
}

Animals
Dynamins/*genetics
Eukaryota/genetics
*Evolution, Molecular
Fungi/genetics
Mitochondria/genetics
Mitochondrial Dynamics/*genetics
Mitochondrial Proteins/*genetics
Phylogeny

@article {pmid32403285,
year = {2020},
author = {Diroma, MA and Varvara, AS and Attimonelli, M and Pesole, G and Picardi, E},
title = {Investigating Human Mitochondrial Genomes in Single Cells.},
journal = {Genes},
volume = {11},
number = {5},
pages = {},
doi = {10.3390/genes11050534},
pmid = {32403285},
issn = {2073-4425},
support = {ROADMAP ESFRI//ELIXIR IIB/ ; },
abstract = {Mitochondria host multiple copies of their own small circular genome that has been extensively studied to trace the evolution of the modern eukaryotic cell and discover important mutations linked to inherited diseases. Whole genome and exome sequencing have enabled the study of mtDNA in a large number of samples and experimental conditions at single nucleotide resolution, allowing the deciphering of the relationship between inherited mutations and phenotypes and the identification of acquired mtDNA mutations in classical mitochondrial diseases as well as in chronic disorders, ageing and cancer. By applying an ad hoc computational pipeline based on our MToolBox software, we reconstructed mtDNA genomes in single cells using whole genome and exome sequencing data obtained by different amplification methodologies (eWGA, DOP-PCR, MALBAC, MDA) as well as data from single cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) in which mtDNA sequences are expected as a byproduct of the technology. We show that assembled mtDNAs, with the exception of those reconstructed by MALBAC and DOP-PCR methods, are quite uniform and suitable for genomic investigations, enabling the study of various biological processes related to cellular heterogeneity such as tumor evolution, neural somatic mosaicism and embryonic development.},
}

@article {pmid31886178,
year = {2019},
author = {Mereu, P and Pirastru, M and Satta, V and Frongia, GN and Kassinis, N and Papadopoulos, M and Hadjisterkotis, E and Xirouchakis, S and Manca, L and Naitana, S and Leoni, GG},
title = {Mitochondrial D-loop Sequence Variability in Three Native Insular Griffon Vulture (Gyps fulvus) Populations from the Mediterranean Basin.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {2073919},
pmid = {31886178},
issn = {2314-6141},
mesh = {Animals ; Birds/*genetics ; *Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Endangered Species ; Genetic Variation/*genetics ; Genetics, Population ; Haplotypes/genetics ; Humans ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {The islands of Sardinia, Crete, and Cyprus are hosting the last native insular griffon populations in the Mediterranean basin. Their states have been evaluated from "vulnerable" to "critically endangered". The sequence analysis of molecular markers, particularly the mtDNA D-loop region, provides useful information in studying the evolution of closely related taxa and the conservation of endangered species. Therefore, a study of D-loop region sequence was carried out to estimate the genetic diversity and phylogenetic relationship within and among these three populations. Among 84 griffon specimens (44 Sardinian, 33 Cretan, and 7 Cypriot), we detected four haplotypes including a novel haplotype (HPT-D) that was exclusively found in the Cretan population with a frequency of 6.1%. When considered as a unique population, haplotype diversity (Hd) and nucleotide diversity (π) were high at 0.474 and 0.00176, respectively. A similar level of Hd and π was found in Sardinian and Cretan populations, both showing three haplotypes. The different haplotype frequencies and exclusivity detected were in accordance with the limited matrilineal gene flow (FST = 0.07097), probably related to the species reluctance to fly over sea masses. The genetic variability we observe today would therefore be the result of an evolutionary process strongly influenced by isolation leading to the appearance of island variants which deserve to be protected. Furthermore, since nesting sites and food availability are essential elements for colony settlement, we may infer that the island's colonization began when the first domestic animals were transferred by humans during the Neolithic. In conclusion, our research presents a first contribution to the genetic characterization of the griffon vulture populations in the Mediterranean islands of Sardinia, Crete and Cyprus and lays the foundation for conservation and restocking programs.},
}

Animals
Birds/*genetics
*Conservation of Natural Resources
DNA, Mitochondrial/genetics
Endangered Species
Genetic Variation/*genetics
Genetics, Population
Haplotypes/genetics
Humans
Mitochondria/*genetics
Phylogeny

@article {pmid31706020,
year = {2020},
author = {Prous, M and Lee, KM and Mutanen, M},
title = {Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106670},
doi = {10.1016/j.ympev.2019.106670},
pmid = {31706020},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial ; Gene Flow ; Genes, Mitochondrial ; Genome, Mitochondrial ; Genomics ; Hymenoptera/*classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtained genomic-scale ddRAD data together with Sanger sequences of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups of the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in the E. immersa group are not recovered as monophyletic according to either mitochondrial or nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within the E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10-20% of recovered loci) cross-contaminated. A reason could be specimen identification tag jumps during sequencing library preparation that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that the cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting of identical sequences in the immersa and longicornis groups, which are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by the small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution against drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using a unique combination of limited number of tags (less than the number of specimens).},
}

Animals
Cell Nucleus/*genetics
DNA, Mitochondrial
Gene Flow
Genes, Mitochondrial
Genome, Mitochondrial
Genomics
Hymenoptera/*classification/*genetics
Mitochondria/*genetics
Phylogeny
Sequence Analysis, DNA

@article {pmid30949694,
year = {2019},
author = {Greiner, S and Lehwark, P and Bock, R},
title = {OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes.},
journal = {Nucleic acids research},
volume = {47},
number = {W1},
pages = {W59-W64},
pmid = {30949694},
issn = {1362-4962},
mesh = {Chromosome Mapping ; Genome, Mitochondrial/*genetics ; Genome, Plastid/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Molecular Sequence Annotation ; Organelles/*genetics ; Phylogeny ; Plastids/genetics ; *Software ; },
abstract = {Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.},
}

Chromosome Mapping
Genome, Mitochondrial/*genetics
Genome, Plastid/*genetics
High-Throughput Nucleotide Sequencing
Mitochondria/genetics
Molecular Sequence Annotation
Organelles/*genetics
Phylogeny
Plastids/genetics
*Software

@article {pmid32397253,
year = {2020},
author = {Kleczewska, M and Grabinska, A and Jelen, M and Stolarska, M and Schilke, B and Marszalek, J and Craig, EA and Dutkiewicz, R},
title = {Biochemical Convergence of Mitochondrial Hsp70 System Specialized in Iron-Sulfur Cluster Biogenesis.},
journal = {International journal of molecular sciences},
volume = {21},
number = {9},
pages = {},
doi = {10.3390/ijms21093326},
pmid = {32397253},
issn = {1422-0067},
support = {UMO-2015/19/B/NZ1/00237//Narodowe Centrum Nauki/ ; TEAM POIR.04.04.00-00-4114 /17-00//Fundacja na rzecz Nauki Polskiej/ ; R35GM127009//National Institutes of Health/ ; },
abstract = {Mitochondria play a central role in the biogenesis of iron-sulfur cluster(s) (FeS), protein cofactors needed for many cellular activities. After assembly on scaffold protein Isu, the cluster is transferred onto a recipient apo-protein. Transfer requires Isu interaction with an Hsp70 chaperone system that includes a dedicated J-domain protein co-chaperone (Hsc20). Hsc20 stimulates Hsp70's ATPase activity, thus stabilizing the critical Isu-Hsp70 interaction. While most eukaryotes utilize a multifunctional mitochondrial (mt)Hsp70, yeast employ another Hsp70 (Ssq1), a product of mtHsp70 gene duplication. Ssq1 became specialized in FeS biogenesis, recapitulating the process in bacteria, where specialized Hsp70 HscA cooperates exclusively with an ortholog of Hsc20. While it is well established that Ssq1 and HscA converged functionally for FeS transfer, whether these two Hsp70s possess similar biochemical properties was not known. Here, we show that overall HscA and Ssq1 biochemical properties are very similar, despite subtle differences being apparent - the ATPase activity of HscA is stimulated to a somewhat higher levels by Isu and Hsc20, while Ssq1 has a higher affinity for Isu and for Hsc20. HscA/Ssq1 are a unique example of biochemical convergence of distantly related Hsp70s, with practical implications, crossover experimental results can be combined, facilitating understanding of the FeS transfer process.},
}

@article {pmid32396817,
year = {2020},
author = {Seebacher, F},
title = {Is Endothermy an Evolutionary By-Product?.},
journal = {Trends in ecology & evolution},
volume = {35},
number = {6},
pages = {503-511},
doi = {10.1016/j.tree.2020.02.006},
pmid = {32396817},
issn = {1872-8383},
abstract = {Endothermy alters the energetic relationships between organisms and their environment and thereby influences fundamental niches. Endothermy is closely tied to energy metabolism. Regulation of energy balance is indispensable for all life and regulatory pathways increase in complexity from bacteria to vertebrates. Increasing complexity of metabolic networks also increase the probability for endothermic phenotypes to appear. Adaptive arguments are problematic epistemologically because the regulatory mechanisms enabling endothermy have not evolved for the 'purpose' of endothermy and the utility of current traits is likely to have changed over evolutionary time. It is most parsimonious to view endothermy as the evolutionary by-product of energy balance regulation rather than as an adaptation and interpret its evolution in the context of metabolic networks.},
}

@article {pmid32396758,
year = {2020},
author = {Puertas, M and Gonzalez-Sanchez, M},
title = {INSERTIONS OF MITOCHONDRIAL DNA INTO THE NUCLEUS. EFFECTS AND ROLE IN CELL EVOLUTION.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2019-0151},
pmid = {32396758},
issn = {1480-3321},
abstract = {We review the insertion of mitochondrial DNA (mtDNA) fragments into nuclear DNA (NUMTS) as a general and ongoing process that has occurred many times during genome evolution. Fragments of mtDNA are generated during the lifetime of organisms in both somatic and germinal cells, by the production of reactive oxygen species in the mitochondria The fragments are inserted into the nucleus during the double strand breaks repair via the non-homologous end joining machinery, followed by genomic instability, giving rise to the high variability observed in NUMT patterns among species, populations or genotypes. Some de novo produced mtDNA insertions show harmful effects, being involved in human diseases, carcinogenesis and ageing. NUMT generation is a non-stop process overpassing the Mendelian transmission. This parasitic property ensures their survival even against their harmful effects. The accumulation of mtDNA fragments mainly at pericentromeric and subtelomeric regions is important to understand the transmission and integration of NUMTs into the genomes. The possible effect on of female meiotic drive for mtDNA insertions at centromeres remains to be studied. In spite of the harmful feature of NUMTs, they are important in cell evolution representing a major source of genomic variation.},
}

@article {pmid32393264,
year = {2020},
author = {De Chiara, M and Friedrich, A and Barré, B and Breitenbach, M and Schacherer, J and Liti, G},
title = {Discordant evolution of mitochondrial and nuclear yeast genomes at population level.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {49},
doi = {10.1186/s12915-020-00786-4},
pmid = {32393264},
issn = {1741-7007},
support = {ANR-10-INBS-09-08//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts.

RESULTS: In contrast with pre-whole genome duplication fungal species, S. cerevisiae mitochondrial genomes show higher genetic diversity compared to the nuclear genomes. Strikingly, mitochondrial genomes appear to be highly admixed, resulting in a complex interconnected phylogeny with a weak grouping of isolates, whereas interspecies introgressions are very rare. Complete genome assemblies revealed that structural rearrangements are nearly absent with rare inversions detected. We tracked intron variation in COX1 and COB to infer gain and loss events throughout the species evolutionary history. Mitochondrial genome copy number is connected with the nuclear genome and linearly scale up with ploidy. We observed rare cases of naturally occurring mitochondrial DNA loss, petite, with a subset of them that do not suffer the expected growth defect in fermentable rich media.

CONCLUSIONS: Overall, our results illustrate how differences in the biology of two genomes coexisting in the same cells can lead to discordant evolutionary histories.},
}

@article {pmid31865652,
year = {2019},
author = {Hamamcı, B and Açıkgöz, G and Kılıç, E and Karaaslan, K and Çetinkaya, Ü and Durgun Yetim, T and Yetim, İ},
title = {Biochemical Analysis of Germinal Membrane and Cyst Fluid by Raman Spectroscopy in Echinococcosis.},
journal = {Turkiye parazitolojii dergisi},
volume = {43},
number = {4},
pages = {175-181},
doi = {10.4274/tpd.galenos.2019.6293},
pmid = {31865652},
issn = {2146-3077},
mesh = {Animals ; Cyst Fluid/chemistry ; DNA, Helminth/chemistry ; Echinococcosis, Hepatic/*diagnostic imaging/parasitology ; Echinococcus granulosus/*classification/genetics ; Electron Transport Complex IV/genetics ; Humans ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction ; Spectrum Analysis, Raman ; Zoonoses/*diagnostic imaging/parasitology ; },
abstract = {Objective: Hydatidosis is a zoonotic parasitic infection caused by the larval stage of Echinococcus granulosus. The aim of this study was to investigate the biochemical structures of germinal membrane and cyst fluids obtained from patients with liver involvement during surgery, by Raman spectroscopy at the molecular level.

Methods: Molecular characterization of germinal membrane and cyst fluid according to mitochondrial gene region was determined and phylogenetic analysis was performed. Raman spectroscopy was used in samples and spectral bands between 300 and 1800 cm-1 were examined.

Results: As a result of PCR, approximately 400 bp DNA band was obtained from germinal membranes and cyst fluids gathered from patients. Peaks were observed at 780, 880, 970, 1151, 1200, 1270 cm-1 for germinal membrane and at 780 and 1200 cm-1 for cyst fluid. The highest spectral bands were obtained at 1333-1335 cm-1 and were determined to be modes indicating the CH3CH2 collagen and polynucleotide chain.

Conclusion: In the identification of microorganisms and biochemical analysis of biological tissues; different diagnostic methods such as molecular, serological and conventional methods are used. In addition to these methods, Raman spectroscopy has been shown in studies to be a fast, non-destructive and noninvasive method. Therefore, it is thought to be an alternative method for analyzing the basic biochemical components of microorganisms at molecular level.},
}

Animals
Cyst Fluid/chemistry
DNA, Helminth/chemistry
Echinococcosis, Hepatic/*diagnostic imaging/parasitology
Echinococcus granulosus/*classification/genetics
Electron Transport Complex IV/genetics
Humans
Mitochondria/enzymology
Phylogeny
Polymerase Chain Reaction
Spectrum Analysis, Raman
Zoonoses/*diagnostic imaging/parasitology

@article {pmid32390938,
year = {2020},
author = {Meduri, GU and Chrousos, GP},
title = {General Adaptation in Critical Illness: Glucocorticoid Receptor-alpha Master Regulator of Homeostatic Corrections.},
journal = {Frontiers in endocrinology},
volume = {11},
number = {},
pages = {161},
doi = {10.3389/fendo.2020.00161},
pmid = {32390938},
issn = {1664-2392},
abstract = {In critical illness, homeostatic corrections representing the culmination of hundreds of millions of years of evolution, are modulated by the activated glucocorticoid receptor alpha (GRα) and are associated with an enormous bioenergetic and metabolic cost. Appreciation of how homeostatic corrections work and how they evolved provides a conceptual framework to understand the complex pathobiology of critical illness. Emerging literature place the activated GRα at the center of all phases of disease development and resolution, including activation and re-enforcement of innate immunity, downregulation of pro-inflammatory transcription factors, and restoration of anatomy and function. By the time critically ill patients necessitate vital organ support for survival, they have reached near exhaustion or exhaustion of neuroendocrine homeostatic compensation, cell bio-energetic and adaptation functions, and reserves of vital micronutrients. We review how critical illness-related corticosteroid insufficiency, mitochondrial dysfunction/damage, and hypovitaminosis collectively interact to accelerate an anti-homeostatic active process of natural selection. Importantly, the allostatic overload imposed by these homeostatic corrections impacts negatively on both acute and long-term morbidity and mortality. Since the bioenergetic and metabolic reserves to support homeostatic corrections are time-limited, early interventions should be directed at increasing GRα and mitochondria number and function. Present understanding of the activated GC-GRα's role in immunomodulation and disease resolution should be taken into account when re-evaluating how to administer glucocorticoid treatment and co-interventions to improve cellular responsiveness. The activated GRα interdependence with functional mitochondria and three vitamin reserves (B1, C, and D) provides a rationale for co-interventions that include prolonged glucocorticoid treatment in association with rapid correction of hypovitaminosis.},
}

@article {pmid31254562,
year = {2019},
author = {Chen, J and Gong, Y and Zheng, H and Ma, H and Aweya, JJ and Zhang, Y and Chen, X and Li, SK},
title = {SpBcl2 promotes WSSV infection by suppressing apoptotic activity of hemocytes in mud crab, Scylla paramamosain.},
journal = {Developmental and comparative immunology},
volume = {100},
number = {},
pages = {103421},
doi = {10.1016/j.dci.2019.103421},
pmid = {31254562},
issn = {1879-0089},
mesh = {Animals ; Apoptosis/immunology ; Aquaculture ; Arthropod Proteins/immunology/*metabolism ; Brachyura/*immunology/virology ; Cytochromes c/immunology/metabolism ; Disease Resistance/immunology ; Gene Expression Profiling ; Hemocytes/cytology/immunology/pathology ; *Immunity, Innate ; Mitochondria/immunology/metabolism ; Phylogeny ; Proto-Oncogene Proteins c-bcl-2/immunology/*metabolism ; Up-Regulation/immunology ; White spot syndrome virus 1/*immunology ; },
abstract = {White spot syndrome virus (WSSV) is one of the most virulent and widespread pathogens that infect almost all marine crustaceans and therefore cause huge economic losses in aquaculture. The Bcl2 protein plays a key role in the mitochondrial apoptosis pathway, which is a crucial immune response in invertebrates. However, the role of Bcl2 in apoptosis and immunoregulation in mud crab, Scylla paramamosain, is poorly understood. Here, the Bcl2 homolog (SpBcl2) in S. paramamosain was cloned and its role in WSSV infection explored. The expression of SpBcl2 increased at both the transcriptional level and post-transcriptional level after WSSV infection, while the hemocytes apoptosis decreased significantly. Furthermore, there was increase in the level of cytochrome c coupled with an upregulation in the expression of SpBcl2. These results indicated that SpBcl2 suppressed apoptosis by preventing the release of cytochrome c from mitochondria, thereby promoting WSSV replication in mud crab. The findings here therefore provide novel insight into the immune response of mud crabs to WSSV infection.},
}

Animals
Apoptosis/immunology
Aquaculture
Arthropod Proteins/immunology/*metabolism
Brachyura/*immunology/virology
Cytochromes c/immunology/metabolism
Disease Resistance/immunology
Gene Expression Profiling
Hemocytes/cytology/immunology/pathology
*Immunity, Innate
Mitochondria/immunology/metabolism
Phylogeny
Proto-Oncogene Proteins c-bcl-2/immunology/*metabolism
Up-Regulation/immunology
White spot syndrome virus 1/*immunology

@article {pmid31066520,
year = {2019},
author = {Gobert, A and Bruggeman, M and Giegé, P},
title = {Involvement of PIN-like domain nucleases in tRNA processing and translation regulation.},
journal = {IUBMB life},
volume = {71},
number = {8},
pages = {1117-1125},
doi = {10.1002/iub.2062},
pmid = {31066520},
issn = {1521-6551},
mesh = {Anticodon/chemistry ; Arabidopsis/enzymology ; Chloroplasts/enzymology ; Cullin Proteins/chemistry ; Escherichia coli/enzymology ; *Gene Expression Regulation ; Homeostasis ; Humans ; Mitochondria/enzymology ; Protein Binding ; *Protein Biosynthesis ; Protein Domains ; Protein Interaction Mapping ; Protein Structure, Secondary ; RNA/chemistry ; RNA Precursors ; RNA, Transfer/*chemistry ; Ribonuclease P/*chemistry ; },
abstract = {Transfer RNAs require essential maturation steps to become functional. Among them, RNase P removes 5' leader sequences of pre-tRNAs. Although RNase P was long thought to occur universally as ribonucleoproteins, different types of protein-only RNase P enzymes were discovered in both eukaryotes and prokaryotes. Interestingly, all these enzymes belong to the super-group of PilT N-terminal-like nucleases (PIN)-like ribonucleases. This wide family of enzymes can be subdivided into major subgroups. Here, we review recent studies at both functional and mechanistic levels on three PIN-like ribonucleases groups containing enzymes connected to tRNA maturation and/or translation regulation. The evolutive distribution of these proteins containing PIN-like domains as well as their organization and fusion with various functional domains is discussed and put in perspective with the diversity of functions they acquired during evolution, for the maturation and homeostasis of tRNA and a wider array of RNA substrates. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1117-1125, 2019.},
}

Anticodon/chemistry
Arabidopsis/enzymology
Chloroplasts/enzymology
Cullin Proteins/chemistry
Escherichia coli/enzymology
*Gene Expression Regulation
Homeostasis
Humans
Mitochondria/enzymology
Protein Binding
*Protein Biosynthesis
Protein Domains
Protein Interaction Mapping
Protein Structure, Secondary
RNA/chemistry
RNA Precursors
RNA, Transfer/*chemistry
Ribonuclease P/*chemistry

@article {pmid32387125,
year = {2020},
author = {Gangloff, EJ and Schwartz, TS and Klabacka, R and Huebschman, N and Liu, AY and Bronikowski, AM},
title = {Mitochondria as central characters in a complex narrative: Linking genomics, energetics, and pace-of-life in natural populations of garter snakes.},
journal = {Experimental gerontology},
volume = {},
number = {},
pages = {110967},
doi = {10.1016/j.exger.2020.110967},
pmid = {32387125},
issn = {1873-6815},
abstract = {As a pacesetter for physiological processes, variation in metabolic rate can determine the shape of energetic trade-offs and thereby drive variation in life-history traits. In turn, such variation in metabolic performance and life-histories can have profound consequences for lifespan and lifetime fitness. Thus, the extent to which metabolic rate variation is due to phenotypic plasticity or fixed genetic differences among individuals or populations is likely to be shaped by natural selection. Here, we first present a generalized framework describing the central role of mitochondria in processes linking environmental, genomic, physiological, and aging variation. We then present a test of these relationships in an exemplary system: populations of garter snakes (Thamnophis elegans) exhibiting contrasting life-history strategies - fast-growing, early-reproducing, and fast-aging (FA) versus slow-growing, late-reproducing, and slow-aging (SA). Previous work has characterized divergences in mitochondrial function, reactive oxygen species processing, and whole-organism metabolic rate between these divergent life-history ecotypes. Here, we report new data on cellular respiration and mitochondrial genomics and synthesize these results with previous work. We test hypotheses about the causes and implications of mitochondrial genome variation within this generalized framework. First, we demonstrate that snakes of the FA ecotype increase cellular metabolic rate across their lifespan, while the opposite pattern holds for SA snakes, implying that reduced energetic throughput is associated with a longer life. Second, we show that variants in mitochondrial genomes are segregating across the landscape in a manner suggesting selection on the physiological consequences of this variation in habitats varying in temperature, food availability, and rates of predation. Third, we demonstrate functional variation in whole-organism metabolic rate related to these mitochondrial genome sequence variants. With this synthesis of numerous datasets, we are able to further characterize how variation across levels of biological organization interact within this generalized framework and how this has resulted in the emergence of distinct life-history ecotypes that vary in their rates of aging and lifespan.},
}

@article {pmid31823814,
year = {2019},
author = {Dubin, A and Jørgensen, TE and Jakt, LM and Johansen, SD},
title = {The mitochondrial transcriptome of the anglerfish Lophius piscatorius.},
journal = {BMC research notes},
volume = {12},
number = {1},
pages = {800},
pmid = {31823814},
issn = {1756-0500},
mesh = {Adenosine Triphosphatases/genetics ; Animals ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport Complex IV/genetics ; Fishes/*genetics/metabolism ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Intracellular Signaling Peptides and Proteins/genetics ; Mitochondria/*genetics/metabolism ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Antisense/genetics ; RNA, Long Noncoding/genetics ; RNA, Messenger/genetics ; RNA, Mitochondrial/genetics ; RNA, Ribosomal/genetics ; Transcriptome/*genetics ; },
abstract = {OBJECTIVE: Analyze key features of the anglerfish Lophius piscatorius mitochondrial transcriptome based on high-throughput total RNA sequencing.

RESULTS: We determined the complete mitochondrial DNA and corresponding transcriptome sequences of L. piscatorius. Key features include highly abundant mitochondrial ribosomal RNAs (10-100 times that of mRNAs), and that cytochrome oxidase mRNAs appeared > 5 times more abundant than both NADH dehydrogenase and ATPase mRNAs. Unusual for a vertebrate mitochondrial mRNA, the polyadenylated COI mRNA was found to harbor a 75 nucleotide 3' untranslated region. The mitochondrial genome expressed several non-canonical genes, including the long noncoding RNAs lncCR-H, lncCR-L and lncCOI. Whereas lncCR-H and lncCR-L mapped to opposite strands in a non-overlapping organization within the control region, lncCOI appeared novel among vertebrates. We found lncCOI to be a highly abundant mitochondrial RNA in antisense to the COI mRNA. Finally, we present the coding potential of a humanin-like peptide within the large subunit ribosomal RNA.},
}

Adenosine Triphosphatases/genetics
Animals
DNA, Mitochondrial/genetics/metabolism
Electron Transport Complex IV/genetics
Fishes/*genetics/metabolism
Genome, Mitochondrial
High-Throughput Nucleotide Sequencing
Intracellular Signaling Peptides and Proteins/genetics
Mitochondria/*genetics/metabolism
NADH Dehydrogenase/genetics
Phylogeny
RNA, Antisense/genetics
RNA, Long Noncoding/genetics
RNA, Messenger/genetics
RNA, Mitochondrial/genetics
RNA, Ribosomal/genetics
Transcriptome/*genetics

@article {pmid31430004,
year = {2019},
author = {Wu, B and Hao, W},
title = {Mitochondrial-encoded endonucleases drive recombination of protein-coding genes in yeast.},
journal = {Environmental microbiology},
volume = {21},
number = {11},
pages = {4233-4240},
doi = {10.1111/1462-2920.14783},
pmid = {31430004},
issn = {1462-2920},
support = {//Wayne State University/International ; },
mesh = {Endonucleases/genetics/*metabolism ; Genome, Mitochondrial/genetics ; Introns/genetics ; Mitochondria/*genetics ; *Recombination, Genetic ; Saccharomyces/*enzymology/*genetics ; },
abstract = {Mitochondrial recombination in yeast is well recognized, yet the underlying genetic mechanisms are not well understood. Recent progress has suggested that mobile introns in mitochondrial genomes (mitogenomes) can facilitate the recombination of their corresponding intron-containing genes through a mechanism known as intron homing. As many mitochondrial genes lack introns, there is a critical need to determine the extent of recombination and underlying mechanism of intron-lacking genes. This study leverages yeast mitogenomes to address these questions. In Saccharomyces cerevisiae, the 3'-end sequences of at least three intron-lacking mitochondrial genes exhibit elevated nucleotide diversity and recombination hotspots. Each of these 3'-end sequences is immediately adjacent to or even fused as overlapping genes with a stand-alone endonuclease. Our findings suggest that SAEs are responsible for recombination and elevated diversity of adjacent intron-lacking genes. SAEs were also evident to drive recombination of intron-lacking genes in Lachancea kluyveri, a yeast species that diverged from S. cerevisiae more than 100 million years ago. These results suggest SAEs as a common driver in recombination of intron-lacking genes during mitogenome evolution. We postulate that the linkage between intron-lacking gene and its adjacent endonuclease gene is the result of co-evolution.},
}

Endonucleases/genetics/*metabolism
Genome, Mitochondrial/genetics
Introns/genetics
Mitochondria/*genetics
*Recombination, Genetic
Saccharomyces/*enzymology/*genetics

@article {pmid32372945,
year = {2020},
author = {Scorziello, A and Borzacchiello, D and Sisalli, MJ and Di Martino, R and Morelli, M and Feliciello, A},
title = {Mitochondrial Homeostasis and Signaling in Parkinson's Disease.},
journal = {Frontiers in aging neuroscience},
volume = {12},
number = {},
pages = {100},
doi = {10.3389/fnagi.2020.00100},
pmid = {32372945},
issn = {1663-4365},
abstract = {The loss of dopaminergic (DA) neurons in the substantia nigra leads to a progressive, long-term decline of movement and other non-motor deficits. The symptoms of Parkinson's disease (PD) often appear later in the course of the disease, when most of the functional dopaminergic neurons have been lost. The late onset of the disease, the severity of the illness, and its impact on the global health system demand earlier diagnosis and better targeted therapy. PD etiology and pathogenesis are largely unknown. There are mutations in genes that have been linked to PD and, from these complex phenotypes, mitochondrial dysfunction emerged as central in the pathogenesis and evolution of PD. In fact, several PD-associated genes negatively impact on mitochondria physiology, supporting the notion that dysregulation of mitochondrial signaling and homeostasis is pathogenically relevant. Derangement of mitochondrial homeostatic controls can lead to oxidative stress and neuronal cell death. Restoring deranged signaling cascades to and from mitochondria in PD neurons may then represent a viable opportunity to reset energy metabolism and delay the death of dopaminergic neurons. Here, we will highlight the relevance of dysfunctional mitochondrial homeostasis and signaling in PD, the molecular mechanisms involved, and potential therapeutic approaches to restore mitochondrial activities in damaged neurons.},
}

@article {pmid32371392,
year = {2020},
author = {Chen, H and Shi, Z and Guo, J and Chang, KJ and Chen, Q and Yao, CH and Haigis, MC and Shi, Y},
title = {The human mitochondrial 12S rRNA m4C methyltransferase METTL15 is required for mitochondrial function.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA119.012127},
pmid = {32371392},
issn = {1083-351X},
abstract = {Mitochondrial DNA (mtDNA) gene expression is coordinately regulated both pre- and post-transcriptionally, and its perturbation can lead to human pathologies. Mitochondrial ribosomal RNAs (mt-rRNAs) undergo a series of nucleotide modifications after release from polycistronic mitochondrial RNA (mtRNA) precursors, which is essential for mitochondrial ribosomal biogenesis. Cytosine N4-methylation (m4C) at position 839 (m4C839) of the 12S small subunit (SSU) mt-rRNA was identified decades ago; however, its biogenesis and function have not been elucidated in detail. Here, using several approaches, including immunofluorescence, RNA immunoprecipitation and methylation assays, and bisulfite mapping, we demonstrate that human methyltransferase-like 15 (METTL15), encoded by a nuclear gene, is responsible for 12S mt-rRNA methylation at m4C839 both in vivo and in vitro We tracked the evolutionary history of RNA m4C methyltransferases and identified a difference in substrate preference between METTL15 and its bacterial ortholog rsmH. Additionally, unlike the very modest impact of a loss of m4C methylation in bacterial SSU rRNA on the ribosome, we found that METTL15 depletion results in impaired translation of mitochondrial protein-coding mRNAs and decreases mitochondrial respiration capacity. Our findings reveal that human METTL15 is required for mitochondrial function, delineate the evolution of methyltransferase substrate specificities and modification patterns in rRNA, and highlight a differential impact of m4C methylation on prokaryotic ribosomes and eukaryotic mitochondrial ribosomes.},
}

@article {pmid31382041,
year = {2019},
author = {De, AK and Muthiyan, R and Ponraj, P and Muniswamy, K and Sunder, J and Kundu, A and Karunakaran, D and George, Z and Kundu, MS and Ahmed, SKZ and Malakar, D and Bhattacharya, D},
title = {Mitogenome analysis of Indian isolate of Rhipicephalus microplus clade A sensu (): A first report from Maritime South-East Asia.},
journal = {Mitochondrion},
volume = {49},
number = {},
pages = {135-148},
doi = {10.1016/j.mito.2019.07.014},
pmid = {31382041},
issn = {1872-8278},
mesh = {Animals ; *Genome, Mitochondrial ; India ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Rhipicephalus/*genetics ; },
abstract = {This communication reports a comprehensive profile of mitogenome analysis of Rhipicephalus microplus, isolated and identified from Andaman and Nicobar islands, a part of Maritime South East Asia. Complete mitogenome of Indian isolate of R. microplus (MK234703) was 14,903 bp. Mitochondrial (mt.) genome had 13 protein coding genes (PCGs), 22 tRNAs, two ribosomal subunits and two control regions. All PCGs were located on the H-strand except nad1, nad5, nad4 and nad4L. All start codons were ATN codon and abbreviated stop codons were seen in cox-2-3, nad-5 and cytb. A purine rich tick-box motif has been identified. A tandem repeat unit (TTTATT), described as a region alike to nad1 was identified in 130 bp insertion in between nad1 and tRNA-Glu and in nad1 sequence. Presence of two control regions (CRs) proved that, two CRs have evolved in concert rather than independently. Strong biasness towards A and T in Indian isolate of R. microplus is a typical feature for most of the arthropods. Subtracted values of dn and ds suggested that, there was least effect of nt. sequence of cox1 gene when Indian isolate was compared with other isolates of Rhipicephalus. On the basis of phylogenetic analysis, species of the genus Rhipicephalus could be clustered in three groups; ticks of the genera belonging to sub-family Rhipicephalinae could be grouped in a single cluster. Finally, cox1 sequence of MK234703 indicated that the isolate belonged to clade A sensu Burger et al., 2014 which has not been reported earlier from India.},
}

Animals
*Genome, Mitochondrial
India
Mitochondria/*genetics
Mitochondrial Proteins/genetics
*Phylogeny
RNA, Ribosomal/genetics
RNA, Transfer/genetics
Rhipicephalus/*genetics

@article {pmid30855674,
year = {2019},
author = {Dobler, R and Dowling, DK and Morrow, EH and Reinhardt, K},
title = {Reply: Mitochondrial replacement and its effects on human health: accounting for non-independence of data in meta-analyses.},
journal = {Human reproduction update},
volume = {25},
number = {3},
pages = {393-394},
doi = {10.1093/humupd/dmz010},
pmid = {30855674},
issn = {1460-2369},
mesh = {*Germ Cells ; Humans ; *Mitochondria ; },
}

*Germ Cells
Humans
*Mitochondria

@article {pmid31742484,
year = {2019},
author = {Woodyard, ET and Stilwell, JM and Camus, AC and Rosser, TG},
title = {Molecular and Histopathological Data on Levisunguis subaequalis Curran, Overstreet, Collins & Benz, 2014 (Pentastomida: Eupentastomida: Porocephalida: Porocephaloidea: Sebekidae: Sebekinae) from Gambusia affinis in Alabama, USA.},
journal = {The Journal of parasitology},
volume = {105},
number = {6},
pages = {827-839},
pmid = {31742484},
issn = {1937-2345},
mesh = {Alabama/epidemiology ; Animals ; Bayes Theorem ; Cyprinodontiformes/*parasitology ; DNA/genetics/isolation & purification ; Electron Transport Complex IV/genetics ; Fish Diseases/epidemiology/*parasitology ; Likelihood Functions ; Lung/parasitology ; Mitochondria/enzymology ; Nymph/anatomy & histology ; Parasitic Diseases, Animal/epidemiology/*parasitology ; Pentastomida/anatomy & histology/classification/*genetics ; Phylogeny ; Prevalence ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Turtles/parasitology ; },
abstract = {Levisunguis subaequalis Curran, Overstreet, Collins & Benz, 2014 , was recently described from the lungs of the definitive hosts, softshell turtles, Apalone ferox (Schneider, 1783), and Apalone spinifera aspera (Agassiz, 1857) as well as the viscera of an intermediate host, the western mosquitofish, Gambusia affinis (Baird and Girard, 1853). However, the original account lacked molecular data. Furthermore, histological examination of infected host tissues in the original account of L. subaequalis did not reveal any pathological changes in the intermediate host. The present work provides a robust morphological description of the nymph and novel molecular data from the 18S and 28S ribosomal gene regions and the cytochrome c oxidase subunit 1 (COI) mitochondrial gene. Phylogenetic analyses using Bayesian inference and maximum likelihood analysis with concatenated sequence data from these 3 regions, as well as each region individually, placed the turtle pentastomid L. subaequalis as a sister clade to the crocodilian pentastomids of the genus Sebekia Sambon, 1922. While only concatenated phylogenetic analyses agreed with the currently accepted classification of the Eupentastomida and phylogenetic signal assessment indicated that the concatenated data set yielded the most phylogenetic signal, data from more taxa are still needed for robust phylogenetic inferences to be made. The intensity of infection ranged from 2 to 171 nymphs per fish, compared with the highest previously reported intensity of 6. These high-intensity infections with L. subaequalis were characterized by the nymphs occupying 5-50% of the coelomic cavity of G. affinis. However, despite this heavy parasite infection, fish exhibited minimal pathology. Observed pathology was characterized by compression or effacement of organs adjacent to the nymphs, particularly liver, swim bladder, and intestines, as well as the formation of granulomas around shed pentastomid cuticles. Nonetheless, the morphological and molecular data provided in the present work will bolster future efforts to identify this pentastomid in other hosts where pathology may be present in addition to aiding in the advancement of the field of molecular pentastomid systematics.},
}

Alabama/epidemiology
Animals
Bayes Theorem
Cyprinodontiformes/*parasitology
DNA/genetics/isolation & purification
Electron Transport Complex IV/genetics
Fish Diseases/epidemiology/*parasitology
Likelihood Functions
Lung/parasitology
Mitochondria/enzymology
Nymph/anatomy & histology
Parasitic Diseases, Animal/epidemiology/*parasitology
Pentastomida/anatomy & histology/classification/*genetics
Phylogeny
Prevalence
RNA, Ribosomal, 18S/genetics
RNA, Ribosomal, 28S/genetics
Turtles/parasitology

@article {pmid30703747,
year = {2019},
author = {Gerosa, C and Fanni, D and Congiu, T and Piras, M and Cau, F and Moi, M and Faa, G},
title = {Liver pathology in Wilson's disease: From copper overload to cirrhosis.},
journal = {Journal of inorganic biochemistry},
volume = {193},
number = {},
pages = {106-111},
doi = {10.1016/j.jinorgbio.2019.01.008},
pmid = {30703747},
issn = {1873-3344},
mesh = {Copper/*metabolism ; Copper-Transporting ATPases/genetics/metabolism ; Epigenesis, Genetic ; Hepatolenticular Degeneration/drug therapy/*pathology ; Humans ; Liver/*pathology ; Liver Cirrhosis/drug therapy ; Mitochondria/metabolism/pathology ; Mutation ; Penicillamine/therapeutic use ; },
abstract = {Wilson's disease (WD) is a genetic metabolic disease strictly associated with liver cirrhosis. In this review, the genetic bases of the disease are discussed, with emphasis on the role of ATP7B (the Wilson disease protein) dysfunction as a determinant factor of systemic copper overload. Regarding the different multiple mutations described in WD patients, the peculiarity of Sardinian population is highlighted, Sardinians carrying a rare deletion in the promoter (5' UTR) of the WD gene. The role of epigenetic changes in the clinical presentation and evolution of liver disease in WD patients is also discussed, nutrition probably representing a relevantly risk factor in WD patients. The role of transmission electron microscopy in the diagnosis of WD-related liver disease is underlined. Mitochondrial changes, increased peroxisomes fat droplets, lipolysosomes and intranuclear glycogen inclusions are reported as the most frequent ultrastructural changes in the liver of WD carriers. The role of histochemical stains for copper is analyzed, and the Timm's method is suggested as the most sensitive one for revealing hepatic copper overload in all stage of WD. The marked variability of the histological liver changes occurring in WD is underlined simple steatosis may represent the only pathological changes, frequently associated with glycogenated nuclei. Mallory-Denk bodies lipogranulomas alcoholic and non-alcoholic fatty liver disease ending with bridging fibrosis and cirrhosis. Finally, the reversal of fibrosis as a possible therapeutic objective in WD is discussed.},
}

Copper/*metabolism
Copper-Transporting ATPases/genetics/metabolism
Epigenesis, Genetic
Hepatolenticular Degeneration/drug therapy/*pathology
Humans
Liver/*pathology
Liver Cirrhosis/drug therapy
Mitochondria/metabolism/pathology
Mutation
Penicillamine/therapeutic use

@article {pmid32362267,
year = {2020},
author = {Pfannschmidt, T and Terry, MJ and Van Aken, O and Quiros, PM},
title = {Retrograde signals from endosymbiotic organelles: a common control principle in eukaryotic cells.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1801},
pages = {20190396},
doi = {10.1098/rstb.2019.0396},
pmid = {32362267},
issn = {1471-2970},
abstract = {Endosymbiotic organelles of eukaryotic cells, the plastids, including chloroplasts and mitochondria, are highly integrated into cellular signalling networks. In both heterotrophic and autotrophic organisms, plastids and/or mitochondria require extensive organelle-to-nucleus communication in order to establish a coordinated expression of their own genomes with the nuclear genome, which encodes the majority of the components of these organelles. This goal is achieved by the use of a variety of signals that inform the cell nucleus about the number and developmental status of the organelles and their reaction to changing external environments. Such signals have been identified in both photosynthetic and non-photosynthetic eukaryotes (known as retrograde signalling and retrograde response, respectively) and, therefore, appear to be universal mechanisms acting in eukaryotes of all kingdoms. In particular, chloroplasts and mitochondria both harbour crucial redox reactions that are the basis of eukaryotic life and are, therefore, especially susceptible to stress from the environment, which they signal to the rest of the cell. These signals are crucial for cell survival, lifespan and environmental adjustment, and regulate quality control and targeted degradation of dysfunctional organelles, metabolic adjustments, and developmental signalling, as well as induction of apoptosis. The functional similarities between retrograde signalling pathways in autotrophic and non-autotrophic organisms are striking, suggesting the existence of common principles in signalling mechanisms or similarities in their evolution. Here, we provide a survey for the newcomers to this field of research and discuss the importance of retrograde signalling in the context of eukaryotic evolution. Furthermore, we discuss commonalities and differences in retrograde signalling mechanisms and propose retrograde signalling as a general signalling mechanism in eukaryotic cells that will be also of interest for the specialist. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.},
}

@article {pmid31095885,
year = {2019},
author = {Vesteg, M and Hadariová, L and Horváth, A and Estraño, CE and Schwartzbach, SD and Krajčovič, J},
title = {Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {94},
number = {5},
pages = {1701-1721},
doi = {10.1111/brv.12523},
pmid = {31095885},
issn = {1469-185X},
mesh = {*Biological Evolution ; DNA-Directed RNA Polymerases/genetics/metabolism ; Euglenida/classification/genetics ; Euglenozoa/*classification/genetics ; Genome/physiology ; Introns/physiology ; Mitochondria/genetics ; *Molecular Biology ; Phototrophic Processes ; Phylogeny ; RNA Interference ; RNA, Ribosomal, 28S/genetics ; Trypanosomatina/classification/enzymology/*genetics ; },
abstract = {Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria-encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual 'J' base (β-D-glucosyl-hydroxymethyluracil), processing of nucleus-encoded precursor messenger RNAs (pre-mRNAs) via spliced-leader RNA (SL-RNA) trans-splicing, post-transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis-spliced introns, polyproteins) is unclear.},
}

*Biological Evolution
DNA-Directed RNA Polymerases/genetics/metabolism
Euglenida/classification/genetics
Euglenozoa/*classification/genetics
Genome/physiology
Introns/physiology
Mitochondria/genetics
*Molecular Biology
Phototrophic Processes
Phylogeny
RNA Interference
RNA, Ribosomal, 28S/genetics
Trypanosomatina/classification/enzymology/*genetics

@article {pmid31249872,
year = {2019},
author = {Peyrégne, S and Slon, V and Mafessoni, F and de Filippo, C and Hajdinjak, M and Nagel, S and Nickel, B and Essel, E and Le Cabec, A and Wehrberger, K and Conard, NJ and Kind, CJ and Posth, C and Krause, J and Abrams, G and Bonjean, D and Di Modica, K and Toussaint, M and Kelso, J and Meyer, M and Pääbo, S and Prüfer, K},
title = {Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe.},
journal = {Science advances},
volume = {5},
number = {6},
pages = {eaaw5873},
pmid = {31249872},
issn = {2375-2548},
mesh = {Animals ; Cell Lineage/genetics ; Cell Nucleus/*genetics ; DNA/*genetics ; Europe ; Evolution, Molecular ; Fossils ; Genome/genetics ; Germany ; Mitochondria/genetics ; Neanderthals/*genetics ; },
abstract = {Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.},
}

Animals
Cell Lineage/genetics
Cell Nucleus/*genetics
DNA/*genetics
Europe
Evolution, Molecular
Fossils
Genome/genetics
Germany
Mitochondria/genetics
Neanderthals/*genetics

@article {pmid32345370,
year = {2020},
author = {Bateman, A},
title = {Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells.},
journal = {Biology direct},
volume = {15},
number = {1},
pages = {8},
doi = {10.1186/s13062-020-00260-9},
pmid = {32345370},
issn = {1745-6150},
abstract = {Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the second model, two prokaryotes, probably an archaeon and a bacterial cell, engaged in prokaryotic endosymbiosis, with the species resident within the host becoming the mitochondrial progenitor. Both models have limitations. A search was therefore undertaken for alternative routes towards the origin of eukaryotic cells. The question was addressed by considering classes of potential pathways from prokaryotic to eukaryotic cells based on considerations of cellular topology. Among the solutions identified, one, called here the "third-space model", has not been widely explored. A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to "merge" as a transitionary complex without obligatory endosymbiosis or phagocytosis and to form a precursor cell. Incipient nuclei and mitochondria diverge by division of labour. The third-space model can accommodate the reorganization of prokaryote-like genomes to a more eukaryote-like genome structure. Nuclei with multiple chromosomes and mitosis emerge as a natural feature of the model. The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic reticulum. Advantages, limitations and variations of the "third-space" models are discussed. REVIEWERS: This article was reviewed by Damien Devos, Buzz Baum and Michael Gray.},
}

@article {pmid32341569,
year = {2020},
author = {López-García, P and Moreira, D},
title = {The Syntrophy hypothesis for the origin of eukaryotes revisited.},
journal = {Nature microbiology},
volume = {5},
number = {5},
pages = {655-667},
doi = {10.1038/s41564-020-0710-4},
pmid = {32341569},
issn = {2058-5276},
abstract = {The discovery of Asgard archaea, phylogenetically closer to eukaryotes than other archaea, together with improved knowledge of microbial ecology, impose new constraints on emerging models for the origin of the eukaryotic cell (eukaryogenesis). Long-held views are metamorphosing in favour of symbiogenetic models based on metabolic interactions between archaea and bacteria. These include the classical Searcy's and Hydrogen hypothesis, and the more recent Reverse Flow and Entangle-Engulf-Endogenize models. Two decades ago, we put forward the Syntrophy hypothesis for the origin of eukaryotes based on a tripartite metabolic symbiosis involving a methanogenic archaeon (future nucleus), a fermentative myxobacterial-like deltaproteobacterium (future eukaryotic cytoplasm) and a metabolically versatile methanotrophic alphaproteobacterium (future mitochondrion). A refined version later proposed the evolution of the endomembrane and nuclear membrane system by invagination of the deltaproteobacterial membrane. Here, we adapt the Syntrophy hypothesis to contemporary knowledge, shifting from the original hydrogen and methane-transfer-based symbiosis (HM Syntrophy) to a tripartite hydrogen and sulfur-transfer-based model (HS Syntrophy). We propose a sensible ecological scenario for eukaryogenesis in which eukaryotes originated in early Proterozoic microbial mats from the endosymbiosis of a hydrogen-producing Asgard archaeon within a complex sulfate-reducing deltaproteobacterium. Mitochondria evolved from versatile, facultatively aerobic, sulfide-oxidizing and, potentially, anoxygenic photosynthesizing alphaproteobacterial endosymbionts that recycled sulfur in the consortium. The HS Syntrophy hypothesis accounts for (endo)membrane, nucleus and metabolic evolution in a realistic ecological context. We compare and contrast the HS Syntrophy hypothesis to other models of eukaryogenesis, notably in terms of the mode and tempo of eukaryotic trait evolution, and discuss several model predictions and how these can be tested.},
}

@article {pmid32337520,
year = {2020},
author = {Pearson, SA and Wachnowsky, C and Cowan, JA},
title = {Defining the mechanism of the mitochondrial Atm1p [2Fe-2S] cluster exporter.},
journal = {Metallomics : integrated biometal science},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9mt00286c},
pmid = {32337520},
issn = {1756-591X},
abstract = {Iron-sulfur cluster proteins play key roles in a multitude of physiological processes; including gene expression, nitrogen and oxygen sensing, electron transfer, and DNA repair. Biosynthesis of iron-sulfur clusters occurs in mitochondria on iron-sulfur cluster scaffold proteins in the form of [2Fe-2S] cores that are then transferred to apo targets within metabolic or respiratory pathways. The mechanism by which cytosolic Fe-S cluster proteins mature to their holo forms remains controversial. The mitochondrial inner membrane protein Atm1p can transport glutathione-coordinated iron-sulfur clusters, which may connect the mitochondrial and cytosolic iron-sulfur cluster assembly systems. Herein we describe experiments on the yeast Atm1p/ABCB7 exporter that provide additional support for a glutathione-complexed cluster as the natural physiological substrate and a reflection of the endosymbiotic model of mitochondrial evolution. These studies provide insight on the mechanism of cluster transport and the molecular basis of human disease conditions related to ABCB7. Recruitment of MgATP following cluster binding promotes a structural transition from closed to open conformations that is mediated by coupling helices, with MgATP hydrolysis facilitating the return to the closed state.},
}

@article {pmid31969697,
year = {2020},
author = {Mishmar, D},
title = {mtDNA in the crossroads of evolution and disease.},
journal = {Nature reviews. Molecular cell biology},
volume = {21},
number = {4},
pages = {181},
doi = {10.1038/s41580-020-0213-4},
pmid = {31969697},
issn = {1471-0080},
mesh = {Alleles ; *DNA, Mitochondrial ; Evolution, Molecular ; *Mitochondria ; Phenotype ; },
}

Alleles
*DNA, Mitochondrial
Evolution, Molecular
*Mitochondria
Phenotype

@article {pmid31329512,
year = {2019},
author = {Cronshaw, M and Parker, S and Arany, P},
title = {Feeling the Heat: Evolutionary and Microbial Basis for the Analgesic Mechanisms of Photobiomodulation Therapy.},
journal = {Photobiomodulation, photomedicine, and laser surgery},
volume = {37},
number = {9},
pages = {517-526},
doi = {10.1089/photob.2019.4684},
pmid = {31329512},
issn = {2578-5478},
mesh = {Analgesia/*methods ; Biological Evolution ; Eukaryota/physiology ; Hot Temperature ; Humans ; Low-Level Light Therapy/*methods ; Mitochondria/physiology ; Patient Safety ; },
abstract = {Background: The clinical therapeutic benefits of Photobiomodulation (PBM) therapy have been well established in many clinical scenarios. However, we are far from having developed a complete understanding of the underlying mechanisms of photon-biological tissue interactions. Concurrent to ongoing PBM studies, there are several parallel fields with evidences from cell and tissue physiology such as evolutionary biology, photobiology, and microbiology among others. Objective: This review is focused on extrapolating evidences from an expanded range of studies that may contribute to a better understanding of PBM mechanisms especially focusing on analgesia. Further, the choice of a PBM device source and relevant dosimetry with regards to specific mechanisms are discussed to enable broader clinical use of PBM therapies. Materials and methods: This discussion article is referenced from an expanded range of peer reviewed publications, including literature associated with evolutionary biology, microbiology, oncology, and photo-optical imaging technology, amongst others. Results and discussion: Materials drawn from many disparate disciplines is described. By inference from the current evidence base, a novel theory is offered to partially explain the cellular basis of PBM-induced analgesia. It is proposed that this may involve the activity of a class of transmembrane proteins known as uncoupling proteins. Furthermore, it is proposed that this may activate the heat stress protein response and that intracellur microthermal inclines may be of significance in PBM analgesia. It is suggested that the PBM dose response as a simple binary model of PBM effects as represented by the Arndt-Schulz law is clinically less useful than a multiphasic biological response. Finally, comments are made concerning the nature of photon to tissue interaction that can have significance in regard to the effective choice and delivery of dose to clinical target. Conclusions: It is suggested that a re-evaluation of phototransduction pathways may lead to an improvement in outcome in phototheraphy. An enhanced knowledge of safe parameters and a better knowledge of the mechanics of action at target level will permit more reliable and predictable clinical gain and assist the acceptance of PBM therapy within the wider medical community.},
}

Analgesia/*methods
Biological Evolution
Eukaryota/physiology
Hot Temperature
Humans
Low-Level Light Therapy/*methods
Mitochondria/physiology
Patient Safety

@article {pmid32334144,
year = {2020},
author = {Waltz, F and Corre, N and Hashem, Y and Giegé, P},
title = {Specificities of the plant mitochondrial translation apparatus.},
journal = {Mitochondrion},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mito.2020.04.008},
pmid = {32334144},
issn = {1872-8278},
abstract = {Mitochondria are endosymbiotic organelles responsible for energy production in most eukaryotic cells. They host a genome and a fully functional gene expression machinery. In plants this machinery involves hundreds of pentatricopeptide repeat (PPR) proteins. Translation, the final step of mitochondrial gene expression is performed by mitochondrial ribosomes (mitoribosomes). The nature of these molecular machines remained elusive for a very long time. Because of their bacterial origin, it was expected that mitoribosomes would closely resemble bacterial ribosomes. However, recent advances in cryo-electron microscopy have revealed the extraordinary diversity of mitoribosome structure and composition. The plant mitoribosome was characterized for Arabidopsis. In plants, in contrast to other species such as mammals and kinetoplastids where rRNA has been largely reduced, the mitoribosome could be described as a protein/RNA-augmented bacterial ribosome. It has an oversized small subunit formed by expanded ribosomal RNAs and additional protein components when compared to bacterial ribosomes. The same holds true for the large subunit. The small subunit is characterized by a new elongated domain on the head. Among its additional proteins, several PPR proteins are core mitoribosome proteins. They mainly act at the structural level to stabilize and maintain the plant-specific ribosomal RNA expansions but could also be involved in translation initiation. Recent advances in plant mitoribosome composition and structure, its specialization for membrane protein synthesis, translation initiation, the regulation and dynamics of mitochondrial translation are reviewed here and put in perspective with the diversity of mitochondrial translation processes in the green lineage and in the wider context of eukaryote evolution.},
}

@article {pmid32333942,
year = {2020},
author = {Kaufer, A and Stark, D and Ellis, J},
title = {A review of the systematics, species identification and diagnostics of the Trypanosomatidae using the maxicircle kinetoplast DNA: from past to present.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2020.03.003},
pmid = {32333942},
issn = {1879-0135},
abstract = {The Trypanosomatid family are a diverse and widespread group of protozoan parasites that belong to the higher order class Kinetoplastida. Containing predominantly monoxenous species (i.e. those having only a single host) that are confined to invertebrate hosts, this class is primarily known for its pathogenic dixenous species (i.e. those that have two hosts), serving as the aetiological agents of the important neglected tropical diseases (NTDs) including leishmaniasis, American trypanosomiasis (Chagas disease) and human African trypanosomiasis. Over the past few decades, a multitude of studies have investigated the diversity, classification and evolutionary history of the trypanosomatid family using different approaches and molecular targets. The mitochondrial-like DNA of the trypanosomatid parasites, also known as the kinetoplast, has emerged as a unique taxonomic and diagnostic target for exploring the evolution of this diverse group of parasitic eukaryotes. This review discusses recent advancements and important developments that have made a significant impact in the field of trypanosomatid systematics and diagnostics in recent years.},
}

@article {pmid32330419,
year = {2020},
author = {Rotterová, J and Salomaki, E and Pánek, T and Bourland, W and Žihala, D and Táborský, P and Edgcomb, VP and Beinart, RA and Kolísko, M and Čepička, I},
title = {Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2020.03.064},
pmid = {32330419},
issn = {1879-0445},
abstract = {Oxygen plays a crucial role in energetic metabolism of most eukaryotes. Yet adaptations to low-oxygen concentrations leading to anaerobiosis have independently arisen in many eukaryotic lineages, resulting in a broad spectrum of reduced and modified mitochondrion-related organelles (MROs). In this study, we present the discovery of two new class-level lineages of free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and Parablepharismea, cl. nov., that, together with the class Armophorea, form a major clade of obligate anaerobes (APM ciliates) within the Spirotrichea, Armophorea, and Litostomatea (SAL) group. To deepen our understanding of the evolution of anaerobiosis in ciliates, we predicted the mitochondrial metabolism of cultured representatives from all three classes in the APM clade by using transcriptomic and metagenomic data and performed phylogenomic analyses to assess their evolutionary relationships. The predicted mitochondrial metabolism of representatives from the APM ciliates reveals functional adaptations of metabolic pathways that were present in their last common ancestor and likely led to the successful colonization and diversification of the group in various anoxic environments. Furthermore, we discuss the possible relationship of Parablepharismea to the uncultured deep-sea class Cariacotrichea on the basis of single-gene analyses. Like most anaerobic ciliates, all studied species of the APM clade host symbionts, which we propose to be a significant accelerating factor in the transitions to an obligately anaerobic lifestyle. Our results provide an insight into the evolutionary mechanisms of early transitions to anaerobiosis and shed light on fine-scale adaptations in MROs over a relatively short evolutionary time frame.},
}

@article {pmid32322241,
year = {2020},
author = {Yang, F and Jin, H and Wang, XQ and Li, Q and Zhang, JT and Cui, N and Jiang, YL and Chen, Y and Wu, QF and Zhou, CZ and Li, WF},
title = {Genomic Analysis of Mic1 Reveals a Novel Freshwater Long-Tailed Cyanophage.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {484},
doi = {10.3389/fmicb.2020.00484},
pmid = {32322241},
issn = {1664-302X},
abstract = {Lake Chaohu, one of the five largest freshwater lakes in China, has been suffering from severe cyanobacterial blooms in the summer for many years. Cyanophages, the viruses that specifically infect cyanobacteria, play a key role in modulating cyanobacterial population, and thus regulate the emergence and decline of cyanobacterial blooms. Here we report a long-tailed cyanophage isolated from Lake Chaohu, termed Mic1, which specifically infects the cyanobacterium Microcystis aeruginosa. Mic1 has an icosahedral head of 88 nm in diameter and a long flexible tail of 400 nm. It possesses a circular genome of 92,627 bp, which contains 98 putative open reading frames. Genome sequence analysis enabled us to define a novel terminase large subunit that consists of two types of intein, indicating that the genome packaging of Mic1 is under fine control via posttranslational maturation of the terminase. Moreover, phylogenetic analysis suggested Mic1 and mitochondria share a common evolutionary origin of DNA polymerase γ gene. All together, these findings provided a start-point for investigating the co-evolution of cyanophages and its cyanobacterial hosts.},
}

@article {pmid32313974,
year = {2020},
author = {Almeida, C and Amaral, MD},
title = {A central role of the endoplasmic reticulum in the cell emerges from its functional contact sites with multiple organelles.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-020-03523-w},
pmid = {32313974},
issn = {1420-9071},
support = {SFRH/BPD/77720/2011//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIM-MEC/2131/2014//Fundação para a Ciência e a Tecnologia/ ; FCT/02/SAICT/2017/28800//Fundação para a Ciência e a Tecnologia/ ; UID/MULTI/04046/2019//Bioisi/ ; SRC 013//Cystic Fibrosis Trust/ ; },
abstract = {Early eukaryotic cells emerged from the compartmentalization of metabolic processes into specific organelles through the development of an endomembrane system (ES), a precursor of the endoplasmic reticulum (ER), which was essential for their survival. Recently, substantial evidence emerged on how organelles communicate among themselves and with the plasma membrane (PM) through contact sites (CSs). From these studies, the ER-the largest single structure in eukaryotic cells-emerges as a central player communicating with all organelles to coordinate cell functions and respond to external stimuli to maintain cellular homeostasis. Herein we review the functional insights into the ER-CSs with other organelles in a physiological perspective. We hypothesize that, in addition to the primitive role by the ES in the appearance of proto-eukaryotes, its successor-the ER-emerges as the key coordinator of inter-organelle/PM communication. The ER thus appears to be the 'maestro' driving eukaryotic cell evolution by incorporating new functions/organelles, while remaining the real coordinator overarching cellular functions and orchestrating them with the external milieu.},
}

@article {pmid32306810,
year = {2020},
author = {Lee, EH and Baek, SY and Park, JY and Kim, YW},
title = {Emodin in Rheum undulatum inhibits oxidative stress in the liver via AMPK with Hippo/Yap signalling pathway.},
journal = {Pharmaceutical biology},
volume = {58},
number = {1},
pages = {333-341},
doi = {10.1080/13880209.2020.1750658},
pmid = {32306810},
issn = {1744-5116},
abstract = {Context: Emodin is a compound in Rheum undulatum Linne (Polygonaceae) that has been reported to exert anti-inflammatory, antibacterial, and antiallergic effects.Objective: Oxidative stress is a causative agent of liver inflammation that may lead to fibrosis and hepato-carcinoma. In this study, we investigated the antioxidant effects of emodin and its mechanism.Materials and methods: We used the hepatocyte stimulated by arachidonic acid (AA) + iron cotreatment and the C57B/6 mice orally injected with acetaminophen (APAP, 500 mg/kg, 6 h), as assessed by immunoblot and next generation sequencing (NGS). Emodin was pre-treated in hepatocyte (3 ∼ 30 μM) for 1 h before AA + iron, and in mice (10 and 30 m/kg, P.O.) for 3 days before APAP.Results:In vitro, emodin treatment inhibited the cell death induced by AA + iron maximally at a dose of 10 μM (EC50 > 3 μM). In addition, emodin attenuated the decrease of anti-apoptotic proteins, and restored mitochondria membrane potential as mediated by the liver kinase B1 (LKB1)-AMP-activated protein kinase (AMPK) pathway. LKB1 mediated AMPK activation was verified using the LKB1 deficient cell line, HeLa. Emodin (10 μM; after 10 min) also induced the phosphorylation of Yes-associated protein 1 (YAP1), the main downstream target of the Hippo signalling pathway that mediated oxidative stress or the ROS-initiated signalling pathway. In vivo, the oral treatment of emodin (10 and 30 m/kg, 3 days) decreased APAP-induced hepatic damage, as indicated by decreases in antioxidant genes as well as tissue damage.Conclusion: Our results show that emodin inhibits oxidative liver injury via the AMPK/YAP mediated pathway.},
}

@article {pmid31817290,
year = {2019},
author = {Arnedo, M and Latorre-Pellicer, A and Lucia-Campos, C and Gil-Salvador, M and Antoñanzas-Peréz, R and Gómez-Puertas, P and Bueno-Lozano, G and Puisac, B and Pié, J},
title = {More Than One HMG-CoA Lyase: The Classical Mitochondrial Enzyme Plus the Peroxisomal and the Cytosolic Ones.},
journal = {International journal of molecular sciences},
volume = {20},
number = {24},
pages = {},
pmid = {31817290},
issn = {1422-0067},
support = {RTC-2017-6494-1//Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación/ ; RTI2018-094434-B-I00//inisterio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación/ ; Grupo de Referencia B32_17R//Diputación General de Aragón - FEDER: European Social Fund/ ; },
mesh = {Cytosol/*enzymology ; Energy Metabolism ; Evolution, Molecular ; Humans ; Isoenzymes/classification/genetics/metabolism ; Ketone Bodies/metabolism ; Liver/enzymology ; Mitochondria/*enzymology ; Oxo-Acid-Lyases/classification/genetics/*metabolism ; Peroxisomes/*enzymology ; },
abstract = {There are three human enzymes with HMG-CoA lyase activity that are able to synthesize ketone bodies in different subcellular compartments. The mitochondrial HMG-CoA lyase was the first to be described, and catalyzes the cleavage of 3-hydroxy-3-methylglutaryl CoA to acetoacetate and acetyl-CoA, the common final step in ketogenesis and leucine catabolism. This protein is mainly expressed in the liver and its function is metabolic, since it produces ketone bodies as energetic fuels when glucose levels are low. Another isoform is encoded by the same gene for the mitochondrial HMG-CoA lyase (HMGCL), but it is located in peroxisomes. The last HMG-CoA lyase to be described is encoded by a different gene, HMGCLL1, and is located in the cytosolic side of the endoplasmic reticulum membrane. Some activity assays and tissue distribution of this enzyme have shown the brain and lung as key tissues for studying its function. Although the roles of the peroxisomal and cytosolic HMG-CoA lyases remain unknown, recent studies highlight the role of ketone bodies in metabolic remodeling, homeostasis, and signaling, providing new insights into the molecular and cellular function of these enzymes.},
}

Cytosol/*enzymology
Energy Metabolism
Evolution, Molecular
Humans
Isoenzymes/classification/genetics/metabolism
Ketone Bodies/metabolism
Liver/enzymology
Mitochondria/*enzymology
Oxo-Acid-Lyases/classification/genetics/*metabolism
Peroxisomes/*enzymology

@article {pmid30638448,
year = {2019},
author = {Phillips, CB and Tsai, CW and Tsai, MF},
title = {The conserved aspartate ring of MCU mediates MICU1 binding and regulation in the mitochondrial calcium uniporter complex.},
journal = {eLife},
volume = {8},
number = {},
pages = {},
pmid = {30638448},
issn = {2050-084X},
support = {R01 GM129345/GM/NIGMS NIH HHS/United States ; R01-GM129345/GM/NIGMS NIH HHS/United States ; },
mesh = {Aspartic Acid/*metabolism ; Biological Transport ; Calcium/metabolism ; Calcium Channels/*chemistry/*metabolism ; Calcium-Binding Proteins/*metabolism ; Cation Transport Proteins/*metabolism ; *Conserved Sequence ; Evolution, Molecular ; HEK293 Cells ; Humans ; Mitochondrial Membrane Transport Proteins/*metabolism ; Models, Biological ; Mutation/genetics ; Protein Binding ; Protein Multimerization ; Static Electricity ; Structure-Activity Relationship ; },
abstract = {The mitochondrial calcium uniporter is a Ca2+ channel that regulates intracellular Ca2+ signaling, oxidative phosphorylation, and apoptosis. It contains the pore-forming MCU protein, which possesses a DIME sequence thought to form a Ca2+ selectivity filter, and also regulatory EMRE, MICU1, and MICU2 subunits. To properly carry out physiological functions, the uniporter must stay closed in resting conditions, becoming open only when stimulated by intracellular Ca2+ signals. This Ca2+-dependent activation, known to be mediated by MICU subunits, is not well understood. Here, we demonstrate that the DIME-aspartate mediates a Ca2+-modulated electrostatic interaction with MICU1, forming an MICU1 contact interface with a nearby Ser residue at the cytoplasmic entrance of the MCU pore. A mutagenesis screen of MICU1 identifies two highly-conserved Arg residues that might contact the DIME-Asp. Perturbing MCU-MICU1 interactions elicits unregulated, constitutive Ca2+ flux into mitochondria. These results indicate that MICU1 confers Ca2+-dependent gating of the uniporter by blocking/unblocking MCU.},
}

Aspartic Acid/*metabolism
Biological Transport
Calcium/metabolism
Calcium Channels/*chemistry/*metabolism
Calcium-Binding Proteins/*metabolism
Cation Transport Proteins/*metabolism
*Conserved Sequence
Evolution, Molecular
HEK293 Cells
Humans
Mitochondrial Membrane Transport Proteins/*metabolism
Models, Biological
Mutation/genetics
Protein Binding
Protein Multimerization
Static Electricity
Structure-Activity Relationship

@article {pmid32297991,
year = {2020},
author = {Waters, ER and Vierling, E},
title = {Plant small heat shock proteins - evolutionary and functional diversity.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.16536},
pmid = {32297991},
issn = {1469-8137},
support = {R01 GM42762/GM/NIGMS NIH HHS/United States ; IBN-0213128//National Science Foundation/ ; IOS 0920611//National Science Foundation/ ; NRICGP 93-02143//US Department of Agriculture/ ; NRICGP 96-351003232//US Department of Agriculture/ ; NRICGP 99-351007618//US Department of Agriculture/ ; },
abstract = {Small heat shock proteins (sHSPs) are an ubiquitous protein family found in archaea, bacteria and eukaryotes. In plants, as in other organisms, sHSPs are upregulated by stress and are proposed to act as molecular chaperones to protect other proteins from stress-induced damage. sHSPs share an 'α-crystallin domain' with a β-sandwich structure and a diverse N-terminal domain. Although sHSPs are 12-25 kDa polypeptides, most assemble into oligomers with ≥ 12 subunits. Plant sHSPs are particularly diverse and numerous; some species have as many as 40 sHSPs. In angiosperms this diversity comprises ≥ 11 sHSP classes encoding proteins targeted to the cytosol, nucleus, endoplasmic reticulum, chloroplasts, mitochondria and peroxisomes. The sHSPs underwent a lineage-specific gene expansion, diversifying early in land plant evolution, potentially in response to stress in the terrestrial environment, and expanded again in seed plants and again in angiosperms. Understanding the structure and evolution of plant sHSPs has progressed, and a model for their chaperone activity has been proposed. However, how the chaperone model applies to diverse sHSPs and what processes sHSPs protect are far from understood. As more plant genomes and transcriptomes become available, it will be possible to explore theories of the evolutionary pressures driving sHSP diversification.},
}

@article {pmid31404599,
year = {2019},
author = {Zhang, Y and Feng, S and Fekrat, L and Jiang, F and Khathutshelo, M and Li, Z},
title = {The first two complete mitochondrial genome of Dacus bivittatus and Dacus ciliatus (Diptera: Tephritidae) by next-generation sequencing and implications for the higher phylogeny of Tephritidae.},
journal = {International journal of biological macromolecules},
volume = {140},
number = {},
pages = {469-476},
doi = {10.1016/j.ijbiomac.2019.08.076},
pmid = {31404599},
issn = {1879-0003},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; *High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Molecular Sequence Annotation ; *Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Tephritidae/*genetics ; Whole Genome Sequencing ; },
abstract = {Dacus bivittatus and Dacus ciliatus are destructive pests of Cucurbitaceae crops including cucumber, zucchini and melons. Recent molecular phylogenetic studies conflicted with morphological taxonomy regarding relationships between Bactrocera, Dacus and Zeugodacus. In this study, we sequenced the complete mitochondrial genomes of the above species which are representatives of two subgenera of Dacus (Dacus and Didacus) not previously sequenced and reconstructed the phylogeny of Tephritidae. The mitochondrial genomes of D. bivittatus and D. ciliatus were 15,833 bp and 15,808 bp in length, respectively. The 37 genes, including 13 protein-coding genes (PCGs), 2 rRNA genes and 22 tRNA genes, with a long non-coding region (A + T-rich control region) were in the same arrangement as the ancestral insect mitochondrial genome. Phylogenetic analysis showed that Dacus has a closer relationship of Zeugodacus rather than Bactrocera. Our phylogenetic results further support the recent proposals that Zeugodacus should be considered as a genus not a subgenus of Bactrocera. Whole mitochondrial genomes of D. bivittatus and D. ciliatus could be useful in further studies for species diagnosis, evolution and phylogeny research within Tephritidae.},
}

Animals
DNA, Mitochondrial/genetics
Genome, Mitochondrial/*genetics
*High-Throughput Nucleotide Sequencing
Mitochondria/genetics
Molecular Sequence Annotation
*Phylogeny
RNA, Transfer/genetics
Sequence Analysis, DNA
Tephritidae/*genetics
Whole Genome Sequencing

@article {pmid32109559,
year = {2020},
author = {Derouiche, L and Irzagh, A and Rahmouni, R and Tahri, R and Hadjeloum, M and Bouhadad, R and Fernandes, C},
title = {Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini).},
journal = {Gene},
volume = {739},
number = {},
pages = {144510},
doi = {10.1016/j.gene.2020.144510},
pmid = {32109559},
issn = {1879-0038},
mesh = {Africa, Northern ; Animals ; Biological Evolution ; Classification ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Endangered Species ; Mitochondria/genetics ; Phylogeography ; Ruminants/classification/*genetics ; },
abstract = {The aoudad or Barbary sheep (Ammotragus lervia) is a threatened ungulate emblematic of North Africa, whose population structure and subspecific taxonomy have not been examined genetically. This knowledge is essential and urgently needed to inform ongoing conservation and management efforts. We analysed the mitochondrial cytochrome b gene and four nuclear genes (casein kappa, spectrin beta nonerythrocytic 1, thyroglobulin, thyrotropin subunit beta) for the first phylogeographic survey of the aoudad, and uncovered a deep Mediterranean-Saharan mitochondrial split separating two highly distinct evolutionary lineages. Their level of divergence is greater than or comparable to those observed between several pairs of congeneric species of different caprine genera. The split was estimated to have occurred in the Early Pleistocene, about 1.3 million years ago. None of the four nuclear genes surveyed, chosen because they have been used in phylogeographic and species-level phylogenetic studies of bovids, allowed us to detect, likely due to their slow evolutionary rate, the substantial and geographically coherent subdivision revealed by mitochondrial DNA. This study is evidence and testament to the ability of mitochondrial DNA, probably unrivalled by any other single-locus marker, as an exploratory tool for investigating population genealogy and history and identifying potential evolutionarily significant units for conservation in animals.},
}

Africa, Northern
Animals
Biological Evolution
Classification
Conservation of Natural Resources
DNA, Mitochondrial/genetics
Endangered Species
Mitochondria/genetics
Phylogeography
Ruminants/classification/*genetics

@article {pmid32001678,
year = {2020},
author = {Barili, V and Fisicaro, P and Montanini, B and Acerbi, G and Filippi, A and Forleo, G and Romualdi, C and Ferracin, M and Guerrieri, F and Pedrazzi, G and Boni, C and Rossi, M and Vecchi, A and Penna, A and Zecca, A and Mori, C and Orlandini, A and Negri, E and Pesci, M and Massari, M and Missale, G and Levrero, M and Ottonello, S and Ferrari, C},
title = {Targeting p53 and histone methyltransferases restores exhausted CD8+ T cells in HCV infection.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {604},
pmid = {32001678},
issn = {2041-1723},
mesh = {Acute Disease ; Adolescent ; Adult ; Aged ; Antiviral Agents/pharmacology/therapeutic use ; Ataxia Telangiectasia Mutated Proteins/metabolism ; CD8-Positive T-Lymphocytes/*immunology ; Chronic Disease ; Epigenesis, Genetic/drug effects ; Gene Expression Profiling ; Gene Regulatory Networks/drug effects ; Glucose/metabolism ; Hepatitis C/blood/genetics/*immunology/virology ; Histone Methyltransferases/*metabolism ; Humans ; Lymphocyte Activation/drug effects/immunology ; Middle Aged ; Mitochondria/drug effects/metabolism ; Principal Component Analysis ; Signal Transduction/drug effects ; Transcription, Genetic/drug effects ; Tumor Suppressor Protein p53/*metabolism ; Young Adult ; },
abstract = {Hepatitis C virus infection (HCV) represents a unique model to characterize, from early to late stages of infection, the T cell differentiation process leading to exhaustion of human CD8+ T cells. Here we show that in early HCV infection, exhaustion-committed virus-specific CD8+ T cells display a marked upregulation of transcription associated with impaired glycolytic and mitochondrial functions, that are linked to enhanced ataxia-telangiectasia mutated (ATM) and p53 signaling. After evolution to chronic infection, exhaustion of HCV-specific T cell responses is instead characterized by a broad gene downregulation associated with a wide metabolic and anti-viral function impairment, which can be rescued by histone methyltransferase inhibitors. These results have implications not only for treatment of HCV-positive patients not responding to last-generation antivirals, but also for other chronic pathologies associated with T cell dysfunction, including cancer.},
}

Acute Disease
Adolescent
Adult
Aged
Antiviral Agents/pharmacology/therapeutic use
Ataxia Telangiectasia Mutated Proteins/metabolism
CD8-Positive T-Lymphocytes/*immunology
Chronic Disease
Epigenesis, Genetic/drug effects
Gene Expression Profiling
Gene Regulatory Networks/drug effects
Glucose/metabolism
Hepatitis C/blood/genetics/*immunology/virology
Histone Methyltransferases/*metabolism
Humans
Lymphocyte Activation/drug effects/immunology
Middle Aged
Mitochondria/drug effects/metabolism
Principal Component Analysis
Signal Transduction/drug effects
Transcription, Genetic/drug effects
Tumor Suppressor Protein p53/*metabolism
Young Adult

@article {pmid31247339,
year = {2019},
author = {Laurimäe, T and Kinkar, L and Romig, T and Umhang, G and Casulli, A and Omer, RA and Sharbatkhori, M and Mirhendi, H and Ponce-Gordo, F and Lazzarini, LE and Soriano, SV and Varcasia, A and Rostami-Nejad, M and Andresiuk, V and Maravilla, P and González, LM and Dybicz, M and Gawor, J and Šarkūnas, M and Šnábel, V and Kuzmina, T and Kia, EB and Saarma, U},
title = {Analysis of nad2 and nad5 enables reliable identification of genotypes G6 and G7 within the species complex Echinococcus granulosus sensu lato.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {74},
number = {},
pages = {103941},
doi = {10.1016/j.meegid.2019.103941},
pmid = {31247339},
issn = {1567-7257},
mesh = {Animals ; Echinococcus granulosus/*classification/genetics ; Genotyping Techniques/*methods ; Helminth Proteins/*genetics ; Mitochondria/genetics ; Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The larval stages of tapeworms in the species complex Echinococcus granulosus sensu lato cause a zoonotic disease known as cystic echinococcosis (CE). Within this species complex, genotypes G6 and G7 are among the most common genotypes associated with human CE cases worldwide. However, our understanding of ecology, biology and epidemiology of G6 and G7 is still limited. An essential first step towards this goal is correct genotype identification, but distinguishing genotypes G6 and G7 has been challenging. A recent analysis based on complete mitogenome data revealed that the conventional sequencing of the cox1 (366 bp) gene fragment mistakenly classified a subset of G7 samples as G6. On the other hand, sequencing complete mitogenomes is not practical if only genotype or haplogroup identification is needed. Therefore, a simpler and less costly method is required to distinguish genotypes G6 and G7. We compared 93 complete mitogenomes of G6 and G7 from a wide geographical range and demonstrate that a combination of nad2 (714 bp) and nad5 (680 bp) gene fragments would be the best option to distinguish G6 and G7. Moreover, this method allows assignment of G7 samples into haplogroups G7a and G7b. However, due to very high genetic variability of G6 and G7, we suggest to construct a phylogenetic network based on the nad2 and nad5 sequences in order to be absolutely sure in genotype assignment. For this we provide a reference dataset of 93 concatenated nad2 and nad5 sequences (1394 bp in total) containing representatives of G6 and G7 (and haplogroups G7a and G7b), which can be used for the reconstruction of phylogenetic networks.},
}

Animals
Echinococcus granulosus/*classification/genetics
Genotyping Techniques/*methods
Helminth Proteins/*genetics
Mitochondria/genetics
Multilocus Sequence Typing
Phylogeny
Sequence Analysis, DNA

@article {pmid29893915,
year = {2018},
author = {Chen, N and Wang, P and Li, C and Wang, Q and Pan, J and Xiao, F and Wang, Y and Zhang, K and Li, C and Yang, B and Sun, C and Deng, X},
title = {A Single Nucleotide Mutation of the IspE Gene Participating in the MEP Pathway for Isoprenoid Biosynthesis Causes a Green-Revertible Yellow Leaf Phenotype in Rice.},
journal = {Plant & cell physiology},
volume = {59},
number = {9},
pages = {1905-1917},
doi = {10.1093/pcp/pcy108},
pmid = {29893915},
issn = {1471-9053},
mesh = {Base Sequence ; Chloroplasts/*metabolism ; Cloning, Molecular ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Mitochondria/metabolism ; Oryza/*genetics ; Photosynthesis/genetics/physiology ; Phylogeny ; Plant Leaves/*metabolism ; Plant Proteins/metabolism ; *Polymorphism, Single Nucleotide ; Terpenes/*metabolism ; },
abstract = {Plant isoprenoids are dependent on two independent pathways, the cytosolic mevalonate (MVA) pathway and the plastidic methylerythritol phosphate (MEP) pathway. IspE is one of seven known enzymes in the MEP pathway. Currently, no IspE gene has been identified in rice. In addition, no virescent mutants have been reported to result from a gene mutation affecting the MEP pathway. In this study, we isolated a green-revertible yellow leaf mutant gry340 in rice. The mutant exhibited a reduced level of photosynthetic pigments, and an arrested development of chloroplasts and mitochondria in its yellow leaves. Map-based cloning revealed a missense mutation in OsIspE (LOC_Os01g58790) in gry340 mutant plants. OsIspE is constitutively expressed in all tissues, and its encoded protein is targeted to the chloroplast. Further, the mutant phenotype of gry340 was rescued by introduction of the wild-type gene. Therefore, we have successfully identified an IspE gene in monocotyledons via map-based cloning, and confirmed that the green-revertible yellow leaf phenotype of gry340 does result from a single nucleotide mutation in the IspE gene. In addition, the ispE ispF double mutant displayed an etiolation lethal phenotype, indicating that the isoprenoid precursors from the cytosol cannot efficiently compensate for the deficiency of the MEP pathway in rice chloroplasts. Furthermore, real-time quantitative reverse transcription-PCR suggested that this functional defect in OsIspE affected the expression of not only other MEP pathway genes but also that of MVA pathway genes, photosynthetic genes and mitochondrial genes.},
}

Base Sequence
Chloroplasts/*metabolism
Cloning, Molecular
Gene Expression Regulation, Plant
Genetic Complementation Test
Mitochondria/metabolism
Oryza/*genetics
Photosynthesis/genetics/physiology
Phylogeny
Plant Leaves/*metabolism
Plant Proteins/metabolism
*Polymorphism, Single Nucleotide
Terpenes/*metabolism

@article {pmid31418651,
year = {2019},
author = {Sato, C and Sasaki, M and Nabeta, H and Tomioka, M and Uga, S and Nakao, M},
title = {A Philophthalmid Eyefluke from a Human in Japan.},
journal = {The Journal of parasitology},
volume = {105},
number = {4},
pages = {619-623},
pmid = {31418651},
issn = {1937-2345},
mesh = {Animals ; Base Sequence ; Conjunctiva/parasitology ; Conjunctivitis/parasitology ; DNA, Helminth/chemistry ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Eye Infections, Parasitic/*parasitology ; Female ; Humans ; Japan ; Middle Aged ; Mitochondria/enzymology ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Trematoda/anatomy & histology/classification/genetics/*isolation & purification ; Trematode Infections/*parasitology ; },
abstract = {Philophthalmid eyeflukes are cosmopolitan parasites of birds and occasionally of mammals, including humans. A gravid adult of Philophthalmus sp. was found from the bulbar conjunctiva of a 64-yr-old woman in Japan, who was diagnosed with acute conjunctivitis. The parasite was morphologically most similar to Philophthalmus hegeneri, but distinctive in lacking an esophagus and in having clearly lobed testes. The DNA sequence analysis of genes for nuclear 28S ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 supported the identification at generic level. The morphological and molecular analyses strongly suggest that the eyefluke from a human in Japan should be treated as an undescribed species of Philophthalmus. The occurrence of human philophthalmosis is very rare. As far as we know, a total of 11 human cases have been reported worldwide to date.},
}

Animals
Base Sequence
Conjunctiva/parasitology
Conjunctivitis/parasitology
DNA, Helminth/chemistry
DNA, Ribosomal/chemistry
Electron Transport Complex IV/genetics
Eye Infections, Parasitic/*parasitology
Female
Humans
Japan
Middle Aged
Mitochondria/enzymology
Phylogeny
RNA, Ribosomal, 28S/genetics
Trematoda/anatomy & histology/classification/genetics/*isolation & purification
Trematode Infections/*parasitology