@article {pmid40343117,
year = {2025},
author = {Meng, D and Lu, T and He, M and Ren, Y and Fu, M and Zhang, Y and Yang, P and Lin, X and Yang, Y and Zhang, Y and Yang, Y and Jin, X},
title = {Organelle genomes of two Scaevola species, S. taccada and S. hainanensis, provide new insights into evolutionary divergence between Scaevola and its related species.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1587750},
pmid = {40343117},
issn = {1664-462X},
abstract = {Chloroplast and mitochondrial genomes harbor crucial information that can be utilized for elucidating plant evolution and environmental adaptation. The organellar genomic characteristics of Goodeniaceae, a sister family to Asteraceae, remain unexplored. Here, using a combination of short-read and long-read sequencing technologies, we successfully assembled the complete organellar genomes of two Goodeniaceae species native to China, Scaevola taccada and S. hainanensis. Chloroplast genome collinearity analysis revealed that Scaevola expanded its genome length through inverted repeat expansion and large single copy fragment duplication, resulting in 181,022 bp (S. taccada) and 182,726 bp (S. hainanensis), ~30 kb increase compared to its related species. Mitochondrial genomes of two Scaevola species exhibit multi-ring topology, forming dual mitochondrial chromosomes of 314,251 bp (S. taccada) and 276,175 bp (S. hainanensis). Sequence variation analysis demonstrated substantial chloroplast sequence divergence (Pi = 0.45) and an increase in gene copy number within the genus. Relative synonymous codon usage (RSCU) analysis revealed that Scaevola chloroplast has a higher bias for A/U-ending codons than mitochondria, with chloroplasts RSCU values ranging from 0.32 to 1.94, whereas mitochondrial RSCU values ranging from 0.38 to 1.62. Phylogenetic analyses support the monophyly of the Asteraceae-Goodeniaceae sister group, whereas the extended evolutionary branches of Scaevola, coupled with mitochondrial collinearity analysis, indicate rapid organellar genome evolution of Scaevola. Organellar-nuclear horizontal gene transfer analysis identified specific increased in the copy numbers of photosynthesis-related genes and chloroplast-nuclear transfer events in S. taccada. Our study not only provides insights for understanding environmental adaptation mechanisms of coastal plants, but also contributes to elucidating organellar genome evolution in Scaevola and Goodeniaceae.},
}

@article {pmid40185233,
year = {2025},
author = {Zhao, HF and Wang, Y and Liu, XH and Liu, XH and Geng, Z and Gao, ZQ and Huang, L and Weng, CJ and Dong, YH and Zhang, H},
title = {Structure-function insights into the dual role of African swine fever virus pB318L: A typical geranylgeranyl-diphosphate synthase and a nuclear import protein.},
journal = {Virologica Sinica},
volume = {40},
number = {2},
pages = {236-246},
doi = {10.1016/j.virs.2025.03.013},
pmid = {40185233},
issn = {1995-820X},
mesh = {*African Swine Fever Virus/genetics/enzymology/physiology ; Animals ; *Viral Proteins/genetics/metabolism/chemistry ; Structure-Activity Relationship ; Swine ; Phylogeny ; Virus Replication ; Active Transport, Cell Nucleus ; Cell Nucleus/metabolism ; Nuclear Localization Signals/genetics ; },
abstract = {African swine fever virus (ASFV) pB318L is an important protein for viral replication that acts as a membrane-bound trans-geranylgeranyl-diphosphate synthase (GGPPS) catalyzing the condensation of isopentenyl diphosphate (IPP) with allylic diphosphates. Recently we solved the crystal structure pB318L lacking N-terminal transmembrane region and performed a preliminary structural analysis. In this study, structure-based mutagenesis study and geranylgeranyl pyrophosphate (GGPP) production assay further revealed the key residues for the GGPPS activity. Structural comparison showed pB318L displays a strong similarity to typical GGPPSs instead of protein prenyltransferases. The phylogenetic analysis indicated pB318L may share a common ancestor with the GGPPSs from Brassicaceae plants rather than from its natural host. The subcellular localization analysis showed pB318L is localized in both nucleus and cytoplasm (including the endoplasmic reticulum membrane and mitochondria outer membrane). A unique N-terminal nuclear localization signal (NLS) following the transmembrane region was discovered in pB318L and the NLS was confirmed to be required for the nuclear import. We further revealed the NLS plays an essential role in the interaction with nuclear transporter karyopherin subunit alpha 1 (KPNA1). Their interaction may suppress signal transducers and activators of transcription 1 (STAT1) translocation and subsequently competitively inhibit nuclear import of IFN-stimulated gene factor 3 (ISGF3) complex. Our biochemical, structural and cellular analyses provide novel insights to pB318L that acts as an essential GGPPS that promotes viral replication and as a nuclear import protein that may be involved in immune evasion of ASFV.},
}

*African Swine Fever Virus/genetics/enzymology/physiology
Animals
*Viral Proteins/genetics/metabolism/chemistry
Structure-Activity Relationship
Swine
Phylogeny
Virus Replication
Active Transport, Cell Nucleus
Cell Nucleus/metabolism
Nuclear Localization Signals/genetics

@article {pmid40338339,
year = {2025},
author = {Li, X and Liu, D and Han, B and Huang, S and Deng, H},
title = {Genome-wide identification of CYP450 in Ganoderma lucidum and expression analysis of genes related to ganoderic acid synthesis.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {137},
pmid = {40338339},
issn = {1432-072X},
support = {2023YFC3503804//The National Key Research and Development Program of China/ ; 2023AH052637//Special Funds for Anhui Dabie Mountain Institute of Traditional Chinese Medicine/ ; Anhui [2023] TG07//the 2023 Central Finance Forestry Science and Technology Promotion Demonstration Funds Project/ ; },
mesh = {*Cytochrome P-450 Enzyme System/genetics/metabolism ; *Reishi/genetics/enzymology/metabolism ; *Triterpenes/metabolism ; *Fungal Proteins/genetics/metabolism ; *Genome, Fungal ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Phylogeny ; Transcriptome ; },
abstract = {The biosynthesis mechanism of ganoderic acid, a class of secondary metabolites of Ganoderma lucidum, is currently unknown. Members of G. lucidum's CYP450 gene family were found in this study by genome-wide analysis. Determination of ganoderic acid content in Jilin, Zhejiang, Jinzhai, Fujian, Yunnan and Shandong regions was performed using high performance liquid chromatography. Expression of CYP450 gene of G. lucidum from Jilin, Jinzhai and Shandong origins was analyzed by transcriptome sequencing. The findings indicated that, through comprehensive sequence analysis and functional annotation, 189 CYP450 genes were detected in the G. lucidum genome, among which 34 CYP450 genes were significantly differentially expressed in transcriptome analysis, and the gene expression was positively correlated with ganoderic acid content. Bioinformatics analysis predicted the conserved motifs, structural features, and subcellular localization of 189 CYP genes, revealing significant differences in gene structure and protein motif composition among GlCYP450 family members. Subcellular localization revealed that they are located in the plasma membrane, cytoplasm, nucleus, mitochondria, peroxisome, endoplasmic reticulum, extracellular space, and cytoskeleton, suggesting that they have multiple functions. A number of cis-regulatory elements associated with stress responses and phytohormones were identified in the promoter regions of these genes. It demonstrates that ganoderic acid production has been significantly controlled by these P450 genes. These findings offer a crucial theoretical foundation for a thorough comprehension of the process of ganoderic acid production, the bioinformatics role of CYP450 genes in G. lucidum, and the selection and breeding of superior G. lucidum resources.},
}

*Cytochrome P-450 Enzyme System/genetics/metabolism
*Reishi/genetics/enzymology/metabolism
*Triterpenes/metabolism
*Fungal Proteins/genetics/metabolism
*Genome, Fungal
Gene Expression Profiling
Gene Expression Regulation, Fungal
Phylogeny
Transcriptome

@article {pmid40333178,
year = {2025},
author = {Rancilhac, L and de Souza, SG and Lukhele, SM and Sebastianelli, M and Ogolowa, BO and Moysi, M and Nikiforou, C and Asfaw, T and Downs, CT and Brelsford, A and vonHoldt, BM and Kirschel, ANG},
title = {Introgression across narrow contact zones shapes the genomic landscape of phylogenetic variation in an African bird clade.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syaf033},
pmid = {40333178},
issn = {1076-836X},
abstract = {Genomic analyses of hybrid zones provide excellent opportunities to investigate the consequences of introgression in nature. In combination with phylogenomics analyses, hybrid zone studies may illuminate the role of ancient and contemporary gene flow in shaping variation of phylogenetic signals across the genome, but this avenue has not been explored yet. We combined phylogenomic and geographic cline analyses in a Pogoniulus tinkerbird clade to determine whether contemporary introgression through hybrid zones contributes to gene-tree heterogeneity across the species ranges. We found diverse phylogenetic signals across the genome with the most common topologies supporting monophyly among taxa connected by secondary contact zones. Remarkably, these systematic conflicts were also recovered when selecting only individuals from each taxon's core range. Using analyses of derived allele sharing and "recombination aware" phylogenomics, we found that introgression shapes gene-tree heterogeneity, and the species tree most likely supports monophyletic red-fronted tinkerbirds, as recovered in previous reconstructions based on mitochondrial DNA. Furthermore, by fitting geographic clines across two secondary contact zones, we found that introgression rates were lower in genomic regions supporting the putative species tree compared to those supporting the two taxa in contact as monophyletic. This demonstrates that introgression through narrow contact zones shapes gene-tree heterogeneity even in allopatric populations. Finally, we did not find evidence that mitochondria-interacting nuclear genes acted as barrier loci. Our results show that species can withstand important amounts of introgression while maintaining their phenotypic integrity and ecological separation, raising questions regarding the genomic architecture of adaptation and barriers to gene flow.},
}

@article {pmid40329166,
year = {2025},
author = {Zhong, T and Huang, S and Liu, R and Zhuo, J and Lu, H and Gan, C and Fu, J and Qian, Q},
title = {The complete mitochondrial genome of Sinojackia microcarpa: evolutionary insights and gene transfer.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {446},
pmid = {40329166},
issn = {1471-2164},
support = {SRSJJD2024005//Off-campus practice education base for design majors of Zhejiang Shuren University/ ; SRSJJD2024005//Off-campus practice education base for design majors of Zhejiang Shuren University/ ; SRSJJD2024005//Off-campus practice education base for design majors of Zhejiang Shuren University/ ; SRSJJD2024005//Off-campus practice education base for design majors of Zhejiang Shuren University/ ; SXSZY202412//Key Specialty Project of Ordinary Colleges and Universities/ ; SXSZY202412//Key Specialty Project of Ordinary Colleges and Universities/ ; SXSZY202412//Key Specialty Project of Ordinary Colleges and Universities/ ; SXSZY202412//Key Specialty Project of Ordinary Colleges and Universities/ ; LGN21C160015//the Basic Public Welfare Research Projects of Zhejiang province/ ; LGN21C160015//the Basic Public Welfare Research Projects of Zhejiang province/ ; LGN21C160015//the Basic Public Welfare Research Projects of Zhejiang province/ ; LGN21C160015//the Basic Public Welfare Research Projects of Zhejiang province/ ; },
mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; Phylogeny ; RNA, Transfer/genetics ; Genomics ; },
abstract = {BACKGROUND: As a dicotyledonous plant within the Styracaceae family, Sinojackia microcarpa (S. microcarpa) is notable for its library-shaped fruit and sparse distribution, serving as a model system for studying the entire tree family. However, the scarcity of genomic data, particularly concerning the mitochondrial and nuclear sequences of S. microcarpa, has substantially impeded our understanding of its evolutionary traits and fundamental biological mechanisms.

RESULTS: This study presents the first complete mitochondrial genome sequence of S. microcarpa and conducts a comparative analysis of its protein-encoding genes across eight plant species. Our analysis revealed that the mitochondrial genome of S. microcarpa spans 687,378 base pairs and contains a total of 59 genes, which include 37 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. Sixteen plastid-derived fragments strongly linked with mitochondrial genes, including one intact plastid-related gene (rps7), were identified. Additionally, Ka/Ks ratio analysis revealed that most mitochondrial genes are under purifying selection, with a few genes, such as nad9 and ccmB, showing signs of relaxed or adaptive evolution. An analysis of twenty-nine protein-coding genes from twenty-four plant species reveals that S. microcarpa exhibits a closer evolutionary relationship with species belonging to the genus Camellia. The findings of this study provide new genomic data that enhance our understanding of S. microcarpa, and reveal its mitochondrial genome's evolutionary proximity to other dicotyledonous species.

CONCLUSIONS: Overall, this research enhances our understanding of the evolutionary and comparative genomics of S. microcarpa and other plants in the Styracaceae family and lays the foundation for future genetic studies and evolutionary analyses in the Styracaceae family.},
}

*Genome, Mitochondrial
*Evolution, Molecular
Phylogeny
RNA, Transfer/genetics
Genomics

@article {pmid40323724,
year = {2025},
author = {Sloan, DB},
title = {Can transcriptome size and off-target effects explain the contrasting evolution of mitochondrial vs nuclear RNA editing?.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf042},
pmid = {40323724},
issn = {1420-9101},
support = {R35GM148134/NH/NIH HHS/United States ; MCB-2048407//National Science Foundation/ ; },
abstract = {Mitochondrial RNA editing has evolved independently in numerous eukaryotic lineages, where it generally restores conserved sequences and functional reading frames in mRNA transcripts derived from altered or disrupted mitochondrial protein-coding genes. In contrast to this "restorative" RNA editing in mitochondria, most editing of nuclear mRNAs introduces novel sequence variants and diversifies the proteome. This Perspective addresses the hypothesis that these completely opposite effects of mitochondrial vs. nuclear RNA editing arise from the enormous difference in gene number between the respective genomes. Because mitochondria produce a much smaller transcriptome, they likely create less opportunity for off-target editing, which has been supported by recent experimental work expressing mitochondrial RNA editing machinery in foreign contexts. In addition, there is recent evidence that the size and complexity of RNA targets may slow the kinetics and reduce efficiency of on-target RNA editing. These findings suggest that efficient targeting and a low risk of off-target editing have facilitated the repeated emergence of disrupted mitochondrial genes and associated restorative RNA editing systems via (potentially non-adaptive) evolutionary pathways that are not feasible in larger nuclear transcriptomes due to lack of precision.},
}

@article {pmid39997180,
year = {2025},
author = {Luccarini, A and Marcheggiani, F and Galeazzi, R and Zuccarotto, A and Castellano, I and Damiani, E},
title = {Characterizing the Ultraviolet (UV) Screening Ability of L-5-Sulfanylhistidine Derivatives on Human Dermal Fibroblasts.},
journal = {Marine drugs},
volume = {23},
number = {2},
pages = {},
pmid = {39997180},
issn = {1660-3397},
support = {2022MJBEK9, CUP E53D23009970006//Next Generation Europe/ ; },
mesh = {Humans ; *Ultraviolet Rays/adverse effects ; *Fibroblasts/drug effects/radiation effects/metabolism ; *Histidine/pharmacology/analogs & derivatives/chemistry ; *Sunscreening Agents/pharmacology/chemistry ; Cell Survival/drug effects/radiation effects ; Reactive Oxygen Species/metabolism ; Apoptosis/drug effects/radiation effects ; Skin/drug effects/radiation effects/cytology ; Antioxidants/pharmacology ; Mitochondria/drug effects/metabolism ; },
abstract = {Using sunscreens is one of the most widespread measures to protect human skin from sun ultraviolet radiation (UVR) damage. However, several studies have highlighted the toxicity of certain inorganic and organic UV filters used in sunscreens for the marine environment and human health. An alternative strategy may involve the use of natural products of marine origin to counteract UVR-mediated damage. Ovothiols are sulfur-containing amino acids produced by marine invertebrates, microalgae, and bacteria, endowed with unique antioxidant and UV-absorption properties. This study aimed to evaluate the protective effect of synthetic L-5-sulfanyl histidine derivatives, inspired by natural ovothiols, on human dermal fibroblasts (HDFs) upon UVA exposure. By using a custom-made experimental set-up to assess the UV screening ability, we measured the levels of cytosolic and mitochondrial reactive oxygen species (ROS), as well as cell viability and apoptosis in HDFs, in the presence of tested compounds, after UVA exposure, using flow cytometry assays with specific fluorescent probes. The results show that L-5-sulfanyl histidine derivatives display a UV screening capacity and prevent loss in cell viability, the production of cytosolic and mitochondrial ROS induced by UVA exposure in HDFs, and subsequent apoptosis. Overall, this study sheds light on the potential applications of marine-inspired sulfur-containing amino acids in developing alternative eco-safe sunscreens for UVR skin protection.},
}

Humans
*Ultraviolet Rays/adverse effects
*Fibroblasts/drug effects/radiation effects/metabolism
*Histidine/pharmacology/analogs & derivatives/chemistry
*Sunscreening Agents/pharmacology/chemistry
Cell Survival/drug effects/radiation effects
Reactive Oxygen Species/metabolism
Apoptosis/drug effects/radiation effects
Skin/drug effects/radiation effects/cytology
Antioxidants/pharmacology
Mitochondria/drug effects/metabolism

@article {pmid39417543,
year = {2025},
author = {Tu, F and Qiao, Y and Zhao, W and Wu, T},
title = {Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {35},
number = {3-4},
pages = {75-83},
doi = {10.1080/24701394.2024.2416179},
pmid = {39417543},
issn = {2470-1408},
mesh = {Animals ; *Sciuridae/genetics/classification ; Phylogeny ; Genome, Mitochondrial ; *Mitochondrial Proteins/genetics ; *Selection, Genetic ; *Genes, Mitochondrial ; },
abstract = {Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.},
}

Animals
*Sciuridae/genetics/classification
Phylogeny
Genome, Mitochondrial
*Mitochondrial Proteins/genetics
*Selection, Genetic
*Genes, Mitochondrial

@article {pmid40313116,
year = {2025},
author = {Li, C and Luo, Y and Li, S},
title = {Mechanistic insights of neuronal death and neuroprotective therapeutic approaches in stroke.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-24-01324},
pmid = {40313116},
issn = {1673-5374},
abstract = {Stroke, particularly ischemic stroke, is the leading cause of long-term disability and mortality worldwide. It occurs due to the occlusion of the cerebral arteries, which significantly reduces the delivery of blood, oxygen, and essential nutrients to brain tissues. This deprivation triggers a cascade of cellular events that ultimately leads to neuronal death. Recent studies have clarified the multifactorial pathogenesis of ischemic stroke, highlighting the roles of energy failure, excitotoxicity, oxidative stress, neuroinflammation, and apoptosis. This review aimed to provide a comprehensive insight into the fundamental mechanisms driving neuronal death triggered by ischemia and to examine the progress of neuroprotective therapeutic approaches designed to mitigate neuronal loss and promote neurological recovery after a stroke. Additionally, we explored widely accepted findings regarding the potential pathways implicated in neuronal death during ischemic stroke, including the interplay of apoptosis, autophagy, pyroptosis, ferroptosis, and necrosis, which collectively influence neuronal fate. We also discussed advancements in neuroprotective therapeutics, encompassing a range of interventions from pharmacological modulation to stem cell-based therapies, aimed at reducing neuronal injury and enhancing functional recovery following ischemic stroke. Despite these advancements, challenges remain in translating mechanistic insights into effective clinical therapies. Although neuroprotective strategies have shown promise in preclinical models, their efficacy in human trials has been inconsistent, often due to the complex pathology of ischemic stroke and the timing of interventions. In conclusion, this review synthesizes mechanistic insights into the intricate interplay of molecular and cellular pathways driving neuronal death post-ischemia. It sheds light on cutting-edge advancements in potential neuroprotective therapeutics, underscores the promise of regenerative medicine, and offers a forward-looking perspective on potential clinical breakthroughs. The ongoing evolution of precision-targeted interventions is expected to significantly enhance preventative strategies and improve clinical outcomes.},
}

@article {pmid40307667,
year = {2025},
author = {Koch, RE and Toomey, MB and Zhang, Y and Hill, GE},
title = {Mechanisms of carotenoid metabolism: understanding the links between red coloration, cellular respiration, and individual quality.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf022},
pmid = {40307667},
issn = {1557-7023},
abstract = {In many species of birds, red carotenoid coloration serves as an honest signal of individual quality, but the mechanisms that link carotenoid coloration to animal performance remain poorly understood. Most birds that display red carotenoid coloration of feathers, bills, or legs ingest yellow carotenoids and metabolically convert the yellow pigments to red. Here, we review two lines of investigation that have rapidly advanced understanding of the production of red carotenoid coloration in birds, potentially providing an explanation for how red coloration serves as a signal of quality: the identification of the genes that enable birds to be red and the confirmation of links between production of red pigments and core cellular function. CYP2J19 and BDH1L were identified as key enzymes that catalyze the conversion of yellow carotenoids to red carotenoids both in the retinas of birds for enhanced color vision and in the feathers and bills of birds for ornamentation. This CYP2J19 and BDH1L pathway was shown to be the mechanism for production of red coloration in diverse species of birds and turtles. In other studies, it was shown that male House Finches (Haemorhous mexicanus) have high concentrations of red carotenoids within liver mitochondria and that redness is positively associated with mitochondrial function. These observations suggested that the CYP2J19 and BDH1L pathway might be tightly associated with mitochondrial function. However, it was subsequently discovered that male House Finches do not use the CYP2J19 and BDH1L pathway to produce red pigments and that both CYP2J19 and BDH1L localize in the endoplasmic reticulum, not the mitochondria. Thus, we have the most detailed understanding of links between cellular function and redness in a bird species for which the enzymes to convert yellow to red pigments remain unknown, while we have the best understanding of the enzymatic pathways to red in species for which links to cellular function are largely unstudied. Deducing whether and how signals of quality arise from these distinct mechanisms of ornamental coloration is a current challenge in for scientists interested in the evolution of honest signaling.},
}

@article {pmid39913674,
year = {2025},
author = {Lavrov, DV and Turner, TL and Vicente, J},
title = {Pervasive Mitochondrial tRNA Gene Loss in Clade B of Haplosclerid Sponges (Porifera, Demospongiae).},
journal = {Genome biology and evolution},
volume = {17},
number = {3},
pages = {},
pmid = {39913674},
issn = {1759-6653},
support = {2048457//National Science Foundation/ ; },
mesh = {Animals ; *Porifera/genetics/classification ; *RNA, Transfer/genetics ; Phylogeny ; Genome, Mitochondrial ; Evolution, Molecular ; *Genes, Mitochondrial ; Mitochondria/genetics ; },
abstract = {Mitochondrial tRNA gene loss and cytosolic tRNA import are two common phenomena in mitochondrial biology, but their importance is often under-appreciated in animals. This is because the mitochondrial DNA (mtDNA) of most bilaterally symmetrical animals (Bilateria) encodes a complete set of tRNAs required for mitochondrial translation. By contrast, the mtDNA of nonbilaterian animals (phyla Cnidaria, Ctenophora, Porifera, and Placozoa) often contains a reduced set of tRNA genes, necessitating tRNA import from the cytosol. Interestingly, in many nonbilaterian lineages, tRNA gene content appears to be set early in evolution and remains conserved thereafter. Here, we report that Clade B of haplosclerid sponges (CBHS) represents an exception to this pattern, displaying considerable variation in tRNA gene content even among relatively closely related species. We determined mt-genome sequences for eight CBHS species and analyzed them in conjunction with six previously available sequences. Additionally, we sequenced mt-genomes for two species of haplosclerid sponges outside the CBHS and used them with eight previously available sequences as outgroups. We found that tRNA gene content varied widely within CBHS, ranging from three in an undescribed Haliclona species (Haliclona sp. TLT785) to 25 in Xestospongia muta and X. testudinaria. Furthermore, we found that all CBHS species outside the genus Xestospongia lacked the atp9 gene, with some also lacking atp8. Analysis of nuclear sequences from Niphates digitalis revealed that both atp8 and atp9 had transferred to the nuclear genome, while the absence of mt-tRNA genes indicated their genuine loss. We argue that CBHS can serve as a valuable system for studying mt-tRNA gene loss, mitochondrial import of cytosolic tRNAs, and the impact of these processes on mitochondrial evolution.},
}

Animals
*Porifera/genetics/classification
*RNA, Transfer/genetics
Phylogeny
Genome, Mitochondrial
Evolution, Molecular
*Genes, Mitochondrial
Mitochondria/genetics

@article {pmid40305847,
year = {2025},
author = {Sarkar, M and Pucadyil, TJ},
title = {Division of Labor among Fission Dynamins Based on Substrate Size.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.4c00862},
pmid = {40305847},
issn = {1520-4995},
abstract = {Membrane fission is necessary for the formation of vesicles in the endolysosomal system and for the division of organelles like peroxisomes, mitochondria, and chloroplasts. In these processes, fission is managed by certain members of the dynamin superfamily of proteins (DSPs). These DSPs are soluble proteins that self-assemble into helical scaffolds that hydrolyze GTP and force the constriction of tubular membrane substrates, leading to their fission. Based on where they function, fission DSPs can be operationally categorized into vesicle dynamins (VDs) or organelle dynamins (ODs). Even though they share conserved domains and display largely similar enzymatic properties, recent results reveal fundamental differences with respect to the size of the tubular membrane substrate that certain VDs and ODs can sever. Substrate sizes encountered during vesicle formation and organelle division are quite different and could have served as physical constraints that forced the evolution of VDs and ODs. Here, we briefly review and rationalize mechanisms for the division of labor among DSPs.The structural basis for substrate size-dependent fission activity among VDs and ODs remains unclear and represents an attractive area for future research.},
}

@article {pmid40302930,
year = {2025},
author = {Scheckhuber, CQ and Maciver, SK and de Obeso Fernandez Del Valle, A},
title = {Unveiling the molecular architecture of the mitochondrial respiratory chain of Acanthamoeba castellanii.},
journal = {Microbial cell (Graz, Austria)},
volume = {12},
number = {},
pages = {65-75},
pmid = {40302930},
issn = {2311-2638},
abstract = {Acanthamoeba castellanii is a ubiquitous free-living amoeba that can cause severe infections in humans. Unlike most other organisms, A. castellanii possesses a "complete" mitochondrial respiratory chain, meaning it con-tains several additional enzymes that contribute to its metabolic versa-tility and survival in diverse environments. This review provides a com-prehensive overview of the mitochondrial respiratory chain in A. castellanii, focusing on the key alternative components in-volved in oxidative phosphorylation and their roles in energy metabo-lism, stress response, and adaptation to various conditions. The func-tional characterization of the alternative oxidase (AOX), uncoupling pro-tein (UCP), and alternative NAD(P)H dehydrogenases, highlight their roles in reducing oxidative stress, modulating proton gradients, and adapting to changes in temperature and nutrient availability. These pro-teins and systems serve a role in the survival of A. castel-lanii under stressful conditions such as starvation and cold con-ditions. Further knowledge of the respiratory chain of the amoeba has potential implications for understanding the evolution of mitochondrial respiration and developing new therapies for treating Acanthamoeba infections.},
}

@article {pmid39834790,
year = {2025},
author = {Arias, E and Crawford, AJ and Hertz, A and Parra Olea, G},
title = {Deep cryptic diversity in the Craugastor podiciferus Species Group (Anura: Craugastoridae) of Isthmian Central America revealed by mitochondrial and nuclear data.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18212},
pmid = {39834790},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; *Anura/genetics/classification ; *DNA, Mitochondrial/genetics ; Central America ; Panama ; *Cell Nucleus/genetics ; *Genetic Variation ; *Mitochondria/genetics ; },
abstract = {The Craugastor podiciferus Species Group contains eleven species of terraranan frogs distributed from eastern Honduras to eastern Panama. All species have remarkable color pattern polymorphisms, which may contribute to potential taxonomic problems. We performed exhaustive sampling throughout the geographic distribution of the group to evaluate the phylogenetic relationships and biogeographic history of all named species based on two mitochondrial markers and nuclear ddRAD loci. We also implemented various species delimitation methods to test for the presence of unconfirmed candidate species within the group. Molecular phylogenetic analyses showed that the group contains four major clades. All currently named species are supported by molecular data, yet species richness within the group is clearly underestimated. Species delimitation was discordant between the mitochondrial and nuclear datasets and among analytical methods. Adopting a conservative approach, we propose that the C. podiciferus species group contains at least 12 unconfirmed candidate species. Ancestral area reconstruction showed that the group originated and diversified in the highlands of the Talamancan montane forest ecoregion of Costa Rica and western Panama.},
}

Animals
Phylogeny
*Anura/genetics/classification
*DNA, Mitochondrial/genetics
Central America
Panama
*Cell Nucleus/genetics
*Genetic Variation
*Mitochondria/genetics

@article {pmid40300602,
year = {2025},
author = {Baumann, N and Wagener, RJ and Javed, A and Conti, E and Abe, P and Lopes, A and Sansevrino, R and Lavalley, A and Magrinelli, E and Szalai, T and Fuciec, D and Ferreira, C and Fièvre, S and Fouassier, A and D'Amico, D and Harschnitz, O and Jabaudon, D},
title = {Regional differences in progenitor metabolism shape brain growth during development.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.04.003},
pmid = {40300602},
issn = {1097-4172},
abstract = {Mammals have particularly large forebrains compared with other brain parts, yet the developmental mechanisms underlying this regional expansion remain poorly understood. Here, we provide a single-cell-resolution birthdate atlas of the mouse brain (www.neurobirth.org), which reveals that while hindbrain neurogenesis is transient and restricted to early development, forebrain neurogenesis is temporally sustained through reduced consumptive divisions of ventricular zone progenitors. This atlas additionally reveals region-specific patterns of direct and indirect neurogenesis. Using single-cell RNA sequencing, we identify evolutionarily conserved cell-cycle programs and metabolism-related molecular pathways that control regional temporal windows of proliferation. We identify the late neocortex-enriched mitochondrial protein FAM210B as a key regulator using in vivo gain- and loss-of-function experiments. FAM210B elongates mitochondria and increases lactate production, which promotes progenitor self-replicative divisions and, ultimately, the larger clonal size of their progeny. Together, these findings indicate that spatiotemporal heterogeneity in mitochondrial function regulates regional progenitor cycling behavior and associated clonal neuronal production during brain development.},
}

@article {pmid40290089,
year = {2025},
author = {Reumann, S and Parasyri, A},
title = {Protein Acetylation as a Novel Post-translational Modification of Plant Peroxisomal Proteins.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf089},
pmid = {40290089},
issn = {1460-2431},
abstract = {Plant peroxisomes compartmentalize many important metabolic functions, but little is known how these pathways are regulated at the post-translational level. Few plant peroxisomal proteins have been shown to be subjected to reversible phosphorylation or ubiquitination, but other post-translational modifications are hardly known for peroxisomes from animals, fungi, and plants. We here address the question whether plant peroxisomal metabolism might be regulated by protein acetylation. We summarize available knowledge on protein acetylation in plastids and mitochondria, focusing on the catalytic machinery and the regulation of target enzymes. We screened global acetylome studies of Arabidopsis for known proteins of peroxisomes that are N-terminally or Lys acetylated. For selected matrix proteins, we mapped the acetylated Lys sites onto their AlphaFold 3D models to predict their effect on enzyme activity and oligomerization. We also summarize knowledge on two Arabidopsis acetyl transferases that have recently been identified as novel peroxisomal matrix proteins. We deduce their evolution in peroxisomes and partly their functions, as far as they can be predicted from available structural models. This information allows us to identify experimental strategies to define the postulated new regulatory mechanism of protein acetylation for plant peroxisomes in the near future. (193 words, <200).},
}

@article {pmid40283904,
year = {2025},
author = {Sakrajda, K and Rybakowski, JK},
title = {The Mechanisms of Lithium Action: The Old and New Findings.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {4},
pages = {},
pmid = {40283904},
issn = {1424-8247},
abstract = {Despite lithium's presence in modern psychiatry for three-quarters of a century, the mechanisms of its therapeutic action have not been fully elucidated. This article presents the evolution of the views on these mechanisms, and both the old and new findings are discussed. Among the old mechanisms, lithium's effect on the purinergic system; electrolyte metabolism; membrane transport; and second messenger systems, namely, cyclic nucleotide and phosphatidylinositol (PI), glycogen synthase kinase-3beta (GSK-3β), brain-derived neurotrophic factor, and neurotransmitters, are discussed. The new data were obtained from in vitro studies, molecular biology, and genetic research. They showed the effects of lithium on the immune system, biological rhythms, telomere functions, and mitochondria. In this article, each lithium mechanism is considered in the light of its association with the pathogenesis of bipolar disorder or/and as a marker of the lithium response. Although not exhaustive, this review elucidates the multiple potential mechanisms of lithium action. It was also observed that many seemingly "old" mechanisms have experienced a resurgence in research conducted during the 21st century. Additionally, many studies converged on the previously postulated mechanisms of lithium inhibiting GSK-3β and PI.},
}

@article {pmid39738580,
year = {2025},
author = {Ahmed, S and Nadeem, MS and Johansson, AM and Jonas, E and Muhammad, K and Mehmood, SA},
title = {Molecular diversity and phylogenetic analysis of ten sheep breeds from Khyber Pakhtunkhwa, Pakistan, based on mitochondrial D-loop sequences.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {36},
number = {1},
pages = {129-139},
pmid = {39738580},
issn = {1432-1777},
mesh = {Animals ; *Phylogeny ; Pakistan ; *DNA, Mitochondrial/genetics/chemistry ; Sheep/genetics/classification ; *Genetic Variation ; Haplotypes ; Female ; Breeding ; *Mitochondria/genetics ; },
abstract = {Livestock farming has a key role in many rural communities both economically and culturally. It plays an important role in overcoming the deficiencies of meat, milk, wool and various by-products. Pakistan has a large number of livestock, well-adapted to local conditions. and has some of the best tropical dairy breeds. Native sheep breeds stand a vital asset to the country's livestock sector because of their adaptability and unique genetic traits. However, knowledge of the genetic diversity of these sheep breeds remains limited. This study aims to investigate the genetic diversity of 10 local sheep breeds from Khyber Pakhtunkhwa by analyzing the mitochondrial D-loop from 159 individual samples of females. The sequenced data from the mtDNA D-loop showed 106 different haplotypes, with a haplotype diversity of 0.9854 ± 0.0041. Analysis of the mitochondrial D-loop revealed three distinct haplogroups (HapA, HapB, and HapC). Out of the 159 sequences, 125 (77.99%) grouped with HapA, 30 (18.87%) with HapB, and 5 (3.14%) with HapC. While HapA and HapB are commonly found in sheep breeds worldwide, the identification of 5 sequences belonging to HapC was unexpected. This haplogroup was seen in four sheep breeds: Afghani, Australian, Gauder and Waziri. Most interestingly, the two Pakistani-origin breeds, the Waziri sheep breed, from South of Waziristan and the Gauder, a crossbreed, have been identified with HapC haplogroup. This indicates that the sheep breeds of Khyber Pakhtunkhwa belong to three distinct phylogenetic lineages, suggesting a probable gene flow from the southwest to the northeast regions of the province.},
}

Animals
*Phylogeny
Pakistan
*DNA, Mitochondrial/genetics/chemistry
Sheep/genetics/classification
*Genetic Variation
Haplotypes
Female
Breeding
*Mitochondria/genetics

@article {pmid40272291,
year = {2025},
author = {Liu, X and Yan, Y},
title = {Advances in origin, evolution, and pathogenesis of optic disc drusen: A narrative review.},
journal = {Indian journal of ophthalmology},
volume = {73},
number = {5},
pages = {637-647},
doi = {10.4103/IJO.IJO_937_24},
pmid = {40272291},
issn = {1998-3689},
mesh = {Humans ; *Optic Disk Drusen/etiology/diagnosis ; *Tomography, Optical Coherence/methods ; *Optic Disk/pathology/diagnostic imaging ; *Visual Fields ; *Retinal Ganglion Cells/pathology ; },
abstract = {Optic disc drusen (ODD) is acellular calcified deposits found mainly in front of the lamina cribrosa within the optic nerve. It can cause chronic or acute vision loss. There has been progress in clinical diagnosis using ophthalmic multimodal imaging in recent years. We conducted a database search on PubMed and Google Scholar (April 2023) with no restrictions on publication year or language. We used the terms: ("optic disc drusen") OR ("optic nerve head drusen") OR ("drusen of optic nerve head"). Other terms included gene, mutation, scleral canal, axonal transport, calcinosis, mitochondria, blood vessel, vasculature, visual field, vision, and optical coherence tomography to identify publications. Etiologically, ODD may stem from congenital genetic defects, aberrant axoplasmic transport, anatomical abnormalities, and mechanical factors during ocular duction. Clinically, ODD is linked to progressive visual field defects and vascular complications. Detection of deeply buried ODD can be challenging, but advances in optical coherence tomography make early identification possible. Structural changes, including retinal nerve fiber layer thinning, can be monitored. Increasing reports indicate vascular complications, including anterior ischemic optic neuropathy, in ODD patients. Currently, ODD-related visual field defects are not effectively treated, and observation remains the primary management approach. Future pathological discoveries or the establishment of animal models may provide new evidence for revealing the pathogenesis of ODD.},
}

Humans
*Optic Disk Drusen/etiology/diagnosis
*Tomography, Optical Coherence/methods
*Optic Disk/pathology/diagnostic imaging
*Visual Fields
*Retinal Ganglion Cells/pathology

@article {pmid39674307,
year = {2025},
author = {Pistolesi, A and Ranieri, G and Calvani, M and Guasti, D and Chiarugi, A and Buonvicino, D},
title = {Microglial suppression by myeloperoxidase inhibitor does not delay neurodegeneration in a mouse model of progressive multiple sclerosis.},
journal = {Experimental neurology},
volume = {385},
number = {},
pages = {115095},
doi = {10.1016/j.expneurol.2024.115095},
pmid = {39674307},
issn = {1090-2430},
mesh = {Animals ; Mice ; *Microglia/drug effects ; Disease Models, Animal ; *Peroxidase/antagonists & inhibitors/metabolism ; Mice, Inbred NOD ; Female ; *Multiple Sclerosis, Chronic Progressive/pathology/drug therapy ; Disease Progression ; Reactive Oxygen Species/metabolism ; *Propionates/pharmacology/therapeutic use ; *Enzyme Inhibitors/therapeutic use/pharmacology ; Mitochondria/drug effects/metabolism ; *Nerve Degeneration/pathology/drug therapy ; Spinal Cord/pathology/drug effects ; Aminopyridines ; Pyrroles ; },
abstract = {Drugs able to efficiently counteract the progression of multiple sclerosis (MS) are still an unmet need. Numerous preclinical evidence indicates that reactive oxygen-generating enzyme myeloperoxidase (MPO), expressed by neutrophils and microglia, might play a key role in neurodegenerative disorders. Then, the MPO inhibition has been evaluated in clinical trials in Parkinson's and multiple system atrophy patients, and a clinical trial for the treatment of amyotrophic lateral sclerosis is underway. The effects of MPO inhibition on MS patients have not yet been explored. In the present study, by adopting the NOD mouse model of progressive MS (PMS), we evaluated the pharmacological effects of the MPO inhibitor verdiperstat (also known as AZD3241) on functional, immune, and mitochondrial parameters during disease evolution. We found that daily treatment with verdiperstat did not affect the pattern of progression as well as survival, despite its ability to reduce mitochondrial reactive oxygen species and microglia activation in the spinal cord of immunized mice. Remarkably, verdiperstat did not affect adaptive immunity, neutrophils invasion as well as mitochondrial derangement in the spinal cords of immunized mice. Data suggest that microglia suppression is not sufficient to prevent disease evolution, corroborating the hypothesis that immune-independent components drive neurodegeneration in progressive MS.},
}

Animals
Mice
*Microglia/drug effects
Disease Models, Animal
*Peroxidase/antagonists & inhibitors/metabolism
Mice, Inbred NOD
Female
*Multiple Sclerosis, Chronic Progressive/pathology/drug therapy
Disease Progression
Reactive Oxygen Species/metabolism
*Propionates/pharmacology/therapeutic use
*Enzyme Inhibitors/therapeutic use/pharmacology
Mitochondria/drug effects/metabolism
*Nerve Degeneration/pathology/drug therapy
Spinal Cord/pathology/drug effects
Aminopyridines
Pyrroles

@article {pmid40271811,
year = {2025},
author = {Bravo-Arévalo, JE},
title = {Tracing the evolutionary pathway: on the origin of mitochondria and eukaryogenesis.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.70109},
pmid = {40271811},
issn = {1742-4658},
support = {CF-2023-I-1545//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; PAPIIT: IN218424//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; },
abstract = {The mito-early hypothesis posits that mitochondrial integration was a key driver in the evolution of defining eukaryotic characteristics (DECs). Building on previous work that identified endosymbiotic selective pressures as central to eukaryotic cell evolution, this study examines how endosymbiotic gene transfer (EGT) and the resulting genomic and bioenergetic constraints shaped mitochondrial protein import systems. These systems were crucial for maintaining cellular function in early eukaryotes and facilitated their subsequent diversification. A primary focus is the co-evolution of mitochondrial import mechanisms and eukaryotic endomembrane complexity. Specifically, I investigate how the necessity for nuclear-encoded mitochondrial protein import drove the adaptation of bacterial secretion components, alongside eukaryotic innovations, to refine translocation pathways. Beyond enabling bioenergetic expansion, mitochondrial endosymbiosis played a fundamental role in the emergence of compartmentalisation and cellular complexity in LECA, driving the evolution of organellar networks. By integrating genomic, structural and phylogenetic evidence, this study aimed to contribute to the mito-early framework, clarifying the mechanisms that linked mitochondrial acquisition to the origin of eukaryotic cells.},
}

@article {pmid39567420,
year = {2025},
author = {Yun, BH and Kim, YH and Han, HS and Bang, IC},
title = {Population genetics analysis based on mitochondrial cytochrome c oxidase subunit I (CO1) gene sequences of Cottus koreanus in South Korea.},
journal = {Genes & genomics},
volume = {47},
number = {2},
pages = {207-221},
pmid = {39567420},
issn = {2092-9293},
support = {NRF-2021R1A6A1A03039503//Ministry of Education/ ; Soonchunhyang University//Soonchunhyang University/ ; },
mesh = {*Electron Transport Complex IV/genetics ; Republic of Korea ; Animals ; Haplotypes ; Genetics, Population ; Genetic Variation ; Phylogeny ; Mitochondria/genetics ; *Fishes/genetics ; },
abstract = {BACKGROUND: The freshwater sculpin Cottus koreanus is endemic to the Korean Peninsula and has a fluvial life history. However, its population has been greatly reduced and it is now listed as an endangered class II species.

OBJECTIVE: To obtain important information for its conservation, we examine the genetic diversity, population structure, and demographic history of C. koreanus through mitochondrial cytochrome c oxidase subunit I (CO1) gene sequence analysis.

METHODS: We analyzed the CO1 gene sequences of 430 individuals of C. koreanus from 23 populations in South Korea.

RESULTS: In all, 32 haplotypes were defined by 124 variable nucleotide sites, of which 28 were unique haplotypes not shared with other regional populations. All sampled populations had high haplotype diversity (Hd = 0.941) and low nucleotide diversity (π = 0.0146). Median-joining network analysis identified two divergent clusters: cluster I that had unique haplotype patterns assigned to each population and cluster II that had a star-like pattern. Each was supported by pairwise FST values and hierarchical analysis of molecular variance. The results of the mismatch distribution, goodness-of-fit test, and extended Bayesian skyline plot analysis showed that cluster I has experienced a gradual population expansion since the last glacial maximum, while cluster II experienced a sudden one. The results of neutrality testing supported the results for cluster II but the signal was weak.

CONCLUSIONS: C. koreanus inhabits the upper reaches of rivers and has extremely low dispersal ability, resulting in unique genetic structure patterns among populations. Therefore, all populations should be managed and conserved separately.},
}

*Electron Transport Complex IV/genetics
Republic of Korea
Animals
Haplotypes
Genetics, Population
Genetic Variation
Phylogeny
Mitochondria/genetics
*Fishes/genetics

@article {pmid40265338,
year = {2025},
author = {Venkatraman, K and Lipp, NF and Budin, I},
title = {Origin and evolution of mitochondrial inner membrane composition.},
journal = {Journal of cell science},
volume = {138},
number = {9},
pages = {},
doi = {10.1242/jcs.263780},
pmid = {40265338},
issn = {1477-9137},
support = {GM142960/NH/NIH HHS/United States ; GBMF9734//Gordon and Betty Moore Foundation/ ; //University of California/ ; },
mesh = {*Mitochondrial Membranes/metabolism/chemistry ; *Mitochondria/metabolism/genetics ; Humans ; Animals ; Mitochondrial Proteins/metabolism ; *Evolution, Molecular ; },
abstract = {Unique membrane architectures and lipid building blocks underlie the metabolic and non-metabolic functions of mitochondria. During eukaryogenesis, mitochondria likely arose from an alphaproteobacterial symbiont of an Asgard archaea-related host cell. Subsequently, mitochondria evolved inner membrane folds known as cristae alongside a specialized lipid composition supported by metabolic and transport machinery. Advancements in phylogenetic methods and genomic and metagenomic data have suggested potential origins for cristae-shaping protein complexes, such as the mitochondrial contact site and cristae-organizing system (MICOS). MICOS protein homologs function in the formation of cristae-like intracytoplasmic membranes (ICMs) in diverse extant alphaproteobacteria. The machinery responsible for synthesizing key mitochondrial phospholipids - which cooperate with cristae-shaping proteins to establish inner membrane architecture - could have also evolved from a bacterial ancestor, but its origins have been less explored. In this Review, we examine the current understanding of mitochondrial membrane evolution, highlighting distinctions between prokaryotic and eukaryotic mitochondrial-specific proteins and lipids and their differing roles in shaping cristae and ICM architecture, and propose a model explaining the concurrent specialization of the mitochondrial lipidome and inner membrane structure in eukaryogenesis. We discuss how advancements across a range of disciplines are shedding light on how multiple membrane components co-evolved to support the central functions of eukaryotic mitochondria.},
}

*Mitochondrial Membranes/metabolism/chemistry
*Mitochondria/metabolism/genetics
Humans
Animals
Mitochondrial Proteins/metabolism
*Evolution, Molecular

@article {pmid40265287,
year = {2025},
author = {Davanzo, GG and Castelucci, BG and de Souza, GF and Muraro, SP and Menezes Dos Reis, L and de Oliveira, IB and Fachi, JL and Virgilio-da-Silva, JV and Berçot, MR and Fernandes, MF and de Oliveira, S and Araujo, NVP and Ribeiro, G and de Castro, G and Costa, WLG and Santoro, AL and Rodrigues-Luiz, GF and do Carmo, HRP and Breder, I and Mori, MA and Farias, AS and Martins-de-Souza, D and Guarnieri, JW and Wallace, DC and Vinolo, MAR and Proença-Módena, JL and Beheshti, A and Sposito, AC and Moraes-Vieira, PM},
title = {Obesity-Induced Metabolic Priming Exacerbates SARS-CoV-2 Inflammation.},
journal = {Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imm.13934},
pmid = {40265287},
issn = {1365-2567},
support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 406974/2023-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2274/20//Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas/ ; 20/04579-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 20/16030-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2015/15626-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 18/15313-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2016/18031-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 21/08354-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 13/07607-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Despite the early recognition that individuals living with obesity are more prone to develop adverse outcomes during COVID-19, the mechanisms underlying these conditions are still unclear. During obesity, an accumulation of free fatty acids (FFAs) in the circulation promotes low-grade inflammation. Here, we show that FFAs induce epigenetic reprogramming of monocytes, exacerbating their inflammatory profile after SARS-CoV-2 infection, a mechanism named metabolic-primed immunity. Monocytes from people with obesity or primed with palmitate, a central component of circulating FFAs, presented elevated viral load and higher gene expression of IL-6. Palmitate-primed monocytes upregulate fatty acid oxidation and FFAs entry into the mitochondria. FFA-derived acetyl-CoA is then converted into citrate, exiting the mitochondria and is used to support H3K18 histone acetylation, which regulates IL-6 accessibility. Ingestion of palm oil by lean and healthy individuals increased circulating FFAs levels and was sufficient to exacerbate the inflammatory profile of monocytes upon SARS-CoV-2 infection. Our findings demonstrate that obesity-derived FFAs induce the metabolic priming of monocytes, which exacerbates the inflammatory response observed in people with severe COVID-19.},
}

@article {pmid40119623,
year = {2025},
author = {Tamburino, R and D'Agostino, N and Aufiero, G and Nicolia, A and Facchiano, A and Giordano, D and Sannino, L and Paparo, R and Arimura, SI and Scotti, N and Cardi, T},
title = {Mitochondrial gene editing and allotopic expression unveil the role of orf125 in the induction of male fertility in some Solanum spp. hybrids and in the evolution of the common potato.},
journal = {Plant biotechnology journal},
volume = {23},
number = {5},
pages = {1862-1875},
doi = {10.1111/pbi.70012},
pmid = {40119623},
issn = {1467-7652},
support = {//European Commission/ ; },
mesh = {*Plant Infertility/genetics ; *Gene Editing ; *Solanum/genetics/physiology ; *Solanum tuberosum/genetics/physiology ; Plant Proteins/genetics/metabolism ; Genome, Mitochondrial/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Genic-cytoplasmic male sterility (CMS) due to interactions between nuclear and cytoplasmic genomes is a well-known phenomenon in some Solanum spp. hybrids, but genes involved are not known. In this study, the chondriomes of two isonuclear male-fertile and sterile somatic hybrids (SH9A and SH9B, respectively) between the common potato (S. tuberosum Group Tuberosum, tbr) and the wild species S. commersonii were sequenced and compared to those of parental species to identify mitochondrial genes involved in the expression of male sterility. A putative novel gene (orf125) was found only in tbr and in male-sterile hybrids. Physical or functional deletion of orf125 by mtDNA editing in SH9B and its allotopic expression in SH9A clearly demonstrated that orf125 affects male fertility. Besides knockout mutants induced by mitoTALEN and DddA-derived cytosine base editing, specific orf125 missense mutations generated by the latter approach also induced reversion to male fertility in edited SH9B plants, prompting further studies on ORF125 structure-function relationship. The organization of the mitochondrial genome region implicated in CMS was found to be conserved across all common potato accessions, while an identical copy of tbr orf125 was detected in accessions belonging to the S. berthaultii species complex (ber). Such findings corroborate the hypothesis that ber accessions with T/β cytoplasm outcrossed as female with Andean potato, giving rise to the differentiation of the Chilean potato, and highlight the origin of mitochondrial factors contributing to genic-cytoplasmic male sterility in some tuber-bearing Solanum hybrids. Our results contribute to the development of innovative breeding approaches in potato.},
}

*Plant Infertility/genetics
*Gene Editing
*Solanum/genetics/physiology
*Solanum tuberosum/genetics/physiology
Plant Proteins/genetics/metabolism
Genome, Mitochondrial/genetics
DNA, Mitochondrial/genetics
Mitochondria/genetics

@article {pmid40252292,
year = {2025},
author = {Cournoyer, JE and De, BC and Mehta, AP},
title = {Molecular and biochemical insights from natural and engineered photosynthetic endosymbiotic systems.},
journal = {Current opinion in chemical biology},
volume = {87},
number = {},
pages = {102598},
doi = {10.1016/j.cbpa.2025.102598},
pmid = {40252292},
issn = {1879-0402},
abstract = {Mitochondria and chloroplasts evolved through the transformation of bacterial endosymbionts established within the host cells. Studies on these organelles have provided several phylogenetic and biochemical insights related to this remarkable evolutionary transformation. Additionally, comparative studies between naturally existing endosymbionts and present-day organelles have allowed us to identify important common features of endosymbiotic evolution. In this review, we discuss hallmarks of photosynthetic endosymbiotic systems, particularly focusing on some of the fascinating molecular changes that occur in the endosymbiont and the host as the endosymbiont/host chimera evolves and transforms endosymbionts into organelles; these include the following: (i) endosymbiont genome minimization and host/endosymbiont gene transfer, (ii) protein import/export systems, (iii) metabolic crosstalk between the endosymbiont, (iv) alterations to the endosymbiont peptidoglycan, and (v) host-controlled replication of endosymbionts/organelles. We discuss these hallmarks in the context of naturally existing photosynthetic endosymbiotic systems and present-day chloroplasts. Further, we also briefly discuss laboratory efforts to engineer endosymbiosis between photosynthetic bacteria and host cells, the lessons learned from these studies, future directions of these studies, and their implications on evolutionary biology and synthetic biology.},
}

@article {pmid40250433,
year = {2025},
author = {Rao, AK and Yee, D and Chevalier, F and LeKieffre, C and Pavie, M and Olivetta, M and Dudin, O and Gallet, B and Hehenberger, E and Seifi, M and Jug, F and Deschamps, J and Wu, TD and Gast, R and Jouneau, PH and Decelle, J},
title = {Hijacking and integration of algal plastids and mitochondria in a polar planktonic host.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.03.076},
pmid = {40250433},
issn = {1879-0445},
abstract = {In oceanic plankton, various hosts are capable of engulfing and temporarily integrating microalgae (photosymbiosis) or just their photosynthetic plastids (kleptoplastidy) from the environment. These cellular interactions have been hypothesized to be representative of evolutionary steps in plastid acquisition in eukaryotes, but the underlying mechanisms are not fully understood. Here, we studied a polar kleptoplastidic dinoflagellate, which is known to steal plastids of the microalga Phaeocystis antarctica. We tracked the morphology and activity of stolen plastids over several months by combining multimodal subcellular imaging and photophysiology. Upon integration inside a host vacuole, the volume of plastids and pyrenoids significantly increased, and photosynthetic activity was boosted. This may be supported by the retention of a 50-fold larger algal nucleus for ∼1 week. Once the algal nucleus was lost, there was a decrease in plastid volume and photosynthesis, but nucleus- and plastid-encoded photosystem subunits were still detected. Carbon fixation and transfer to the host were also maintained after >2 months. We also showed that the algal mitochondrion was stolen and retained for several months, transforming into an extensive network interacting with plastids. This highlights a complex strategy in plankton along the continuum of plastid symbioses, where both plastids and mitochondria of a microalga are hijacked by a host for several months without the algal nucleus. This association, which we found to be widely distributed in polar regions, suggests that plastid-mitochondrion interaction may have played a role in the evolution of plastid acquisition and opens new questions about host control and organelle maintenance.},
}

@article {pmid39932860,
year = {2025},
author = {Zhao, S and Hou, J and Deng, L and Qi, Z and Tao, N and Ruan, W and Zheng, J and Wang, W and Xu, Q and Saiding, Q and Kong, N and Liu, YN and Tao, W},
title = {Lactate-Modulating Nanozyme-Mediated Mitochondrial Respiration Block for Tumor Immunosuppression Remodeling.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {64},
number = {17},
pages = {e202422203},
doi = {10.1002/anie.202422203},
pmid = {39932860},
issn = {1521-3773},
support = {22238013//National Natural Science Foundation of China/ ; 22178393//National Natural Science Foundation of China/ ; 2019TP1001//Hunan Provincial Science and Technology Plan Project/ ; 2020JJ3044//Hunan Provincial Science and Technology Plan Project/ ; //High-Performance Computing Center of Central South University/ ; 2024M764247//China Postdoctoral Science Foundation/ ; LCD1034625//American Lung Association Cancer Discovery award/ ; 2022A017206//American Lung Association Courtney Cox Cole Lung Cancer Research award/ ; 2023A004452//Harvard/Brigham Health & Technology Innovation Fund/ ; 2022A002721//Nanotechnology Foundation/ ; 018129//Distinguished Chair Professorship Foundation/ ; },
mesh = {Humans ; *Lactic Acid/metabolism ; *Mitochondria/metabolism/drug effects ; Tumor Microenvironment/drug effects ; *Neoplasms/metabolism/immunology ; Mixed Function Oxygenases/metabolism ; Copper/chemistry ; Cell Line, Tumor ; },
abstract = {Abnormal lactate metabolism in tumor cells leads to immune escape in the tumor microenvironment. Intervening in specific lactate metabolic pathways while blocking downstream pyruvate influx holds great promise for overcoming conventional lactate-targeted therapy limitations such as short half-life, insufficient lactate consumption, and pathological microenvironment elasticity. Herein, a nanocatalytic medicine based on carbondoping engineered copper nitride enzyme (Cu3N-C NE) with enhanced lactate oxidase (LOX) activity was carefully designed. Computational results revealed that the introduction of C favors activation of the hydroxyalkyl C-H bond in lactate by the polarization of adjacent hydroxyl groups, correspondingly facilitating the abstraction of hydrogen atoms from the desired α-C-H and α-C-O-H groups in lactate via the hydrogen atom-transfer (HAT) process. The Cu3N-C NEs could downregulate lactate levels in tumor cells for robust remodeling of the immunosuppressive microenvironment and further block as-generated pyruvate to influx into the mitochondrial respiration, achieving lactate homeostasis reprogramming. Our study provides a proof-of-concept design of next-generation lactate-modulation nanomedicine via heteroatom-doping and evolution with the additional potential to expedite the industrial production of lactate to pyruvate.},
}

Humans
*Lactic Acid/metabolism
*Mitochondria/metabolism/drug effects
Tumor Microenvironment/drug effects
*Neoplasms/metabolism/immunology
Mixed Function Oxygenases/metabolism
Copper/chemistry
Cell Line, Tumor

@article {pmid40239883,
year = {2025},
author = {Wallnoefer, O and Formaggioni, A and Plazzi, F and Passamonti, M},
title = {Convergent evolution in nuclear and mitochondrial OXPHOS subunits underlies the phylogenetic discordance in deep lineages of Squamata.},
journal = {Molecular phylogenetics and evolution},
volume = {208},
number = {},
pages = {108358},
doi = {10.1016/j.ympev.2025.108358},
pmid = {40239883},
issn = {1095-9513},
abstract = {The order Squamata is a good candidate for detecting unusual patterns of mitochondrial evolution. The lineages leading to the snake and agamid clades likely experienced convergent evolution in mitochondrial OXidative PHOSphorylation (OXPHOS) genes, which provides strong support for the sister relationship of these two groups. The OXPHOS subunits are encoded by both the nuclear and mitochondrial genomes, which are subject to distinct evolutionary pressures. Nevertheless, the cooperation between OXPHOS subunits is essential for proper OXPHOS function, as incompatibilities between subunits can be highly deleterious. In the present study, we annotated OXPHOS genes of 56 Squamata species. The nuclear OXPHOS subunits that physically interact with mitochondrial proteins also support the clade sister relationship between snakes and agamids. Additionally, we found a significant number of convergent amino acid changes between agamids and snakes, not only in mitochondrial OXPHOS genes, but also in nuclear ones, with a higher rate of convergence in the nuclear OXPHOS subunits that play central roles in the OXPHOS complexes, like COX4 and NDUFA4. Overall, the common selective pressures in two distinct lineages can lead two sets of genes, encoded by two different genomes, to exhibit similar patterns of convergent evolution, as well as similar evolutionary rates. As a consequence, the coevolution of interdependent subunits and their adaptation to specific evolutionary pressures can heavily influence the molecular structure of cytonuclear enzyme complexes and blur phylogenetic signals.},
}

@article {pmid40238856,
year = {2025},
author = {Lawson, LP and Bittencourt-Silva, GB and Conradie, W and Portik, DM and Loader, SP},
title = {A phylogenomic perspective reveals mitochondrial-nuclear discordance and previously undescribed species nested within a widespread East African Reed frog species (Hyperolius substriatus Ahl, 1931).},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0318951},
pmid = {40238856},
issn = {1932-6203},
mesh = {Animals ; Female ; Africa, Eastern ; *Anura/genetics/classification ; *Cell Nucleus/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; *Phylogeny ; Phylogeography ; },
abstract = {The sub-montane East African Reed Frog, Hyperolius substriatus Ahl, 1931 (Spotted Reed Frog) has a fragmented highland distribution throughout East Africa. Previous studies show extensive mitochondrial divergence between four lineages of African Spotted Reed Frogs that roughly correspond to previously-recognized subspecies. These may have conservation implications if formally described. However, as mitochondrial-based population models only track maternal patterns, further genomic datasets are necessary to assess the distinctness of these lineages in relation to historically recognized morphological subspecies. In this study, we expanded sampling to newly discovered localities and assessed mitochondrial and genomic data to better understand phylogeography and landscape genomics of this species. We found that genomic clades (biparentally inherited) confirm some of the mitochondrial structure (female inherited), but also revealed multiple cases of mitonuclear discordance particularly within the Udzungwa Mountain block, which may have two separate founding events based on peripatric mitochondrial lineages and panmictic genomic signals. Taken together, the three clades within the geographical range of H. substriatus through Tanzania, Malawi, and Mozambique correspond to three previously-identified subspecies and lineages, and have both spatially cohesive and population-specific patterns of geneflow and isolation with neighboring highland locations.},
}

Animals
Female
Africa, Eastern
*Anura/genetics/classification
*Cell Nucleus/genetics
*DNA, Mitochondrial/genetics
*Mitochondria/genetics
*Phylogeny
Phylogeography

@article {pmid40237040,
year = {2025},
author = {Kervella, M and Bertile, F and Bouillaud, F and Criscuolo, F},
title = {The cell origin of reactive oxygen species and its implication for evolutionary trade-offs.},
journal = {Open biology},
volume = {15},
number = {4},
pages = {240312},
pmid = {40237040},
issn = {2046-2441},
support = {//Centre National de la Recherche Scientifique/ ; },
mesh = {*Reactive Oxygen Species/metabolism ; Animals ; *Mitochondria/metabolism ; Humans ; *Biological Evolution ; Oxidative Stress ; Energy Metabolism ; Homeostasis ; Antioxidants/metabolism ; Oxidation-Reduction ; },
abstract = {The allocation of resources in animals is shaped by adaptive trade-offs aimed at maximizing fitness. At the heart of these trade-offs, lies metabolism and the conversion of food resources into energy, a process mostly occurring in mitochondria. Yet, the conversion of nutrients to utilizable energy molecules (adenosine triphosphate) inevitably leads to the by-production of reactive oxygen species (ROS) that may cause damage to important biomolecules such as proteins or lipids. The 'ROS theory of ageing' has thus proposed that the relationship between lifespan and metabolic rate may be mediated by ROS production. However, the relationship is not as straightforward as it may seem: not only are mitochondrial ROS crucial for various cellular functions, but mitochondria are also actually equipped with antioxidant systems, and many extra-mitochondrial sources also produce ROS. In this review, we discuss how viewing the mitochondrion as a regulator of cellular oxidative homeostasis, not merely a ROS producer, may provide new insights into the role of oxidative stress in the reproduction-survival trade-off. We suggest several avenues to test how mitochondrial oxidative buffering capacity might complement current bioenergetic and evolutionary studies.},
}

*Reactive Oxygen Species/metabolism
Animals
*Mitochondria/metabolism
Humans
*Biological Evolution
Oxidative Stress
Energy Metabolism
Homeostasis
Antioxidants/metabolism
Oxidation-Reduction

@article {pmid40231068,
year = {2025},
author = {Bagdonaitė, L and Leder, EH and Lifjeld, JT and Johnsen, A and Mauvisseau, Q},
title = {Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mitochondrial DNA copy number in songbird blood and sperm cells.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19278},
pmid = {40231068},
issn = {2167-8359},
mesh = {Animals ; Male ; *DNA, Mitochondrial/genetics/blood/analysis ; *Spermatozoa/chemistry ; Reproducibility of Results ; *DNA Copy Number Variations ; *Songbirds/genetics/blood ; *Polymerase Chain Reaction/methods ; *Real-Time Polymerase Chain Reaction/methods ; },
abstract = {Mitochondrial DNA (mtDNA) copy number varies across species, individuals, and cell types. In birds, there are two types of cells with a relatively low number of mitochondria: red blood cells and spermatozoa. Previous studies investigating variation of mitochondrial abundance in animal sperm have generally used quantitative PCR (qPCR), but this method shows potential limitations when quantifying targets at low abundance. To mitigate such issues, we investigated and compared the reliability and accuracy of qPCR, digital PCR (dPCR) and droplet digital PCR (ddPCR) to quantify high and low concentration DNA. We used synthetic DNA targets, to calculate the limit of detection and the limit of quantification and found that with both dPCR and ddPCR, these limits were lower than with qPCR. Then, to compare quantification accuracy and repeatability, we used DNA extracted from blood and sperm cells of Eurasian siskin. We found that qPCR, dPCR and ddPCR all reliably quantified mitochondrial DNA in sperm samples but showed significant differences when analyzing the typically lower levels of mtDNA in blood, with ddPCR consistently showing lower variation among replicates. Our study provides critical insights and recommendations for future studies aiming to quantify target mtDNA and indicates that dPCR and ddPCR are the preferred methods when working with samples with low abundance of mtDNA.},
}

Animals
Male
*DNA, Mitochondrial/genetics/blood/analysis
*Spermatozoa/chemistry
Reproducibility of Results
*DNA Copy Number Variations
*Songbirds/genetics/blood
*Polymerase Chain Reaction/methods
*Real-Time Polymerase Chain Reaction/methods

@article {pmid40229680,
year = {2025},
author = {Liu, M and Fan, R and Wang, C and Dai, L and Chu, S},
title = {Complete analysis and phylogenetic analysis of Polygonatum sibiricum mitochondria.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {471},
pmid = {40229680},
issn = {1471-2229},
mesh = {*Polygonatum/genetics/classification ; *Phylogeny ; *Genome, Mitochondrial/genetics ; RNA, Transfer/genetics ; Base Composition ; RNA, Ribosomal/genetics ; },
abstract = {In this project, we studied the complete mitogenome of the liliaceae medicinal plant Polygonatum sibiricum. The genome is represented by a circular ring molecule with a length of 691,910 bp and a GC content of 46.33%. Mitochondrial genome composition is slightly biased towards A+T, with AT accounting for 53.67%, and AT skewness slightly positive (0.092%). The complete mitogenome has a total of sixty-three unique genes, including thirty-nine protein-coding genes, twenty-one transfer RNAs (tRNAs) and three ribosomal RNAs (rRNAs). We examined codon use, repeat sequence, RNA editing in the mitogenome of P. sibiricum, and elucidated species classification based on phylogenetic trees of mitogenome of twenty-three species. Our results provide comprehensive information on the mitogenome of P. sibiricum and show for the first time the evolutionary relationship between the mitogenome of P. sibiricum and Chlorophytum comosum in the Asparagales family.},
}

*Polygonatum/genetics/classification
*Phylogeny
*Genome, Mitochondrial/genetics
RNA, Transfer/genetics
Base Composition
RNA, Ribosomal/genetics

@article {pmid39993485,
year = {2025},
author = {Li, W and Yang, G and Fan, Y and Yan, X and Li, Z and Guo, Y and Wang, Q and Li, X and Gu, W and Ning, M and Zhou, J and Meng, Q},
title = {Eriocheir sinensis CD63 activate mitochondria-mediated apoptosis to resist Spiroplasma eriocheiris infection.},
journal = {Fish & shellfish immunology},
volume = {161},
number = {},
pages = {110227},
doi = {10.1016/j.fsi.2025.110227},
pmid = {39993485},
issn = {1095-9947},
mesh = {Animals ; *Spiroplasma/physiology ; *Tetraspanin 30/genetics/immunology/chemistry ; *Apoptosis ; *Brachyura/immunology/genetics/microbiology ; Mitochondria ; *Arthropod Proteins/genetics/immunology/chemistry ; *Immunity, Innate/genetics ; Hemocytes/immunology ; Phylogeny ; Amino Acid Sequence ; Sequence Alignment ; },
abstract = {CD63, a member of the tetraspanins, is involved in cell movement, adhesion, immune response. Nevertheless, the role of CD63 in combating pathogen infections in invertebrates remains largely unclear. Tremor disease, whose pathogen is Spiroplasma eriocheiris, is one of the most prevalent illnesses affecting Eriocheir sinensis. EsCD63 is 1474 bp, with a 756 bp open reading frame that encodes for 252 amino acids. The qPCR data demonstrated that gills showed significant levels of transcription for EsCD63, followed by hemocytes, hepatopancreas, intestines and nerves, while showing low levels of transcription in the heart and muscles. After infection with S. eriocheiris, an obvious drop in the transcription level of EsCD63 was observed. Both the amount of S. eriocheiris copies in hemocytes and the mortality of E. sinensis significantly increased after the injection of chemically synthesized EsCD63 siRNA and stimulation with S. eriocheiris. After EsCD63 interference, the phagocytosis of hemocytes to S. eriocheiris, the apoptosis of hemocytes, and reactive oxygen species level of hemocytes were all decreased significantly, by laser scanning confocal microscopy and flow cytometry analysis. Meanwhile, the mitochondrial membrane potential of hemocytes was increased after EsCD63 interference. These findings indicated that EsCD63 was crucial for E. sinensis immunity and defense mechanisms against infection of S. eriocheiris.},
}

Animals
*Spiroplasma/physiology
*Tetraspanin 30/genetics/immunology/chemistry
*Apoptosis
*Brachyura/immunology/genetics/microbiology
Mitochondria
*Arthropod Proteins/genetics/immunology/chemistry
*Immunity, Innate/genetics
Hemocytes/immunology
Phylogeny
Amino Acid Sequence
Sequence Alignment

@article {pmid39540328,
year = {2024},
author = {Pham, LTK and Van Quyen, D and Saijuntha, W and Doan, HTT and Le, TH and Lawton, SP},
title = {Mitogenomics of the zoonotic parasite Echinostoma miyagawai and insights into the evolution of tandem repeat regions within the mitochondrial non-coding control region.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/S0031182024001422},
pmid = {39540328},
issn = {1469-8161},
support = {108.02-2020.07//National Foundation for Science and Technology Development/ ; },
abstract = {Echinostoma miyagawai is a cosmopolitan parasite within the Echinostomatidae and is a cause of human echinostomiasis. Species within the family have been a challenge to disentangle with E. miyagawai being synonyms of several other Echinostoma species. However, complete mitochondrial genomes have been shown to be vital in distinguishing echinostomatid species, but detailed comparisons of not only gene content but also structural features have been limited. Using long range sequencing techniques, the complete mitochondrial genome of E. miyagawai was sequenced and compared to other members of Echinostomatidae. In total 12 protein coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes were identified, as was an extensive noncoding control region (CR), consisting of 2 types of multiple tandem repeat units. Phylogenetic analyses of complete mitochondrial genomes corresponded to previous studies on single mitochondrial genes and nuclear ribosomal nuclear markers confirmed E. miyagawai to be within in the ‘Echinostoma revolutum’ group. The tandem repeat units found in the CR contained promoter sequences containing domains typical of initiation sites for replication and transcription as well as several palindromic regions which were shared between echinostomatid species. The study illustrates not only the utility complete mitogenomes in disentangling the relationship between these parasite species, but also provides some insight into the potential adaptations and other evolutionary processes that may govern the divergence of mitochondrial genomes for the first time in echinostomatids.},
}

@article {pmid40229603,
year = {2025},
author = {Li, X and Hu, L and Hu, Q and Jin, H},
title = {Research dynamics and drug treatment of renal fibrosis from a mitochondrial perspective: a historical text data analysis based on bibliometrics.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {40229603},
issn = {1432-1912},
support = {82274307//National Natural Science Foundation of China/ ; 2023CXMMTCM018//Research Funds of Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM/ ; },
abstract = {Renal fibrosis (RF) represents a significant public health challenge, necessitating the urgent identification of effective and safe therapeutic agents. Mitochondrial-targeted strategies have demonstrated considerable promise in restoring renal function and mitigating fibrosis. This study aims to examine the evolution of research and therapeutic interventions for RF from a mitochondrial perspective through bibliometric analysis. Literature retrieval was primarily conducted using the Web of Science Core Collection. Visual analysis was performed utilizing the Bibliometrix package (R- 4.4.2), CiteSpace 6.3.R1, and VOSviewer 1.6.19. A total of 819 documents were included for analysis. Significant contributions were made by researchers from China and the USA, with Nanjing Medical University leading in publication volume. Zhang Aihua and Huang Songming emerge as key scholars in the field, while the International Journal of Molecular Sciences is the journal with the highest publication output. Key research themes include oxidative stress, expression, injury, activation, mechanisms, and mitochondrial dysfunction. Mitochondrial-targeted approaches for treating RF can be categorized into six main strategies: mitochondrial biogenesis regulators, mitochondrial dynamics modulators, mitophagy inducers, oxidative stress regulators, NLRP3 inhibitors, and other mitochondrial-targeted therapeutic approaches. This study comprehensively examines the current state of RF research from a mitochondrial standpoint, summarizing key drugs and potential mechanisms of mitochondrial regulation. The findings aim to enhance scholarly understanding of the ongoing research trends and provide valuable insights for the development of targeted therapeutic agents.},
}

@article {pmid40214180,
year = {2025},
author = {Takahashi, K and Lum, WM and Hehenberger, E and Iwataki, M},
title = {Kapelodiniopsis flava n. g., n. sp. (Dinophyceae), a new katodinioid with haptophyte-derived plastids of multiple origins: Implications for the plastid integration process.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {3},
pages = {e13082},
doi = {10.1111/jeu.13082},
pmid = {40214180},
issn = {1550-7408},
support = {LQ200962204//The Czech Academy of Sciences, Lumina Quaeruntur fellowship/ ; 19KK0160//Japan Society for the Promotion of Science/ ; 21K15150//Japan Society for the Promotion of Science/ ; },
mesh = {*Plastids/genetics/ultrastructure ; Phylogeny ; *Dinoflagellida/genetics/classification/ultrastructure/isolation & purification ; *Haptophyta/genetics/ultrastructure ; DNA, Protozoan/genetics/chemistry ; Japan ; DNA, Ribosomal/genetics/chemistry ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {An autotrophic unarmored dinoflagellate species with haptophyte-derived plastids, Kapelodiniopsis flava n. g., n. sp., was described as a sister taxon of Kapelodinium vestifici, which was formerly well characterized by its low-positioned cingulum and heterotrophic nature. The isolates from several Japanese coastal locations were observed using light microscopy, scanning and transmission electron microscopy, and their phylogeny was inferred from nuclear-encoded rRNA genes and multiple plastid-encoded genes. To date of this publication, a representative culture of Ks. flava has grown autotrophically for 98 months in the absence of prey or organic matter. This dinoflagellate lacked nonplastid haptophyte cell components (e.g. nucleus or mitochondria). In the host dinoflagellate phylogeny, Ks. flava was distantly related to the other two dinoflagellate lineages known to be associated with haptophyte-derived plastids, thus representing the third of such lineage. Plastid origins differed among Ks. flava strains (>99.8% 18S rRNA gene identity), with plastids being derived from at least three haptophytes and an especially strong genetic similarity to two distantly related extant haptophytes (>99.9% 16S rRNA gene identity). This indicates that Ks. flava recently integrated plastids from multiple haptophyte lineages to an extent that allows the host to replicate the plastids without other haptophyte components.},
}

*Plastids/genetics/ultrastructure
Phylogeny
*Dinoflagellida/genetics/classification/ultrastructure/isolation & purification
*Haptophyta/genetics/ultrastructure
DNA, Protozoan/genetics/chemistry
Japan
DNA, Ribosomal/genetics/chemistry
RNA, Ribosomal, 18S/genetics
Sequence Analysis, DNA

@article {pmid40207624,
year = {2025},
author = {Mathieu, S and Lesch, E and Garcia, S and Graindorge, S and Schallenberg-Rüdinger, M and Hammani, K},
title = {De novo RNA base editing in plant organelles with engineered synthetic P-type PPR editing factors.},
journal = {Nucleic acids research},
volume = {53},
number = {7},
pages = {},
pmid = {40207624},
issn = {1362-4962},
support = {ANR-18-CE20-0013//Agence National de la Recherche/ ; //Centre National de la Recherche Scientifique/ ; SCHA 1952/2-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*RNA Editing ; Nicotiana/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Mitochondria/genetics/metabolism ; Escherichia coli/genetics ; *Plant Proteins/genetics/metabolism ; Cytidine Deaminase/genetics/metabolism ; },
abstract = {In plant mitochondria and chloroplasts, cytidine-to-uridine RNA editing is necessary for the production of functional proteins. While natural PLS-type PPR proteins are specialized in this process, synthetic PPR proteins offer significant potential for targeted RNA editing. In this study, we engineered chimeric editing factors by fusing synthetic P-type PPR guides with the DYW cytidine deaminase domain of a moss mitochondrial editing factor, PPR56. These designer PPR editors (dPPRe) elicited efficient and precise de novo RNA editing in Escherichia coli as well as in the chloroplasts and mitochondria of Nicotiana benthamiana. Chloroplast transcriptome-wide analysis of the most efficient dPPRe revealed minimal off-target effects, with only three nontarget C sites edited due to sequence similarity with the intended target. This study introduces a novel and precise method for RNA base editing in plant organelles, paving the way for new approaches in gene regulation applicable to plants and potentially other organisms.},
}

*RNA Editing
Nicotiana/genetics/metabolism
Chloroplasts/genetics/metabolism
Mitochondria/genetics/metabolism
Escherichia coli/genetics
*Plant Proteins/genetics/metabolism
Cytidine Deaminase/genetics/metabolism

@article {pmid40225169,
year = {2023},
author = {Lazarian, G and Leroy, B and Theves, F and Hormi, M and Letestu, R and Eclache, V and Tueur, G and Ameur, A and Bidet, A and Cornillet-Lefebvre, P and Davi, F and Delabesse, E and Estienne, MH and Etancelin, P and Kosmider, O and Laibe, S and Muller, M and Nadal, N and Naguib, D and Pastoret, C and Poulain, S and Sujobert, P and Veronese, L and Imache, S and Lefebvre, V and Cymbalista, F and Baran-Marszak, F and Soussi, T and , },
title = {The Broad Spectrum of TP53 Mutations in CLL: Evidence of Multiclonality and Novel Mutation Hotspots.},
journal = {Human mutation},
volume = {2023},
number = {},
pages = {4880113},
pmid = {40225169},
issn = {1098-1004},
mesh = {Humans ; *Leukemia, Lymphocytic, Chronic, B-Cell/genetics ; *Tumor Suppressor Protein p53/genetics ; *Mutation ; },
abstract = {TP53 aberrations are a major predictive factor of resistance to chemoimmunotherapy in chronic lymphocytic leukemia (CLL), and an assessment of them before each line of treatment is required for theranostic stratification. Acquisition of subclonal TP53 abnormalities underlies the evolution of CLL. To better characterize the distribution, combination, and impact of TP53 variants in CLL, 1,056 TP53 variants collected from 683 patients included in a multicenter collaborative study in France were analyzed and compared to UMD_CLL, a dataset built from published articles collectively providing 5,173 TP53 variants detected in 3,808 patients. Our analysis confirmed the presence of several CLL-specific hotspot mutations, including a two-base pair deletion in codon 209 and a missense variant at codon 234, the latter being associated with alkylating treatment. Our analysis also identified a novel CLL-specific variant in the splice acceptor signal of intron 6 leading to the use of a cryptic splice site, similarly utilized by TP53 to generate p53psi, a naturally truncated p53 isoform localized in the mitochondria. Examination of both UMD_CLL and several recently released large-scale genomic analyses of CLL patients confirmed that this splice variant is highly enriched in this disease when compared to other cancer types. Using a TP53-specific single-nucleotide polymorphism, we also confirmed that copy-neutral loss of heterozygosity is frequent in CLL. This event can lead to misinterpretation of TP53 status. Unlike other cancers, CLL displayed a high proportion of patients harboring multiple TP53 variants. Using both in silico analysis and single molecule smart sequencing, we demonstrated the coexistence of distinct subclones harboring mutations on distinct alleles. In summary, our study provides a detailed TP53 mutational architecture in CLL and gives insights into how treatments may shape the genetic landscape of CLL patients.},
}

Humans
*Leukemia, Lymphocytic, Chronic, B-Cell/genetics
*Tumor Suppressor Protein p53/genetics
*Mutation

@article {pmid40205193,
year = {2025},
author = {Lu, Q and Luo, W},
title = {Comparative analysis of the complete mitochondrial genomes of Firmiana danxiaensis and F. kwangsiensis (Malvaceae), two endangered Firmiana species in China.},
journal = {Planta},
volume = {261},
number = {5},
pages = {107},
pmid = {40205193},
issn = {1432-2048},
support = {31960083//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial/genetics ; Endangered Species ; China ; Phylogeny ; RNA, Transfer/genetics ; Genome, Chloroplast/genetics ; },
abstract = {We reported the mitogenomes of F. danxiaensis and F. kwangsiensis for the first time. Mitogenome size and structure differ significantly between them. Firmiana danxiaensis and F. kwangsiensis belong to the Firmiana genus and are distributed in the Danxia and Karst regions of southern China. Both species have been designated as endangered. Currently, the chloroplast genomes of F. danxiaensis and F. kwangsiensis have been sequenced, but the mitochondrial genome (mitogenome) of these two species has not been reported. To further understand the mitogenome characteristics, evolution, and phylogeny of F. danxiaensis and F. kwangsiensis, we assembled the mitogenomes of these two species based on a combination of Illumina and Nanopore sequencing methods. The mitogenome of F. danxiaensis exhibits a branching structure consisting of nine circular molecules with a total length of 938,890 bp, while the F. kwangsiensis has a circular structure with a length of 736,334 bp. Compared to F. kwangsiensis, F. danxiaensis has more tRNA genes, SSRs, tandem repeats, and dispersed repeats, while the codon use patterns are similar in these two species. There were 24 and 23 homologous sequences between mitogenome and chloroplast genome of F. danxiaensis and F. kwangsiensis, accounting for 0.37% and 0.49% of the mitogenome, respectively. In addition, the Ka/Ks ratio and the nucleic acid diversity analysis revealed that most of the mitochondria protein-coding genes in F. danxiaensis and F. kwangsiensis are highly conserved and may have undergone purifying selection. Furthermore, the collinear and comparative analysis showed that extensive genomic rearrangement events existed among the Malvaceae species. Lastly, a phylogenetic tree based on shared mitochondrial PCGs of 29 species revealed that F. danxiaensis and F. kwangsiensis form a sister group with high support values. Overall, the current study reports two mitogenomes (F. danxiaensis and F. kwangsiensis) in the Firmiana genus for the first time, which will help enhance comprehension of the mitogenome evolutionary patterns within Firmiana and promote the evolutionary and comparative genomic analyses within Malvaceae species.},
}

*Genome, Mitochondrial/genetics
Endangered Species
China
Phylogeny
RNA, Transfer/genetics
Genome, Chloroplast/genetics

@article {pmid40197538,
year = {2025},
author = {Zhao, P and Tian, R and Song, D and Zhu, Q and Ding, X and Zhang, J and Cao, B and Zhang, M and Xu, Y and Fang, J and Tan, J and Yi, C and Xia, H and Liu, W and Zou, W and Sun, Q},
title = {Rab GTPases are evolutionarily conserved signals mediating selective autophagy.},
journal = {The Journal of cell biology},
volume = {224},
number = {5},
pages = {},
pmid = {40197538},
issn = {1540-8140},
support = {92254307//National Natural Science Foundation of China/ ; 2024YFA1803003//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {*rab GTP-Binding Proteins/metabolism/genetics ; Humans ; *Autophagy ; Animals ; *Signal Transduction ; HeLa Cells ; Mitochondria/metabolism ; Mitophagy ; *Evolution, Molecular ; },
abstract = {Selective autophagy plays a crucial role in maintaining cellular homeostasis by specifically targeting unwanted cargo labeled with "autophagy cues" signals for autophagic degradation. In this study, we identify Rab GTPases as a class of such autophagy cues signals involved in selective autophagy. Through biochemical and imaging screens, we reveal that human Rab GTPases are common autophagy substrates. Importantly, we confirm the conservation of Rab GTPase autophagic degradation in different model organisms. Rab GTPases translocate to damaged mitochondria, lipid droplets, and invading Salmonella-containing vacuoles (SCVs) to serve as degradation signals. Furthermore, they facilitate mitophagy, lipophagy, and xenophagy, respectively, by recruiting receptors. This interplay between Rab GTPases and receptors may ensure the de novo synthesis of isolation membranes around Rab-GTPase-labeled cargo, thereby mediating selective autophagy. These processes are further influenced by upstream regulators such as LRRK2, GDIs, and RabGGTase. In conclusion, this study unveils a conserved mechanism involving Rab GTPases as autophagy cues signals and proposes a model for the spatiotemporal control of selective autophagy.},
}

*rab GTP-Binding Proteins/metabolism/genetics
Humans
*Autophagy
Animals
*Signal Transduction
HeLa Cells
Mitochondria/metabolism
Mitophagy
*Evolution, Molecular

@article {pmid40196624,
year = {2025},
author = {Ly, J and Tao, YF and Di Bernardo, M and Khalizeva, E and Giuliano, CJ and Lourido, S and Fleming, MD and Cheeseman, IM},
title = {Alternative start codon selection shapes mitochondrial function during evolution, homeostasis, and disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.27.645657},
pmid = {40196624},
issn = {2692-8205},
abstract = {Mitochondrial endosymbiosis was a pivotal event in eukaryotic evolution, requiring core proteins to adapt to function both within the mitochondria and in the host cell. Here, we systematically profile the localization of protein isoforms generated by alternate start codon selection during translation. We identify hundreds of pairs of differentially-localized protein isoforms, many of which affect mitochondrial targeting and are essential for mitochondrial function. The emergence of dual-localized mitochondrial protein isoforms coincides with mitochondrial acquisition during early eukaryotic evolution. We further reveal that eukaryotes use diverse mechanisms-such as leaky ribosome scanning, alternative transcription, and paralog duplication-to maintain the production of dual-localized isoforms. Finally, we identify multiple isoforms that are specifically dysregulated by rare disease patient mutations and demonstrate how these mutations can help explain unique clinical presentations. Together, our findings illuminate the evolutionary and pathological relevance of alternative translation initiation, offering new insights into the molecular underpinnings of mitochondrial biology.},
}

@article {pmid40188039,
year = {2025},
author = {Liang, H and Deng, J and Wang, Y and Gao, G and Yang, R},
title = {The first complete mitochondrial genome of Curcuma amarissima (Zingiberaceae): insights into multi-branch structure, codon usage, and phylogenetic evolution.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {343},
pmid = {40188039},
issn = {1471-2164},
support = {ITH2024ZD02//Basic scientific research business expenses of HAAS/ ; 32001390//Natural Science Foundation of Shenyang Municipality/ ; },
mesh = {*Phylogeny ; *Codon Usage ; *Curcuma/genetics/classification ; *Genome, Mitochondrial ; *Evolution, Molecular ; Base Composition ; RNA, Transfer/genetics ; },
abstract = {BACKGROUND: As a key genus in Zingiberaceae, Curcuma is widely studied for its taxonomic diversity, the presence of bioactive curcuminoids and volatile oils, and its extensive applications in traditional medicine and economic products such as spices and cosmetics. Although chloroplast genomes have been assembled and published for over 20 Curcuma species, mitochondrial genomic data remain limited.

RESULTS: We successfully sequenced, assembled, and annotated the mitogenome of Curcuma amarissima (C. amarissima) using both Illumina short reads and Nanopore long reads, achieving the first complete mitogenome characterization in the Zingiberaceae family. The C. amarissima mitogenome features a unique multi-branched structure, spanning 6,505,655 bp and consisting of 39 distinct segments. It contains a total of 43 protein-coding genes, 63 tRNA genes, and 4 rRNA genes, with a GC content of 44.04%. Codon usage analysis indicated a weak bias, with neutrality plot analysis suggesting natural selection as a key factor shaping mitochondrial codon usage in C. amarissima. The mitogenome provides valuable insights into genome size, coding genes, structural features, RNA editing, repetitive sequences, and sequence migration, enhancing our understanding of the evolution and molecular biology of multi-branched mitochondria in Zingiberaceae. The high frequency of repeat sequences may contribute to the structural stability of the mitochondria. Comparing chloroplast genome, phylogenetic analysis based on the mitochondrial genome establishes a foundation for further exploration of evolutionary relationships within Zingiberaceae.

CONCLUSIONS: In short, the mitochondrial genome characterized here advances our understanding of multi-branched mitogenome organization in Zingiberaceae and offers useful genomic resources that may support future breeding, germplasm conservation, and phylogenetic studies, though further research is necessary.},
}

*Phylogeny
*Codon Usage
*Curcuma/genetics/classification
*Genome, Mitochondrial
*Evolution, Molecular
Base Composition
RNA, Transfer/genetics

@article {pmid40183649,
year = {2025},
author = {Zielenkiewicz, U and Kaushal, V and Kaczanowski, S},
title = {On the origins and evolution of apoptosis: the predator‒mitochondrial prey hypothesis.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf039},
pmid = {40183649},
issn = {1420-9101},
abstract = {Different types of programmed cell death have been described both in unicellular and multicellular organisms. The fundamental mode of eukaryotic cell death is programmed cell death initiated by mitochondria, which is frequently referred to as apoptosis (or mitochondrial apoptosis). It is initiated by mitochondria through mitochondrial permeability transition and the release of apoptotic factors. It is widely thought that mitochondrial apoptosis evolved concurrently with mitochondrial domestication. Programmed cell death initiated by mitochondria is observed in various multicellular and unicellular eukaryotes. We discuss key hypotheses-namely, the "pleiotropy", "addiction", "immunological", and our "predator-mitochondrial prey" hypotheses-to explain the mechanisms of mitochondrial domestication that lead to apoptosis. In this perspective paper, we present evidence from various phylogenetic and experimental studies that strongly indicates our hypothesis is the most plausible. For the first time, we also present evidence that challenges the assumptions underlying all other hypotheses.},
}

@article {pmid40181281,
year = {2025},
author = {Degnan, PH and Percy, DM and Hansen, AK},
title = {Coupled evolutionary rates shape a Hawaiian insect-symbiont system.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {336},
pmid = {40181281},
issn = {1471-2164},
support = {DEB 1241253//NSF/ ; 2019-70016-29066//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Symbiosis/genetics ; *Evolution, Molecular ; Phylogeny ; Hawaii ; *Hemiptera/genetics/microbiology/classification ; Genome, Mitochondrial ; Genome, Insect ; },
abstract = {BACKGROUND: The Hawaiian Pariaconus psyllid radiation represents a unique system to study the co-evolution of nuclear, mitochondrial, and endosymbiont genomes. These psyllids, which diversified across the Hawaiian Islands during the last 3-3.5 million years vary with their ecological niches on their plant host 'Ōhi'a lehua (Metrosideros polymorpha) (free-living, open-gall, and closed-gall lifestyles) and harbor one to three beneficial bacterial endosymbionts. Co-evolutionary studies of other multi-endosymbiont insect systems have shown decoupled rates of sequence evolution between mitochondria and endosymbionts. Here we examine the evolutionary trends in Pariaconus psyllids, their mitochondria and their endosymbionts to determine if they fit this paradigm.

RESULTS: We sequenced a new Carsonella genome from the ohialoha species group (closed-gall, one symbiont), revealing a remarkable degree of gene conservation between two of the most divergent species from this diverse species group that has dispersed across multiple islands. Further, despite the rapid radiation of psyllid species, we observed complete synteny among mitochondrial genomes from all six Pariaconus species in this study, suggesting the preservation of genome structure due to strong purifying selection. Phylogenetic analyses of the nuclear, mitochondrial, and endosymbiont genomes across these six Pariaconus species revealed correlated rates of substitutions, contrary to prior reports of decoupling between mitochondrial and endosymbiont genomes in other insect systems with multiple symbiont partners. Finally, we found that free-living psyllids with three symbionts exhibited elevated mutation rates (~ 1.2-1.6x) across all genomes and elevated rates of fixation of nonsynonymous substitutions in the insect nuclear genome and one of the endosymbionts.

CONCLUSIONS: This study highlights the interplay between ecological diversification and genomic evolution in Pariaconus. Further, these data indicate that multiple endosymbiont partners alone are not sufficient to result in decoupling rates of sequence evolution. Future work on basal members of this species radiation will refine our understanding of the mechanisms shaping this dynamic insect-symbiont system and its implications for genome evolution.},
}

Animals
*Symbiosis/genetics
*Evolution, Molecular
Phylogeny
Hawaii
*Hemiptera/genetics/microbiology/classification
Genome, Mitochondrial
Genome, Insect

@article {pmid40174913,
year = {2025},
author = {Rubens, P and Mayeur, A and Chatzovoulou, K and Gigarel, N and Monnot, S and Rötig, A and Munnich, A and Frydman, N and Steffann, J},
title = {Profiling mitochondrial DNA variant segregation during human preimplantation development: a prerequisite to preimplantation genetic testing for mitochondrial DNA-related disorders.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/deaf050},
pmid = {40174913},
issn = {1460-2350},
support = {//Association Française contre les Myopathies/ ; },
abstract = {STUDY QUESTION: Is preimplantation genetic testing for mitochondrial DNA (mtDNA) disorders (PGT-mt) feasible at early compaction and blastocyst stages?

SUMMARY ANSWER: Pathogenic mtDNA variants segregate evenly among cell types and various lineages of a given embryo during preimplantation development, supporting the relevance of genetic analyses performed on Day 4 blastomere and on Day 5 or 6 trophectoderm (TE) samples.

WHAT IS KNOWN ALREADY: PGT-mt is validated at cleavage stage (Day 3 of development). However, its feasibility at later stages is questionable, as little is known regarding the segregation of pathogenic mtDNA variants during preimplantation development. Since mtDNA replication is silenced until the blastocyst stage (Day 5 or 6), uneven mtDNA segregation between preimplantation embryo cellular lineages known as a 'bottleneck' effect, cannot be excluded, posing a challenge for PGT-mt.

STUDY DESIGN, SIZE, DURATION: We analyzed 112 'mito' embryos carrying pathogenic mtDNA variants and 28 control embryos with mtDNA polymorphism. Heteroplasmy levels were assessed in single cells of the TE, in different parts of blastocysts (inner cell mass and TE), and at three time points of development, namely cleavage (Day 3), early compaction (Day 4), and blastocyst stages (Day 5 or 6).

As part of clinical PGT, a blastomere biopsy was performed at cleavage or early compaction stages (Day 3 or 4) on 112 'mito' and 21/28 control embryos. Further analysis was carried out at Day 5 or 6 on 51 embryos deemed unsuitable for uterine transfer and donated to research. Heteroplasmy levels were determined by semi-quantitative PCR amplification of (i) the mtDNA pathogenic variants with additional enzymatic digestion or (ii) the mtDNA polymorphic hypervariable region 2.

Here, we first show that mtDNA variants segregate evenly among blastomeres during early compaction (Day 4), supporting the feasibility of PGT-mt at this stage. We also found that mtDNA ratios remain stable between cleavage and blastocyst stages. Yet, the substantial variation of heteroplasmy levels occurring among single TE cells in 1/8 embryos suggests that PGT is only feasible when at least 5-10 cells are collected by standard TE biopsy.

This study sheds light on mtDNA segregation in human preimplantation embryo development. Its limitation lies in the scarcity of the material and the small number of embryos carrying a specific pathogenic mtDNA variant. Furthermore, the study of single cells from TE was performed on control embryos only.

By supporting the relevance of blastocyst biopsy in the context of PGT for pathogenic mtDNA variants, this study contributes to the general trend of postponing the biopsy to later stages of embryonic development. However, particular attention should be paid to the number of TE cells tested. Due to the potential variation of mutant load during in utero development, a control amniocentesis for evolutive pregnancies following the transfer of heteroplasmic embryos is still recommended.

This work was funded by 'Association Française contre les Myopathies/AFM Téléthon' (22112, 24317, 28525); and EUR G.E.N.E. (No. ANR-17-EURE-0013). The authors have no competing interests to declare.

TRIAL REGISTRATION NUMBER: N/A.},
}

@article {pmid40174813,
year = {2025},
author = {Xu, J and Shen, Z and Hao, T and Su, H and Chen, M and Pan, X and Yi, Z},
title = {Exploring the evolution of anaerobes within ciliate class Prostomatea by transcriptomics.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108345},
doi = {10.1016/j.ympev.2025.108345},
pmid = {40174813},
issn = {1095-9513},
abstract = {Mitochondrion-related organelles (MROs) enable anaerobic eukaryotes to thrive in anoxic environments, and the independent ciliate lineages of anaerobes serve as excellent candidates for investigating the convergent evolutionary transition from mitochondria to MROs. Previous studies have demonstrated that the adaptations of ciliates to anaerobic conditions may be lineage-specific. However, our understanding of the diverse metabolic peculiarities of MROs is limited to a few ciliate lineages. In this study, we sequenced the transcriptomes of four anaerobic species from two genera (Apolagynus and Holophrya), which are classified within the predominantly aerobic class Prostomatea, and predicted their mitochondrial metabolism. The ecological niches of prostomatean anaerobes were mapped onto newly constructed phylogenomic trees and small subunit (SSU) rDNA trees. Results showed that paraphyletic class Prostomatea containing six clades (Clade I-Ⅵ) has a close relationship with Oligohymenophorea and Plagiopylea. Notably, all prostomatean species within Clade II are anaerobic, while anaerobes are only sporadically present in other clades. The MROs of anaerobic prostomatean species display at least two distinct phenotypes. Holophrya ovum in Clade I produces ATP by oxidative phosphorylation under aerobic conditions and via substrate-level phosphorylation via acetate: succinate CoA transferase (ASCT) and succinyl CoA synthetase (SCS) as well as adenylate kinase (AK) under anaerobic conditions. In contrast, three species of Apolagynus in Clade II possess reduced electron transport chain (ETC), and are capable of ATP generation via substrate-level phosphorylation mediated by ASCT/SCS and propionyl-CoA. Additionally, these three Apolagynus species possess [FeFe] hydrogenase probably producing H2. A comparison of the ETC pathways among various anaerobic ciliates further showed that the MROs of these organisms have originated from repeated convergent evolution. Our findings shed lights on evolutionary history of anaerobes within the ciliate class Prostomatea.},
}

@article {pmid40167337,
year = {2025},
author = {Koch, RE and Truong, CN and Reeb, HR and Joski, BH and Hill, GE and Zhang, Y and Toomey, MB},
title = {Multiple Pathways to Red Carotenoid Coloration: House Finches (Haemorhous mexicanus) Do Not Use CYP2J19 to Produce Red Plumage.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17744},
doi = {10.1111/mec.17744},
pmid = {40167337},
issn = {1365-294X},
support = {NSF-IOS-2037735//Directorate for Biological Sciences/ ; NSF-IOS-2037739//Directorate for Biological Sciences/ ; NSF-IOS-2037741//Directorate for Biological Sciences/ ; NSF-IOS-2224556//Directorate for Biological Sciences/ ; },
abstract = {The carotenoid-based colours of birds are a celebrated example of biological diversity and an important system for the study of evolution. Recently, a two-step mechanism, with the enzymes cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like (BDH1L), was described for the biosynthesis of red ketocarotenoids from yellow dietary carotenoids in the retina and plumage of birds. A common assumption has been that all birds with ketocarotenoid-based plumage coloration used this CYP2J19/BDH1L mechanism to produce red feathers. We tested this assumption in house finches (Haemorhous mexicanus) by examining the catalytic function of the house finch homologues of these enzymes and tracking their expression in birds growing new feathers. We found that CYP2J19 and BDH1L did not catalyse the production of 3-hydroxy-echinenone (3-OH-echinenone), the primary red plumage pigment of house finches, when provided with common dietary carotenoid substrates. Moreover, gene expression analyses revealed little to no expression of CYP2J19 in liver tissue or growing feather follicles, the putative sites of pigment metabolism in moulting house finches. Finally, although the hepatic mitochondria of house finches have high concentrations of 3-OH-echinenone, observations using fluorescent markers suggest that both CYP2J19 and BDH1L localise to the endomembrane system rather than the mitochondria. We propose that house finches and other birds that deposit 3-OH-echinenone as their primary red plumage pigment use an alternative enzymatic pathway to produce their characteristic red ketocarotenoid-based coloration.},
}

@article {pmid40141318,
year = {2025},
author = {Prado-Souza, LFLD and Ferraz, LS and Citrangulo Tortelli, T and Ribeiro, CAJ and Amaral, DTD and Arruda, DC and Oliveira, ÉA and Chammas, R and Maria-Engler, SS and Rodrigues, T},
title = {Exploiting Paradoxical Activation of Oncogenic MAPK Signaling by Targeting Mitochondria to Sensitize NRAS Mutant-Melanoma to Vemurafenib.},
journal = {International journal of molecular sciences},
volume = {26},
number = {6},
pages = {},
pmid = {40141318},
issn = {1422-0067},
support = {2021/14650-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 306681/2023-4//Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Humans ; *Melanoma/drug therapy/genetics/metabolism/pathology ; *Vemurafenib/pharmacology/therapeutic use ; *GTP Phosphohydrolases/genetics/metabolism ; *Mitochondria/metabolism/drug effects ; *Membrane Proteins/genetics/metabolism ; Cell Line, Tumor ; *Mutation ; *MAP Kinase Signaling System/drug effects ; Mitochondrial Dynamics/drug effects ; Antineoplastic Agents/pharmacology/therapeutic use ; Drug Resistance, Neoplasm/genetics/drug effects ; Cell Proliferation/drug effects ; Dynamins ; },
abstract = {Vemurafenib is a BRAF (rapidly accelerated fibrosarcoma B-type)-targeted therapy used to treat patients with advanced, unresectable melanoma. It inhibits the MAPK (mitogen-activated protein kinase)/ERK (extracellular signal-regulated kinase) pathway and tumor proliferation in BRAF[V600E]-mutated melanoma cells. Resistance to vemurafenib has been reported in melanoma patients due to secondary NRAS (neuroblastoma RAS viral oncogene homolog) mutations, which lead to paradoxical MAPK pathway activation and tumor proliferation. However, the impact of this paradoxical activation on mitochondrial dynamics and function in NRAS-mutated melanoma is unclear. Here, we investigated the effects of vemurafenib on NRAS[Q61R]-mutated melanoma cells, focusing on mitochondrial dynamics and function. As expected, vemurafenib did not exhibit cytotoxicity in SK-MEL-147 NRAS[Q61R]-mutated melanoma cells, even after 72 h of incubation. However, it significantly enhanced the MAPK/ERK signaling through paradoxical activation, accompanied by decreased expression of mitochondrial fusion proteins and activation of the fission protein DRP1 (dynamin-related protein 1), leading to small, rounded mitochondrial morphology. These observations were corroborated by transcriptome data obtained from NRAS-mutated melanoma patients, showing MFN1 (mitofusin 1) and OPA1 (optic atrophy 1) downregulation and DNM1L (DRP1 gene) upregulation. Interestingly, inhibition of mitochondrial fission with mdivi-1 or modulation of oxidative phosphorylation via respiratory chain inhibition or uncoupling significantly sensitized NRAS[Q61R]-mutated melanoma cells to vemurafenib. Despite vemurafenib's low cytotoxicity in NRAS-mutated melanoma, targeting mitochondrial dynamics and/or oxidative phosphorylation may offer a promising strategy for combined therapy.},
}

Humans
*Melanoma/drug therapy/genetics/metabolism/pathology
*Vemurafenib/pharmacology/therapeutic use
*GTP Phosphohydrolases/genetics/metabolism
*Mitochondria/metabolism/drug effects
*Membrane Proteins/genetics/metabolism
Cell Line, Tumor
*Mutation
*MAP Kinase Signaling System/drug effects
Mitochondrial Dynamics/drug effects
Antineoplastic Agents/pharmacology/therapeutic use
Drug Resistance, Neoplasm/genetics/drug effects
Cell Proliferation/drug effects
Dynamins

@article {pmid39950816,
year = {2025},
author = {Guo, B and Guo, G and Qi, W and Aizezi, M and Wu, C and Tian, M and Casulli, A and Zhang, W and Li, J},
title = {The genetic variation of mitochondrial sequences and pathological differences of Echinococcus multilocularis strains from different continents.},
journal = {Microbiology spectrum},
volume = {13},
number = {4},
pages = {e0131824},
pmid = {39950816},
issn = {2165-0497},
support = {2023TSYCTD0017//Tianshan talent training program/ ; 32072886,U1803282//MOST | National Natural Science Foundation of China (NSFC)/ ; 81830066//MOST | National Natural Science Foundation of China (NSFC)/ ; SKLHIDCA-2022-BC4//State Key Laboratory/ ; },
mesh = {Animals ; *Echinococcus multilocularis/genetics/classification ; Mice ; *Genetic Variation ; *Phylogeny ; *Echinococcosis/parasitology/pathology ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Japan ; Humans ; },
abstract = {Alveolar echinococcosis is a lethal zoonotic disease caused by the fox tapeworm Echinococcus multilocularis. The parasite is widely distributed in the Northern Hemisphere and exhibits low genetic diversity among populations. To compare the differences among four E. multilocularis strains from different geographical locations, namely, Alaska (EM-AK), Japan (EM-JP), Xinjiang (EM-XJ), and Ningxia (EM-NX), their complete mitochondrial (mt) sequences were compared, and their induced pathological lesions were analyzed in mouse models. The complete mt sequence of EM-AK resulted in 0.84%-0.86% variation as compared with the other strains, which had a lower variation. Phylogenetic analysis and parsimony network indicated that EM-AK resulted in 30,000 years of evolutionary distance from the other three strains. EM-AK induced more pathological damage than the other three strains, which was likely to induce more host cell infiltration and acute granuloma in the liver. More importantly, EM-AK produced more protoscoleces than the other three strains, which may impact the transmission dynamics of the parasite. Given the geographical location of four strains, which is far from each other, and also the pathological differences, the strains of E. multilocularis are likely models for addressing the relationship and interfacial immune response between the host and the helminth.IMPORTANCEEchinococcus multilocularis is the causative agent of alveolar echinococcosis, which is considered the most serious parasitic disease in the Northern Hemisphere. There are many genotypes, but the pathogenic and mitochondria sequence and differences are still unclear. Therefore, this study showed both pathological and genetic differences between the four strains of E. multilocularis. EM-AK induced more severe immune responses and especially induced more host cell infiltration, which resulted in more severe granuloma in the liver. EM-JP has metacestode lesions morphologically closer to those of E. granulosus with clear cyst fluid. However, this strain produced much fewer protoscoleces (PSCs). Genetically, EM-AK is more distant from other strains.},
}

Animals
*Echinococcus multilocularis/genetics/classification
Mice
*Genetic Variation
*Phylogeny
*Echinococcosis/parasitology/pathology
Mitochondria/genetics
DNA, Mitochondrial/genetics
Japan
Humans

@article {pmid40128668,
year = {2025},
author = {Song, S and Cao, J and Xiang, H and Liu, Z and Jiang, W},
title = {Comparative mitogenomic analysis of Chinese cavefish Triplophysa (Cypriniformes: Nemacheilidae): novel gene tandem duplication and evolutionary implications.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {293},
pmid = {40128668},
issn = {1471-2164},
support = {32060128//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Cypriniformes/genetics ; *Genome, Mitochondrial ; *Evolution, Molecular ; *Gene Duplication ; *Phylogeny ; RNA, Transfer/genetics ; },
abstract = {BACKGROUND: Cavefish exhibit significant morphological changes that result in trade-offs in metabolic requirements and energy utilization in perpetual darkness. As cellular "powerhouses", mitochondria play crucial roles in energy metabolism, suggesting that mitochondrial genes have likely experienced selective pressures during cavefish evolution.

RESULTS: This study presents the first assembly of the complete mitogenome of Triplophysa yangi, a typical cavefish species in China. The mitogenome is 17,068 bp long, marking the longest recorded for the genus Triplophysa, and includes 13 protein-coding genes (PCGs), 2 rRNAs, 25 tRNAs, and a noncoding control region. An ~ 500 bp insertion between ND2 and WANCY regions was observed, comprising a large intact tandem repeat unit (A'-N'-OL'-C') flanked by two unannotated sequences (U1/U2). The evolutionary origin of this repeat unit may involve either in situ duplication events with subsequent functional divergence-where neofunctionalization, subfunctionalization, or pseudogenization drove differential mutation rates between paralogs-or alternatively, horizontal acquisition from exogenous genetic material that became functionally integrated into the ancestral T. yangi mitogenome through co-option mechanisms. Phylogenetic analyses revealed two major clades within Triplophysa-epigean and hypogean lineages-consistent with previous classifications, while cave-restricted species exhibited signs of parallel evolution within the hypogean lineage. Selective pressure analysis indicated that the hypogean lineage (cave-dwelling groups, II & III) have a significantly increased ratio of nonsynonymous to synonymous substitution rates (ω) compared to the epigean lineage (surface-dwelling group, I), suggesting a combination of adaptive selection and relaxed functional constraints in cave-dwelling species.

CONCLUSIONS: The duplication of tRNAs in T. yangi and the potential positive selection sites identified in Triplophysa cavefish further indicated adaptive evolution in mitochondrial PCGs in response to extreme subterranean conditions.},
}

Animals
*Cypriniformes/genetics
*Genome, Mitochondrial
*Evolution, Molecular
*Gene Duplication
*Phylogeny
RNA, Transfer/genetics

@article {pmid40127832,
year = {2025},
author = {Liu, Q and Mao, W and Wang, Y and Xiao, J and Saha, S and Gao, T and Liu, F},
title = {Whole genome sequencing and phylogenetic analyses of the Sillaginidae family fish.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108340},
doi = {10.1016/j.ympev.2025.108340},
pmid = {40127832},
issn = {1095-9513},
abstract = {For a long time, the taxonomic study of the Sillaginidae family of fish has been relatively slow, leaving the evolutionary relationships among species unclear. Previous research has mainly relied on morphological characteristics, with molecular studies limited primarily to mitochondrial genomics, including analyses of gene fragments and whole mitochondrial genomic sequence. This approach resulted in less precise and comprehensive species identification. In this study, we employed high-depth whole-genome sequencing (WGS) and genome surveys on 13 specimens representing 9 species of Sillaginidae fish collected from the wild. Our analysis included a thorough genomic survey and the assembly of draft genomes for each specimen. The genome sizes of Sillaginidae species are highly similar, ranging from 511.71 Mb to 578.27 Mb, with most individuals exhibiting repeat sequences content below 34.69 %. After the genome draft assembly of each sample, we identified conserved genes and shared consistent sequences among individuals and constructed a species phylogenetic tree based on these data. The results revealed that Sillago ingenua occupies the basal branch, followed by S. maculata and S. aeolus, then Sillaginopsis panijus, S. japonica and S. asiatica, and finally S. nigrofasciata and S. cf. sihama. Subsequently, we validated the phylogenetic tree using genome-wide single nucleotide variations, and the results were highly consistent. This research provides, for the first time, a whole-genome perspective on the evolutionary relationships among Sillaginidae species, offering valuable insights into their taxonomy and historical evolution.},
}

@article {pmid40123256,
year = {2025},
author = {Richmond, JQ and Gottscho, AD and Jockusch, EL and Leaché, AD and Fisher, RN and Reeder, TW},
title = {Genomic discordance throws a wrench in the parallel speciation hypothesis for scincid lizards.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpaf059},
pmid = {40123256},
issn = {1558-5646},
abstract = {Parallel evolution of the same reproductive isolation barrier within a taxon is an indicator of ecology's role in speciation (i.e., parallel speciation), yet spatiotemporal variability in the efficacy of the barrier can present challenges to retracing how it evolved. Here, we revisit the evidence for a candidate example of parallel speciation in a clade of scincid lizards (the Plestiodon skiltonianus complex) using genomic data, with emphasis on determining whether hybridization may have confounded the phylogenetic signals of parallelism for this group. Our results show a striking case of genealogical discordance, where mitochondrial loci support multiple origins of a derived large-bodied morphotype (Plestiodon gilberti) within a small-bodied ancestor (Plestiodon skiltonianus), while nuclear loci indicate a single origin. We attribute the discordance to separate, temporally-spaced hybridization events that led to asymmetric capture of P. skiltonianus mitochondria in different regional lineages of P. gilberti. Nuclear introgression showed a similar directional bias but was less pervasive. We demonstrate how a mechanical reproductive barrier previously identified for this group explains the asymmetry of mitochondrial introgression, given that hybrid matings are most likely when the male is P. gilberti and the female is P. skiltonianus. We then use permutation tests of morphological data to provide evidence that the mechanical barrier is less stringent in areas where hybridization is inferred to have occurred. Our results demonstrate how biased hybridization can dictate which genetic variants are transmitted between species and emphasize the importance of accounting for introgression and deep coalescence in identifying phyletic signatures of parallel speciation.},
}

@article {pmid40114504,
year = {2025},
author = {Iverson, ENK and Criswell, A and Havird, JC},
title = {Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf061},
pmid = {40114504},
issn = {1537-1719},
abstract = {Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.},
}

@article {pmid40112915,
year = {2025},
author = {Park, YJ and Pang, WK and Ryu, DY and Rahman, MS and Pang, MG},
title = {Spatiotemporal translation of sperm acrosome associated proteins during early capacitation modulates sperm fertilizing ability.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.03.035},
pmid = {40112915},
issn = {2090-1224},
abstract = {INTRODUCTION: Despite the lack of essential cytoplasmic organelles in mature spermatozoa, which creates unfavorable conditions for transcription and translation, the presence of various mRNA and proteins during capacitation suggests potential for de novo protein synthesis.

OBJECTIVES: We applied a metabolic labeling method using a fluorescent noncanonical amino acid tagging system (FUNCAT) and proximity ligation method (PLA) in normal and reduced fertility spermatozoa to detect different translation phenomena during sperm capacitation according to their fertility.

METHODS: We explored different proteome changes in spermatozoa according to the time-sequential capacitation process (0, 20, 40, 60, and 120 min) between normal [average fertility rate (FR) = 77.44 % ± 1.51] and reduced fertility (average FR = 58.57 % ± 1.64) spermatozoa bull spermatozoa, as the representative male fertility models owing to their broad spectrum of fertility phenotypes. Moreover, the FUNCAT/PLA method was used to detect and visualize different translation phenomena during sperm capacitation according to fertility.

RESULTS: We found that sperm-associated protein (SPACA) 1 and SPACA5 were newly synthesized in the head of normal-fertility spermatozoa, whereas a lack of newly synthesized proteins in the head and a relatively earlier loss of SPACA1 and SPACA5 were observed in the reduced-fertility spermatozoa. Moreover, the mitochondrial translation inhibitor, chloramphenicol, partially inhibited sperm translation and delayed translocation, suggesting that mitochondria participate in sperm translation.

CONCLUSION: Our results unveil time-sequential microenvironmental changes in sperm proteomes during capacitation, which lead to the orchestra of proteins that complete fertilization. Fertile spermatozoa are selected through inter-competition during the journey of fertilization in the female reproductive tract. This study provides an overview of how translation dynamics acts on the sperm selection and influence the evolution of sperm fertility.},
}

@article {pmid40107722,
year = {2025},
author = {Dondi, A and Borgsmüller, N and Ferreira, PF and Haas, BJ and Jacob, F and Heinzelmann-Schwarz, V and , and Beerenwinkel, N},
title = {De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279281.124},
pmid = {40107722},
issn = {1549-5469},
abstract = {In cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging high-quality LR scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy number alterations (CNAs), and gene fusions, to reconstruct the tumor clonal heterogeneity. Before somatic variant calling, LongSom reannotates marker gene-based cell types using cell mutational profiles. LongSom distinguishes somatic SNVs from noise and germline polymorphisms by applying an extensive set of hard filters and statistical tests. Applying LongSom to human ovarian cancer samples, we detected clinically relevant somatic SNVs that were validated against matched DNA samples. Leveraging somatic SNVs and fusions, LongSom found subclones with different predicted treatment outcomes. In summary, LongSom enables de novo variant detection without the need for normal samples, facilitating the study of cancer evolution, clonal heterogeneity, and treatment resistance.},
}

@article {pmid40107618,
year = {2025},
author = {Thalhofer, V and Doktor, C and Philipp, L and Betat, H and Mörl, M},
title = {An alternative adaptation strategy of the CCA-adding enzyme to accept non-canonical tRNA substrates in Ascaris suum.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {108414},
doi = {10.1016/j.jbc.2025.108414},
pmid = {40107618},
issn = {1083-351X},
abstract = {Playing a central role in translation, tRNAs act as an essential adapter linking the correct amino acid to the corresponding mRNA codon in translation. Due to this function, all tRNAs exhibit a typical secondary and tertiary structure to be recognized by the tRNA maturation enzymes as well as many components of the translation machinery. Yet, there is growing evidence for structurally deviating tRNAs in metazoan mitochondria, requiring a co-evolution and adaptation of these enzymes to the unusual structures of their substrates. Here, it is shown that the CCA-adding enzyme of Ascaris suum carries such a specific adaptation in form of a C-terminal extension. The corresponding enzymes of other nematodes also carry such extensions, and many of them have an additional adaptation in a small region of their N-terminal catalytic core. Thus, the presented data indicates that these enzymes evolved two distinct strategies to tolerate non-canonical tRNAs as substrates for CCA-incorporation. The identified C-terminal extension represents a surprising case of convergent evolution in tRNA substrate adaptation, as the nematode mitochondrial translation factor EF-Tu1 carries a similar extension that is essential for efficient binding to such structurally deviating tRNAs.},
}

@article {pmid40090735,
year = {2025},
author = {Yabuki, A and Fujii, C and Yazaki, E and Tame, A and Mizuno, K and Obayashi, Y and Takao, Y},
title = {Massive RNA Editing in Ascetosporean Mitochondria.},
journal = {Microbes and environments},
volume = {40},
number = {1},
pages = {},
doi = {10.1264/jsme2.ME24070},
pmid = {40090735},
issn = {1347-4405},
mesh = {*RNA Editing ; *Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing ; Eukaryota/genetics/classification ; Phylogeny ; Adenosine Deaminase/genetics/metabolism ; },
abstract = {Ascetosporeans are parasitic protists of invertebrates. A deep sequencing ana-lysis of species within the orders Mikrocytida, Paramyxida, and Haplosporida using metagenomic approaches revealed that their mitochondria were functionally reduced and their organellar genomes were lacking. Ascetosporeans belonging to the order Paradinida have not been sequenced, and the nature of their mitochondria remains unclear. We herein established two cultures of Paradinida and conducted DNA and RNA sequencing ana-lyses. The results obtained indicate that mitochondrial function in paradinids was not reduced and their organellar genomes were retained. In contrast, their mitochondrial genomes were involved in massive A-to-I and C-to-U substitution types of RNA editing. All edits in protein-coding genes were nonsynonymous substitutions, and likely had a restorative function against negative mutations. Furthermore, we detected possible sequences of DYW type of pentatricopeptide repeat (PPR-DYW) protein and a homologue of adenosine deaminase acting on RNA (ADAR-like), which are key enzymes for C-to-U and A-to-I substitutions, respectively. An immunofluorescence ana-lysis showed that ADAR-like of paradinids may specifically localize within mitochondria. These results expand our knowledge of the diversity and complexity of organellar RNA editing phenomena.},
}

*RNA Editing
*Mitochondria/genetics
*Genome, Mitochondrial/genetics
High-Throughput Nucleotide Sequencing
Eukaryota/genetics/classification
Phylogeny
Adenosine Deaminase/genetics/metabolism

@article {pmid40081380,
year = {2025},
author = {Morel, CA and Asencio, C and Moreira, D and Blancard, C and Salin, B and Gontier, E and Duvezin-Caubet, S and Rojo, M and Bringaud, F and Tetaud, E},
title = {A new member of the dynamin superfamily modulates mitochondrial membrane branching in Trypanosoma brucei.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.02.033},
pmid = {40081380},
issn = {1879-0445},
abstract = {Unlike most other eukaryotes, where mitochondria continuously fuse and divide, the mitochondrion of trypanosome cells forms a single and continuously interconnected network that divides only during cytokinesis. However, the machinery governing mitochondrial remodeling and interconnection of trypanosome mitochondrion remain largely unknown. We functionally characterize a new member of the dynamin superfamily protein (DSP) from T. brucei (TbMfnL), which shares similarity with a family of homologs present in various eukaryotic and prokaryotic phyla but not in opisthokonts like mammals and budding yeast. The sequence and domain organization of TbMfnL is distinct, and it is phylogenetically very distant from the yeast and mammalian dynamin-related proteins involved in mitochondrial fusion/fission dynamics, such as optic atrophy 1 (Opa1) and mitofusin (Mfn). TbMfnL localizes to the inner mitochondrial membrane facing the matrix and, upon overexpression, induces a strong increase in the interconnection and branching of mitochondrial filaments in a GTPase-dependent manner. TbMfnL is a component of a novel membrane remodeling machinery with an unprecedented matrix-side localization that is able to modulate the degree of inter-mitochondrial connections.},
}

@article {pmid40037840,
year = {2025},
author = {Medini, H and Mishmar, D},
title = {Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth.},
journal = {Genome research},
volume = {35},
number = {3},
pages = {459-474},
doi = {10.1101/gr.279700.124},
pmid = {40037840},
issn = {1549-5469},
mesh = {Animals ; *Gene Expression Regulation, Developmental ; Vertebrates/genetics ; Cell Nucleus/metabolism/genetics ; Mitochondria/genetics/metabolism ; Genes, Mitochondrial ; Humans ; Oxidative Phosphorylation ; Chickens/genetics ; },
abstract = {Interactions between mitochondrial and nuclear factors are essential to life. Nevertheless, the importance of coordinated regulation of mitochondrial-nuclear gene expression (CMNGE) to changing physiological conditions is poorly understood and is limited to certain tissues and organisms. We hypothesized that CMNGE is important for development across vertebrates and, hence, should be conserved. As a first step, we analyzed more than 1400 RNA-seq experiments performed during prenatal development, in neonates, and in adults across vertebrate evolution. We find conserved sharp elevation of CMNGE after birth, including oxidative phosphorylation (OXPHOS) and mitochondrial ribosome genes, in the heart, hindbrain, forebrain, and kidney across mammals, as well as in Gallus gallus and in the lizard Anolis carolinensis This is accompanied by elevated expression of TCA cycle enzymes and reduction in hypoxia response genes, suggesting a conserved cross-tissue metabolic switch after birth/hatching. Analysis of about 70 known regulators of mitochondrial gene expression reveals consistently elevated expression of PPARGC1A (also known as Pgc-1alpha) and CEBPB after birth/hatching across organisms and tissues, thus highlighting them as candidate regulators of CMNGE upon transition to the neonate. Analyses of Danio rerio, Xenopus tropicalis, Caenorhabditis elegans, and Drosophila melanogaster reveal elevated CMNGE prior to hatching in X. tropicalis and in D. melanogaster, which is associated with the emergence of muscle activity. Lack of such an ancient pattern in mammals and in chickens suggests that it was lost during radiation of terrestrial vertebrates. Taken together, our results suggest that regulated CMNGE after birth reflects an essential metabolic switch that is under strong selective constraints.},
}

Animals
*Gene Expression Regulation, Developmental
Vertebrates/genetics
Cell Nucleus/metabolism/genetics
Mitochondria/genetics/metabolism
Genes, Mitochondrial
Humans
Oxidative Phosphorylation
Chickens/genetics

@article {pmid39893979,
year = {2025},
author = {Duan, C and Zhao, Y and Xiao, Y and Hou, Y and Gong, W and Zhang, H and Wang, Y and Nie, X},
title = {Lithium with environmentally relevant concentrations interferes with mitochondrial function, antioxidant response, and autophagy processes in Daphnia magna, leading to changes in life-history traits and behavior.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137420},
doi = {10.1016/j.jhazmat.2025.137420},
pmid = {39893979},
issn = {1873-3336},
mesh = {Animals ; *Daphnia/drug effects ; *Autophagy/drug effects ; *Water Pollutants, Chemical/toxicity ; *Mitochondria/drug effects ; *Lithium/toxicity ; Oxidative Stress/drug effects ; Antioxidants/metabolism ; Life History Traits ; Behavior, Animal/drug effects ; Reactive Oxygen Species/metabolism ; Female ; Daphnia magna ; },
abstract = {With the increasing production and use of lithium-based products, concerns over lithium pollution in aquatic ecosystems are increasing, whereas research on its toxicity mechanisms in aquatic organisms remains limited. The main objective of the present study was to explore the effects of environmentally relevant concentrations of lithium exposure on the life-history strategy, behavior, antioxidant system, and autophagy process of Daphnia magna. Acute (24-96 h) and chronic (21 days) exposure experiments under three lithium treatments (low: 8.34 μg/L, medium: 83.44 μg/L, and high: 834.41 μg/L) were conducted. The results indicated that exposure to medium and high lithium concentrations led to eye and tail deformities in D. magna. Furthermore, developmental and reproductive parameters such as body length, total neonates per female, and average neonates per time were negatively influenced. Lithium also interfered with energy metabolism to cause the decreasing swimming speed and the reduction in the swimming range. In addition, lithium exposure affected the expression of gsk-3β, further disrupting the dynamic balance of mitochondrial fission, fusion, and regeneration, which caused ROS accumulation and induced oxidative stress. D. magna attenuated the stress by activating the FoxO/SESN and Nrf2/Keap1 pathways, synergistically enhancing downstream antioxidant enzymes expression. Concurrently, D. magna also mitigated oxidative stress and mitochondrial damage by promoting autophagy and inhibiting apoptosis. In summary, lithium harmed the physiological and biochemical functions of D. magna through multiple mechanisms, suggesting that environmental lithium pollution may pose a potential threat to aquatic organisms.},
}

Animals
*Daphnia/drug effects
*Autophagy/drug effects
*Water Pollutants, Chemical/toxicity
*Mitochondria/drug effects
*Lithium/toxicity
Oxidative Stress/drug effects
Antioxidants/metabolism
Life History Traits
Behavior, Animal/drug effects
Reactive Oxygen Species/metabolism
Female
Daphnia magna

@article {pmid40076588,
year = {2025},
author = {Zhou, W and Cao, X and Li, H and Cui, X and Diao, X and Qiao, Z},
title = {Genomic Analysis of Hexokinase Genes in Foxtail Millet (Setaria italica): Haplotypes and Expression Patterns Under Abiotic Stresses.},
journal = {International journal of molecular sciences},
volume = {26},
number = {5},
pages = {},
pmid = {40076588},
issn = {1422-0067},
mesh = {*Setaria Plant/genetics ; *Stress, Physiological/genetics ; *Gene Expression Regulation, Plant ; *Phylogeny ; *Hexokinase/genetics/metabolism ; *Haplotypes ; Plant Proteins/genetics/metabolism ; Evolution, Molecular ; },
abstract = {Hexokinases (HXKs) in plants are multifunctional enzymes that not only phosphorylate hexose but also function as glucose sensors, integrating nutrient, light, and hormone signaling networks to regulate cell metabolism and signaling pathways, thereby controlling growth and development in response to environmental changes. To date, limited information is available regarding the HXKs of foxtail millet (Setaria italica L.). In this study, six HXK genes were identified and characterized in foxtail millet. Phylogenetic analysis revealed that the foxtail millet hexokinases were classified into three subfamilies, corresponding to the two types (B-type and C-type) of hexokinases in plants. Gene structure and conserved motif analysis showed that the SiHXKs exhibited varying numbers of introns and exons, with proteins in each subfamily showing similar motif organization. Evolutionary divergence analysis indicated that the foxtail millet HXK and green foxtail HXK genes families underwent both positive and negative selection and experienced a large-scale duplication event approximately 1.18-154.84 million years ago. Expression analysis revealed that these genes are widely expressed in roots, stems, leaves, panicles, anthers, and seeds, with most genes showing significantly increased expression in roots under abiotic stress conditions, including 20% PEG 6000 (drought stress), 200 μmol/L NaCl (salt stress), and 1 μmol/L BR (brassinosteroid-mediated stress response). These results suggest that these genes may play a pivotal role in enhancing stress tolerance. Subcellular localization assay showed that SiHXK5 and SiHXK6 were predominantly localized in mitochondria. Haplotype analysis revealed that SiHXK3-H1 was associated with higher plant height and grain yield. These findings provide valuable insights into the functional characteristics of HXK genes, especially in the context of marker-assisted selection and the pyramiding of advantageous haplotypes in foxtail millet breeding programs.},
}

*Setaria Plant/genetics
*Stress, Physiological/genetics
*Gene Expression Regulation, Plant
*Phylogeny
*Hexokinase/genetics/metabolism
*Haplotypes
Plant Proteins/genetics/metabolism
Evolution, Molecular

@article {pmid40075306,
year = {2025},
author = {Zhou, N and Wang, X and Xia, Y and Liu, Z and Luo, L and Jin, R and Tong, X and Shi, Z and Wang, Z and Sui, H and Ma, Y and Li, Y and Cao, Z and Zhang, Y},
title = {Comparatively profiling the transcriptome of human, Porcine and mouse oocytes undergoing meiotic maturation.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {236},
pmid = {40075306},
issn = {1471-2164},
support = {2020LCX015//Anhui Province Innovation and Entrepreneurship Support Program for Returnee Scholar/ ; 2021YFA0805905//Sub-project of National Key Research and Development Program of China/ ; AHCYJSTX-04//Special Fund for Anhui Agriculture Research System/ ; },
mesh = {Animals ; *Oocytes/metabolism ; Mice ; *Meiosis/genetics ; Humans ; Swine ; *Gene Expression Profiling ; *Transcriptome ; Female ; Oogenesis/genetics ; Species Specificity ; },
abstract = {BACKGROUND: Oocyte maturation is a critical process responsible for supporting preimplantation embryo development and full development to term. Understanding oocyte gene expression is relevant given the unique molecular mechanism present in this gamete. Comparative transcriptome analysis across species offers a powerful approach to uncover conserved and species-specific genes involved in the molecular regulation of oocyte maturation throughout evolution.

RESULTS: Transcriptome analysis identified 4,625, 3,824, 4,972 differentially expressed genes (DEGs) between the germinal vesicle (GV) and metaphase II (MII) stage in human, porcine and mouse oocytes respectively. These DEGs showed dynamic changes associated with oocyte maturation. Functional enrichment analysis revealed that the DEGs in all three species were mainly involved in DNA replication, cell cycle and redox regulation. Comparative transcriptome analysis identified 551 conserved DEGs in the three species with significant enrichment in mitochondria and mitochondrial intima.

CONCLUSIONS: This study provides a systematic comparative analysis of oocyte meiotic maturation in humans, pigs and mice identifying both conserved and species-specific patterns during oocyte meiosis. Our findings also implied that the selection of oocyte expressed genes among these three species could form a basis for further exploring their functional roles in human oocyte maturation.},
}

Animals
*Oocytes/metabolism
Mice
*Meiosis/genetics
Humans
Swine
*Gene Expression Profiling
*Transcriptome
Female
Oogenesis/genetics
Species Specificity

@article {pmid40043709,
year = {2025},
author = {Ping, J and Liu, X and Lu, Y and Quan, C and Fan, P and Lu, H and Li, Q and Wang, C and Zhang, Z and Liu, M and Chen, S and Chang, L and Jiang, Y and Huang, Q and Liu, J and Wuren, T and Liu, H and Hao, Y and Kang, L and Liu, G and Lu, H and Wei, X and Wang, Y and Li, Y and Guo, H and Cui, Y and Zhang, H and Zhang, Y and Zhai, Y and He, Y and Zheng, W and Qi, X and Ouzhuluobu, and Ma, H and Yang, L and Wang, X and Jin, W and Cui, Y and Ge, R and Wu, S and Wei, Y and Su, B and He, F and Zhang, H and Zhou, G},
title = {A highland-adaptation variant near MCUR1 reduces its transcription and attenuates erythrogenesis in Tibetans.},
journal = {Cell genomics},
volume = {5},
number = {3},
pages = {100782},
doi = {10.1016/j.xgen.2025.100782},
pmid = {40043709},
issn = {2666-979X},
mesh = {Humans ; *Erythropoiesis/genetics ; Tibet ; *Calcium/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Kinase/genetics/metabolism ; Quantitative Trait Loci ; Mitochondria/metabolism/genetics ; Male ; Altitude ; TOR Serine-Threonine Kinases/metabolism/genetics ; Adaptation, Physiological/genetics ; Transcription, Genetic/genetics ; Female ; Adult ; Calcium Channels/genetics/metabolism ; Polymorphism, Single Nucleotide ; East Asian People ; },
abstract = {To identify genomic regions subject to positive selection that might contain genes involved in high-altitude adaptation (HAA), we performed a genome-wide scan by whole-genome sequencing of Tibetan highlanders and Han lowlanders. We revealed a collection of candidate genes located in 30 genomic loci under positive selection. Among them, MCUR1 at 6p23 was a novel pronounced candidate. By single-cell RNA sequencing and comprehensive functional studies, we demonstrated that MCUR1 depletion leads to impairment of erythropoiesis under hypoxia and normoxia. Mechanistically, MCUR1 knockdown reduced mitochondrial Ca[2+] uptake and then concomitantly increased cytosolic Ca[2+] levels, which thereby reduced erythropoiesis via the CAMKK2-AMPK-mTOR axis. Further, we revealed rs61644582 at 6p23 as an expression quantitative trait locus for MCUR1 and a functional variant that confers an allele-specific transcriptional regulation of MCUR1. Overall, MCUR1-mediated mitochondrial Ca[2+] homeostasis is highlighted as a novel regulator of erythropoiesis, deepening our understanding of the genetic mechanism of HAA.},
}

Humans
*Erythropoiesis/genetics
Tibet
*Calcium/metabolism
Calcium-Calmodulin-Dependent Protein Kinase Kinase/genetics/metabolism
Quantitative Trait Loci
Mitochondria/metabolism/genetics
Male
Altitude
TOR Serine-Threonine Kinases/metabolism/genetics
Adaptation, Physiological/genetics
Transcription, Genetic/genetics
Female
Adult
Calcium Channels/genetics/metabolism
Polymorphism, Single Nucleotide
East Asian People

@article {pmid40072502,
year = {2025},
author = {Kemph, A and Kharel, K and Tindell, SJ and Arkov, AL and Lynch, JA},
title = {Novel structure and composition of the unusually large germline determinant of the wasp Nasonia vitripennis.},
journal = {Molecular biology of the cell},
volume = {},
number = {},
pages = {mbcE24110499},
doi = {10.1091/mbc.E24-11-0499},
pmid = {40072502},
issn = {1939-4586},
abstract = {Specialized, maternally derived ribonucleoprotein (RNP) granules play an important role in specifying the primordial germ cells in many animal species. Typically, these germ granules are small (∼100 nm to a few microns in diameter) and numerous; in contrast, a single, extremely large granule called the oosome plays the role of germline determinant in the wasp Nasonia vitripennis. The organizational basis underlying the form and function of this unusually large membraneless RNP granule remains an open question. Here we use a combination of super-resolution and transmission electron microscopy to investigate the composition and morphology of the oosome. We show evidence which suggests the oosome has properties of a viscous liquid or elastic solid. The most prominent feature of the oosome is a branching mesh-like network of high abundance mRNAs that pervades the entire structure. Homologs of the core germ granule proteins Vasa and Oskar do not appear to nucleate this network but rather are distributed adjacently as separate puncta. Low abundance RNAs appear to cluster in puncta that similarly do not overlap with the protein puncta. Several membrane-bound organelles, including lipid droplets and rough ER-like vesicles, are incorporated within the oosome, whereas mitochondria are nearly entirely excluded. Our findings show that the remarkably large size of the oosome is reflected in a complex sub-granular organization and suggest that the oosome is a powerful model for probing interactions between membraneless and membrane-bound organelles, structural features that contribute to granule size, and the evolution of germ plasm in insects. [Media: see text] [Media: see text].},
}

@article {pmid40056111,
year = {2025},
author = {Sun, A and Wang, WX},
title = {Photodegradation Controls of Potential Toxicity of Secondary Sunscreen-Derived Microplastics and Associated Leachates.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12077},
pmid = {40056111},
issn = {1520-5851},
abstract = {The escalating environmental concern over secondary microplastics (SMPs) stems from their physicochemical evolution from primary microplastics (PMPs), yet the contribution of varying physicochemical transformations to the ultimate environmental risks remains unknown. In this study, a photomechanical degradation process was employed to convert the primary sunscreen-derived microplastics (SDMPs) into secondary SDMPs. While mechanical degradation caused physical fragmentation, photodegradation induced both physical and chemical alterations, introducing surface oxidation, chemical bond scission, and cross-linking to the secondary SDMPs. Employing a combination of alkaline digestion and pyrolysis GC-MS techniques, it was observed that both physical fragmentation and photooxidation led to heightened intracellular sequestration of MPs. Although the bioaccumulated SDMPs could be indicated by the enlarged lysosomes and fragmented mitochondria, toxicity of secondary SDMPs at the cellular level was primarily driven by chemical transformations post-photodegradation. A nontargeted analysis employing high-resolution mass spectrometry identified 46 plastic-associated compounds in the leachate, with photodegradation-induced chemical transformations playing a crucial role in the dissociation of hydrophobic additives and oxidative conversion of leached compounds. The toxicity of the leachate was exacerbated by photodegradation, with mitochondrial fragmentation serving as the primary subcellular biomarker, indicative of leachate toxicity. This study elucidates the pivotal role of photodegradation in augmenting the cytotoxicity of secondary SDMPs, shedding light on the intricate interplay between physicochemical transformations and environmental risks.},
}

@article {pmid40043708,
year = {2025},
author = {Thomas, HB and Demain, LAM and Cabrera-Orefice, A and Schrauwen, I and Shamseldin, HE and Rea, A and Bharadwaj, T and Smith, TB and Oláhová, M and Thompson, K and He, L and Kaur, N and Shukla, A and Abukhalid, M and Ansar, M and Rehman, S and Riazuddin, S and Abdulwahab, F and Smith, JM and Stark, Z and Mancilar, H and Tumer, S and Esen, FN and Uctepe, E and Topcu, V and Yesilyurt, A and Afzal, E and Salari, M and Carroll, C and Zifarelli, G and Bauer, P and Kor, D and Bulut, FD and Houlden, H and Maroofian, R and Carrera, S and Yue, WW and Munro, KJ and Alkuraya, FS and Jamieson, P and Ahmed, ZM and Leal, SM and Taylor, RW and Wittig, I and O'Keefe, RT and Newman, WG},
title = {Bi-allelic variants in MRPL49 cause variable clinical presentations, including sensorineural hearing loss, leukodystrophy, and ovarian insufficiency.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2025.02.005},
pmid = {40043708},
issn = {1537-6605},
abstract = {Combined oxidative phosphorylation deficiency (COXPD) is a rare multisystem disorder that is clinically and genetically heterogeneous. Genome sequencing identified bi-allelic MRPL49 variants in individuals from nine unrelated families with presentations ranging from Perrault syndrome (primary ovarian insufficiency and sensorineural hearing loss) to severe childhood onset of leukodystrophy, learning disability, microcephaly, and retinal dystrophy. Complexome profiling of fibroblasts from affected individuals revealed reduced levels of the small mitochondrial ribosomal subunits and a more pronounced reduction of the large mitochondrial ribosomal subunits. There was no evidence of altered mitoribosomal assembly. The reductions in levels of oxidative phosphorylation (OXPHOS) enzyme complexes I and IV are consistent with a form of COXPD associated with bi-allelic MRPL49 variants, expanding the understanding of how disruption of the mitochondrial ribosomal large subunit results in multisystem phenotypes.},
}

@article {pmid40029892,
year = {2025},
author = {Paul, SK and Islam, MSU and Akter, N and Zohra, FT and Rashid, SB and Ahmed, MS and Rahman, SM and Sarkar, MAR},
title = {Genome-wide identification and characterization of FORMIN gene family in cotton (Gossypium hirsutum L.) and their expression profiles in response to multiple abiotic stress treatments.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0319176},
pmid = {40029892},
issn = {1932-6203},
mesh = {*Gossypium/genetics ; *Stress, Physiological/genetics ; *Phylogeny ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; *Multigene Family ; Formins/genetics/metabolism ; Genome, Plant ; Evolution, Molecular ; Genes, Plant ; },
abstract = {FORMIN proteins distinguished by FH2 domain, are conserved throughout evolution and widely distributed in eukaryotic organisms. These proteins interact with various signaling molecules and cytoskeletal proteins, playing crucial roles in both biotic and abiotic stress responses. However, the functions of FORMINs in cotton (Gossypium hirsutum L.) remain uncovered. In this study, 46 FORMIN genes in G. hirsutum (referred to as GhFH) were systematically identified. The gene structures, conserved domains, and motifs of these GhFH genes were thoroughly explored. Phylogenetic and structural analysis classified these 46 GhFH genes into five distinct groups. In silico subcellular localization, prediction suggested that GhFH genes are distributed across various cellular compartments, including the nucleus, extracellular space, cytoplasm, mitochondria, cytoskeleton, plasma membrane, endoplasmic reticulum, and chloroplasts. Evolutionary and functional diversification analyses, based on on-synonymous (Ka) and synonymous (Ks) ratios and gene duplication events, indicated that GhFH genes have evolved under purifying selection. The analysis of cis-acting elements suggested that GhFH genes may be involved in plant growth, hormone regulation, light response, and stress response. Results from transcriptional factors TFs and gene ontology analysis indicate that FORMIN proteins regulate cell wall structure and cytoskeleton dynamics by reacting to hormone signals associated with environmental stress. Additionally, 45 putative ghr-miRNAs were identified from 32 families targeting 33 GhFH genes. Expression analysis revealed that GhFH1, GhFH10, GhFH20, GhFH24, and GhFH30 exhibited the highest levels of expression under red, blue, and white light conditions. Further, GhFH9, GhFH20, and GhFH30 displayed higher expression levels under heat stress, while GhFH20 and GhFH30 showed increased expression under salt stress compared to controls. The result suggests that GhFH20 and GhFH30 genes could play significant roles in the development of G. hirsutum under heat and salt stresses. Overall these findings enhance our understanding of the biological functions of the cotton FORMIN family, offering prospects for developing stress-resistant cotton varieties through manipulation of GhFH gene expression.},
}

*Gossypium/genetics
*Stress, Physiological/genetics
*Phylogeny
*Gene Expression Regulation, Plant
*Plant Proteins/genetics/metabolism
*Multigene Family
Formins/genetics/metabolism
Genome, Plant
Evolution, Molecular
Genes, Plant

@article {pmid39993486,
year = {2025},
author = {He, M and Li, S and Sun, J and Lv, X and Li, Y and Song, L},
title = {CgVDAC2 participated in haemocyte mitophagy induced by Vibrio splendidus in the Pacific oyster Crassostrea gigas.},
journal = {Fish & shellfish immunology},
volume = {160},
number = {},
pages = {110226},
doi = {10.1016/j.fsi.2025.110226},
pmid = {39993486},
issn = {1095-9947},
mesh = {Animals ; *Vibrio/physiology ; *Crassostrea/immunology/genetics ; *Hemocytes/immunology ; *Mitophagy/immunology ; *Voltage-Dependent Anion Channel 2/genetics/immunology ; Immunity, Innate/genetics ; Gene Expression Regulation/immunology ; Phylogeny ; },
abstract = {VDAC2 (Voltage dependent anion channel 2) is a highly conserved pore-forming protein expressed in the outer membrane of eukaryotic mitochondria. In the present study, CgVDAC2 identified from Crassostrea gigas regulated the mitophagy of haemocytes induced by Vibrio splendidus. CgVDAC2 was distributed in the cytoplasm of three subpopulations of haemocytes. After V. splendidus stimulation, the mRNA and protein expressions of CgVDAC2 were induced in haemocytes. Furthermore, the green signals of CgVDAC2 were colocalized with the red signals of mitochondria and Mtphagy Dye, respectively. And their co-localization values were both increased significantly in haemocytes at 12 h after V. splendidus stimulation, respectively. In siCgVDAC2-treated oysters, the mRNA expressions of mitophagy-related genes (CgLC3, CgPINK1, CgParkin1, CgPHB2, and CgATG16L) and the levels of mitophagy decreased significantly in haemocytes after V. splendidus stimulation. In addition, both the fluorescence intensities of the JC-1 monomer/aggregate ratio (Q4/Q2) and mitochondrial reactive oxygen species (mtROS) increased significantly. Collectively, all the results indicated that CgVDAC2 participated in oyster antibacterial immune response through regulating the haemocyte mitophagy.},
}

Animals
*Vibrio/physiology
*Crassostrea/immunology/genetics
*Hemocytes/immunology
*Mitophagy/immunology
*Voltage-Dependent Anion Channel 2/genetics/immunology
Immunity, Innate/genetics
Gene Expression Regulation/immunology
Phylogeny

@article {pmid40027421,
year = {2025},
author = {Bagdonaitė, L and Mauvisseau, Q and Johnsen, A and Lifjeld, JT and Leder, EH},
title = {Sperm mtDNA Copy Number Is Not Associated With Midpiece Size Among Songbirds.},
journal = {Ecology and evolution},
volume = {15},
number = {3},
pages = {e71055},
pmid = {40027421},
issn = {2045-7758},
abstract = {Tremendous variation in sperm morphology is observed across the animal kingdom. Within avian taxa, the songbirds (infraorder Passerides) have the largest variation in sperm morphology. Their spermatozoa move by using energy generated in the midpiece, which is formed by multiple mitochondria fusing together during spermatogenesis. However, very little is known regarding the number of mitochondria required to form the songbird midpiece. Based on previous research showing an association of midpiece length and mitochondrial DNA (mtDNA) copy number in the zebra finch Taeniopygia guttata, we hypothesize that songbird species with longer sperm midpieces have more copies of mtDNA. We estimated the sperm mtDNA copy number in 19 species from 10 families within Passerides, covering a broad range of midpiece sizes. Mitochondrial and nuclear DNA abundance were determined using droplet digital PCR (ddPCR) and the ratio between mitochondrial and single-copy nuclear genes was used to estimate mtDNA copy number per spermatozoon. We found that species differ in their average mtDNA copy number, but the variation was small and not significantly related to midpiece length. A possible explanation is that mitochondrial genomes are eliminated in the spermatids during spermatogenesis.},
}

@article {pmid40027321,
year = {2025},
author = {Zhang, T and Fu, J and Li, C and Gong, R and Al-Rasheid, KAS and Stover, NA and Shao, C and Cheng, T},
title = {Novel findings on the mitochondria in ciliates, with description of mitochondrial genomes of six representatives.},
journal = {Marine life science & technology},
volume = {7},
number = {1},
pages = {79-95},
pmid = {40027321},
issn = {2662-1746},
abstract = {UNLABELLED: Determining and comparing mitochondrial genomes (mitogenomes) are essential for assessing the diversity and evolution of mitochondria. Ciliates are ancient and diverse unicellular eukaryotes, and thus are ideal models for elucidating the early evolution of mitochondria. Here, we report on six new mitogenomes of spirotrichs, a dominant ciliate group, and perform comparative analyses on 12 representative species. We show that: (1) the mitogenomes of spirotrichs are linear structures with high A+T contents (61.12-81.16%), bidirectional transcription, and extensive synteny (except for the nad5, ccmf and cob genes in Euplotia); (2) the non-split of NADH dehydrogenase subunit 2 gene (nad2) is a plesiomorphy of ciliates, whereas it has evolved into a split gene in Spirotrichea (apart from Euplotes taxa), Oligohymenophorea, and Armophorea; (3) the number of small subunit ribosomal proteins (rps) encoded in mitogenomes increases in the later branching classes of ciliates, whereas rps8 shows a loss trend during the evolution of Euplotes taxa; (4) the mitogenomes of spirotrichs exhibit A/T codon bias at the third position, and the codon bias is mainly due to DNA mutation in oligotrichs, hypotrichs and Diophrys appendiculata; (5) the phylogenetic position of D. appendiculata is unstable and controversial based on both phylogenetic analyses and mitogenome evidence. In summary, we investigated the mitogenome diversity of spirotrichs and broadened our understanding of the evolution of mitochondria in ciliates.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00249-7.},
}

@article {pmid40022150,
year = {2025},
author = {Shalata, A and Saada, A and Mahroum, M and Hadid, Y and Furman, C and Shalata, ZE and Desnick, RJ and Lorber, A and Khoury, A and Higazi, A and Shaag, A and Barash, V and Spiegel, R and Vlodavsky, E and Rustin, P and Pietrokovski, S and Manov, I and Gieger, D and Tal, G and Salzberg, A and Mandel, H},
title = {Sengers syndrome caused by biallelic TIMM29 variants and RNAi silencing in Drosophila orthologue recapitulates the human phenotype.},
journal = {Human genomics},
volume = {19},
number = {1},
pages = {21},
pmid = {40022150},
issn = {1479-7364},
mesh = {Humans ; Animals ; Male ; Female ; *Drosophila melanogaster/genetics ; *Phenotype ; *Acidosis, Lactic/genetics/pathology ; *Drosophila Proteins/genetics ; Alleles ; Cataract/genetics/pathology ; RNA Interference ; Mutation/genetics ; Pedigree ; Cardiomyopathy, Hypertrophic/genetics/pathology ; Child ; Mitochondrial Precursor Protein Import Complex Proteins ; Muscular Diseases/genetics/pathology ; Mitochondria/genetics/pathology/metabolism ; Homozygote ; },
abstract = {PURPOSE: Sengers-syndrome (S.S) is a genetic disorder characterized by congenital cataracts, hypertrophic cardiomyopathy, skeletal myopathy and lactic acidosis. All reported cases were genetically caused by biallelic mutations in the AGK gene. We herein report a pathogenic variant in TIMM29 gene, encoding Tim29 protein, as a novel cause of S.S. Notably, AGK and Tim29 proteins are components of the TIM22 complex, which is responsible for importing carrier proteins into the inner mitochondrial membrane.

METHOD: Clinical data of 17 consanguineous patients featuring S.S was obtained. Linkage analysis, and sequencing were used to map and identify the disease-causing gene. Tissues derived from the study participants and a Drosophila melanogaster model were used to evaluate the effects of TIMM29 variant on S.S.

RESULTS: The patients presented with a severe phenotype of S.S, markedly elevated serum creatine-phosphokinase, combined mitochondrial-respiratory-chain-complexes deficiency, reduced pyruvate-dehydrogenase complex activity, and reduced adenine nucleotide translocator 1 protein. Histopathological studies showed accumulation of abnormal mitochondria. Homozygosity mapping and gene sequencing revealed a biallelic variant in TIMM29 NM_138358.4:c.514T > C NP_612367.1:p.(Trp172Arg). The knockdown of the Drosophila TIMM29 orthologous gene (CG14270) recapitulated the phenotype and pathology observed in the studied cohort. We expand the clinical phenotype of S.S and provide substantial evidence supporting TIMM29 as the second causal gene of a severe type of S.S, designated as S.S- TIMM29.

CONCLUSION: The present study uncovers several biochemical differences between the two S.S types, including the hyperCPKemia being almost unique for S.S-TIMM29 cohort, the different frequency of MMRCC and PDHc deficiencies among the two S.S types. We propose to designate the S.S associated with TIMM29 homozygous variant as S.S-TIMM29.},
}

Humans
Animals
Male
Female
*Drosophila melanogaster/genetics
*Phenotype
*Acidosis, Lactic/genetics/pathology
*Drosophila Proteins/genetics
Alleles
Cataract/genetics/pathology
RNA Interference
Mutation/genetics
Pedigree
Cardiomyopathy, Hypertrophic/genetics/pathology
Child
Mitochondrial Precursor Protein Import Complex Proteins
Muscular Diseases/genetics/pathology
Mitochondria/genetics/pathology/metabolism
Homozygote

@article {pmid40021962,
year = {2025},
author = {Dong, S and Li, X and Liu, Q and Zhu, T and Tian, A and Chen, N and Tu, X and Ban, L},
title = {Comparative genomics uncovers evolutionary drivers of locust migratory adaptation.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {203},
pmid = {40021962},
issn = {1471-2164},
support = {2022YFD1400500//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Animal Migration ; *Grasshoppers/genetics/physiology ; *Genomics/methods ; Adaptation, Physiological/genetics ; Evolution, Molecular ; Selection, Genetic ; Phylogeny ; Phenotype ; Biological Evolution ; Energy Metabolism/genetics ; },
abstract = {BACKGROUND: Locust migration is one of the main causes of locust plagues. While existing research has highlighted the adaptive migratory capabilities of locusts, the evolutionary patterns of their migration remain elusive. This study aims to explore these evolutionary patterns of locust migratory behavior at the genomic level. To achieve this, we conducted comparative genomics analysis using genomic data from 10 locust species with diverse migratory tendencies.

RESULTS: We identified 1064 genes showing signatures of positive selection in five migratory locust species using a dN/dS model. The BUSTED-PH model revealed 116 genes associated with migratory phenotypes. Gene ontology enrichment analysis indicated that these genes were predominantly related to metabolism and mitochondria-related pathways through both methods. Additionally, the evolutionary rate (RER) analysis between migratory and non-migratory locusts revealed significant divergence in energy metabolism pathways. Notably, of the genes analyzed, the SETX gene consistently showed evidence of positive selection across all five migratory species.

CONCLUSIONS: The findings suggest that the evolution of migratory behavior is associated with increased selective pressure on metabolism and mitochondria-related pathways. Hundreds of genes undergo selective changes during repetitive transitions to migratory behavior. These findings enhance our understanding of the genetic and phenotypic relationships underlying different locust migratory behaviors, providing important data for understanding the biological mechanisms behind locust outbreaks.},
}

Animals
*Animal Migration
*Grasshoppers/genetics/physiology
*Genomics/methods
Adaptation, Physiological/genetics
Evolution, Molecular
Selection, Genetic
Phylogeny
Phenotype
Biological Evolution
Energy Metabolism/genetics

@article {pmid40008059,
year = {2025},
author = {Nielsen, TL and Nielsen, SH and Novosolov, M and Gravlund, P and Allentoft, ME},
title = {Deeply Diverged but Morphologically Conserved Lineages in Tornier's Cat Snake (Crotaphopeltis tornieri) of the Eastern Arc Mountains.},
journal = {Ecology and evolution},
volume = {15},
number = {2},
pages = {e70452},
pmid = {40008059},
issn = {2045-7758},
abstract = {The Eastern Arc Mountain (EAM) forests in Tanzania have remarkably high endemism. Closely-related forest-adapted species are found isolated on different "sky islands" testifying to allopatry as a major driver for speciation in this region. However, some species defy this pattern. Tornier's cat snake (Crotaphopeltis tornieri) occupies most of the isolated mountain rainforest, despite presumably not being able to move across the arid savannah landscape that separates them. To test contrasting hypotheses of recent dispersal vs morphological conservatism we examined scale characters of 218 C. tornieri individuals and sequenced 80 full mitochondrial genomes covering populations from eight mountain blocks across the EAM and Southern Highlands of Tanzania (SHT). The morphological examination revealed no differentiation between populations except the Usambara Mountain populations showing significant differences in some scale characters. This was in stark contrast to the genetic analyses showing very high divergence between mountain populations. On average the mitochondrial genome showed > 12% genetic differentiation with cytB and COI showing interpopulation distances of up to 28.5% and 15.1%, respectively. Both Bayesian coalescent and maximum-likelihood based phylogenies, uncovered a highly distinct clade structure in C. tornieri defined by the mountains. Divergence times were estimated at c. 21 million years for the split between the EAM and SHT populations and 5.4-1.4 millions years for population splits within EAM. Our results point towards old isolation events but with a highly conserved morphology resulting in just one recognized species. By including presumed outgroups of C. degeni and C. hotamboeia in the phylogeny we found C. tornieri to be paraphyletic. These results have implications for understanding evolution in the EAM and warrant a revision of the number of species in this genus.},
}

@article {pmid40006901,
year = {2025},
author = {Stefano, GB and Kream, RM},
title = {Primordial Biochemicals Within Coacervate-Like Droplets and the Origins of Life.},
journal = {Viruses},
volume = {17},
number = {2},
pages = {},
pmid = {40006901},
issn = {1999-4915},
mesh = {*Mitochondria/metabolism ; *Viruses/metabolism/genetics ; *Origin of Life ; Humans ; Energy Metabolism ; },
abstract = {An organism is considered "alive" if it can grow, reproduce, respond to external stimuli, metabolize nutrients, and maintain stability. By this definition, both mitochondria and viruses exhibit the key characteristics of independent life. In addition to their capacity for self-replication under specifically defined conditions, both mitochondria and viruses can communicate via shared biochemical elements, alter cellular energy metabolism, and adapt to their local environment. To explain this phenomenon, we hypothesize that early viral prototype species evolved from ubiquitous environmental DNA and gained the capacity for self-replication within coacervate-like liquid droplets. The high mutation rates experienced in this environment streamlined their acquisition of standard genetic codes and adaptation to a diverse set of host environments. Similarly, mitochondria, eukaryotic intracellular organelles that generate energy and resolve oxygen toxicity, originally evolved from an infectious bacterial species and maintain their capacity for active functionality within the extracellular space. Thus, while mitochondria contribute profoundly to eukaryotic cellular homeostasis, their capacity for freestanding existence may lead to functional disruptions over time, notably, the overproduction of reactive oxygen species, a phenomenon strongly linked to aging-related disorders. Overall, a more in-depth understanding of the full extent of the evolution of both viruses and mitochondria from primordial precursors may lead to novel insights and therapeutic strategies to address neurodegenerative processes and promote healthy aging.},
}

*Mitochondria/metabolism
*Viruses/metabolism/genetics
*Origin of Life
Humans
Energy Metabolism

@article {pmid40002411,
year = {2025},
author = {Peña, FJ and Martín-Cano, FE and Becerro-Rey, L and da Silva-Álvarez, E and Gaitskell-Phillips, G and Aparicio, IM and Gil, MC and Ortega-Ferrusola, C},
title = {Redox Regulation and Glucose Metabolism in the Stallion Spermatozoa.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/antiox14020225},
pmid = {40002411},
issn = {2076-3921},
abstract = {Stallion spermatozoa are cells which exhibit intense metabolic activity, where oxidative phosphorylation in the mitochondria is the primary ATP generator. However, metabolism must be viewed as a highly interconnected network of oxidation-reduction reactions that generate the energy necessary for life. An unavoidable side effect of metabolism is the generation of reactive oxygen species, leading to the evolution of sophisticated mechanisms to maintain redox homeostasis. In this paper, we provide an updated overview of glucose metabolism in stallion spermatozoa, highlighting recent evidence on the role of aerobic glycolysis in these cells, and the existence of an intracellular lactate shuttle that may help to explain the particular metabolism of the stallion spermatozoa in the context of their redox regulation.},
}

@article {pmid40000832,
year = {2025},
author = {Du, W and Sun, Q and Hu, S and Yu, P and Kan, S and Zhang, W},
title = {Equus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6803},
pmid = {40000832},
issn = {2045-2322},
support = {ZR2023QC278//Natural Science Foundation of Shandong Province/ ; 2022YFC3341002-2//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Equidae/genetics ; *Genome, Mitochondrial ; *Domestication ; Horses/genetics ; *Phylogeny ; Genetic Variation ; Mitochondria/genetics ; Animals, Domestic/genetics ; },
abstract = {Mitochondria are semi-autonomous organelles that play a crucial role in the energy budget of animal cells and are closely related to the locomotor abilities of animals. Equidae is renowned for including two domesticated species with distinct purposes: the endurance-oriented donkey and the power-driven horse, making it an ideal system for studying the relationship between mitochondria and locomotor abilities. In this study, to cover the genetic diversity of donkeys, we sequenced and assembled six new mitochondrial genomes from China. Meanwhile, we downloaded the published mitochondrial genomes of all species within Equus and conducted a comprehensive pan-mitochondrial genome analysis. We found that the mitochondrial genomes of Equus are highly conserved, each encoding 37 genes, including 13 protein-coding genes (PCGs). Phylogenetic analysis based on mitochondrial genomes supports previous research, indicating that the extant species in Equus are divided into three main branches: horses, donkeys, and zebras. Specifically, 761 genetic variants were identified between donkeys and horses, 68 of which were non-synonymous mutations in PCGs, potentially linked to their different locomotor abilities. Structural protein modeling indicated that despite genetic differences, the overall protein structures between donkeys and horses remain similar. This study revealed the mitochondrial genome variation patterns of domesticated animals, offering novelty perspectives on domestication imprints. Additionally, it provides reliable candidate molecular markers for the identification of donkeys and horses.},
}

Animals
*Equidae/genetics
*Genome, Mitochondrial
*Domestication
Horses/genetics
*Phylogeny
Genetic Variation
Mitochondria/genetics
Animals, Domestic/genetics

@article {pmid39998089,
year = {2025},
author = {Lan, X and Yang, M and Wang, J and Huang, C and Wu, A and Cui, L and Guo, Y and Zeng, L and Guo, X and Zhang, Y and Xiang, Y and Wang, Q},
title = {Pore-Forming Protein LIN-24 Enhances Starvation Resilience in Caenorhabditis elegans by Modulating Lipid Metabolism and Mitochondrial Dynamics.},
journal = {Toxins},
volume = {17},
number = {2},
pages = {},
pmid = {39998089},
issn = {2072-6651},
support = {82471591, 82460283, 32360136//National Natural Science Foundation of China/ ; 2023YFC3603300, 2023YFF1001000//National Key R&D Program, Ministry of Science and Technology of China/ ; 2024SSY07161 and 20221ZDG020070//Natural Science Foundation of Jiangxi Province/ ; 28740105//Foundation of Nanchang University/ ; },
mesh = {Animals ; *Caenorhabditis elegans/genetics/physiology/metabolism ; *Caenorhabditis elegans Proteins/genetics/metabolism ; *Lipid Metabolism ; *Mitochondrial Dynamics ; *Starvation/metabolism ; Mitochondria/metabolism ; },
abstract = {The ability to survive starvation is a critical evolutionary adaptation, yet the molecular mechanisms underlying this capability remain incompletely understood. Pore-forming proteins (PFPs) are typically associated with immune defense, where they disturb the membranes of target cells. However, the role of PFPs in non-immune functions, particularly in metabolic and structural adaptations to starvation, is less explored. Here, we investigate the aerolysin-like PFP LIN-24 in Caenorhabditis elegans and uncover its novel function in enhancing starvation resistance. We found that LIN-24 expression is upregulated during starvation, leading to increased expression of the lipase-encoding gene lipl-3. This upregulation accelerates the mobilization and degradation of lipid stores, thereby sustaining energy levels. Additionally, LIN-24 overexpression significantly preserves muscle integrity, as evidenced by the maintenance of muscle structure compared to wild-type worms. Furthermore, we demonstrate that LIN-24 induces the formation of donut-shaped mitochondria, a structural change likely aimed at reducing ATP production to conserve energy during prolonged nutrient deprivation. This mitochondrial remodeling depends on genes involved in mitochondrial dynamics, including mff-1, mff-2, drp-1, and clk-1. Collectively, these findings expand our understanding of PFPs, demonstrating their multifaceted role in stress resistance beyond immune defense. LIN-24's involvement in regulating metabolism, preserving muscle structure, and remodeling mitochondria highlights its crucial role in the adaptive response to starvation, offering novel insights into the evolution of stress resistance mechanisms and potential therapeutic targets for conditions related to muscle preservation and metabolic regulation.},
}

Animals
*Caenorhabditis elegans/genetics/physiology/metabolism
*Caenorhabditis elegans Proteins/genetics/metabolism
*Lipid Metabolism
*Mitochondrial Dynamics
*Starvation/metabolism
Mitochondria/metabolism

@article {pmid39990427,
year = {2025},
author = {Cai, L and Havird, JC and Jansen, RK},
title = {Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.14.637881},
pmid = {39990427},
issn = {2692-8205},
abstract = {The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated in cross-species and inter-organelle transfers. Based on this, we propose a generalized dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we describe a universal roadmap for mitochondrial evolution in heterotrophic plants where increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.},
}

@article {pmid39988053,
year = {2025},
author = {Monesi, N and Fernandes, GM and Valer, FB and Cardoso Uliana, JV and Trinca, V and Caleiro Seixas Azzolini, AE and Gorab, E and Alberici, LC},
title = {Identification and characterization of a laterally transferred alternative oxidase (AOX) in a terrestrial insect, the dipteran Pseudolycoriella hygida.},
journal = {Biochimie},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biochi.2025.02.007},
pmid = {39988053},
issn = {1638-6183},
abstract = {Alternative oxidase (AOX) (EC 1.10.3.11) is a terminal oxidase in the mitochondrial inner membrane that branches the canonical electron transport system (ETS). AOX is ubiquitous in plants, frequently found in fungi and protists and presents a more sporadic distribution in metazoans. More recently, AOX has gained attention due to its potential application in gene therapy for treatment of mitochondrial diseases. Here we characterized the AOX in the basal Dipteran, Pseudolycoriella hygida using a combination of genomic analyses, molecular, functional and in vivo survival assays. AOX is a single copy gene that encodes three developmental stage specific protein isoforms. AOX localizes to the mitochondria in adult thoracic muscles, which present cyanide-resistant respiration that is sensitive to the AOX inhibitor salicylhydroxamic acid (SHAM). Both the cyanide-resistant respiration and AOX levels gradually increase during aging, but are not influenced by thermal stress. Thoracic mitochondria respire using substrates derived from several metabolic routes, such as pyruvate, proline, acylcarnitine, NADH and glycerol-3P, and present values of oxidative phosphorylation capacity ((P-L)/E = 0.70) and coupling (P/L = 4.35; L/E = 0.21). Adult flies exhibit a high survival resistance for SHAM-sensitive complex III inhibition. Together, our results demonstrate the presence of a functional AOX in a terrestrial arthropod and provide insights regarding AOX function in animals and evolution of respiratory systems in metazoans. Psl. hygida emerges as a natural and valuable model for comprehensive AOX research at the whole-organism level which complements models expressing the heterologous enzyme.},
}

@article {pmid39980242,
year = {2025},
author = {Yonemitsu, MA and Sevigny, JK and Vandepas, LE and Dimond, JL and Giersch, RM and Gurney-Smith, HJ and Abbott, CL and Supernault, J and Withler, R and Smith, PD and Weinandt, SA and Garrett, FES and Child, ZJ and Sigo, RLW and Unsell, E and Crim, RN and Metzger, MJ},
title = {Multiple Lineages of Transmissible Neoplasia in the Basket Cockle (C. nuttallii) With Repeated Horizontal Transfer of Mitochondrial DNA.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17682},
doi = {10.1111/mec.17682},
pmid = {39980242},
issn = {1365-294X},
support = {//National Research Council/ ; 2208081//Division of Ocean Sciences/ ; A19AP00215//Bureau of Indian Affairs/ ; },
abstract = {Transmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from 11 locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.},
}

@article {pmid39977315,
year = {2025},
author = {Elling, FJ and Pierrel, F and Chobert, SC and Abby, SS and Evans, TW and Reveillard, A and Pelosi, L and Schnoebelen, J and Hemingway, JD and Boumendjel, A and Becker, KW and Blom, P and Cordes, J and Nathan, V and Baymann, F and Lücker, S and Spieck, E and Leadbetter, JR and Hinrichs, KU and Summons, RE and Pearson, A},
title = {A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {8},
pages = {e2421994122},
doi = {10.1073/pnas.2421994122},
pmid = {39977315},
issn = {1091-6490},
support = {1702262//NSF (NSF)/ ; 1843285//NSF (NSF)/ ; NA//Gordon and Betty Moore Foundation (GBMF)/ ; 441217575//Deutsche Forschungsgemeinschaft (DFG)/ ; ANR-21-CE02-0018//Agence Nationale de la Recherche (ANR)/ ; ANR-15-IDEX-02//Agence Nationale de la Recherche (ANR)/ ; IDEX-IRS 2020//Grenoble-Alpes University/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft (DFG)/ ; NA//Alexander von Humboldt-Stiftung (AvH)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; 18-EXXO18-0039//NASA | NASA Astrobiology Institute (NAI)/ ; 946150//EC | European Research Council (ERC)/ ; 80NSSC19K0480//NASA | NASA Astrobiology Institute (NAI)/ ; },
mesh = {Aerobiosis ; *Biosynthetic Pathways ; Quinones/metabolism ; Plastoquinone/metabolism ; Oxidation-Reduction ; Biological Evolution ; Phylogeny ; Bacteria/metabolism/genetics ; Cyanobacteria/metabolism/genetics ; Evolution, Molecular ; },
abstract = {The dominant organisms in modern oxic ecosystems rely on respiratory quinones with high redox potential (HPQs) for electron transport in aerobic respiration and photosynthesis. The diversification of quinones, from low redox potential (LPQ) in anaerobes to HPQs in aerobes, is assumed to have followed Earth's surface oxygenation ~2.3 billion years ago. However, the evolutionary origins of HPQs remain unresolved. Here, we characterize the structure and biosynthetic pathway of an ancestral HPQ, methyl-plastoquinone (mPQ), that is unique to bacteria of the phylum Nitrospirota. mPQ is structurally related to the two previously known HPQs, plastoquinone from Cyanobacteriota/chloroplasts and ubiquinone from Pseudomonadota/mitochondria, respectively. We demonstrate a common origin of the three HPQ biosynthetic pathways that predates the emergence of Nitrospirota, Cyanobacteriota, and Pseudomonadota. An ancestral HPQ biosynthetic pathway evolved ≥ 3.4 billion years ago in an extinct lineage and was laterally transferred to these three phyla ~2.5 to 3.2 billion years ago. We show that Cyanobacteriota and Pseudomonadota were ancestrally aerobic and thus propose that aerobic metabolism using HPQs significantly predates Earth's surface oxygenation. Two of the three HPQ pathways were later obtained by eukaryotes through endosymbiosis forming chloroplasts and mitochondria, enabling their rise to dominance in modern oxic ecosystems.},
}

Aerobiosis
*Biosynthetic Pathways
Quinones/metabolism
Plastoquinone/metabolism
Oxidation-Reduction
Biological Evolution
Phylogeny
Bacteria/metabolism/genetics
Cyanobacteria/metabolism/genetics
Evolution, Molecular

@article {pmid39972273,
year = {2025},
author = {Zhou, B and Sui, R and Yu, L and Qi, D and Fu, S and Luo, Y and Qi, H and Li, X and Zhao, K and Liu, S and Tian, F},
title = {Transcriptomics and proteomics provide insights into the adaptative strategies of Tibetan naked carps (Gymnocypris przewalskii) to saline-alkaline variations.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {162},
pmid = {39972273},
issn = {1471-2164},
support = {32071489//National Natural Science Foundation of China/ ; 32401305//National Natural Science Foundation of China/ ; LHZX-2021-03//Joint Foundation from the Chinese Academy of Sciences -People's Government of Qinghai Province on Sanjiangyuan National Park/ ; LHZX-2021-03//Joint Foundation from the Chinese Academy of Sciences -People's Government of Qinghai Province on Sanjiangyuan National Park/ ; },
mesh = {Animals ; *Proteomics/methods ; *Salinity ; *Gills/metabolism ; Carps/genetics/metabolism ; Transcriptome ; Adaptation, Physiological/genetics ; Gene Expression Profiling ; Kidney/metabolism ; Alkalies ; Fish Proteins/genetics/metabolism ; Proteome/metabolism ; Tibet ; Osmoregulation/genetics ; Lakes ; },
abstract = {Gymnocypris przewalskii is an exclusively cyprinid fish that inhabits Lake Qinghai, which is characterized by high salinity and alkalinity. To elucidate the molecular basis of the adaptation of G. przewalskii to a wide range of salinity‒alkalinity conditions, we performed morphological, biochemical, transcriptomic and proteomic analyses of the major osmoregulatory organs of the gills and kidney. Morphological examination revealed that mitochondria-rich cells were replaced by mucus cells in the gills during the transition of G. przewalskii from freshwater to lake water. In the kidney, the tight junction formed dense structure in the renal tubules under lake water condition compared with the loose structure in freshwater. The results of the biochemical assays revealed an increased content of total amino acids, indicating their potential roles as osmolytes and energy supplies in freshwater. The decreased urea concentration suggested that urea synthesis might not be involved in the detoxicity of ammonia. The transcriptomic and proteomic data revealed that genes involved in ion absorption and ammonia excretion were activated in freshwater and that genes involved in cell junction and glutamine synthesis were induced in lake water, which was consistent with the morphological and biochemical observations. Together with the higher levels of glutamine and glutamate, we proposed that G. przewalskii alleviated the toxic effect of ammonia direct excretion through gills under freshwater and the activation of the conversion of glutamate to glutamine under high saline-alkaline condition. Our results revealed different expression profiles of genes involved in metabolic pathways, including the upregulation of genes involved in energy production in freshwater and the induction of genes involved in the synthesis of acetylneuramic acid and sphingolipid in soda lake water. In conclusion, the appearance of mitochondria-rich cells and increased energy production might contribute to ion absorption in G. przewalskii to maintain ion and solute homeostasis in freshwater. The existence of mucus cells and dense junctions, which are associated with increased gene expression, might be related to the adaptation of G. przewalskii to high salinity-alkalinity.},
}

Animals
*Proteomics/methods
*Salinity
*Gills/metabolism
Carps/genetics/metabolism
Transcriptome
Adaptation, Physiological/genetics
Gene Expression Profiling
Kidney/metabolism
Alkalies
Fish Proteins/genetics/metabolism
Proteome/metabolism
Tibet
Osmoregulation/genetics
Lakes

@article {pmid39962375,
year = {2025},
author = {Kim, SC and Kang, ES and Kim, TH and Choi, YR and Kim, HJ},
title = {Report on the complete organelle genomes of Orobanche Filicicola Nakai ex Hyun, Y. S. Lim & H. C. Shin (Orobanchaceae): insights from comparison with Orobanchaceae plant genomes.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {157},
pmid = {39962375},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Genome, Chloroplast ; Base Composition ; Orobanchaceae/genetics/classification ; Orobanche/genetics ; Genome, Plant ; Evolution, Molecular ; },
abstract = {BACKGROUND: Orobanche is a parasitic plant distributed in the temperate zone of Northern Hemisphere, with approximately 200 species found worldwide. In the Republic of Korea, two species of Orobanche, namely O. coerulescens Stephan ex Willd. and O. filicicola Nakai ex Hyun, Y. S. Lim & H. C. Shin, are present, with O. filicicola being endemic. Genome analysis of this species has not yet been performed, and characterizing its complete organelle genome will provide valuable insights into the phylogeny and genome evolution of parasitic plants.

RESULTS: The chloroplast and mitochondrial genomes were analyzed, revealing distinct characteristics. The chloroplast genome is 91,529 bp long with a GC content of 33.6%, containing 33 protein-coding, 30 tRNA, and 4 rRNA genes. In contrast, the mitochondrial genome is 1,058,991 bp long with a GC content of 45.5%, featuring 31 protein-coding, 16 tRNA, and 3 rRNA genes. The mitochondrial genome has over three times more simple sequence repeats and longer long repeats than the chloroplast genome. Analysis of synonymous codon usage in protein-coding genes from nine Orobanchaceae species revealed significant differences between chloroplasts and mitochondria, with codons ending in A or T exhibiting higher coding rates. Ka/Ks ratio calculations indicated that psbI and atpB had the smallest and largest ratios in chloroplasts, respectively, while ccmFC was identified as the only gene under positive selection in mitochondria genomes. Sequence alignment identified 30 homologous fragments between the two genomes, totaling 7,247 bp. Comparison of O. filicicola's chloroplast genome with related species showed gene loss and conserved inverted repeat sequences. Numerous homologous collinear blocks were found in mitochondrial genomes of related species, but some regions lacked homology. Phylogenetic analysis indicated identical topologies for chloroplasts and mitochondria, with Orobanchaceae forming a strong monophyletic group.

CONCLUSIONS: Characterizing the complete organelle genome of O. filicicola enabled a comprehensive analysis of the Orobanchaceae organelle genome, providing important baseline data for its structure and evolution.},
}

*Genome, Mitochondrial
*Phylogeny
*Genome, Chloroplast
Base Composition
Orobanchaceae/genetics/classification
Orobanche/genetics
Genome, Plant
Evolution, Molecular

@article {pmid39961891,
year = {2025},
author = {Larkum, AWD and Falkowski, PG and Edwards, D and Osmond, CB and Lambers, H and Sanchez-Baracaldo, P and Ritchie, RJ and Runcie, JW and Ralph, PJ and Westoby, M and Maberly, S and Griffiths, H and Smith, FA and Beardall, J},
title = {John Raven, FRS, FRSE: a truly great innovator in plant physiology, photosynthesis and much more.},
journal = {Photosynthesis research},
volume = {163},
number = {2},
pages = {18},
pmid = {39961891},
issn = {1573-5079},
mesh = {*Photosynthesis/physiology ; History, 20th Century ; History, 21st Century ; Plant Physiological Phenomena ; Botany/history ; },
abstract = {This is a tribute to a truly inspirational plant biologist, Prof. John A. Raven, FRS, FRSE (25th June 1941- 23rd May 2024), who died at the age of 82. He was a leader in the field of evolution and physiology of algae and land plants. His research touched on many areas including photosynthesis, ion transport, carbon utilisation, mineral use, such as silicon, iron and molybdenum, the evolution of phytoplankton, the evolution of root systems, the impact of global change, especially on the acidification of the oceans, carbon gain and water use in early land plants, and ways of detecting extraterrestrial photosynthesis. Beginning his research career in the Botany School, University of Cambridge, John studied ion uptake in a giant algal cell. This was at the time of great strides brought about by Peter Mitchell (1920-1992) in elucidating the role of energy generation in mitochondria and chloroplasts and the coupling of ion transport systems to energy generation. With Enid MacRobbie and Andrew Smith, John pioneered early work on the involvement of ion transport in the growth and metabolism of plant cells.On leaving Cambridge John took up a lectureship at the University of Dundee in 1971, where he was still attached upon his death. His primary focus over the years, with one of us (Paul Falkowski), was on phytoplankton, the photosynthetic microalgae of the oceans. Still, his publication list of 5 books and over 600 scientific papers spans a very broad range. The many highly cited papers (see Table 1) attest to an outstanding innovator, who influenced a multitude of students and coworkers and a very wide readership worldwide. At the personal level, John Raven was a wonderful human being; he had an extraordinary memory, dredging up facts and little-known scientific papers, like a scientific magician, but at the same time making humorous jokes and involving his colleagues in fun and sympathetic appreciation. Table 1 Ten best cited articles (from google scholar) Citations Date Aquatic Photosynthesis, 3rd Edition P.G. Falkowski & J.A. Raven Princeton University Press, 2013 3854 2013 The evolution of modern eukaryotic phytoplankton P.G. Falkowski, M.E. Katz, A.H. Knoll, A. Quigg, J.A. Raven, et al Science 305, 354-360 1790 2004 CO2 concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution M. Giordano, J. Beardall & J.A. Raven Annu. Rev. Plant Biol. 56 (1), 99-131 1648 2005 Algae as nutritional food sources: revisiting our understanding M.L. Wells, P. Potin, J.S. Craigie, J.A. Raven, S.S. Merchant, et al Journal of applied phycology 29, 949-982 1527 2017 Plant Nutrient acquisition strategies change with soil age H. Lambers, J.A. Raven, G.R. Shaver & S.E. Smith Trends in ecology & evolution 23, 95-103 1488 2008 Ocean acidification due to increasing atmospheric carbon dioxide J. Raven, K. Caldeira, H. Elderfield, O. Hoegh-Guldberg, P. Liss, et al The Royal Society, Policy Document, June 2005 1470 2005 Phytoplankton in a changing world: cell size and elemental stoichiometry Z.V. Finkel, J. Beardall, K.J. Flynn, A. Quigg, T.A.V. Rees & J.A. Raven Journal of plankton research 32, 119-137 1198 2010 Opportunities for improving phosphorus efficiency in crop plants E.J. Veneklaas, H. Lambers, J. Bragg, P.M. Finnegan, C.E. Lovelock, et al New phytologist 195, 306-320 951 2012 Adaptation of unicellular algae to irradiance: an analysis of strategies K. Richardson, J. Beardall & J.A. Raven New Phytologist 93, 157-191 914 1983 Nitrogen assimilation and transport in vascular land plants in relation to Intracellular pH regulation J.A. Raven & F.A. Smith New Phytologist 76, 415-431 893 1976 Temperature and algal growth J.A. Raven & R.J. Geider New phytologist 110, 441-461 867 1988 The role of trace metals in photosynthetic electron transport in O2 -evolving organisms J.A. Raven, M.C.W. Evans & R.E. Korb Photosynthesis Research 60, 111-150 840 1999.},
}

*Photosynthesis/physiology
History, 20th Century
History, 21st Century
Plant Physiological Phenomena
Botany/history

@article {pmid39949038,
year = {2025},
author = {Ratajczak, MZ and Thetchinamoorthy, K and Wierzbicka, D and Konopko, A and Ratajczak, J and Kucia, M},
title = {Extracellular microvesicles/exosomes - magic bullets in horizontal transfer between cells of mitochondria and molecules regulating mitochondria activity.},
journal = {Stem cells (Dayton, Ohio)},
volume = {},
number = {},
pages = {},
doi = {10.1093/stmcls/sxae086},
pmid = {39949038},
issn = {1549-4918},
abstract = {Extracellular microvesicles (ExMVs) were one of the first communication platforms between cells that emerged early in evolution. Evidence indicates that all types of cells secrete these small circular structures surrounded by a lipid membrane that plays an important role in cellular physiology and some pathological processes. ExMVs interact with target cells and may stimulate them by ligands expressed on their surface and/or transfer to the target cells their cargo comprising various RNA species, proteins, bioactive lipids, and signaling nucleotides. These small vesicles can also hijack some organelles from the cells and, in particular, transfer mitochondria, which are currently the focus of scientific interest for their potential application in clinical settings. Different mechanisms exist for transferring mitochondria between cells, including their encapsulation in ExMVs or their uptake in a "naked" form. It has also been demonstrated that mitochondria transfer may involve direct cell-cell connections by signaling nanotubules. In addition, evidence accumulated that ExMVs could be enriched for regulatory molecules, including some miRNA species and proteins that regulate the function of mitochondria in the target cells. Recently, a new beneficial effect of mitochondrial transfer has been reported based on inducing the mitophagy process, removing damaged mitochondria in the recipient cells to improve their energetic state. Based on this novel role of ExMVs in powering the energetic state of target cells, we present a current point of view on this topic and review some selected most recent discoveries and recently published most relevant papers.},
}

@article {pmid39946260,
year = {2025},
author = {Waneka, G and Broz, AK and Wold-McGimsey, F and Zou, Y and Wu, Z and Sloan, DB},
title = {Disruption of recombination machinery alters the mutational landscape in plant organellar genomes.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf029},
pmid = {39946260},
issn = {2160-1836},
support = {R35 GM148134/GM/NIGMS NIH HHS/United States ; },
abstract = {Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targeted mutS homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in Arabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of A. thaliana mutant lines lacking radA, recA1, or recA3. In contrast, osb2 and why2 mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from A. thaliana organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and msh1 mutants. Finally, using long-read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.},
}

@article {pmid39945506,
year = {2025},
author = {Van Gaever, M and Dupuy, O and Dupont, E and Canu, MH and Daussin, F},
title = {Early sensorimotor restriction in rats induces age-dependent mitochondrial alterations in skeletal muscles and brain structures.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP287765},
pmid = {39945506},
issn = {1469-7793},
abstract = {A sedentary lifestyle can lead to motor and cognitive deficits, increasing the risk of neurodegenerative diseases in ageing. Emerging hypotheses suggest that these functional alterations may be related to energy metabolism. Indeed, ATP produced by mitochondria is essential for muscle contraction, neurotransmission and brain plasticity processes. Although a sedentary lifestyle has been associated with mitochondrial alterations in skeletal muscle, the potential effects on brain structures have yet to be investigated. The present study aimed to determine whether early sensorimotor restriction (SMR) alters mitochondrial metabolism in rat muscles and brain structures. Enzyme activities of citrate synthase (CS) and respiratory chain complexes I, II and IV were measured using a spectrophotometric technique and mitochondrial respiration was assessed using high-resolution respirometry in two hind limb muscles [soleus and extensor digitorum longus (EDL)] and four brain structures (sensorimotor cortex, striatum, prefrontal cortex and hippocampus) in control rats and rats experiencing early SMR from birth to day 28. Mitochondrial enzyme activities decreased in the soleus (complexes I and II), in the EDL (complex I) and in the hippocampus (complexes I and IV) in an age-dependent manner, whereas no effect was observed in other brain structures. CS activity decreases in the soleus and increases transiently in the striatum and sensorimotor cortex at postnatal day 15. Mitochondrial respiration was reduced in the soleus and in the sensorimotor cortex (CI and CI+CII). Early SMR appears to induce quantitative and qualitative mitochondrial alterations in skeletal muscles and certain brain structures involved in cognitive and motor processes. KEY POINTS: Early sensorimotor restriction (SMR) alters mitochondrial enzyme activities and mitochondrial respiration in skeletal muscles and brain. Mitochondrial alterations induced by early SMR are age-dependent, structure-dependent and complex-dependent. Mitochondrial enzyme activities increase during development and the evolution pattern is specific to the different structures.},
}

@article {pmid39944907,
year = {2025},
author = {Ruiz, E and Leprieur, F and Sposito, G and Lüthi, M and Schmidlin, M and Panfili, J and Pellissier, L and Albouy, C},
title = {Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae.},
journal = {Ecology and evolution},
volume = {15},
number = {2},
pages = {e70645},
pmid = {39944907},
issn = {2045-7758},
abstract = {While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non-invasive, and precise way of estimating a wild animal's age. DNA methylation from tissue DNA (tDNA) was recently proposed as a method to overcome these issues and showed more accurate results than telomere-length-based age assessments. Here, we used environmental DNA (eDNA) for the first time as a template for age estimation, focusing on the larval phase (10-24 days post-hatch) of cultured Dicentrarchus labrax (seabass), a species of major economic and conservation interest. Using third-generation sequencing, we were able to directly detect various modification types (e.g., cytosine and adenosine methylation in all contexts) across the whole genome using amplification-free nanopore sequencing. However, aging sites were only present in the mitogenome, which could be a specific feature of eDNA methylation or the consequence of better DNA protection within mitochondria. By considering qualitative and quantitative information about aging sites according to an objective model selection framework, our epigenetic clock reached a cross-validated accuracy of 2.6 days (Median Absolute Error). Such performances are higher than those of previous clocks, notably for adult seabass even when scaling MAE to the age range, which could be linked to a more dynamic epigenome during early life stages. Overall, our pilot study proposes new methods to determine the potential of eDNA for simultaneous age and biodiversity assessments, although robust validation of our preliminary results along with methodological developments are needed before field applications can be envisaged.},
}

@article {pmid39944804,
year = {2024},
author = {Vorozheykin, PS and Titov, II},
title = {Computer analysis shows differences between mitochondrial miRNAs and other miRNAs.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {28},
number = {8},
pages = {834-842},
doi = {10.18699/vjgb-24-91},
pmid = {39944804},
issn = {2500-0462},
abstract = {A subclass of miRNAs with as yet unknown specific functions is mitomiRs - mitochondrial miRNAs that are mainly derived from nuclear DNA and are imported into mitochondria; moreover, changes in the expression levels of mitomiRs are associated with some diseases. To identify the most pronounced characteristics of mitochondrial miRNAs that distinguish them from other miRNAs, we classified mitomiR sequences using the Random Forest algorithm. The analysis revealed, for the first time, a significant difference between mitomiRs and other microRNAs by the following criteria (in descending order of importance in the classification): mitomiRs are evolutionarily older (have a lower phylostratigraphic age index, PAI); have more targets and disease associations, including mitochondrial ones (two-sided Fisher's exact test, average p-values 1.82 × 10-89/1.13 × 10-96 for all mRNA/diseases and 6.01 × 10-22/1.09 × 10-9 for mitochondria, respectively); and are in the class of "circulating" miRNAs (average p- value 1.20 × 10-56). The identified differences between mitomiRs and other miRNAs may help uncover the mode of miRNA delivery into mitochondria, indicate the evolutionary conservation and importance of mitomiRs in the regulation of mitochondrial function and metabolism, and generally show that mitomiRs are not randomly encountered miRNAs. Information on 1,312 experimentally validated mitomiR sequences for three organisms (Homo sapiens, Mus musculus and Rattus norvegicus) is collected in the mitomiRdb database (https://mitomiRdb.org).Key words: mitomiR; mitochondria; miRNA; evolution; database.},
}

@article {pmid39940743,
year = {2025},
author = {Zeng, Q and Yu, Q and Mo, Y and Liang, H and Chen, B and Meng, J},
title = {Genome-Wide Identification and Functional Characterization of the Acyl-CoA Dehydrogenase (ACAD) Family in Fusarium sacchari.},
journal = {International journal of molecular sciences},
volume = {26},
number = {3},
pages = {},
doi = {10.3390/ijms26030973},
pmid = {39940743},
issn = {1422-0067},
support = {31960031//National Natural Science Foundation of China/ ; 2024GXNSFAA010041//Guangxi Natural Science Foundation/ ; },
mesh = {*Fusarium/genetics/pathogenicity/enzymology ; *Phylogeny ; Fatty Acids/metabolism ; Fungal Proteins/genetics/metabolism ; Acyl-CoA Dehydrogenase/genetics/metabolism ; Genome, Fungal ; Gene Expression Regulation, Fungal ; Multigene Family ; Plant Diseases/microbiology/genetics ; },
abstract = {Fusarium sacchari is one of the primary causal agents of Pokkah boeng disease (PBD), an important disease of sugarcane worldwide. The acyl-CoA dehydrogenases (ACADs) constitute a family of flavoenzymes involved in the β-oxidation of fatty acids and amino acid catabolism in mitochondria. However, the role of ACADs in the pathogenesis of F. sacchari is unclear. Here, 14 ACAD-encoding genes (FsACAD-1-FsACAD-14) were identified by screening the entire genome sequence of F. sacchari. The FsACAD genes are distributed across seven chromosomes and were classified into seven clades based on phylogenetic analysis of the protein sequences. In vivo mRNA quantification revealed that the FsACAD genes are differentially expressed during sugarcane infection, and their expression patterns differ significantly in response to the in vitro induction of fatty acids of different classes. Fatty acid utilization assays of the FsACAD-deletion mutants revealed that the FsACADs varied in their preference and ability to break down different fatty acids and amino acids. There was variation in the adverse impact of FsACAD-deletion mutants on fungal traits, including growth, conidiation, stress tolerance, and virulence. These findings provide insights into the roles of FsACADs in F. sacchari, and the identification of FsACADs offers potential new targets for the improved control of PBD.},
}

*Fusarium/genetics/pathogenicity/enzymology
*Phylogeny
Fatty Acids/metabolism
Fungal Proteins/genetics/metabolism
Acyl-CoA Dehydrogenase/genetics/metabolism
Genome, Fungal
Gene Expression Regulation, Fungal
Multigene Family
Plant Diseases/microbiology/genetics

@article {pmid39936990,
year = {2025},
author = {Zhang, Y and Sun, J and Li, S and Wang, L and Song, L},
title = {The Potential Mechanism of Cuproptosis in Hemocytes of the Pacific Oyster Crassostrea gigas upon Elesclomol Treatment.},
journal = {Cells},
volume = {14},
number = {3},
pages = {},
pmid = {39936990},
issn = {2073-4409},
support = {32222086, 32230110//National Natural Science Foundation of China/ ; CARS-49//the fund for China Agriculture Research System/ ; No//Outstanding Talents and Innovative Teams of Agricultural Scientific Research in MARA/ ; LT202009//innovation team of Aquaculture Environment Safety from Liaoning Province/ ; XLYC2203087//Liaoning Revitalization Talents Program/ ; 2022RG14//Dalian High Level Talent Innovation Support Program/ ; 2022RY01//Dalian Outstanding Young Scientific and Technological Talent/ ; },
mesh = {Animals ; *Hemocytes/metabolism/drug effects ; *Crassostrea/drug effects/genetics ; *Copper/metabolism/pharmacology ; Mitochondria/metabolism/drug effects ; Cell Death/drug effects ; },
abstract = {Cuproptosis is a novel cell death dependent on mitochondrial respiration and regulated by copper. While the study of it is mainly focused on tumor therapy, in the present study, two key cuproptosis-related genes, ferredoxin (FDX1) and dihydrolipoamide S-acetyltransferase (DLAT) homologs (designated as CgFDX1 and CgDLAT), were identified from Crassostrea gigas. CgFDX1 has a Fer2 domain with a 2Fe-2S cluster forming a unique ferredoxin. CgDLAT is composed of a biotin_lipoyl domain, an E3-binding domain, and a 2-oxoacid_dh domain. CgFDX1 and CgDLAT mRNA were expressed in all the examined tissues. After elesclomol treatment, both mRNA and protein expressions of them were reduced in the hemocytes. The mortality rate of the hemocytes increased significantly, and the hemocytes were accompanied with noticeable adhesive abnormalities and heightened secretion after elesclomol treatment. Additionally, the accumulation or depletion of actin was observed in the hemocytes. The integrity of the double membrane structure of the mitochondria was compromised, and the organization of mitochondrial cristae was disrupted. The contents of copper, malondialdehyde (MDA), pyruvic acid and mitoSOX as well as the ratio of cells with low mitochondrial potential increased significantly in the hemocytes upon elesclomol treatment and the content of citric acid decreased significantly. These findings suggest the potential presence of cuproptosis in oysters and its activation mechanism is relatively conserved in evolution.},
}

Animals
*Hemocytes/metabolism/drug effects
*Crassostrea/drug effects/genetics
*Copper/metabolism/pharmacology
Mitochondria/metabolism/drug effects
Cell Death/drug effects

@article {pmid39933620,
year = {2025},
author = {Tatarczuch, A and Gogola-Mruk, J and Kotarska, K and Polański, Z and Ptak, A},
title = {Mitochondrial activity and steroid secretion in mouse ovarian granulosa cells are suppressed by a PFAS mixture.},
journal = {Toxicology},
volume = {512},
number = {},
pages = {154083},
doi = {10.1016/j.tox.2025.154083},
pmid = {39933620},
issn = {1879-3185},
abstract = {The accumulation of a number of per- and polyfluoroalkyl substances (PFASs) in ovarian follicular fluid (FF) has been documented, raising serious questions about their impact on female fertility. Here, we tested the hypothesis that a mixture of PFASs acts in a paracrine manner on granulosa cells (GCs) as a metabolism-disrupting chemical. We selected perfluorooctane sulfonate (PFOS; 22.4 ng/mL), perfluorooctanoic acid (PFOA; 14.5 ng/mL), perfluorohexane sulfonate (PFHxS; 21.3 ng/mL), perfluorodecanoic acid (PFDA; 0.9 ng/mL), perfluoroheptane sulphonate (PFHpA; 0.6 ng/mL), perfluoroundecanoic acid (PFUnDA; 0.4 ng/mL), and perfluorononanoic acid (PFNA; 2 ng/mL), which were the most commonly detected PFASs in FF of women undergoing assisted reproductive technology treatment. Exposure of mouse GCs to the PFAS mixture decreased the amount of active mitochondria and the mitochondrial membrane potential, which correlated with a reduction in ATP production and inhibition of oxidative phosphorylation (OXPHOS). At the same time, expression of the mitochondrial membrane-associated steroidogenic enzyme 3-beta-hydroxysteroid dehydrogenase (3βHSD) and production of the major steroids progesterone and estradiol were decreased. In addition, expression and activity of superoxide dismutase 1 (SOD1), an enzyme that neutralizes reactive oxygen species (ROS), were decreased while ROS levels and lipid peroxidation were increased without cell death, indicating that the PFAS mixture had subtoxic effects. Our results show that PFAS mixtures, at concentrations similar to those found in human FF led to GC dysfunction by impairing mitochondrial function and steroid secretions and therefore may have implications for reproductive health.},
}

@article {pmid39921600,
year = {2025},
author = {Shi, X and Ma, C and Chen, N and Xu, MM and Kambal, S and Cai, ZF and Yang, Q and Adeola, AC and Liu, LS and Wang, J and Lu, WF and Li, Y and Msalya, GM and Lei, C and Mwacharo, JM and Han, JL and Hanotte, O and Zhang, YP and Peng, MS},
title = {Selection increases mitonuclear DNA discordance but reconciles incompatibility in African cattle.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf039},
pmid = {39921600},
issn = {1537-1719},
abstract = {Mitochondrial function relies on the coordinated interactions between genes in the mitochondrial (mtDNA) and nuclear genomes. Imperfect interactions following mitonuclear incompatibility may lead to reduced fitness. MtDNA introgressions across species and populations are common and well documented. Various strategies may be expected to reconcile mitonuclear incompatibility in hybrids or admixed individuals. African admixed cattle (Bos taurus × B. indicus) show sex-biased admixture, with taurine (B. taurus) mtDNA and a nuclear genome predominantly of humped zebu (B. indicus). Here, we leveraged local ancestry inference approaches to identify the ancestry and distribution patterns of nuclear functional genes associated with the mitochondrial oxidative phosphorylation process in the genomes of African admixed cattle. We show that most of the nuclear genes involved in mitonuclear interactions are under selection and of humped zebu ancestry. Variation in mtDNA copy number (mtDNA-CN) may have contributed to the recovery of optimal mitochondrial function following admixture with the regulation of gene expression, alleviating or nullifying mitochondrial dysfunction. Interestingly, some nuclear mitochondrial genes with enrichment in taurine ancestry may have originated from ancient African aurochs (B. primigenius africanus) introgression. They may have contributed to the local adaptation of African cattle to pathogen burdens. Our study provides further support and new evidence showing that the successful settlement of cattle across the continent was a complex mechanism involving adaptive introgression, mtDNA-CN variation, regulation of gene expression, and selection of ancestral mitochondria-related genes.},
}

@article {pmid39906580,
year = {2025},
author = {Erkosar, B and Dupuis, C and Savary, L and Kawecki, TJ},
title = {Shared genetic architecture links energy metabolism, behavior and starvation resistance along a power-endurance axis.},
journal = {Evolution letters},
volume = {9},
number = {1},
pages = {150-162},
pmid = {39906580},
issn = {2056-3744},
abstract = {Shared developmental, physiological, and molecular mechanisms can generate strong genetic covariances across suites of traits, constraining genetic variability, and evolvability to certain axes in multivariate trait space ("variational modules" or "syndromes"). Such trait suites will not only respond jointly to selection; they will also covary across populations that diverged from one another by genetic drift. We report evidence for such a genetically correlated trait suite that links traits related to energy metabolism along a "power-endurance" axis in Drosophila melanogaster. The "power" pole of the axis is characterized by high potential for energy generation and expenditure-high expression of glycolysis and TCA cycle genes, high abundance of mitochondria, and high spontaneous locomotor activity. The opposite "endurance" pole is characterized by high triglyceride (fat) reserves, locomotor endurance, and starvation resistance (and low values of traits associated with the "power" pole). This trait suite also aligns with the first principal component of metabolome; the "power" direction is characterized by low levels of trehalose (blood sugar) and high levels of some amino acids and their derivatives, including creatine, a compound known to facilitate energy production in muscles. Our evidence comes from six replicate "Selected" populations adapted to a nutrient-poor larval diet regime during 250 generations of experimental evolution and six "Control" populations evolved in parallel on a standard diet regime. We found that, within each of these experimental evolutionary regimes, the above traits strongly covaried along this "power-endurance" axis across replicate populations which diversified by drift, indicating a shared genetic architecture. The two evolutionary regimes also drove divergence along this axis, with Selected populations on average displaced towards the "power" direction compared to Controls. Aspects of this "power-endurance" axis resemble the "pace of life" syndrome and the "thrifty phenotype"; it may have evolved as part of a coordinated organismal response to nutritional conditions.},
}

@article {pmid39903101,
year = {2025},
author = {Iliushchenko, D and Efimenko, B and Mikhailova, AG and Shamanskiy, V and Saparbaev, MK and Matkarimov, BT and Mazunin, I and Voronka, A and Knorre, D and Kunz, WS and Kapranov, P and Denisov, S and Fellay, J and Khrapko, K and Gunbin, K and Popadin, K},
title = {Deciphering the Foundations of Mitochondrial Mutational Spectra: Replication-Driven and Damage-Induced Signatures Across Chordate Classes.},
journal = {Molecular biology and evolution},
volume = {42},
number = {2},
pages = {},
pmid = {39903101},
issn = {1537-1719},
support = {//Federal Academic Leadership Program Priority 2030/ ; //Immanuel Kant Baltic Federal University/ ; 21-75-20143//Russian Science Foundation/ ; 075-15-2021-1084//Ministry of Science and Higher Education of the Russian Federation/ ; KU 911/22-1//Deutsche Forschungsgemeinschaft/ ; AP23485899//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {*DNA, Mitochondrial/genetics ; Animals ; *DNA Replication ; DNA Damage ; Mutation ; Mutagenesis ; DNA Repair ; Urochordata/genetics ; Cytochromes b/genetics ; DNA-Directed DNA Polymerase/genetics ; DNA Mismatch Repair ; },
abstract = {Mitochondrial DNA (mtDNA) mutagenesis remains poorly understood despite its crucial role in disease, aging, and evolutionary tracing. In this study, we reconstructed a comprehensive 192-component mtDNA mutational spectrum for chordates by analyzing 118,397 synonymous mutations in the CytB gene across 1,697 species and five classes. This analysis revealed three primary forces shaping mtDNA mutagenesis: (i) symmetrical, replication-driven errors by mitochondrial polymerase (POLG), resulting in C > T and A > G mutations that are highly conserved across classes; (ii) asymmetrical, damage-driven C > T mutations on the single-stranded heavy strand with clock-like dynamics; and (iii) asymmetrical A > G mutations on the heavy strand, with dynamics suggesting sensitivity to oxidative damage. The third component, sensitive to oxidative damage, positions mtDNA mutagenesis as a promising marker for metabolic and physiological processes across various classes, species, organisms, tissues, and cells. The deconvolution of the mutational spectra into mutational signatures uncovered deficiencies in both base excision repair (BER) and mismatch repair (MMR) pathways. Further analysis of mutation hotspots, abasic sites, and mutational asymmetries underscores the critical role of single-stranded DNA damage (components ii and iii), which, uncorrected due to BER and MMR deficiencies, contributes roughly as many mutations as POLG-induced errors (component i).},
}

*DNA, Mitochondrial/genetics
Animals
*DNA Replication
DNA Damage
Mutation
Mutagenesis
DNA Repair
Urochordata/genetics
Cytochromes b/genetics
DNA-Directed DNA Polymerase/genetics
DNA Mismatch Repair

@article {pmid39901091,
year = {2025},
author = {Park, S and Hwang, Y and Kim, H and Choi, K},
title = {Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {102},
pmid = {39901091},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; *Genome, Plastid ; *Cell Nucleus/genetics ; *Apiaceae/genetics ; Phylogeny ; Evolution, Molecular ; Genome, Plant ; DNA, Plant/genetics ; Plastids/genetics ; },
abstract = {BACKGROUND: Gene transfer between the organelles and the nucleus plays a central role in shaping plant genome evolution. The identification and analysis of nuclear DNA of plastid (NUPTs) and mitochondrial (NUMTs) origins are important for exploring the extent of intracellular DNA transfer in genomes.

RESULTS: We report the complete plastid and mitochondrial genomes (plastome and mitogenome) of Cicuta virosa (Apiaceae) as well as a draft nuclear genome using high-fidelity (HiFi) PacBio sequencing technologies. The C. virosa plastome (154,449 bp) is highly conserved, with a quadripartite structure, whereas the mitogenome (406,112 bp) exhibits two chromosomes (352,718 bp and 53,394 bp). The mitochondrial-encoded genes (rpl2, rps14, rps19, and sdh3) were successfully transferred to the nuclear genome. Our findings revealed extensive DNA transfer from organelles to the nucleus, with 6,686 NUPTs and 6,237 NUMTs detected, covering nearly the entire plastome (99.93%) and a substantial portion of the mitogenome (77.04%). These transfers exhibit a range of sequence identities (80-100%), suggesting multiple transfer events over evolutionary timescales. Recent DNA transfer between organelles and the nucleus is more frequent in mitochondria than that in plastids.

CONCLUSIONS: This study contributes to the understanding of ongoing genome evolution in C. virosa and underscores the significance of the organelle-nuclear genome interplay in plant species. Our findings provide valuable insights into the evolutionary processes that shape organelle genomes in Apiaceae, with implications for broader plant genome evolution.},
}

*Genome, Mitochondrial
*Genome, Plastid
*Cell Nucleus/genetics
*Apiaceae/genetics
Phylogeny
Evolution, Molecular
Genome, Plant
DNA, Plant/genetics
Plastids/genetics

@article {pmid39893444,
year = {2025},
author = {Hao, J and Liang, Y and Wang, T and Su, Y},
title = {Correlations of gene expression, codon usage bias, and evolutionary rates of the mitochondrial genome show tissue differentiation in Ophioglossum vulgatum.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {134},
pmid = {39893444},
issn = {1471-2229},
support = {31872670//National Natural Science Foundation of China/ ; 32071781//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Mitochondrial ; *Codon Usage ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Transcriptome ; Codon/genetics ; Plant Leaves/genetics ; },
abstract = {BACKGROUND: Mitochondria are crucial for energy production in plant tissues, but their quantity and activity vary in different tissues and developmental processes. Determining the factors underlying differential molecular evolutionary rates has long been a central question in evolutionary biology, with expression level emerging as the prime predictor. Although we have previously observed an anti-correlation between expression level (E) and evolutionary rate (R) in chloroplast genes, it remains unclear whether such an anti-correlation exists in plant mitochondrial genes. Ophioglossum vulgatum is a typical plant belonging to the Ophioglossaceae, characterized by its unique morphology with only a single leaf above ground. It holds significant scientific and medicinal value. Using the mitochondrial genome and transcriptome data of O. vulgatum, we first analyzed the correlation between mitochondrial gene expression, codon usage bias, and evolutionary rates in different tissues.

RESULTS: Our findings indicated that mitochondrial gene expression level was the strongest between stem and leaf, while the weakest was between sporangium and root. Kruskal-Wallis tests revealed significant differences across various tissue types. Codon usage bias was influenced by both mutation and selection, with selection exerting a greater impact. The Spearman's rank correlation coefficients between codon adaptation index and expression levels of sporangium, stem, leaf, and root were 0.1178, 0.3926, 0.4463, and 0.2945, respectively, with significance in stem and leaf (P < 0.05). The correlation coefficients between the nonsynonymous substitution rate (dN) and expression levels in sporangium, stem, leaf, and root were -0.0840, -0.1786, -0.1714, and -0.0857, respectively, yet none are statistically significant. The correlation coefficient between the synonymous substitution rate (dS) and expression levels in sporangium was negative, whereas those between dS and the stem, leaf, and root were positive, although they were not significant. The dN/dS ratio exhibited a significant negative correlation with expression levels in both leaf and root (P < 0.05).

CONCLUSIONS: For the first time, our study revealed differences in the correlation between mitochondrial gene expression and codon usage bias, as well as evolutionary rates, across various tissues of O. vulgatum. Moreover, we also provide novel insights into understanding the effects of plant mitochondrial gene expression on evolutionary patterns.},
}

*Genome, Mitochondrial
*Codon Usage
*Evolution, Molecular
Gene Expression Regulation, Plant
Transcriptome
Codon/genetics
Plant Leaves/genetics

@article {pmid39892694,
year = {2025},
author = {Uzoigwe, CE},
title = {Nuclear Quantum Effects Explain Chemiosmosis: The Power of the Proton.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105407},
doi = {10.1016/j.biosystems.2025.105407},
pmid = {39892694},
issn = {1872-8324},
abstract = {ATP is a universal bio-currency, with chemiosmosis the metabolic mint by which currency is printed. Chemiosmosis leverages a membrane potential and ion gradient, typically a proton gradient, to generate ATP. The current chemiosmotic hypothesis is both cannon and dogma. However, there are obstacles to the unqualified and uncritical acceptance of this model. Intriguingly the proton is sufficiently small to exhibit quantum phenomena of wave-particle duality, often thought the exclusive prerogative of smaller subcellular particles. Evidence shows that chemiosmosis is by necessity critically dependent upon these nuclear quantum effects (NQE) of hydrogen, most notably as a proton. It is well established scientific orthodoxy that protons in water and hydrogen atoms of water molecules exhibit quantum phenomena. The effect is amplified by the hydrogen bonding and juxta-membrane location of protons in mitochondria and chloroplasts. NQE explains the otherwise inexplicable features of chemiosmosis, including the paucity of protons, the rate of the proton movement and ATP genesis in otherwise subliminal proton motive forces and thus functionality of alkaliphiles. It also accounts for the efficiencies of chemiosmosis reported at greater than 100% in certain contexts, which violates the second law of thermodynamics under the paradigm of classical physics. Mitochondria may have evolved to exploit quantum biology with notable features such as dimeric ATP synthases adumbrating the first double-slip experiment with the protons. The dramatic global deceleration of mitochondrial chemiosmosis and all cellular function following proton substitution with is heavier isotopes, deuterium and tritium: "deuteruction", is testimony to the primacy of nuclear quantum effects in this Quantum Chemiosmosis. Indeed the speed of evolution itself and its inexorable route to homeothermy may be due to the power of nuclear quantum effects of the smallest nucleus, the proton. The atom that is almost nothing was selected to bring about the most important processes and complex manifestations of life.},
}

@article {pmid39888573,
year = {2025},
author = {Brzezniakiewicz-Janus, K and Jarczak, J and Konopko, A and Ratajczak, J and Kucia, M and Ratajczak, MZ},
title = {Mitochondria Express Functional Signaling Ligand-Binding Receptors that Regulate their Biological Responses - the Novel Role of Mitochondria as Stress-Response Sentinels.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {39888573},
issn = {2629-3277},
support = {UMO-2022/45/B/NZ6/00475//Narodowe Centrum Nauki/ ; },
abstract = {Evidence accumulated mitochondria, as the "powerplants of the cell," express several functional receptors for external ligands that modify their function and regulate cell biology. This review sheds new light on the role of these organelles in sensing external stimuli to facilitate energy production for cellular needs. This is possible because mitochondria express some receptors on their membranes that are responsible for their autonomous responses. This is not surprising given the widely accepted hypothesis that these intracellular organelles originated from prokaryotic ancestors that fused with eukaryotic cells during early evolution. It has been reported that mitochondria express functional estrogen, androgen, glucocorticoid, 5-hydroxytryptamine, melatonin, and cannabinoid receptors. What is intriguing is recent evidence showing that mitochondria could also be directly regulated by active mediators of intracellular complement (complosome) and intrinsic mediators of purinergic signaling. Accordingly, they express receptors for intracellular complement cleavage fragments (C5a and C3a) as well as for adenosine triphosphate (ATP), which, besides its crucial role in transferring energy in the cells, is also an important signaling molecule interacting with P2X7 receptor expressed not only on the cell surface but also on the mitochondria membrane. Based on this, intrinsic complosome and purinergic signaling mediators emerge as important cooperating regulators of reactive oxygen species (ROS) release from mitochondria and activators of intracellular pattern recognition receptor Nlrp3 inflammasome. This activation within the beneficial "hormetic zone response" regulates cell metabolism, proliferation, migration, and adaptation to the surrounding challenges of the microenvironment in a favorable way.},
}