@article {pmid35614856,
year = {2022},
author = {Xu, JJ and Hu, M and Yang, L and Chen, XY},
title = {How plants synthesize coenzyme Q.},
journal = {Plant communications},
volume = {},
number = {},
pages = {100341},
doi = {10.1016/j.xplc.2022.100341},
pmid = {35614856},
issn = {2590-3462},
abstract = {Coenzyme Q (CoQ) is a conserved redox-active lipid that has a wide distribution across life domains. CoQ plays a key role in the oxidative electron transfer chain and serves as a crucial antioxidant in cellular membranes. The knowledge of CoQ biosynthesis in eukaryotes mostly came from the studies of yeast. Recently, significant advances have been made in understanding CoQ biosynthesis in plants, from which unique mitochondrial flavin-dependent monooxygenase and benzenoid ring precursor biosynthetic pathways have been discovered, generating new insight into the diversity of CoQ biosynthetic pathways and the evolution of phototrophic eukaryotes. We summarize the research progress of CoQ biosynthesis and regulation in plants, and recent efforts to increase CoQ content in plant foods.},
}

@article {pmid35483362,
year = {2022},
author = {David, P and Degletagne, C and Saclier, N and Jennan, A and Jarne, P and Plénet, S and Konecny, L and François, C and Guéguen, L and Garcia, N and Lefébure, T and Luquet, E},
title = {Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination.},
journal = {Current biology : CB},
volume = {32},
number = {10},
pages = {2325-2333.e6},
doi = {10.1016/j.cub.2022.04.014},
pmid = {35483362},
issn = {1879-0445},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/genetics ; },
abstract = {Cytoplasmic male sterility (CMS) is a form of genetic conflict over sex determination that results from differences in modes of inheritance between genomic compartments.1-3 Indeed, maternally transmitted (usually mitochondrial) genes sometimes enhance their transmission by suppressing the male function in a hermaphroditic organism to the detriment of biparentally inherited nuclear genes. Therefore, these hermaphrodites become functionally female and may coexist with regular hermaphrodites in so-called gynodioecious populations.3 CMS has been known in plants since Darwin's times4 but is previously unknown in the animal kingdom.5-8 We relate the first observation of CMS in animals. It occurs in a freshwater snail population, where some individuals appear unable to sire offspring in controlled crosses and show anatomical, physiological, and behavioral characters consistent with a suppression of the male function. Male sterility is associated with a mitochondrial lineage that underwent a spectacular acceleration of DNA substitution rates, affecting the entire mitochondrial genome-this acceleration concerns both synonymous and non-synonymous substitutions and therefore results from increased mitogenome mutation rates. Consequently, mitochondrial haplotype divergence within the population is exceptionally high, matching that observed between snail taxa that diverged 475 million years ago. This result is reminiscent of similar accelerations in mitogenome evolution observed in plant clades where gynodioecy is frequent,9,10 both being consistent with arms-race evolution of genome regions implicated in CMS.11,12 Our study shows that genomic conflicts can trigger independent evolution of similar sex-determination systems in plants and animals and dramatically accelerate molecular evolution.},
}

Animals
*DNA, Mitochondrial/genetics
Evolution, Molecular
Female
*Genome, Mitochondrial
Haplotypes
Mitochondria/genetics

@article {pmid35587988,
year = {2022},
author = {Huynen, MA and Elurbe, DM},
title = {Mitochondrial complex complexification.},
journal = {Science (New York, N.Y.)},
volume = {376},
number = {6595},
pages = {794-795},
doi = {10.1126/science.abq0368},
pmid = {35587988},
issn = {1095-9203},
mesh = {*Electron Transport Complex I/chemistry/genetics ; *Electron Transport Complex IV/chemistry/genetics ; Evolution, Molecular ; *Mitochondria/enzymology ; Oxidative Phosphorylation ; Protein Subunits/chemistry/genetics ; *Tetrahymena thermophila/enzymology ; },
abstract = {Variation in complex composition provides clues about the function of individual subunits.},
}

*Electron Transport Complex I/chemistry/genetics
*Electron Transport Complex IV/chemistry/genetics
Evolution, Molecular
*Mitochondria/enzymology
Oxidative Phosphorylation
Protein Subunits/chemistry/genetics
*Tetrahymena thermophila/enzymology

@article {pmid35609548,
year = {2022},
author = {Schärer, L},
title = {Evolution: Mitochondrial lodgers can take over in hermaphroditic snails.},
journal = {Current biology : CB},
volume = {32},
number = {10},
pages = {R477-R479},
doi = {10.1016/j.cub.2022.04.039},
pmid = {35609548},
issn = {1879-0445},
abstract = {Mitochondria - the cell's power stations - are inherited uniparentally via eggs, not sperm. In hermaphroditic plants, they sometimes prevent their hosts from making pollen (and sperm), causing cytoplasmic male sterility. New evidence from a hermaphroditic freshwater snail now documents cytoplasmic male sterility in animals.},
}

@article {pmid35452707,
year = {2022},
author = {Chen, Q and Chen, L and Liao, CQ and Wang, X and Wang, M and Huang, GH},
title = {Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species.},
journal = {Gene},
volume = {830},
number = {},
pages = {146516},
doi = {10.1016/j.gene.2022.146516},
pmid = {35452707},
issn = {1879-0038},
mesh = {Animals ; *Butterflies/genetics ; *Genome, Mitochondrial ; *Lepidoptera/genetics ; Mitochondria/genetics ; *Moths/genetics ; Phylogeny ; RNA, Transfer/genetics ; },
abstract = {Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as "ATGATAA". Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).},
}

Animals
*Butterflies/genetics
*Genome, Mitochondrial
*Lepidoptera/genetics
Mitochondria/genetics
*Moths/genetics
Phylogeny
RNA, Transfer/genetics

@article {pmid34818432,
year = {2022},
author = {Jiang, Y and Yue, L and Yang, F and Gillung, JP and Winterton, SL and Price, BW and Contreras-Ramos, A and Hayashi, F and Aspöck, U and Aspöck, H and Yeates, DK and Yang, D and Liu, X},
title = {Similar pattern, different paths: tracing the biogeographical history of Megaloptera (Insecta: Neuropterida) using mitochondrial phylogenomics.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {38},
number = {3},
pages = {374-391},
doi = {10.1111/cla.12494},
pmid = {34818432},
issn = {1096-0031},
support = {32170448//National Natural Science Foundation of China/ ; 31322051//National Natural Science Foundation of China/ ; 31972871//National Natural Science Foundation of China/ ; 31672322//National Natural Science Foundation of China/ ; 31320103902//National Natural Science Foundation of China/ ; 41271063//National Natural Science Foundation of China/ ; 2018//Changjiang Scholars Program/ ; 2020TC158//Chinese Universities Scientific Fund/ ; },
mesh = {Animals ; *Genome, Mitochondrial/genetics ; *Holometabola/genetics ; Insecta/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The sequential breakup of the supercontinent Pangaea since the Middle Jurassic is one of the crucial factors that has driven the biogeographical patterns of terrestrial biotas. Despite decades of effort searching for concordant patterns between diversification and continental fragmentation among taxonomic groups, increasing evidence has revealed more complex and idiosyncratic scenarios resulting from a mixture of vicariance, dispersal and extinction. Aquatic insects with discreet ecological requirements, low vagility and disjunct distributions represent a valuable model for testing biogeographical hypotheses by reconstructing their distribution patterns and temporal divergences. Insects of the order Megaloptera have exclusively aquatic larvae, their adults have low vagility, and the group has a highly disjunct geographical distribution. Here we present a comprehensive phylogeny of Megaloptera based on a large-scale mitochondrial genome sequencing of 99 species representing >90% of the world genera from all major biogeographical regions. Molecular dating suggests that the deep divergence within Megaloptera pre-dates the breakup of Pangaea. Subsequently, the intergeneric divergences within Corydalinae (dobsonflies), Chauliodinae (fishflies) and Sialidae (alderflies) might have been driven by both vicariance and dispersal correlated with the shifting continent during the Cretaceous, but with strikingly different and incongruent biogeographical signals. The austral distribution of many corydalids appears to be a result of colonization from Eurasia through southward dispersal across Europe and Africa during the Cretaceous, whereas a nearly contemporaneous dispersal via northward rafting of Gondwanan landmasses may account for the colonization of extant Eurasian alderflies from the south.},
}

Animals
*Genome, Mitochondrial/genetics
*Holometabola/genetics
Insecta/genetics
Mitochondria/genetics
Phylogeny

@article {pmid35596716,
year = {2022},
author = {Yu, G and Nakajima, K and Gruber, A and Rio Bartulos, C and Schober, AF and Lepetit, B and Yohannes, E and Matsuda, Y and Kroth, PG},
title = {Mitochondrial PEP Carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.18268},
pmid = {35596716},
issn = {1469-8137},
abstract = {Photosynthetic carbon fixation is often limited by CO2 availability, which led to the evolution of CO2 concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C4 plants, but it is controversially discussed whether biochemical CCMs are a commonly found in diatoms. In the diatom Phaeodactylum tricornutum, Phosphoenolpyruvate Carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real-time quantitative PCR, western blots, and enzymatic assays to examine PEPC expression and PEPC activities, under low and high concentrations of dissolved inorganic carbon (DIC). We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double-knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double-knockout strains grown under ambient air or lower DIC availability, showed reduced growth and photosynthetic affinity to DIC, while behaving similarly as WT cells at high DIC concentrations. These mutants furthermore exhibited significantly lower 13 C/12 C ratios compared to WT. Our data implies that in P. tricornutum at least parts of the CCM relies on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.},
}

@article {pmid35585601,
year = {2022},
author = {Vujovic, F and Hunter, N and Farahani, RM},
title = {Notch ankyrin domain: evolutionary rise of a thermodynamic sensor.},
journal = {Cell communication and signaling : CCS},
volume = {20},
number = {1},
pages = {66},
pmid = {35585601},
issn = {1478-811X},
mesh = {Animals ; *Ankyrins/metabolism ; Mice ; *Neural Stem Cells/metabolism ; Phylogeny ; Signal Transduction ; Thermodynamics ; },
abstract = {Notch signalling pathway plays a key role in metazoan biology by contributing to resolution of binary decisions in the life cycle of cells during development. Outcomes such as proliferation/differentiation dichotomy are resolved by transcriptional remodelling that follows a switch from Notchon to Notchoff state, characterised by dissociation of Notch intracellular domain (NICD) from DNA-bound RBPJ. Here we provide evidence that transitioning to the Notchoff state is regulated by heat flux, a phenomenon that aligns resolution of fate dichotomies to mitochondrial activity. A combination of phylogenetic analysis and computational biochemistry was utilised to disclose structural adaptations of Notch1 ankyrin domain that enabled function as a sensor of heat flux. We then employed DNA-based micro-thermography to measure heat flux during brain development, followed by analysis in vitro of the temperature-dependent behaviour of Notch1 in mouse neural progenitor cells. The structural capacity of NICD to operate as a thermodynamic sensor in metazoans stems from characteristic enrichment of charged acidic amino acids in β-hairpins of the ankyrin domain that amplify destabilising inter-residue electrostatic interactions and render the domain thermolabile. The instability emerges upon mitochondrial activity which raises the perinuclear and nuclear temperatures to 50 °C and 39 °C, respectively, leading to destabilization of Notch1 transcriptional complex and transitioning to the Notchoff state. Notch1 functions a metazoan thermodynamic sensor that is switched on by intercellular contacts, inputs heat flux as a proxy for mitochondrial activity in the Notchon state via the ankyrin domain and is eventually switched off in a temperature-dependent manner. Video abstract.},
}

Animals
*Ankyrins/metabolism
Mice
*Neural Stem Cells/metabolism
Phylogeny
Signal Transduction
Thermodynamics

@article {pmid35575078,
year = {2022},
author = {Lee, J and Willett, CS},
title = {Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids.},
journal = {The Journal of heredity},
volume = {113},
number = {2},
pages = {171-183},
doi = {10.1093/jhered/esab068},
pmid = {35575078},
issn = {1465-7333},
support = {NSF IOS-1155325//National Science Foundation/ ; //University of North Carolina at Chapel Hill/ ; },
mesh = {Animals ; *Copepoda/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.},
}

Animals
*Copepoda/genetics
DNA, Mitochondrial/genetics
Genes, Mitochondrial
Haplotypes
Mitochondria/genetics
Phylogeny

@article {pmid35580923,
year = {2022},
author = {Maldonado, J and Firneno, TJ and Hall, AS and Fujita, M},
title = {Parthenogenesis Doubles the Rate of Amino Acid Substitution in Whiptail Mitochondria.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1111/evo.14509},
pmid = {35580923},
issn = {1558-5646},
abstract = {Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious mutations. We tested this prediction by estimating the dN/dS ratios in asexual vertebrate lineages in the genus Aspidoscelis using whole mitochondrial genomes from seven asexual and five sexual species. We found higher dN/dS ratios in asexual Aspidoscelis species, indicating that asexual whiptails accumulate non-synonymous substitutions due to weaker purifying selection. Additionally, we estimated nucleotide diversity and found that asexuals harbor significantly less diversity. Thus, despite their recent origins, slightly deleterious mutations accumulated rapidly enough in asexual lineages to be detected. We provided empirical evidence to corroborate the connection between asexuality and increased amino acid substitutions in asexual vertebrate lineages. This article is protected by copyright. All rights reserved.},
}

@article {pmid35577958,
year = {2022},
author = {Bates, M and Keller-Findeisen, J and Przybylski, A and Hüper, A and Stephan, T and Ilgen, P and Cereceda Delgado, AR and D'Este, E and Egner, A and Jakobs, S and Sahl, SJ and Hell, SW},
title = {Optimal precision and accuracy in 4Pi-STORM using dynamic spline PSF models.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {35577958},
issn = {1548-7105},
support = {ALTF 800-2010//European Molecular Biology Organization (EMBO)/ ; SFB1286/A0//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Coherent fluorescence imaging with two objective lenses (4Pi detection) enables single-molecule localization microscopy with sub-10 nm spatial resolution in three dimensions. Despite its outstanding sensitivity, wider application of this technique has been hindered by complex instrumentation and the challenging nature of the data analysis. Here we report the development of a 4Pi-STORM microscope, which obtains optimal resolution and accuracy by modeling the 4Pi point spread function (PSF) dynamically while also using a simpler optical design. Dynamic spline PSF models incorporate fluctuations in the modulation phase of the experimentally determined PSF, capturing the temporal evolution of the optical system. Our method reaches the theoretical limits for precision and minimizes phase-wrapping artifacts by making full use of the information content of the data. 4Pi-STORM achieves a near-isotropic three-dimensional localization precision of 2-3 nm, and we demonstrate its capabilities by investigating protein and nucleic acid organization in primary neurons and mammalian mitochondria.},
}

@article {pmid35563133,
year = {2022},
author = {Bonturi, CR and Silva Teixeira, AB and Rocha, VM and Valente, PF and Oliveira, JR and Filho, CMB and Fátima Correia Batista, I and Oliva, MLV},
title = {Plant Kunitz Inhibitors and Their Interaction with Proteases: Current and Potential Pharmacological Targets.},
journal = {International journal of molecular sciences},
volume = {23},
number = {9},
pages = {},
pmid = {35563133},
issn = {1422-0067},
support = {2017/06630-7 and 2019/22243-9//São Paulo Research Foundation/ ; Finance Code 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 301721/2016-5//National Council for Scientific and Technological Development/ ; },
mesh = {Endopeptidases ; Fungi/metabolism ; Humans ; *Plants/metabolism ; *Protease Inhibitors/chemistry/pharmacology/therapeutic use ; Serine Proteases/metabolism ; },
abstract = {The action of proteases can be controlled by several mechanisms, including regulation through gene expression; post-translational modifications, such as glycosylation; zymogen activation; targeting specific compartments, such as lysosomes and mitochondria; and blocking proteolysis using endogenous inhibitors. Protease inhibitors are important molecules to be explored for the control of proteolytic processes in organisms because of their ability to act on several proteases. In this context, plants synthesize numerous proteins that contribute to protection against attacks by microorganisms (fungi and bacteria) and/or invertebrates (insects and nematodes) through the inhibition of proteases in these organisms. These proteins are widely distributed in the plant kingdom, and are present in higher concentrations in legume seeds (compared to other organs and other botanical families), motivating studies on their inhibitory effects in various organisms, including humans. In most cases, the biological roles of these proteins have been assigned based mostly on their in vitro action, as is the case with enzyme inhibitors. This review highlights the structural evolution, function, and wide variety of effects of plant Kunitz protease inhibitors, and their potential for pharmaceutical application based on their interactions with different proteases.},
}

Endopeptidases
Fungi/metabolism
Humans
*Plants/metabolism
*Protease Inhibitors/chemistry/pharmacology/therapeutic use
Serine Proteases/metabolism

@article {pmid35547863,
year = {2021},
author = {Benz, R},
title = {Historical Perspective of Pore-Forming Activity Studies of Voltage-Dependent Anion Channel (Eukaryotic or Mitochondrial Porin) Since Its Discovery in the 70th of the Last Century.},
journal = {Frontiers in physiology},
volume = {12},
number = {},
pages = {734226},
pmid = {35547863},
issn = {1664-042X},
abstract = {Eukaryotic porin, also known as Voltage-Dependent Anion Channel (VDAC), is the most frequent protein in the outer membrane of mitochondria that are responsible for cellular respiration. Mitochondria are most likely descendants of strictly aerobic Gram-negative bacteria from the α-proteobacterial lineage. In accordance with the presumed ancestor, mitochondria are surrounded by two membranes. The mitochondrial outer membrane contains besides the eukaryotic porins responsible for its major permeability properties a variety of other not fully identified channels. It encloses also the TOM apparatus together with the sorting mechanism SAM, responsible for the uptake and assembly of many mitochondrial proteins that are encoded in the nucleus and synthesized in the cytoplasm at free ribosomes. The recognition and the study of electrophysiological properties of eukaryotic porin or VDAC started in the late seventies of the last century by a study of Schein et al., who reconstituted the pore from crude extracts of Paramecium mitochondria into planar lipid bilayer membranes. Whereas the literature about structure and function of eukaryotic porins was comparatively rare during the first 10years after the first study, the number of publications started to explode with the first sequencing of human Porin 31HL and the recognition of the important function of eukaryotic porins in mitochondrial metabolism. Many genomes contain more than one gene coding for homologs of eukaryotic porins. More than 100 sequences of eukaryotic porins are known to date. Although the sequence identity between them is relatively low, the polypeptide length and in particular, the electrophysiological characteristics are highly preserved. This means that all eukaryotic porins studied to date are anion selective in the open state. They are voltage-dependent and switch into cation-selective substates at voltages in the physiological relevant range. A major breakthrough was also the elucidation of the 3D structure of the eukaryotic pore, which is formed by 19 β-strands similar to those of bacterial porin channels. The function of the presumed gate an α-helical stretch of 20 amino acids allowed further studies with respect to voltage dependence and function, but its exact role in channel gating is still not fully understood.},
}

@article {pmid35543999,
year = {2022},
author = {Corsaro, D},
title = {Insights into Microsporidia Evolution from Early Diverging Microsporidia.},
journal = {Experientia supplementum (2012)},
volume = {114},
number = {},
pages = {71-90},
pmid = {35543999},
issn = {1664-431X},
mesh = {Animals ; Fungi ; *Microsporidia/genetics ; *Parasites ; Phylogeny ; },
abstract = {Microsporidia have drastically modified genomes and cytology resulting from their high level of adaptation to intracytoplasmic parasitism. Their origins, which had long remained enigmatic, were placed within the line of Rozella, a primitive endoparasitic chytrid. These origins became more and more refined with the discovery of various parasites morphologically similar to the primitive lines of microsporidia (Metchnikovellids and Chytridiopsids) but which possess fungal-like genomes and functional mitochondria. These various parasites turn out to be distinct missing links between a large assemblage of chytrid-like rozellids and the true microsporidians, which are actually a very evolved branch of the rozellids themselves. The question of how to consider the historically known Microsporidia and the various microsporidia-like organisms within paraphyletic rozellids is discussed.},
}

Animals
Fungi
*Microsporidia/genetics
*Parasites
Phylogeny

@article {pmid35508562,
year = {2022},
author = {Kidd, KK and Evsanaa, B and Togtokh, A and Brissenden, JE and Roscoe, JM and Dogan, M and Neophytou, PI and Gurkan, C and Bulbul, O and Cherni, L and Speed, WC and Murtha, M and Kidd, JR and Pakstis, AJ},
title = {North Asian population relationships in a global context.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7214},
pmid = {35508562},
issn = {2045-2322},
support = {NIJ grant 2018-75-CX-0041//National Institute of Justice, Office of Justice Programs of the United States Department of Justice/ ; },
mesh = {*Asians/genetics ; Ethnicity/genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Humans ; Phylogeny ; Principal Component Analysis ; },
abstract = {Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.},
}

*Asians/genetics
Ethnicity/genetics
Genetic Variation
*Genetics, Population
Haplotypes
Humans
Phylogeny
Principal Component Analysis

@article {pmid35504558,
year = {2022},
author = {Zhou, W and Zhao, Z and Yu, Z and Hou, Y and Keerthiga, R and Fu, A},
title = {Mitochondrial transplantation therapy inhibits the proliferation of malignant hepatocellular carcinoma and its mechanism.},
journal = {Mitochondrion},
volume = {65},
number = {},
pages = {11-22},
doi = {10.1016/j.mito.2022.04.004},
pmid = {35504558},
issn = {1872-8278},
abstract = {Mitochondrial dysfunction plays a vital role in growth and malignancy of tumors. In recent scenarios, mitochondrial transplantation therapy is considered as an effective method to remodel mitochondrial function in mitochondria-related diseases. However, the mechanism by which mitochondrial transplantation blocks tumor cell proliferation is still not determined. In addition, mitochondria are maternal inheritance in evolution, and mitochondria obtained from genders exhibit differences in mitochondrial activity. Therefore, the study indicates the inhibitory effect of mitochondria from different genders on hepatocellular carcinoma and explores the molecular mechanism. The results reveal that the healthy mitochondria can retard the proliferation of the hepatocellular carcinoma cells in vitro and in vivo through arresting cell cycle and inducing apoptosis. The molecular mechanism suggests that mitochondrial transplantation therapy can decrease aerobic glycolysis, and down-regulate the expression of cycle-related proteins while up-regulate apoptosis-related proteins in tumor cells. In addition, the antitumor activity of mitochondria from female mice (F-Mito) is relatively higher than that of mitochondria from male mice (M-Mito), which would be related to the evidence that the F-Mito process higher activity than the M-Mito. This study clarifies the mechanism of exogenous mitochondria inhibiting the proliferation of hepatocellular carcinoma and contributes a new biotechnology for therapy of mitochondria-related diseases from different genders.},
}

@article {pmid35503755,
year = {2022},
author = {Niu, Y and Lu, Y and Song, W and He, X and Liu, Z and Zheng, C and Wang, S and Shi, C and Liu, J},
title = {Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla).},
journal = {PloS one},
volume = {17},
number = {5},
pages = {e0263545},
pmid = {35503755},
issn = {1932-6203},
mesh = {Genome Size ; *Genome, Chloroplast ; *Genome, Mitochondrial/genetics ; Genome, Plant ; Macadamia/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Macadamia is a true dicotyledonous plant that thrives in a mild, humid, low wind environment. It is cultivated and traded internationally due to its high-quality nuts thus, has significant development prospects and scientific research value. However, information on the genetic resources of Macadamia spp. remains scanty.

RESULTS: The mitochondria (mt) genomes of three economically important Macadamia species, Macadamia integrifolia, M. ternifolia and M. tetraphylla, were assembled through the Illumina sequencing platform. The results showed that each species has 71 genes, including 42 protein-coding genes, 26 tRNAs, and 3 rRNAs. Repeated sequence analysis, RNA editing site prediction, and analysis of genes migrating from chloroplast (cp) to mt were performed in the mt genomes of the three Macadamia species. Phylogenetic analysis based on the mt genome of the three Macadamia species and 35 other species was conducted to reveal the evolution and taxonomic status of Macadamia. Furthermore, the characteristics of the plant mt genome, including genome size and GC content, were studied through comparison with 36 other plant species. The final non-synonymous (Ka) and synonymous (Ks) substitution analysis showed that most of the protein-coding genes in the mt genome underwent negative selections, indicating their importance in the mt genome.

CONCLUSION: The findings of this study provide a better understanding of the Macadamia genome and will inform future research on the genus.},
}

Genome Size
*Genome, Chloroplast
*Genome, Mitochondrial/genetics
Genome, Plant
Macadamia/genetics
Phylogeny

@article {pmid35501686,
year = {2022},
author = {Liu, H and Zhao, W and Hua, W and Liu, J},
title = {A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {339},
pmid = {35501686},
issn = {1471-2164},
support = {31871664//National Natural Science Foundation of China/ ; CAAS-ZDRW2019003//Agricultural Science and Technology Innovation Program/ ; },
mesh = {Brassica/genetics ; *Brassica napus/genetics ; Brassica rapa/genetics ; Chloroplasts/genetics ; Genetic Variation ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genome, Plant ; Mitochondria/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Allotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea.

RESULTS: Based on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus.

CONCLUSIONS: The phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.},
}

Brassica/genetics
*Brassica napus/genetics
Brassica rapa/genetics
Chloroplasts/genetics
Genetic Variation
*Genome, Chloroplast
*Genome, Mitochondrial
Genome, Plant
Mitochondria/genetics
Phylogeny

@article {pmid35490656,
year = {2022},
author = {Das, R and Kumar, A and Dalai, R and Goswami, C},
title = {Cytochrome C interacts with the pathogenic mutational hotspot region of TRPV4 and forms complexes that differ in mutation and metal ion-sensitive manner.},
journal = {Biochemical and biophysical research communications},
volume = {611},
number = {},
pages = {172-178},
doi = {10.1016/j.bbrc.2022.04.066},
pmid = {35490656},
issn = {1090-2104},
abstract = {The importance of TRPV4 in physiology and disease has been reported by several groups. Recently we have reported that TRPV4 localizes in the mitochondria in different cellular systems, regulates mitochondrial metabolism and electron transport chain functions. Here, we show that TRPV4 colocalizes with Cytochrome C (Cyt C), both in resting as well as in activated conditions. Amino acid region 592-630 of TRPV4 (termed as Fr592-630) that also covers TM4-Loop-TM5 region (which is also a hotspot of several pathogenic mutations) interacts with Cyt C, in a Ca2+-sensitive manner. This interaction is also variable and sensitive to other divalent and trivalent cations (i.e., Cu2+, Mn2+, Ni2+, Zn2+, Fe3+). Key residues of TRPV4 involved in these interactions remain conserved throughout the vertebrate evolution. Accordingly, this interaction is variable in the case of different pathogenic mutations (R616Q, F617L, L618P, V620I). Our data suggest that the TRPV4-Cyt C complex differs due to different mutations and is sensitive to the presence of different metal ions. We propose that TRPV4-Cyt C complex formation is important for physiological functions and relevant for TRPV4-induced channelopathies.},
}

@article {pmid35480047,
year = {2022},
author = {De Pinto, V and Mahalakshmi, R and Messina, A},
title = {Editorial: VDAC Structure and Function: An Up-to-Date View.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {871586},
pmid = {35480047},
issn = {1664-042X},
}

@article {pmid35463435,
year = {2022},
author = {Yi, L and Liu, B and Nixon, PJ and Yu, J and Chen, F},
title = {Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {837528},
pmid = {35463435},
issn = {1664-462X},
abstract = {The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologs form homo- and heterocomplexes with specialized functions in maintaining photosynthesis and respiration. The diversification of FtsH homologs combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarize recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.},
}

@article {pmid35460877,
year = {2022},
author = {Kodagoda, YK and Liyanage, DS and Omeka, WKM and Kwon, H and Hwang, SD and Lee, J},
title = {Molecular characterization, expression, and functional analysis of cystatin B in the big-belly seahorse (Hippocampus abdominalis).},
journal = {Fish & shellfish immunology},
volume = {124},
number = {},
pages = {442-453},
doi = {10.1016/j.fsi.2022.04.020},
pmid = {35460877},
issn = {1095-9947},
mesh = {Animals ; *Cyprinidae/genetics ; Cystatin B/genetics ; *Cystatins/genetics ; *Fish Diseases ; Fish Proteins/chemistry ; Male ; Phylogeny ; Poly I-C/pharmacology ; Sequence Alignment ; *Smegmamorpha ; },
abstract = {Cystatins are a diverse group of cysteine protease inhibitors widely present among various organisms. Beyond their protease inhibitor function, cystatins play a crucial role in diverse pathophysiological conditions in animals, including neurodegenerative disorders, tumor progression, inflammatory diseases, and immune response. However, the role of cystatins in immunity against viral and bacterial infections in fish remains to be elucidated. In this study, the cystatin B from big-belly seahorse, Hippocampus abdominalis, designated as HaCSTB, was identified and characterized. HaCSTB shared the highest homology with type 1 cystatin family members of teleosts and had three cystatin catalytic domains with no signal peptides or disulfide bonds. HaCSTB transcripts were mainly expressed in peripheral blood cells (PBCs), followed by the testis and pouch of healthy big-belly seahorses. Immune challenge with lipopolysaccharides (LPS), polyinosinic:polycytidylic acid (Poly I:C), and Streptococcus iniae induced upregulation of relative HaCSTB mRNA expression in PBCs. Subcellular localization analysis revealed the distribution of HaCSTB in the cytosol, mitochondria, and nuclei of fathead minnow cells (FHM). Recombinant HaCSTB (rHaCSTB) exhibited potent in vitro inhibitory activity against papain, a cysteine protease, in a concentration-, pH-, and temperature-dependent manner. Overexpression of HaCSTB in viral hemorrhagic septicemia virus (VHSV)-susceptible FHM cells increased cell viability and reduced VHSV-induced apoptosis. Collectively, these results suggest that HaCSTB might engage in the teleostean immune protection against bacteria and viruses.},
}

Animals
*Cyprinidae/genetics
Cystatin B/genetics
*Cystatins/genetics
*Fish Diseases
Fish Proteins/chemistry
Male
Phylogeny
Poly I-C/pharmacology
Sequence Alignment
*Smegmamorpha

@article {pmid35457201,
year = {2022},
author = {Juskeviciene, R and Fritz, AK and Brilkova, M and Akbergenov, R and Schmitt, K and Rehrauer, H and Laczko, E and Isnard-Petit, P and Thiam, K and Eckert, A and Schacht, J and Wolfer, DP and Böttger, EC and Shcherbakov, D},
title = {Phenotype of Mrps5-Associated Phylogenetic Polymorphisms Is Intimately Linked to Mitoribosomal Misreading.},
journal = {International journal of molecular sciences},
volume = {23},
number = {8},
pages = {},
pmid = {35457201},
issn = {1422-0067},
mesh = {Animals ; Mice ; *Mitochondrial Proteins/genetics ; Mutation ; Phenotype ; Phylogeny ; Protein Biosynthesis ; *Ribosomal Proteins/genetics ; },
abstract = {We have recently identified point mutation V336Y in mitoribosomal protein Mrps5 (uS5m) as a mitoribosomal ram (ribosomal ambiguity) mutation conferring error-prone mitochondrial protein synthesis. In vivo in transgenic knock-in animals, homologous mutation V338Y was associated with a discrete phenotype including impaired mitochondrial function, anxiety-related behavioral alterations, enhanced susceptibility to noise-induced hearing damage, and accelerated metabolic aging in muscle. To challenge the postulated link between Mrps5 V338Y-mediated misreading and the in vivo phenotype, we introduced mutation G315R into the mouse Mrps5 gene as Mrps5 G315R is homologous to the established bacterial ram mutation RpsE (uS5) G104R. However, in contrast to bacterial translation, the homologous G → R mutation in mitoribosomal Mrps5 did not affect the accuracy of mitochondrial protein synthesis. Importantly, in the absence of mitochondrial misreading, homozygous mutant MrpS5G315R/G315R mice did not show a phenotype distinct from wild-type animals.},
}

Animals
Mice
*Mitochondrial Proteins/genetics
Mutation
Phenotype
Phylogeny
Protein Biosynthesis
*Ribosomal Proteins/genetics

@article {pmid35453648,
year = {2022},
author = {Russo, C and Valle, MS and Casabona, A and Spicuzza, L and Sambataro, G and Malaguarnera, L},
title = {Vitamin D Impacts on Skeletal Muscle Dysfunction in Patients with COPD Promoting Mitochondrial Health.},
journal = {Biomedicines},
volume = {10},
number = {4},
pages = {},
pmid = {35453648},
issn = {2227-9059},
abstract = {Skeletal muscle dysfunction is frequently associated with chronic obstructive pulmonary disease (COPD), which is characterized by a permanent airflow limitation, with a worsening respiratory disorder during disease evolution. In COPD, the pathophysiological changes related to the chronic inflammatory state affect oxidant-antioxidant balance, which is one of the main mechanisms accompanying extra-pulmonary comorbidity such as muscle wasting. Muscle impairment is characterized by alterations on muscle fiber architecture, contractile protein integrity, and mitochondrial dysfunction. Exogenous and endogenous sources of reactive oxygen species (ROS) are present in COPD pathology. One of the endogenous sources of ROS is represented by mitochondria. Evidence demonstrated that vitamin D plays a crucial role for the maintenance of skeletal muscle health. Vitamin D deficiency affects oxidative stress and mitochondrial function influencing disease course through an effect on muscle function in COPD patients. This review will focus on vitamin-D-linked mechanisms that could modulate and ameliorate the damage response to free radicals in muscle fibers, evaluating vitamin D supplementation with enough potent effect to contrast mitochondrial impairment, but which avoids potential severe side effects.},
}

@article {pmid35453370,
year = {2022},
author = {Hambardikar, V and Guitart-Mampel, M and Scoma, ER and Urquiza, P and Nagana, GGA and Raftery, D and Collins, JA and Solesio, ME},
title = {Enzymatic Depletion of Mitochondrial Inorganic Polyphosphate (polyP) Increases the Generation of Reactive Oxygen Species (ROS) and the Activity of the Pentose Phosphate Pathway (PPP) in Mammalian Cells.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
pmid = {35453370},
issn = {2076-3921},
support = {1K99AG055701-01A1//National Institute of Health/ ; R00 AG055701/AG/NIA NIH HHS/United States ; 4R00AG055701-03//National Institute of Health/ ; Start Up Funds//Rutgers, The State University of New Jersey/ ; K99 AG055701/AG/NIA NIH HHS/United States ; },
abstract = {Inorganic polyphosphate (polyP) is an ancient biopolymer that is well preserved throughout evolution and present in all studied organisms. In mammals, it shows a high co-localization with mitochondria, and it has been demonstrated to be involved in the homeostasis of key processes within the organelle, including mitochondrial bioenergetics. However, the exact extent of the effects of polyP on the regulation of cellular bioenergetics, as well as the mechanisms explaining these effects, still remain poorly understood. Here, using HEK293 mammalian cells under Wild-type (Wt) and MitoPPX (cells enzymatically depleted of mitochondrial polyP) conditions, we show that depletion of polyP within mitochondria increased oxidative stress conditions. This is characterized by enhanced mitochondrial O2- and intracellular H2O2 levels, which may be a consequence of the dysregulation of oxidative phosphorylation (OXPHOS) that we have demonstrated in MitoPPX cells in our previous work. These findings were associated with an increase in basal peroxiredoxin-1 (Prx1), superoxide dismutase-2 (SOD2), and thioredoxin (Trx) antioxidant protein levels. Using 13C-NMR and immunoblotting, we assayed the status of glycolysis and the pentose phosphate pathway (PPP) in Wt and MitoPPX cells. Our results show that MitoPPX cells display a significant increase in the activity of the PPP and an increase in the protein levels of transaldolase (TAL), which is a crucial component of the non-oxidative phase of the PPP and is involved in the regulation of oxidative stress. In addition, we observed a trend towards increased glycolysis in MitoPPX cells, which corroborates our prior work. Here, for the first time, we show the crucial role played by mitochondrial polyP in the regulation of mammalian redox homeostasis. Moreover, we demonstrate a significant effect of mitochondrial polyP on the regulation of global cellular bioenergetics in these cells.},
}

@article {pmid35453058,
year = {2022},
author = {Coleman, PS and Parlo, RA},
title = {Cancer's camouflage: Microvesicle shedding from cholesterol-rich tumor plasma membranes might blindfold first-responder immunosurveillance strategies.},
journal = {European journal of cell biology},
volume = {101},
number = {2},
pages = {151219},
doi = {10.1016/j.ejcb.2022.151219},
pmid = {35453058},
issn = {1618-1298},
mesh = {Animals ; Cell Membrane/metabolism ; Cholesterol/metabolism ; *Lipid Bilayers ; Mammals/metabolism ; Membrane Lipids/metabolism ; Monitoring, Immunologic ; *Neoplasms ; },
abstract = {Intermediary metabolism of tumors is characterized, in part, by a dysregulation of the cholesterol biosynthesis pathway at its rate-controlling enzyme providing the molecular basis for tumor membranes (mitochondria, plasma membrane) to become enriched with cholesterol (Bloch, 1965; Feo et al., 1975; Brown and Goldstein, 1980; Goldstein and Brown, 1990). Cholesterol enriched tumor mitochondria manifest preferential citrate export, thereby providing a continuous supply of substrate precursor for the tumor's dysregulated cholesterogenesis via a "truncated" Krebs/TCA cycle (Kaplan et al., 1986; Coleman et al., 1997). Proliferating tumors shed elevated amounts of plasma membrane-derived extracellular vesicles (pmEV) compared with normal tissues (van Blitterswijk et al., 1979; Black, 1980). Coordination of these metabolic phenomena in tumors supports the enhanced intercalation of cholesterol within the plasma membrane lipid bilayer's cytoplasmic face, the promotion of outward protrusions from the plasma membrane, and the evolution of cholesterol enriched pmEV. The pmEV shed by tumors possess elevated cholesterol and concentrated cell surface antigen clusters found on the tumor cells themselves (Kim et al., 2002). Upon exfoliation, saturation of the extracellular milieu with tumor-derived pmEV could allow early onset mammalian immune surveillance mechanisms to become "blind" to an evolving cancer and lose their ability to detect and initiate strategies to destroy the cancer. However, a molecular mechanism is lacking that would help explain how cholesterol enrichment of the pmEV inner lipid bilayer might allow the tumor cell to evade the host immune system. We offer a hypothesis, endorsed by published mathematical modeling of biomembrane structure as well as by decades of in vivo data with diverse cancers, that a cholesterol enriched inner bilayer leaflet, coupled with a logarithmic expansion in surface area of shed tumor pmEV load relative to its derivative cancer cell, conspire to force exposure of otherwise unfamiliar membrane integral protein domains as antigenic epitopes to the host's circulating immune surveillance system, allowing the tumor cells to evade destruction. We provide elementary numerical estimations comparing the amount of pmEV shed from tumor versus normal cells.},
}

Animals
Cell Membrane/metabolism
Cholesterol/metabolism
*Lipid Bilayers
Mammals/metabolism
Membrane Lipids/metabolism
Monitoring, Immunologic
*Neoplasms

@article {pmid35446942,
year = {2022},
author = {Gil Del Alcazar, CR and Trinh, A and Aleckovic, M and Rojas Jimenez, E and Harper, NW and Oliphant, MU and Xie, S and Krop, ED and Lulseged, B and Murphy, KC and Keenan, TE and Van Allen, EM and Tolaney, SM and Freeman, GJ and Dillon, DA and Muthuswamy, SK and Polyak, K},
title = {Insights into immune escape during tumor evolution and response to immunotherapy using a rat model of breast cancer.},
journal = {Cancer immunology research},
volume = {},
number = {},
pages = {},
doi = {10.1158/2326-6066.CIR-21-0804},
pmid = {35446942},
issn = {2326-6074},
abstract = {Animal models are critical for the preclinical validation of cancer immunotherapies. Unfortunately, mouse breast cancer models do not faithfully reproduce the molecular subtypes and immune environment of the human disease. In particular, there are no good murine models of estrogen receptor-positive (ER+) breast cancer, the predominant subtype in patients. Here, we show that Nitroso-N-methylurea-induced mammary tumors in outbred Sprague-Dawley rats recapitulate the heterogeneity for mutational profiles, ER expression, and immune evasive mechanisms observed in human breast cancer. We demonstrate the utility of this model for preclinical studies by dissecting mechanisms of response to immunotherapy using combination TGFBR inhibition and PD-L1 blockade. Short-term treatment of early-stage tumors induced durable responses. Gene expression profiling and spatial mapping classified tumors as inflammatory and non-inflammatory, and identified IFN, TCR and BCR signaling, CD74/MHC II, and epithelium-interacting CD8+ T cells as markers of response, whereas the complement system, M2 macrophage phenotype, and translation in mitochondria were associated with resistance. We found that the expression of CD74 correlated with leukocyte fraction and TCR diversity in human breast cancer. We identified a subset of rat ER+ tumors marked by expression of antigen-processing genes that had an active immune environment and responded to treatment. A gene signature characteristic of these tumors predicted disease-free survival in ER+ Luminal A breast cancer patients and overall survival in metastatic breast cancer patients receiving anti-PD-L1 therapy. We demonstrate the usefulness of this preclinical model for immunotherapy and suggest examination to expand immunotherapy to a subset of patients with ER+ disease.},
}

@article {pmid35446419,
year = {2022},
author = {Fields, PD and Waneka, G and Naish, M and Schatz, MC and Henderson, IR and Sloan, DB},
title = {Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome.},
journal = {Genome biology and evolution},
volume = {14},
number = {5},
pages = {},
doi = {10.1093/gbe/evac059},
pmid = {35446419},
issn = {1759-6653},
support = {R01 GM118046/GM/NIGMS NIH HHS/United States ; },
mesh = {*Arabidopsis/genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; In Situ Hybridization, Fluorescence ; Mitochondria/genetics ; Sequence Analysis, DNA ; },
abstract = {Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mitochondrial genome. The primary Arabidopsis nuclear reference genome contains less than half of the numt because of its structural complexity and repetitiveness. Recent data sets generated with improved long-read sequencing technologies (PacBio HiFi) provide an opportunity to finally determine the accurate sequence and structure of this numt. We performed a de novo assembly using sequencing data from recent initiatives to span the Arabidopsis centromeres, producing a gap-free sequence of the Chromosome 2 numt, which is 641 kb in length and has 99.933% nucleotide sequence identity with the actual mitochondrial genome. The numt assembly is consistent with the repetitive structure previously predicted from fiber-based fluorescent in situ hybridization. Nanopore sequencing data indicate that the numt has high levels of cytosine methylation, helping to explain its biased spectrum of nucleotide sequence divergence and supporting previous inferences that it is transcriptionally inactive. The original numt insertion appears to have involved multiple mitochondrial DNA copies with alternative structures that subsequently underwent an additional duplication event within the nuclear genome. This work provides insights into numt evolution, addresses one of the last unresolved regions of the Arabidopsis reference genome, and represents a resource for distinguishing between highly similar numt and mitochondrial sequences in studies of transcription, epigenetic modifications, and de novo mutations.},
}

*Arabidopsis/genetics
Cell Nucleus/genetics
DNA, Mitochondrial/genetics
*Genome, Mitochondrial
In Situ Hybridization, Fluorescence
Mitochondria/genetics
Sequence Analysis, DNA

@article {pmid35444563,
year = {2022},
author = {Mendez-Romero, O and Ricardez-García, C and Castañeda-Tamez, P and Chiquete-Félix, N and Uribe-Carvajal, S},
title = {Thriving in Oxygen While Preventing ROS Overproduction: No Two Systems Are Created Equal.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {874321},
pmid = {35444563},
issn = {1664-042X},
abstract = {From 2.5 to 2.0 billion years ago, atmospheric oxygen concentration [O2] rose thousands of times, leading to the first mass extinction. Reactive Oxygen Species (ROS) produced by the non-catalyzed partial reduction of O2 were highly toxic eliminating many species. Survivors developed different strategies to cope with ROS toxicity. At the same time, using O2 as the final acceptor in respiratory chains increased ATP production manifold. Thus, both O2 and ROS were strong drivers of evolution, as species optimized aerobic metabolism while developing ROS-neutralizing mechanisms. The first line of defense is preventing ROS overproduction and two mechanisms were developed in parallel: 1) Physiological uncoupling systems (PUS), which increase the rate of electron fluxes in respiratory systems. 2) Avoidance of excess [O2]. However, it seems that as avoidance efficiency improved, PUSs became less efficient. PUS includes branched respiratory chains and proton sinks, which may be proton specific, the mitochondrial uncoupling proteins (UCPs) or unspecific, the mitochondrial permeability transition pore (PTP). High [O2] avoidance also involved different strategies: 1) Cell association, as in biofilms or in multi-cellularity allowed gas-permeable organisms (oxyconformers) from bacterial to arthropods to exclude O2. 2) Motility, to migrate from hypoxic niches. 3) Oxyregulator organisms: as early as in fish, and O2-impermeable epithelium excluded all gases and only exact amounts entered through specialized respiratory systems. Here we follow the parallel evolution of PUS and O2-avoidance, PUS became less critical and lost efficiency. In regard, to proton sinks, there is fewer evidence on their evolution, although UCPs have indeed drifted in function while in some species it is not clear whether PTPs exist.},
}

@article {pmid35441886,
year = {2022},
author = {Egusquiza-Alvarez, CA and Robles-Flores, M},
title = {An approach to p32/gC1qR/HABP1: a multifunctional protein with an essential role in cancer.},
journal = {Journal of cancer research and clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {35441886},
issn = {1432-1335},
support = {IV200220//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; IN229420//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; FOSSIS 2017-289600//Consejo Nacional de Ciencia y Tecnología/ ; },
abstract = {P32/gC1qR/HABP1 is a doughnut-shaped acidic protein, highly conserved in eukaryote evolution and ubiquitous in the organism. Although its canonical subcellular localization is the mitochondria, p32 can also be found in the cytosol, nucleus, cytoplasmic membrane, and it can be secreted. Therefore, it is considered a multicompartmental protein. P32 can interact with many physiologically divergent ligands in each subcellular location and modulate their functions. The main ligands are C1q, hyaluronic acid, calreticulin, CD44, integrins, PKC, splicing factor ASF/SF2, and several microbial proteins. Among the functions in which p32 participates are mitochondrial metabolism and dynamics, apoptosis, splicing, immune response, inflammation, and modulates several cell signaling pathways. Notably, p32 is overexpressed in a significant number of epithelial tumors, where its expression level negatively correlates with patient survival. Several studies of gain and/or loss of function in cancer cells have demonstrated that p32 is a promoter of malignant hallmarks such as proliferation, cell survival, chemoresistance, angiogenesis, immunoregulation, migration, invasion, and metastasis. All of this strongly suggests that p32 is a potential diagnostic molecule and therapeutic target in cancer. Indeed, preclinical advances have been made in developing therapeutic strategies using p32 as a target. They include tumor homing peptides, monoclonal antibodies, an intracellular inhibitor, a p32 peptide vaccine, and p32 CAR T cells. These advances are promising and will allow soon to include p32 as part of targeted cancer therapies.},
}

@article {pmid35418016,
year = {2022},
author = {Yuan, F and Lan, X},
title = {Sequencing the organelle genomes of Bougainvillea spectabilis and Mirabilis jalapa (Nyctaginaceae).},
journal = {BMC genomic data},
volume = {23},
number = {1},
pages = {28},
pmid = {35418016},
issn = {2730-6844},
mesh = {*Genome, Chloroplast/genetics ; *Genome, Mitochondrial/genetics ; *Mirabilis/genetics ; Mitochondria/genetics ; *Nyctaginaceae/genetics ; },
abstract = {OBJECTIVES: Mirabilis jalapa L. and Bougainvillea spectabilis are two Mirabilis species known for their ornamental and pharmaceutical values. The organelle genomes are highly conserved with a rapid evolution rate making them suitable for evolutionary studies. Therefore, mitochondrial and chloroplast genomes of B. spectabilis and M. jalapa were sequenced to understand their evolutionary relationship with other angiosperms.

DATA DESCRIPTION: Here, we report the complete mitochondrial genomes of B. spectabilis and M. jalapa (343,746 bp and 267,334 bp, respectively) and chloroplast genomes of B. spectabilis (154,520 bp) and M. jalapa (154,532 bp) obtained from Illumina NovaSeq. The mitochondrial genomes of B. spectabilis and M. jalapa consisted of 70 and 72 genes, respectively. Likewise, the chloroplast genomes of B. spectabilis and M. jalapa contained 131 and 132 genes, respectively. The generated genomic data will be useful for molecular characterization and evolutionary studies.},
}

*Genome, Chloroplast/genetics
*Genome, Mitochondrial/genetics
*Mirabilis/genetics
Mitochondria/genetics
*Nyctaginaceae/genetics

@article {pmid35409414,
year = {2022},
author = {Tsai, HC and Hsieh, CH and Hsu, CW and Hsu, YH and Chien, LF},
title = {Cloning and Organelle Expression of Bamboo Mitochondrial Complex I Subunits Nad1, Nad2, Nad4, and Nad5 in the Yeast Saccharomyces cerevisiae.},
journal = {International journal of molecular sciences},
volume = {23},
number = {7},
pages = {},
pmid = {35409414},
issn = {1422-0067},
support = {NSC96-2313-B-005-030-MY2, NSC96-2752-B-005-013-PAE, MOST110-2221-E-005-078//Ministry of Science and Technology of Taiwan/ ; },
mesh = {Cloning, Molecular ; DNA, Mitochondrial/genetics ; *Electron Transport Complex I/genetics ; Mitochondria/genetics ; Phylogeny ; *Saccharomyces cerevisiae/genetics ; },
abstract = {Mitochondrial respiratory complex I catalyzes electron transfer from NADH to ubiquinone and pumps protons from the matrix into the intermembrane space. In particular, the complex I subunits Nad1, Nad2, Nad4, and Nad5, which are encoded by the nad1, nad2, nad4, and nad5 genes, reside at the mitochondrial inner membrane and possibly function as proton (H+) and ion translocators. To understand the individual functional roles of the Nad1, Nad2, Nad4, and Nad5 subunits in bamboo, each cDNA of these four genes was cloned into the pYES2 vector and expressed in the mitochondria of the yeast Saccharomyces cerevisiae. The mitochondrial targeting peptide mt gene (encoding MT) and the egfp marker gene (encoding enhanced green fluorescent protein, EGFP) were fused at the 5'-terminal and 3'-terminal ends, respectively. The constructed plasmids were then transformed into yeast. RNA transcripts and fusion protein expression were observed in the yeast transformants. Mitochondrial localizations of the MT-Nad1-EGFP, MT-Nad2-EGFP, MT-Nad4-EGFP, and MT-Nad5-EGFP fusion proteins were confirmed by fluorescence microscopy. The ectopically expressed bamboo subunits Nad1, Nad2, Nad4, and Nad5 may function in ion translocation, which was confirmed by growth phenotype assays with the addition of different concentrations of K+, Na+, or H+.},
}

Cloning, Molecular
DNA, Mitochondrial/genetics
*Electron Transport Complex I/genetics
Mitochondria/genetics
Phylogeny
*Saccharomyces cerevisiae/genetics

@article {pmid35409376,
year = {2022},
author = {Kasperski, A},
title = {Life Entrapped in a Network of Atavistic Attractors: How to Find a Rescue.},
journal = {International journal of molecular sciences},
volume = {23},
number = {7},
pages = {},
pmid = {35409376},
issn = {1422-0067},
mesh = {Cell Physiological Phenomena ; Cell Transformation, Neoplastic/metabolism ; *Energy Metabolism ; Humans ; Mitochondria/metabolism ; *Neoplasms/metabolism ; },
abstract = {In view of unified cell bioenergetics, cell bioenergetic problems related to cell overenergization can cause excessive disturbances in current cell fate and, as a result, lead to a change of cell-fate. At the onset of the problem, cell overenergization of multicellular organisms (especially overenergization of mitochondria) is solved inter alia by activation and then stimulation of the reversible Crabtree effect by cells. Unfortunately, this apparently good solution can also lead to a much bigger problem when, despite the activation of the Crabtree effect, cell overenergization persists for a long time. In such a case, cancer transformation, along with the Warburg effect, may occur to further reduce or stop the charging of mitochondria by high-energy molecules. Understanding the phenomena of cancer transformation and cancer development has become a real challenge for humanity. To date, many models have been developed to understand cancer-related mechanisms. Nowadays, combining all these models into one coherent universal model of cancer transformation and development can be considered a new challenge. In this light, the aim of this article is to present such a potentially universal model supported by a proposed new model of cellular functionality evolution. The methods of fighting cancer resulting from unified cell bioenergetics and the two presented models are also considered.},
}

Cell Physiological Phenomena
Cell Transformation, Neoplastic/metabolism
*Energy Metabolism
Humans
Mitochondria/metabolism
*Neoplasms/metabolism

@article {pmid35408834,
year = {2022},
author = {Scaltsoyiannes, V and Corre, N and Waltz, F and Giegé, P},
title = {Types and Functions of Mitoribosome-Specific Ribosomal Proteins across Eukaryotes.},
journal = {International journal of molecular sciences},
volume = {23},
number = {7},
pages = {},
pmid = {35408834},
issn = {1422-0067},
support = {ANR 16 CE11-0024; ANR 20 CE11-0021//Agence Nationale de la Recherche/ ; },
mesh = {Cryoelectron Microscopy ; Eukaryota/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; *Mitochondrial Ribosomes/metabolism ; RNA, Ribosomal/metabolism ; *Ribosomal Proteins/metabolism ; },
abstract = {Mitochondria are key organelles that combine features inherited from their bacterial endosymbiotic ancestor with traits that arose during eukaryote evolution. These energy producing organelles have retained a genome and fully functional gene expression machineries including specific ribosomes. Recent advances in cryo-electron microscopy have enabled the characterization of a fast-growing number of the low abundant membrane-bound mitochondrial ribosomes. Surprisingly, mitoribosomes were found to be extremely diverse both in terms of structure and composition. Still, all of them drastically increased their number of ribosomal proteins. Interestingly, among the more than 130 novel ribosomal proteins identified to date in mitochondria, most of them are composed of a-helices. Many of them belong to the nuclear encoded super family of helical repeat proteins. Here we review the diversity of functions and the mode of action held by the novel mitoribosome proteins and discuss why these proteins that share similar helical folds were independently recruited by mitoribosomes during evolution in independent eukaryote clades.},
}

Cryoelectron Microscopy
Eukaryota/genetics/metabolism
Mitochondrial Proteins/genetics/metabolism
*Mitochondrial Ribosomes/metabolism
RNA, Ribosomal/metabolism
*Ribosomal Proteins/metabolism

@article {pmid35406135,
year = {2022},
author = {Snell, TW and Carberry, J},
title = {Astaxanthin Bioactivity Is Determined by Stereoisomer Composition and Extraction Method.},
journal = {Nutrients},
volume = {14},
number = {7},
pages = {},
pmid = {35406135},
issn = {2072-6643},
mesh = {Animals ; *Antioxidants/pharmacology ; Reactive Oxygen Species/metabolism ; Stereoisomerism ; *Xanthophylls/chemistry/pharmacology ; },
abstract = {Astaxanthin (ASX) is a natural product and one of the most powerful antioxidants known. It has significant effects on the metabolism of many animals, increasing fecundity, egg yolk volume, growth rates, immune responses, and disease resistance. A large part of the bioactivity of ASX is due to its targeting of mitochondria, where it inserts itself into cell membranes. Here, ASX stabilizes membranes and acts as a powerful antioxidant, protecting mitochondria from damage by reactive oxygen species (ROS). ROS are ubiquitous by-products of energy metabolism that must be tightly regulated by cells, lest they bind to and inactivate proteins, DNA and RNA, lipids, and signaling molecules. Most animals cannot synthesize ASX, so they need to acquire it in their diet. ASX is easily thermally denatured during extraction, and its high hydrophobicity limits its bioavailability. Our focus in this review is to contrast the bioactivity of different ASX stereoisomers and how extraction methods can denature ASX, compromising its bioavailability and bioactivity. We discuss the commercial sources of astaxanthin, structure of stereoisomers, relative bioavailability and bioactivity of ASX stereoisomers, mechanisms of ASX bioactivity, evolution of carotenoids, and why mitochondrial targeting makes ASX such an effective antioxidant.},
}

Animals
*Antioxidants/pharmacology
Reactive Oxygen Species/metabolism
Stereoisomerism
*Xanthophylls/chemistry/pharmacology

@article {pmid35397926,
year = {2022},
author = {Zhu, D and Li, X and Tian, Y},
title = {Mitochondrial-to-nuclear communication in aging: an epigenetic perspective.},
journal = {Trends in biochemical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibs.2022.03.008},
pmid = {35397926},
issn = {0968-0004},
abstract = {Age-associated changes in mitochondria are closely involved in aging. Apart from the established roles in bioenergetics and biosynthesis, mitochondria are signaling organelles that communicate their fitness to the nucleus, triggering transcriptional programs to adapt homeostasis stress that is essential for organismal health and aging. Emerging studies revealed that mitochondrial-to-nuclear (mito-nuclear) communication via altered levels of mitochondrial metabolites or stress signals causes various epigenetic changes, facilitating efforts to maintain homeostasis and affect aging. Here, we summarize recent studies on the mechanisms by which mito-nuclear communication modulates epigenomes and their effects on regulating the aging process. Insights into understanding how mitochondrial metabolites serve as prolongevity signals and how aging affects this communication will help us develop interventions to promote longevity and health.},
}

@article {pmid35391231,
year = {2022},
author = {Chen, Z and Liu, F and Li, D and Xu, X},
title = {Four new species of the primitively segmented spider genus Songthela (Mesothelae, Liphistiidae) from Chongqing Municipality, China.},
journal = {Zootaxa},
volume = {5091},
number = {4},
pages = {546-558},
doi = {10.11646/zootaxa.5091.4.2},
pmid = {35391231},
issn = {1175-5334},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Female ; Male ; Mitochondria/genetics ; *Spiders/genetics ; },
abstract = {This paper reports four new species of the primitively segmented spider genus Songthela from Chongqing Municipality, China, based on morphological characters of both males and females: S. jinyun sp. nov., S. longbao sp. nov., S. serriformis sp. nov. and S. wangerbao sp. nov. We also provide the GenBank accession codes of mitochondrial DNA barcode gene, cytochrome c oxidase subunit I (COI), for the holotype of four new species for future identification.},
}

Animals
China
DNA Barcoding, Taxonomic
DNA, Mitochondrial/genetics
Female
Male
Mitochondria/genetics
*Spiders/genetics

@article {pmid35391113,
year = {2022},
author = {Lobon-Rovira, J and Conradie, W and Pinto, PV and Keates, C and Edwards, S and Plessis, AD and Branch, WR},
title = {Systematic revision of Afrogecko ansorgii (Boulenger, 1907) (Sauria: Gekkonidae) from western Angola.},
journal = {Zootaxa},
volume = {5124},
number = {4},
pages = {401-430},
doi = {10.11646/zootaxa.5124.4.1},
pmid = {35391113},
issn = {1175-5334},
mesh = {Angola ; Animals ; Cell Nucleus/genetics ; *Lizards/genetics ; Male ; Mitochondria ; Phylogeny ; },
abstract = {Here we provide the first phylogenetic analysis that include Afrogecko ansorgii and a detailed morphological comparison with other species of leaf-toed geckos. For this purpose, we used two mitochondrial (16S, ND2) and four nuclear (RAG1, RAG2, CMOS, PDC) genes to produce a robust phylogenetic reconstruction. This allowed us to show that A. ansorgii is not related as previously believed to circum-Indian Ocean leaf-toed geckos and is rather more closely related to other Malagasy leaf-toed geckos. Additionally, we explore and compare osteological variation in A. ansorgii skulls through High Resolution X-ray Computed Tomography with previously published material. This allowed us to describe herein a new genus, Bauerius gen. nov., and additionally provide a detailed redescription of the species (including the first description of male material), supplementing the limited original description and type series, which consisted of only two females.},
}

Angola
Animals
Cell Nucleus/genetics
*Lizards/genetics
Male
Mitochondria
Phylogeny

@article {pmid35390830,
year = {2021},
author = {Takano, KT and Gao, JJ and Hu, YG and Li, NN and Yafuso, M and Suwito, A and Repin, R and Pungga, RAS and Meleng, PA and Kaliang, CH and Chong, L and Toda, MJ},
title = {Phylogeny, taxonomy and flower-breeding ecology of the Colocasiomyia cristata species group (Diptera: Drosophilidae), with descriptions of ten new species.},
journal = {Zootaxa},
volume = {5079},
number = {1},
pages = {170},
doi = {10.11646/zootaxa.5079.1.1},
pmid = {35390830},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; *Drosophilidae ; Flowers ; Mitochondria ; Phylogeny ; Plant Breeding ; },
abstract = {The phylogeny of the Colocasiomyia cristata species group is reconstructed as a hypothesis, based on DNA sequences of two mitochondrial and six nuclear genes and 51 morphological characters. The resulting tree splits this species group into two clades, one of which corresponds to the colocasiae subgroup. Therefore, a new species subgroup named as the cristata subgroup is established for the other clade. Within the cristata subgroup, three subclades are recognized and each of them is defined as a species complex: the cristata complex composed of five species (including three new ones: C. kinabaluana sp. nov., C. kotana sp. nov. and C. matthewsi sp. nov.), the sabahana complex of two species (C. sabahana sp. nov. and C. sarawakana sp. nov.), and the xenalocasiae complex of five species (including C. sumatrana sp. nov. and C. leucocasiae sp. nov.). There are, however, three new species (C. ecornuta sp. nov., C. grandis sp. nov. and C. vieti sp. nov.) not assigned to any species complex. In addition, breeding habits are described for four cristata-subgroup species, each of which monopolizes its specific host plant. And, data of host-plant use are compiled for all species of the cristata group from records at various localities in the Oriental and Papuan regions. The evolution of host-plant selection and sharing modes is considered by mapping host-plant genera of each species on the phylogenetic tree resulting from the present study.},
}

Animals
*Diptera
*Drosophilidae
Flowers
Mitochondria
Phylogeny
Plant Breeding

@article {pmid35390639,
year = {2022},
author = {Schneider, A},
title = {Evolution and diversification of mitochondrial protein import systems.},
journal = {Current opinion in cell biology},
volume = {75},
number = {},
pages = {102077},
doi = {10.1016/j.ceb.2022.102077},
pmid = {35390639},
issn = {1879-0410},
mesh = {Animals ; Carrier Proteins/metabolism ; Mammals/metabolism ; Membrane Proteins/metabolism ; Mitochondria/metabolism ; *Mitochondrial Membranes/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Protein Transport/physiology ; Saccharomyces cerevisiae/metabolism ; },
abstract = {More than 95% of mitochondrial proteins are encoded in the nucleus, synthesised in the cytosol and imported into the organelle. The evolution of mitochondrial protein import systems was therefore a prerequisite for the conversion of the α-proteobacterial mitochondrial ancestor into an organelle. Here, I review that the origin of the mitochondrial outer membrane import receptors can best be understood by convergent evolution. Subsequently, I discuss an evolutionary scenario that was proposed to explain the diversification of the inner membrane carrier protein translocases between yeast and mammals. Finally, I illustrate a scenario that can explain how the two specialised inner membrane protein translocase complexes found in most eukaryotes were reduced to a single multifunctional one in trypanosomes.},
}

Animals
Carrier Proteins/metabolism
Mammals/metabolism
Membrane Proteins/metabolism
Mitochondria/metabolism
*Mitochondrial Membranes/metabolism
*Mitochondrial Proteins/genetics/metabolism
Protein Transport/physiology
Saccharomyces cerevisiae/metabolism

@article {pmid35383845,
year = {2022},
author = {Sharbrough, J and Conover, JL and Fernandes Gyorfy, M and Grover, CE and Miller, ER and Wendel, JF and Sloan, DB},
title = {Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.},
journal = {Molecular biology and evolution},
volume = {39},
number = {4},
pages = {},
pmid = {35383845},
issn = {1537-1719},
mesh = {Cell Nucleus/genetics ; Evolution, Molecular ; Genome, Plant ; *Magnoliopsida/genetics ; Plastids/genetics ; Polyploidy ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.},
}

Cell Nucleus/genetics
Evolution, Molecular
Genome, Plant
*Magnoliopsida/genetics
Plastids/genetics
Polyploidy
Ribulose-Bisphosphate Carboxylase/genetics

@article {pmid35377454,
year = {2022},
author = {de Brito Monteiro, L and Silveira Prodonoff, J and Favero de Aguiar, C and Correa-da-Silva, F and Castoldi, A and van Teijlingen Bakker, N and Gastão Davanzo, G and Castelucci, B and Aparecida da Silva Pereira, J and Curtis, J and Büscher, J and Menezes Dos Reis, L and Castro, G and Ribeiro, G and Victor Virgílio-da-Silva, J and Adamoski, D and Martha Gomes Dias, S and Consonni, SR and Donato, J and Pearce, EJ and Câmara, NOS and Moraes-Vieira, PM},
title = {Leptin Signaling Suppression in Macrophages Improves Immunometabolic Outcomes in Obesity.},
journal = {Diabetes},
volume = {},
number = {},
pages = {},
doi = {10.2337/db21-0842},
pmid = {35377454},
issn = {1939-327X},
abstract = {Obesity is a major concern for global healthcare systems. Systemic low-grade inflammation in obesity is a major risk factor for insulin resistance. Leptin is an adipokine secreted by the adipose tissue that functions by controlling food intake, leading to satiety. Leptin levels are increased in obesity. Here, we show that leptin enhances the effects of LPS in macrophages, intensifying the production of cytokines, glycolytic rates and morphological and functional changes in the mitochondria through an mTORC2-dependent, mTORC1-independent mechanism. Leptin also boosts the effects of IL-4 in macrophages, leading to increased oxygen consumption, expression of macrophage markers associated with a tissue repair phenotype, and wound healing. In vivo, hyperleptinemia caused by diet-induced obesity increases the inflammatory response by macrophages. Deletion of leptin receptor and subsequently of leptin signaling in myeloid cells (ObR-/-) is sufficient to improve insulin resistance in obese mice and decrease systemic inflammation. Our results indicate that leptin acts as a systemic nutritional checkpoint to regulate macrophage fitness and contributes to obesity-induced inflammation and insulin resistance. Thus, specific interventions aimed at downstream modulators of leptin signaling may represent new therapeutic targets to treat obesity-induced systemic inflammation.},
}

@article {pmid35360860,
year = {2022},
author = {Bever, BW and Dietz, ZP and Sullins, JA and Montoya, AM and Bergthorsson, U and Katju, V and Estes, S},
title = {Mitonuclear Mismatch is Associated With Increased Male Frequency, Outcrossing, and Male Sperm Size in Experimentally-Evolved C. elegans.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {742272},
pmid = {35360860},
issn = {1664-8021},
abstract = {We provide a partial test of the mitonuclear sex hypothesis with the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. Among facultatively outcrossing lines, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested-nuclear isp-1, mitochondrial cox-1 and ctb-1, and an isp-1 IV; ctb-1M mitonuclear double mutant-and confirmed for a single line set (cox-1) that increased male frequency also resulted in successful outcrossing. We previously found the same result for lines evolved from another nuclear ETC mutant, gas-1. For several lines in the current experiment, however, male frequency declined to wildtype levels (near 0%) in later generations. Male frequency did not change in lines evolved from a wildtype control strain. Additional phenotypic assays of lines evolved from the mitochondrial cox-1 mutant indicated that evolution of high male frequency was accompanied by evolution of increased male sperm size and mating success with tester females, but that it did not translate into increased mating success with coevolved hermaphrodites. Rather, hermaphrodites' self-crossed reproductive fitness increased, consistent with sexually antagonistic coevolution. In accordance with evolutionary theory, males and sexual outcrossing may be most beneficial to populations evolving from a state of low ancestral fitness (gas-1, as previously reported) and less beneficial or deleterious to those evolving from a state of higher ancestral fitness (cox-1). In support of this idea, the obligately outcrossing fog-2 V; cox-1 M lines exhibited no fitness evolution compared to their ancestor, while facultatively outcrossing lines showed slight upward evolution of fitness, and all but one of the obligately selfing xol-1 X; cox-1 M lines evolved substantially increased fitness-even beyond wildtype levels. This work provides a foundation to directly test the effect of reproductive mode on the evolutionary dynamics of mitonuclear genomes, as well as whether compensatory mutations (nuclear or mitochondrial) can rescue populations from mitochondrial dysfunction.},
}

@article {pmid35359176,
year = {2022},
author = {Ceriotti, LF and Gatica-Soria, L and Sanchez-Puerta, MV},
title = {Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes.},
journal = {Plant molecular biology},
volume = {},
number = {},
pages = {},
pmid = {35359176},
issn = {1573-5028},
support = {PICT-2017-0691//Agencia Nacional de Promoción Científica y Tecnológica/ ; 06/A724//Universidad Nacional de Cuyo/ ; },
abstract = {KEY MESSAGE: Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.},
}

@article {pmid35358979,
year = {2022},
author = {Risser, C and Tran Ba Loc, P and Binder-Foucard, F and Fabacher, T and Lefèvre, H and Sauvage, C and Sauleau, EA and Wolff, V},
title = {COVID-19 Impact on Stroke Admissions during France's First Epidemic Peak: An Exhaustive, Nationwide, Observational Study.},
journal = {Cerebrovascular diseases (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-7},
pmid = {35358979},
issn = {1421-9786},
abstract = {INTRODUCTION: The coronavirus disease 2019 (COVID-19) pandemic continues to have great impacts on the care of non-COVID-19 patients. This was especially true during the first epidemic peak in France, which coincided with the national lockdown. The aim of this study was to identify whether a decrease in stroke admissions occurred in spring 2020, by analyzing the evolution of all stroke admissions in France from January 2019 to June 2020.

METHODS: We conducted a nationwide cohort study using the French national database of hospital admissions (Information Systems Medicalization Program) to extract exhaustive data on all hospitalizations in France with at least one stroke diagnosis between January 1, 2019, and June 30, 2020. The primary endpoint was the difference in the slope gradients of stroke hospitalizations between pre-epidemic, epidemic peak, and post-epidemic peak phases. Modeling was carried out using Bayesian techniques.

RESULTS: Stroke hospitalizations dropped from March 10, 2020 (slope gradient: -11.70), and began to rise again from March 22 (slope gradient: 2.090) to May 7. In total, there were 23,873 stroke admissions during the period March-April 2020, compared to 29,263 at the same period in 2019, representing a decrease of 18.42%. The percentage change was -15.63%, -25.19%, -18.62% for ischemic strokes, transient ischemic attacks, and hemorrhagic strokes, respectively.

DISCUSSION/CONCLUSION: Stroke hospitalizations in France experienced a decline during the first lockdown period, which cannot be explained by a sudden change in stroke incidence. This decline is therefore likely to be a direct, or indirect, result of the COVID-19 pandemic.},
}

@article {pmid35353639,
year = {2022},
author = {Lipko, NB},
title = {Photobiomodulation: Evolution and Adaptation.},
journal = {Photobiomodulation, photomedicine, and laser surgery},
volume = {40},
number = {4},
pages = {213-233},
doi = {10.1089/photob.2021.0145},
pmid = {35353639},
issn = {2578-5478},
mesh = {Humans ; Lasers ; *Low-Level Light Therapy/methods ; Mitochondria ; },
abstract = {Photobiomodulation (PBM) can be described as the intentional use of low-power laser or light-emitting diode light in the visible and near-infrared light spectra as a medical treatment to living biological tissues. This article describes the evolution of photochemical reactions on Earth, the mitochondria, and their implications in PBM; the science of light and energy (necessary to understand the mechanisms of PBM); and the clinical science of light as therapeutic medicine. Finally, selected reviews of current treatment protocols and ongoing research regarding the possibilities for the use of PBM in the human body are examined.},
}

Humans
Lasers
*Low-Level Light Therapy/methods
Mitochondria

@article {pmid35351912,
year = {2022},
author = {Lessios, HA and Hendler, G},
title = {Mitochondrial phylogeny of the brittle star genus Ophioderma.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {5304},
pmid = {35351912},
issn = {2045-2322},
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Echinodermata/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Phylogeny ; },
abstract = {We reconstructed the mitochondrial phylogeny of the species of the brittle star genus Ophioderma, using sequences of the Cytochrome Oxidase I gene (COI) to address four questions: (i) Are the species of Ophioderma described on morphological evidence reflected in mitochondrial genealogy? (ii) Which species separated from which? (iii) When did speciation events occur? (iv) What is the rate of COI evolution in ophiuroids? We found that most of the 22 described species we sampled coincide with monophyletic clusters of COI sequences, but there are exceptions, most notably in the eastern Pacific, in which three undescribed species were indicated. The COI phylogeny lacks resolution in the deeper nodes, but it does show that there are four species pairs, the members of which are found on either side of the central American Isthmus. Two pairs with a genetic distance of ~ 4% between Atlantic and Pacific members were probably split during the final stages of Isthmus completion roughly 3 million years ago. The rate of divergence provided by these pairs allowed the calibration of a relaxed molecular clock. Estimated dates of divergence indicate that the lineages leading to extant species coalesce at times much older than congeneric species in other classes of echinoderms, suggesting that low extinction rates may be one of the reasons that ophiuroids are species-rich. The mean rate of COI substitution in Ophioderma is three times slower than that of echinoids. Conclusions of previous mitochondrial DNA studies of ophiuroids that relied on echinoid calibrations to determine divergence times need to be revised.},
}

Animals
DNA, Mitochondrial/genetics
*Echinodermata/genetics
*Evolution, Molecular
Mitochondria/genetics
Phylogeny

@article {pmid35348760,
year = {2022},
author = {Azuma, T and Pánek, T and Tice, AK and Kayama, M and Kobayashi, M and Miyashita, H and Suzaki, T and Yabuki, A and Brown, MW and Kamikawa, R},
title = {An Enigmatic Stramenopile Sheds Light on Early Evolution in Ochrophyta Plastid Organellogenesis.},
journal = {Molecular biology and evolution},
volume = {39},
number = {4},
pages = {},
pmid = {35348760},
issn = {1537-1719},
mesh = {Ecosystem ; Evolution, Molecular ; *Genome, Plastid ; Phylogeny ; Plants/genetics ; Plastids/genetics ; *Stramenopiles/genetics ; },
abstract = {Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (nonphotosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRSs) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened before the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host-plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions.},
}

Ecosystem
Evolution, Molecular
*Genome, Plastid
Phylogeny
Plants/genetics
Plastids/genetics
*Stramenopiles/genetics

@article {pmid35342946,
year = {2022},
author = {Senarat, S and Kettratad, J and Pairohakul, S and Ampawong, S and Huggins, BP and Coleman, MM and Kaneko, G},
title = {An update on the evolutionary origin of aglomerular kidney with structural and ultrastructural descriptions of the kidney in three fish species.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.15045},
pmid = {35342946},
issn = {1095-8649},
support = {//Johnson Foundation/ ; //Chulalongkorn University/ ; },
abstract = {The kidney of fish contains numerous nephrons, each of which is divided into the renal corpuscle and renal tubules. This glomerular structure is the filtration unit of the nephron and is important for the kidney function, but it has been reported that the renal corpuscle was lost in at least four independent linages of fish (i.e., aglomerular kidney). In this study, the authors newly described renal structures for three species by histological and ultrastructural observations: two aglomerular kidneys from a seahorse Hippocampus barbouri and a toadfish Allenbatrachus grunniens and a glomerular kidney from a snake eel Pisodonophis boro. The renal development of H. barbouri was also described during 1-35 days after birth. In all species tested, the anterior kidney was comprised of haematopoietic tissues and a few renal tubules, whereas the posterior kidney contained more renal tubules. Although the glomerular structure was present in P. boro, light microscopic observations identified no glomeruli in the kidney of H. barbouri and A. grunniens. Ultrastructurally, abundant deep basal infoldings with mitochondria in the renal tubules were observed in A. grunniens compared to H. barbouri and P. boro, suggesting the possible role of basal infoldings in maintaining the osmotic balance. By integrating the results from the three species and comprehensive literature search, the authors further showed that 56 species have been reported to be aglomerular, and that the aglomerular kidney has evolved at least eight times in bony fishes.},
}

@article {pmid35340599,
year = {2022},
author = {Hickey, T and Devaux, J and Rajagopal, V and Power, A and Crossman, D},
title = {Paradoxes of Hymenoptera flight muscles, extreme machines.},
journal = {Biophysical reviews},
volume = {14},
number = {1},
pages = {403-412},
pmid = {35340599},
issn = {1867-2450},
abstract = {In the Carboniferous, insects evolved flight. Intense selection drove for high performance and approximately 100 million years later, Hymenoptera (bees, wasps and ants) emerged. Some species had proportionately small wings, with apparently impossible aerodynamic challenges including a need for high frequency flight muscles (FMs), powered exclusively off aerobic pathways and resulting in extreme aerobic capacities. Modern insect FMs are the most refined and form large dense blocks that occupy 90% of the thorax. These can beat wings at 200 to 230 Hz, more than double that achieved by standard neuromuscular systems. To do so, rapid repolarisation was circumvented through evolution of asynchronous stimulation, stretch activation, elastic recoil and a paradoxically slow Ca2+ reuptake. While the latter conserves ATP, considerable ATP is demanded at the myofibrils. FMs have diminished sarcoplasmic volumes, and ATP is produced solely by mitochondria, which pack myocytes to maximal limits and have very dense cristae. Gaseous oxygen is supplied directly to mitochondria. While FMs appear to be optimised for function, several unusual paradoxes remain. FMs lack any significant equivalent to the creatine kinase shuttle, and myofibrils are twice as wide as those of within cardiomyocytes. The mitochondrial electron transport systems also release large amounts of reactive oxygen species (ROS) and respiratory complexes do not appear to be present at any exceptional level. Given that the loss of the creatine kinase shuttle and elevated ROS impairs heart function, we question how do FM shuttle adenylates at high rates and tolerate oxidative stress conditions that occur in diseased hearts?},
}

@article {pmid35333655,
year = {2022},
author = {Jackson, TD and Crameri, JJ and Muellner-Wong, L and Frazier, AE and Palmer, CS and Formosa, LE and Hock, DH and Fujihara, KM and Stait, T and Sharpe, AJ and Thorburn, DR and Ryan, MT and Stroud, DA and Stojanovski, D},
title = {Sideroflexin 4 is a complex I assembly factor that interacts with the MCIA complex and is required for the assembly of the ND2 module.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {13},
pages = {e2115566119},
pmid = {35333655},
issn = {1091-6490},
mesh = {Adenosine Triphosphate/metabolism ; *Electron Transport Complex I/metabolism ; Humans ; Membrane Proteins ; Mitochondria/genetics/metabolism ; *Mitochondrial Diseases/genetics ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; },
abstract = {SignificanceMitochondria are double-membraned eukaryotic organelles that house the proteins required for generation of ATP, the energy currency of cells. ATP generation within mitochondria is performed by five multisubunit complexes (complexes I to V), the assembly of which is an intricate process. Mutations in subunits of these complexes, or the suite of proteins that help them assemble, lead to a severe multisystem condition called mitochondrial disease. We show that SFXN4, a protein that causes mitochondrial disease when mutated, assists with the assembly of complex I. This finding explains why mutations in SFXN4 cause mitochondrial disease and is surprising because SFXN4 belongs to a family of amino acid transporter proteins, suggesting that it has undergone a dramatic shift in function through evolution.},
}

Adenosine Triphosphate/metabolism
*Electron Transport Complex I/metabolism
Humans
Membrane Proteins
Mitochondria/genetics/metabolism
*Mitochondrial Diseases/genetics
Mitochondrial Proteins/genetics/metabolism
Mutation

@article {pmid35325186,
year = {2022},
author = {Ye, Z and Zhao, C and Raborn, RT and Lin, M and Wei, W and Hao, Y and Lynch, M},
title = {Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa.},
journal = {Molecular biology and evolution},
volume = {39},
number = {4},
pages = {},
pmid = {35325186},
issn = {1537-1719},
support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; R35-GM122566-01/GF/NIH HHS/United States ; IOS-1922914//NSF EDGE/ ; },
mesh = {Animals ; DNA, Mitochondrial/genetics ; Daphnia/genetics ; *Genome, Mitochondrial ; Heteroplasmy ; *Pulicaria/genetics ; Recombination, Genetic ; },
abstract = {Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.},
}

Animals
DNA, Mitochondrial/genetics
Daphnia/genetics
*Genome, Mitochondrial
Heteroplasmy
*Pulicaria/genetics
Recombination, Genetic

@article {pmid35322502,
year = {2022},
author = {Cantoni, D and Osborne, A and Taib, N and Thompson, G and Martín-Escolano, R and Kazana, E and Edrich, E and Brown, IR and Gribaldo, S and Gourlay, CW and Tsaousis, AD},
title = {Localization and functional characterization of the alternative oxidase in Naegleria.},
journal = {The Journal of eukaryotic microbiology},
volume = {},
number = {},
pages = {e12908},
doi = {10.1111/jeu.12908},
pmid = {35322502},
issn = {1550-7408},
support = {//Alfonso Martín Escudero Foundation/ ; //Gordon and Betty Moore Foundation/ ; BB/M009971/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {The alternative oxidase (AOX) is a protein involved in supporting enzymatic reactions of the Krebs cycle in instances when the canonical (cytochrome-mediated) respiratory chain has been inhibited, while allowing for the maintenance of cell growth and necessary metabolic processes for survival. Among eukaryotes, alternative oxidases have dispersed distribution and are found in plants, fungi, and protists, including Naegleria ssp. Naegleria species are free-living unicellular amoeboflagellates and include the pathogenic species of N. fowleri, the so-called "brain-eating amoeba." Using a multidisciplinary approach, we aimed to understand the evolution, localization, and function of AOX and the role that plays in Naegleria's biology. Our analyses suggest that AOX was present in last common ancestor of the genus and structure prediction showed that all functional residues are also present in Naegleria species. Using cellular and biochemical techniques, we also functionally characterize N. gruberi's AOX in its mitochondria, and we demonstrate that its inactivation affects its proliferation. Consequently, we discuss the benefits of the presence of this protein in Naegleria species, along with its potential pathogenicity role in N. fowleri. We predict that our findings will spearhead new explorations to understand the cell biology, metabolism, and evolution of Naegleria and other free-living relatives.},
}

@article {pmid35318703,
year = {2022},
author = {Hammond, M and Dorrell, RG and Speijer, D and Lukeš, J},
title = {Eukaryotic cellular intricacies shape mitochondrial proteomic complexity.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {44},
number = {5},
pages = {e2100258},
doi = {10.1002/bies.202100258},
pmid = {35318703},
issn = {1521-1878},
support = {LL1601//ERC CZ/ ; 20-071856S//Czech Grant Agency/ ; 21-09283S//Czech Grant Agency/ ; 16_019/0000759//ERD Fund/ ; },
mesh = {Biological Evolution ; Eukaryota/physiology ; *Eukaryotic Cells/metabolism ; Mitochondria/metabolism ; Organelles/metabolism ; Phylogeny ; *Proteomics ; },
abstract = {Mitochondria have been fundamental to the eco-physiological success of eukaryotes since the last eukaryotic common ancestor (LECA). They contribute essential functions to eukaryotic cells, above and beyond classical respiration. Mitochondria interact with, and complement, metabolic pathways occurring in other organelles, notably diversifying the chloroplast metabolism of photosynthetic organisms. Here, we integrate existing literature to investigate how mitochondrial metabolism varies across the landscape of eukaryotic evolution. We illustrate the mitochondrial remodelling and proteomic changes undergone in conjunction with major evolutionary transitions. We explore how the mitochondrial complexity of the LECA has been remodelled in specific groups to support subsequent evolutionary transitions, such as the acquisition of chloroplasts in photosynthetic species and the emergence of multicellularity. We highlight the versatile and crucial roles played by mitochondria during eukaryotic evolution, extending from its huge contribution to the development of the LECA itself to the dynamic evolution of individual eukaryote groups, reflecting both their current ecologies and evolutionary histories.},
}

Biological Evolution
Eukaryota/physiology
*Eukaryotic Cells/metabolism
Mitochondria/metabolism
Organelles/metabolism
Phylogeny
*Proteomics

@article {pmid35307029,
year = {2022},
author = {Smith, AJ and Advani, J and Brock, DC and Nellissery, J and Gumerson, J and Dong, L and Aravind, L and Kennedy, B and Swaroop, A},
title = {GATD3A, a mitochondrial deglycase with evolutionary origins from gammaproteobacteria, restricts the formation of advanced glycation end products.},
journal = {BMC biology},
volume = {20},
number = {1},
pages = {68},
pmid = {35307029},
issn = {1741-7007},
support = {ZIAEY000450/EY/NEI NIH HHS/United States ; ZIAEY000546/EY/NEI NIH HHS/United States ; },
mesh = {Animals ; *Gammaproteobacteria/metabolism ; *Glycation End Products, Advanced/metabolism ; Mammals ; Mice ; Mitochondrial Proteins/genetics ; Protein Deglycase DJ-1/metabolism ; },
abstract = {BACKGROUND: Functional complexity of the eukaryotic mitochondrial proteome is augmented by independent gene acquisition from bacteria since its endosymbiotic origins. Mammalian homologs of many ancestral mitochondrial proteins have uncharacterized catalytic activities. Recent forward genetic approaches attributed functions to proteins in established metabolic pathways, thereby limiting the possibility of identifying novel biology relevant to human disease. We undertook a bottom-up biochemistry approach to discern evolutionarily conserved mitochondrial proteins with catalytic potential.

RESULTS: Here, we identify a Parkinson-associated DJ-1/PARK7-like protein-glutamine amidotransferase-like class 1 domain-containing 3A (GATD3A), with bacterial evolutionary affinities although not from alphaproteobacteria. We demonstrate that GATD3A localizes to the mitochondrial matrix and functions as a deglycase. Through its amidolysis domain, GATD3A removes non-enzymatic chemical modifications produced during the Maillard reaction between dicarbonyls and amines of nucleotides and amino acids. GATD3A interacts with factors involved in mitochondrial mRNA processing and translation, suggestive of a role in maintaining integrity of important biomolecules through its deglycase activity. The loss of GATD3A in mice is associated with accumulation of advanced glycation end products (AGEs) and altered mitochondrial dynamics.

CONCLUSIONS: An evolutionary perspective helped us prioritize a previously uncharacterized but predicted mitochondrial protein GATD3A, which mediates the removal of early glycation intermediates. GATD3A restricts the formation of AGEs in mitochondria and is a relevant target for diseases where AGE deposition is a pathological hallmark.},
}

Animals
*Gammaproteobacteria/metabolism
*Glycation End Products, Advanced/metabolism
Mammals
Mice
Mitochondrial Proteins/genetics
Protein Deglycase DJ-1/metabolism

@article {pmid35306886,
year = {2022},
author = {Zluvova, J and Kubat, Z and Hobza, R and Janousek, B},
title = {Adaptive changes of the autosomal part of the genome in a dioecious clade of Silene.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {377},
number = {1850},
pages = {20210228},
pmid = {35306886},
issn = {1471-2970},
mesh = {Chromosomes, Plant ; Evolution, Molecular ; *Magnoliopsida ; Sex Chromosomes ; *Silene/genetics ; },
abstract = {The genus Silene brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in Silene subgenus Silene and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (ca 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy, as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the formation of general conclusions. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.},
}

Chromosomes, Plant
Evolution, Molecular
*Magnoliopsida
Sex Chromosomes
*Silene/genetics

@article {pmid35294555,
year = {2022},
author = {Karmin, M and Flores, R and Saag, L and Hudjashov, G and Brucato, N and Crenna-Darusallam, C and Larena, M and Endicott, PL and Jakobsson, M and Lansing, JS and Sudoyo, H and Leavesley, M and Metspalu, M and Ricaut, FX and Cox, MP},
title = {Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages.},
journal = {Molecular biology and evolution},
volume = {39},
number = {3},
pages = {},
pmid = {35294555},
issn = {1537-1719},
mesh = {Asia, Southeastern ; *Asians ; *DNA, Mitochondrial/genetics ; Humans ; Male ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Island Southeast Asia (ISEA) and Oceania host one of the world's richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region's male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region's initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40-25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world's least understood regions.},
}

Asia, Southeastern
*Asians
*DNA, Mitochondrial/genetics
Humans
Male
Mitochondria/genetics
Phylogeny

@article {pmid35289381,
year = {2022},
author = {Drechsel, V and Schneebauer, G and Sandbichler, AM and Fiechtner, B and Pelster, B},
title = {Oxygen consumption and acid secretion in isolated gas gland cells of the European eel Anguilla anguilla.},
journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology},
volume = {},
number = {},
pages = {},
pmid = {35289381},
issn = {1432-136X},
support = {I2984-B25//Österreichische Forschungsförderungsgesellschaft/ ; },
abstract = {Swimbladder gas gland cells are known to produce lactic acid required for the acidification of swimbladder blood and decreasing the oxygen carrying capacity of swimbladder blood, i.e., the onset of the Root effect. Gas gland cells have also been shown to metabolize glucose via the pentose phosphate shunt, but the role of the pentose phosphate shunt for acid secretion has not yet been evaluated. Similarly, aerobic metabolism of gas gland cells has been largely neglected so far. In the present study, we therefore simultaneously assessed the role of glycolysis and of the pentose phosphate shunt for acid secretion and recorded oxygen consumption of isolated swimbladder gas gland cells of the European eel. Presence of glucose was essential for acid secretion, and at glucose concentrations of about 1.5 mmol l-1 acid secretion of gas gland cells reached a maximum, indicating that glucose concentrations in swimbladder blood should not be limiting acid production and secretion under physiological conditions. The data revealed that most of the acid was produced in the glycolytic pathway, but a significant fraction was also contributed by the pentose phosphate shunt. Addition of glucose to gas gland cells incubated in a glucose-free medium resulted in a reduction of oxygen uptake. Inhibition of mitochondrial respiration significantly reduced oxygen consumption, but a fraction of mitochondria-independent respiration remained in presence of rotenone and antimycin A. In the presence of glucose, application of either iodo-acetate inhibiting glycolysis or 6-AN inhibiting the pentose phosphate shunt did not significantly affect oxygen uptake, indicating an independent regulation of oxidative phosphorylation and of acid production. Inhibition of the muscarinic acetylcholine receptor caused a slight elevation in acid secretion, while forskolin caused a concentration-dependent reduction in acid secretion, indicating muscarinic and c-AMP-dependent control of acid secretion in gas gland cells.},
}

@article {pmid35279439,
year = {2022},
author = {Zhou, B and Qi, D and Liu, S and Qi, H and Wang, Y and Zhao, K and Tian, F},
title = {Physiological, morphological and transcriptomic responses of Tibetan naked carps (Gymnocypris przewalskii) to salinity variations.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {42},
number = {},
pages = {100982},
doi = {10.1016/j.cbd.2022.100982},
pmid = {35279439},
issn = {1878-0407},
mesh = {Animals ; *Carps ; *Cyprinidae/genetics ; Gills ; Lakes ; Salinity ; Tibet ; Transcriptome ; },
abstract = {Gymnocypris przewalskii is a native cyprinid fish that dwells in the Lake Qinghai with salinity of 12-13‰. It migrates annually to the freshwater rivers for spawning, experiencing the significant changes in salinity. In the present study, we performed the physiological, morphological and transcriptomic analyses to understand the osmoregulation in G. przewalskii. The physiological assay showed that the osmotic pressure of G. przewalskii was almost isosmotic to the brackish lake water. The low salinity reduced its ionic concentrations and osmotic pressure. The plasticity of gill microstructure was linked to the salinity variations, including the presence of mucus and intact tight junctions in brackish water and the development of the mitochondria-rich cells and the loosened tight junctions in freshwater. RNA-seq analysis identified 1926 differentially expressed genes, including 710 and 1216 down- and up-regulated genes in freshwater, which were enriched in ion transport, cell-cell adhesion, and mucus secretion. Genes in ion uptake were activated in low salinity, and mucus pathways and tight junction showed the higher transcription in brackish water. The isosmoticity between the body fluid and the environment suggested G. przewalskii was in the metabolic-saving condition in the brackish water. The decreased salinity disrupted this balance, which activated the ion uptake in freshwater to maintain osmotic homeostasis. The gill remodeling was involved in this process through the development of the mitochondria-rich cells to enhance ion uptake. The current finding provided insights into the potential mechanisms of G. przewalskii to cope with salinity alteration.},
}

Animals
*Carps
*Cyprinidae/genetics
Gills
Lakes
Salinity
Tibet
Transcriptome

@article {pmid35277964,
year = {2022},
author = {Lam, SM and Li, J and Sun, H and Mao, W and Lu, Z and Zhao, Q and Han, C and Gong, X and Jiang, B and Chua, GH and Zhao, Z and Meng, F and Shui, G},
title = {Quantitative Lipidomics and Spatial MS-Imaging Uncovered Neurological and Systemic Lipid Metabolic Pathways Underlying Troglomorphic Adaptations in Cave-Dwelling Fish.},
journal = {Molecular biology and evolution},
volume = {39},
number = {4},
pages = {},
pmid = {35277964},
issn = {1537-1719},
mesh = {Animals ; Biological Evolution ; Caves ; *Characidae/genetics ; *Cyprinidae ; *Demyelinating Diseases ; Lipidomics ; Metabolic Networks and Pathways ; Phospholipids ; },
abstract = {Sinocyclocheilus represents a rare, freshwater teleost genus endemic to China that comprises the river-dwelling surface fish and the cave-dwelling cavefish. Using a combinatorial approach of quantitative lipidomics and mass-spectrometry imaging (MSI), we demonstrated that neural compartmentalization of lipid distribution and lipid metabolism is associated with the evolution of troglomorphic traits in Sinocyclocheilus. Attenuated docosahexaenoic acid (DHA) biosynthesis via the Δ4 desaturase pathway led to reductions in DHA-phospholipids in cavefish cerebellum. Instead, cavefish accumulates arachidonic acid-phospholipids that may disfavor retinotectal arbor growth. Importantly, MSI of sulfatides coupled with immunostaining of myelin basic protein and transmission electron microscopy images of hindbrain axons revealed demyelination in cavefish raphe serotonergic neurons. Demyelination in cavefish parallels the loss of neuroplasticity governing social behavior such as aggressive dominance. Outside the brain, quantitative lipidomics and qRT-PCR revealed systemic reductions in membrane esterified DHAs in the liver, attributed to suppression of genes along the Sprecher pathway (elovl2, elovl5, and acox1). Development of fatty livers was observed in cavefish; likely mediated by an impeded mobilization of storage lipids, as evident in the diminished expressions of pnpla2, lipea, lipeb, dagla, and mgll; and suppressed β-oxidation of fatty acyls via both mitochondria and peroxisomes as reflected in the reduced expressions of cpt1ab, hadhaa, cpt2, decr1, and acox1. These neurological and systemic metabolic adaptations serve to reduce energy expenditure, forming the basis of recessive evolution that eliminates nonessential morphological and behavioral traits and giving cavefish a selective advantage to thrive in caves where proper resource allocation becomes a major determinant of survival.},
}

Animals
Biological Evolution
Caves
*Characidae/genetics
*Cyprinidae
*Demyelinating Diseases
Lipidomics
Metabolic Networks and Pathways
Phospholipids

@article {pmid35272287,
year = {2022},
author = {Ho, KM and Morgan, DJR},
title = {The Proximal Tubule as the Pathogenic and Therapeutic Target in Acute Kidney Injury.},
journal = {Nephron},
volume = {},
number = {},
pages = {1-9},
doi = {10.1159/000522341},
pmid = {35272287},
issn = {2235-3186},
abstract = {BACKGROUND: In 2004, the term acute kidney injury (AKI) was introduced with the intention of broadening our understanding of rapid declines in renal function and to replace the historical terms of acute renal failure and acute tubular necrosis (ATN). Despite this evolution in terminology, the mechanisms of AKI have stayed largely elusive with the pathophysiological concepts of ATN remaining the mainstay in our understanding of AKI.

SUMMARY: The proximal tubule (PT), having the highest mitochondrial content in the kidney and relying heavily on oxidative phosphorylation to generate ATP, is vulnerable to ischaemic insults and mitochondrial dysfunction. Histologically, pathological changes in the PT are more consistent than changes to the glomeruli or the loop of Henle in AKI. Physiologically, activation of tubuloglomerular feedback due to PT dysfunction leads to an increase in preglomerular afferent arteriole resistance and a reduction in glomerular filtration. Pharmacologically, frusemide - a drug commonly used in the setting of oliguric AKI - is actively secreted by the PT and its diuretic effect is compromised by its failure to be secreted into the urine and thus be delivered to its site of action at the loop of Henle in AKI. Increases in the urinary, but not plasma biomarkers, of PT injury within 1 h of shock suggest that the PT as the initiation pathogenic target of AKI.

KEY MESSAGE: Therapeutic agents targeting specifically the PT epithelial cells, in particular its mitochondria - including amino acid ergothioneine and superoxide scavenger MitoTEMPO - show great promises in ameliorating AKI.},
}

@article {pmid35259985,
year = {2022},
author = {Perez, M and Breusing, C and Angers, B and Beinart, RA and Won, YJ and Young, CR},
title = {Divergent paths in the evolutionary history of maternally transmitted clam symbionts.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1970},
pages = {20212137},
pmid = {35259985},
issn = {1471-2954},
mesh = {Animals ; Bacteria/genetics ; *Bivalvia/genetics ; *Gammaproteobacteria/genetics ; Genome Size ; Genome, Bacterial ; Phylogeny ; Symbiosis/genetics ; },
abstract = {Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017-1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.},
}

Animals
Bacteria/genetics
*Bivalvia/genetics
*Gammaproteobacteria/genetics
Genome Size
Genome, Bacterial
Phylogeny
Symbiosis/genetics

@article {pmid35258392,
year = {2022},
author = {Magalhaes-Novais, S and Blecha, J and Naraine, R and Mikesova, J and Abaffy, P and Pecinova, A and Milosevic, M and Bohuslavova, R and Prochazka, J and Khan, S and Novotna, E and Sindelka, R and Machan, R and Dewerchin, M and Vlcak, E and Kalucka, J and Stemberkova Hubackova, S and Benda, A and Goveia, J and Mracek, T and Barinka, C and Carmeliet, P and Neuzil, J and Rohlenova, K and Rohlena, J},
title = {Mitochondrial respiration supports autophagy to provide stress resistance during quiescence.},
journal = {Autophagy},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/15548627.2022.2038898},
pmid = {35258392},
issn = {1554-8635},
abstract = {Mitochondrial oxidative phosphorylation (OXPHOS) generates ATP, but OXPHOS also supports biosynthesis during proliferation. In contrast, the role of OXPHOS during quiescence, beyond ATP production, is not well understood. Using mouse models of inducible OXPHOS deficiency in all cell types or specifically in the vascular endothelium that negligibly relies on OXPHOS-derived ATP, we show that selectively during quiescence OXPHOS provides oxidative stress resistance by supporting macroautophagy/autophagy. Mechanistically, OXPHOS constitutively generates low levels of endogenous ROS that induce autophagy via attenuation of ATG4B activity, which provides protection from ROS insult. Physiologically, the OXPHOS-autophagy system (i) protects healthy tissue from toxicity of ROS-based anticancer therapy, and (ii) provides ROS resistance in the endothelium, ameliorating systemic LPS-induced inflammation as well as inflammatory bowel disease. Hence, cells acquired mitochondria during evolution to profit from oxidative metabolism, but also built in an autophagy-based ROS-induced protective mechanism to guard against oxidative stress associated with OXPHOS function during quiescence.Abbreviations: AMPK: AMP-activated protein kinase; AOX: alternative oxidase; Baf A: bafilomycin A1; CI, respiratory complexes I; DCF-DA: 2',7'-dichlordihydrofluorescein diacetate; DHE: dihydroethidium; DSS: dextran sodium sulfate; ΔΨmi: mitochondrial inner membrane potential; EdU: 5-ethynyl-2'-deoxyuridine; ETC: electron transport chain; FA: formaldehyde; HUVEC; human umbilical cord endothelial cells; IBD: inflammatory bowel disease; LC3B: microtubule associated protein 1 light chain 3 beta; LPS: lipopolysaccharide; MEFs: mouse embryonic fibroblasts; MTORC1: mechanistic target of rapamycin kinase complex 1; mtDNA: mitochondrial DNA; NAC: N-acetyl cysteine; OXPHOS: oxidative phosphorylation; PCs: proliferating cells; PE: phosphatidylethanolamine; PEITC: phenethyl isothiocyanate; QCs: quiescent cells; ROS: reactive oxygen species; PLA2: phospholipase A2, WB: western blot.},
}

@article {pmid35255175,
year = {2022},
author = {Treidel, LA and Quintanilla Ramirez, GS and Chung, DJ and Menze, MA and Vázquez-Medina, JP and Williams, CM},
title = {Selection on dispersal drives evolution of metabolic capacities for energy production in female wing-polymorphic sand field crickets, Gryllus firmus.},
journal = {Journal of evolutionary biology},
volume = {35},
number = {4},
pages = {599-609},
doi = {10.1111/jeb.13996},
pmid = {35255175},
issn = {1420-9101},
support = {//Society for Integrative and Comparative Biology (SICB)/ ; //University of California Berkeley/ ; //Hellman Family Foundation/ ; },
mesh = {Animals ; Energy Metabolism ; Female ; *Gryllidae/physiology ; Phenotype ; Wings, Animal/metabolism ; },
abstract = {Life history and metabolism covary, but the mechanisms and individual traits responsible for these linkages remain unresolved. Dispersal capability is a critical component of life history that is constrained by metabolic capacities for energy production. Conflicting relationships between metabolism and life histories may be explained by accounting for variation in dispersal and maximal metabolic rates. We used female wing-polymorphic sand field crickets, Gryllus firmus, selected either for long wings (LW, flight-capable) or short wings (SW, flightless) to test the hypothesis that selection on dispersal capability drives the evolution of metabolic capacities. While resting metabolic rates were similar, long-winged crickets reached higher maximal metabolic rates than short-winged crickets, resulting in improved running performance. We further provided insight into the mechanisms responsible for covariation between life history and metabolism by comparing mitochondrial content of tissues involved in powering locomotion and assessing the function of mitochondria isolated from long- and short-winged crickets. Our results demonstrated that larger metabolic capacities in long-winged crickets were underpinned by increases in mitochondrial content of dorsoventral flight muscle and enhanced bioenergetic capacities of mitochondria within the fat body, a tissue responsible for fuel storage and mobilization. Thus, selection on flight capability correlates with increases in maximal, but not resting metabolic rates, through modifications of tissues powering locomotion at the cellular and organelle levels. This allows organisms to meet high energetic demands of activity for life history. Dispersal capability should therefore explicitly be considered as a potential factor driving the evolution of metabolic capacities.},
}

Animals
Energy Metabolism
Female
*Gryllidae/physiology
Phenotype
Wings, Animal/metabolism

@article {pmid35248958,
year = {2022},
author = {Rodríguez-Martín, D and Murciano, A and Herráiz, M and de Francisco, P and Amaro, F and Gutiérrez, JC and Martín-González, A and Díaz, S},
title = {Arsenate and arsenite differential toxicity in Tetrahymena thermophila.},
journal = {Journal of hazardous materials},
volume = {431},
number = {},
pages = {128532},
doi = {10.1016/j.jhazmat.2022.128532},
pmid = {35248958},
issn = {1873-3336},
mesh = {Animals ; Arsenates/metabolism/toxicity ; *Arsenic/metabolism/toxicity ; *Arsenites/metabolism/toxicity ; Metallothionein ; *Tetrahymena thermophila/genetics ; },
abstract = {A comparative analysis of toxicities of both arsenic forms (arsenite and arsenate) in the model eukaryotic microorganism Tetrahymena thermophila (ciliate protozoa) has shown the presence of various detoxification mechanisms and cellular effects comparable to those of animal cells under arsenic stress. In the wild type strain SB1969 arsenate is almost 2.5 times more toxic than arsenite. According to the concentration addition model used in binary metallic mixtures their toxicities show an additive effect. Using fluorescent assays and flow cytometry, it has been detected that As(V) generates elevated levels of ROS/RNS compared to As(III). Both produce the same levels of superoxide anion, but As(V) also causes greater increases in hydrogen peroxide and peroxynitrite. The mitochondrial membrane potential is affected by both As(V) and As(III), and electron microscopy has also revealed that mitochondria are the main target of both arsenic ionic forms. Fusion/fission and swelling mitochondrial and mitophagy, together with macroautophagy, vacuolization and mucocyst extruction are mainly associated to As(V) toxicity, while As(III) induces an extensive lipid metabolism dysfunction (adipotropic effect). Quantitative RT-PCR analysis of some genes encoding antioxidant proteins or enzymes has shown that glutathione and thioredoxin metabolisms are involved in the response to arsenic stress. Likewise, the function of metallothioneins seems to be crucial in arsenic detoxification processes, after using both metallothionein knockout and knockdown strains and cells overexpressing metallothionein genes from this ciliate. The analysis of the differential toxicity of As(III) and As(V) shown in this study provides cytological and molecular tools to be used as biomarkers for each of the two arsenic ionic forms.},
}

Animals
Arsenates/metabolism/toxicity
*Arsenic/metabolism/toxicity
*Arsenites/metabolism/toxicity
Metallothionein
*Tetrahymena thermophila/genetics

@article {pmid35247316,
year = {2022},
author = {Moorthy, BT and Jiang, C and Patel, DM and Ban, Y and O'Shea, CR and Kumar, A and Yuan, T and Birnbaum, MD and Gomes, AV and Chen, X and Fontanesi, F and Lampidis, TJ and Barrientos, A and Zhang, F},
title = {The evolutionarily conserved arginyltransferase 1 mediates a pVHL-independent oxygen-sensing pathway in mammalian cells.},
journal = {Developmental cell},
volume = {57},
number = {5},
pages = {654-669.e9},
pmid = {35247316},
issn = {1878-1551},
support = {R01 GM138557/GM/NIGMS NIH HHS/United States ; R35 GM118141/GM/NIGMS NIH HHS/United States ; },
mesh = {*Aminoacyltransferases/genetics/metabolism ; Animals ; Humans ; Mammals/metabolism ; *Oxygen ; Phylogeny ; Proteolysis ; },
abstract = {The response to oxygen availability is a fundamental process concerning metabolism and survival/death in all mitochondria-containing eukaryotes. However, the known oxygen-sensing mechanism in mammalian cells depends on pVHL, which is only found among metazoans but not in other species. Here, we present an alternative oxygen-sensing pathway regulated by ATE1, an enzyme ubiquitously conserved in eukaryotes that influences protein degradation by posttranslational arginylation. We report that ATE1 centrally controls the hypoxic response and glycolysis in mammalian cells by preferentially arginylating HIF1α that is hydroxylated by PHD in the presence of oxygen. Furthermore, the degradation of arginylated HIF1α is independent of pVHL E3 ubiquitin ligase but dependent on the UBR family proteins. Bioinformatic analysis of human tumor data reveals that the ATE1/UBR and pVHL pathways jointly regulate oxygen sensing in a transcription-independent manner with different tissue specificities. Phylogenetic analysis suggests that eukaryotic ATE1 likely evolved during mitochondrial domestication, much earlier than pVHL.},
}

*Aminoacyltransferases/genetics/metabolism
Animals
Humans
Mammals/metabolism
*Oxygen
Phylogeny
Proteolysis

@article {pmid35243551,
year = {2022},
author = {Choi, H and Lee, K and Kim, D and Kim, S and Lee, JH},
title = {The implication of holocytochrome c synthase mutation in Korean familial hypoplastic amelogenesis imperfecta.},
journal = {Clinical oral investigations},
volume = {},
number = {},
pages = {},
pmid = {35243551},
issn = {1436-3771},
support = {2021R1F1A104718511//National Research Foundation of Korea/ ; 2020R1A6A1A03047902//National Research Foundation of Korea/ ; 2021R1A2B5B01001903//National Research Foundation of Korea/ ; },
abstract = {OBJECTIVES: This study aimed to comprehensively characterise genetic variants of amelogenesis imperfecta in a single Korean family through whole-exome sequencing and bioinformatics analysis.

MATERIAL AND METHODS: Thirty-one individuals of a Korean family, 9 of whom were affected and 22 unaffected by amelogenesis imperfecta, were enrolled. Whole-exome sequencing was performed on 12 saliva samples, including samples from 8 affected and 4 unaffected individuals. The possible candidate genes associated with the disease were screened by segregation analysis and variant filtering. In silico mutation impact analysis was then performed on the filtered variants based on sequence conservation and protein structure.

RESULTS: Whole-exome sequencing data revealed an X-linked dominant, heterozygous genomic missense mutation in the mitochondrial gene holocytochrome c synthase (HCCS). We also found that HCCS is potentially related to the role of mitochondria in amelogenesis. The HCCS variant was expected to be deleterious in both evolution-based and large population-based analyses. Further, the variant was predicted to have a negative effect on catalytic function of HCCS by in silico analysis of protein structure. In addition, HCCS had significant association with amelogenesis in literature mining analysis.

CONCLUSIONS: These findings suggest new evidence for the relationship between amelogenesis and mitochondria function, which could be implicated in the pathogenesis of amelogenesis imperfecta.

CLINICAL RELEVANCE: The discovery of HCCS mutations and a deeper understanding of the pathogenesis of amelogenesis imperfecta could lead to finding solutions for the fundamental treatment of this disease. Furthermore, it enables dental practitioners to establish predictable prosthetic treatment plans at an early stage by early detection of amelogenesis imperfecta through personalised medicine.},
}

@article {pmid35242350,
year = {2022},
author = {Pearman, WS and Wells, SJ and Dale, J and Silander, OK and Freed, NE},
title = {Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod.},
journal = {Royal Society open science},
volume = {9},
number = {1},
pages = {211550},
pmid = {35242350},
issn = {2054-5703},
abstract = {Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda, species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod, Isocladus armatus. Data from long- and short-read DNA sequencing suggest that I. armatus has two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda. Additionally, we find that an asymmetrical site previously observed across many species within Isopoda is absent in I. armatus, but confirm the presence of two asymmetrical sites recently reported in two other isopod species.},
}

@article {pmid35231030,
year = {2022},
author = {Güngör, B and Flohr, T and Garg, SG and Herrmann, JM},
title = {The ER membrane complex (EMC) can functionally replace the Oxa1 insertase in mitochondria.},
journal = {PLoS biology},
volume = {20},
number = {3},
pages = {e3001380},
pmid = {35231030},
issn = {1545-7885},
mesh = {Amino Acid Sequence ; Cell Respiration/genetics ; Electron Transport Complex IV/genetics/*metabolism ; Endoplasmic Reticulum/*metabolism ; Membrane Proteins/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Mitochondrial Proton-Translocating ATPases/genetics/metabolism ; Mutation ; Nuclear Proteins/genetics/*metabolism ; Phylogeny ; Protein Biosynthesis/genetics ; Protein Transport/genetics ; Saccharomyces cerevisiae/genetics/growth & development/*metabolism ; Saccharomyces cerevisiae Proteins/classification/genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Two multisubunit protein complexes for membrane protein insertion were recently identified in the endoplasmic reticulum (ER): the guided entry of tail anchor proteins (GET) complex and ER membrane complex (EMC). The structures of both of their hydrophobic core subunits, which are required for the insertion reaction, revealed an overall similarity to the YidC/Oxa1/Alb3 family members found in bacteria, mitochondria, and chloroplasts. This suggests that these membrane insertion machineries all share a common ancestry. To test whether these ER proteins can functionally replace Oxa1 in yeast mitochondria, we generated strains that express mitochondria-targeted Get2-Get1 and Emc6-Emc3 fusion proteins in Oxa1 deletion mutants. Interestingly, the Emc6-Emc3 fusion was able to complement an Δoxa1 mutant and restored its respiratory competence. The Emc6-Emc3 fusion promoted the insertion of the mitochondrially encoded protein Cox2, as well as of nuclear encoded inner membrane proteins, although was not able to facilitate the assembly of the Atp9 ring. Our observations indicate that protein insertion into the ER is functionally conserved to the insertion mechanism in bacteria and mitochondria and adheres to similar topological principles.},
}

Amino Acid Sequence
Cell Respiration/genetics
Electron Transport Complex IV/genetics/*metabolism
Endoplasmic Reticulum/*metabolism
Membrane Proteins/genetics/*metabolism
Mitochondria/genetics/*metabolism
Mitochondrial Proteins/genetics/*metabolism
Mitochondrial Proton-Translocating ATPases/genetics/metabolism
Mutation
Nuclear Proteins/genetics/*metabolism
Phylogeny
Protein Biosynthesis/genetics
Protein Transport/genetics
Saccharomyces cerevisiae/genetics/growth & development/*metabolism
Saccharomyces cerevisiae Proteins/classification/genetics/metabolism
Sequence Homology, Amino Acid

@article {pmid35222958,
year = {2022},
author = {Zárate, D and Lima, TG and Poole, JD and Calfee, E and Burton, RS and Kohn, JR},
title = {Admixture in Africanized honey bees (Apis mellifera) from Panamá to San Diego, California (U.S.A.).},
journal = {Ecology and evolution},
volume = {12},
number = {2},
pages = {e8580},
pmid = {35222958},
issn = {2045-7758},
abstract = {The Africanized honey bee (AHB) is a New World amalgamation of several subspecies of the western honey bee (Apis mellifera), a diverse taxon historically grouped into four major biogeographic lineages: A (African), M (Western European), C (Eastern European), and O (Middle Eastern). In 1956, accidental release of experimentally bred "Africanized" hybrids from a research apiary in Sao Paulo, Brazil initiated a hybrid species expansion that now extends from northern Argentina to northern California (U.S.A.). Here, we assess nuclear admixture and mitochondrial ancestry in 60 bees from four countries (Panamá; Costa Rica, Mexico; U.S.A) across this expansive range to assess ancestry of AHB several decades following initial introduction and test the prediction that African ancestry decreases with increasing latitude. We find that AHB nuclear genomes from Central America and Mexico have predominately African genomes (76%-89%) with smaller contributions from Western and Eastern European lineages. Similarly, nearly all honey bees from Central America and Mexico possess mitochondrial ancestry from the African lineage with few individuals having European mitochondria. In contrast, AHB from San Diego (CA) shows markedly lower African ancestry (38%) with substantial genomic contributions from all four major honey bee lineages and mitochondrial ancestry from all four clades as well. Genetic diversity measures from all New World populations equal or exceed those of ancestral populations. Interestingly, the feral honey bee population of San Diego emerges as a reservoir of diverse admixture and high genetic diversity, making it a potentially rich source of genetic material for honey bee breeding.},
}

@article {pmid35219813,
year = {2022},
author = {Xia, L and Cheng, C and Zhao, X and He, X and Yu, X and Li, J and Wang, Y and Chen, J},
title = {Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops.},
journal = {Gene},
volume = {823},
number = {},
pages = {146342},
doi = {10.1016/j.gene.2022.146342},
pmid = {35219813},
issn = {1879-0038},
mesh = {Crops, Agricultural/genetics ; Cucumis/*genetics ; Cucurbitaceae/classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Mitochondrial ; Genomics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The mitochondria ofCucumis genus contain several intriguing features such as paternal inheritance and three-ring genome structure. However, the evolutionary relationships of mitochondria inCucumisremain elusive. Here, we assembled the mitochondrial genome ofC. hystrixand performed a comparative genomic analysis with other crops inthe Cucurbitaceae. The mitochondrial genome ofC. hystrixhas three circular-mapping chromosomes of lengths 1,113,461 bp, 110,683 bp, and 92,288 bp, which contain 73 genes including 38 protein-coding genes, 31tRNAgenes, and 4rRNAgenes. Repeat sequences, RNA editing, and horizontal gene transfer events were identified. The results of phylogenetic analyses, collinearity and gene clusters revealed thatC. hystrixis closer toC. sativus than to C. melo. Meanwhile, wedemonstrated mitochondrial paternal inheritance inC. hystrixbymolecular markers. In comparison with other cucurbitcrops, wefound amarker foridentification of germplasm resources ofCucumis. Collectively, our findings provide a tool to help clarify the paternal lineage within that genus in the evolution of Cucumis.},
}

Crops, Agricultural/genetics
Cucumis/*genetics
Cucurbitaceae/classification/*genetics
Evolution, Molecular
Gene Transfer, Horizontal
Genome Size
*Genome, Mitochondrial
Genomics
High-Throughput Nucleotide Sequencing
Mitochondria/*genetics
Phylogeny
Sequence Analysis, DNA/*methods

@article {pmid35215562,
year = {2022},
author = {Levy, D and Giannini, M and Oulehri, W and Riou, M and Marcot, C and Pizzimenti, M and Debrut, L and Charloux, A and Geny, B and Meyer, A},
title = {Long Term Follow-Up of Sarcopenia and Malnutrition after Hospitalization for COVID-19 in Conventional or Intensive Care Units.},
journal = {Nutrients},
volume = {14},
number = {4},
pages = {},
pmid = {35215562},
issn = {2072-6643},
mesh = {Aged ; *COVID-19/complications ; Follow-Up Studies ; Hand Strength ; Hospitalization ; Humans ; Intensive Care Units ; *Malnutrition/diagnosis/epidemiology ; Quality of Life ; SARS-CoV-2 ; *Sarcopenia/diagnosis/epidemiology/etiology ; },
abstract = {BACKGROUND: The post-COVID-19 condition, defined as COVID-19-related signs and symptoms lasting at least 2 months and persisting more than 3 months after infection, appears now as a public health issue in terms of frequency and quality of life alterations. Nevertheless, few data are available concerning long term evolution of malnutrition and sarcopenia, which deserve further attention.

METHOD: Sarcopenia was investigated prospectively, together with weight evolution, at admission and at 3 and 6 months after hospital discharge in 139 COVID-19 patients, using the European Working Group on Sarcopenia in Older People (EWGSOP2) criteria, associating both decreased muscle strength and muscle mass, assessed, respectively, with hand dynamometer and dual-energy X-ray absorptiometry.

RESULTS: Of the 139 patients, 22 presented with sarcopenia at 3 months; intensive care units (ICU) length of stay was the sole factor associated with sarcopenia after multivariate analysis. Although the entire group did not demonstrate significant weight change, weight decreased significantly in the sarcopenia group (Five and eight patients, showing, respectively, >5 or >10% weight decrease). Interestingly, at 6 months, 16 of the 22 patients recovered from sarcopenia and their weight returned toward baseline values.

CONCLUSIONS: Sarcopenia and malnutrition are frequently observed in patients hospitalized for COVID-19, even 3 months after infection occurrence, but can largely be reversed at 6 months after discharge. Enhanced patient care is needed in sarcopenic patients, particularly during long stays in an ICU.},
}

Aged
*COVID-19/complications
Follow-Up Studies
Hand Strength
Hospitalization
Humans
Intensive Care Units
*Malnutrition/diagnosis/epidemiology
Quality of Life
SARS-CoV-2
*Sarcopenia/diagnosis/epidemiology/etiology

@article {pmid35208909,
year = {2022},
author = {Cevallos, MA and Degli Esposti, M},
title = {New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient.},
journal = {Microorganisms},
volume = {10},
number = {2},
pages = {},
pmid = {35208909},
issn = {2076-2607},
abstract = {We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new 'oxycline' clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments.},
}

@article {pmid35207539,
year = {2022},
author = {Lei, L and Burton, ZF},
title = {"Superwobbling" and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {35207539},
issn = {2075-1729},
abstract = {The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code. We posit that EF-Tu, the closing mechanism of the 30S ribosomal subunit, methylation of wobble U34 at the 5-carbon and suppression of wobbling at the tRNA-36 position were partly redundant and overlapping functions that coevolved to establish the code. The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). "Superwobbling" or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome. In superwobbling, unmodified wobble tRNA-U34 can recognize all four codon wobble bases (A, G, C and U), allowing a single unmodified tRNA-U34 to read a 4-codon box. During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base. TRNA-37 modifications help maintain the translation frame during elongation.},
}

@article {pmid35205291,
year = {2022},
author = {Zhang, BQ and Song, XP and Zhang, XQ and Huang, YX and Liang, YJ and Zhou, S and Yang, CF and Yang, LT and Huang, X and Li, YR},
title = {Differential Gene Expression Analysis of SoCBL Family Calcineurin B-like Proteins: Potential Involvement in Sugarcane Cold Stress.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205291},
issn = {2073-4425},
mesh = {Calcineurin/genetics ; Cold-Shock Response/genetics ; Gene Expression ; Phylogeny ; *Saccharum/genetics ; },
abstract = {Sugarcan e is a major crop for sugar and biofuel production and is cultivated in tropical and subtropical areas worldwide. Sugarcane growth is constrained because of winter's low-temperature stress, and cold resistance is an important limitation in sugarcane growth enhancement. Therefore, in this study, we identified a gene involved in the low-temperature stress response of sugarcane. Calcineurin B-like (CBL) protein is a calcium signal receptor involved in the cold stress response. Five sugarcane CBL genes were cloned, sequenced, and named SoCBL1, SoCBL3, SoCBL5, SoCBL6, and SoCBL9. The protein sequences of these genes were analyzed. The calculated molecular weight of these proteins was 24.5, 25.9, 25.2, 25.6, and 26.3 kD, respectively. Subcellular localization analysis revealed that SoCBL1, SoCBL3, SoCBL6, and SoCBL9 were situated in the cytoplasm, while SoCBL5 was present in mitochondria. Secondary structure analysis showed that these five CBL proteins had similar secondary structures. Conserved domain analysis displayed that each sugarcane CBL protein contained three conserved EF domains. According to the self-expanding values of the phylogenetic tree, the CBL gene family was divided into four groups. The CBL1 and CBL9 genes were classified into one group, illustrating that these two genes might possess a similar function. The expression analysis of the SoCBL gene under low temperatures showed that SoCBL3 and SoCBL5 were affected significantly, while SoCBL1 and SoCBL9 were less affected. These results demonstrate that the CBL genes in sugarcane have similar characteristics and present differences in genetic diversity and gene expression response to low temperatures. Therefore, these genes might be novel candidates for fighting cold stress in sugarcane.},
}

Calcineurin/genetics
Cold-Shock Response/genetics
Gene Expression
Phylogeny
*Saccharum/genetics

@article {pmid35205149,
year = {2022},
author = {Zhu, Y},
title = {Gap Junction-Dependent and -Independent Functions of Connexin43 in Biology.},
journal = {Biology},
volume = {11},
number = {2},
pages = {},
pmid = {35205149},
issn = {2079-7737},
abstract = {For the first time in animal evolution, the emergence of gap junctions allowed direct exchanges of cellular substances for communication between two cells. Innexin proteins constituted primordial gap junctions until the connexin protein emerged in deuterostomes and took over the gap junction function. After hundreds of millions of years of gene duplication, the connexin gene family now comprises 21 members in the human genome. Notably, GJA1, which encodes the Connexin43 protein, is one of the most widely expressed and commonly studied connexin genes. The loss of Gja1 in mice leads to swelling and a blockage of the right ventricular outflow tract and death of the embryos at birth, suggesting a vital role of Connexin43 gap junction in heart development. Since then, the importance of Connexin43-mediated gap junction function has been constantly expanded to other types of cells. Other than forming gap junctions, Connexin43 can also form hemichannels to release or uptake small molecules from the environment or even mediate many physiological processes in a gap junction-independent manner on plasma membranes. Surprisingly, Connexin43 also localizes to mitochondria in the cell, playing important roles in mitochondrial potassium import and respiration. At the molecular level, Connexin43 mRNA and protein are processed with very distinct mechanisms to yield carboxyl-terminal fragments with different sizes, which have their unique subcellular localization and distinct biological activities. Due to many exciting advancements in Connexin43 research, this review aims to start with a brief introduction of Connexin43 and then focuses on updating our knowledge of its gap junction-independent functions.},
}

@article {pmid35199854,
year = {2022},
author = {Lane, N},
title = {Ursula Mittwoch: Pioneering geneticist who solved the riddle of sexes.},
journal = {Annals of human genetics},
volume = {86},
number = {3},
pages = {153-158},
doi = {10.1111/ahg.12461},
pmid = {35199854},
issn = {1469-1809},
}

@article {pmid35199143,
year = {2022},
author = {Helmstetter, N and Chybowska, AD and Delaney, C and Da Silva Dantas, A and Gifford, H and Wacker, T and Munro, C and Warris, A and Jones, B and Cuomo, CA and Wilson, D and Ramage, G and Farrer, RA},
title = {Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets.},
journal = {Genetics},
volume = {221},
number = {1},
pages = {},
pmid = {35199143},
issn = {1943-2631},
support = {215239/Z/19/Z//Wellcome Trust Seed Award/ ; 812969//European Union's Horizon 2020, Innovative Training Network: FunHoMic/ ; MR/N006364/2//Medical Research Council Centre for Medical Mycology/ ; 214317/Z/18/Z//Wellcome Trust Senior Research Fellowship/ ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Adult ; Antifungal Agents/pharmacology ; *Candida glabrata/genetics ; Drug Resistance, Fungal/genetics ; Genetics, Population ; *Genome, Mitochondrial ; Humans ; Virulence/genetics ; },
abstract = {Candida glabrata is the second most common etiological cause of worldwide systemic candidiasis in adult patients. Genome analysis of 68 isolates from 8 hospitals across Scotland, together with 83 global isolates, revealed insights into the population genetics and evolution of C. glabrata. Clinical isolates of C. glabrata from across Scotland are highly genetically diverse, including at least 19 separate sequence types that have been recovered previously in globally diverse locations, and 1 newly discovered sequence type. Several sequence types had evidence for ancestral recombination, suggesting transmission between distinct geographical regions has coincided with genetic exchange arising in new clades. Three isolates were missing MATα1, potentially representing a second mating type. Signatures of positive selection were identified in every sequence type including enrichment for epithelial adhesins thought to facilitate fungal adhesin to human epithelial cells. In patent microevolution was identified from 7 sets of recurrent cases of candidiasis, revealing an enrichment for nonsynonymous and frameshift indels in cell surface proteins. Microevolution within patients also affected epithelial adhesins genes, and several genes involved in drug resistance including the ergosterol synthesis gene ERG4 and the echinocandin target FKS1/2, the latter coinciding with a marked drop in fluconazole minimum inhibitory concentration. In addition to nuclear genome diversity, the C. glabrata mitochondrial genome was particularly diverse, with reduced conserved sequence and conserved protein-encoding genes in all nonreference ST15 isolates. Together, this study highlights the genetic diversity within the C. glabrata population that may impact virulence and drug resistance, and 2 major mechanisms generating this diversity: microevolution and genetic exchange/recombination.},
}

Adult
Antifungal Agents/pharmacology
*Candida glabrata/genetics
Drug Resistance, Fungal/genetics
Genetics, Population
*Genome, Mitochondrial
Humans
Virulence/genetics

@article {pmid35197365,
year = {2022},
author = {Łabędzka-Dmoch, K and Rażew, M and Gapińska, M and Piątkowski, J and Kolondra, A and Salmonowicz, H and Wenda, JM and Nowotny, M and Golik, P},
title = {The Pet127 protein is a mitochondrial 5'-to-3' exoribonuclease from the PD-(D/E)XK superfamily involved in RNA maturation and intron degradation in yeasts.},
journal = {RNA (New York, N.Y.)},
volume = {28},
number = {5},
pages = {711-728},
pmid = {35197365},
issn = {1469-9001},
mesh = {Candida albicans ; *Exoribonucleases/genetics ; Fungal Proteins/genetics/metabolism ; Introns/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; *RNA ; },
abstract = {Pet127 is a mitochondrial protein found in multiple eukaryotic lineages, but absent from several taxa, including plants and animals. Distant homology suggests that it belongs to the divergent PD-(D/E)XK superfamily which includes various nucleases and related proteins. Earlier yeast genetics experiments suggest that it plays a nonessential role in RNA degradation and 5' end processing. Our phylogenetic analysis suggests that it is a primordial eukaryotic invention that was retained in diverse groups, and independently lost several times in the evolution of other organisms. We demonstrate for the first time that the fungal Pet127 protein in vitro is a processive 5'-to-3' exoribonuclease capable of digesting various substrates in a sequence nonspecific manner. Mutations in conserved residues essential in the PD-(D/E)XK superfamily active site abolish the activity of Pet127. Deletion of the PET127 gene in the pathogenic yeast Candida albicans results in a moderate increase in the steady-state levels of several transcripts and in accumulation of unspliced precursors and intronic sequences of three introns. Mutations in the active site residues result in a phenotype identical to that of the deletant, confirming that the exoribonuclease activity is related to the physiological role of the Pet127 protein. Pet127 activity is, however, not essential for maintaining the mitochondrial respiratory activity in C. albicans.},
}

Candida albicans
*Exoribonucleases/genetics
Fungal Proteins/genetics/metabolism
Introns/genetics
Mitochondrial Proteins/genetics
Phylogeny
*RNA

@article {pmid35191499,
year = {2022},
author = {Zamudio-Ochoa, A and Morozov, YI and Sarfallah, A and Anikin, M and Temiakov, D},
title = {Mechanisms of mitochondrial promoter recognition in humans and other mammalian species.},
journal = {Nucleic acids research},
volume = {50},
number = {5},
pages = {2765-2781},
pmid = {35191499},
issn = {1362-4962},
support = {R35 GM131832/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; DNA, Mitochondrial/genetics ; DNA-Directed RNA Polymerases/metabolism ; Humans ; Mammals/genetics/metabolism ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/metabolism ; Transcription Factors/chemistry/genetics ; Transcription Initiation Site ; *Transcription, Genetic ; },
abstract = {Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for > 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of the DNA in the initiation complex and permitted investigation of the sequence-specific protein-DNA interactions. We determined the molecular basis of promoter recognition by mtRNAP and TFB2M, which cooperatively recognize bases near TSS in a species-specific manner. Our findings reveal a role of mitochondrial transcription machinery in mitonuclear coevolution and speciation.},
}

Animals
DNA, Mitochondrial/genetics
DNA-Directed RNA Polymerases/metabolism
Humans
Mammals/genetics/metabolism
Mitochondria/enzymology/*genetics
Mitochondrial Proteins/metabolism
Transcription Factors/chemistry/genetics
Transcription Initiation Site
*Transcription, Genetic

@article {pmid35189365,
year = {2022},
author = {Hawlitschek, O and Ortiz, EM and Noori, S and Webster, KC and Husemann, M and Pereira, RJ},
title = {Transcriptomic data reveals nuclear-mitochondrial discordance in Gomphocerinae grasshoppers (Insecta: Orthoptera: Acrididae).},
journal = {Molecular phylogenetics and evolution},
volume = {170},
number = {},
pages = {107439},
doi = {10.1016/j.ympev.2022.107439},
pmid = {35189365},
issn = {1095-9513},
mesh = {Animals ; *Grasshoppers/genetics ; Hybridization, Genetic ; Mitochondria/genetics ; *Orthoptera/genetics ; Phylogeny ; Transcriptome ; },
abstract = {The phylogeny of many groups of Orthoptera remains poorly understood. Previous phylogenetic studies largely restricted to few mitochondrial markers found many species in the grasshopper subfamily Gomphocerinae to be para- or polyphyletic, presumably because of incomplete lineage sorting and ongoing hybridization between putatively young lineages. Resolving the phylogeny of the Chorthippus biguttulus species complex is important because many morphologically cryptic species occupy overlapping ranges across Eurasia and serve important ecological functions. We investigated whether multispecies coalescent analysis of 540 genes generated by transcriptome sequencing could resolve the phylogeny of the C. biguttulus complex and related Gomphocerinae species. Our divergence time estimates confirm that Gomphocerinae is a very young radiation, with an age estimated at 1.38 (2.35-0.77) mya for the C. biguttulus complex. Our estimated topology based on complete mitogenomes recovered some species as para- or polyphyletic. In contrast, the multispecies coalescent based on nuclear genes retrieved all species as monophyletic clusters, corroborating most taxonomic hypotheses. Our results underline the importance of using nuclear multispecies coalescent methods for studying young radiations and highlight the need of further taxonomic revision in Gomphocerinae grasshoppers.},
}

Animals
*Grasshoppers/genetics
Hybridization, Genetic
Mitochondria/genetics
*Orthoptera/genetics
Phylogeny
Transcriptome

@article {pmid35188099,
year = {2022},
author = {De La Rossa, A and Laporte, MH and Astori, S and Marissal, T and Montessuit, S and Sheshadri, P and Ramos-Fernández, E and Mendez, P and Khani, A and Quairiaux, C and Taylor, EB and Rutter, J and Nunes, JM and Carleton, A and Duchen, MR and Sandi, C and Martinou, JC},
title = {Paradoxical neuronal hyperexcitability in a mouse model of mitochondrial pyruvate import deficiency.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35188099},
issn = {2050-084X},
mesh = {3-Hydroxybutyric Acid/pharmacology ; Animals ; Anion Transport Proteins/genetics/*metabolism ; Biological Transport ; Calcium/physiology ; Gene Expression Regulation/drug effects ; Homeostasis/drug effects/physiology ; Ketone Bodies ; Mice ; Mice, Knockout ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Monocarboxylic Acid Transporters/genetics/*metabolism ; Neurons/drug effects/metabolism ; Oxidation-Reduction ; Pentylenetetrazole/toxicity ; Phosphorylation ; Pyruvic Acid/*metabolism ; Seizures/chemically induced ; Tamoxifen/pharmacology ; },
abstract = {Neuronal excitation imposes a high demand of ATP in neurons. Most of the ATP derives primarily from pyruvate-mediated oxidative phosphorylation, a process that relies on import of pyruvate into mitochondria occuring exclusively via the mitochondrial pyruvate carrier (MPC). To investigate whether deficient oxidative phosphorylation impacts neuron excitability, we generated a mouse strain carrying a conditional deletion of MPC1, an essential subunit of the MPC, specifically in adult glutamatergic neurons. We found that, despite decreased levels of oxidative phosphorylation and decreased mitochondrial membrane potential in these excitatory neurons, mice were normal at rest. Surprisingly, in response to mild inhibition of GABA mediated synaptic activity, they rapidly developed severe seizures and died, whereas under similar conditions the behavior of control mice remained unchanged. We report that neurons with a deficient MPC were intrinsically hyperexcitable as a consequence of impaired calcium homeostasis, which reduced M-type potassium channel activity. Provision of ketone bodies restored energy status, calcium homeostasis and M-channel activity and attenuated seizures in animals fed a ketogenic diet. Our results provide an explanation for the seizures that frequently accompany a large number of neuropathologies, including cerebral ischemia and diverse mitochondriopathies, in which neurons experience an energy deficit.},
}

3-Hydroxybutyric Acid/pharmacology
Animals
Anion Transport Proteins/genetics/*metabolism
Biological Transport
Calcium/physiology
Gene Expression Regulation/drug effects
Homeostasis/drug effects/physiology
Ketone Bodies
Mice
Mice, Knockout
Mitochondria/*metabolism
Mitochondrial Membrane Transport Proteins/genetics/*metabolism
Monocarboxylic Acid Transporters/genetics/*metabolism
Neurons/drug effects/metabolism
Oxidation-Reduction
Pentylenetetrazole/toxicity
Phosphorylation
Pyruvic Acid/*metabolism
Seizures/chemically induced
Tamoxifen/pharmacology

@article {pmid35175958,
year = {2022},
author = {Buja, LM},
title = {PATHOBIOLOGY OF MYOCARDIAL ISCHEMIA AND REPERFUSION INJURY: MODELS, MODES, MOLECULAR MECHANISMS, MODULATION AND CLINICAL APPLICATIONS.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000000440},
pmid = {35175958},
issn = {1538-4683},
abstract = {This review presents an integrated approach to the analysis of myocardial ischemia and reperfusion injury and the modulating influence of myocardial conditioning during the evolution of acute myocardial infarction (AMI) and other clinical settings. Experimental studies have involved a spectrum of in vitro, ex vivo and in vivo models, and guidelines have been developed for the conduct of rigorous pre-clinical studies and for the identification of various forms of cell injury and death in evolving AMI. AMI in vivo is dominated by oncosis (cell injury with swelling) leading to necroptosis and final necrosis of ischemic cardiomyocytes (CMCs), without or with contraction band formation. Early after coronary occlusion, reperfusion salvages a significant amount of ischemic myocardium in the subepicardium while reperfusion injury contributes up to 50% of the final subendocardial infarct. AMI progression is mediated by damage (or danger)-associated molecular patterns (DAMPs), also known as alarmins, which activate pattern recognition receptors (PRRs) and initiate the inflammatory response. In pre-clinical studies, lethal reperfusion injury can largely be prevented with preconditioning or postconditioning by pharmacologic or physical means due to effects on both the CMC and microvasculature. Conditioning involves triggers, cytosolic mediators, and intracellular effectors. Mitochondria have a central role in the maintenance and loss of viability of CMCs. Reperfusion of severely ischemic myocardium leads to sustained opening of the mitochondrial permeability transition pore (MPTP). Once the MPTP is opened, the mitochondrial membrane potential (ΔΨm) is rapidly lost and energy production ceases. Conditioning blocks the sustained opening of the MPTP. Translation of conditioning strategies to the clinical management of patients has been challenging. The status of translation of experimental findings to approaches to modulate and ameliorate ischemic and reperfusion injury is discussed for the clinical settings of acute coronary syndromes (ACS) treated with percutaneous interventions (PCI) and cardiac preservation during open heart surgery and cardiac transplantation.},
}

@article {pmid35174241,
year = {2021},
author = {Ahmad, HI and Afzal, G and Iqbal, MN and Iqbal, MA and Shokrollahi, B and Mansoor, MK and Chen, J},
title = {Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals.},
journal = {Frontiers in veterinary science},
volume = {8},
number = {},
pages = {814765},
pmid = {35174241},
issn = {2297-1769},
abstract = {The regulated production of filamentous protein complexes is essential in many biological processes and provides a new paradigm in signal transmission. The mitochondrial antiviral signaling protein (MAVS) is a critical signaling hub in innate immunity that is activated when a receptor induces a shift in the globular caspase activation and recruitment domain of MAVS into helical superstructures (filaments). It is of interest whether adaptive evolution affects the proteins involved in innate immunity. Here, we explore and confer the role of selection and diversification on mitochondrial antiviral signaling protein in mammalian species. We obtined the MAVS proteins of mammalian species and examined their differences in evolutionary patterns. We discovered evidence for these proteins being subjected to substantial positive selection. We demonstrate that immune system proteins, particularly those encoding recognition proteins, develop under positive selection using codon-based probability methods. Positively chosen regions within recognition proteins cluster in domains involved in microorganism recognition, implying that molecular interactions between hosts and pathogens may promote adaptive evolution in the mammalian immune systems. These significant variations in MAVS development in mammalian species highlights the involvement of MAVS in innate immunity. Our findings highlight the significance of accounting for how non-synonymous alterations affect structure and function when employing sequence-level studies to determine and quantify positive selection.},
}

@article {pmid35163839,
year = {2022},
author = {Davoudi, M and Chen, J and Lou, Q},
title = {Genome-Wide Identification and Expression Analysis of Heat Shock Protein 70 (HSP70) Gene Family in Pumpkin (Cucurbita moschata) Rootstock under Drought Stress Suggested the Potential Role of these Chaperones in Stress Tolerance.},
journal = {International journal of molecular sciences},
volume = {23},
number = {3},
pages = {},
pmid = {35163839},
issn = {1422-0067},
support = {BE2021357 and 2021YFD1200201-04//the Key Research and Development Program/ ; },
mesh = {Cucurbita/genetics/*physiology ; *Down-Regulation ; Droughts ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant ; Genomics/*methods ; HSP70 Heat-Shock Proteins/*genetics ; Multigene Family ; Phylogeny ; Plant Proteins/genetics ; Promoter Regions, Genetic ; Selection, Genetic ; Stress, Physiological ; },
abstract = {Heat shock protein 70s (HSP70s) are highly conserved proteins that are involved in stress responses. These chaperones play pivotal roles in protein folding, removing the extra amounts of oxidized proteins, preventing protein denaturation, and improving the antioxidant system activities. This conserved family has been characterized in several crops under drought stress conditions. However, there is no study on HSP70s in pumpkin (Cucurbita moschata). Therefore, we performed a comprehensive analysis of this gene family, including phylogenetic relationship, motif and gene structure analysis, gene duplication, collinearity, and promoter analysis. In this research, we found 21 HSP70s that were classified into five groups (from A to E). These genes were mostly localized in the cytoplasm, chloroplast, mitochondria, nucleus, and endoplasmic reticulum (ER). We could observe more similarity in closely linked subfamilies in terms of motifs, the number of introns/exons, and the corresponding cellular compartments. According to the collinearity analysis, gene duplication had occurred as a result of purifying selection. The results showed that the occurrence of gene duplication for all nine gene pairs was due to segmental duplication (SD). Synteny analysis revealed a closer relationship between pumpkin and cucumber than pumpkin and Arabidopsis. Promoter analysis showed the presence of various cis-regulatory elements in the up-stream region of the HSP70 genes, such as hormones and stress-responsive elements, indicating a potential role of this gene family in stress tolerance. We furtherly performed the gene expression analysis of the HSP70s in pumpkin under progressive drought stress. Pumpkin is widely used as a rootstock to improve stress tolerance, as well as fruit quality of cucumber scion. Since stress-responsive mobile molecules translocate through vascular tissue from roots to the whole plant body, we used the xylem of grafted materials to study the expression patterns of the HSP70 (potentially mobile) gene family. The results indicated that all CmoHSP70s had very low expression levels at 4 days after stress (DAS). However, the genes showed different expression patterns by progressing he drought period. For example, the expression of CmoHSP70-4 (in subgroup E) and CmoHSP70-14 (in subgroup C) sharply increased at 6 and 11 DAS, respectively. However, the expression of all genes belonging to subgroup A did not change significantly in response to drought stress. These findings indicated the diverse roles of this gene family under drought stress and provided valuable information for further investigation on the function of this gene family, especially under stressful conditions.},
}

Cucurbita/genetics/*physiology
*Down-Regulation
Droughts
Gene Expression Profiling/*methods
Gene Expression Regulation, Plant
Genomics/*methods
HSP70 Heat-Shock Proteins/*genetics
Multigene Family
Phylogeny
Plant Proteins/genetics
Promoter Regions, Genetic
Selection, Genetic
Stress, Physiological

@article {pmid35163579,
year = {2022},
author = {Lin, YH and Lim, SN and Chen, CY and Chi, HC and Yeh, CT and Lin, WR},
title = {Functional Role of Mitochondrial DNA in Cancer Progression.},
journal = {International journal of molecular sciences},
volume = {23},
number = {3},
pages = {},
pmid = {35163579},
issn = {1422-0067},
support = {MOST 109-2314-B-182A-068-//Ministry of Science and Technology of the Republic of China/ ; MOST 110-2314-B-182A-095-//Ministry of Science and Technology of the Republic of China/ ; MOST 110-2311-B-182A-001-MY3//Ministry of Science and Technology of the Republic of China/ ; CMRPG3K2292//Chang Gung Memorial Hospital, Taiwan/ ; CMRPG3J0693//Chang Gung Memorial Hospital, Taiwan/ ; CMRPG3J1681//Chang Gung Memorial Hospital, Taiwan/ ; NRRPG3L6011//Chang Gung Memorial Hospital, Taiwan/ ; },
mesh = {*DNA, Mitochondrial/genetics/metabolism ; *DNA, Neoplasm/genetics/metabolism ; Humans ; *Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; *Mutation ; Neoplasm Proteins/genetics/metabolism ; *Neoplasms/genetics/metabolism ; *Polymorphism, Single Nucleotide ; },
abstract = {Mitochondrial DNA (mtDNA) has been identified as a significant genetic biomarker in disease, cancer and evolution. Mitochondria function as modulators for regulating cellular metabolism. In the clinic, mtDNA variations (mutations/single nucleotide polymorphisms) and dysregulation of mitochondria-encoded genes are associated with survival outcomes among cancer patients. On the other hand, nuclear-encoded genes have been found to regulate mitochondria-encoded gene expression, in turn regulating mitochondrial homeostasis. These observations suggest that the crosstalk between the nuclear genome and mitochondrial genome is important for cellular function. Therefore, this review summarizes the significant mechanisms and functional roles of mtDNA variations (DNA level) and mtDNA-encoded genes (RNA and protein levels) in cancers and discusses new mechanisms of crosstalk between mtDNA and the nuclear genome.},
}

*DNA, Mitochondrial/genetics/metabolism
*DNA, Neoplasm/genetics/metabolism
Humans
*Mitochondria/genetics/metabolism
Mitochondrial Proteins/genetics/metabolism
*Mutation
Neoplasm Proteins/genetics/metabolism
*Neoplasms/genetics/metabolism
*Polymorphism, Single Nucleotide

@article {pmid35163574,
year = {2022},
author = {Falchi, FA and Pizzoccheri, R and Briani, F},
title = {Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase.},
journal = {International journal of molecular sciences},
volume = {23},
number = {3},
pages = {},
pmid = {35163574},
issn = {1422-0067},
mesh = {*Evolution, Molecular ; *Exoribonucleases/genetics/metabolism ; Humans ; *Mutation ; *RNA/genetics/metabolism ; *RNA Stability ; *RNA-Binding Proteins/genetics/metabolism ; },
abstract = {Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.},
}

*Evolution, Molecular
*Exoribonucleases/genetics/metabolism
Humans
*Mutation
*RNA/genetics/metabolism
*RNA Stability
*RNA-Binding Proteins/genetics/metabolism

@article {pmid35163296,
year = {2022},
author = {Amaroli, A and Ravera, S and Zekiy, A and Benedicenti, S and Pasquale, C},
title = {A Narrative Review on Oral and Periodontal Bacteria Microbiota Photobiomodulation, through Visible and Near-Infrared Light: From the Origins to Modern Therapies.},
journal = {International journal of molecular sciences},
volume = {23},
number = {3},
pages = {},
pmid = {35163296},
issn = {1422-0067},
mesh = {Bacteria ; Humans ; Infrared Rays ; Light ; Low-Level Light Therapy/methods/*trends ; Microbiota/*radiation effects ; Mitochondria ; Periodontal Diseases/*microbiology/radiotherapy ; Phototherapy/methods/trends ; Stomatitis/radiotherapy ; },
abstract = {Photobiomodulation (PBM) consists of a photon energy transfer to the cell, employing non-ionizing light sources belonging to the visible and infrared spectrum. PBM acts on some intrinsic properties of molecules, energizing them through specific light wavelengths. During the evolution of life, semiconducting minerals were energized by sun radiation. The molecules that followed became photoacceptors and were expressed into the first proto-cells and prokaryote membranes. Afterward, the components of the mitochondria electron transport chain influenced the eukaryotic cell physiology. Therefore, although many organisms have not utilized light as an energy source, many of the molecules involved in their physiology have retained their primordial photoacceptive properties. Thus, in this review, we discuss how PBM can affect the oral microbiota through photo-energization and the non-thermal effect of light on photoacceptors (i.e., cytochromes, flavins, and iron-proteins). Sometimes, the interaction of photons with pigments of an endogenous nature is followed by thermal or photodynamic-like effects. However, the preliminary data do not allow determining reliable therapies but stress the need for further knowledge on light-bacteria interactions and microbiota management in the health and illness of patients through PBM.},
}

Bacteria
Humans
Infrared Rays
Light
Low-Level Light Therapy/methods/*trends
Microbiota/*radiation effects
Mitochondria
Periodontal Diseases/*microbiology/radiotherapy
Phototherapy/methods/trends
Stomatitis/radiotherapy

@article {pmid35162994,
year = {2022},
author = {Phillips, MA and Arnold, KR and Vue, Z and Beasley, HK and Garza-Lopez, E and Marshall, AG and Morton, DJ and McReynolds, MR and Barter, TT and Hinton, A},
title = {Combining Metabolomics and Experimental Evolution Reveals Key Mechanisms Underlying Longevity Differences in Laboratory Evolved Drosophila melanogaster Populations.},
journal = {International journal of molecular sciences},
volume = {23},
number = {3},
pages = {},
pmid = {35162994},
issn = {1422-0067},
mesh = {Aging/*genetics/metabolism ; Animals ; Carbohydrate Metabolism ; Citric Acid Cycle ; Directed Molecular Evolution ; Drosophila melanogaster/genetics/*physiology ; Genomics/*methods ; Longevity ; Metabolomics/*methods ; Mitochondria/metabolism ; Multifactorial Inheritance ; NAD/metabolism ; Polymorphism, Single Nucleotide ; },
abstract = {Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups of experimentally evolved D. melanogaster populations with different aging and longevity patterns. Our metabolomic analysis found that aging alters mitochondrial metabolism through increased consumption of NAD+ and increased usage of the TCA cycle. Combining our genomic and metabolomic data produced a list of biologically relevant candidate genes. Among these candidates, we found significant enrichment for genes and pathways associated with neurological development and function, and carbohydrate metabolism. While we do not explicitly find enrichment for aging canonical genes, neurological dysregulation and carbohydrate metabolism are both known to be associated with accelerated aging and reduced longevity. Taken together, our results provide plausible genetic mechanisms for what might be driving longevity differences in this experimental system. More broadly, our findings demonstrate the value of combining multiple types of omic data with experimental evolution when attempting to dissect mechanisms underlying complex and highly polygenic traits such as aging.},
}

Aging/*genetics/metabolism
Animals
Carbohydrate Metabolism
Citric Acid Cycle
Directed Molecular Evolution
Drosophila melanogaster/genetics/*physiology
Genomics/*methods
Longevity
Metabolomics/*methods
Mitochondria/metabolism
Multifactorial Inheritance
NAD/metabolism
Polymorphism, Single Nucleotide

@article {pmid35157851,
year = {2022},
author = {Grass, M and McDougal, AD and Blazeski, A and Kamm, RD and García-Cardeña, G and Dewey, CF},
title = {A computational model of cardiomyocyte metabolism predicts unique reperfusion protocols capable of reducing cell damage during ischemia/reperfusion.},
journal = {The Journal of biological chemistry},
volume = {298},
number = {5},
pages = {101693},
doi = {10.1016/j.jbc.2022.101693},
pmid = {35157851},
issn = {1083-351X},
abstract = {If a coronary blood vessel is occluded and the neighboring cardiomyocytes deprived of oxygen, subsequent reperfusion of the ischemic tissue can lead to oxidative damage due to excessive generation of reactive oxygen species. Cardiomyocytes and their mitochondria are the main energy producers and consumers of the heart, and their metabolic changes during ischemia seem to be a key driver of reperfusion injury. Here, we hypothesized that tracking changes in cardiomyocyte metabolism, such as oxygen and ATP concentrations, would help in identifying points of metabolic failure during ischemia and reperfusion. To track some of these changes continuously from the onset of ischemia through reperfusion, we developed a system of differential equations representing the chemical reactions involved in the production and consumption of 67 molecular species. This model was validated and used to identify conditions present during periods of critical transition in ischemia and reperfusion that could lead to oxidative damage. These simulations identified a range of oxygen concentrations that lead to reverse mitochondrial electron transport at complex I of the respiratory chain and a spike in mitochondrial membrane potential, which are key suspects in the generation of reactive oxygen species at the onset of reperfusion. Our model predicts that a short initial reperfusion treatment with reduced oxygen content (5% of physiological levels) could reduce the cellular damage from both of these mechanisms. This model should serve as an open-source platform to test ideas for treatment of the ischemia reperfusion process by following the temporal evolution of molecular concentrations in the cardiomyocyte.},
}

@article {pmid35148829,
year = {2022},
author = {Loconte, V and Singla, J and Li, A and Chen, JH and Ekman, A and McDermott, G and Sali, A and Le Gros, M and White, KL and Larabell, CA},
title = {Soft X-ray tomography to map and quantify organelle interactions at the mesoscale.},
journal = {Structure (London, England : 1993)},
volume = {30},
number = {4},
pages = {510-521.e3},
pmid = {35148829},
issn = {1878-4186},
support = {P30 GM138441/GM/NIGMS NIH HHS/United States ; P41 GM103445/GM/NIGMS NIH HHS/United States ; P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 GM083960/GM/NIGMS NIH HHS/United States ; },
mesh = {*Imaging, Three-Dimensional/methods ; Insulin ; Mitochondria/ultrastructure ; Organelles ; *Tomography, X-Ray/methods ; },
abstract = {Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due to the range of scales encountered in cell biology and the throughput limitations of traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used to rapidly map ultrastructural reorganization and inter-organelle interactions in intact cells. SXT takes advantage of the naturally occurring, differential X-ray absorption of the carbon-rich compounds in each organelle. Specifically, we use SXT to map the spatiotemporal evolution of insulin vesicles and their co-localization and interaction with mitochondria in pancreatic β cells during insulin secretion and in response to different stimuli. We quantify changes in the morphology, biochemical composition, and relative position of mitochondria and insulin vesicles. These findings highlight the importance of a comprehensive and unbiased mapping at the mesoscale to characterize cell reorganization that would be difficult to detect with other existing methodologies.},
}

*Imaging, Three-Dimensional/methods
Insulin
Mitochondria/ultrastructure
Organelles
*Tomography, X-Ray/methods

@article {pmid35145105,
year = {2022},
author = {Elsemman, IE and Rodriguez Prado, A and Grigaitis, P and Garcia Albornoz, M and Harman, V and Holman, SW and van Heerden, J and Bruggeman, FJ and Bisschops, MMM and Sonnenschein, N and Hubbard, S and Beynon, R and Daran-Lapujade, P and Nielsen, J and Teusink, B},
title = {Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {801},
pmid = {35145105},
issn = {2041-1723},
support = {BB/M025748/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M025756/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Fermentation ; Gene Expression Regulation, Fungal ; Glucose/metabolism ; *Metabolic Networks and Pathways/genetics ; Mitochondria/metabolism ; Proteome/*metabolism ; *Proteomics ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Yeasts/*genetics/growth & development/*metabolism ; },
abstract = {When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation-known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells.},
}

Fermentation
Gene Expression Regulation, Fungal
Glucose/metabolism
*Metabolic Networks and Pathways/genetics
Mitochondria/metabolism
Proteome/*metabolism
*Proteomics
Saccharomyces cerevisiae/genetics/metabolism
Saccharomyces cerevisiae Proteins/genetics/metabolism
Yeasts/*genetics/growth & development/*metabolism

@article {pmid35143947,
year = {2022},
author = {Sai Satyanarayana, D and Ahlawat, S and Sharma, R and Arora, R and Sharma, A and Tantia, MS and Vijh, RK},
title = {Mitochondrial DNA diversity divulges high levels of haplotype diversity and lack of genetic structure in the Indian camels.},
journal = {Gene},
volume = {820},
number = {},
pages = {146279},
doi = {10.1016/j.gene.2022.146279},
pmid = {35143947},
issn = {1879-0038},
mesh = {Animals ; Biodiversity ; Camelus/*genetics ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Haplotypes ; India ; Male ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {Camels represent an important genetic resource of the desert ecosystems of India, with the dromedary and Bactrian camels inhabiting the hot and cold deserts, respectively. This study is the first attempt to investigate mitochondrial DNA based genetic diversity in the Indian camel populations and explores their relationship in the context of global genetic diversity of all the three large camel species (Camelus ferus, Camelus bactrianus and Camelus dromedaries). A mitochondrial DNA fragment encompassing part of cytochrome b gene, tRNAThr, tRNAPro and the beginning of the control region was amplified and analyzed in 72 dromedary and 8 Bactrian camels of India. Sequence analysis revealed that the haplotype and nucleotide diversity (Hd: 0.937 and π: 0.00431) in the Indian dromedaries was higher than the indices reported so far for the dromedary or Bactrian camels across the globe. The corresponding values in the Indian Bactrian camels were 1.000 and 0.00393, respectively. Signals of population expansion were evident in the dromedaries of India on the basis of mismatch analysis and Fu's Fs values. The analysis of molecular variance attributed most of the genetic variance (92.15%) between the dromedary, wild Bactrian and domestic Bactrian camels indicating separate maternal origins. The existence of three mitochondrial lineages in the old world camels (C. bactrianus: Lineage A; C. ferus: Lineage B and C. dromedarius: Lineage C) was also substantiated by the topology of the Median-Joining network.},
}

Animals
Biodiversity
Camelus/*genetics
DNA, Mitochondrial/*genetics
Female
*Genetic Variation
Haplotypes
India
Male
Mitochondria/*genetics
Phylogeny

@article {pmid35135343,
year = {2022},
author = {Horrell, HD and Lindeque, A and Farrell, AP and Seymour, RS and White, CR and Kruger, KM and Snelling, EP},
title = {Relationship between capillaries, mitochondria and maximum power of the heart: a meta-study from shrew to elephant.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1968},
pages = {20212461},
pmid = {35135343},
issn = {1471-2954},
mesh = {Animals ; *Capillaries ; *Elephants ; Humans ; Mitochondria ; Oxygen ; Oxygen Consumption ; Phylogeny ; Shrews ; },
abstract = {This meta-study uses phylogenetic scaling models across more than 30 species, spanning five orders of magnitude in body mass, to show that cardiac capillary numerical density and mitochondrial volume density decrease with body mass raised to the -0.07 ± 0.03 and -0.04 ± 0.01 exponents, respectively. Thus, while an average 10 g mammal has a cardiac capillary density of approximately 4150 mm-2 and a mitochondrial density of 33%, a 1 t mammal has considerably lower corresponding values of 1850 mm-2 and 21%. These similar scaling trajectories suggest quantitative matching for the primary oxygen supply and oxygen consuming structures of the heart, supporting economic design at the cellular level of the oxygen cascade in this aerobic organ. These scaling trajectories are nonetheless somewhat shallower than the exponent of -0.11 calculated for the maximum external mechanical power of the cardiac tissue, under conditions of heavy exercise, when oxygen flow between capillaries and mitochondria is probably fully exploited. This mismatch, if substantiated, implies a declining external mechanical efficiency of the heart with increasing body mass, whereby larger individuals put more energy in but get less energy out, a scenario with implications for cardiovascular design, aerobic capacity and limits of body size.},
}

Animals
*Capillaries
*Elephants
Humans
Mitochondria
Oxygen
Oxygen Consumption
Phylogeny
Shrews

@article {pmid35133488,
year = {2022},
author = {Shumenko, PG and Tatonova, YV},
title = {Assessing the population structure of trematode Metagonimus suifunensis using three mitochondrial markers.},
journal = {Parasitology research},
volume = {121},
number = {3},
pages = {915-923},
pmid = {35133488},
issn = {1432-1955},
mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; Far East ; Genetic Variation ; *Heterophyidae/genetics ; Mitochondria/genetics ; Phylogeny ; Russia ; },
abstract = {In this work, for the first time, the genetic variability of the Metagonimus suifunensis population in the Russian southern Far East was estimated based on the full-length sequences of the nad1 gene of mitochondrial DNA. In addition, for a sample of the same size, the sequences of cox1 and cytb genes, previously used for population studies for M. suifunensis, were reanalysed. Three markers were combined to a common sequence, and the obtained data were studied. Despite the higher level of variability, nad1 and cox1 mtDNA genes did not reveal subdivisions within the population. The combined dataset made it possible to determine that the sample from the Odyr River was the centre of the species' range formation and clarified the continental migration route of the parasite from south to north. According to the data obtained, it was presumed that piscivorous birds participate in the life cycle of the parasite. The subdivision within population revealed that using all three mitochondrial markers is consistent with the features of differentiation within populations of related species, but the reasons for its formation remain unclear due to the insufficient amount of data and the use of different markers in studies of different species.},
}

Animals
DNA, Mitochondrial/chemistry/genetics
Far East
Genetic Variation
*Heterophyidae/genetics
Mitochondria/genetics
Phylogeny
Russia

@article {pmid35132109,
year = {2022},
author = {Verma, RK and Kalyakulina, A and Mishra, A and Ivanchenko, M and Jalan, S},
title = {Role of mitochondrial genetic interactions in determining adaptation to high altitude human population.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {2046},
pmid = {35132109},
issn = {2045-2322},
mesh = {Adaptation, Physiological/*genetics ; *Altitude ; Epistasis, Genetic/*genetics ; Ethiopia ; Genes, Mitochondrial/*genetics/*physiology ; Humans ; Mitochondria/*genetics/*physiology ; Polymorphism, Genetic ; South America ; Tibet ; },
abstract = {Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a near-by polymorphism on the same DNA sample making them connected in terms of evolution. Here, first, we provide a method to model these mitochondrial polymorphisms as "co-mutation networks" for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions of CYB and CO3 genes in Tibetan and Andean populations, while NADH dehydrogenase genes in the Ethiopian population playing a significant role in high altitude adaptation. These co-mutation based genetic networks provide insights into the role of different set of genes in high-altitude adaptation in human sub-populations.},
}

Adaptation, Physiological/*genetics
*Altitude
Epistasis, Genetic/*genetics
Ethiopia
Genes, Mitochondrial/*genetics/*physiology
Humans
Mitochondria/*genetics/*physiology
Polymorphism, Genetic
South America
Tibet

@article {pmid35129136,
year = {2022},
author = {Balasubramaniam, S and Soman, M and Katneni, VK and Tomy, S and Gopalapillay, G and Vijayan, KK},
title = {Mitochondrial DNA based diversity studies reveal distinct and substructured populations of pearlspot, Etroplus suratensis (Bloch, 1790) in Indian waters.},
journal = {Journal of genetics},
volume = {101},
number = {},
pages = {},
pmid = {35129136},
issn = {0973-7731},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; India ; *Mitochondria/genetics ; Phylogeny ; },
abstract = {Pearlspot (Etroplus suratensis) is one of the most commercially important brackish water fish species widely found along the coastal regions of peninsular India and Sri Lanka. Pearlspot is known for its tender flesh, delectable taste, culinary tourism and highyielding market value. Information on the genetic makeup of stocks/populations is extremely vital as it forms the basis for future genetic studies. For this, we utilized ATPase6/8 genes of mtDNA of pearlspot populations collected from nine different locations ranging from Ratnagiri in Maharashtra state on the west coast to Chilika in Odisha on the east coast. Sequence analyses of these genes revealed 33 polymorphic sites, which include 17 singleton and 16 parsimony informative sites. Pair-wise genetic differentiation study (FST = 0.75) indicated significant (P<0.001) differences among all the pairs of stocks except those from Chilika and Nagayalanka. The spatial analysis of molecular variance (SAMOVA) significantly delineated the population into four groups (FCT = 0.69, P = 0.0001), namely northwest (Ratnagiri and Goa); southwest (Mangalore and lakes at Vembanad, Ashtamudi and Vellayani in Kerala); southeast (Pulicat in Tamil Nadu) and northeast (Chilika in Odisha and Nagayalanka in Andhra Pradesh). The above delineation is supported by clades of the phylogenetic tree and also the clusters of median joining haplotype network. The high haplotype diversity (0.84), low nucleotide diversity (0.003), and negative values of Tajima's D (-1.47) and Fu's Fs statistic (-14.89) are characteristic of populations having recently undergone demographic expansion. Mantel test revealed significant isolation by distance. The study identifies highly delineated structured populations with restricted gene flow. If such a stock is overfished, it is highly unlikely that it would recover through migration. For any future breeding programme in this species, it would be desirable to form a base population which incorporates the genetic material from all the locations so that we get a wide gene pool to select from.},
}

Animals
*DNA, Mitochondrial/genetics
Genetic Variation
Genetics, Population
Haplotypes/genetics
India
*Mitochondria/genetics
Phylogeny

@article {pmid35122922,
year = {2022},
author = {Baratange, C and Paris-Palacios, S and Bonnard, I and Delahaut, L and Grandjean, D and Wortham, L and Sayen, S and Gallorini, A and Michel, J and Renault, D and Breider, F and Loizeau, JL and Cosio, C},
title = {Metabolic, cellular and defense responses to single and co-exposure to carbamazepine and methylmercury in Dreissena polymorpha.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {300},
number = {},
pages = {118933},
doi = {10.1016/j.envpol.2022.118933},
pmid = {35122922},
issn = {1873-6424},
mesh = {Animals ; Carbamazepine/analysis/toxicity ; *Dreissena/metabolism ; Gills/metabolism ; *Methylmercury Compounds/metabolism/toxicity ; *Water Pollutants, Chemical/analysis ; },
abstract = {Carbamazepine (CBZ) and Hg are widespread and persistent micropollutants in aquatic environments. Both pollutants are known to trigger similar toxicity mechanisms, e.g. reactive oxygen species (ROS) production. Here, their effects were assessed in the zebra mussel Dreissena polymorpha, frequently used as a freshwater model in ecotoxicology and biomonitoring. Single and co-exposures to CBZ (3.9 μg L-1) and MeHg (280 ng L-1) were performed for 1 and 7 days. Metabolomics analyses evidenced that the co-exposure was the most disturbing after 7 days, reducing the amount of 25 metabolites involved in protein synthesis, energy metabolism, antioxidant response and osmoregulation, and significantly altering cells and organelles' structure supporting a reduction of functions of gills and digestive glands. CBZ alone after 7 days decreased the amount of α-aminobutyric acid and had a moderate effect on the structure of mitochondria in digestive glands. MeHg alone had no effect on mussels' metabolome, but caused a significant alteration of cells and organelles' structure in gills and digestive glands. Single exposures and the co-exposure increased antioxidant responses vs control in gills and digestive glands, without resulting in lipid peroxidation, suggesting an increased ROS production caused by both pollutants. Data globally supported that a higher number of hyperactive cells compensated cellular alterations in the digestive gland of mussels exposed to CBZ or MeHg alone, while CBZ + MeHg co-exposure overwhelmed this compensation after 7 days. Those effects were unpredictable based on cellular responses to CBZ and MeHg alone, highlighting the need to consider molecular toxicity pathways for a better anticipation of effects of pollutants in biota in complex environmental conditions.},
}

Animals
Carbamazepine/analysis/toxicity
*Dreissena/metabolism
Gills/metabolism
*Methylmercury Compounds/metabolism/toxicity
*Water Pollutants, Chemical/analysis

@article {pmid35119574,
year = {2022},
author = {Munekage, YN and Taniguchi, YY},
title = {A scheme for C4 evolution derived from a comparative analysis of the closely related C3, C3-C4 intermediate, C4-like, and C4 species in the genus Flaveria.},
journal = {Plant molecular biology},
volume = {},
number = {},
pages = {},
pmid = {35119574},
issn = {1573-5028},
support = {17K07456//Japan Society for the Promotion of Science/ ; 16H06557//Japan Society for the Promotion of Science/ ; 21K05520//Japan Society for the Promotion of Science/ ; },
abstract = {KEY MESSAGE: A comparative analysis of the genus Flaveria showed a C4 evolutionary process in which the anatomical and metabolic features of C4 photosynthesis were gradually acquired through C3-C4 intermediate stages. C4 photosynthesis has been acquired in multiple lineages of angiosperms during evolution to suppress photorespiration. Crops that perform C4 photosynthesis exhibit high rates of CO2 assimilation and high grain production even under high-temperature in semiarid environments; therefore, engineering C4 photosynthesis in C3 plants is of great importance in the application field. The genus Flaveria contains a large number of C3, C3-C4 intermediate, C4-like, and C4 species, making it a good model genus to study the evolution of C4 photosynthesis, and these studies indicate the direction for C4 engineering. C4 photosynthesis was acquired gradually through the C3-C4 intermediate stage. First, a two-celled C2 cycle called C2 photosynthesis was acquired by localizing glycine decarboxylase activity in the mitochondria of bundle sheath cells. With the development of two-cell metabolism, anatomical features also changed. Next, the replacement of the two-celled C2 cycle by the two-celled C4 cycle was induced by the acquisition of cell-selective expression in addition to the upregulation of enzymes in the C4 cycle during the C3-C4 intermediate stage. This was supported by an increase in cyclic electron transport activity in response to an increase in the ATP/NADPH demand for metabolism. Suppression of the C3 cycle in mesophyll cells was induced after the functional establishment of the C4 cycle, and optimization of electron transport by suppressing the activity of photosystem II also occurred during the final phase of C4 evolution.},
}

@article {pmid35113355,
year = {2022},
author = {Singh, P and Lim, B},
title = {Targeting Apoptosis in Cancer.},
journal = {Current oncology reports},
volume = {24},
number = {3},
pages = {273-284},
pmid = {35113355},
issn = {1534-6269},
mesh = {*Antineoplastic Agents/pharmacology/therapeutic use ; Apoptosis ; Humans ; Mitochondria/metabolism ; *Neoplasms/drug therapy/metabolism ; Proto-Oncogene Proteins c-bcl-2 ; },
abstract = {PURPOSE OF REVIEW: Apoptosis is a major mechanism of cancer cell death. Thus, evasion of apoptosis results in therapy resistance. Here, we review apoptosis modulators in cancer and their recent developments, including MDM2 inhibitors and kinase inhibitors that can induce effective apoptosis.

RECENT FINDINGS: Both extrinsic pathways (external stimuli through cell surface death receptor) and intrinsic pathways (mitochondrial-mediated regulation upon genotoxic stress) regulate the complex process of apoptosis through orchestration of various proteins such as members of the BCL-2 family. Dysregulation within these complex steps can result in evasion of apoptosis. However, via the combined evolution of medicinal chemistry and molecular biology, omics assays have led to innovative inducers of apoptosis and inhibitors of anti-apoptotic regulators. Many of these agents are now being tested in cancer patients in early-phase trials. We believe that despite a sluggish speed of development, apoptosis targeting holds promise as a relevant strategy in cancer therapeutics.},
}

*Antineoplastic Agents/pharmacology/therapeutic use
Apoptosis
Humans
Mitochondria/metabolism
*Neoplasms/drug therapy/metabolism
Proto-Oncogene Proteins c-bcl-2