@article {pmid40570835,
year = {2025},
author = {Allard, CAH and Thies, AB and Mitra, R and Vaelli, PM and Leto, OD and Walsh, BL and Laetz, EMJ and Tresguerres, M and Lee, ASY and Bellono, NW},
title = {A host organelle integrates stolen chloroplasts for animal photosynthesis.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.06.003},
pmid = {40570835},
issn = {1097-4172},
abstract = {Eukaryotic life evolved over a billion years ago when ancient cells engulfed and integrated prokaryotes to become modern mitochondria and chloroplasts. Sacoglossan "solar-powered" sea slugs possess the ability to acquire organelles within a single lifetime by selectively retaining consumed chloroplasts that remain photosynthetically active for nearly a year. The mechanism for this "animal photosynthesis" remains unknown. Here, we discovered that foreign chloroplasts are housed within novel, host-derived organelles we term "kleptosomes." Kleptosomes use ATP-sensitive ion channels to maintain a luminal environment that supports chloroplast photosynthesis and longevity. Upon slug starvation, kleptosomes digest stored chloroplasts for additional nutrients, thereby serving as a food source. We leveraged this discovery to find that organellar retention and digestion of photosynthetic cargo has convergently evolved in other photosynthetic animals, including corals and anemones. Thus, our study reveals mechanisms underlying the long-term acquisition and evolutionary incorporation of intracellular symbionts into organelles that support complex cellular function.},
}

@article {pmid40564954,
year = {2025},
author = {Stefano, GB and Buttiker, P and Michaelsen, MM and Esch, T},
title = {The Anatomical and Evolutionary Impact of Pain, Pleasure, Motivation, and Cognition: Integrating Energy Metabolism and the Mind-Body BERN (Behavior, Exercise, Relaxation, and Nutrition) Framework.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125491},
pmid = {40564954},
issn = {1422-0067},
mesh = {Humans ; *Energy Metabolism ; *Exercise/physiology ; *Cognition/physiology ; Mitochondria/metabolism ; *Motivation ; *Pain/metabolism/physiopathology ; Animals ; *Pleasure/physiology ; Biological Evolution ; },
abstract = {In this manuscript, we highlight the evolutionary origins of mitochondria from bacterial endosymbionts and explore their contributions to health, energy metabolism, and neural-immune communication. Mitochondrial adaptability and the roles played by these organelles in promoting oxygen-dependent ATP production provide critical regulation of cognition, motivation, and inflammation. Hypoxia has been identified as an important initiator of inflammation, neurodegeneration, and mitochondrial dysfunction, emphasizing the overall importance of oxygen homeostasis to health and well-being. The Behavior, Exercise, Relaxation, and Nutrition framework highlights these observations as tools that can be used to optimize mitochondrial efficiency. Interestingly, mitochondrial dysfunction may also be linked to psychiatric disorders (e.g., schizophrenia), a hypothesis that focuses on energy dynamics, a proposal that may extend our understanding of these disorders beyond traditional neurotransmitter-focused concepts. Collectively, these perspectives underscore the critical contributions of mitochondria to health and disease and offer a novel framework that may help to explain the connections featured in mind-body medicine.},
}

Humans
*Energy Metabolism
*Exercise/physiology
*Cognition/physiology
Mitochondria/metabolism
*Motivation
*Pain/metabolism/physiopathology
Animals
*Pleasure/physiology
Biological Evolution

@article {pmid40562331,
year = {2025},
author = {Martin, WF},
title = {ATP requirements for growth reveal the bioenergetic impact of mitochondrial symbiosis.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {},
number = {},
pages = {149564},
doi = {10.1016/j.bbabio.2025.149564},
pmid = {40562331},
issn = {1879-2650},
abstract = {Studies by microbiologists in the 1970s provided robust estimates for the energy supply and demand of a prokaryotic cell. The amount of ATP needed to support growth was calculated from the chemical composition of the cell and known enzymatic pathways that synthesize its constituents from known substrates in culture. Starting in 2015, geneticists and evolutionary biologists began investigating the bioenergetic role of mitochondria at eukaryote origin and energy in metazoan evolution using their own, widely trusted-but hitherto unvetted-model for the costs of growth in terms of ATP per cell. The more recent model contains, however, a severe and previously unrecognized error that systematically overestimates the ATP cost of amino acid synthesis up to 200-fold. The error applies to all organisms studied by such models and leads to conspicuously false inferences, for example that the synthesis of an average amino acid in humans requires 30 ATP, which no biochemistry textbook will confirm. Their ATP 'cost' calculations would require that E. coli obtains ~100 ATP per glucose and that mammals obtain ~240 ATP per glucose, untenable propositions that invalidate and void all evolutionary inferences so based. By contrast, established methods for estimating the ATP cost of microbial growth show that the first mitochondrial endosymbionts could have easily doubled the host's available ATP pool, provided (i) that genes for growth on environmental amino acids were transferred from the mitochondrial symbiont to the archaeal host, and (ii) that the host for mitochondrial origin was an autotroph using the acetyl-CoA pathway. SIGNIFICANCE STATEMENT: Life is a chemical reaction. It requires energy release in order to proceed. The currency of energy in cells is adenosine triphosphate ATP. Five decades ago, microbiologists were able to measure and understand the amount of ATP that cells require to grow. New studies by evolutionary biologists have appeared in the meantime that brush aside the older microbiological findings, using their own methods to calculate the ATP cost of growth instead. Science is, however, an imperfect undertaking. The new studies contain a major error, similar to conflating centimeters with yards. The error affects many publications and their conclusions. Using the old methods, we can still meaningfully study the role of energy in evolution, including the origin of complex, nucleus-bearing cells.},
}

@article {pmid40550401,
year = {2025},
author = {Daplan, E and Rodriguez, E and Lane, N and Turin, L},
title = {A chance insight into phosgene toxicity.},
journal = {Free radical biology & medicine},
volume = {238},
number = {},
pages = {113-122},
doi = {10.1016/j.freeradbiomed.2025.06.033},
pmid = {40550401},
issn = {1873-4596},
abstract = {It has long been known that phosgene, a war gas and an industrial reagent, causes intense oxidative stress, but how it does so remains unclear. Here we report an accidental discovery: Electron spin resonance spectroscopy (ESR) of live fruit flies reveals that phosgene exposure results in a distinctive manganese (Ⅱ) hyperfine structure. After exposure to phosgene, every batch of flies consistently displays the Mn (Ⅱ) signal. Regardless of the aftercare provided, these flies inevitably perish, making the signal a diagnostic of phosgene poisoning in flies. The intensity of the signal is dependent on both exposure time and concentration, resembling the kinetics of phosgene poisoning. The signal of Mn (Ⅱ) correlates with the presence of a functional superoxide dismutase Sod2. After exposure, heterozygous Sod2 mutants have a markedly lower intensity of Mn (Ⅱ) in their ESR spectrum. We suggest that phosgene disturbs Mn redox cycling between ESR-silent Mn (Ⅲ) and ESR-active Mn (Ⅱ) that is required for superoxide dismutation. Accordingly, mitochondria of phosgene-treated flies show reduced rates of hydrogen peroxide production, and severely compromised complex I-linked respiration. It is likely that phosgene damages mitochondria through MnSOD and complex I, which contributes to its toxicity. This work uses Drosophila melanogaster for the first time in phosgene research.},
}

@article {pmid40549685,
year = {2025},
author = {Yu, X and Hu, J and Tan, Y and Pan, M and Zhang, H and Li, B},
title = {MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.},
journal = {PLoS computational biology},
volume = {21},
number = {6},
pages = {e1013090},
doi = {10.1371/journal.pcbi.1013090},
pmid = {40549685},
issn = {1553-7358},
mesh = {Humans ; *Mutation/genetics ; Algorithms ; Computational Biology/methods ; *Mitochondria/genetics ; Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Neoplasms/genetics ; *DNA, Mitochondrial/genetics ; Proto-Oncogene Proteins B-raf/genetics ; },
abstract = {Mitochondrial (MT) mutations serve as natural genetic markers for inferring clonal relationships using single cell sequencing data. However, the fundamental challenge of MT mutation-based lineage tracing is automated identification of informative MT mutations. Here, we introduced an open-source computational algorithm called "MitoTracer", which accurately identified clonally informative MT mutations and inferred evolutionary lineage from scRNA-seq or scATAC-seq samples. We benchmarked MitoTracer using the ground-truth experimental lineage sequencing data and demonstrated its superior performance over the existing methods measured by high sensitivity and specificity. MitoTracer is compatible with multiple single cell sequencing platforms. Its application to a cancer evolution dataset revealed the genes related to primary BRAF-inhibitor resistance from scRNA-seq data of BRAF-mutated cancer cells. Overall, our work provided a valuable tool for capturing real informative MT mutations and tracing the lineages among cells.},
}

Humans
*Mutation/genetics
Algorithms
Computational Biology/methods
*Mitochondria/genetics
Single-Cell Analysis/methods
*Cell Lineage/genetics
Neoplasms/genetics
*DNA, Mitochondrial/genetics
Proto-Oncogene Proteins B-raf/genetics

@article {pmid40547468,
year = {2025},
author = {Panagopoulos, DJ and Yakymenko, I and De Iuliis, GN and Chrousos, GP},
title = {A comprehensive mechanism of biological and health effects of anthropogenic extremely low frequency and wireless communication electromagnetic fields.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1585441},
pmid = {40547468},
issn = {2296-2565},
mesh = {*Electromagnetic Fields/adverse effects ; Humans ; *Wireless Technology ; *Environmental Exposure/adverse effects ; Oxidative Stress ; DNA Damage ; Microwaves/adverse effects ; },
abstract = {Exposure to anthropogenic electromagnetic fields (EMFs), especially those of wireless communications (WC) has increased tremendously. This is an unprecedented phenomenon throughout biological evolution because, all anthropogenic EMFs, being fully polarized, coherent, and, especially WC EMFs, highly variable, differ substantially from the natural EMFs. WC EMFs consist of Microwave (MW) carrier waves, modulated, by Extremely Low Frequency (ELF) signals, and included in on/off pulses repeated at various ELF rates. Moreover, they exhibit intense random variability, mainly in the Ultra Low Frequency (ULF) band. Thus, WC EMFs are a combination of MW and ELF/ULF EMFs. The combination of polarization/coherence and intense low-frequency (ELF/ULF) variability seems to be the key to EMF-bioactivity. Epidemiological and laboratory studies highlight a connection between ELF or WC EMF exposure and cancer, infertility, electro-hypersensitivity, and various other pathologies. Studies also find DNA damage and Oxidative Stress (OS) which explain these pathologies. While man-made EMFs cannot directly ionize molecules, they are capable of doing this indirectly in biological tissue, by triggering the biosynthesis of Reactive Oxygen Species (ROS) which can damage biomolecules, including DNA. The (over)production of ROS and the consequent OS are triggered by irregular gating of Voltage-Gated Ion Channels (VGICs) in the cell membranes as described by the Ion Forced Oscillation (IFO)-VGIC mechanism: Mobile ions within VGICs forced to oscillate by the applied ELF/ULF EMFs exert forces on the voltage sensors of the VGICs, similar to or greater than the forces that physiologically gate those channels, resulting in their irregular gating (dysfunction). Dysfunction of ion channels disrupts intracellular ionic concentrations. This triggers ROS overproduction and OS by the ROS-generating systems/enzymes in the cells, such as the electron transport chain (ETC) in the mitochondria, or the NADPH/NADH oxidases (NOXs), the Nitric Oxide synthases (NOS), etc. The IFO-VGIC mechanism and the consequent OS constitute a comprehensive mechanism that explains all known adverse biological and health effects reported to be induced by anthropogenic EMFs.},
}

*Electromagnetic Fields/adverse effects
Humans
*Wireless Technology
*Environmental Exposure/adverse effects
Oxidative Stress
DNA Damage
Microwaves/adverse effects

@article {pmid40545685,
year = {2025},
author = {Benning, FMC and Bell, TA and Nguyen, TH and Syau, D and Connell, LB and Liao, YT and Keating, MP and Coughlin, M and Nordstrom, AEH and Ericsson, M and daCosta, CJB and Chao, LH},
title = {Ancestral sequence reconstruction of the Mic60 Mitofilin domain reveals residues supporting respiration in yeast.},
journal = {Protein science : a publication of the Protein Society},
volume = {34},
number = {7},
pages = {e70207},
doi = {10.1002/pro.70207},
pmid = {40545685},
issn = {1469-896X},
support = {NFRFE-2018-00064//New Frontiers in Research Fund/ ; 377068/CAPMC/CIHR/Canada ; R35GM142553/NH/NIH HHS/United States ; 9736//Simons Foundation/ ; //Gordon and Betty Moore Foundation/ ; 34475//Canada Foundation for Innovation/ ; RGPIN-2016-04801//Natural Sciences and Engineering Research Council of Canada/ ; //Helen Hay Whitney Foundation/ ; P180777//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Keystone Future of Science Fund/ ; },
mesh = {*Saccharomyces cerevisiae/metabolism/genetics ; *Mitochondrial Proteins/genetics/chemistry/metabolism ; *Saccharomyces cerevisiae Proteins/genetics/chemistry/metabolism ; Protein Domains ; Evolution, Molecular ; Phylogeny ; },
abstract = {In eukaryotes, cellular respiration takes place in the cristae of mitochondria. The mitochondrial inner membrane protein Mic60, a core component of the mitochondrial contact site and cristae organizing system, is crucial for the organization and stabilization of crista junctions and its associated functions. While the C-terminal Mitofilin domain of Mic60 is necessary for cellular respiration, the sequence determinants for this function have remained unclear. Here, we used ancestral sequence reconstruction to generate Mitofilin ancestors up to and including the last opisthokont common ancestor (LOCA). We found that yeast-lineage derived Mitofilin ancestors as far back as the LOCA rescue respiration. By comparing Mitofilin ancestors, we identified four residues sufficient to explain the respiratory difference between yeast- and animal-derived Mitofilin ancestors. Our results provide a foundation for investigating the conservation of Mic60-mediated cristae junction interactions.},
}

*Saccharomyces cerevisiae/metabolism/genetics
*Mitochondrial Proteins/genetics/chemistry/metabolism
*Saccharomyces cerevisiae Proteins/genetics/chemistry/metabolism
Protein Domains
Evolution, Molecular
Phylogeny

@article {pmid40542427,
year = {2025},
author = {Katsafadou, AI and Nebert, DW and Krupenko, SA and Thompson, DC and Vasiliou, V},
title = {Update of the sideroflexin (SLC56) gene family.},
journal = {Human genomics},
volume = {19},
number = {1},
pages = {69},
pmid = {40542427},
issn = {1479-7364},
support = {ES033815/NH/NIH HHS/United States ; },
mesh = {Humans ; Mitochondria/metabolism/genetics ; *Multigene Family ; Iron/metabolism ; Animals ; *Mitochondrial Membrane Transport Proteins/genetics ; *Mitochondrial Proteins/genetics/metabolism ; Evolution, Molecular ; },
abstract = {The human sideroflexin (SFXN) gene family, also classified as solute carrier family 56 (SLC56), encodes a group of five mitochondrial transmembrane proteins (SFXN1-SFXN5) involved in key aspects of mitochondrial metabolism, cellular homeostasis, and development. SFXNs are highly conserved across eukaryotic species, with evolutionary the origin traced back to the earliest metazoans. Functionally, each of the five family members exhibits distinct functional specialization. Particularly, SFXN1 and SFXN3 facilitate mitochondrial serine transport, supporting one-carbon metabolism. SFXN2 and SFXN4 are implicated in mitochondrial iron regulation, heme biosynthesis, and iron-sulfur cluster assembly. SFXN5, predominantly expressed in the brain, is proposed to regulate citrate metabolism and immune cell functions. Mutations or dysregulation of SFXN genes have been linked to certain human diseases, including congenital sideroblastic anemia, oxidative phosphorylation disorders, neurodegenerative conditions, and cancers. Structurally, SFXNs share conserved transmembrane domains and key motifs critical for substrate transport, mitochondrial iron homeostasis, and overall mitochondrial function. The evolutionary trajectory of the SFXN family-from amino acid transport to functionally specialized roles in higher organisms-highlights their biological and clinical significance. Comparative studies across model organisms reveal both conserved and divergent functions, emphasizing their importance in health and disease. A comprehensive understanding of the SFXN family not only advances fundamental mitochondrial research but also opens avenues for novel therapeutic interventions.},
}

Humans
Mitochondria/metabolism/genetics
*Multigene Family
Iron/metabolism
Animals
*Mitochondrial Membrane Transport Proteins/genetics
*Mitochondrial Proteins/genetics/metabolism
Evolution, Molecular

@article {pmid39798085,
year = {2025},
author = {Martell, E and Kuzmychova, H and Senthil, H and Chawla, U and Kaul, E and Grewal, A and Banerji, V and Anderson, CM and Venugopal, C and Miller, D and Werbowetski-Ogilvie, TE and Singh, SK and Sharif, T},
title = {Disease stage-specific role of the mitochondrial pyruvate carrier suppresses differentiation in temozolomide and radiation-treated glioblastoma.},
journal = {Neuro-oncology},
volume = {27},
number = {5},
pages = {1193-1209},
doi = {10.1093/neuonc/noaf008},
pmid = {39798085},
issn = {1523-5866},
support = {/CAPMC/CIHR/Canada ; //Natural Sciences and Engineering Research Council/ ; //Manitoba Medical Services Foundation/ ; },
mesh = {Humans ; *Glioblastoma/pathology/metabolism/therapy/drug therapy/radiotherapy ; *Temozolomide/pharmacology/therapeutic use ; Animals ; *Brain Neoplasms/pathology/metabolism/therapy/drug therapy ; Mice ; Antineoplastic Agents, Alkylating/pharmacology/therapeutic use ; Mitochondria/metabolism/drug effects ; *Cell Differentiation/drug effects ; Xenograft Model Antitumor Assays ; *Mitochondrial Membrane Transport Proteins/metabolism ; Tumor Cells, Cultured ; Neoplasm Staging ; *Monocarboxylic Acid Transporters/metabolism ; },
abstract = {BACKGROUND: The mitochondrial pyruvate carrier (MPC), a central metabolic conduit linking glycolysis and mitochondrial metabolism, is instrumental in energy production. However, the role of the MPC in cancer is controversial. In particular, the importance of the MPC in glioblastoma (GBM) disease progression following standard temozolomide (TMZ) and radiation therapy (RT) remains unexplored.

METHODS: Leveraging in vitro and in vivo patient-derived models of TMZ-RT treatment in GBM, we characterize the temporal dynamics of MPC abundance and downstream metabolic consequences using state-of-the-art molecular, metabolic, and functional assays.

RESULTS: Our findings unveil a disease stage-specific role for the MPC, where in posttreatment GBM, but not therapy-naïve tumors, the MPC acts as a central metabolic regulator that suppresses differentiation. Temporal profiling reveals a dynamic metabolic rewiring where a steady increase in MPC abundance favors a shift towards enhanced mitochondrial metabolic activity across patient GBM samples. Intriguingly, while overall mitochondrial metabolism is increased, acetyl-CoA production is reduced in posttreatment GBM cells, hindering histone acetylation and silencing neural differentiation genes in an MPC-dependent manner. Finally, the therapeutic translations of these findings are highlighted by the successful pre-clinical patient-derived orthotopic xenograft trials utilizing a blood-brain-barrier permeable MPC inhibitor, MSDC-0160, which augments standard TMZ-RT therapy to mitigate disease relapse and prolong animal survival.

CONCLUSION: Our findings demonstrate the critical role of the MPC in mediating GBM aggressiveness and molecular evolution following standard TMZ-RT treatment, illuminating a therapeutically-relevant metabolic vulnerability to potentially improve survival outcomes for GBM patients.},
}

Humans
*Glioblastoma/pathology/metabolism/therapy/drug therapy/radiotherapy
*Temozolomide/pharmacology/therapeutic use
Animals
*Brain Neoplasms/pathology/metabolism/therapy/drug therapy
Mice
Antineoplastic Agents, Alkylating/pharmacology/therapeutic use
Mitochondria/metabolism/drug effects
*Cell Differentiation/drug effects
Xenograft Model Antitumor Assays
*Mitochondrial Membrane Transport Proteins/metabolism
Tumor Cells, Cultured
Neoplasm Staging
*Monocarboxylic Acid Transporters/metabolism

@article {pmid40546076,
year = {2025},
author = {Liu, S and Powell, V and Yang, SM and Lam, F and Bowler, C and Obornik, M and Dorrell, RG},
title = {Dynamic Relocalization and Divergent Expression of a Major Facilitator Carrier Subfamily in Diatoms.},
journal = {Physiologia plantarum},
volume = {177},
number = {3},
pages = {e70355},
doi = {10.1111/ppl.70355},
pmid = {40546076},
issn = {1399-3054},
support = {101039760//European Research Council/International ; 835067//European Research Council/International ; CZ.02.2.69/0.0/0.0/18_054/0014649//Jihočeská Univerzita v Českých Budějovicích/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche/ ; ANR-10-LABX-54//Agence Nationale de la Recherche/ ; ANR-11-BTBR-0008//Agence Nationale de la Recherche/ ; ANR-11-IDEX-0001-02//Agence Nationale de la Recherche/ ; ANR-19-CE20-0020//Agence Nationale de la Recherche/ ; 23-06203S//Grantová Agentura České Republiky/ ; },
abstract = {Eukaryotic organisms, including microbial members such as protists and green algae, utilize suites of transporter proteins to move essential metabolites across cell organelle membranes. Amongst these different transporter families, the mitochondrial carrier family (MCF) is one of the most diverse, encompassing essential NAD+ and ADP/ATP translocators, as well as amino acid, sugar and cofactor transporters. They are typically associated with the mitochondrial inner membrane, but some display more dynamic localization. Here, we perform a census of predicted MCF domains in the genome of the model diatom alga Phaeodactylum tricornutum, identifying a new family of three proteins (termed here and elsewhere "MCFc") with strong internal sequence conservation but limited similarity to other MCF proteins encoded in its genome. Considering both phylogenetic data and experimental localization, we posit that MCFc is widespread across algae with complex red chloroplasts alongside some primary green algae, and contains multiple subfamilies targeted to diatom mitochondria, plastids, and endomembranes. Finally, using data from Tara Oceans, we identify putative roles for MCFc in diatom cells, including a possible association of the plastid-targeted Phatr3_J46742 subfamily in cellular nitrate assimilation. Our data provide insights into the evolutionary diversification of the membrane transport mechanisms associated with diatoms and other eukaryotic algae.},
}

@article {pmid40536996,
year = {2025},
author = {Yañez, IM and Torres-Cuevas, I and Corral-Debrinski, M},
title = {Neuroglobin: A promising candidate to treat neurological diseases.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-24-01503},
pmid = {40536996},
issn = {1673-5374},
abstract = {Neurodevelopmental and neurodegenerative illnesses constitute a global health issue and a foremost economic burden since they are a large cause of incapacity and death worldwide. Altogether, the burden of neurological disorders has increased considerably over the past 30 years because of population aging. Overall, neurological diseases significantly impair cognitive and motor functions and their incidence will increase as societies age and the world's population continues to grow. Autism spectrum disorder, motor neuron disease, encephalopathy, epilepsy, stroke, ataxia, Alzheimer's disease, amyotrophic lateral sclerosis, Huntington's disease, and Parkinson's disease represent a non-exhaustive list of neurological illnesses. These affections are due to perturbations in cellular homeostasis leading to the progressive injury and death of neurons in the nervous system. Among the common features of neurological handicaps, we find protein aggregation, oxidative stress, neuroinflammation, and mitochondrial impairment in the target tissues, e.g., the brain, cerebellum, and spinal cord. The high energy requirements of neurons and their inability to produce sufficient adenosine triphosphate by glycolysis, are responsible for their dependence on functional mitochondria for their integrity. Reactive oxygen species, produced along with the respiration process within mitochondria, can lead to oxidative stress, which compromises neuronal survival. Besides having an essential role in energy production and oxidative stress, mitochondria are indispensable for an array of cellular processes, such as amino acid metabolism, iron-sulfur cluster biosynthesis, calcium homeostasis, intrinsic programmed cell death (apoptosis), and intraorganellar signaling. Despite the progress made in the last decades in the understanding of a growing number of genetic and molecular causes of central nervous diseases, therapies that are effective to diminish or halt neuronal dysfunction/death are rare. Given the genetic complexity responsible for neurological disorders, the development of neuroprotective strategies seeking to preserve mitochondrial homeostasis is a realistic challenge to lastingly diminish the harmful evolution of these pathologies and so to recover quality of life. A promising candidate is the neuroglobin, a globin superfamily member of 151 amino acids, which is found at high levels in the brain, the eye, and the cerebellum. The protein, which localizes to mitochondria, is involved in electron transfer, oxygen storage and defence against oxidative stress; hence, possessing neuroprotective properties. This review surveys up-to-date knowledge and emphasizes on existing investigations regarding neuroglobin physiological functions, which remain since its discovery in 2000 under intense debate and the possibility of using neuroglobin either by gene therapy or its direct delivery into the brain to treat neurological disorders.},
}

@article {pmid40527924,
year = {2025},
author = {Cal, K and Leyva, A and Rodríguez-Duarte, J and Ruiz, S and Santos, L and Garat, MP and Colella, L and Ingold, M and Benitez-Rosendo, A and Pérez-Torrado, V and Vilaseca, C and Galliussi, G and Ziegler, L and Peclat, TR and Bresque, M and Handy, RM and King, R and Menezes Dos Reis, L and Alves, JM and Espasandín, C and de la Sovera, V and Breining, P and Dapueto, R and Lopez, A and Thompson, KL and Lino, CA and França, JV and Vieira, TS and Rattan, R and Agorrody, G and DeVallance, E and Haag, J and Meadows, E and Lewis, SE and Santana Barbosa, GC and Lai de Souza, LO and Chichierchio, MS and Valez, V and Aicardo, A and Contreras, P and Vendelbo, MH and Jakobsen, S and Kamaid, A and Porcal, W and Calliari, A and Verdes, JM and Du, J and Wang, Y and Hollander, JM and White, TA and Radi, R and Moyna, G and Quijano, C and O'Doherty, R and Moraes-Vieira, P and Giri, S and Holloway, GP and Festuccia, WT and Leiria, LO and Leonardi, R and Mori, MA and Camacho-Pereira, J and Kelley, EE and Duran, R and López, GV and Chini, EN and Batthyány, C and Escande, C},
title = {A nitroalkene derivative of salicylate, SANA, induces creatine-dependent thermogenesis and promotes weight loss.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {40527924},
issn = {2522-5812},
support = {R01 HL-128485//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01 HL-168290//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; NS 112727//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NS AI144004//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM119528//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK124510-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01HL153532//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 19TPA34850089//American Heart Association (American Heart Association, Inc.)/ ; },
abstract = {The emergence of glucagon-like peptide-1 agonists represents a notable advancement in the pharmacological treatment of obesity, yet complementary approaches are essential. Through phenotypic drug discovery, we developed promising nitroalkene-containing small molecules for obesity-related metabolic dysfunctions. Here, we present SANA, a nitroalkene derivative of salicylate, demonstrating notable efficacy in preclinical models of diet-induced obesity. SANA reduces liver steatosis and insulin resistance by enhancing mitochondrial respiration and increasing creatine-dependent energy expenditure in adipose tissue, functioning effectively in thermoneutral conditions and independently of uncoupling protein 1 and AMPK activity. Finally, we conducted a randomized, double-blind, placebo-controlled phase 1A/B clinical trial, which consisted of two parts, each with four arms: (A) single ascending doses (200-800 mg) in healthy lean volunteers; (B) multiple ascending doses (200-400 mg per day for 15 days) in healthy volunteers with overweight or obesity. The primary endpoint assessed safety and tolerability. Secondary and exploratory endpoints included pharmacokinetics, tolerability, body weight and metabolic markers. SANA shows good safety and tolerability, and demonstrates beneficial effects on body weight and glucose management within 2 weeks of treatment. Overall, SANA appears to be a first-in-class activator of creatine-dependent energy expenditure and thermogenesis, highlighting its potential as a therapeutic candidate for 'diabesity'. Australian New Zealand Clinical Trials Registry registration: ACTRN12622001519741 .},
}

@article {pmid40523936,
year = {2025},
author = {Muthukumar, G and Weissman, JS},
title = {Shaping the composition of the mitochondrial outer membrane.},
journal = {Nature cell biology},
volume = {},
number = {},
pages = {},
pmid = {40523936},
issn = {1476-4679},
support = {T32GM007287//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Mitochondria are critical double-membraned organelles that act as biosynthetic and bioenergetic cellular factories, with the outer membrane providing an interface with the rest of the cell. Mitochondrial outer membrane proteins regulate a variety of processes, including metabolism, innate immunity and apoptosis. Although the biophysical and functional diversity of these proteins is highly documented, the mechanisms of their biogenesis and the integration of that into cellular homeostasis are just starting to take shape. Here, focusing on α-helical outer membrane proteins, we review recent insights into the mechanisms of synthesis and cytosolic chaperoning, insertion and assembly in the lipid bilayer, and quality control of unassembled or mislocalized transmembrane domains. We further discuss the role convergent evolution played in this process, comparing key biogenesis players from lower eukaryotes, including yeast and trypanosomes, with multicellular metazoan systems, and draw comparisons with the endoplasmic reticulum biogenesis system, in which membrane proteins face similar challenges.},
}

@article {pmid39985363,
year = {2025},
author = {Ganetzky, R and Stanley, KD and MacMullen, LE and George-Sankoh, I and Wang, J and Goldstein, A and Xiao, R and Falk, MJ},
title = {Recognizing the evolution of clinical syndrome spectrum progression in individuals with single large-scale mitochondrial DNA deletion syndromes (SLSMDS).},
journal = {Genetics in medicine : official journal of the American College of Medical Genetics},
volume = {27},
number = {5},
pages = {101386},
doi = {10.1016/j.gim.2025.101386},
pmid = {39985363},
issn = {1530-0366},
mesh = {Humans ; Female ; Male ; *Mitochondrial Diseases/genetics/pathology ; *DNA, Mitochondrial/genetics ; Child ; *Kearns-Sayre Syndrome/genetics/pathology ; Adult ; Adolescent ; Quality of Life ; Retrospective Studies ; Phenotype ; Child, Preschool ; Disease Progression ; Middle Aged ; Young Adult ; Sequence Deletion/genetics ; *Lipid Metabolism, Inborn Errors/genetics/pathology ; Syndrome ; Ophthalmoplegia, Chronic Progressive External/genetics/pathology ; Acyl-CoA Dehydrogenase, Long-Chain/genetics/deficiency ; Mitochondria/genetics ; Congenital Bone Marrow Failure Syndromes ; Muscular Diseases ; },
abstract = {PURPOSE: Single large-scale mtDNA deletions (SLSMD) result in single large-scale deletion syndromes (SLSMDS). SLSMDS presentations have classically been recognized to encompass at least 3 distinct clinical phenotypes: Pearson syndrome (PS), Kearns-Sayre syndrome (KSS), and chronic progressive ophthalmoplegia.

METHODS: A facilitated review of electronic medical records, manual charts, and Research Electronic Data Capture research databases was performed to complete a retrospective natural history study of 30 participants with SLSMDS in a single health system between 2002 and 2020. The evaluated characteristics included genetic and clinical laboratory test values, growth parameters, signs and symptoms, demographics, and patient-reported outcome measures of fatigue, quality of life, and overall function.

RESULTS: Detailed cohort characterization highlighted that a recurrent deleted region involving MT-ND5 (HGNC:7641) occurs in 96% of participants with SLSMDS regardless of the clinical phenotype, which tends to evolve over time. Higher blood heteroplasmy correlated with an earlier age of onset. Growth differentiation factor 15 levels were elevated in all participants with SLSMDS. A history of PS was associated with poor survival prognosis. Furthermore, increased fatigue and decreased quality of life have been reported in patients with SLSMD with advanced age.

CONCLUSION: A retrospective natural history study of patients with SLSMDS demonstrated the evolution of classically considered PS, Kearns-Sayre syndrome, and chronic progressive ophthalmoplegia clinical presentations in affected individuals, which may inform future clinical trial developments.},
}

Humans
Female
Male
*Mitochondrial Diseases/genetics/pathology
*DNA, Mitochondrial/genetics
Child
*Kearns-Sayre Syndrome/genetics/pathology
Adult
Adolescent
Quality of Life
Retrospective Studies
Phenotype
Child, Preschool
Disease Progression
Middle Aged
Young Adult
Sequence Deletion/genetics
*Lipid Metabolism, Inborn Errors/genetics/pathology
Syndrome
Ophthalmoplegia, Chronic Progressive External/genetics/pathology
Acyl-CoA Dehydrogenase, Long-Chain/genetics/deficiency
Mitochondria/genetics
Congenital Bone Marrow Failure Syndromes
Muscular Diseases

@article {pmid40509913,
year = {2025},
author = {Gonçalves, LT and Pezzi, PH and Deprá, M and Françoso, E},
title = {Mitonuclear coevolution in bumblebees (Bombus): genomic signatures and its role in climatic niche adaptation.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf123},
pmid = {40509913},
issn = {1759-6653},
abstract = {Mitochondria play a central role in cellular respiration, but require close coevolution with the nuclear genome for proper function. This process, termed mitonuclear coevolution, is poorly understood on species-level evolutionary timescales, despite its role in speciation. Here, we investigate mitonuclear coevolution in bumblebees (Bombus), a group of ecologically diverse pollinators with rapid mitochondrial (mt) DNA evolution. Leveraging genomic data from a comprehensive set of 55 bumblebee species, we quantified the evolutionary rate correlation (ERC) between mt genes and nuclear genes that interact with mitochondria (N-mt). We found a strong ERC between mt and N-mt genes, but not among mt genes and random nuclear genes, supporting the mitonuclear coevolution hypothesis. Additionally, we found the strength of mitonuclear ERC seems to be consistent across bumblebee lineages, contrasting with observations in other taxa. Finally, bumblebee species from colder environments showed increased mt evolutionary rates relative to both N-mt genes and random nuclear genes. This suggests potential implications to bumblebee climatic niche adaptation and the thermoregulation of cold-adapted species, possibly driven by selection for enhanced mt function to sustain thermogenesis and flight in low-temperature environments. Our findings are discussed considering the dynamics of mitonuclear coevolution in bumblebees and its potential role in shaping their adaptation to diverse ecological niches.},
}

@article {pmid40509562,
year = {2025},
author = {Terraza-Silvestre, E and Bandera-Linero, J and Oña-Sánchez, D and Pimentel-Muinos, FX},
title = {Unconventional role of ATG16L1 in the control of ATP compartmentalization during apoptosis.},
journal = {Autophagy},
volume = {},
number = {},
pages = {},
doi = {10.1080/15548627.2025.2519051},
pmid = {40509562},
issn = {1554-8635},
abstract = {The autophagy mediator ATG16L1 forms part of a complex that is essential for MAP1LC3/LC3 lipidation and autophagosome formation in the canonical macroautophagic/autophagic pathway. However, ATG16L1 is also involved in unconventional activities where LC3 becomes lipidated in single-membrane structures unrelated to double-membrane autophagosomes. Such atypical activities usually require the C-terminal domain of the molecule that includes 7 WD40-type repetitions (WD40 domain, WDD). The WDD acts as a docking site for upstream inducers that engage the LC3 lipidation ability of ATG16L1 in alternative membrane compartments. Given that this domain is absent in the yeast Atg16 ortholog, an intriguing idea proposes that it was added to the primitive protein during evolution to perform new physiological roles required by the appearance of multicellularity. Identification of such atypical activities and their physiological implications at the organismal level are important issues that remain to be clarified. In a recent report we describe an unconventional autophagic pathway that restrains the immunogenic potential of apoptosis, a key feature of homeostatic and developmentally regulated cell death in multicellular organisms. This signaling route emanates from apoptotic mitochondria and induces the formation of single-membrane, LC3-positive vesicles through a mechanism that requires the WDD of ATG16L1. The induced vesicles sequester ATP to inhibit the amount of ATP released from apoptotic cells and, consequently, prevent the activation of co-cultured phagocytes. Thus, this is a pathway that contributes to maintain the immunosilent nature of apoptotic cell death.},
}

@article {pmid39155336,
year = {2025},
author = {Prajapati, MR and Diksha, D and Thapa, P and Sharma, SK and Gupta, N and Baranwal, VK},
title = {Identification of a novel mitovirus in grapevine through high-throughput sequencing.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {5},
pages = {909-916},
pmid = {39155336},
issn = {1618-1905},
support = {Ag.Edn.F.No./27/01/NP/2022-HRD//Indian Council of Agricultural Research/ ; },
mesh = {*Vitis/virology ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Phylogeny ; Open Reading Frames ; *RNA Viruses/genetics/classification/isolation & purification ; RNA, Viral/genetics ; Plant Diseases/virology ; RNA-Dependent RNA Polymerase/genetics ; *Plant Viruses/genetics/classification/isolation & purification ; Viral Proteins/genetics ; },
abstract = {BACKGROUND: Transcriptome data from a plant sample frequently include numerous reads originating from RNA virus genomes that were concurrently isolated during RNA preparation. These high-throughput sequencing reads from the virus can be assembled to form a new sequence for the plant RNA genome.

METHODS AND RESULTS: Here, we identify putative novel mitovirus, grapevine mitovirus 1 (GMV1) through high-throughput sequencing (HTS) of grapevine rootstocks (Vitis spp.), and the identified virus was confirmed using virus-specific primers in RT-PCR assay. The genomic RNA of GMV1 encodes complete open reading frame (ORF) of 2,496 nucleotides (nts) in length. RNA-dependent RNA polymerase (RdRp) encoded by the viral genome contained one RdRp conserved domain. BLASTx analysis of GMV1 genome showed sequence identity of 33.18-56.75% with the existing mitovirus sequences. Phylogenetic analysis based on genome sequences showed that GMV1 clustered in a distinct clade to other mitoviruses.

CONCLUSION: Grapevine mitovirus 1 represents a newly discovered species within the Unuamitovirus genus of the Mitoviridae family, targeting fungal mitochondria. While the majority of recognized mitoviruses typically lack a functional RdRp as per the plant mitochondrial genetic code, GMV1 encodes a complete RdRp in accordance with both fungal and plant mitochondrial genetic codes.},
}

*Vitis/virology
High-Throughput Nucleotide Sequencing
Genome, Viral
Phylogeny
Open Reading Frames
*RNA Viruses/genetics/classification/isolation & purification
RNA, Viral/genetics
Plant Diseases/virology
RNA-Dependent RNA Polymerase/genetics
*Plant Viruses/genetics/classification/isolation & purification
Viral Proteins/genetics

@article {pmid40381604,
year = {2025},
author = {He, Q and Cao, S and Yu, W and Li, Z and Liu, W and Tian, C and Li, D and Zou, Y and Yu, B and Zhan, Y and Jiang, Y and Wu, J and Yang, Y and Wang, N},
title = {hnRNP K regulates mitochondrial apoptosis induced by porcine circovirus type 3 capsid protein.},
journal = {Veterinary microbiology},
volume = {306},
number = {},
pages = {110557},
doi = {10.1016/j.vetmic.2025.110557},
pmid = {40381604},
issn = {1873-2542},
mesh = {*Circovirus/genetics ; *Apoptosis ; Animals ; *Capsid Proteins/genetics/metabolism ; Swine ; *Mitochondria/metabolism ; *Heterogeneous-Nuclear Ribonucleoprotein K/metabolism/genetics ; Cell Line ; Circoviridae Infections/virology/veterinary ; Molecular Docking Simulation ; },
abstract = {Porcine circovirus type 3 (PCV3) is a globally emerging circovirus affecting pigs and other animals. The capsid protein (Cap) is the sole structural protein of PCV, with a crucial role in virus evolution and pathogenesis. Through interactions with host factors, Cap enables viral entry, transport, and replication while modifying various cellular processes. Cap protein-induced apoptosis has important implications for viral pathogenesis, but remains poorly defined. Herein, we demonstrated for the first time that PCV3 Cap induced cell cycle arrest of PK-15 cells in S-phase and initiated apoptosis via a mitochondrial Caspase-9-dependent pathway. Truncation analysis localized the apoptotic determinant to the N-terminal 1-34 aa of PCV3 Cap and heterogeneous nuclear ribonucleoprotein K (hnRNP K) was identified as a host protein that binds to PCV3 Cap. Overexpression of hnRNP K reduced PCV3 Cap-induced release of Cyt-c into the cytoplasm, implying a regulatory role in apoptosis. Based on structural modelling and molecular docking, amino acids at sites 24 and 27 of Cap from PCV3 variants, which define genotypes (PCV3a/b/c), affected binding with hnRNP K. Specifically, PCV3c Cap (V24/K27 and V24/R27) had higher affinity than PCV3a Cap (A24/R27) or PCV3b Cap (A24/K27), consistent with its superior apoptosis-inducing capacity compared to PCV3a/b variants, highlighting the importance of Cap interactions with hnRNP K. In summary, we identified novel molecular determinants of PCV3 pathogenesis that will inform development of vaccines and diagnostics.},
}

*Circovirus/genetics
*Apoptosis
Animals
*Capsid Proteins/genetics/metabolism
Swine
*Mitochondria/metabolism
*Heterogeneous-Nuclear Ribonucleoprotein K/metabolism/genetics
Cell Line
Circoviridae Infections/virology/veterinary
Molecular Docking Simulation

@article {pmid40494286,
year = {2025},
author = {Sprecher, BN and Johnson, MD},
title = {Kleptoplasty: Letting the cart lead the horse.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R414-R417},
doi = {10.1016/j.cub.2025.04.068},
pmid = {40494286},
issn = {1879-0445},
mesh = {*Dinoflagellida/physiology/genetics ; Animals ; *Chloroplasts/physiology/metabolism ; *Plastids/physiology ; Photosynthesis/genetics ; Mitochondria ; Biological Evolution ; },
abstract = {Some chloroplast-stealing dinoflagellates remodel their kleptoplastids, form an extensive network with stollen mitochondria, and likely benefit from photosynthetic genes that they inherited or acquired from prey. These adaptations allow these protists to exploit kleptoplastids for months and shed light on past plastid acquisitions.},
}

*Dinoflagellida/physiology/genetics
Animals
*Chloroplasts/physiology/metabolism
*Plastids/physiology
Photosynthesis/genetics
Mitochondria
Biological Evolution

@article {pmid40490602,
year = {2025},
author = {Lerouley, O and Larrieu, I and Ducrocq, TL and Pinson, B and Giraud, MF and Mourier, A},
title = {An alternative mechanism by which If1 prevents ATP hydrolysis by the ATP synthase subcomplex in S. cerevisiae.},
journal = {EMBO reports},
volume = {},
number = {},
pages = {},
pmid = {40490602},
issn = {1469-3178},
support = {ANR-22-CE14-0040//Agence Nationale de la Recherche (ANR)/ ; AAPPF2021-2020-12000110//Region Nouvelle Aquitaine/ ; MetabOptic 2022-24564910//Region Nouvelle Aquitaine/ ; COMUNCAN//SIRIC BRIO/ ; SBM-AAPG-2024//Université de Bordeaux (University of Bordeaux)/ ; },
abstract = {The mitochondrial F1F0-ATP synthase is crucial for maintaining the ATP/ADP balance which is critical for cell metabolism, ion homeostasis and cell proliferation. This enzyme, conserved across evolution, is found in the mitochondria or chloroplasts of eukaryotic cells and the plasma membrane of bacteria. In vitro studies have shown that the mitochondrial F1F0-ATP synthase is reversible, capable of hydrolyzing instead of synthesizing ATP. In vivo, its reversibility is inhibited by the endogenous peptide If1 (Inhibitory Factor 1), which specifically prevents ATP hydrolysis in a pH-dependent manner. Despite its presumed importance, the loss of If1 in various model organisms does not cause severe phenotypes, suggesting its role may be confined to specific stress or metabolic conditions yet to be discovered. Our analyses indicate that inhibitory peptides are crucial in mitigating mitochondrial depolarizing stress under glyco-oxidative metabolic conditions. Additionally, we found that the absence of If1 destabilizes the nuclear-encoded free F1 subcomplex. This mechanism highlights the role of If1 in preventing harmful ATP wastage, offering new insights into its function under physiological and pathological conditions.},
}

@article {pmid40481010,
year = {2025},
author = {Tao, A and Tao, J and Gan, Z and Zhang, Y and Yin, C and Jiang, G},
title = {The characterisation of the complete mitochondrial genome of Polygonatum Kingianum reveals recombination mediated by repeats associated with DNA replication.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19980},
pmid = {40481010},
issn = {2045-2322},
support = {NO. 202301AT070898, NO. 202101AT070001//Ai-en Tao/ ; },
mesh = {*Genome, Mitochondrial ; *DNA Replication/genetics ; *Polygonatum/genetics ; DNA, Mitochondrial/genetics ; Phylogeny ; *Recombination, Genetic ; RNA, Transfer/genetics ; *Repetitive Sequences, Nucleic Acid ; },
abstract = {Polygonatum kingianum Coll et Hemsl (P. kingianum) is recognized as one of the most valuable medicinal species, demonstrating a diverse range of bioactivities, including antidiabetic effects, reduction of blood lipids, anti-tumor properties, and hyperglycemic activity. However, the mitochondrial genome of P. kingianum has not yet been reported. Therefore, we sequenced and assembled the mitochondrial DNA (mtDNA) of P. kingianum. The results indicate that the mitochondrial genome possesses a multi-branched conformational structure. Further annotation of the mitochondrial genome reveals that it is 647,110 bp in length, containing a total of 35 distinct protein-coding genes, 22 tRNA genes, and 4 rRNA genes. The analysis of gene loss revealed that a total of seven genes were absent in the mitochondrial genome of P. kingianum. This includes six ribosomal protein genes (rpl2, rpl6, rpl10, rps7, rps8, rps11) and two succinate dehydrogenase genes (sdh3 and sdh4), as well as one pseudogene. Furthermore, Analysis of mitochondrial genome coding sequences of ten closely related species revealed a total of 24 shared genes. The Ka/Ks values of all shared coding protein genes are less than 1, indicating that these genes have undergone purification selection during evolution and their protein functions are relatively stable. In addition, codon studies on P. kingianum mitochondria showed 29 high-frequency codons (RSCU > 1). The preference for codon usage is influenced by mutations and natural selection, but mainly determined by natural selection. Furthermore, we identified 31 homologous fragments spanning both chloroplast and mitochondrial genomes and 585 C-to-U RNA editing sites were predicted in mitochondrial PCGs. The phylogenetic tree established a close relationship between P. kingianum and the 27 closely related species. To sum up, this study will contribute to the application of population genetics and evolutionary research in the genus Polygonatum and other genera in the Asparagales family.},
}

*Genome, Mitochondrial
*DNA Replication/genetics
*Polygonatum/genetics
DNA, Mitochondrial/genetics
Phylogeny
*Recombination, Genetic
RNA, Transfer/genetics
*Repetitive Sequences, Nucleic Acid

@article {pmid40267584,
year = {2025},
author = {Costa, JAS and da Silva Medeiros, C and Furtado, LFV and Rabelo, ÉML},
title = {From selection to resistance: Mitochondrial findings in hookworm evolution under drug pressure.},
journal = {Veterinary parasitology},
volume = {337},
number = {},
pages = {110470},
doi = {10.1016/j.vetpar.2025.110470},
pmid = {40267584},
issn = {1873-2550},
mesh = {Animals ; *Selection, Genetic ; *Drug Resistance/genetics ; Phylogeny ; *Anthelmintics/pharmacology ; *Ancylostoma/genetics/drug effects ; Albendazole/pharmacology ; Mitochondria/genetics ; Polymorphism, Single Nucleotide ; Evolution, Molecular ; Electron Transport Complex IV/genetics ; Genetic Variation ; NADH Dehydrogenase/genetics ; },
abstract = {Single nucleotide polymorphisms (SNPs) in codons 134, 167, 198, and 200 of the β-tubulin isotype 1 gene are associated with benzimidazole resistance in nematodes. Our group previously selected an Ancylostoma ceylanicum strain resistant to albendazole through drug-induced selective pressure, derived from a wild-type strain maintained under laboratory conditions for over 15 years. This study aimed to investigate mitochondrial genetic variability in the resistant strain compared to its wild-type counterpart. A total of 151 worms from both strains, collected during and 42 months after the selection process, were analyzed for partial sequences of the mitochondrial COI and NAD1 genes. Nucleotide variations were detected exclusively in the resistant strain, with low divergence levels of 0.16 % (1/612 bp) in COI and 0.25 % (1/398 bp) in NAD1. All COI substitutions were synonymous, while NAD1 presented one nonsynonymous mutation. Phylogenetic analyses based on Maximum Likelihood and Bayesian inference revealed strong clustering between resistant and wild-type laboratory samples (COI: 99 % bootstrap; NAD1: 96 %), distinct from field-derived sequences. These findings suggest that genetically homogeneous populations, resulting from isolation and restricted gene flow, may be more susceptible to genetic pressures, including selection, potentially leading to the establishment of resistant parasites. This study underscores the role of population genetics in the evolution of drug resistance and emphasizes the importance of managing genetic diversity to mitigate resistance development.},
}

Animals
*Selection, Genetic
*Drug Resistance/genetics
Phylogeny
*Anthelmintics/pharmacology
*Ancylostoma/genetics/drug effects
Albendazole/pharmacology
Mitochondria/genetics
Polymorphism, Single Nucleotide
Evolution, Molecular
Electron Transport Complex IV/genetics
Genetic Variation
NADH Dehydrogenase/genetics

@article {pmid40474826,
year = {2025},
author = {Yang, X and Zhou, Y and Zhang, B and Tao, X and Qi, W and Wu, H},
title = {Irradiation-induced increase in nuclear p62 levels contributes to chromosomal fragmentation and chromothripsis.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000002643},
pmid = {40474826},
issn = {1743-9159},
abstract = {Chromosomal instability (CIN) is a hallmark of cancer, closely associated with tumor evolution, metastasis, immune evasion, and resistance to treatment. CIN is driven by persistent chromosome missegregation, resulting in abnormal chromosomal copy numbers and promoting tumor progression through mitotic errors, faulty chromosome segregation, and the formation of micronuclei or chromosome bridges. Previous studies have demonstrated that p62 localizes to micronuclei, where it interacts with mitochondria, enhancing ROS-mediated cysteine oxidation and promoting p62 homo-oligomerization. This disrupts repair by recruiting CHMP7 and other ESCRT-III components, impairing their function in restoring the micronuclear envelope. Notably, we observed a time-dependent increase in nuclear p62 levels following radiation therapy, which correlated with enhanced chromatin fragmentation and chromothripsis. While p62 inhibits homologous recombination repair and promotes non-homologous end joining, we hypothesize that radiation-induced nuclear p62 accumulation impairs nuclear envelope resealing by inhibiting ESCRT-III components, thereby contributing to chromosomal fragmentation and chromothripsis. These chromosomal alterations may play a significant role in tumor evolution and treatment resistance. Our findings suggest that irradiation-induced p62 accumulation is crucial for chromothripsis and may affect nuclear repair processes, impacting chromosomal stability. Future research will focus on elucidating how p62 contributes to these abnormalities and their implications for tumor progression and treatment resistance.},
}

@article {pmid40464854,
year = {2025},
author = {Gruber, A and Vohnoutová, M and McKay, C and Rocap, G and Oborník, M},
title = {ASAFind 2.0: multi-class protein targeting prediction for diatoms and algae with complex plastids.},
journal = {The Plant journal : for cell and molecular biology},
volume = {122},
number = {5},
pages = {e70138},
doi = {10.1111/tpj.70138},
pmid = {40464854},
issn = {1365-313X},
support = {//Parazitologický ústav, Akademie Věd České Republiky/ ; //National Science Foundation/ ; LM2023055//Ministry of Education, Youth and Science/ ; 21-26115S//Czech Science Foundation/ ; 23-06203S//Czech Science Foundation/ ; },
mesh = {*Diatoms/metabolism/genetics ; *Plastids/metabolism ; Proteome ; Rhodophyta/metabolism ; *Algal Proteins/metabolism ; *Software ; *Computational Biology/methods ; },
abstract = {Plastids of diatoms and related algae with complex plastids of red algal origin are surrounded by four membranes, which also define the periplastidic compartment (PPC), the space between the second and third membranes. Metabolic reactions as well as cell biological processes take place in the PPC; however, genome-wide predictions of the proteins targeted to this compartment were so far based on manual annotation work. Using published experimental protein localizations as reference data, we developed the first automatic prediction method for PPC proteins, which we included as a new feature in an updated version of the plastid protein predictor ASAFind. With our method, at least a subset of the PPC proteins can be predicted with high specificity, with an estimate of at least 81 proteins (0.7% of the predicted proteome) targeted to the PPC in the model diatom Phaeodactylum tricornutum. The proportion of PPC proteins varies, since 180 PPC proteins (1.3% of the predicted proteome) were predicted in the genome of the diatom Thalassiosira pseudonana. The new ASAFind version can also generate a newly designed graphical output that visualizes the contribution of each position in the sequence to the score and accepts the output of the recent versions of SignalP (5.0) and TargetP (2.0) as input data. Furthermore, we release a script to calculate custom scoring matrices that can be used for predictions in a simplified score cut-off mode. This allows for adjustments of the method to other groups of algae.},
}

*Diatoms/metabolism/genetics
*Plastids/metabolism
Proteome
Rhodophyta/metabolism
*Algal Proteins/metabolism
*Software
*Computational Biology/methods

@article {pmid40463036,
year = {2025},
author = {Xu, P and Mancuso, RI and Leonzino, M and Zeiss, CJ and Krause, DS and De Camilli, P},
title = {Defect in hematopoiesis and embryonic lethality at midgestation of Vps13a/Vps13c double knockout mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.09.653147},
pmid = {40463036},
issn = {2692-8205},
abstract = {VPS13 is the founding member of a family of proteins that mediate lipid transfer at intracellular membrane contact sites by a bridge-like mechanism. Mammalian genomes comprise 4 VPS13 genes encoding proteins with distinct localizations and function. The gene duplication resulting in VPS13A and VPS13C is the most recent in evolution and, accordingly, these two proteins are the most similar to each other. However, they have distinct subcellular localizations and their loss of function mutations in humans are compatible with life but result in two different age-dependent neurodegenerative diseases, chorea-acanthocytosis and Parkinson's disease, respectively. Thus, it remains unclear whether these two proteins have overlapping functions. Here, we show that while Vps13a KO and Vps13c KO mice are viable, embryonic development of Vps13a/Vps13c double knockout (DKO) mice is arrested at midgestation. Prior to death, DKO embryos were smaller than controls, were anemic and had a smaller liver, the key erythropoietic site at this developmental stage. Further analyses of erythroid precursor cells showed that their differentiation was impaired and that this defect was accompanied by activation of innate immunity as revealed by upregulation of interferon stimulated genes (ISGs). Additionally, the RIG-I and MDA5 components of dsRNA triggered innate immunity were found upregulated in the DKO fetal liver. Activation of innate immunity may result from loss of integrity of the membranes of intracellular organelles, such as mitochondria and autophagic lysosomes, due to the absence of these lipid transport proteins. The surprising and striking synthetic effect resulting for the combined loss of VPS13A and VPS13C suggests that despite of the different localization of these two proteins, the lipid fluxes that they mediate are partially redundant.},
}

@article {pmid40456292,
year = {2025},
author = {Dormegny-Jeanjean, LC and Lenoir, S and Humbert, I and Mainberger, OAE and Lozere, C and Meyer, C and Geny, B and Michel, B and Foucher, JR and de Crespin de Billy, C},
title = {Cardiovascular Effects of Non-Selective Monoamine Oxidase Inhibitors and Intranasal Esketamine Combination in Depression - A Quasi-Experimental Design with Bayesian Analyses.},
journal = {Pharmacopsychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2590-3469},
pmid = {40456292},
issn = {1439-0795},
abstract = {Ketamine and esketamine (ESK) offer new treatment options for resistant depression. Unlike traditional antidepressants, they can be used in combination with non-selective monoamine oxidase inhibitors (NS-MAOI) without the risk of serotonergic syndrome. However, potential sympathomimetic synergy may lead to elevated blood pressure (BP). This series investigates whether cardiovascular parameters (heart rate, systolic [SP], and diastolic [DP] pressures) increase during ESK sessions and whether the ESK+NS-MAOI combination is associated with BP elevations.We collected cardiovascular parameters for ESK sessions conducted between 2018 and 2022. These parameters were measured at baseline and every 30 min for 2 h. Patients were categorized into two non-equivalent groups: those receiving ESK alone and those receiving ESK+NS-MAOI. A Bayesian random model was used to estimate the evolution of these parameters, while a Bayesian hierarchical model assessed factors contributing to BP elevation.ESK sessions (n=193), of which 116 involved NS-MAOI, were performed in 13 patients. SP, DP, and heart rate showed peak increases during sessions, but these changes were not clinically significant (SP+8.68 mmHg, DP+6.57 mmHg, and heart rate+3.5 bpm). No significant differences were found between the ESK-alone and ESK+NS-MAOI groups. The combination was not identified as a factor linked to BP elevations.These findings align with previous research on ketamine derivatives and suggest minimal peripheric sympathomimetic synergy with NS-MAOI. Bayesian models were used to account for biases intrinsically related to these ecological data and provide a foundation for future open adversarial collaborations. Registration NCT05530668.},
}

@article {pmid40451764,
year = {2025},
author = {Zhu, W and Wu, J and Kang, Y and Xue, P},
title = {Cu2O/CuVO3 Nano-Heterojunction as a Highly Active Therapeutic Catalyst for Aggravating Redox Dyshomeostasis of Neoplastic Cells.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2502407},
doi = {10.1002/adma.202502407},
pmid = {40451764},
issn = {1521-4095},
support = {2024YFFK0249//Key Research and Development Project of Sichuan Provincial Science and Technology Plan/ ; KFKT202405//Open Research Project from Anhui Provincial Key Laboratory of Tumor Evolution and Intelligent Diagnosis and Treatment/ ; 2023YFF0713900//National Key Research and Development Program of China/ ; XNDX2022020013//Shuangcheng Cooperative Agreement Research Grant of Yibin/ ; KJQN202400202//Scientific and Technological Research Program of Chongqing Municipal Education Commission/ ; },
abstract = {Redox dyshomeostasis is both a hallmark and a vulnerability of cancer cells, offering multiple avenues for therapeutic intervention. Herein, a belt-like nano-heterojunction Cu2O/CuVO3 (CVO) is developed as a potential redox dyshomeostasis inducer by exacerbating ROS levels and compromising antioxidant defense without the need of exogenous stimulations. Steady-state analysis reveals that CVO exhibits extraordinary reaction velocity and catalytic efficiency (Vmax = 2.32 µm s[-1], Kcat = 0.49 s[-1]) in the production of hydroxyl radicals (·OH). Likewise, density functional theory (DFT) calculations indicate that the superb charge-transferring properties in the heterojunction structure and unique surface coverage rate of CVO primarily dominate the high-efficient catalytic reactions. Noteworthy, CVO is capable of inducing mitochondria dysfunction by aggravating the cellular redox imbalance, thereby triggering multiple cell death pathways and generating synergistic effects. Transcriptomics analysis outcomes further demonstrate that CVO exerts significant and distinct effects on key biological processes in tumor cells, encompassing but not limited to canonical pathways such as apoptosis, ferroptosis, and cuprotosis. Both in vitro and in vivo studies demonstrate the pronounced tumor-inhibitory efficacy of CVO, which paves a promising pathway for the development of novel nanocatalysts that effectively target cancer through the amplification of redox dyshomeostasis.},
}

@article {pmid40444636,
year = {2025},
author = {Tanouti, Y and Roovers, M and Wolff, P and Lechner, A and Van Elder, D and Feller, A and Soin, R and Gueydan, C and Kruys, V and Droogmans, L and Labar, G},
title = {Structural insight into the novel Thermus thermophilus SPOUT methyltransferase RlmR catalysing Um2552 formation in the 23S rRNA A-loop: a case of convergent evolution.},
journal = {Nucleic acids research},
volume = {53},
number = {10},
pages = {},
pmid = {40444636},
issn = {1362-4962},
support = {//Fonds de la Recherche Scientifique - FNRS/ ; //Fonds Jean Brachet/ ; //French National Program Investissement d'Avenir/ ; ANR-10-LABX-0036_NETRNA//Agence Nationale de la Recherche/ ; //Interdisciplinary Thematic Institute IMCBio/ ; //University of Strasbourg/ ; ANR-10-IDEX-0002//IdEx Unistra/ ; ANR-20-SFRI-0012//IdEx Unistra/ ; ANR-17-EURE-750023//IdEx Unistra/ ; 20210875//French Investments for the Future Program/ ; 20232022//French Investments for the Future Program/ ; //Institut de Recherche LABIRIS-Commission communautaire française-COCOF/ ; },
mesh = {*Thermus thermophilus/enzymology/genetics ; *RNA, Ribosomal, 23S/chemistry/metabolism/genetics ; *Methyltransferases/chemistry/metabolism/genetics ; Evolution, Molecular ; Humans ; Nucleic Acid Conformation ; Escherichia coli/genetics ; Models, Molecular ; *Bacterial Proteins/chemistry/metabolism/genetics ; Crystallography, X-Ray ; Methylation ; },
abstract = {The A-loop of the 23S ribosomal RNA is a critical region of the ribosome involved in stabilizing the CCA-end of A-site-bound transfer RNA. Within this loop, nucleotide U2552 is frequently 2'-O-methylated (Um2552) in various organisms belonging to the three domains of life. Until now, two enzymatic systems are known to modify this position, relying on either a Rossmann fold-like methyltransferase (RFM) or a small RNA-guided system. Here, we report the identification of a third system involved in Um2552 formation, consisting of a methyltransferase of the SPOUT (SpoU-TrmD) superfamily encoded by the ttc1712 open reading frame of Thermus thermophilus, herein renamed RlmR. In Escherichia coli and human mitochondria, the absence of the RFM enzyme responsible for Um2552 formation is known to cause severe defects in ribogenesis and ribosome function. In contrast, no comparable effect was observed upon ttc1712 gene invalidation in T. thermophilus. We also report the high-resolution crystal structure of RlmR in complex with a 59-mer substrate RNA. The structure highlights significant conformational rearrangements of the A-loop and provides a new insight into the catalytic mechanism, revealing structural features that may be generalized to other SpoU methyltransferases.},
}

*Thermus thermophilus/enzymology/genetics
*RNA, Ribosomal, 23S/chemistry/metabolism/genetics
*Methyltransferases/chemistry/metabolism/genetics
Evolution, Molecular
Humans
Nucleic Acid Conformation
Escherichia coli/genetics
Models, Molecular
*Bacterial Proteins/chemistry/metabolism/genetics
Crystallography, X-Ray
Methylation

@article {pmid40441921,
year = {2025},
author = {Liu, F and Zhao, Z and Fernie, AR and Zhang, Y},
title = {Towards establishing functional nitrogenase activities within plants.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.04.020},
pmid = {40441921},
issn = {1879-3096},
abstract = {Biological nitrogen fixation, catalyzed by nitrogenase, can convert atmospheric N2 into NH3 for plant growth. Legumes form symbioses with nitrogen-fixing bacteria, but non-legumes rely on excessive nitrogen fertilizers. Efforts to engineer nitrogenase in non-legumes face major challenges, including oxygen sensitivity, metal cluster assembly complexity, and high energy demands. Nonetheless, advances in synthetic biology, and artificial intelligence (AI)-driven design - shown by partial nitrogenase reconstitution in Escherichia coli and yeast - offer promising solutions. Engineering nitrogenase in yeast mitochondria under low-oxygen conditions also helps circumvent oxygen constraints. Fully overcoming energy costs and feedback loops responsive to nitrogen levels could yield nitrogen-fixing crops, transforming sustainable agriculture and ensuring global food security. Such breakthroughs would reduce fertilizer dependence, cut pollution, and stabilize yields in diverse farming systems.},
}

@article {pmid40432501,
year = {2025},
author = {Macdonald, JR and Arnold, MS and Luth, MR and Cihalova, D and Quinn, RJ and Winzeler, EA and Lee, MC and van Dooren, GG and Maier, AG and Skinner-Adams, TS and Andrews, KT and Fisher, GM},
title = {Inner-mitochondrial membrane protein PfMPV17 is linked to P. falciparum in vitro resistance to the indoloquinolizidine alkaloid alstonine.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1093/jac/dkaf141},
pmid = {40432501},
issn = {1460-2091},
support = {//Griffith University Postgraduate Research Scholarship/ ; //Commonwealth Government Research Training programme/ ; //Griffith University GRIDD ECR/ ; //Ruth L. Kirschstein Institutional National Research Award/ ; T32 GM008666MRL//National Institute for General Medical Sciences/ ; /NH/NIH HHS/United States ; 1R01AI152533//Bill & Melinda Gates Foundation/ ; INV-039628//Bill & Melinda Gates Foundation/ ; GNT1182369//National Health and Medical Research Council/ ; },
abstract = {BACKGROUND: There are an estimated 260 million malaria cases and ∼600 000 deaths annually. Challenges to malaria eradication include the lack of highly effective and broadly applicable vaccines and parasite drug resistance. This is driving the need for new tools, including novel drugs and drug targets. The indoloquinolizidine alkaloid alstonine was previously shown to have in vitro activity against Plasmodium falciparum malaria parasites and a slow-action activity that is different from other slow-action antiplasmodial compounds such as clindamycin.

OBJECTIVES: To investigate the action of the antiplasmodial compound alstonine by validating a putative resistance mutation and determining whether the activity of alstonine is linked to the mitochondrial electron transport chain.

MATERIALS AND METHODS: In vitro evolution of resistance was used to generate alstonine-resistant P. falciparum, followed by whole-genome sequencing and CRISPR/Cas9 gene editing of wildtype parasites to validate a putative resistance-associated mutation. Links to mitochondrial function were assessed using oxygen consumption rate measurements and activity of alstonine in P. falciparum expressing the yeast dihydroorotate dehydrogenase.

RESULTS: P. falciparum parasites were selected with ∼20-fold reduced sensitivity to alstonine compared to wild-type parasites. Whole-genome sequencing of alstonine-resistant P. falciparum sub-clones identified several mutations including a copy number variation and point mutation (A318P) in a gene encoding a putative inner-mitochondrial membrane protein (PfMPV17). Introduction of the A318P mutation into the PfMPV17 gene in wild-type P. falciparum yielded parasites with reduced alstonine sensitivity. While a direct link between alstonine action and mitochondrial respiratory function was not found, a transgenic P. falciparum line resistant to the cytochrome bc1 inhibitor atovaquone and pyrimidine synthesis inhibitor DSM265 had reduced sensitivity to alstonine.

CONCLUSIONS: These data demonstrate that PfMPV17 is linked to alstonine resistance and suggest that alstonine action is linked to the mitochondria and/or pyrimidine biosynthesis pathways.},
}

@article {pmid40427588,
year = {2025},
author = {Luo, Y and Bähler, J and Huang, Y},
title = {The Insertion Domain of Mti2 Facilitates the Association of Mitochondrial Initiation Factors with Mitoribosomes in Schizosaccharomyces pombe.},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
pmid = {40427588},
issn = {2218-273X},
support = {302608/Z/23/Z//Wellcome Discovery Award/ ; },
mesh = {*Schizosaccharomyces/metabolism/genetics ; *Schizosaccharomyces pombe Proteins/metabolism/genetics/chemistry ; *Mitochondrial Proteins/metabolism/genetics/chemistry ; *Mitochondrial Ribosomes/metabolism ; *Mitochondria/metabolism/genetics ; Protein Domains ; *Peptide Initiation Factors/metabolism/genetics/chemistry ; },
abstract = {Translation initiation in mitochondria involves unique mechanisms distinct from those in the cytosol or in bacteria. The Schizosaccharomyces pombe mitochondrial translation initiation factor 2 (Mti2) is the ortholog of human MTIF2, which plays a vital role in synthesizing proteins in mitochondria. Here, we investigate the insertion domain of Mti2, which stabilizes its interaction with the ribosome and is crucial for efficient translation initiation. Our results show that the insertion domain is critical for the proper folding and function of Mti2. The absence of the insertion domain disrupts cell growth and affects the expression of genes encoded by mitochondrial DNA. Additionally, we show that Mti2 physically interacts with the small subunits of mitoribosomes (mtSSU), and deletion of the insertion domain dissociates mitochondrial initiation factors from the mitoribosome, reducing the efficiency of mitochondrial translation. Altogether, these findings highlight the conserved role of the insertion domain in facilitating translation initiation in fission yeast and thus reveal shared principles of mitochondrial translation initiation in both fission yeast and humans.},
}

*Schizosaccharomyces/metabolism/genetics
*Schizosaccharomyces pombe Proteins/metabolism/genetics/chemistry
*Mitochondrial Proteins/metabolism/genetics/chemistry
*Mitochondrial Ribosomes/metabolism
*Mitochondria/metabolism/genetics
Protein Domains
*Peptide Initiation Factors/metabolism/genetics/chemistry

@article {pmid40419126,
year = {2025},
author = {Bernier, D and Grafl, N and Gnauck, J and Betat, H and Dengler, S and Huc, I and Mörl, M},
title = {Armless hairpin-like tRNAs in Romanomermis culicivorax: evolutionary adaptation of a mitochondrial elongation factor EF-Tu.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {110294},
doi = {10.1016/j.jbc.2025.110294},
pmid = {40419126},
issn = {1083-351X},
abstract = {tRNAs are central players in translation, delivering cognate amino acids to the ribosome. To fulfill this essential function, secondary and tertiary structures of tRNAs are highly conserved. In metazoan, however, several mitochondrial tRNAs show strong structural deviations and lack D- or T-arms. As these elements are important for the interaction with tRNA-binding proteins, these proteins are adapted to recognize such unusual targets. A prominent example is mitochondrial EF-Tu, delivering aminoacylated tRNAs to the ribosome. In nematode mitochondria, two variants of mt-EF-Tu exist. While mt-EF-Tu2 is specific for D-armless mt-tRNA[Ser], mt-EF-Tu1 recognizes the remaining 20 tRNAs. The most bizarre mt-tRNAs are found in Romanomermis culicivorax, where hairpin-like structures were described lacking both D- and T-arm. To ensure functional translation with such extremely reduced tRNAs, the corresponding mt-EF-Tu1 must have undergone a further adaptation. In a comparative analysis, the tRNA binding behavior of recombinant mitochondrial EF-Tu1 versions from several nematodes was investigated. They all carry a C-terminal extension that is required for an efficient interaction with non-canonical tRNAs. Furthermore, in mt-EF-Tu1 from R. culicivorax and C. elegans, a basic residue in domain III was identified that represents an additional adaptation in the transition from canonical towards hairpin-like tRNA substrates. The results indicate that nematode mt-EF-Tu1 proteins are in principle able to interact with hairpin-like tRNAs, although such transcripts are only found in some of these species. Hence, concerning mt-EF-Tu, the evolutionary stage is set for a further truncation of mitochondrial tRNAs towards armless structures.},
}

@article {pmid40406718,
year = {2025},
author = {Zhang, R and Liu, S and Liu, Y and Wei, P and Xiang, N and Zhao, Y and Gao, X and Yin, Y and Qin, L and Yuan, T},
title = {Comparative analysis of the organelle genomes of seven Rosa species (Rosaceae): insights into structural variation and phylogenetic position.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1584289},
pmid = {40406718},
issn = {1664-462X},
abstract = {INTRODUCTION: The genus Rosa belongs to the family Rosaceae within the order Rosales, which is one of the more ancient plant lineages. At present, the complete mitochondrial genome of Rosa spp. is still rarely reported, and studies on the mitochondrial genome of Rosa spp. are limited.

METHODS: In this study, the R. laevigata mitochondrial genome was sequenced using both Pacbio Sequel II and DNB-SEQ-T7 platforms. The second- and third-generation data for the other five Rosa species were downloaded from the NCBI database. Genome annotation was performed using Geneious, with structural visualization via CPGview. In-depth analyses were conducted, including assessments of non-synonymous/synonymous mutation ratios (Ka/Ks), codon usage bias, collinearity, and the identification of homologous fragments between chloroplast and mitochondrial genomes. Finally, we employed the maximum likelihood (ML) methods to analyze the phylogenetic relationships among R. laevigata and other Rosa species.

RESULTS: The chloroplast genome sizes ranged from 156,342 bp (R. laevigata) to 157,214 bp (R. agrestis). The GC content varied from 37.2% to 37.3%, and the number of genes ranged from 129 to 131. The mitochondrial genomes were all circular, with lengths between 271,191 bp and 338,975 bp, containing 52 to 59 genes. Codon usage analysis indicated a preference for A/T-ending codons in both chloroplast and mitochondrial genes. Four highly differentiated regions (rps19, ndhF, ycf1, and psbM-trnD-GUC) in the plastomes of the 7 Rosa species were identified, which can serve as molecular markers for future species identification and studies of genetic diversity. Compared to PCGs of plastome, mitochondrial PCGs displayed a higher non-synonymous to synonymous ratio. We also observed extensive gene transfer between the mitochondria and chloroplasts, particularly with the rrn16 and rpl23 genes, which are commonly found in Rosa species. These gene transfer events likely occurred in the ancestor of Rosa around 4.46 Mya. Estimates of divergence events indicate that rapid differentiation among Rosa species took place around 4.46 Mya, potentially influenced by the uplift of the Qinghai-Tibet Plateau during the Late Miocene.

DISCUSSION: This study enriches the genetic resources of the Rosa genus and lays the groundwork for the development of molecular markers, phylogenetic analyses, and research into the evolution of organelle genomes.},
}

@article {pmid40394395,
year = {2025},
author = {Sekine, H and Akaike, T and Motohashi, H},
title = {Oxygen needs sulfur, sulfur needs oxygen: a relationship of interdependence.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40394395},
issn = {1460-2075},
support = {18H05277//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23H02672//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21H05263//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22K19397//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K20040//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 24H00063//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21H04799//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21H05258//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21H05264//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 24H00605//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJCR2024//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JP24gm6710026//Japan Agency for Medical Research and Development (AMED)/ ; },
abstract = {Oxygen and sulfur, both members of the chalcogen group (group 16 elements), play fundamental roles in life. Ancient organisms primarily utilized sulfur for energy metabolism, while the rise in atmospheric oxygen facilitated the evolution of aerobic organisms, enabling highly efficient energy production. Nevertheless, all modern organisms, both aerobes and anaerobes, must protect themselves from oxygen toxicity. Interestingly, aerobes still rely on sulfur for survival. This dependence has been illuminated by the recent discovery of supersulfides, a novel class of biomolecules, made possible through advancements in technology and analytical methods. These breakthroughs are reshaping our understanding of biological processes and emphasizing the intricate interplay between oxygen and sulfur in regulating essential redox reactions. This review summarizes the latest insights into the biological roles of sulfur and oxygen, their interdependence in key processes, and their contributions to adaptive responses to environmental stressors. By exploring these interactions, we aim to provide a comprehensive perspective on how these elements drive survival strategies across diverse life forms, highlighting their indispensable roles in both human health and the sustenance of life.},
}

@article {pmid40392717,
year = {2025},
author = {Bryner, J},
title = {Hopeful Sunshine and Quantum Bubbles: The June 2025 issue of Scientific American is packed with exciting features, from magnificent mitochondria and a plan to refreeze the Arctic to the universe's first light and recent human evolution.},
journal = {Scientific American},
volume = {332},
number = {6},
pages = {4},
doi = {10.1038/scientificamerican062025-YZxzd1kSxUa63TFsqt7QZ},
pmid = {40392717},
issn = {0036-8733},
}

@article {pmid40388856,
year = {2025},
author = {Liu, J and Pan, L and Cheng, Y and Ruan, M and Ye, Q and Wang, R and Yao, Z and Zhou, G and Liu, C and Wan, H},
title = {Evolution and functional roles of neutral/alkaline invertases in plant growth, development, and stress response.},
journal = {Plant physiology and biochemistry : PPB},
volume = {225},
number = {},
pages = {110011},
doi = {10.1016/j.plaphy.2025.110011},
pmid = {40388856},
issn = {1873-2690},
abstract = {Neutral/alkaline invertases (N/A-Invs) are crucial enzymes in sucrose metabolism, playing essential roles in plant growth, development, and stress responses. Unlike acidic invertases, N/A-Invs are localized in various subcellular compartments, including the cytoplasm, mitochondria, chloroplasts, and plastids, with distinct functions in each organelle. These enzymes regulate sugar homeostasis and are involved in key processes such as root development, carbon partitioning, and osmotic stress responses. Recent studies have identified two subfamilies of N/A-Invs, α and β, with the β subfamily being more conserved and primarily localized in the cytoplasm, whereas the α subfamily is associated with mitochondria and plastids. Despite significant advances, many aspects of N/A-Invs remain unclear, particularly their interaction with signaling pathways and their differential roles across plant species. Future research should focus on understanding the molecular mechanisms underlying N/A-Invs' regulation, their evolutionary history, and their potential applications in improving crop resilience and productivity. This growing body of knowledge promises to enhance our understanding of plant physiology and offer insights into agricultural biotechnology.},
}

@article {pmid40384044,
year = {2025},
author = {Harada, R and Shiratori, T and Yabuki, A and Inagaki, Y and Roger, AJ and Kamikawa, R},
title = {Complete Mitochondrial Genomes of Ancyromonads Provide Clues for the Gene Content and Genome Structures of Ancestral Mitochondria.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {3},
pages = {e70012},
pmid = {40384044},
issn = {1550-7408},
support = {18J02091//Japan Society for the Promotion of Science/ ; 22KJ0401//Japan Society for the Promotion of Science/ ; 24K21929//Japan Society for the Promotion of Science/ ; 23K27226//Japan Society for the Promotion of Science/ ; BPI06050//Japan Society for the Promotion of Science/ ; RGPIN-2022-05430//Natural Sciences and Engineering Research Council of Canada/ ; G-2024-1-011//Institute for Fermentation, Osaka/ ; //World Premier International Research Center Initiative/ ; },
mesh = {*Genome, Mitochondrial ; Phylogeny ; Evolution, Molecular ; *Mitochondria/genetics ; Eukaryota/genetics ; },
abstract = {Mitochondria of eukaryotic cells are direct descendants of an endosymbiotic bacterium related to Alphaproteobacteria. These organelles retain their own genomes, which are highly reduced and divergent when compared to those of their bacterial relatives. To better understand the trajectory of mitochondrial genome evolution from the last eukaryotic common ancestor (LECA) to extant species, mitochondrial genome sequences from phylogenetically diverse lineages of eukaryotes-particularly protists-are essential. For this reason, we focused on the mitochondrial genomes of Ancyromonadida, an independent and understudied protist lineage in the eukaryote tree of life. Here we report the mitochondrial genomes from three Ancyromonadida: Ancyromonas sigmoides, Nutomonas longa, and Fabomonas tropica. Our analyses reveal that these mitochondrial genomes are circularly mapping molecules with inverted repeats that carry genes. This inverted repeat structure has been observed in other mitochondrial genomes but is patchily distributed over the tree of eukaryotes. Ancyromonad mitochondrial genomes possess several protein-coding genes, which have not been detected from any other mitochondrial genomes of eukaryotes sequenced to date, thereby extending the known mitochondrial gene repertoire of ancestral eukaryotes, including LECA. These findings significantly expand our understanding of mitochondrial genome diversity across eukaryotes, shedding light on the early phases of mitochondrial genome evolution.},
}

*Genome, Mitochondrial
Phylogeny
Evolution, Molecular
*Mitochondria/genetics
Eukaryota/genetics

@article {pmid40373020,
year = {2025},
author = {Mu, W and Liu, J and Zhang, H},
title = {Characterization of the complete mitochondrial genomes of two sea cucumbers, Deima validum and Oneirophanta mutabilis (Holothuroidea, Synallactida, Deimatidae): Insight into deep-sea adaptive evolution of Deimatidae.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323612},
pmid = {40373020},
issn = {1932-6203},
mesh = {Animals ; *Genome, Mitochondrial ; *Sea Cucumbers/genetics/classification ; Phylogeny ; *Evolution, Molecular ; RNA, Transfer/genetics ; *Adaptation, Physiological/genetics ; },
abstract = {The deep-sea is the largest and most extensive ecosystem on our planet with limited food availability, extreme pressure reaching hundreds of bars, perpetual darkness, frigid temperatures, and minimal oxygen levels. Mitochondria plays a key role in energy metabolism and oxygen usage, thus it may undergo adaptive evolution in response to pressures from extreme harsh environments. In this study, we present the mitochondrial genome sequences of the sea cucumbers Deima validum and Oneirophanta mutabilis collected from the South China Sea. To our knowledge, they are the first reported mitogenomes from the family Deimatidae. Similar to other sea cucumbers, both mitogenomes contain 13 PCGs, 2 rRNA genes, 22 tRNA genes (including duplication of trnS and trnL) and 1 non-coding regions. The genes in both species are distributed on the positive and negative strands, with six genes encoded on the L-strand and 31 genes encoded on the H-strand. We compared the order of genes from the 13 available holothurian mitogenomes and found a novel gene arrangement in D. validum. Phylogenetic analysis revealed that D. validum clustered with O. mutabilis, forming the deep-sea Deimatidae clade. The analysis of individual genes revealed the presence of three sites (90 L, 147 S, 192 V) in nad2 and one site (28 S) in nad5 with high posterior probabilities indicating positive selection. By comparing these features with those of shallow sea cucumbers, we predict that nad2 and nad5 may provide valuable insights into the molecular mechanisms at the mitochondrial level involved in Deimatidae's adaptation to the deep-sea habitat.},
}

Animals
*Genome, Mitochondrial
*Sea Cucumbers/genetics/classification
Phylogeny
*Evolution, Molecular
RNA, Transfer/genetics
*Adaptation, Physiological/genetics

@article {pmid40359376,
year = {2025},
author = {Belinchon-Moreno, J and Berard, A and Canaguier, A and Le-Clainche, I and Rittener-Ruff, V and Lagnel, J and Hinsinger, D and Boissot, N and Faivre-Rampant, P},
title = {Nuclear and organelle genome assemblies of five Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais and Zhimali, belonging to diverse botanical groups.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf098},
pmid = {40359376},
issn = {2160-1836},
abstract = {The construction of accurate whole genome sequences is pivotal for characterizing the genetic diversity of plant species, identifying genes controlling important traits, or understanding their evolutionary dynamics. Here, we generated the nuclear, mitochondrial and chloroplast high-quality assemblies of five melon (Cucumis melo L.) accessions representing five botanical groups, using the Oxford Nanopore sequencing technology. The accessions here studied included varied origins, fruit shapes, sizes, and resistance traits, providing a holistic view of melon genomic diversity. The final chromosome-level genome assemblies ranged in size from 359 to 365 Mb, with approximately 25× coverage for four of them multiplexed in half of a PromethION flowcell, and 48× coverage for the fifth, sequenced individually in another half of a PromethION flowcell. Contigs N50 ranged from seven to 15 Mb for all the assemblies, and very long contigs reaching sizes of 20-25 Mb, almost compatible with complete chromosomes, were assembled in all the accessions. Quality assessment through BUSCO and Merqury indicated the high completeness and accuracy of the assemblies, with BUSCO values exceeding 96% for all accessions, and Merqury QV values ranging between 41 and 47. We focused on the complex NLR resistance gene regions to validate the accuracy of the assemblies in highly complex and repetitive regions. Through Nanopore adaptive sampling, we generated accurate targeted assemblies of these regions with a significantly higher coverage, enabling the comparison to our whole genome assemblies. Overall, these chromosome-level assembled genomes constitute a valuable resource for research focused on melon diversity, disease resistance, evolution, and breeding applications.},
}

@article {pmid40359151,
year = {2025},
author = {Garlovsky, MD and Dobler, R and Guo, R and Voigt, S and Dowling, DK and Reinhardt, K},
title = {Testing for age- and sex- specific mitonuclear epistasis in Drosophila.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpaf096},
pmid = {40359151},
issn = {1558-5646},
abstract = {The need for efficient ATP production is predicted to result in the evolution of cooperation between the mitochondrial and nuclear encoded components of the electron transport system. Genotypes where mitochondrial and nuclear genomes from different geographic populations are combined (mismatched), are therefore predicted to result in negative fitness consequences. Such negative fitness effects are expected to be prominent in males, since maternal inheritance of mitochondria can lead to accumulation of male-harming mutations (the mother's curse hypothesis), and they may become more prevalent with ageing. To test these predictions, we measured fertility traits of females and males at different ages using a genetically diverse panel of 27 mitonuclear populations of Drosophila melanogaster with matched or experimentally mismatched mitonuclear genomes. We found no evidence that novel mitonuclear combinations had reduced fitness in females. In males, we found limited evidence of mitonuclear interactions affecting fitness in old age, however, not in the direction predicted. Novel mitonuclear combinations were associated with males that sired more offspring. Sex-specific advantages of mismatched males might arise if novel nuclear alleles compensate for deleterious mitochondrial alleles that have accumulated. If such compensatory effects of novel mitonuclear combinations increasing fitness occur in nature, they could represent a possible counterforce to the mother's curse.},
}

@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 {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 {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 {pmid40305847,
year = {2025},
author = {Sarkar, M and Pucadyil, TJ},
title = {Division of Labor among Fission Dynamins Based on Substrate Size.},
journal = {Biochemistry},
volume = {64},
number = {10},
pages = {2117-2122},
doi = {10.1021/acs.biochem.4c00862},
pmid = {40305847},
issn = {1520-4995},
mesh = {Humans ; *Dynamins/metabolism/chemistry ; Animals ; Guanosine Triphosphate/metabolism ; Organelles/metabolism ; },
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.},
}

Humans
*Dynamins/metabolism/chemistry
Animals
Guanosine Triphosphate/metabolism
Organelles/metabolism

@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 {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 {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},
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 {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 {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 {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 {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},
mesh = {*Phylogeny ; Animals ; *Oxidative Phosphorylation ; *Evolution, Molecular ; Cell Nucleus/genetics ; *Lizards/genetics/classification ; Mitochondria/genetics ; Snakes/genetics/classification ; Genome, Mitochondrial ; },
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.},
}

*Phylogeny
Animals
*Oxidative Phosphorylation
*Evolution, Molecular
Cell Nucleus/genetics
*Lizards/genetics/classification
Mitochondria/genetics
Snakes/genetics/classification
Genome, Mitochondrial

@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 {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 {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 {pmid40199161,
year = {2025},
author = {Xia, J and Ma, R and Cai, Y and Xie, T and Zhang, Y and Lv, M and Liu, Y and You, H and Zhang, C and Yu, D and Hua, X},
title = {The functional conservation of SSR1 homologs in plants.},
journal = {Plant physiology and biochemistry : PPB},
volume = {223},
number = {},
pages = {109855},
doi = {10.1016/j.plaphy.2025.109855},
pmid = {40199161},
issn = {1873-2690},
mesh = {*Arabidopsis Proteins/metabolism/genetics/chemistry ; *Arabidopsis/metabolism/genetics ; *Mitochondrial Proteins/metabolism/genetics/chemistry ; Amino Acid Sequence ; Phylogeny ; Mitochondria/metabolism ; Plant Proteins/metabolism/genetics ; Bryopsida/genetics/metabolism ; },
abstract = {AtSSR1 (Arabidopsis thaliana short and swollen root 1) is a plant-specific gene that encodes a mitochondrial protein containing TPR (tetratricopeptide repeat) domains, and was shown to be required for maintaining mitochondrial function. However, the evolution of its function in the plant lineage is not known. In this paper, SSR1 homologs were cloned from seven representative plant species ranging from lower to higher plants. Their structural and functional conservation were characterized in detail. The results demonstrated that most of the SSR1 homologs are predicted to have mitochondrial localization except for the one from Physcomitrella patens and all of them possess various numbers of TPR domains. Upon introduction into the Arabidopsis ssr1-2 knock-out mutant, all SSR1 homologs were capable of fully rescuing the short-root and stress hypersensitive phenotype of the mutant. In addition, in vitro pull-down analysis showed that similar to AtSSR1, the selected SSR1 homologs were also able to interact with AtHSCA2 and AtISU1, two components of mitochondrial iron-sulfur cluster assembly pathway, suggesting that SSR1 homologs from various plant species are functionally conserved. Despite the conserved function, different SSR1 homologs shared relatively low sequence identity with AtSSR1. Instead, their 3D structures display a common feature of a globular shape, mainly dominated by α-helices and two β-sheets embedded in the center. Taken together, our results suggest that SSR1, as a plant-specific mitochondrial protein, might have complete functionality in plant development and stress response already in the early stage of plant evolution.},
}

*Arabidopsis Proteins/metabolism/genetics/chemistry
*Arabidopsis/metabolism/genetics
*Mitochondrial Proteins/metabolism/genetics/chemistry
Amino Acid Sequence
Phylogeny
Mitochondria/metabolism
Plant Proteins/metabolism/genetics
Bryopsida/genetics/metabolism

@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 = {},
pmid = {40196624},
issn = {2692-8205},
support = {R01 AI144369/AI/NIAID NIH HHS/United States ; R01 AI158501/AI/NIAID NIH HHS/United States ; R35 GM126930/GM/NIGMS NIH HHS/United States ; R24 DK094746/DK/NIDDK NIH HHS/United States ; R01 DK087992/DK/NIDDK NIH HHS/United States ; },
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 {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 {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 = {40},
number = {5},
pages = {956-961},
doi = {10.1093/humrep/deaf050},
pmid = {40174913},
issn = {1460-2350},
support = {//Association Française contre les Myopathies/ ; //Université Paris Cité/ ; },
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Preimplantation Diagnosis/methods ; Female ; *Blastocyst/metabolism ; *Embryonic Development/genetics ; *Mitochondrial Diseases/genetics/diagnosis ; *Genetic Testing/methods ; Pregnancy ; Heteroplasmy ; Blastomeres ; },
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.},
}

Humans
*DNA, Mitochondrial/genetics
*Preimplantation Diagnosis/methods
Female
*Blastocyst/metabolism
*Embryonic Development/genetics
*Mitochondrial Diseases/genetics/diagnosis
*Genetic Testing/methods
Pregnancy
Heteroplasmy
Blastomeres

@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 = {207},
number = {},
pages = {108345},
doi = {10.1016/j.ympev.2025.108345},
pmid = {40174813},
issn = {1095-9513},
mesh = {*Phylogeny ; *Ciliophora/genetics/classification/metabolism ; Anaerobiosis ; *Transcriptome ; *Evolution, Molecular ; Mitochondria/genetics/metabolism ; Biological Evolution ; },
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 metabolisms. 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.},
}

*Phylogeny
*Ciliophora/genetics/classification/metabolism
Anaerobiosis
*Transcriptome
*Evolution, Molecular
Mitochondria/genetics/metabolism
Biological Evolution

@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 = {34},
number = {9},
pages = {e17744},
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/ ; },
mesh = {Animals ; *Feathers/metabolism ; *Finches/genetics/metabolism/physiology ; *Carotenoids/metabolism ; *Pigmentation/genetics ; *Cytochrome P-450 Enzyme System/genetics/metabolism ; },
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.},
}

Animals
*Feathers/metabolism
*Finches/genetics/metabolism/physiology
*Carotenoids/metabolism
*Pigmentation/genetics
*Cytochrome P-450 Enzyme System/genetics/metabolism

@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/genetics/drug therapy/metabolism/pathology ; *Vemurafenib/pharmacology ; *Mitochondria/metabolism/drug effects ; Cell Line, Tumor ; *GTP Phosphohydrolases/genetics/metabolism ; *Membrane Proteins/genetics ; *Mutation ; *MAP Kinase Signaling System/drug effects ; Mitochondrial Dynamics/drug effects ; Dynamins/metabolism/genetics ; Mitochondrial Proteins/metabolism/genetics ; Cell Proliferation/drug effects ; Drug Resistance, Neoplasm/drug effects ; },
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/genetics/drug therapy/metabolism/pathology
*Vemurafenib/pharmacology
*Mitochondria/metabolism/drug effects
Cell Line, Tumor
*GTP Phosphohydrolases/genetics/metabolism
*Membrane Proteins/genetics
*Mutation
*MAP Kinase Signaling System/drug effects
Mitochondrial Dynamics/drug effects
Dynamins/metabolism/genetics
Mitochondrial Proteins/metabolism/genetics
Cell Proliferation/drug effects
Drug Resistance, Neoplasm/drug effects

@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/classification ; *Genome, Mitochondrial ; *Evolution, Molecular ; *Gene Duplication ; Phylogeny ; China ; RNA, Transfer/genetics ; *Genomics/methods ; },
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/classification
*Genome, Mitochondrial
*Evolution, Molecular
*Gene Duplication
Phylogeny
China
RNA, Transfer/genetics
*Genomics/methods

@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 = {207},
number = {},
pages = {108340},
doi = {10.1016/j.ympev.2025.108340},
pmid = {40127832},
issn = {1095-9513},
mesh = {Animals ; *Phylogeny ; Whole Genome Sequencing ; Evolution, Molecular ; *Fishes/genetics/classification ; Genome, Mitochondrial ; },
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.},
}

Animals
*Phylogeny
Whole Genome Sequencing
Evolution, Molecular
*Fishes/genetics/classification
Genome, Mitochondrial

@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 {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},
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 {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 = {42},
number = {4},
pages = {},
pmid = {40114504},
issn = {1537-1719},
support = {R35 GM142836/GM/NIGMS NIH HHS/United States ; 1R35GM142836/NH/NIH HHS/United States ; //Stengl-Wyer Endowment/ ; },
mesh = {Animals ; *Selection, Genetic ; *DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Altitude ; Genome, Mitochondrial ; Fishes/genetics ; Vertebrates/genetics ; Arthropods/genetics ; Adaptation, Biological/genetics ; Biological Evolution ; Adaptation, Physiological/genetics ; },
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 selection, 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.},
}

Animals
*Selection, Genetic
*DNA, Mitochondrial/genetics
*Evolution, Molecular
Altitude
Genome, Mitochondrial
Fishes/genetics
Vertebrates/genetics
Arthropods/genetics
Adaptation, Biological/genetics
Biological Evolution
Adaptation, Physiological/genetics

@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 = {35},
number = {4},
pages = {900-913},
pmid = {40107722},
issn = {1549-5469},
support = {U24 CA180922/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Single-Cell Analysis/methods ; *Polymorphism, Single Nucleotide ; DNA Copy Number Variations ; Female ; *Ovarian Neoplasms/genetics/pathology ; *Sequence Analysis, RNA/methods ; *Neoplasms/genetics ; Computational Biology/methods ; },
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.},
}

Humans
*Single-Cell Analysis/methods
*Polymorphism, Single Nucleotide
DNA Copy Number Variations
Female
*Ovarian Neoplasms/genetics/pathology
*Sequence Analysis, RNA/methods
*Neoplasms/genetics
Computational Biology/methods

@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 noncanonical tRNA substrates in Ascaris suum.},
journal = {The Journal of biological chemistry},
volume = {301},
number = {4},
pages = {108414},
pmid = {40107618},
issn = {1083-351X},
mesh = {*Ascaris suum/enzymology/genetics ; Animals ; *RNA, Transfer/metabolism/chemistry/genetics ; *RNA Nucleotidyltransferases/metabolism/genetics/chemistry ; Substrate Specificity ; *Helminth Proteins/metabolism/genetics/chemistry ; Peptide Elongation Factor Tu/metabolism/genetics/chemistry ; },
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 coevolution 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 indicate that these enzymes evolved two distinct strategies to tolerate noncanonical 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.},
}

*Ascaris suum/enzymology/genetics
Animals
*RNA, Transfer/metabolism/chemistry/genetics
*RNA Nucleotidyltransferases/metabolism/genetics/chemistry
Substrate Specificity
*Helminth Proteins/metabolism/genetics/chemistry
Peptide Elongation Factor Tu/metabolism/genetics/chemistry

@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 = {35},
number = {6},
pages = {1337-1352.e5},
doi = {10.1016/j.cub.2025.02.033},
pmid = {40081380},
issn = {1879-0445},
mesh = {*Trypanosoma brucei brucei/genetics/metabolism/physiology ; *Mitochondrial Membranes/metabolism ; *Dynamins/metabolism/genetics ; *Protozoan Proteins/metabolism/genetics ; Mitochondrial Dynamics ; Mitochondria/metabolism ; Phylogeny ; },
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.},
}

*Trypanosoma brucei brucei/genetics/metabolism/physiology
*Mitochondrial Membranes/metabolism
*Dynamins/metabolism/genetics
*Protozoan Proteins/metabolism/genetics
Mitochondrial Dynamics
Mitochondria/metabolism
Phylogeny

@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/enzymology ; Phylogeny ; *Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; *Haplotypes ; *Hexokinase/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; Genomics/methods ; 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/enzymology
Phylogeny
*Gene Expression Regulation, Plant
*Stress, Physiological/genetics
*Haplotypes
*Hexokinase/genetics/metabolism
*Plant Proteins/genetics/metabolism
Genomics/methods
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/cytology ; Mice ; *Meiosis/genetics ; Humans ; Swine ; *Gene Expression Profiling ; *Transcriptome ; Female ; 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/cytology
Mice
*Meiosis/genetics
Humans
Swine
*Gene Expression Profiling
*Transcriptome
Female
Species Specificity

@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 = {36},
number = {5},
pages = {ar55},
pmid = {40072502},
issn = {1939-4586},
support = {R01 GM129153/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Wasps/metabolism ; *Germ Cells/metabolism/ultrastructure ; Ribonucleoproteins/metabolism ; Female ; Insect Proteins/metabolism ; RNA, Messenger/metabolism ; Cytoplasmic Granules/metabolism/ultrastructure ; Microscopy, Electron, Transmission ; },
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 (TEM) 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. Homologues 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 endoplasmic reticulum (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 subgranular 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.},
}

Animals
*Wasps/metabolism
*Germ Cells/metabolism/ultrastructure
Ribonucleoproteins/metabolism
Female
Insect Proteins/metabolism
RNA, Messenger/metabolism
Cytoplasmic Granules/metabolism/ultrastructure
Microscopy, Electron, Transmission

@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 = {59},
number = {10},
pages = {5223-5236},
pmid = {40056111},
issn = {1520-5851},
mesh = {*Microplastics/toxicity ; *Sunscreening Agents ; Photolysis ; Water Pollutants, Chemical/toxicity ; },
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.},
}

*Microplastics/toxicity
*Sunscreening Agents
Photolysis
Water Pollutants, Chemical/toxicity

@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},
pmid = {40043709},
issn = {2666-979X},
mesh = {Humans ; Tibet ; *Erythropoiesis/genetics ; Altitude ; Calcium/metabolism ; Mitochondria/metabolism ; Quantitative Trait Loci/genetics ; Polymorphism, Single Nucleotide/genetics ; *Adaptation, Physiological/genetics ; Male ; Transcription, Genetic ; Female ; 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
Tibet
*Erythropoiesis/genetics
Altitude
Calcium/metabolism
Mitochondria/metabolism
Quantitative Trait Loci/genetics
Polymorphism, Single Nucleotide/genetics
*Adaptation, Physiological/genetics
Male
Transcription, Genetic
Female
East Asian People

@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 = {112},
number = {4},
pages = {952-962},
pmid = {40043708},
issn = {1537-6605},
mesh = {Humans ; Female ; *Hearing Loss, Sensorineural/genetics/pathology ; *Primary Ovarian Insufficiency/genetics/pathology ; Child ; Alleles ; Child, Preschool ; Pedigree ; Male ; *Ribosomal Proteins/genetics ; *Mitochondrial Proteins/genetics ; Oxidative Phosphorylation ; Adolescent ; Phenotype ; Adult ; *Gonadal Dysgenesis, 46,XX/genetics ; Mutation ; Infant ; },
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.},
}

Humans
Female
*Hearing Loss, Sensorineural/genetics/pathology
*Primary Ovarian Insufficiency/genetics/pathology
Child
Alleles
Child, Preschool
Pedigree
Male
*Ribosomal Proteins/genetics
*Mitochondrial Proteins/genetics
Oxidative Phosphorylation
Adolescent
Phenotype
Adult
*Gonadal Dysgenesis, 46,XX/genetics
Mutation
Infant

@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},
pmid = {40037840},
issn = {1549-5469},
mesh = {Animals ; *Gene Expression Regulation, Developmental ; *Vertebrates/genetics/growth & development ; *Genes, Mitochondrial ; *Mitochondria/genetics/metabolism ; *Cell Nucleus/genetics ; Oxidative Phosphorylation ; Transcription Factors/genetics ; Chickens/genetics ; Zebrafish/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/growth & development
*Genes, Mitochondrial
*Mitochondria/genetics/metabolism
*Cell Nucleus/genetics
Oxidative Phosphorylation
Transcription Factors/genetics
Chickens/genetics
Zebrafish/genetics

@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/metabolism ; *Stress, Physiological/genetics ; Phylogeny ; *Gene Expression Regulation, Plant ; *Formins/genetics ; *Plant Proteins/genetics/metabolism ; *Multigene Family ; Gene Expression Profiling ; Genome, 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/metabolism
*Stress, Physiological/genetics
Phylogeny
*Gene Expression Regulation, Plant
*Formins/genetics
*Plant Proteins/genetics/metabolism
*Multigene Family
Gene Expression Profiling
Genome, Plant

@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},
support = {P40 OD010964/OD/NIH HHS/United States ; },
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 = {Animals ; Humans ; Male ; Phenotype ; Female ; Drosophila melanogaster/genetics ; *Cataract/genetics/pathology/congenital ; Alleles ; *Drosophila Proteins/genetics ; RNA Interference ; Mutation ; Pedigree ; *Cardiomyopathy, Hypertrophic/genetics/pathology ; *Acidosis, Lactic/genetics/pathology ; Disease Models, Animal ; Adult ; Mitochondria/pathology/genetics ; },
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.},
}

Animals
Humans
Male
Phenotype
Female
Drosophila melanogaster/genetics
*Cataract/genetics/pathology/congenital
Alleles
*Drosophila Proteins/genetics
RNA Interference
Mutation
Pedigree
*Cardiomyopathy, Hypertrophic/genetics/pathology
*Acidosis, Lactic/genetics/pathology
Disease Models, Animal
Adult
Mitochondria/pathology/genetics

@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 ; *Evolution, Molecular ; Selection, Genetic ; *Adaptation, Physiological/genetics ; Phylogeny ; Phenotype ; },
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
*Evolution, Molecular
Selection, Genetic
*Adaptation, Physiological/genetics
Phylogeny
Phenotype

@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.},
}