@article {pmid33808521,
year = {2021},
author = {Gînguță, A and Rusu, I and Mircea, C and Ioniță, A and Banciu, HL and Kelemen, B},
title = {Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania).},
journal = {Genes},
volume = {12},
number = {3},
pages = {},
pmid = {33808521},
issn = {2073-4425},
mesh = {Asia/ethnology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics/*history ; European Continental Ancestry Group/*genetics ; Genetics, Population ; History, Medieval ; Humans ; Mitochondria/*genetics ; Phylogeny ; Population Dynamics ; Romania/ethnology ; },
abstract = {The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe.},
}

Asia/ethnology
DNA, Ancient/*analysis
DNA, Mitochondrial/genetics/*history
European Continental Ancestry Group/*genetics
Genetics, Population
History, Medieval
Humans
Mitochondria/*genetics
Phylogeny
Population Dynamics
Romania/ethnology

@article {pmid33807111,
year = {2021},
author = {Maár, K and Varga, GIB and Kovács, B and Schütz, O and Maróti, Z and Kalmár, T and Nyerki, E and Nagy, I and Latinovics, D and Tihanyi, B and Marcsik, A and Pálfi, G and Bernert, Z and Gallina, Z and Varga, S and Költő, L and Raskó, I and Török, T and Neparáczki, E},
title = {Maternal Lineages from 10-11th Century Commoner Cemeteries of the Carpathian Basin.},
journal = {Genes},
volume = {12},
number = {3},
pages = {},
pmid = {33807111},
issn = {2073-4425},
mesh = {Cemeteries ; DNA, Mitochondrial/*genetics ; Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing ; History, Medieval ; Humans ; Hungary/ethnology ; Maternal Inheritance ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; Transients and Migrants/*history ; },
abstract = {Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10-11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10-11th century commoners most likely represent local populations of the Carpathian Basin, which admixed with the eastern immigrant groups (which included conquering Hungarians).},
}

Cemeteries
DNA, Mitochondrial/*genetics
Genetics, Population
Haplotypes
High-Throughput Nucleotide Sequencing
History, Medieval
Humans
Hungary/ethnology
Maternal Inheritance
Mitochondria/*genetics
Phylogeny
Polymorphism, Single Nucleotide
Sequence Analysis, DNA/*methods
Transients and Migrants/*history

@article {pmid32891682,
year = {2020},
author = {Darriba, S and Lee, RS and López, C},
title = {Mikrocytos mytilicoli n.sp. (Cercozoa, Mikrocytida, Mikrocytiidae) infecting the copepod Mytilicola intestinalis (Arthropoda, Cyclopoida, Mytilicolidae), a symbiont of Mytilus galloprovincialis in Galicia (NW Spain).},
journal = {Journal of invertebrate pathology},
volume = {176},
number = {},
pages = {107460},
doi = {10.1016/j.jip.2020.107460},
pmid = {32891682},
issn = {1096-0805},
mesh = {Animals ; Cercozoa/*classification/cytology/genetics/ultrastructure ; Copepoda/*parasitology/physiology ; DNA, Protozoan/analysis ; DNA, Ribosomal Spacer/analysis ; *Host-Parasite Interactions ; Microscopy ; Microscopy, Electron, Transmission ; Mytilus/physiology ; Phylogeny ; RNA, Ribosomal, 18S/analysis ; RNA, Ribosomal, 28S/analysis ; Spain ; Symbiosis ; },
abstract = {During a histopathological survey of Mytilus galloprovincialis in Galicia (NW Spain), microcells were observed infecting several organs of the symbiont copepod Mytilicola intestinalis. Positive results of PCR assay with specific primers for genus Mikrocytos and a clear signal of in situ hybridization with MACKINI-1 digoxigenin- labelled DNA probe (DIG-ISH) indicated a protozoan parasite of Mikrocytos genus. The ultrastructural study revealed intra and extracellular locations, polymorphic nuclei, intracellular round vesicles in the cytoplasm and absence of mitochondria. The present paper reports the characterization of the Mikrocytos sp. infecting M. intestinalis and proposes a novel species in the genus: Mikrocytos mytilicoli n. sp. A sequence of 18S-28S rDNA was obtained with 95.6% maximum identity (query cover 100%) with Mikrocytos mackini. Phylogenetic analysis showed that M. mytilicoli n. sp. and M. mackini share a common ancestor. However, comparison of the ITS1 rDNA region showed low similarity (75.8%) with M. mackini, which, combined with differences in ultrastructural details, host and geographic location, support the designation of a new species. This is the first description of a microcytid parasite of the genus Mikrocytos from a non-bivalve host.},
}

Animals
Cercozoa/*classification/cytology/genetics/ultrastructure
Copepoda/*parasitology/physiology
DNA, Protozoan/analysis
DNA, Ribosomal Spacer/analysis
*Host-Parasite Interactions
Microscopy
Microscopy, Electron, Transmission
Mytilus/physiology
Phylogeny
RNA, Ribosomal, 18S/analysis
RNA, Ribosomal, 28S/analysis
Spain
Symbiosis

@article {pmid33561119,
year = {2021},
author = {De, AK and Sawhney, S and Bhattacharya, D and Sujatha, T and Sunder, J and Ponraj, P and Ravi, SK and Mondal, S and Malakar, D and Kundu, A},
title = {Origin, genetic diversity and evolution of Andaman local duck, a native duck germplasm of an insular region of India.},
journal = {PloS one},
volume = {16},
number = {2},
pages = {e0245138},
pmid = {33561119},
issn = {1932-6203},
mesh = {Animals ; Animals, Domestic/genetics ; Biological Evolution ; DNA, Mitochondrial/analysis/*genetics ; Ducks/*genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Haplotypes/genetics ; India ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Domestic ducks are of paramount importance as a cheap source of protein in rural India. Andaman local duck (ALD) is an indigenous avian genetic resource of Andaman and Nicobar islands (ANI) and is mainly distributed in Middle and Northern parts of these islands. Negligence has brought this breed on the edge of extinction necessitating immediate conservation efforts. Here, we report the genetic diversity, population structure and matrilineal genetic root of ALD. Partial mtDNA D-loop sequences were analyzed in 71 ALD samples and analysis revealed 19 polymorphic sites and 13 haplotypes. Estimated haplotype (Hd ± SD) and nucleotide diversity (π ± SD) were 0.881 ± 0.017 and 0.00897 ± 0.00078 respectively. The high genetic diversity of ALD indicates introgression of genetic material from other local duck breeds. In addition, it can be postulated that ALD bearing high genetic diversity has strong ability to adapt to environmental changes and can withstand impending climate change. Phylogenetic and network analysis indicate that ALD falls under Eurasian clade of mallard and ALD forms three clusters; one cluster is phylogenetically close to Southeast Asian countries, one close to Southern part of mainland India and the third one forms an independent cluster. Therefore, ALD might have migrated either from Southeast Asian countries which enjoy a close cultural bondage with ANI from time immemorial or from Southern part of India. The independent cluster may have evolved locally in these islands and natural selection pressure imposed by environmental conditions might be the driving force for evaluation of these duck haplotypes; which mimics Darwin's theory of natural selection. The results of the study will be beneficial for formulating future breeding programme and conservation strategy towards sustainable development of the duck breed.},
}

Animals
Animals, Domestic/genetics
Biological Evolution
DNA, Mitochondrial/analysis/*genetics
Ducks/*genetics
Genetic Variation/genetics
Genetics, Population/methods
Haplotypes/genetics
India
Mitochondria/genetics
Phylogeny
Sequence Analysis, DNA/methods

@article {pmid33494532,
year = {2021},
author = {Kirkland, C and Farré, M},
title = {Mitochondrial Genome Evolution, Genetic Diversity, and Population Structure in British Water Voles (Arvicola amphibius).},
journal = {Genes},
volume = {12},
number = {2},
pages = {},
pmid = {33494532},
issn = {2073-4425},
mesh = {Animals ; Arvicolinae/classification/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, the impact that captive breeding programs in Britain are having on the genetic diversity of water voles is unknown. We use available mitochondrial genomes to construct the phylogeny of species within Arvicolinae, followed by sequencing the mitochondrial DNA control region of 17 individuals from a captive population of water voles in Britain to assess their genetic diversity and population structure. Our study first provides an updated phylogenetic tree of Arvicolinae using the mitochondrial genome of 31 species. Second, our results show considerable genetic diversity in the captive population of water voles, when compared with natural populations in Britain. We confirm the grouping of British water voles into two clades, with all captive individuals found in the English/Welsh clade. Moreover, captive water voles clustered closely with populations in the South East and East of England. The mitochondrial genome provides a useful marker to study the phylogenetics of this rodent clade and in addition, our study provides support for the breeding program at Wildwood Trust and provides a framework for future conservation genetics studies in this species.},
}

Animals
Arvicolinae/classification/*genetics
*Evolution, Molecular
*Genetic Variation
Genetics, Population
*Genome, Mitochondrial
Haplotypes
Mitochondria/*genetics
Phylogeny

@article {pmid34309123,
year = {2021},
author = {Fernandes Gyorfy, M and Miller, ER and Conover, JL and Grover, CE and Wendel, JF and Sloan, DB and Sharbrough, J},
title = {Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.15436},
pmid = {34309123},
issn = {1365-313X},
abstract = {The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication events (WGDs) in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follow WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR (ddPCR) to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.},
}

@article {pmid34175396,
year = {2021},
author = {Lin, C and Tang, D and Gao, X and Jiang, H and Du, C and Zhu, J},
title = {Molecular characterization, dynamic transcription, and potential function of KIF3A/KIF3B during spermiogenesis in Opsariichthys bidens.},
journal = {Gene},
volume = {798},
number = {},
pages = {145795},
doi = {10.1016/j.gene.2021.145795},
pmid = {34175396},
issn = {1879-0038},
mesh = {Animals ; Cyprinidae/genetics/*physiology ; Kinesin/chemistry/genetics/*physiology ; Male ; Microtubules/metabolism ; Mitochondria/metabolism ; Phylogeny ; Protein Conformation ; RNA, Messenger/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sperm Tail/physiology ; Spermatids/physiology/ultrastructure ; Spermatogenesis/genetics/*physiology ; Testis/metabolism ; Transcription, Genetic ; },
abstract = {Spermiogenesis is the final phase of spermatogenesis, wherein the spermatids differentiate into mature spermatozoa via complex morphological transformation. In this process, kinesin plays an important role. Here, we observed the morphological transformation of spermatids and analyzed the characterization, dynamic transcription, and potential function of kinesin KIF3A/KIF3B during spermiogenesis in Chinese hook snout carp (Opsariichthys bidens). We found that the full-length cDNAs of O. bidens kif3a and kif3b were 2544 and 2806 bp in length comprising 119 bp and 259 bp 5' untranslated region (UTR), 313 bp and 222 bp 3' UTR, and 2112 bp and 2325 bp open reading frame encoding 703 and 774 amino acids, respectively. Ob-KIF3A/KIF3B proteins have three domains, namely N-terminal head, coiled-coil stalk, and C-terminal tail, and exhibit high similarity with homologous proteins in vertebrates and invertebrates. Ob-kif3a/kif3b mRNAs were ubiquitously expressed in all tissues examined, with the highest expression in the brain and stage-IV testis. Immunofluorescence results showed that Ob-KIF3A was co-localized with tubulin and the mitochondria. Particularly, in early spermatids, Ob-KIF3A, tubulin, and the mitochondrial signals were evenly distributed in the cytoplasm, whereas in middle spermatids, they were distributed around the nucleus. In the late stage, the signals were concentrated on one side of the nucleus, where the tail is formed, whereas in mature sperms, they were detected in the midpiece and flagellum. These results indicate that Ob-KIF3A/KIF3B may participate in nuclear reshaping, flagellum formation, and mitochondrial aggregation in the midpiece during spermiogenesis.},
}

Animals
Cyprinidae/genetics/*physiology
Kinesin/chemistry/genetics/*physiology
Male
Microtubules/metabolism
Mitochondria/metabolism
Phylogeny
Protein Conformation
RNA, Messenger/metabolism
Sequence Alignment
Sequence Analysis, DNA
Sperm Tail/physiology
Spermatids/physiology/ultrastructure
Spermatogenesis/genetics/*physiology
Testis/metabolism
Transcription, Genetic

@article {pmid33396901,
year = {2020},
author = {Cucini, C and Fanciulli, PP and Frati, F and Convey, P and Nardi, F and Carapelli, A},
title = {Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data.},
journal = {Genes},
volume = {12},
number = {1},
pages = {},
pmid = {33396901},
issn = {2073-4425},
mesh = {Animals ; Antarctic Regions ; Arthropods/classification/*genetics ; Bayes Theorem ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/genetics ; *Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition.},
}

Animals
Antarctic Regions
Arthropods/classification/*genetics
Bayes Theorem
Biological Evolution
DNA, Mitochondrial/*genetics
Gene Order
*Genome, Mitochondrial
Mitochondria/genetics
*Models, Genetic
*Phylogeny
Sequence Analysis, DNA

@article {pmid33228188,
year = {2020},
author = {Peralta-Castro, A and García-Medel, PL and Baruch-Torres, N and Trasviña-Arenas, CH and Juarez-Quintero, V and Morales-Vazquez, CM and Brieba, LG},
title = {Plant Organellar DNA Polymerases Evolved Multifunctionality through the Acquisition of Novel Amino Acid Insertions.},
journal = {Genes},
volume = {11},
number = {11},
pages = {},
pmid = {33228188},
issn = {2073-4425},
mesh = {Amino Acids/genetics/metabolism ; Arabidopsis/genetics ; Arabidopsis Proteins/genetics/metabolism ; DNA End-Joining Repair/physiology ; DNA Repair/*physiology ; DNA-Directed DNA Polymerase/*genetics/metabolism ; Evolution, Molecular ; Organelles/*enzymology ; Plant Proteins/*genetics/metabolism ; },
abstract = {The majority of DNA polymerases (DNAPs) are specialized enzymes with specific roles in DNA replication, translesion DNA synthesis (TLS), or DNA repair. The enzymatic characteristics to perform accurate DNA replication are in apparent contradiction with TLS or DNA repair abilities. For instance, replicative DNAPs incorporate nucleotides with high fidelity and processivity, whereas TLS DNAPs are low-fidelity polymerases with distributive nucleotide incorporation. Plant organelles (mitochondria and chloroplast) are replicated by family-A DNA polymerases that are both replicative and TLS DNAPs. Furthermore, plant organellar DNA polymerases from the plant model Arabidopsis thaliana (AtPOLIs) execute repair of double-stranded breaks by microhomology-mediated end-joining and perform Base Excision Repair (BER) using lyase and strand-displacement activities. AtPOLIs harbor three unique insertions in their polymerization domain that are associated with TLS, microhomology-mediated end-joining (MMEJ), strand-displacement, and lyase activities. We postulate that AtPOLIs are able to execute those different functions through the acquisition of these novel amino acid insertions, making them multifunctional enzymes able to participate in DNA replication and DNA repair.},
}

Amino Acids/genetics/metabolism
Arabidopsis/genetics
Arabidopsis Proteins/genetics/metabolism
DNA End-Joining Repair/physiology
DNA Repair/*physiology
DNA-Directed DNA Polymerase/*genetics/metabolism
Evolution, Molecular
Organelles/*enzymology
Plant Proteins/*genetics/metabolism

@article {pmid33477742,
year = {2021},
author = {Sunagar, K and Khochare, S and Senji Laxme, RR and Attarde, S and Dam, P and Suranse, V and Khaire, A and Martin, G and Captain, A},
title = {A Wolf in Another Wolf's Clothing: Post-Genomic Regulation Dictates Venom Profiles of Medically-Important Cryptic Kraits in India.},
journal = {Toxins},
volume = {13},
number = {1},
pages = {},
pmid = {33477742},
issn = {2072-6651},
support = {IAVI/BES/KASU/0002//Department for International Development, UK Government/ ; SR/FST/LS-II/2018/233//DST-FIST/ ; },
mesh = {Animals ; Antivenins/chemistry ; Biological Evolution ; Bungarotoxins/*chemistry ; Bungarus/classification/*genetics/*metabolism ; Gene Expression Profiling ; Gene Regulatory Networks ; Humans ; India ; Male ; Mice ; Mitochondria/genetics ; Molecular Typing ; Pakistan ; Phylogeny ; *Proteome ; Proteomics ; Species Specificity ; },
abstract = {The Common Krait (Bungarus caeruleus) shares a distribution range with many other 'phenotypically-similar' kraits across the Indian subcontinent. Despite several reports of fatal envenomings by other Bungarus species, commercial Indian antivenoms are only manufactured against B. caeruleus. It is, therefore, imperative to understand the distribution of genetically distinct lineages of kraits, the compositional differences in their venoms, and the consequent impact of venom variation on the (pre)clinical effectiveness of antivenom therapy. To address this knowledge gap, we conducted phylogenetic and comparative venomics investigations of kraits in Southern and Western India. Phylogenetic reconstructions using mitochondrial markers revealed a new species of krait, Romulus' krait (Bungarus romulusi sp. nov.), in Southern India. Additionally, we found that kraits with 17 mid-body dorsal scale rows in Western India do not represent a subspecies of the Sind Krait (B. sindanus walli) as previously believed, but are genetically very similar to B. sindanus in Pakistan. Furthermore, venom proteomics and comparative transcriptomics revealed completely contrasting venom profiles. While the venom gland transcriptomes of all three species were highly similar, venom proteomes and toxicity profiles differed significantly, suggesting the prominent role of post-genomic regulatory mechanisms in shaping the venoms of these cryptic kraits. In vitro venom recognition and in vivo neutralisation experiments revealed a strong negative impact of venom variability on the preclinical performance of commercial antivenoms. While the venom of B. caeruleus was neutralised as per the manufacturer's claim, performance against the venoms of B. sindanus and B. romulusi was poor, highlighting the need for regionally-effective antivenoms in India.},
}

Animals
Antivenins/chemistry
Biological Evolution
Bungarotoxins/*chemistry
Bungarus/classification/*genetics/*metabolism
Gene Expression Profiling
Gene Regulatory Networks
Humans
India
Male
Mice
Mitochondria/genetics
Molecular Typing
Pakistan
Phylogeny
*Proteome
Proteomics
Species Specificity

@article {pmid33669879,
year = {2021},
author = {Zapelloni, F and Jurado-Rivera, JA and Jaume, D and Juan, C and Pons, J},
title = {Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea).},
journal = {Genes},
volume = {12},
number = {2},
pages = {},
pmid = {33669879},
issn = {2073-4425},
mesh = {Amphipoda/classification/*genetics ; Animals ; Codon/genetics ; Codon Usage/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; },
abstract = {We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson-Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.},
}

Amphipoda/classification/*genetics
Animals
Codon/genetics
Codon Usage/genetics
DNA, Mitochondrial/*genetics
*Evolution, Molecular
Genome, Mitochondrial/*genetics
Mitochondria/genetics
Phylogeny
RNA, Transfer/genetics

@article {pmid34279226,
year = {2021},
author = {Colnaghi, M and Pomiankowski, A and Lane, N},
title = {The need for high-quality oocyte mitochondria at extreme ploidy dictates mammalian germline development.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
doi = {10.7554/eLife.69344},
pmid = {34279226},
issn = {2050-084X},
support = {EP/F500351/1//Engineering and Physical Sciences Research Council/ ; EP/I017909/1//Engineering and Physical Sciences Research Council/ ; NE/R010579/1//Natural Environment Research Council/ ; BB/S003681/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; .none.//bgc3/ ; BB/V003542/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Selection against deleterious mitochondrial mutations is facilitated by germline processes, lowering the risk of genetic diseases. How selection works is disputed: experimental data are conflicting and previous modelling work has not clarified the issues. Here we develop computational and evolutionary models that compare the outcome of selection at the level of individuals, cells and mitochondria. Using realistic de novo mutation rates and germline development parameters from mouse and humans, the evolutionary model predicts the observed prevalence of mitochondrial mutations and diseases in human populations. We show the importance of organelle-level selection, seen in the selective pooling of mitochondria into the Balbiani body, in achieving high-quality mitochondria at extreme ploidy in mature oocytes. Alternative mechanisms debated in the literature, bottlenecks and follicular atresia, are unlikely to account for the clinical data, because neither process effectively eliminates mitochondrial mutations under realistic conditions. Our findings explain the major features of female germline architecture, notably the longstanding paradox of over-proliferation of primordial germ cells followed by massive loss. The near-universality of these processes across animal taxa makes sense in light of the need to maintain mitochondrial quality at extreme ploidy in mature oocytes, in the absence of sex and recombination.},
}

@article {pmid34277616,
year = {2021},
author = {Xu, X and Ma, A and Li, T and Cui, W and Wang, X and Li, J and Li, Q and Pang, Y},
title = {Genetic and Functional Characterization of Novel Brown-Like Adipocytes Around the Lamprey Brain.},
journal = {Frontiers in cell and developmental biology},
volume = {9},
number = {},
pages = {674939},
doi = {10.3389/fcell.2021.674939},
pmid = {34277616},
issn = {2296-634X},
abstract = {During the process of vertebrate evolution, many thermogenic organs and mechanisms have appeared. Mammalian brown adipose tissue (BAT) generates heat through the uncoupling oxidative phosphorylation of mitochondria, acts as a natural defense against hypothermia and inhibits the development of obesity. Although the existence, cellular origin and molecular identity of BAT in humans have been well studied, the genetic and functional characteristics of BAT from lampreys remain unknown. Here, we identified and characterized a novel, naturally existing brown-like adipocytes at the lamprey brain periphery. Similar to human BAT, the lamprey brain periphery contains brown-like adipocytes that maintain the same morphology as human brown adipocytes, containing multilocular lipid droplets and high mitochondrion numbers. Furthermore, we found that brown-like adipocytes in the periphery of lamprey brains responded to thermogenic reagent treatment and cold exposure and that lamprey UCP2 promoted precursor adipocyte differentiation. Molecular mapping by RNA-sequencing showed that inflammation in brown-like adipocytes treated with LPS and 25HC was enhanced compared to controls. The results of this study provide new evidence for human BAT research and demonstrate the multilocular adipose cell functions of lampreys, including: (1) providing material energy and protecting structure, (2) generating additional heat and contributing to adaptation to low-temperature environments, and (3) resisting external pathogens.},
}

@article {pmid34274481,
year = {2021},
author = {Kimball, RT and Guido, M and Hosner, PA and Braun, EL},
title = {When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes).},
journal = {Gene},
volume = {},
number = {},
pages = {145841},
doi = {10.1016/j.gene.2021.145841},
pmid = {34274481},
issn = {1879-0038},
abstract = {Mitochondrial sequences were among the first molecular data collected for phylogenetic studies and they plentiful in DNA sequence archives. However, the future value of mitogenomic data in phylogenetics is uncertain, because its phylogenetic signal sometimes conflicts with that of the nuclear genome. A thorough understanding of the causes and prevalence of cyto-nuclear discordance would aid in reconciling different results owing to sequence data type, and provide a framework for interpreting megaphylogenies when taxa which lack substantial nuclear data are placed using mitochondrial data. Here, we examine the prevalence and possible causes of cyto-nuclear discordance in the landfowl (Aves: Galliformes), leveraging 47 new mitogenomes assembled from off-target reads recovered as part of a target-capture study. We evaluated two hypotheses, that cyto-nuclear discordance is "genuine" and a result of biological processes such as incomplete lineage sorting or introgression, and that cyto-nuclear discordance is an artifact of inaccurate mitochondrial tree estimation (the "inaccurate estimation" hypothesis). We identified seven well-supported topological differences between the mitogenomic tree and trees based on nuclear data. These well-supported topological differences were robust to model selection. An examination of sites suggests these differences were driven by small number of sites, particularly from third-codon positions, suggesting that they were not confounded by convergent directional selection. Hence, the hypothesis of genuine discordance was supported.},
}

@article {pmid33529628,
year = {2021},
author = {Yan, L and Xu, W and Zhang, D and Li, J},
title = {Comparative analysis of the mitochondrial genomes of flesh flies and their evolutionary implication.},
journal = {International journal of biological macromolecules},
volume = {174},
number = {},
pages = {385-391},
doi = {10.1016/j.ijbiomac.2021.01.188},
pmid = {33529628},
issn = {1879-0003},
mesh = {Animals ; Base Composition ; Evolution, Molecular ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sarcophagidae/*classification/genetics ; Whole Genome Sequencing/*methods ; },
abstract = {Flesh flies (Diptera: Sarcophagidae) include a large and widely distributed rapid radiation within the Calyptratae. They are vital for the ecosystem, as well as economic, forensic, and evolutionary studies, because of their extremely diverse habits as larvae. Phylogenetic studies of Sarcophagidae have been reaching convergence, which leads the opportunity to elucidate the evolution of these fast-evolving insects from the perspective of mitochondrial genome. Complete mitochondrial genomes of eight species were sequenced, and comparative mitochondrial genomic analysis between subfamilies were conducted. Mitochondrial genomes of these flesh flies are conserved in gene content with gene arrangement, same as the inferred ancestral insect, and the nucleotide composition is highly biased towards A + T like other flesh flies. The evolutionary rates of Sarcophagidae vary considerably across subfamilies, with that of Miltogramminae higher than the other two subfamilies. Phylogenetic analysis strongly supports monophyly of Sarcophagidae and each subfamily, with subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). The main topological inconsistency of all reconstructions is the relationship within Miltogramminae and Sarcophaga, which might be caused by their rapid evolution. Our study indicates that the mitochondrial genomes of flesh flies are highly conserved, and they are practically useful for phylogenetic inference of calyptrates.},
}

Animals
Base Composition
Evolution, Molecular
Genome Size
Genome, Mitochondrial
High-Throughput Nucleotide Sequencing
Mitochondria/*genetics
Phylogeny
Sarcophagidae/*classification/genetics
Whole Genome Sequencing/*methods

@article {pmid34222053,
year = {2021},
author = {Li, T and Fang, Z and He, Q and Wang, C and Meng, X and Yu, B and Zhou, Z},
title = {Characterizing the Xenoma of Vairimorpha necatrix Provides Insights Into the Most Efficient Mode of Microsporidian Proliferation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {699239},
pmid = {34222053},
issn = {2235-2988},
mesh = {Animals ; Cell Proliferation ; Humans ; In Situ Hybridization, Fluorescence ; *Microsporidia/genetics ; Phylogeny ; },
abstract = {Microsporidia are a group of obligated intracellular parasites that can infect nearly all vertebrates and invertebrates, including humans and economic animals. Microsporidian Vairimorpha necatrix is a natural pathogen of multiple insects and can massively proliferate by making tumor-like xenoma in host tissue. However, little is known about the subcellular structures of this xenoma and the proliferation features of the pathogens inside. Here, we characterized the V. necatrix xenoma produced in muscle cells of silkworm midgut. In result, the whitish xenoma was initially observed on the 12th day post infection on the outer surface of the midgut and later became larger and numerous. The observation by scanning electronic microscopy showed that the xenoma is mostly elliptical and spindle with dense pathogen-containing protrusions and spores on the surface, which were likely shedding off the xenoma through exocytosis and could be an infection source of other tissues. Demonstrated with transmission electron microscopy and fluorescent staining, the xenoma was enveloped by a monolayer membrane, and full of vesicle structures, mitochondria, and endoplasmic reticulum around parasites in development, suggesting that high level of energy and nutrients were produced to support the massive proliferation of the parasites. Multiple hypertrophic nuclei were found in one single xenoma, indicating that the cyst was probably formed by fusion of multiple muscle cells. Observed by fluorescence in situ hybridization, pathogens in the xenoma were in merongony, sporogony, and octosporogony, and mature stages. And mature spores were pushed to the center while vegetative pathogens were in the surface layer of the xenoma. The V. necatrix meront usually contained two to three nuclei, and sporont contained two nuclei and was wrapped by a thick membrane with high electron density. The V. necatrix sporogony produces two types of spores, the ordinary dikaryotic spore and unicellular octospores, the latter of which were smaller in size and packed in a sporophorous vesicle. In summary, V. necatrix xenoma is a specialized cyst likely formed by fusion of multiple muscle cells and provides high concentration of energy and nutrients with increased number of mitochondria and endoplasmic reticulum for the massive proliferation of pathogens inside.},
}

Animals
Cell Proliferation
Humans
In Situ Hybridization, Fluorescence
*Microsporidia/genetics
Phylogeny

@article {pmid34204357,
year = {2021},
author = {Richtová, J and Sheiner, L and Gruber, A and Yang, SM and Kořený, L and Striepen, B and Oborník, M},
title = {Using Diatom and Apicomplexan Models to Study the Heme Pathway of Chromera velia.},
journal = {International journal of molecular sciences},
volume = {22},
number = {12},
pages = {},
pmid = {34204357},
issn = {1422-0067},
support = {21-03224S//Grantová Agentura České Republiky/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//ERDF/ESF, Centre for Research of Pathogenicity and Virulence of Parasites/ ; },
mesh = {Alveolata/*physiology ; Amino Acid Sequence ; Apicomplexa/*metabolism ; Biological Transport ; Diatoms/*metabolism ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Heme/*metabolism ; *Metabolic Networks and Pathways ; Mitochondria/genetics/metabolism/ultrastructure ; Protozoan Proteins/chemistry/genetics/metabolism ; },
abstract = {Heme biosynthesis is essential for almost all living organisms. Despite its conserved function, the pathway's enzymes can be located in a remarkable diversity of cellular compartments in different organisms. This location does not always reflect their evolutionary origins, as might be expected from the history of their acquisition through endosymbiosis. Instead, the final subcellular localization of the enzyme reflects multiple factors, including evolutionary origin, demand for the product, availability of the substrate, and mechanism of pathway regulation. The biosynthesis of heme in the apicomonad Chromera velia follows a chimeric pathway combining heme elements from the ancient algal symbiont and the host. Computational analyses using different algorithms predict complex targeting patterns, placing enzymes in the mitochondrion, plastid, endoplasmic reticulum, or the cytoplasm. We employed heterologous reporter gene expression in the apicomplexan parasite Toxoplasma gondii and the diatom Phaeodactylum tricornutum to experimentally test these predictions. 5-aminolevulinate synthase was located in the mitochondria in both transfection systems. In T. gondii, the two 5-aminolevulinate dehydratases were located in the cytosol, uroporphyrinogen synthase in the mitochondrion, and the two ferrochelatases in the plastid. In P. tricornutum, all remaining enzymes, from ALA-dehydratase to ferrochelatase, were placed either in the endoplasmic reticulum or in the periplastidial space.},
}

Alveolata/*physiology
Amino Acid Sequence
Apicomplexa/*metabolism
Biological Transport
Diatoms/*metabolism
Evolution, Molecular
Gene Expression Regulation, Enzymologic
Heme/*metabolism
*Metabolic Networks and Pathways
Mitochondria/genetics/metabolism/ultrastructure
Protozoan Proteins/chemistry/genetics/metabolism

@article {pmid32998193,
year = {2020},
author = {Marshall, C and Sturk-Andreaggi, K and Ring, JD and Dür, A and Parson, W},
title = {Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting.},
journal = {Genes},
volume = {11},
number = {10},
pages = {},
pmid = {32998193},
issn = {2073-4425},
mesh = {*Algorithms ; DNA, Mitochondrial/analysis/*genetics ; *Genetic Variation ; *Genetics, Population ; *Genome, Mitochondrial ; *Haplotypes ; Humans ; Mitochondria/*genetics/metabolism/pathology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Given the enhanced discriminatory power of the mitochondrial DNA (mtDNA) genome (mitogenome) over the commonly sequenced control region (CR) portion, the scientific merit of mitogenome sequencing is generally accepted. However, many laboratories remain beholden to CR sequencing due to privacy policies and legal requirements restricting the use of disease information or coding region (codR) information. In this report, we present an approach to obviate the reporting of sensitive codR data in forensic haplotypes. We consulted the MitoMap database to identify 92 mtDNA codR variants with confirmed pathogenicity. We determined the frequencies of these pathogenic variants in literature-quality and forensic-quality databases to be very low, at 1.2% and 0.36%, respectively. The observed effect of pathogenic variant filtering on random match statistics in 2488 forensic-quality mitogenome haplotypes from four populations was nil. We propose that pathogenic variant filtering should be incorporated into variant calling algorithms for mitogenome haplotype reporting to maximize the discriminatory power of the locus while minimizing the reveal of sensitive genetic information.},
}

*Algorithms
DNA, Mitochondrial/analysis/*genetics
*Genetic Variation
*Genetics, Population
*Genome, Mitochondrial
*Haplotypes
Humans
Mitochondria/*genetics/metabolism/pathology
Phylogeny
Sequence Analysis, DNA

@article {pmid32769116,
year = {2020},
author = {MacEwen, MJ and Markhard, AL and Bozbeyoglu, M and Bradford, F and Goldberger, O and Mootha, VK and Sancak, Y},
title = {Evolutionary divergence reveals the molecular basis of EMRE dependence of the human MCU.},
journal = {Life science alliance},
volume = {3},
number = {10},
pages = {},
pmid = {32769116},
issn = {2575-1077},
support = {R01 AR071942/AR/NIAMS NIH HHS/United States ; R01 HL130143/HL/NHLBI NIH HHS/United States ; T32 GM007750/GM/NIGMS NIH HHS/United States ; },
mesh = {Biological Evolution ; Calcium/metabolism ; Calcium Channels/*metabolism/physiology ; Dictyostelium/genetics/metabolism ; Evolution, Molecular ; HEK293 Cells ; Humans ; Ion Transport/genetics/physiology ; Mitochondria/metabolism ; Protein Domains ; },
abstract = {The mitochondrial calcium uniporter (MCU) is a calcium-activated calcium channel critical for signaling and bioenergetics. MCU, the pore-forming subunit of the uniporter, contains two transmembrane domains and is found in all major eukaryotic taxa. In amoeba and fungi, MCU homologs are sufficient to form a functional calcium channel, whereas human MCU exhibits a strict requirement for the metazoan protein essential MCU regulator (EMRE) for conductance. Here, we exploit this evolutionary divergence to decipher the molecular basis of human MCU's dependence on EMRE. By systematically generating chimeric proteins that consist of EMRE-independent Dictyostelium discoideum MCU and Homo sapiens MCU (HsMCU), we converged on a stretch of 10 amino acids in D. discoideum MCU that can be transplanted to HsMCU to render it EMRE independent. We call this region in human MCU the EMRE dependence domain (EDD). Crosslinking experiments show that EMRE directly interacts with HsMCU at its transmembrane domains as well as the EDD. Our results suggest that EMRE stabilizes the EDD of MCU, permitting both channel opening and calcium conductance, consistent with recently published structures of MCU-EMRE.},
}

Biological Evolution
Calcium/metabolism
Calcium Channels/*metabolism/physiology
Dictyostelium/genetics/metabolism
Evolution, Molecular
HEK293 Cells
Humans
Ion Transport/genetics/physiology
Mitochondria/metabolism
Protein Domains

@article {pmid34257835,
year = {2021},
author = {Cheung, NJ and John Peter, AT and Kornmann, B},
title = {Leri: A web-server for identifying protein functional networks from evolutionary couplings.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {3556-3563},
pmid = {34257835},
issn = {2001-0370},
abstract = {Information on the co-evolution of amino acid pairs in a protein can be used for endeavors such as protein engineering, mutation design, and structure prediction. Here we report a method that captures significant determinants of proteins using estimated co-evolution information to identify networks of residues, termed "residue communities", relevant to protein function. On the benchmark dataset (67 proteins with both catalytic and allosteric residues), the Pearson's correlation between the identified residues in the communities at functional sites is 0.53, and it is higher than 0.8 by taking account of conserved residues derived from the method. On the endoplasmic reticulum-mitochondria encounter structure complex, the results indicate three distinguishable residue communities that are relevant to functional roles in the protein family, suggesting that the residue communities could be general evolutionary signatures in proteins. Based on the method, we provide a webserver for the scientific community to explore the signatures in protein families, which establishes a powerful tool to analyze residue-level profiling for the discovery of functional sites and biological pathway identification. This web-server is freely available for non-commercial users at https://kornmann.bioch.ox.ac.uk/leri/services/ecs.html, neither login nor e-mail required.},
}

@article {pmid34256922,
year = {2021},
author = {Husnik, F and Tashyreva, D and Boscaro, V and George, EE and Lukeš, J and Keeling, PJ},
title = {Bacterial and archaeal symbioses with protists.},
journal = {Current biology : CB},
volume = {31},
number = {13},
pages = {R862-R877},
doi = {10.1016/j.cub.2021.05.049},
pmid = {34256922},
issn = {1879-0445},
abstract = {Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms - the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly.},
}

@article {pmid33247794,
year = {2021},
author = {Bagherfard, S and Najafi, N and Gharzi, A and Akmali, V},
title = {Lack of intraspecific variations of the mitochondrial cytochrome b gene in the greater mouse-tailed bat Rhinopoma microphyllum (Chiroptera: Rhinopomatidae) in Iran.},
journal = {Genetica},
volume = {149},
number = {1},
pages = {37-45},
pmid = {33247794},
issn = {1573-6857},
mesh = {Animals ; Chiroptera/classification/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Speciation ; Genetic Variation/genetics ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeography ; Species Specificity ; },
abstract = {Rhinopoma microphyllum is one of the species of bats that lives in arid and semi-arid areas of Iran. The initial suggestion of the presence of two subspecies R. m. microphyllum and R. m. harrisoni based on their morphological characteristics has been questioned on the basis of small differences between the populations. Later, other researchers assigned Iranian populations of this species to one or two subspecies based on their morphological and molecular characteristics. The present study provides a phylogeographical analysis of this species using 687 bp of the mitochondrial cytochrome b in 81 bats in Iran, Jordan, Levant and Ethiopia. Based on mtDNA sequences, we found a low degree of genetic diversity in the Iranian populations of R. microphyllum (π = 0.0025), which shows a close relationship between the haplotypes. The analysis of genetic distance (0.15-1.93%), phylogenetic trees, and statistical parsimony network showed that all Iranian samples were grouped in the same clade, while Levant, Jordan and Ethiopian samples belonged to a different clade. Molecular dating suggested the Iranian R. microphyllum lineage split from the R. microphyllum of the Levant and Jordan clade during the Pliocene 3.18 (2.11-4.32 Ma). Taking these results into consideration, we can conclude that all Iranian specimens belong to the same subspecies as R. m. harrisoni since molecular results indicate that Iranian samples are differ from Levant subspecies (R. m. microphyllum).},
}

Animals
Chiroptera/classification/*genetics
Cytochromes b/*genetics
DNA, Mitochondrial/*genetics
*Genetic Speciation
Genetic Variation/genetics
Genetics, Population
Haplotypes/genetics
Mitochondria/genetics
Phylogeography
Species Specificity

@article {pmid34254168,
year = {2021},
author = {Igloi, GL},
title = {The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {34254168},
issn = {1432-1432},
abstract = {During the endosymbiotic evolution of mitochondria, the genes for aminoacyl-tRNA synthetases were transferred to the ancestral nucleus. A further reduction of mitochondrial function resulted in mitochondrion-related organisms (MRO) with a loss of the organelle genome. The fate of the now redundant ancestral mitochondrial aminoacyl-tRNA synthetase genes is uncertain. The derived protein sequence for arginyl-tRNA synthetase from thirty mitosomal organisms have been classified as originating from the ancestral nuclear or mitochondrial gene and compared to the identity element at position 20 of the cognate tRNA that distinguishes the two enzyme forms. The evolutionary choice between loss and retention of the ancestral mitochondrial gene for arginyl-tRNA synthetase reflects the coevolution of arginyl-tRNA synthetase and tRNA identity elements.},
}

@article {pmid34252921,
year = {2021},
author = {Anselmetti, Y and El-Mabrouk, N and Lafond, M and Ouangraoua, A},
title = {Gene tree and species tree reconciliation with endosymbiotic gene transfer.},
journal = {Bioinformatics (Oxford, England)},
volume = {37},
number = {Suppl_1},
pages = {i120-i132},
doi = {10.1093/bioinformatics/btab328},
pmid = {34252921},
issn = {1367-4811},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Fonds de recherche Nature et Technologie, Québec/ ; },
abstract = {MOTIVATION: It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree.

RESULTS: We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees.

EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.},
}

@article {pmid34235856,
year = {2021},
author = {Mori, MP and Penjweini, R and Knutson, JR and Wang, PY and Hwang, PM},
title = {Mitochondria and Oxygen Homeostasis.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.16115},
pmid = {34235856},
issn = {1742-4658},
abstract = {Molecular oxygen possesses a dual nature due to its highly reactive free radical property: it is capable of oxidizing metabolic substrates to generate cellular energy, but can also serve as a substrate for genotoxic reactive oxygen species generation. As a labile substance upon which aerobic life depends, the mechanisms for handling cellular oxygen have been finely tuned and orchestrated in evolution. Protection from atmospheric oxygen toxicity as originally posited by the Endosymbiotic Theory of the Mitochondrion is likely to be one basic principle underlying oxygen homeostasis. We briefly review the literature on oxygen homeostasis both in vitro and in vivo with a focus on the role of the mitochondrion where the majority of cellular oxygen is consumed. The insights gleaned from these basic mechanisms are likely to be important for understanding disease pathogenesis and developing strategies for maintaining health.},
}

@article {pmid34212085,
year = {2021},
author = {Sheng, L and Zhou, T and Shi, Z and Pan, X and Weng, X and Ma, J and Wu, S},
title = {The complete mitochondrial genome of Trictenotoma davidi Deyrolle, 1875 (Coleoptera: Trictenotomidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {7},
pages = {2026-2027},
pmid = {34212085},
issn = {2380-2359},
abstract = {Trictenotoma davidi Deyrolle, 1875 is a beetle of the Trictenotomidae family. The length of the complete mitochondria genome of T. davidi was 15,910 bp with 24.1% GC content, including 39.9% A, 15.1% C, 9.0% G, and 36.0% T. The genome encoded 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. Phylogenetic analysis showed that T. davidi was closely related to Vincenzellus ruficollis. This study provided useful genetic information for the evolution of T. davidi and Trictenotomidae insects.},
}

@article {pmid34211444,
year = {2021},
author = {Degli Esposti, M and Moya-Beltrán, A and Quatrini, R and Hederstedt, L},
title = {Respiratory Heme A-Containing Oxidases Originated in the Ancestors of Iron-Oxidizing Bacteria.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {664216},
pmid = {34211444},
issn = {1664-302X},
abstract = {Respiration is a major trait shaping the biology of many environments. Cytochrome oxidase containing heme A (COX) is a common terminal oxidase in aerobic bacteria and is the only one in mammalian mitochondria. The synthesis of heme A is catalyzed by heme A synthase (CtaA/Cox15), an enzyme that most likely coevolved with COX. The evolutionary origin of COX in bacteria has remained unknown. Using extensive sequence and phylogenetic analysis, we show that the ancestral type of heme A synthases is present in iron-oxidizing Proteobacteria such as Acidithiobacillus spp. These bacteria also contain a deep branching form of the major COX subunit (COX1) and an ancestral variant of CtaG, a protein that is specifically required for COX biogenesis. Our work thus suggests that the ancestors of extant iron-oxidizers were the first to evolve COX. Consistent with this conclusion, acidophilic iron-oxidizing prokaryotes lived on emerged land around the time for which there is the earliest geochemical evidence of aerobic respiration on earth. Hence, ecological niches of iron oxidation have apparently promoted the evolution of aerobic respiration.},
}

@article {pmid34211399,
year = {2021},
author = {García-Casas, P and Alvarez-Illera, P and Gómez-Orte, E and Cabello, J and Fonteriz, RI and Montero, M and Alvarez, J},
title = {The Mitochondrial Na+/Ca2+ Exchanger Inhibitor CGP37157 Preserves Muscle Structure and Function to Increase Lifespan and Healthspan in Caenorhabditis elegans.},
journal = {Frontiers in pharmacology},
volume = {12},
number = {},
pages = {695687},
pmid = {34211399},
issn = {1663-9812},
abstract = {We have reported recently that the mitochondrial Na+/Ca2+ exchanger inhibitor CGP37157 extends lifespan in Caenorhabditis elegans by a mechanism involving mitochondria, the TOR pathway and the insulin/IGF1 pathway. Here we show that CGP37157 significantly improved the evolution with age of the sarcomeric regular structure, delaying development of sarcopenia in C. elegans body wall muscle and increasing the average and maximum speed of the worms. Similarly, CGP37157 favored the maintenance of a regular mitochondrial structure during aging. We have also investigated further the mechanism of the effect of CGP37157 by studying its effect in mutants of aak-1;aak-2/AMP-activated kinase, sir-2.1/sirtuin, rsks-1/S6 kinase and daf-16/FOXO. We found that this compound was still effective increasing lifespan in all these mutants, indicating that these pathways are not involved in the effect. We have then monitored pharynx cytosolic and mitochondrial Ca2+ signalling and our results suggest that CGP37157 is probably inhibiting not only the mitochondrial Na+/Ca2+ exchanger, but also Ca2+ entry through the plasma membrane. Finally, a transcriptomic study detected that CGP37157 induced changes in lipid metabolism enzymes and a four-fold increase in the expression of ncx-6, one of the C. elegans mitochondrial Na+/Ca2+ exchangers. In summary, CGP37157 increases both lifespan and healthspan by a mechanism involving changes in cytosolic and mitochondrial Ca2+ homeostasis. Thus, Ca2+ signalling could be a promising target to act on aging.},
}

@article {pmid34202821,
year = {2021},
author = {Purnomo, GA and Mitchell, KJ and O'Connor, S and Kealy, S and Taufik, L and Schiller, S and Rohrlach, A and Cooper, A and Llamas, B and Sudoyo, H and Teixeira, JC and Tobler, R},
title = {Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact.},
journal = {Genes},
volume = {12},
number = {7},
pages = {},
doi = {10.3390/genes12070965},
pmid = {34202821},
issn = {2073-4425},
support = {IN18010007//Australian Research Council/ ; DE190101069//Australian Research Council/ ; //Indonesian Ministry of Research and Technology/National Research and Innovation Agency/ ; },
abstract = {The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul-i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level-by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000-4000 years ago (3-4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.},
}

@article {pmid34192514,
year = {2021},
author = {Amine, AAA and Liao, CW and Hsu, PC and Opoc, FJG and Leu, JY},
title = {Experimental evolution improves mitochondrial genome quality control in Saccharomyces cerevisiae and extends its replicative lifespan.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2021.06.026},
pmid = {34192514},
issn = {1879-0445},
abstract = {The mitochondrion is an ancient endosymbiotic organelle that performs many essential functions in eukaryotic cells.1-3 Mitochondrial impairment often results in physiological defects or diseases.2-8 Since most mitochondrial genes have been copied into the nuclear genome during evolution,9 the regulatory and interaction mechanisms between the mitochondrial and nuclear genomes are very complex. Multiple mechanisms, including antioxidant, DNA repair, mitophagy, and mitochondrial biogenesis pathways, have been shown to monitor the quality and quantity of mitochondria.10-12 Nonetheless, it remains unclear if these pathways can be further modified to enhance mitochondrial stability. Previously, experimental evolution has been used to adapt cells to novel growth conditions. By analyzing the resulting evolved populations, insights have been gained into the underlying molecular mechanisms.13 Here, we experimentally evolved yeast cells under conditions that selected for efficient respiration while continuously assaulting the mitochondrial genome (mtDNA) with ethidium bromide (EtBr). We found that the ability to maintain functional mtDNA was enhanced in most of the evolved lines when challenged with mtDNA-damaging reagents. We identified mutations of the mitochondrial NADH dehydrogenase NDE1 in most of the evolved lines, but other pathways are also involved. Finally, we show that cells displaying enhanced mtDNA retention also exhibit a prolonged replicative lifespan. Our work reveals potential evolutionary trajectories by which cells can maintain functional mitochondria in response to mtDNA stress, as well as the physiological implications of such adaptations.},
}

@article {pmid34188831,
year = {2021},
author = {Yang, M and Dong, D and Li, X},
title = {The complete mitogenome of Phymorhynchus sp. (Neogastropoda, Conoidea, Raphitomidae) provides insights into the deep-sea adaptive evolution of Conoidea.},
journal = {Ecology and evolution},
volume = {11},
number = {12},
pages = {7518-7531},
pmid = {34188831},
issn = {2045-7758},
abstract = {The deep-sea environment is characterized by darkness, hypoxia, and high hydrostatic pressure. Mitochondria play a vital role in energy metabolism; thus, they may endure the selection process during the adaptive evolution of deep-sea organisms. In the present study, the mitogenome of Phymorhynchus sp. from the Haima methane seep was completely assembled and characterized. This mitogenome is 16,681 bp in length and contains 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of most sequenced conoidean gastropods. Some special elements, such as tandem repeat sequences and AT-rich sequences, which are involved in the regulation of the replication and transcription of the mitogenome, were observed in the control region. Phylogenetic analysis revealed that Conoidea is divided into two separate clades with high nodal support. Positive selection analysis revealed evidence of adaptive changes in the mitogenomes of deep-sea conoidean gastropods. Eight residues located in atp6, cox1, cytb, nad1, nad4, and nad5 were determined to have undergone positive selection. This study explores the adaptive evolution of deep-sea conoidean gastropods and provides valuable clues at the mitochondrial level regarding the exceptional adaptive ability of organisms in deep-sea environments.},
}

@article {pmid34171617,
year = {2021},
author = {Iwata, R and Vanderhaeghen, P},
title = {Regulatory roles of mitochondria and metabolism in neurogenesis.},
journal = {Current opinion in neurobiology},
volume = {69},
number = {},
pages = {231-240},
doi = {10.1016/j.conb.2021.05.003},
pmid = {34171617},
issn = {1873-6882},
abstract = {Neural stem cells (NSCs) undergo massive molecular and cellular changes during neuronal differentiation. These include mitochondria and metabolism remodelling, which were thought to be mostly permissive cues, but recent work indicates that they are causally linked to neurogenesis. Striking remodelling of mitochondria occurs right after mitosis of NSCs, which influences the postmitotic daughter cells towards self-renewal or differentiation. The transitioning to neuronal fate requires metabolic rewiring including increased oxidative phosphorylation activity, which drives transcriptional and epigenetic effects to influence cell fate. Mitochondria metabolic pathways also contribute in an essential way to the regulation of NSC proliferation and self-renewal. The influence of mitochondria and metabolism on neurogenesis is conserved from fly to human systems, but also displays striking differences linked to cell context or species. These new findings have important implications for our understanding of neurodevelopmental diseases and possibly human brain evolution.},
}

@article {pmid34155201,
year = {2021},
author = {Evers, F and Cabrera-Orefice, A and Elurbe, DM and Kea-Te Lindert, M and Boltryk, SD and Voss, TS and Huynen, MA and Brandt, U and Kooij, TWA},
title = {Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3820},
pmid = {34155201},
issn = {2041-1723},
mesh = {Electron Transport Chain Complex Proteins/metabolism/ultrastructure ; Evolution, Molecular ; *Life Cycle Stages ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/metabolism/ultrastructure ; Multiprotein Complexes/metabolism/ultrastructure ; Oxidative Phosphorylation ; Plasmodium falciparum/growth & development/*metabolism/ultrastructure ; Protozoan Proteins/metabolism/ultrastructure ; Species Specificity ; },
abstract = {Our current understanding of mitochondrial functioning is largely restricted to traditional model organisms, which only represent a fraction of eukaryotic diversity. The unusual mitochondrion of malaria parasites is a validated drug target but remains poorly understood. Here, we apply complexome profiling to map the inventory of protein complexes across the pathogenic asexual blood stages and the transmissible gametocyte stages of Plasmodium falciparum. We identify remarkably divergent composition and clade-specific additions of all respiratory chain complexes. Furthermore, we show that respiratory chain complex components and linked metabolic pathways are up to 40-fold more prevalent in gametocytes, while glycolytic enzymes are substantially reduced. Underlining this functional switch, we find that cristae are exclusively present in gametocytes. Leveraging these divergent properties and stage dynamics for drug development presents an attractive opportunity to discover novel classes of antimalarials and increase our repertoire of gametocytocidal drugs.},
}

Electron Transport Chain Complex Proteins/metabolism/ultrastructure
Evolution, Molecular
*Life Cycle Stages
Mitochondria/*metabolism/ultrastructure
Mitochondrial Proteins/metabolism/ultrastructure
Multiprotein Complexes/metabolism/ultrastructure
Oxidative Phosphorylation
Plasmodium falciparum/growth & development/*metabolism/ultrastructure
Protozoan Proteins/metabolism/ultrastructure
Species Specificity

@article {pmid34145919,
year = {2021},
author = {Dymek, AM and Pecio, A and Piprek, RP},
title = {Diversity of Balbiani body formation in internally and externally fertilizing representatives of Osteoglossiformes (Teleostei: Osteoglossomorpha).},
journal = {Journal of morphology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jmor.21387},
pmid = {34145919},
issn = {1097-4687},
support = {N18/DBS/000005//Ministerstwo Nauki i Szkolnictwa Wyższego/ ; //PhD Students Society of Jagiellonian University/ ; K/DSC/005532//Uniwersytet Jagielloński w Krakowie/ ; },
abstract = {During the early stages of oogenesis, the Balbiani body is formed in the primary oocytes. It consists of the Golgi apparatus, endoplasmic reticulum (ER), and numerous mitochondria aggregated with germ plasm, but its form may differ among animals. Hypothetically, during oogenesis oocytes become adapted to future development in two different environments depending on internal or external fertilization. We aimed to investigate, using light and transmission electron microscopy, the development of the Balbiani body during oogenesis in representatives of Osteoglossiformes, one of the most basal Teleostei groups. We analyzed the structure of oogonia and primary oocytes in the internally fertilizing butterflyfish Pantodon buchholzi and the externally fertilizing Osteoglossum bicirrhosum and Arapaima gigas to compare formation of the Balbiani body in relation to modes of fertilization. We demonstrated that the presence of the germ plasm as well as the fusion and fission of mitochondria are the conserved features of the Bb. However, each species exhibited also some peculiar features, including the presence of three types of ooplasm with different electron density and mitochondria-associated membranes in P. buchholzi; annulate lamellae, complexes of the Golgi apparatus, ER network, and lysosome-like bodies in O. bicirrhosum; as well as karmellae and whorls formed by the lamellae of the ER in A. gigas. Moreover, the form of the germ plasm observed in close contact with mitochondria differed between osteoglossiforms, with a "net-like" structure in P. buchholzi, the presence of numerous strings in O. bicirrhosum, and irregular accumulations in A. gigas. These unique features indicate that the extreme diversity of gamete structure observed so far only in the spermatozoa of osteoglossiforms is also characteristic for oocyte development in these basal teleosts. Possible reason of this variability is a period of about 150 million years of independent evolution of the lineages.},
}

@article {pmid34140474,
year = {2021},
author = {Jin, L and Tang, Q and Hu, S and Chen, Z and Zhou, X and Zeng, B and Wang, Y and He, M and Li, Y and Gui, L and Shen, L and Long, K and Ma, J and Wang, X and Chen, Z and Jiang, Y and Tang, G and Zhu, L and Liu, F and Zhang, B and Huang, Z and Li, G and Li, D and Gladyshev, VN and Yin, J and Gu, Y and Li, X and Li, M},
title = {A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3715},
pmid = {34140474},
issn = {2041-1723},
mesh = {Adipose Tissue/*metabolism ; Alternative Splicing ; Animals ; Biological Evolution ; Cell Line ; Cell Lineage ; Cell Nucleus/genetics/metabolism ; Enhancer Elements, Genetic ; Evolution, Molecular ; Gene Expression Profiling ; Gene Regulatory Networks ; MicroRNAs/genetics/*metabolism ; Mitochondria/metabolism ; Molecular Conformation ; Muscle, Skeletal/*metabolism ; Myofibrils/genetics/metabolism ; Phylogeny ; Promoter Regions, Genetic ; RNA, Circular/genetics/*metabolism ; RNA, Long Noncoding/genetics/*metabolism ; RNA, Messenger/genetics/*metabolism ; Spatial Analysis ; Swine ; Transcriptome/*genetics ; },
abstract = {A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter-enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits.},
}

Adipose Tissue/*metabolism
Alternative Splicing
Animals
Biological Evolution
Cell Line
Cell Lineage
Cell Nucleus/genetics/metabolism
Enhancer Elements, Genetic
Evolution, Molecular
Gene Expression Profiling
Gene Regulatory Networks
MicroRNAs/genetics/*metabolism
Mitochondria/metabolism
Molecular Conformation
Muscle, Skeletal/*metabolism
Myofibrils/genetics/metabolism
Phylogeny
Promoter Regions, Genetic
RNA, Circular/genetics/*metabolism
RNA, Long Noncoding/genetics/*metabolism
RNA, Messenger/genetics/*metabolism
Spatial Analysis
Swine
Transcriptome/*genetics

@article {pmid34136489,
year = {2021},
author = {Gažová, I and Lefevre, L and Bush, SJ and Rojo, R and Hume, DA and Lengeling, A and Summers, KM},
title = {CRISPR-Cas9 Editing of Human Histone Deubiquitinase Gene USP16 in Human Monocytic Leukemia Cell Line THP-1.},
journal = {Frontiers in cell and developmental biology},
volume = {9},
number = {},
pages = {679544},
pmid = {34136489},
issn = {2296-634X},
abstract = {USP16 is a histone deubiquitinase which facilitates G2/M transition during the cell cycle, regulates DNA damage repair and contributes to inducible gene expression. We mutated the USP16 gene in a high differentiation clone of the acute monocytic leukemia cell line THP-1 using the CRISPR-Cas9 system and generated four homozygous knockout clones. All were able to proliferate and to differentiate in response to phorbol ester (PMA) treatment. One line was highly proliferative prior to PMA treatment and shut down proliferation upon differentiation, like wild type. Three clones showed sustained expression of the progenitor cell marker MYB, indicating that differentiation had not completely blocked proliferation in these clones. Network analysis of transcriptomic differences among wild type, heterozygotes and homozygotes showed clusters of genes that were up- or down-regulated after differentiation in all cell lines. Prior to PMA treatment, the homozygous clones had lower levels than wild type of genes relating to metabolism and mitochondria, including SRPRB, encoding an interaction partner of USP16. There was also apparent loss of interferon signaling. In contrast, a number of genes were up-regulated in the homozygous cells compared to wild type at baseline, including other deubiquitinases (USP12, BAP1, and MYSM1). However, three homozygotes failed to fully induce USP3 during differentiation. Other network clusters showed effects prior to or after differentiation in the homozygous clones. Thus the removal of USP16 affected the transcriptome of the cells, although all these lines were able to survive, which suggests that the functions attributed to USP16 may be redundant. Our analysis indicates that the leukemic line can adapt to the extreme selection pressure applied by the loss of USP16, and the harsh conditions of the gene editing and selection protocol, through different compensatory pathways. Similar selection pressures occur during the evolution of a cancer in vivo, and our results can be seen as a case study in leukemic cell adaptation. USP16 has been considered a target for cancer chemotherapy, but our results suggest that treatment would select for escape mutants that are resistant to USP16 inhibitors.},
}

@article {pmid34133204,
year = {2021},
author = {Cadena, LR and Gahura, O and Panicucci, B and Zíková, A and Hashimi, H},
title = {Mitochondrial Contact Site and Cristae Organization System and F1FO-ATP Synthase Crosstalk Is a Fundamental Property of Mitochondrial Cristae.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0032721},
doi = {10.1128/mSphere.00327-21},
pmid = {34133204},
issn = {2379-5042},
abstract = {Mitochondrial cristae are polymorphic invaginations of the inner membrane that are the fabric of cellular respiration. Both the mitochondrial contact site and cristae organization system (MICOS) and the F1FO-ATP synthase are vital for sculpting cristae by opposing membrane-bending forces. While MICOS promotes negative curvature at crista junctions, dimeric F1FO-ATP synthase is crucial for positive curvature at crista rims. Crosstalk between these two complexes has been observed in baker's yeast, the model organism of the Opisthokonta supergroup. Here, we report that this property is conserved in Trypanosoma brucei, a member of the Discoba clade that separated from the Opisthokonta ∼2 billion years ago. Specifically, one of the paralogs of the core MICOS subunit Mic10 interacts with dimeric F1FO-ATP synthase, whereas the other core Mic60 subunit has a counteractive effect on F1FO-ATP synthase oligomerization. This is evocative of the nature of MICOS-F1FO-ATP synthase crosstalk in yeast, which is remarkable given the diversification that these two complexes have undergone during almost 2 eons of independent evolution. Furthermore, we identified a highly diverged, putative homolog of subunit e, which is essential for the stability of F1FO-ATP synthase dimers in yeast. Just like subunit e, it is preferentially associated with dimers and interacts with Mic10, and its silencing results in severe defects to cristae and the disintegration of F1FO-ATP synthase dimers. Our findings indicate that crosstalk between MICOS and dimeric F1FO-ATP synthase is a fundamental property impacting crista shape throughout eukaryotes. IMPORTANCE Mitochondria have undergone profound diversification in separate lineages that have radiated since the last common ancestor of eukaryotes some eons ago. Most eukaryotes are unicellular protists, including etiological agents of infectious diseases, like Trypanosoma brucei. Thus, the study of a broad range of protists can reveal fundamental features shared by all eukaryotes and lineage-specific innovations. Here, we report that two different protein complexes, MICOS and F1FO-ATP synthase, known to affect mitochondrial architecture, undergo crosstalk in T. brucei, just as in baker's yeast. This is remarkable considering that these complexes have otherwise undergone many changes during their almost 2 billion years of independent evolution. Thus, this crosstalk is a fundamental property needed to maintain proper mitochondrial structure even if the constituent players considerably diverged.},
}

@article {pmid34131078,
year = {2021},
author = {Hoshino, Y and Gaucher, EA},
title = {Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {25},
pages = {},
pmid = {34131078},
issn = {1091-6490},
support = {R01 AR069137/AR/NIAMS NIH HHS/United States ; },
abstract = {Steroids are components of the eukaryotic cellular membrane and have indispensable roles in the process of eukaryotic endocytosis by regulating membrane fluidity and permeability. In particular, steroids may have been a structural prerequisite for the acquisition of mitochondria via endocytosis during eukaryogenesis. While eukaryotes are inferred to have evolved from an archaeal lineage, there is little similarity between the eukaryotic and archaeal cellular membranes. As such, the evolution of eukaryotic cellular membranes has limited our understanding of eukaryogenesis. Despite evolving from archaea, the eukaryotic cellular membrane is essentially a fatty acid bacterial-type membrane, which implies a substantial bacterial contribution to the evolution of the eukaryotic cellular membrane. Here, we address the evolution of steroid biosynthesis in eukaryotes by combining ancestral sequence reconstruction and comprehensive phylogenetic analyses of steroid biosynthesis genes. Contrary to the traditional assumption that eukaryotic steroid biosynthesis evolved within eukaryotes, most steroid biosynthesis genes are inferred to be derived from bacteria. In particular, aerobic deltaproteobacteria (myxobacteria) seem to have mediated the transfer of key genes for steroid biosynthesis to eukaryotes. Analyses of resurrected steroid biosynthesis enzymes suggest that the steroid biosynthesis pathway in early eukaryotes may have been similar to the pathway seen in modern plants and algae. These resurrected proteins also experimentally demonstrate that molecular oxygen was required to establish the modern eukaryotic cellular membrane during eukaryogenesis. Our study provides unique insight into relationships between early eukaryotes and other bacteria in addition to the well-known endosymbiosis with alphaproteobacteria.},
}

@article {pmid34129020,
year = {2021},
author = {Mixão, V and Hegedűsová, E and Saus, E and Pryszcz, LP and Cillingová, A and Nosek, J and Gabaldón, T},
title = {Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsab006},
pmid = {34129020},
issn = {1756-1663},
abstract = {Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, C. subhashii was initially described as the causative agent of a case of peritonitis. Considering the relevance of whole-genome sequencing and analysis for our understanding of genome evolution and pathogenicity, we sequenced, assembled and annotated the genome of C. subhashii type strain. Our results show that C. subhashii presents a highly heterozygous genome and other signatures that point to a hybrid ancestry. The presence of functional pathways for assimilation of hydroxyaromatic compounds goes in line with the affiliation of this yeast with soil microbial communities involved in lignin decomposition. Furthermore, we observed that different clones of this strain may present circular or linear mitochondrial DNA. Re-sequencing and comparison of strains with differential mitochondrial genome topology revealed five candidate genes potentially associated with this conformational change: MSK1, SSZ1, ALG5, MRPL9 and OYE32.},
}

@article {pmid34118265,
year = {2021},
author = {Manoj, KM and Bazhin, NM},
title = {The murburn precepts for aerobic respiration and redox homeostasis.},
journal = {Progress in biophysics and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pbiomolbio.2021.05.010},
pmid = {34118265},
issn = {1873-1732},
abstract = {Murburn concept is a new perspective to metabolism which posits that certain redox enzymes/proteins mediate catalysis outside their active site, via diffusible reactive oxygen species (DROS, usually deemed as toxic wastes). We have recently questioned the proton-centric chemiosmotic rotary ATP synthesis (CRAS) explanation for mitochondrial oxidative phosphorylation (mOxPhos) and proposed an oxygen-centric murburn model in lieu. Herein, the chemical equations and thermodynamic foundations for this new model of mOxPhos are detailed. Standard transformed Gibbs free energy values of respiratory reactions are calculated to address the spontaneity, control, and efficiency of oxidative phosphorylation. Unlike the deterministic/multi-molecular and 'irreducibly complex' CRAS model, the stochastic/bimolecular and parsimonious murburn reactions afford a more viable precept for the variable and non-integral stoichiometry, higher yield for NADH than FADH2, and origin/evolution of oxygen-centric cellular life. Also, we present tangible DROS-based explanations for the multiple roles of various reaction components, HCN > H2S order of cellular toxicity in aerobes, and explain why oxygen inhibits anaerobes. We highlight the thermodynamic significance of proton deficiency in NADH/mitochondria and link the 'oxygen → DROS → water' metabolic pathway to the macroscopic physiologies of ATP-synthesis, trans-membrane potential, thermogenesis, and homeostasis. We also provide arguments for the extension of the murburn bioenergetics model to life under anoxic and extreme/unique habitats. In the context of mOxPhos, our findings imply that DROS should be seen as an essential requisite for life, and not merely as pathophysiological manifestations.},
}

@article {pmid34097987,
year = {2021},
author = {Capitanio, G and Papa, F and Papa, S},
title = {The allosteric protein interactions in the proton-motive function of mammalian redox enzymes of the respiratory chain.},
journal = {Biochimie},
volume = {189},
number = {},
pages = {1-12},
doi = {10.1016/j.biochi.2021.05.018},
pmid = {34097987},
issn = {1638-6183},
abstract = {Insight into mammalian respiratory complexes defines the role of allosteric protein interactions in their proton-motive activity. In cytochrome c oxidase (CxIV) conformational change of subunit I, caused by O2 binding to heme a32+-CuB+ and reduction, and stereochemical transitions coupled to oxidation/reduction of heme a and CuA, combined with electrostatic effects, determine the proton pumping activity. In ubiquinone-cytochrome c oxidoreductase (CxIII) conformational movement of Fe-S protein between cytochromes b and c1 is the key element of the proton-motive activity. In NADH-ubiquinone oxidoreductase (CxI) ubiquinone binding and reduction result in conformational changes of subunits in the quinone reaction structure which initiate proton pumping.},
}

@article {pmid34087614,
year = {2021},
author = {Mazzocca, A and Fais, S},
title = {New hypotheses for cancer generation and progression.},
journal = {Medical hypotheses},
volume = {152},
number = {},
pages = {110614},
doi = {10.1016/j.mehy.2021.110614},
pmid = {34087614},
issn = {1532-2777},
mesh = {Biological Evolution ; Carcinogenesis ; Humans ; Mutation ; *Neoplasms ; Phenotype ; Tumor Microenvironment ; },
abstract = {Since Nixon famously declared war on cancer in 1971, trillions of dollars have been spent on cancer research but the life expectancy for most forms of cancer is still poor. There are many reasons for the partial success of cancer translational research. One of these can be the predominance of certain paradigms that potentially narrowed the vision in interpreting cancer. The main paradigm to explain carcinogenesis is based on DNA mutations, which is well interpreted by the somatic mutation theory (SMT). However, a different theory claims that cancer is instead a tissue disease as proposed by the Tissue Organization Field Theory (TOFT). Here, we propose new hypotheses to explain the origin and pathogenesis of cancer. In this perspective, the systemic-evolutionary theory of cancer (SETOC) is discussed as well as how the microenvironment affects the adaptation of transformed cells and the reversion to a unicellular-like or embryo-like phenotype.},
}

Biological Evolution
Carcinogenesis
Humans
Mutation
*Neoplasms
Phenotype
Tumor Microenvironment

@article {pmid34083540,
year = {2021},
author = {Wang, S and Luo, H},
title = {Dating Alphaproteobacteria evolution with eukaryotic fossils.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3324},
pmid = {34083540},
issn = {2041-1723},
mesh = {Alphaproteobacteria/*classification/*genetics ; Animals ; Cyanobacteria/classification/genetics ; Eukaryota/*classification/*genetics ; *Evolution, Molecular ; *Fossils/history/microbiology ; Genome, Bacterial ; Genome, Mitochondrial ; History, Ancient ; Mitochondria/genetics/microbiology ; Models, Biological ; Models, Genetic ; Phylogeny ; Rickettsiales/classification/genetics ; Symbiosis/genetics ; Time Factors ; },
abstract = {Elucidating the timescale of the evolution of Alphaproteobacteria, one of the most prevalent microbial lineages in marine and terrestrial ecosystems, is key to testing hypotheses on their co-evolution with eukaryotic hosts and Earth's systems, which, however, is largely limited by the scarcity of bacterial fossils. Here, we incorporate eukaryotic fossils to date the divergence times of Alphaproteobacteria, based on the mitochondrial endosymbiosis that mitochondria evolved from an alphaproteobacterial lineage. We estimate that Alphaproteobacteria arose ~1900 million years (Ma) ago, followed by rapid divergence of their major clades. We show that the origin of Rickettsiales, an order of obligate intracellular bacteria whose hosts are mostly animals, predates the emergence of animals for ~700 Ma but coincides with that of eukaryotes. This, together with reconstruction of ancestral hosts, strongly suggests that early Rickettsiales lineages had established previously underappreciated interactions with unicellular eukaryotes. Moreover, the mitochondria-based approach displays higher robustness to uncertainties in calibrations compared with the traditional strategy using cyanobacterial fossils. Further, our analyses imply the potential of dating the (bacterial) tree of life based on endosymbiosis events, and suggest that previous applications using divergence times of the modern hosts of symbiotic bacteria to date bacterial evolution might need to be revisited.},
}

Alphaproteobacteria/*classification/*genetics
Animals
Cyanobacteria/classification/genetics
Eukaryota/*classification/*genetics
*Evolution, Molecular
*Fossils/history/microbiology
Genome, Bacterial
Genome, Mitochondrial
History, Ancient
Mitochondria/genetics/microbiology
Models, Biological
Models, Genetic
Phylogeny
Rickettsiales/classification/genetics
Symbiosis/genetics
Time Factors

@article {pmid34073133,
year = {2021},
author = {Cramer, ERA and Garcia-Del-Rey, E and Johannessen, LE and Laskemoen, T and Marthinsen, G and Johnsen, A and Lifjeld, JT},
title = {Longer Sperm Swim More Slowly in the Canary Islands Chiffchaff.},
journal = {Cells},
volume = {10},
number = {6},
pages = {},
pmid = {34073133},
issn = {2073-4409},
support = {301592//Norges Forskningsråd/ ; 196554//Norges Forskningsråd/ ; },
abstract = {Sperm swimming performance affects male fertilization success, particularly in species with high sperm competition. Understanding how sperm morphology impacts swimming performance is therefore important. Sperm swimming speed is hypothesized to increase with total sperm length, relative flagellum length (with the flagellum generating forward thrust), and relative midpiece length (as the midpiece contains the mitochondria). We tested these hypotheses and tested for divergence in sperm traits in five island populations of Canary Islands chiffchaff (Phylloscopus canariensis). We confirmed incipient mitochondrial DNA differentiation between Gran Canaria and the other islands. Sperm swimming speed correlated negatively with total sperm length, did not correlate with relative flagellum length, and correlated negatively with relative midpiece length (for Gran Canaria only). The proportion of motile cells increased with relative flagellum length on Gran Canaria only. Sperm morphology was similar across islands. We thus add to a growing number of studies on passerine birds that do not support sperm morphology-swimming speed hypotheses. We suggest that the swimming mechanics of passerine sperm are sufficiently different from mammalian sperm that predictions from mammalian hydrodynamic models should no longer be applied for this taxon. While both sperm morphology and sperm swimming speed are likely under selection in passerines, the relationship between them requires further elucidation.},
}

@article {pmid34072215,
year = {2021},
author = {Dür, A and Huber, N and Parson, W},
title = {Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences.},
journal = {International journal of molecular sciences},
volume = {22},
number = {11},
pages = {},
pmid = {34072215},
issn = {1422-0067},
mesh = {Algorithms ; Computational Biology/methods ; DNA, Mitochondrial/chemistry/*genetics ; Genome, Mitochondrial ; Genomics/methods ; *Haplotypes ; Humans ; Mitochondria/genetics ; *Phylogeny ; Regulatory Sequences, Nucleic Acid ; },
abstract = {In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.},
}

Algorithms
Computational Biology/methods
DNA, Mitochondrial/chemistry/*genetics
Genome, Mitochondrial
Genomics/methods
*Haplotypes
Humans
Mitochondria/genetics
*Phylogeny
Regulatory Sequences, Nucleic Acid

@article {pmid34070437,
year = {2021},
author = {Ai, D and Peng, L and Qin, D and Zhang, Y},
title = {Characterization of Three Complete Mitogenomes of Flatidae (Hemiptera: Fulgoroidea) and Compositional Heterogeneity Analysis in the Planthoppers' Mitochondrial Phylogenomics.},
journal = {International journal of molecular sciences},
volume = {22},
number = {11},
pages = {},
pmid = {34070437},
issn = {1422-0067},
support = {31420103911//National Natural Science Foundation of China/ ; 2015FY210300//Ministry of Science and Technology of the People's Republic of China/ ; 2005DKA21402//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Animals ; Base Composition ; Codon Usage ; Gene Order ; *Genome, Mitochondrial ; Hemiptera/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Tandem Repeat Sequences/genetics ; },
abstract = {Although sequences of mitogenomes have been widely used for investigating phylogenetic relationship, population genetics, and biogeography in many members of Fulgoroidea, only one complete mitogenome of a member of Flatidae has been sequenced. Here, the complete mitogenomes of Cerynia lineola, Cromna sinensis, and Zecheuna tonkinensis are sequenced. The gene arrangements of the three new mitogenomes are consistent with ancestral insect mitogenomes. The strategy of using mitogenomes in phylogenetics remains in dispute due to the heterogeneity in base composition and the possible variation in evolutionary rates. In this study, we found compositional heterogeneity and variable evolutionary rates among planthopper mitogenomes. Phylogenetic analysis based on site-homogeneous models showed that the families (Delphacidae and Derbidae) with high values of Ka/Ks and A + T content tended to fall together at a basal position on the trees. Using a site-heterogeneous mixture CAT + GTR model implemented in PhyloBayes yielded almost the same topology. Our results recovered the monophyly of Fulgoroidea. In this study, we apply the heterogeneous mixture model to the planthoppers' phylogenetic analysis for the first time. Our study is based on a large sample and provides a methodological reference for future phylogenetic studies of Fulgoroidea.},
}

Animals
Base Composition
Codon Usage
Gene Order
*Genome, Mitochondrial
Hemiptera/*genetics
High-Throughput Nucleotide Sequencing
Mitochondria/*genetics
Mitochondrial Proteins/genetics
Phylogeny
RNA, Ribosomal/genetics
RNA, Transfer/genetics
Sequence Alignment
Tandem Repeat Sequences/genetics

@article {pmid34070384,
year = {2021},
author = {Di Gregorio, E and Miolo, G and Saorin, A and Steffan, A and Corona, G},
title = {From Metabolism to Genetics and Vice Versa: The Rising Role of Oncometabolites in Cancer Development and Therapy.},
journal = {International journal of molecular sciences},
volume = {22},
number = {11},
pages = {},
pmid = {34070384},
issn = {1422-0067},
mesh = {Cell Transformation, Neoplastic/*metabolism/pathology ; Humans ; Metabolic Diseases/*metabolism/pathology ; Mitochondria/*metabolism/pathology ; Neoplasms/*metabolism/pathology ; *Signal Transduction ; },
abstract = {Over the last decades, the study of cancer metabolism has returned to the forefront of cancer research and challenged the role of genetics in the understanding of cancer development. One of the major impulses of this new trend came from the discovery of oncometabolites, metabolic intermediates whose abnormal cellular accumulation triggers oncogenic signalling and tumorigenesis. These findings have led to reconsideration and support for the long-forgotten hypothesis of Warburg of altered metabolism as oncogenic driver of cancer and started a novel paradigm whereby mitochondrial metabolites play a pivotal role in malignant transformation. In this review, we describe the evolution of the cancer metabolism research from a historical perspective up to the oncometabolites discovery that spawned the new vision of cancer as a metabolic disease. The oncometabolites' mechanisms of cellular transformation and their contribution to the development of new targeted cancer therapies together with their drawbacks are further reviewed and discussed.},
}

Cell Transformation, Neoplastic/*metabolism/pathology
Humans
Metabolic Diseases/*metabolism/pathology
Mitochondria/*metabolism/pathology
Neoplasms/*metabolism/pathology
*Signal Transduction

@article {pmid34067626,
year = {2021},
author = {Yamaguchi, K and Kitamura, S and Furutake, Y and Murakami, R and Yamanoi, K and Taki, M and Ukita, M and Hamanishi, J and Mandai, M},
title = {Acquired Evolution of Mitochondrial Metabolism Regulated by HNF1B in Ovarian Clear Cell Carcinoma.},
journal = {Cancers},
volume = {13},
number = {10},
pages = {},
pmid = {34067626},
issn = {2072-6694},
abstract = {Clear cell carcinoma (CCC) of the ovary exhibits a unique morphology and clinically malignant behavior. The eosinophilic cytoplasm includes abundant glycogen. Although the growth is slow, the prognosis is poor owing to resistance to conventional chemotherapies. CCC often arises in endometriotic cysts and is accompanied by endometriosis. Based on these characteristics, three clinical questions are considered: why does ovarian cancer, especially CCC and endometrioid carcinoma, frequently occur in endometriotic cysts, why do distinct histological subtypes (CCC and endometrioid carcinoma) arise in the endometriotic cyst, and why does ovarian CCC possess unique characteristics? Mutations in AT-rich interacting domain-containing protein 1A and phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit alpha genes may contribute to the carcinogenesis of ovarian CCC, whereas hepatocyte nuclear factor-1-beta (HNF1B) plays crucial roles in sculpting the unique characteristics of ovarian CCC through metabolic alterations. HNF1B increases glutathione synthesis, activates anaerobic glycolysis called the Warburg effect, and suppresses mitochondria. These metabolic changes may be induced in stressful environments. Life has evolved to utilize and control energy; eukaryotes require mitochondria to transform oxygen reduction into useful energy. Because mitochondrial function is suppressed in ovarian CCC, these cancer cells probably acquired further metabolic evolution during the carcinogenic process in order to survive stressful environments.},
}

@article {pmid34065848,
year = {2021},
author = {Lyu, D and Msimbira, LA and Nazari, M and Antar, M and Pagé, A and Shah, A and Monjezi, N and Zajonc, J and Tanney, CAS and Backer, R and Smith, DL},
title = {The Coevolution of Plants and Microbes Underpins Sustainable Agriculture.},
journal = {Microorganisms},
volume = {9},
number = {5},
pages = {},
pmid = {34065848},
issn = {2076-2607},
support = {RGPIN 2020-07047.//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Terrestrial plants evolution occurred in the presence of microbes, the phytomicrobiome. The rhizosphere microbial community is the most abundant and diverse subset of the phytomicrobiome and can include both beneficial and parasitic/pathogenic microbes. Prokaryotes of the phytomicrobiome have evolved relationships with plants that range from non-dependent interactions to dependent endosymbionts. The most extreme endosymbiotic examples are the chloroplasts and mitochondria, which have become organelles and integral parts of the plant, leading to some similarity in DNA sequence between plant tissues and cyanobacteria, the prokaryotic symbiont of ancestral plants. Microbes were associated with the precursors of land plants, green algae, and helped algae transition from aquatic to terrestrial environments. In the terrestrial setting the phytomicrobiome contributes to plant growth and development by (1) establishing symbiotic relationships between plant growth-promoting microbes, including rhizobacteria and mycorrhizal fungi, (2) conferring biotic stress resistance by producing antibiotic compounds, and (3) secreting microbe-to-plant signal compounds, such as phytohormones or their analogues, that regulate aspects of plant physiology, including stress resistance. As plants have evolved, they recruited microbes to assist in the adaptation to available growing environments. Microbes serve themselves by promoting plant growth, which in turn provides microbes with nutrition (root exudates, a source of reduced carbon) and a desirable habitat (the rhizosphere or within plant tissues). The outcome of this coevolution is the diverse and metabolically rich microbial community that now exists in the rhizosphere of terrestrial plants. The holobiont, the unit made up of the phytomicrobiome and the plant host, results from this wide range of coevolved relationships. We are just beginning to appreciate the many ways in which this complex and subtle coevolution acts in agricultural systems.},
}

@article {pmid34061590,
year = {2021},
author = {Siscar-Lewin, S and Gabaldón, T and Aldejohann, AM and Kurzai, O and Hube, B and Brunke, S},
title = {Transient Mitochondria Dysfunction Confers Fungal Cross-Resistance against Phagocytic Killing and Fluconazole.},
journal = {mBio},
volume = {12},
number = {3},
pages = {e0112821},
doi = {10.1128/mBio.01128-21},
pmid = {34061590},
issn = {2150-7511},
support = {//FSU | Jena School for Microbial Communication, Friedrich-Schiller-Universität Jena (JSMC, FSU)/ ; ID 390713860//Friedrich-Schiller-Universität Jena (FSU)/ ; },
abstract = {Loss or inactivation of antivirulence genes is an adaptive strategy in pathogen evolution. Candida glabrata is an important opportunistic pathogen related to baker's yeast, with the ability to both quickly increase its intrinsic high level of azole resistance and persist within phagocytes. During C. glabrata's evolution as a pathogen, the mitochondrial DNA polymerase CgMip1 has been under positive selection. We show that CgMIP1 deletion not only triggers loss of mitochondrial function and a petite phenotype, but increases C. glabrata's azole and endoplasmic reticulum (ER) stress resistance and, importantly, its survival in phagocytes. The same phenotype is induced by fluconazole and by exposure to macrophages, conferring a cross-resistance between antifungals and immune cells, and can be found in clinical isolates despite a slow growth of petite strains. This suggests that petite constitutes a bet-hedging strategy of C. glabrata and, potentially, a relevant cause of azole resistance. Mitochondrial function may therefore be considered a potential antivirulence factor. IMPORTANCE Candida glabrata is an opportunistic pathogen whose incidence has been increasing in the last 40 years. It has risen to become the most prominent non-Candida albicans Candida (NCAC) species to cause candidemia, constituting about one-third of isolates in the United States, and steadily increasing in European countries and in Australia. Despite its clinical importance, C. glabrata's pathogenicity strategies remain poorly understood. Our research shows that loss of mitochondrial function and the resulting petite phenotype is advantageous for C. glabrata to cope with infection-related stressors, such as antifungals and host immune defenses. The (cross-)resistance against both these factors may have major implications in the clinical outcome of infections with this major fungal pathogen.},
}

@article {pmid34039261,
year = {2021},
author = {Awadi, A and Ben Slimen, H and Schaschl, H and Knauer, F and Suchentrunk, F},
title = {Positive selection on two mitochondrial coding genes and adaptation signals in hares (genus Lepus) from China.},
journal = {BMC ecology and evolution},
volume = {21},
number = {1},
pages = {100},
pmid = {34039261},
issn = {2730-7182},
mesh = {Animals ; China ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; *Hares/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection.

RESULTS: Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of Δ vibrational entropy energy between wild and mutant type. Moreover, our PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. Our statistical models indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgression, which is not uncommon in a number of hare species.

CONCLUSIONS: Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.},
}

Animals
China
DNA, Mitochondrial/genetics
Genes, Mitochondrial
*Hares/genetics
Phylogeny

@article {pmid34037779,
year = {2021},
author = {Burskaia, V and Artyushin, I and Potapova, NA and Konovalov, K and Bazykin, GA},
title = {Convergent Adaptation in Mitochondria of Phylogenetically Distant Birds: Does it Exist?.},
journal = {Genome biology and evolution},
volume = {13},
number = {7},
pages = {},
pmid = {34037779},
issn = {1759-6653},
abstract = {In a wide range of taxa, proteins encoded by mitochondrial genomes are involved in adaptation to lifestyle that requires oxygen starvation or elevation of metabolism rate. It remains poorly understood to what extent adaptation to similar conditions is associated with parallel changes in these proteins. We search for a genetic signal of parallel or convergent evolution in recurrent molecular adaptation to high altitude, migration, diving, wintering, unusual flight abilities, or loss of flight in mitochondrial genomes of birds. Developing on previous work, we design an approach for the detection of recurrent coincident changes in genotype and phenotype, indicative of an association between the two. We describe a number of candidate sites involved in recurrent adaptation in ND genes. However, we find that the majority of convergence events can be explained by random coincidences without invoking adaptation.},
}

@article {pmid34034879,
year = {2021},
author = {Chowrasia, S and Nishad, J and Pandey, R and Mondal, TK},
title = {Oryza coarctata is a triploid plant with initial events of C4 photosynthesis evolution.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {308},
number = {},
pages = {110878},
doi = {10.1016/j.plantsci.2021.110878},
pmid = {34034879},
issn = {1873-2259},
mesh = {*Biological Evolution ; *Carbon Cycle ; Oryza/*anatomy & histology/genetics ; *Photosynthesis ; Plant Leaves/anatomy & histology ; *Triploidy ; },
abstract = {Oryza coarctata is an obligate halophyte of wild species of rice which thrives well under high saline as well as submerged conditions. We report here for the first time that O. coarctata is triploid (2n = 3x = 36), though it was previously known as tetraploid (2n = 4x = 48). The chromosome number of O. coarctata was determined from mitotic plates of root tips and ploidy level was determined by flow cytometer, where it was found to be triploid (2n = 3x = 36). In addition, this species was found to possess several unique anatomical features in leaves such as presence of Kranz-anatomy, increased vein density and higher ratio of bundle sheath to mesophyll cell area as compared to rice variety (IR-29). Ultra-structure of leaf showed the presence of bundle sheath cells with significant number of chloroplasts and mitochondria which were arranged centrifugally. Chloroplasts lack grana in bundle sheath cell whereas, mesophyll cell contain well-developed grana. These anatomical and ultra structural characteristics indicate that this plant is in initial stage of evolving towards C4 photosynthesis due to high selection pressure which might help it to survive in wide range of ecological conditions i.e. from submerged saline to non-saline terrestrial condition.},
}

*Biological Evolution
*Carbon Cycle
Oryza/*anatomy & histology/genetics
*Photosynthesis
Plant Leaves/anatomy & histology
*Triploidy

@article {pmid34029916,
year = {2021},
author = {Zhu, D and Liu, Z and Li, Y and Huang, Q and Xia, L and Li, K},
title = {Delivery of manganese carbonyl to the tumor microenvironment using Tumor-Derived exosomes for cancer gas therapy and low dose radiotherapy.},
journal = {Biomaterials},
volume = {274},
number = {},
pages = {120894},
doi = {10.1016/j.biomaterials.2021.120894},
pmid = {34029916},
issn = {1878-5905},
mesh = {Cell Line, Tumor ; *Exosomes ; Manganese ; *Nanoparticles ; *Neoplasms/radiotherapy ; Tumor Microenvironment ; },
abstract = {The development of novel radiosensitizer with high selectivity and controllability is highly desirable. CO gas could cause damage to mitochondria and thus enhance RT effect. Controlled delivery of CO in tumor is important both to achieve high-efficiency of CO gas therapy and to decrease the risk of CO poisoning. In this study, manganese carbonyl (MnCO) loaded exosome nano-vesicles (MMV) to overcome this conundrum for tumor therapy is developed. After administration, MMV showed its admirable performance in active tumor-targeting, mitochondria damage and radiosensitization therapy. These MMV nanoparticles were able to facilitate robust CO evolution and consequent ROS generation in response to X-ray irradiation both in vitro and in vivo. Significantly, MMV could facilitate a 90% inhibition effect of tumor growth under very low dose (only 2Gy) RT, which is better than high dose (6Gy) radiotherapy. Overall, this study highlights a novel and practical approach to enhancing the efficacy of tumor RT, underscoring the value of future research in the field of CO medicine.},
}

Cell Line, Tumor
*Exosomes
Manganese
*Nanoparticles
*Neoplasms/radiotherapy
Tumor Microenvironment

@article {pmid34027666,
year = {2021},
author = {Zheng, Y and Ye, Z and Liu, Z and Yang, W and Zhang, X and Yang, Y and Xiao, Y},
title = {Nitroso-Caged Rhodamine: A Superior Green Light-Activatable Fluorophore for Single-Molecule Localization Super-Resolution Imaging.},
journal = {Analytical chemistry},
volume = {93},
number = {22},
pages = {7833-7842},
doi = {10.1021/acs.analchem.1c00175},
pmid = {34027666},
issn = {1520-6882},
mesh = {*Fluorescent Dyes ; Ionophores ; Microscopy, Fluorescence ; Rhodamines ; *Single Molecule Imaging ; },
abstract = {The evolution of super-resolution imaging techniques, especially single-molecule localization microscopy, demands the engineering of switchable fluorophores with labeling functionality. Yet, the switching of these fluorophores depends on the exterior conditions of UV light and enhancing buffers, which is bioincompatible for living-cell applications. Herein, to surpass these limitations, a nitroso-caging strategy is employed to cage rhodamines into leuco forms, which for the first time, is discovered to uncage highly bright zwitterions by green light. Further, clickable construction grants the specificity and versatility for labeling various components in living cells. The simultaneous photoactivation and excitation of these novel probes allow for single-laser super-resolution imaging without any harmful additives. Super-resolution imaging of microtubules in fixed cells or mitochondria and the distribution of glycans and H2B proteins in living cells are achieved at a molecular scale with robust integrity. We envision that our nitroso-caging probes would set a platform for the development of future visible-activatable probes.},
}

*Fluorescent Dyes
Ionophores
Microscopy, Fluorescence
Rhodamines
*Single Molecule Imaging

@article {pmid34018613,
year = {2021},
author = {Stephens, TG and Gabr, A and Calatrava, V and Grossman, AR and Bhattacharya, D},
title = {Why is primary endosymbiosis so rare?.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.17478},
pmid = {34018613},
issn = {1469-8137},
support = {//Carnegie Institution for Science/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K0462/NASA/NASA/United States ; },
abstract = {Endosymbiosis is a relationship between two organisms wherein one cell resides inside the other. This affiliation, when stable and beneficial for the 'host' cell, can result in massive genetic innovation with the foremost examples being the evolution of eukaryotic organelles, the mitochondria and plastids. Despite its critical evolutionary role, there is limited knowledge about how endosymbiosis is initially established and how host-endosymbiont biology is integrated. Here, we explore this issue, using as our model the rhizarian amoeba Paulinella, which represents an independent case of primary plastid origin that occurred c. 120 million yr ago. We propose the 'chassis and engine' model that provides a theoretical framework for understanding primary plastid endosymbiosis, potentially explaining why it is so rare.},
}

@article {pmid34017941,
year = {2021},
author = {Kamrad, S and Rodríguez-López, M and Dey, S and Hoti, M and Wallace, H and Ralser, M and Bähler, J},
title = {Recombination and biased segregation of mitochondrial genomes during crossing and meiosis of different Schizosaccharomyces pombe strains.},
journal = {microPublication biology},
volume = {2021},
number = {},
pages = {},
pmid = {34017941},
issn = {2578-9430},
support = {/WT_/Wellcome Trust/United Kingdom ; FC001134/ARC_/Arthritis Research UK/United Kingdom ; },
abstract = {During meiosis, tethering of parental mitochondria to opposite cell poles inhibits the mixing of mitochondria with different genomes and ensures uniparental inheritance in thestandard laboratory strain of fission yeast. We here investigate mitochondrial inheritance in crosses between natural isolates using tetrad dissection and next-generation sequencing. We find that colonies grown from single spores can sometimes carry a mix of mitochondrial genotypes, that mitochondrial genomes can recombine during meiosis, that in some cases tetrads do not follow the 2:2 segregation pattern, and that certain crosses may feature a weak bias towards one of the parents. Together, these findings paint a more nuanced picture of mitochondrial inheritance in the wild.},
}

@article {pmid34011950,
year = {2021},
author = {Horváthová, L and Žárský, V and Pánek, T and Derelle, R and Pyrih, J and Motyčková, A and Klápšťová, V and Vinopalová, M and Marková, L and Voleman, L and Klimeš, V and Petrů, M and Vaitová, Z and Čepička, I and Hryzáková, K and Harant, K and Gray, MW and Chami, M and Guilvout, I and Francetic, O and Franz Lang, B and Vlček, Č and Tsaousis, AD and Eliáš, M and Doležal, P},
title = {Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2947},
pmid = {34011950},
issn = {2041-1723},
mesh = {Amino Acid Sequence ; Conserved Sequence ; Eukaryota/classification/genetics/metabolism ; *Evolution, Molecular ; Gram-Negative Bacteria/classification/genetics/metabolism ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/classification/genetics/metabolism ; Models, Biological ; Models, Molecular ; Naegleria/classification/genetics/metabolism ; Peroxisomes/metabolism ; Phylogeny ; Protozoan Proteins/classification/genetics/metabolism ; Sequence Homology, Amino Acid ; Type II Secretion Systems/classification/*genetics/*metabolism ; },
abstract = {The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion.},
}

Amino Acid Sequence
Conserved Sequence
Eukaryota/classification/genetics/metabolism
*Evolution, Molecular
Gram-Negative Bacteria/classification/genetics/metabolism
Mitochondria/*genetics/*metabolism
Mitochondrial Proteins/classification/genetics/metabolism
Models, Biological
Models, Molecular
Naegleria/classification/genetics/metabolism
Peroxisomes/metabolism
Phylogeny
Protozoan Proteins/classification/genetics/metabolism
Sequence Homology, Amino Acid
Type II Secretion Systems/classification/*genetics/*metabolism

@article {pmid34011275,
year = {2021},
author = {Porter, TM and Hajibabaei, M},
title = {Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {256},
pmid = {34011275},
issn = {1471-2105},
mesh = {Cell Nucleus ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; *Pseudogenes/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes.

RESULTS: Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place.

CONCLUSIONS: Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.},
}

Cell Nucleus
*DNA Barcoding, Taxonomic
DNA, Mitochondrial
Mitochondria/genetics
Phylogeny
*Pseudogenes/genetics
Sequence Analysis, DNA

@article {pmid34009340,
year = {2021},
author = {Phua, SY and De Smet, B and Remacle, C and Chan, KX and Van Breusegem, F},
title = {Reactive Oxygen Species and Organellar Signaling.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erab218},
pmid = {34009340},
issn = {1460-2431},
abstract = {The evolution of photosynthesis and its associated metabolic pathways has been crucial to the successful establishment of plants, but has also challenged plant cells in the form of reactive oxygen species (ROS) production. Intriguingly, multiple forms of ROS are generated in virtually every plant cell compartment through diverse pathways. As a result, a sophisticated network of ROS detoxification and signaling that is simultaneously tailored to individual organelles and safeguards the entire cell is necessary. Here we take an organelle-centric view on the principal sources and sinks of ROS across the plant cell and give insights into the ROS-induced organelle-to-nucleus retrograde signaling pathways needed for operational readjustments during environmental stresses.},
}

@article {pmid34008202,
year = {2021},
author = {Speijer, D},
title = {Zombie ideas about early endosymbiosis: Which entry mechanisms gave us the "endo" in different endosymbionts?.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {43},
number = {7},
pages = {e2100069},
doi = {10.1002/bies.202100069},
pmid = {34008202},
issn = {1521-1878},
abstract = {Recently, a review regarding the mechanics and evolution of mitochondrial fission appeared in Nature. Surprisingly, it stated authoritatively that the mitochondrial outer membrane, in contrast with the inner membrane of bacterial descent, was acquired from the host, presumably during uptake. However, it has been known for quite some time that this membrane was also derived from the Gram-negative, alpha-proteobacterium related precursor of present-day mitochondria. The zombie idea of the host membrane still surrounding the endosymbiont is not only wrong, but more importantly, might hamper the proper conception of possible scenarios of eukaryogenesis. Why? Because it steers the imagination not only with regard to possible uptake mechanisms, but also regarding what went on before. Here I critically discuss both the evidence for the continuity of the bacterial outer membrane, the reasons for the persistence of the erroneous host membrane hypothesis and the wider implications of these misconceptions for the ideas regarding events occurring during the first steps towards the evolution of the eukaryotes and later major eukaryotic differentiations. I will also highlight some of the latest insights regarding different instances of endosymbiont evolution.},
}

@article {pmid34006275,
year = {2021},
author = {Hirakawa, Y and Senda, M and Fukuda, K and Yu, HY and Ishida, M and Taira, M and Kinbara, K and Senda, T},
title = {Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {105},
pmid = {34006275},
issn = {1741-7007},
support = {18K06358, 19H03280//Japan Society for the Promotion of Science/ ; 18H05419//Japan Society for the Promotion of Science/ ; JP20am0101071//Japan Agency for Medical Research and Development/ ; },
abstract = {BACKGROUND: Carbonic anhydrases (CAs) are universal metalloenzymes that catalyze the reversible conversion of carbon dioxide (CO2) and bicarbonate (HCO3-). They are involved in various biological processes, including pH control, respiration, and photosynthesis. To date, eight evolutionarily unrelated classes of CA families (α, β, γ, δ, ζ, η, θ, and ι) have been identified. All are characterized by an active site accommodating the binding of a metal cofactor, which is assumed to play a central role in catalysis. This feature is thought to be the result of convergent evolution.

RESULTS: Here, we report that a previously uncharacterized protein group, named "COG4337," constitutes metal-independent CAs from the newly discovered ι-class. Genes coding for COG4337 proteins are found in various bacteria and photosynthetic eukaryotic algae. Biochemical assays demonstrated that recombinant COG4337 proteins from a cyanobacterium (Anabaena sp. PCC7120) and a chlorarachniophyte alga (Bigelowiella natans) accelerated CO2 hydration. Unexpectedly, these proteins exhibited their activity under metal-free conditions. Based on X-ray crystallography and point mutation analysis, we identified a metal-free active site within the cone-shaped α+β barrel structure. Furthermore, subcellular localization experiments revealed that COG4337 proteins are targeted into plastids and mitochondria of B. natans, implicating their involvement in CO2 metabolism in these organelles.

CONCLUSIONS: COG4337 proteins shared a short sequence motif and overall structure with ι-class CAs, whereas they were characterized by metal independence, unlike any known CAs. Therefore, COG4337 proteins could be treated as a variant type of ι-class CAs. Our findings suggested that this novel type of ι-CAs can function even in metal-poor environments (e.g., the open ocean) without competition with other metalloproteins for trace metals. Considering the widespread prevalence of ι-CAs across microalgae, this class of CAs may play a role in the global carbon cycle.},
}

@article {pmid34001130,
year = {2021},
author = {Záhonová, K and Lax, G and Sinha, SD and Leonard, G and Richards, TA and Lukeš, J and Wideman, JG},
title = {Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {103},
pmid = {34001130},
issn = {1741-7007},
support = {20-07186S//Grantová Agentura České Republiky/ ; ERC CZ LL1601//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; URF\R\191005//Royal Society/ ; 16_019/0000759//Czech Ministry of Education/ ; },
abstract = {BACKGROUND: The supergroup Euglenozoa unites heterotrophic flagellates from three major clades, kinetoplastids, diplonemids, and euglenids, each of which exhibits extremely divergent mitochondrial characteristics. Mitochondrial genomes (mtDNAs) of euglenids comprise multiple linear chromosomes carrying single genes, whereas mitochondrial chromosomes are circular non-catenated in diplonemids, but circular and catenated in kinetoplastids. In diplonemids and kinetoplastids, mitochondrial mRNAs require extensive and diverse editing and/or trans-splicing to produce mature transcripts. All known euglenozoan mtDNAs exhibit extremely short mitochondrial small (rns) and large (rnl) subunit rRNA genes, and absence of tRNA genes. How these features evolved from an ancestral bacteria-like circular mitochondrial genome remains unanswered.

RESULTS: We sequenced and assembled 20 euglenozoan single-cell amplified genomes (SAGs). In our phylogenetic and phylogenomic analyses, three SAGs were placed within kinetoplastids, 14 within diplonemids, one (EU2) within euglenids, and two SAGs with nearly identical small subunit rRNA gene (18S) sequences (EU17/18) branched as either a basal lineage of euglenids, or as a sister to all euglenozoans. Near-complete mitochondrial genomes were identified in EU2 and EU17/18. Surprisingly, both EU2 and EU17/18 mitochondrial contigs contained multiple genes and one tRNA gene. Furthermore, EU17/18 mtDNA possessed several features unique among euglenozoans including full-length rns and rnl genes, six mitoribosomal genes, and nad11, all likely on a single chromosome.

CONCLUSIONS: Our data strongly suggest that EU17/18 is an early-branching euglenozoan with numerous ancestral mitochondrial features. Collectively these data contribute to untangling the early evolution of euglenozoan mitochondria.},
}

@article {pmid33991648,
year = {2021},
author = {Moreno-Carmona, M and Cameron, SL and Prada Quiroga, CF},
title = {How are the mitochondrial genomes reorganized in Hexapoda? Differential evolution and the first report of convergences within Hexapoda.},
journal = {Gene},
volume = {791},
number = {},
pages = {145719},
doi = {10.1016/j.gene.2021.145719},
pmid = {33991648},
issn = {1879-0038},
mesh = {Animals ; Databases, Genetic ; Evolution, Molecular ; Gene Order/genetics ; Gene Rearrangement/genetics ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Insecta/classification/*genetics ; Mitochondria/classification/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The evolution of the Hexapoda mitochondrial genome has been the focus of several genetic and evolutionary studies over the last decades. However, they have concentrated on certain taxonomic orders of economic or health importance. The recent increase of mitochondrial genomes sequencing of diverse taxonomic orders generates an important opportunity to clarify the evolution of this group of organisms. However, there is no comparative study that investigates the evolution of the Hexapoda mitochondrial genome. In order to verify the level of rearrangement and the mitochondrial genome evolution, we performed a comparative genomic analysis of the Hexapoda mitochondrial genome available in the NCBI database. Using a combination of bioinformatics methods to carefully examine the mitochondrial gene rearrangements in 1198 Hexapoda species belonging to 32 taxonomic orders, we determined that there is a great variation in the rate of rearrangement by gene and by taxonomic order. A higher rate of genetic reassortment is observed in Phthiraptera, Thysanoptera, Protura, and Hymenoptera; compared to other taxonomic orders. Twenty-four events of convergence in the genetic order between different taxonomic orders were determined, most of them not previously reported; which proves the great evolutionary dynamics within Hexapoda.},
}

Animals
Databases, Genetic
Evolution, Molecular
Gene Order/genetics
Gene Rearrangement/genetics
Genes, Mitochondrial/*genetics
Genome, Mitochondrial/*genetics
Insecta/classification/*genetics
Mitochondria/classification/genetics
Phylogeny
Sequence Analysis, DNA/methods

@article {pmid33984441,
year = {2021},
author = {Lim, LWK and Chung, HH and Lau, MML and Aziz, F and Gan, HM},
title = {Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers.},
journal = {Gene},
volume = {791},
number = {},
pages = {145708},
doi = {10.1016/j.gene.2021.145708},
pmid = {33984441},
issn = {1879-0038},
mesh = {Animals ; Base Sequence/genetics ; Biomarkers ; Cyprinidae/*classification/*genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Indonesia ; Malaysia ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.},
}

Animals
Base Sequence/genetics
Biomarkers
Cyprinidae/*classification/*genetics
DNA, Mitochondrial/genetics
Genes, Mitochondrial/genetics
Genome, Mitochondrial/*genetics
Haplotypes/genetics
Indonesia
Malaysia
Mitochondria/genetics
Phylogeny
Sequence Analysis, DNA/methods

@article {pmid33983431,
year = {2021},
author = {Dellière, S and Hamane, S and Aissaoui, N and Gits-Muselli, M and Bretagne, S and Alanio, A},
title = {Increased sensitivity of a new commercial reverse transcriptase-quantitative PCR for the detection of Pneumocystis jirovecii in respiratory specimens.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myab029},
pmid = {33983431},
issn = {1460-2709},
abstract = {Optimal sensitivity to detect low Pneumocystis loads is of importance to take individual and collective measures to avoid evolution towards Pneumocystis pneumonia and outbreaks in immunocompromised patients. This study compares two qPCR procedures, a new automated RTqPCR using the GeneLEAD VIII extractor/thermocycler (GLVIII; ∼2.2 hrs workflow) and a previously validated in-house qPCR assays (IH; ∼5 hrs workflow) both targeting mtSSU and mtLSU for detecting P. jirovecii in 213 respiratory samples. GLVIII was found to be more sensitive than IH, detecting 8 more specimens. Bland-Altman analysis between the two procedures showed a Cq bias of 1.17 ± 0.07 in favor of GLVIII. The fungus Pneumocystis needs to be detected early in respiratory samples to prevent pneumonia in immunocompromised hosts. We evaluated a new commercial RTqPCR on 213 respiratory samples to detect Pneumocystis and found it more sensitive and faster than our routine sensitive in-house qPCR assay.},
}

@article {pmid33974849,
year = {2021},
author = {Mathur, V and Wakeman, KC and Keeling, PJ},
title = {Parallel functional reduction in the mitochondria of apicomplexan parasites.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2021.04.028},
pmid = {33974849},
issn = {1879-0445},
abstract = {Gregarines are an early-diverging lineage of apicomplexan parasites that hold many clues into the origin and evolution of the group, a remarkable transition from free-living phototrophic algae into obligate parasites of animals.1 Using single-cell transcriptomics targeting understudied lineages to complement available sequencing data, we characterized the mitochondrial metabolic repertoire across the tree of apicomplexans. In contrast to the large suite of proteins involved in aerobic respiration in well-studied parasites like Toxoplasma or Plasmodium,2 we find that gregarine trophozoites have significantly reduced energy metabolism: most lack respiratory complexes III and IV, and some lack the electron transport chains (ETCs) and tricarboxylic acid (TCA) cycle entirely. Phylogenomic analyses show that these reductions took place several times in parallel, resulting in a functional range from fully aerobic organelles to extremely reduced "mitosomes" restricted to Fe-S cluster biosynthesis. The mitochondrial genome has also been lost repeatedly: in species with severe functional reduction simply by gene loss but in one species with a complete ETC by relocating cox1 to the nuclear genome. Severe functional reduction of mitochondria is generally associated with structural reduction, resulting in small, nondescript mitochondrial-related organelles (MROs).3 By contrast, gregarines retain distinctive mitochondria with tubular cristae, even the most functionally reduced cases that also lack genes associated with cristae formation. Overall, the parallel, severe reduction of gregarine mitochondria expands the diversity of organisms that contain MROs and further emphasizes the role of parallel transitions in apicomplexan evolution.},
}

@article {pmid33963405,
year = {2021},
author = {Skejo, J and Garg, SG and Gould, SB and Hendriksen, M and Tria, FDK and Bremer, N and Franjević, D and Blackstone, NW and Martin, WF},
title = {Evidence for a syncytial origin of eukaryotes from ancestral state reconstruction.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evab096},
pmid = {33963405},
issn = {1759-6653},
abstract = {Modern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor, LECA, is seldom, if ever, questioned, even though cells harboring multiple (syncytia, coenocytes, polykaryons) are surprisingly common across eukaryotic supergroups. Here we present a survey of multinucleated forms. Ancestral character state reconstruction for representatives of 106 eukaryotic taxa using 16 different possible roots and supergroup sister relationships, indicate that LECA, in addition to being mitochondriate, sexual, and meiotic, was multinucleate. LECA exhibited closed mitosis, which is the rule for modern syncytial forms, shedding light on the mechanics of its chromosome segregation. A simple mathematical model shows that within LECA's multinucleate cytosol, relationships among mitochondria and nuclei were neither one-to-one, nor one-to-many, but many-to-many, placing mitonuclear interactions and cytonuclear compatibility at the evolutionary base of eukaryotic cell origin. Within a syncytium, individual nuclei and individual mitochondria function as the initial lower-level evolutionary units of selection, as opposed to individual cells, during eukaryogenesis. Nuclei within a syncytium rescue each other's lethal mutations, thereby postponing selection for viable nuclei and cytonuclear compatibility to the generation of spores, buffering transitional bottlenecks at eukaryogenesis. The prokaryote-to-eukaryote transition is traditionally thought to have left no intermediates, yet if eukaryogenesis proceeded via a syncytial common ancestor, intermediate forms have persisted to the present throughout the eukaryotic tree as syncytia, but have so far gone unrecognized.},
}

@article {pmid33952666,
year = {2021},
author = {Reinke, AW},
title = {mSphere of Influence: Where the Pathogen Proteins Are.},
journal = {mSphere},
volume = {6},
number = {3},
pages = {},
pmid = {33952666},
issn = {2379-5042},
abstract = {Aaron Reinke studies microsporidian evolution and how microsporidia interact with their hosts. In this mSphere of Influence article, he reflects on how the papers "A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells" (K. J. Roux, D. I. Kim, M. Raida, and B. Burke, J Cell Biol 196:801-810, 2012, https://doi.org/10.1083/jcb.201112098) and "Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging" (H.-W. Rhee, P. Zou, N. D. Udeshi, J. D. Martell, et al., Science 339:1328-1331, 2013, https://doi.org/10.1126/science.1230593) impacted his thinking on how to determine where proteins from intracellular pathogens are located within host cells.},
}

@article {pmid33946769,
year = {2021},
author = {Oborník, M},
title = {Enigmatic Evolutionary History of Porphobilinogen Deaminase in Eukaryotic Phototrophs.},
journal = {Biology},
volume = {10},
number = {5},
pages = {},
pmid = {33946769},
issn = {2079-7737},
support = {21-03224S//Czech Science Foundation/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//European Regional Development Fund/ ; },
abstract = {In most eukaryotic phototrophs, the entire heme synthesis is localized to the plastid, and enzymes of cyanobacterial origin dominate the pathway. Despite that, porphobilinogen deaminase (PBGD), the enzyme responsible for the synthesis of hydroxymethybilane in the plastid, shows phylogenetic affiliation to α-proteobacteria, the supposed ancestor of mitochondria. Surprisingly, no PBGD of such origin is found in the heme pathway of the supposed partners of the primary plastid endosymbiosis, a primarily heterotrophic eukaryote, and a cyanobacterium. It appears that α-proteobacterial PBGD is absent from glaucophytes but is present in rhodophytes, chlorophytes, plants, and most algae with complex plastids. This may suggest that in eukaryotic phototrophs, except for glaucophytes, either the gene from the mitochondrial ancestor was retained while the cyanobacterial and eukaryotic pseudoparalogs were lost in evolution, or the gene was acquired by non-endosymbiotic gene transfer from an unspecified α-proteobacterium and functionally replaced its cyanobacterial and eukaryotic counterparts.},
}

@article {pmid33931054,
year = {2021},
author = {Li, F and Lv, Y and Wen, Z and Bian, C and Zhang, X and Guo, S and Shi, Q and Li, D},
title = {The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders.},
journal = {BMC ecology and evolution},
volume = {21},
number = {1},
pages = {72},
pmid = {33931054},
issn = {2730-7182},
mesh = {Animals ; Base Sequence ; *Genome, Mitochondrial/genetics ; Phylogeny ; Silk/genetics ; *Spiders/genetics ; },
abstract = {BACKGROUND: Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders.

RESULTS: We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene.

CONCLUSIONS: Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.},
}

Animals
Base Sequence
*Genome, Mitochondrial/genetics
Phylogeny
Silk/genetics
*Spiders/genetics

@article {pmid33924228,
year = {2021},
author = {Kolchanova, S and Komissarov, A and Kliver, S and Mazo-Vargas, A and Afanador, Y and Velez-Valentín, J and de la Rosa, RV and Castro-Marquez, S and Rivera-Colon, I and Majeske, AJ and Wolfsberger, WW and Hains, T and Corvelo, A and Martinez-Cruzado, JC and Glenn, TC and Robinson, O and Koepfli, KP and Oleksyk, TK},
title = {Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles.},
journal = {Genes},
volume = {12},
number = {4},
pages = {},
pmid = {33924228},
issn = {2073-4425},
support = {DUE 1044714//National Science Foundation/ ; 2012-2013//Toyota Foundation/ ; 2012//U.S. Fish and Wildlife Service/ ; start up funds//Oakland University/ ; 17-00-00144//Russian Foundation for Basic Research/ ; 17-00-00148//Russian Foundation for Basic Research/ ; ITMO Fellowship and Professorship Program//Government of the Russian Federation/ ; },
abstract = {Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full mitochondrial genomes of all the extant Amazon parrot species from the Greater Antillean (A. leucocephala (Cuba), A. agilis, A. collaria (both from Jamaica), A. ventralis (Hispaniola), and A. vittata (Puerto Rico)), A. albifrons from mainland Central America, and A. rhodocorytha from the Atlantic Forest in Brazil. The assembled and annotated mitogenome maps provide information on sequence organization, variation, population diversity, and evolutionary history for the Caribbean species including the critically endangered A. vittata. Despite the larger number of available samples from the Puerto Rican Parrot Recovery Program, the sequence diversity of the A. vittata population in Puerto Rico was the lowest among all parrot species analyzed. Our data support the stepping-stone dispersal and speciation hypothesis that has started approximately 3.47 MYA when the ancestral population arrived from mainland Central America and led to diversification across the Greater Antilles, ultimately reaching the island of Puerto Rico 0.67 MYA. The results are presented and discussed in light of the geological history of the Caribbean and in the context of recent parrot evolution, island biogeography, and conservation. This analysis contributes to understating evolutionary history and empowers subsequent assessments of sequence variation and helps design future conservation efforts in the Caribbean.},
}

@article {pmid33923118,
year = {2021},
author = {Filip, E and Skuza, L},
title = {Horizontal Gene Transfer Involving Chloroplasts.},
journal = {International journal of molecular sciences},
volume = {22},
number = {9},
pages = {},
pmid = {33923118},
issn = {1422-0067},
mesh = {Cell Nucleus/*genetics ; Chloroplasts/*genetics ; Endophytes/genetics ; *Gene Transfer, Horizontal ; Genome ; Mitochondria/*genetics ; Plants/genetics ; Plastids/genetics ; },
abstract = {Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.},
}

Cell Nucleus/*genetics
Chloroplasts/*genetics
Endophytes/genetics
*Gene Transfer, Horizontal
Genome
Mitochondria/*genetics
Plants/genetics
Plastids/genetics

@article {pmid33921106,
year = {2021},
author = {Bonora, M and Missiroli, S and Perrone, M and Fiorica, F and Pinton, P and Giorgi, C},
title = {Mitochondrial Control of Genomic Instability in Cancer.},
journal = {Cancers},
volume = {13},
number = {8},
pages = {},
pmid = {33921106},
issn = {2072-6694},
support = {IG-23670//Associazione Italiana per la Ricerca sul Cancro/ ; IG-19803//Associazione Italiana per la Ricerca sul Cancro/ ; GGP11139B//Fondazione Telethon/ ; GR-2013-02356747//Ministero della Salute/ ; PRIN2017E5L5P3//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; PRIN20177E9EPY//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; 853057-InflaPML/ERC_/European Research Council/International ; },
abstract = {Mitochondria are well known to participate in multiple aspects of tumor formation and progression. They indeed can alter the susceptibility of cells to engage regulated cell death, regulate pro-survival signal transduction pathways and confer metabolic plasticity that adapts to specific tumor cell demands. Interestingly, a relatively poorly explored aspect of mitochondria in neoplastic disease is their contribution to the characteristic genomic instability that underlies the evolution of the disease. In this review, we summarize the known mechanisms by which mitochondrial alterations in cancer tolerate and support the accumulation of DNA mutations which leads to genomic instability. We describe recent studies elucidating mitochondrial responses to DNA damage as well as the direct contribution of mitochondria to favor the accumulation of DNA alterations.},
}

@article {pmid33892508,
year = {2021},
author = {Breton, S and Ghiselli, F and Milani, L},
title = {Mitochondrial short-term plastic responses and long-term evolutionary dynamics in animal species.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evab084},
pmid = {33892508},
issn = {1759-6653},
abstract = {How do species respond or adapt to environmental changes? The answer to this depends partly on mitochondrial epigenetics and genetics, new players in promoting adaptation to both short- and long-term environmental changes. In this review, we explore how mitochondrial epigenetics and genetics mechanisms, such as mtDNA methylation, mtDNA-derived non-coding RNAs, micropeptides, mtDNA mutations and adaptations, can contribute to animal plasticity and adaptation. We also briefly discuss the challenges in assessing mtDNA adaptive evolution. In sum, this review covers new advances in the field of mitochondrial genomics, many of which are still controversial, and discusses processes still somewhat obscure, and some of which are still quite speculative and require further robust experimentation.},
}

@article {pmid33891594,
year = {2021},
author = {Milner, DS and Wideman, JG and Stairs, CW and Dunn, CD and Richards, TA},
title = {A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist.},
journal = {PLoS biology},
volume = {19},
number = {4},
pages = {e3001126},
pmid = {33891594},
issn = {1545-7885},
abstract = {The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin-antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.},
}

@article {pmid33878294,
year = {2021},
author = {Kummer, E and Schubert, KN and Schoenhut, T and Scaiola, A and Ban, N},
title = {Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.},
journal = {Molecular cell},
volume = {81},
number = {12},
pages = {2566-2582.e6},
doi = {10.1016/j.molcel.2021.03.042},
pmid = {33878294},
issn = {1097-4164},
abstract = {The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.},
}

@article {pmid33871590,
year = {2021},
author = {Helfenrath, K and Sauer, M and Kamga, M and Wisniewsky, M and Burmester, T and Fabrizius, A},
title = {The More, the Merrier? Multiple Myoglobin Genes in Fish Species, Especially in Gray Bichir (Polypterus senegalus) and Reedfish (Erpetoichthys calabaricus).},
journal = {Genome biology and evolution},
volume = {13},
number = {7},
pages = {},
doi = {10.1093/gbe/evab078},
pmid = {33871590},
issn = {1759-6653},
abstract = {The members of the globin superfamily are a classical model system to investigate gene evolution and their fates as well as the diversity of protein function. One of the best-known globins is myoglobin (Mb), which is mainly expressed in heart muscle and transports oxygen from the sarcolemma to the mitochondria. Most vertebrates harbor a single copy of the myoglobin gene, but some fish species have multiple myoglobin genes. Phylogenetic analyses indicate an independent emergence of multiple myoglobin genes, whereby the origin is mostly the last common ancestor of each order. By analyzing different transcriptome data sets, we found at least 15 multiple myoglobin genes in the polypterid gray bichir (Polypterus senegalus) and reedfish (Erpetoichthys calabaricus). In reedfish, the myoglobin genes are expressed in a broad range of tissues but show very different expression values. In contrast, the Mb genes of the gray bichir show a rather scattered expression pattern; only a few Mb genes were found expressed in the analyzed tissues. Both, gray bichir and reedfish possess lungs which enable them to inhabit shallow and swampy waters throughout tropical Africa with frequently fluctuating and low oxygen concentrations. The myoglobin repertoire probably reflects the molecular adaptation to these conditions. The sequence divergence, the substitution rate, and the different expression pattern of multiple myoglobin genes in gray bichir and reedfish imply different functions, probably through sub- and neofunctionalization during evolution.},
}

@article {pmid33871031,
year = {2021},
author = {de Melo Teixeira, M and Lang, BF and Matute, DR and Stajich, JE and Barker, B},
title = {The mitochondrial genomes of the human pathogens Coccidioides immitis and C. posadasii.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkab132},
pmid = {33871031},
issn = {2160-1836},
support = {R01 AI153523/AI/NIAID NIH HHS/United States ; R21 AI128536/AI/NIAID NIH HHS/United States ; },
abstract = {Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation of nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify fourteen mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.},
}

@article {pmid33863338,
year = {2021},
author = {Salomaki, ED and Terpis, KX and Rueckert, S and Kotyk, M and Varadínová, ZK and Čepička, I and Lane, CE and Kolisko, M},
title = {Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans.},
journal = {BMC biology},
volume = {19},
number = {1},
pages = {77},
pmid = {33863338},
issn = {1741-7007},
support = {CZ.02.2.69/0.0/0.0/16_027/0008357//Ministerstvo Školství, Mládeže a Tělovýchovy (CZ)/ ; CZ.02.2.69/0.0/0.0/20_079/0017809//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; 1541510//Directorate for Biological Sciences/ ; 1158119//Grantová Agentura, Univerzita Karlova/ ; 19-19297S//Grantová Agentura České Republiky/ ; 18-28103S//Grantová Agentura České Republiky/ ; Fellowship Purkyne//Akademie Věd České Republiky/ ; OIA-1655221//National Science Foundation/ ; GBMF9327//Gordon and Betty Moore Foundation/ ; },
abstract = {BACKGROUND: Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria.

RESULTS: Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines.

CONCLUSIONS: Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.},
}

@article {pmid33860546,
year = {2021},
author = {Brandeis, M},
title = {Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {43},
number = {6},
pages = {e2000256},
doi = {10.1002/bies.202000256},
pmid = {33860546},
issn = {1521-1878},
abstract = {I hypothesize that the appearance of sex facilitated the merging of the endosymbiont and host genomes during early eukaryote evolution. Eukaryotes were formed by symbiosis between a bacterium that entered an archaeon, eventually giving rise to mitochondria. This entry was followed by the gradual transfer of most bacterial endosymbiont genes into the archaeal host genome. I argue that the merging of the mitochondrial genes into the host genome was vital for the evolution of genuine eukaryotes. At the time this process commenced it was unprecedented and required a novel mechanism. I suggest that this mechanism was meiotic sex, and that its appearance might have been THE crucial step that enabled the evolution of proper eukaryotes from early endosymbiont containing proto-eukaryotes. Sex might continue to be essential today for keeping genome insertions in check. Also see the video abstract here: https://youtu.be/aVMvWMpomac.},
}

@article {pmid33857537,
year = {2021},
author = {Deonath, A},
title = {Evolution of eukaryotes as a story of survival and growth of mitochondrial DNA over two billion years.},
journal = {Bio Systems},
volume = {206},
number = {},
pages = {104426},
doi = {10.1016/j.biosystems.2021.104426},
pmid = {33857537},
issn = {1872-8324},
abstract = {Mitochondria's significance in human diseases and in functioning, health and death of eukaryotic cell has been acknowledged widely. Yet our perspective in cell biology and evolution remains nucleocentric. Mitochondrial DNA, by virtue of its omnipresence and species-level conservation, is used as a barcode in animal taxonomy. This article analyses various levels of containment structures that enclose mitochondrial DNA and advocates a fresh perspective wherein evolution of organic structures of the eukarya domain seem to support and facilitate survival and proliferation of mitochondrial DNA by splitting containers as they age and by directing them along two distinct pathways: destruction of containers with more mutant mitochondrial DNA and rejuvenation of containers with less mutant mitochondrial DNA.},
}

@article {pmid33857516,
year = {2021},
author = {Dores-Silva, PR and Kiraly, VTR and Moritz, MNO and Serrão, VHB and Dos Passos, PMS and Spagnol, V and Teixeira, FR and Gava, LM and Cauvi, DM and Ramos, CHI and De Maio, A and Borges, JC},
title = {New insights on human Hsp70-escort protein 1: Chaperone activity, interaction with liposomes, cellular localizations and HSPA's self-assemblies remodeling.},
journal = {International journal of biological macromolecules},
volume = {182},
number = {},
pages = {772-784},
doi = {10.1016/j.ijbiomac.2021.04.048},
pmid = {33857516},
issn = {1879-0003},
abstract = {The 70 kDa heat shock proteins (Hsp70) are prone to self-assembly under thermal stress conditions, forming supramolecular assemblies (SMA), what may have detrimental consequences for cellular viability. In mitochondria, the cochaperone Hsp70-escort protein 1 (Hep1) maintains mitochondrial Hsp70 (mtHsp70) in a soluble and functional state, contributing to preserving proteostasis. Here we investigated the interaction between human Hep1 (hHep1) and HSPA9 (human mtHsp70) or HSPA1A (Hsp70-1A) in monomeric and thermic SMA states to unveil further information about the involved mechanisms. hHep1 was capable of blocking the formation of HSPA SMAs under a thermic treatment and stimulated HSPA ATPase activity in both monomeric and preformed SMA. The interaction of hHep1 with both monomeric and SMA HSPAs displayed a stoichiometric ratio close to 1, suggesting that hHep1 has access to most protomers within the SMA. Interestingly, hHep1 remodeled HSPA9 and HSPA1A SMAs into smaller forms. Furthermore, hHep1 was detected in the mitochondria and nucleus of cells transfected with the respective coding DNA and interacted with liposomes resembling mitochondrial membranes. Altogether, these new features reinforce that hHep1 act as a "chaperone for a chaperone", which may play a critical role in cellular proteostasis.},
}

@article {pmid33839167,
year = {2021},
author = {García-Catalán, S and González-Moreno, L and Del Arco, A},
title = {Ca2+-regulated mitochondrial carriers of ATP-Mg2+/Pi: Evolutionary insights in protozoans.},
journal = {Biochimica et biophysica acta. Molecular cell research},
volume = {1868},
number = {7},
pages = {119038},
doi = {10.1016/j.bbamcr.2021.119038},
pmid = {33839167},
issn = {1879-2596},
abstract = {In addition to its uptake across the Ca2+ uniporter, intracellular calcium signals can stimulate mitochondrial metabolism activating metabolite exchangers of the inner mitochondrial membrane belonging to the mitochondrial carrier family (SLC25). One of these Ca2+-regulated mitochondrial carriers (CaMCs) are the reversible ATP-Mg2+/Pi transporters, or SCaMCs, required for maintaining optimal adenine nucleotide (AdN) levels in the mitochondrial matrix representing an alternative transporter to the ADP/ATP translocases (AAC). This CaMC has a distinctive Calmodulin-like (CaM-like) domain fused to the carrier domain that makes its transport activity strictly dependent on cytosolic Ca2+ signals. Here we investigate about its origin analysing its distribution and features in unicellular eukaryotes. Unexpectedly, we find two types of ATP-Mg2+/Pi carriers, the canonical ones and shortened variants lacking the CaM-like domain. Phylogenetic analysis shows that both SCaMC variants have a common origin, unrelated to AACs, suggesting in turn that recurrent losses of the regulatory module have occurred in the different phyla. They are excluding variants that show a more limited distribution and less conservation than AACs. Interestingly, these truncated variants of SCaMC are found almost exclusively in parasitic protists, such as apicomplexans, kinetoplastides or animal-patogenic oomycetes, and in green algae, suggesting that its lost could be related to certain life-styles. In addition, we find an intricate structural diversity in these variants that may be associated with their pathogenicity. The consequences on SCaMC functions of these new SCaMC-b variants are discussed.},
}

@article {pmid33837778,
year = {2021},
author = {Pyrih, J and Pánek, T and Durante, IM and Rašková, V and Cimrhanzlová, K and Kriegová, E and Tsaousis, AD and Eliáš, M and Lukeš, J},
title = {Vestiges of the bacterial signal recognition particle-based protein targeting in mitochondria.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msab090},
pmid = {33837778},
issn = {1537-1719},
abstract = {The main bacterial pathway for inserting proteins into the plasma membrane relies on the signal recognition particle (SRP), composed of the Ffh protein and an associated RNA component, and the SRP-docking protein FtsY. Eukaryotes use an equivalent system of archaeal origin to deliver proteins into the endoplasmic reticulum, whereas a bacteria-derived SRP and FtsY function in the plastid. Here we report on the presence of homologs of the bacterial Ffh and FtsY proteins in various unrelated plastid-lacking unicellular eukaryotes, namely Heterolobosea, Alveida, Goniomonas, and Hemimastigophora. The monophyly of novel eukaryotic Ffh and FtsY groups, predicted mitochondrial localization experimentally confirmed for Naegleria gruberi, and a strong alphaproteobacterial affinity of the Ffh group, collectively suggest they constitute parts of an ancestral mitochondrial signal peptide-based protein-targeting system inherited from the last eukaryotic common ancestor, but lost from the majority of extant eukaryotes. The ability of putative signal peptides, predicted in a subset of mitochondrial-encoded N. gruberi proteins, to target a reporter fluorescent protein into the endoplasmic reticulum of Trypanosoma brucei, likely through their interaction with the cytosolic SRP, provided further support for this notion. We also illustrate that known mitochondrial ribosome-interacting proteins implicated in membrane protein targeting in opisthokonts (Mba1, Mdm38, and Mrx15) are broadly conserved in eukaryotes and non-redundant with the mitochondrial SRP system. Finally, we identified a novel mitochondrial protein (MAP67) present in diverse eukaryotes and related to the signal peptide-binding domain of Ffh, which may well be a hitherto unrecognized component of the mitochondrial membrane protein-targeting machinery.},
}

@article {pmid33829092,
year = {2021},
author = {Lee, SH and Lee, SH},
title = {Complete mitochondrial genome of Oregonia gracilis Dana, 1851 (Crustacea: Decapoda: Majoidea).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {3},
pages = {1236-1237},
pmid = {33829092},
issn = {2380-2359},
abstract = {The complete mitochondrial genome of the majoid crab, Oregonia gracilis, was determined from a specimen collected in Korea. The mitochondrial genome is 15,737 bp long and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. A maximum-likelihood phylogenetic tree based on the 13 PCGs of the mitochondria showed that O. gracilis is closely related to the genus Chinoecetes. The complete mitochondrial genome of O. gracilis provides valuable information on the mitochondrial evolution of majoid crabs.},
}

@article {pmid33818247,
year = {2021},
author = {Schwartz, JH},
title = {Evolution, systematics, and the unnatural history of mitochondrial DNA.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {32},
number = {4},
pages = {126-151},
doi = {10.1080/24701394.2021.1899165},
pmid = {33818247},
issn = {2470-1408},
abstract = {The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the opposite - only the head enters the egg - became fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra- and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.},
}

@article {pmid33813887,
year = {2021},
author = {Ghiselli, F and Gomes-Dos-Santos, A and Adema, CM and Lopes-Lima, M and Sharbrough, J and Boore, JL},
title = {Molluscan mitochondrial genomes break the rules.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {376},
number = {1825},
pages = {20200159},
pmid = {33813887},
issn = {1471-2970},
abstract = {The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.},
}

@article {pmid33811236,
year = {2021},
author = {Alqahtani, AA and Jansen, RK},
title = {The evolutionary fate of rpl32 and rps16 losses in the Euphorbia schimperi (Euphorbiaceae) plastome.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7466},
pmid = {33811236},
issn = {2045-2322},
abstract = {Gene transfers from mitochondria and plastids to the nucleus are an important process in the evolution of the eukaryotic cell. Plastid (pt) gene losses have been documented in multiple angiosperm lineages and are often associated with functional transfers to the nucleus or substitutions by duplicated nuclear genes targeted to both the plastid and mitochondrion. The plastid genome sequence of Euphorbia schimperi was assembled and three major genomic changes were detected, the complete loss of rpl32 and pseudogenization of rps16 and infA. The nuclear transcriptome of E. schimperi was sequenced to investigate the transfer/substitution of the rpl32 and rps16 genes to the nucleus. Transfer of plastid-encoded rpl32 to the nucleus was identified previously in three families of Malpighiales, Rhizophoraceae, Salicaceae and Passifloraceae. An E. schimperi transcript of pt SOD-1-RPL32 confirmed that the transfer in Euphorbiaceae is similar to other Malpighiales indicating that it occurred early in the divergence of the order. Ribosomal protein S16 (rps16) is encoded in the plastome in most angiosperms but not in Salicaceae and Passifloraceae. Substitution of the E. schimperi pt rps16 was likely due to a duplication of nuclear-encoded mitochondrial-targeted rps16 resulting in copies dually targeted to the mitochondrion and plastid. Sequences of RPS16-1 and RPS16-2 in the three families of Malpighiales (Salicaceae, Passifloraceae and Euphorbiaceae) have high sequence identity suggesting that the substitution event dates to the early divergence within Malpighiales.},
}

@article {pmid33807810,
year = {2021},
author = {S Ten, V and Stepanova, AA and Ratner, V and Neginskaya, M and Niatsetskaya, Z and Sosunov, S and Starkov, A},
title = {Mitochondrial Dysfunction and Permeability Transition in Neonatal Brain and Lung Injuries.},
journal = {Cells},
volume = {10},
number = {3},
pages = {},
pmid = {33807810},
issn = {2073-4409},
support = {P01 AG014930/AG/NIA NIH HHS/United States ; R01 NS099109/NS/NINDS NIH HHS/United States ; R01 NS100850/NS/NINDS NIH HHS/United States ; NS099109, NS100850, PO AG14930/NH/NIH HHS/United States ; },
abstract = {This review discusses the potential mechanistic role of abnormally elevated mitochondrial proton leak and mitochondrial bioenergetic dysfunction in the pathogenesis of neonatal brain and lung injuries associated with premature birth. Providing supporting evidence, we hypothesized that mitochondrial dysfunction contributes to postnatal alveolar developmental arrest in bronchopulmonary dysplasia (BPD) and cerebral myelination failure in diffuse white matter injury (WMI). This review also analyzes data on mitochondrial dysfunction triggered by activation of mitochondrial permeability transition pore(s) (mPTP) during the evolution of perinatal hypoxic-ischemic encephalopathy. While the still cryptic molecular identity of mPTP continues to be a subject for extensive basic science research efforts, the translational significance of mitochondrial proton leak received less scientific attention, especially in diseases of the developing organs. This review is focused on the potential mechanistic relevance of mPTP and mitochondrial dysfunction to neonatal diseases driven by developmental failure of organ maturation or by acute ischemia-reperfusion insult during development.},
}

@article {pmid33805626,
year = {2021},
author = {Schirrmacher, V},
title = {Less Can Be More: The Hormesis Theory of Stress Adaptation in the Global Biosphere and Its Implications.},
journal = {Biomedicines},
volume = {9},
number = {3},
pages = {},
pmid = {33805626},
issn = {2227-9059},
abstract = {A dose-response relationship to stressors, according to the hormesis theory, is characterized by low-dose stimulation and high-dose inhibition. It is non-linear with a low-dose optimum. Stress responses by cells lead to adapted vitality and fitness. Physical stress can be exerted through heat, radiation, or physical exercise. Chemical stressors include reactive species from oxygen (ROS), nitrogen (RNS), and carbon (RCS), carcinogens, elements, such as lithium (Li) and silicon (Si), and metals, such as silver (Ag), cadmium (Cd), and lead (Pb). Anthropogenic chemicals are agrochemicals (phytotoxins, herbicides), industrial chemicals, and pharmaceuticals. Biochemical stress can be exerted through toxins, medical drugs (e.g., cytostatics, psychopharmaceuticals, non-steroidal inhibitors of inflammation), and through fasting (dietary restriction). Key-lock interactions between enzymes and substrates, antigens and antibodies, antigen-presenting cells, and cognate T cells are the basics of biology, biochemistry, and immunology. Their rules do not obey linear dose-response relationships. The review provides examples of biologic stressors: oncolytic viruses (e.g., immuno-virotherapy of cancer) and hormones (e.g., melatonin, stress hormones). Molecular mechanisms of cellular stress adaptation involve the protein quality control system (PQS) and homeostasis of proteasome, endoplasmic reticulum, and mitochondria. Important components are transcription factors (e.g., Nrf2), micro-RNAs, heat shock proteins, ionic calcium, and enzymes (e.g., glutathion redox enzymes, DNA methyltransferases, and DNA repair enzymes). Cellular growth control, intercellular communication, and resistance to stress from microbial infections involve growth factors, cytokines, chemokines, interferons, and their respective receptors. The effects of hormesis during evolution are multifarious: cell protection and survival, evolutionary flexibility, and epigenetic memory. According to the hormesis theory, this is true for the entire biosphere, e.g., archaia, bacteria, fungi, plants, and the animal kingdoms.},
}

@article {pmid33805166,
year = {2021},
author = {Lyu, D and Zajonc, J and Pagé, A and Tanney, CAS and Shah, A and Monjezi, N and Msimbira, LA and Antar, M and Nazari, M and Backer, R and Smith, DL},
title = {Plant Holobiont Theory: The Phytomicrobiome Plays a Central Role in Evolution and Success.},
journal = {Microorganisms},
volume = {9},
number = {4},
pages = {},
pmid = {33805166},
issn = {2076-2607},
support = {G250030 AAFC BioFuelNet//Agriculture and Agri-Food Canada/ ; RGPIN 2020-07047.//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Under natural conditions, plants are always associated with a well-orchestrated community of microbes-the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the "plant" is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.},
}

@article {pmid33803683,
year = {2021},
author = {Proulex, GCR and Meade, MJ and Manoylov, KM and Cahoon, AB},
title = {Mitochondrial mRNA Processing in the Chlorophyte Alga Pediastrum duplex and Streptophyte Alga Chara vulgaris Reveals an Evolutionary Branch in Mitochondrial mRNA Processing.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {3},
pages = {},
pmid = {33803683},
issn = {2223-7747},
abstract = {Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing has only been explored in Chlamydomonas reinhardtii (Class: Chlorophyceae) and the mature mRNAs are different than higher plants, having no 5' UnTranslated Regions (UTRs), much shorter and more variable 3' UTRs and polycytidylated mature mRNAs. In this study, we analyzed transcript termini using circular RT-PCR and PacBio Iso-Seq to survey the 3' and 5' UTRs and termini for two green algae, Pediastrum duplex (Class: Chlorophyceae) and Chara vulgaris (Class: Charophyceae). This enabled the comparison of processing in the chlorophyte and charophyte clades of green algae to determine if the differences in mitochondrial mRNA processing pre-date the invasion of land by embryophytes. We report that the 5' mRNA termini and non-template 3' termini additions in P. duplex resemble those of C. reinhardtii, suggesting a conservation of mRNA processing among the chlorophyceae. We also report that C. vulgaris mRNA UTRs are much longer than chlorophytic examples, lack polycytidylation, and are polyadenylated similar to embryophytes. This demonstrates that some mitochondrial mRNA processing events diverged with the split between chlorophytic and streptophytic algae.},
}

@article {pmid33803147,
year = {2021},
author = {Arcila-Galvis, JE and Arango, RE and Torres-Bonilla, JM and Arias, T},
title = {The Mitochondrial Genome of a Plant Fungal Pathogen Pseudocercospora fijiensis (Mycosphaerellaceae), Comparative Analysis and Diversification Times of the Sigatoka Disease Complex Using Fossil Calibrated Phylogenies.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {3},
pages = {},
pmid = {33803147},
issn = {2075-1729},
support = {221356934854//Instituto para el desarrollo de la Ciencia y la Tecnología "Francisco José de Caldas/ ; 755-2017//Jovenes Investigadores e Innovadores por la Paz convocatoria/ ; },
abstract = {Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora fijiensis, and (ii) compare it with closely related species (Sphaerulina musiva, S. populicola, P. musae and P. eumusae) available online, paying particular attention to the Sigatoka disease's complex causal agents. The mitochondrial genome of P. fijiensis is a circular molecule of 74,089 bp containing typical genes coding for the 14 proteins related to oxidative phosphorylation, 2 rRNA genes and a set of 38 tRNAs. P. fijiensis mitogenome has two truncated cox1 copies, and bicistronic transcription of nad2-nad3 and atp6-atp8 confirmed experimentally. Comparative analysis revealed high variability in size and gene order among selected Mycosphaerellaceae mitogenomes likely to be due to rearrangements caused by mobile intron invasion. Using fossil calibrated Bayesian phylogenies, we found later diversification times for Mycosphaerellaceae (66.6 MYA) and the Sigatoka disease complex causal agents, compared to previous strict molecular clock studies. An early divergent Pseudocercospora fijiensis split from the sister species P. musae + P. eumusae 13.31 MYA while their sister group, the sister species P. eumusae and P. musae, split from their shared common ancestor in the late Miocene 8.22 MYA. This newly dated phylogeny suggests that species belonging to the Sigatoka disease complex originated after wild relatives of domesticated bananas (section Eumusae; 27.9 MYA). During this time frame, mitochondrial genomes expanded significantly, possibly due to invasions of introns into different electron transport chain genes.},
}

@article {pmid33802618,
year = {2021},
author = {Zhang, T and Li, C and Zhang, X and Wang, C and Roger, AJ and Gao, F},
title = {Characterization and Comparative Analyses of Mitochondrial Genomes in Single-Celled Eukaryotes to Shed Light on the Diversity and Evolution of Linear Molecular Architecture.},
journal = {International journal of molecular sciences},
volume = {22},
number = {5},
pages = {},
pmid = {33802618},
issn = {1422-0067},
support = {31922013//National Natural Science Foundation of China/ ; 32030015//National Natural Science Foundation of China/ ; 31772428//National Natural Science Foundation of China/ ; 201841013//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Amino Acid Sequence ; Cells, Cultured ; Eukaryota/*genetics ; Eukaryotic Cells/physiology ; Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitogens/genetics ; Phylogeny ; Plankton/genetics ; Replication Origin/genetics ; },
abstract = {Determination and comparisons of complete mitochondrial genomes (mitogenomes) are important to understand the origin and evolution of mitochondria. Mitogenomes of unicellular protists are particularly informative in this regard because they are gene-rich and display high structural diversity. Ciliates are a highly diverse assemblage of protists and their mitogenomes (linear structure with high A+T content in general) were amongst the first from protists to be characterized and have provided important insights into mitogenome evolution. Here, we report novel mitogenome sequences from three representatives (Strombidium sp., Strombidium cf. sulcatum, and Halteria grandinella) in two dominant ciliate lineages. Comparative and phylogenetic analyses of newly sequenced and previously published ciliate mitogenomes were performed and revealed a number of important insights. We found that the mitogenomes of these three species are linear molecules capped with telomeric repeats that differ greatly among known species. The genomes studied here are highly syntenic, but larger in size and more gene-rich than those of other groups. They also all share an AT-rich tandem repeat region which may serve as the replication origin and modulate initiation of bidirectional transcription. More generally we identified a split version of ccmf, a cytochrome c maturation-related gene that might be a derived character uniting taxa in the subclasses Hypotrichia and Euplotia. Finally, our mitogenome comparisons and phylogenetic analyses support to reclassify Halteria grandinella from the subclass Oligotrichia to the subclass Hypotrichia. These results add to the growing literature on the unique features of ciliate mitogenomes, shedding light on the diversity and evolution of their linear molecular architecture.},
}

Amino Acid Sequence
Cells, Cultured
Eukaryota/*genetics
Eukaryotic Cells/physiology
Evolution, Molecular
Genome, Mitochondrial/*genetics
Mitogens/genetics
Phylogeny
Plankton/genetics
Replication Origin/genetics

@article {pmid33798681,
year = {2021},
author = {Ennis, CC and Haeffner, NN and Keyser, CD and Leonard, ST and Macdonald-Shedd, AC and Savoie, AM and Cronin, TJ and Veldsman, WP and Barden, P and Chak, STC and Baeza, JA},
title = {Comparative mitochondrial genomics of sponge-dwelling snapping shrimps in the genus Synalpheus: Exploring differences between eusocial and non-eusocial species and insights into phylogenetic relationships in caridean shrimps.},
journal = {Gene},
volume = {786},
number = {},
pages = {145624},
doi = {10.1016/j.gene.2021.145624},
pmid = {33798681},
issn = {1879-0038},
mesh = {Animals ; Codon Usage ; Decapoda/*classification/genetics ; Genome Size ; Genome, Mitochondrial ; Genomics/*methods ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Selection, Genetic ; },
abstract = {The genus Synalpheus is a cosmopolitan clade of marine shrimps found in most tropical regions. Species in this genus exhibit a range of social organizations, including pair-forming, communal breeding, and eusociality, the latter only known to have evolved within this genus in the marine realm. This study examines the complete mitochondrial genomes of seven species of Synalpheus and explores differences between eusocial and non-eusocial species considering that eusociality has been shown before to affect the strength of purifying selection in mitochondrial protein coding genes. The AT-rich mitochondrial genomes of Synalpheus range from 15,421 bp to 15,782 bp in length and comprise, invariably, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 648 bp to 994 bp long intergenic space is assumed to be the D-loop. Mitochondrial gene synteny is identical among the studied shrimps. No major differences occur between eusocial and non-eusocial species in nucleotide composition and codon usage profiles of PCGs and in the secondary structure of tRNA genes. Maximum likelihood phylogenetic analysis of the complete concatenated PCG complement of 90 species supports the monophyly of the genus Synalpheus and its family Alpheidae. Moreover, the monophyletic status of the caridean families Alvinocaridae, Atyidae, Thoridae, Lysmatidae, Palaemonidae, and Pandalidae within caridean shrimps are fully or highly supported by the analysis. We therefore conclude that mitochondrial genomes contain sufficient phylogenetic information to resolve relationships at high taxonomic levels within the Caridea. Our analysis of mitochondrial genomes in the genus Synalpheus contributes to the understanding of the coevolution between genomic architecture and sociality in caridean shrimps and other marine organisms.},
}

Animals
Codon Usage
Decapoda/*classification/genetics
Genome Size
Genome, Mitochondrial
Genomics/*methods
Mitochondria/*genetics
Phylogeny
RNA, Transfer/genetics
Selection, Genetic

@article {pmid33793863,
year = {2020},
author = {Considine, MJ and Foyer, CH},
title = {Oxygen and reactive oxygen species-dependent regulation of plant growth and development.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
pmid = {33793863},
issn = {1532-2548},
abstract = {Oxygen and reactive oxygen species (ROS) have been co-opted during evolution into the regulation of plant growth, development and differentiation. ROS and oxidative signals arising from metabolism or phytohormone-mediated processes control almost every aspect of plant development from seed and bud dormancy, liberation of meristematic cells from the quiescent state, root and shoot growth and architecture, to flowering and seed production. Moreover, the phytochrome and phytohormone-dependent transmission of ROS waves is central to the systemic whole plant signaling pathways that integrate root and shoot growth. The sensing of oxygen availability through the Cys/Arg N-degron pathway functions alongside ROS production and signaling but how these pathways interact in developing organs remains poorly understood. Considerable progress has been made in our understanding of the nature hydrogen peroxide sensors and the role of thiol-dependent signaling networks in the transmission of ROS signals. Reduction/oxidation (redox) changes in the glutathione pool (GSH), glutaredoxins (GRX) and thioredoxins (TRX) are important in the control of growth mediated by phytohormone pathways. Although, it is clear that the redox states of proteins involved in plant growth and development are controlled by the NADPH/NADPH thioredoxin reductase (NTR)/thioredoxin (TRX) and reduced GSH/GRX systems of the cytosol, chloroplasts, mitochondria and nucleus, we have only scratched the surface of this multilayered control and how redox-regulated processes interact with other cell signaling systems.},
}

@article {pmid33791336,
year = {2021},
author = {Mortz, M and Levivier, A and Lartillot, N and Dufresne, F and Blier, PU},
title = {Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates.},
journal = {Frontiers in molecular biosciences},
volume = {8},
number = {},
pages = {626042},
pmid = {33791336},
issn = {2296-889X},
abstract = {Bivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1-2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies have shown that mitochondrial DNA mutation rates are linked to lifespan in vertebrate species, but no study has explored this in invertebrates. To this end, we performed a Bayesian Phylogenetic Covariance model of evolution analysis using 12 mitochondrial protein-coding genes of 76 bivalve species. Three life history traits (maximum longevity, generation time and mean temperature tolerance) were tested against 1) synonymous substitution rates (dS), 2) conservative amino acid replacement rates (Kc) and 3) ratios of radical over conservative amino acid replacement rates (Kr/Kc). Our results confirm the already known correlation between longevity and generation time and show, for the first time in an invertebrate class, a significant negative correlation between dS and longevity. This correlation was not as strong when generation time and mean temperature tolerance variations were also considered in our model (marginal correlation), suggesting a confounding effect of these traits on the relationship between longevity and mtDNA substitution rate. By confirming the negative correlation between dS and longevity previously documented in birds and mammals, our results provide support for a general pattern in substitution rates.},
}

@article {pmid33770399,
year = {2021},
author = {Bazer, FW and Seo, H and Johnson, GA and Wu, G},
title = {One-Carbon Metabolism and Development of the Conceptus During Pregnancy: Lessons from Studies with Sheep and Pigs.},
journal = {Advances in experimental medicine and biology},
volume = {1285},
number = {},
pages = {1-15},
pmid = {33770399},
issn = {0065-2598},
mesh = {Animals ; Carbon ; *Embryo, Mammalian ; Endometrium ; Female ; Fetal Development ; *Interferon Type I ; Placenta ; Pregnancy ; Sheep ; Swine ; Uterus ; },
abstract = {The pregnancy recognition signal from the conceptus (embryo/fetus and associated membranes) to the mother is interferon tau (IFNT) in ruminants and estradiol, possibly in concert with interferons gamma and delta in pigs. Those pregnancy recognition signals silence expression of interferon stimulated genes (ISG) in uterine luminal (LE) and superficial glandular (sGE) epithelia while inducing expression of genes for transport of nutrients, including glucose and amino acids, into the uterine lumen to support growth and development of the conceptus. In sheep and pigs, glucose not utilized immediately by the conceptus is converted to fructose. Glucose, fructose, serine and glycine in uterine histotroph can contribute to one carbon (1C) metabolism that provides one-carbon groups for the synthesis of purines and thymidylate, as well as S-adenosylmethionine for epigenetic methylation reactions. Serine and glycine are transported into the mitochondria of cells and metabolized to formate that is transported into the cytoplasm for the synthesis of purines, thymidine and S-adenosylmethionine. The unique aspects of one-carbon metabolism are discussed in the context of the hypoxic uterine environment, aerobic glycolysis, and similarities in metabolism between cancer cells and cells of the rapidly developing fetal-placental tissues during pregnancy. Further, the evolution of anatomical and functional aspects of the placentae of sheep and pigs versus primates is discussed in the context of mechanisms to efficiently obtain, store and utilize nutrients required for rapid fetal growth in the last one-half of gestation.},
}

Animals
Carbon
*Embryo, Mammalian
Endometrium
Female
Fetal Development
*Interferon Type I
Placenta
Pregnancy
Sheep
Swine
Uterus

@article {pmid33750312,
year = {2021},
author = {Cheng, Y and He, X and Priyadarshani, SVGN and Wang, Y and Ye, L and Shi, C and Ye, K and Zhou, Q and Luo, Z and Deng, F and Cao, L and Zheng, P and Aslam, M and Qin, Y},
title = {Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {167},
pmid = {33750312},
issn = {1471-2164},
support = {31671267//National Natural Science Foundation of China/ ; 31970333//National Natural Science Foundation of China/ ; },
mesh = {*Chenopodiaceae/genetics ; Genome Size ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Phylogeny ; },
abstract = {BACKGROUND: Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific research value. The S. glauca chloroplast (cp) genome has recently been reported; however, the mitochondria (mt) genome is still unexplored.

RESULTS: The mt genome of S. glauca were assembled based on the reads from Pacbio and Illumina sequencing platforms. The circular mt genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (28.00%), T (27.93%), C (21.62%), and G (22.45%). S. glauca mt genome contains 61 genes, including 27 protein-coding genes, 29 tRNA genes, and 5 rRNA genes. The sequence repeats, RNA editing, and gene migration from cp to mt were observed in S. glauca mt genome. Phylogenetic analysis based on the mt genomes of S. glauca and other 28 taxa reflects an exact evolutionary and taxonomic status of S. glauca. Furthermore, the investigation on mt genome characteristics, including genome size, GC contents, genome organization, and gene repeats of S. gulaca genome, was investigated compared to other land plants, indicating the variation of the mt genome in plants. However, the subsequently Ka/Ks analysis revealed that most of the protein-coding genes in mt genome had undergone negative selections, reflecting the importance of those genes in the mt genomes.

CONCLUSIONS: In this study, we reported the mt genome assembly and annotation of a halophytic model plant S. glauca. The subsequent analysis provided us a comprehensive understanding of the S. glauca mt genome, which might facilitate the research on the salt-tolerant plant species.},
}

*Chenopodiaceae/genetics
Genome Size
*Genome, Chloroplast
*Genome, Mitochondrial
Phylogeny