bims-mirnam Biomed News
on Mitochondrial RNA metabolism
Issue of 2025–12–21
eighteen papers selected by
Hana Antonicka, McGill University
  1. A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA.
  2. Two genomes, one destiny: Mitophagy at the crossroads of inheritance and disease.
  3. A systematic bi-genomic split-GFP assay illuminates the mitochondrial matrix proteome and protein targeting routes.
  4. How Tailored Ribo-Seq Methods Probe Unique Translation Events.
  5. Reprogramming ribosomes during viral protein synthesis.
  6. Pathogen-induced mitochondrial dysfunction: mechanistic insights, immune crosstalk, and therapeutic opportunities.
  7. fpocketR: A Platform for Identification and Analysis of Ligand-Binding Pockets in RNA.
  8. High-stoichiometry m6A sites are evolutionarily conserved.
  9. Mitochondrial RNA cytosolic leakage drives the SASP.
  10. RAPMS 2.0 Improves Specificity and Throughput for Proteomic Identification of RNA Binding Proteins.
  11. Engineered base editors with reduced bystander editing through directed evolution.
  12. Mutant CHCHD10 disrupts cytochrome c oxidation and activates mitochondrial retrograde signaling.
  13. The TIM22 carrier translocase supports cell proliferation by facilitating mitochondrial iron uptake for Fe-S biogenesis.
  14. Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation.
  15. NSUNs-driven dysregulation: the next frontier in targeted cancer therapy?
  16. An efficient preprocessing workflow tailored for mitochondrial genome assembly from fragmented DNA.
  17. Beyond translation: systematic insight of the multifaceted roles of GARS1 in cellular biology and disease.
  18. MRPL47 Deficiency Drives Mitochondrial Dysfunction via ROS-p38-p21 Signaling in Non-Small Cell Lung Cancer.
  1. Nucleic Acids Res. 2025 Nov 26. pii: gkaf1327. [Epub ahead of print]53(22):
    A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA.
    Simona Amodeo, Mauro Fischli, Silke Oeljeklaus, Salvatore Calderaro, Bettina Warscheid, André Schneider.
      Unlike most eukaryotes, Trypanosoma brucei processes its cytosolic large subunit (LSU) RNA into six fragments. The factors responsible for these processing events were previously unknown. Here, we identify TbLrRP1 and TbLrRP2 as essential components of this trypanosome-specific LSU RNA processing pathway. Each contains a single transmembrane domain and localizes to the ER membrane and the nuclear envelope, forming a heterodimeric complex. Depletion of either protein disrupts LSU RNA processing, causing accumulation of unprocessed intermediates that are incorporated into translationally active cytosolic polysomes. This disruption impairs, but does not fully halt, growth of both procyclic and bloodstream form trypanosomes. The nuclease-related domain (NERD) of TbLrRP2 is essential for LSU RNA processing. Intriguingly, NERD-containing proteins were predicted to have DNase activity; however, our results suggest that the NERD of TbLrRP2 is a ribonuclease. In contrast, the DEDDh domain of TbLrRP1 is dispensable for LSU RNA processing, indicating it may have a scaffolding role. Both proteins require their transmembrane domains for full functionality. Our findings reveal a lineage-specific processing complex acting at a late stage of LSU RNA maturation, highlighting the unique adaptations of trypanosomal cytosolic ribosome biogenesis.
    DOI:  https://doi.org/10.1093/nar/gkaf1327
  2. Cell Chem Biol. 2025 Dec 18. pii: S2451-9456(25)00390-3. [Epub ahead of print]32(12): 1439-1441
    Two genomes, one destiny: Mitophagy at the crossroads of inheritance and disease.
    Chih-Yao Chung, Kritarth Singh, Brigida R Pinho, Jorge M A Oliveira, Michael R Duchen.
      Mechanisms ensuring mito-nuclear compatibility are poorly understood. In a recent study published in Science,1 Frison et al. found that a mouse mitochondrial DNA (mtDNA) mutation can escape mitochondrial surveillance in embryogenesis by repressing the ubiquitin-proteasome system. Inhibition of USP30 restored ubiquitin-mediated mitophagy and reduced mutant burden, suggesting a potential therapeutic target for mtDNA disorders.
    DOI:  https://doi.org/10.1016/j.chembiol.2025.11.010
  3. Elife. 2025 Dec 16. pii: RP98889. [Epub ahead of print]13
    A systematic bi-genomic split-GFP assay illuminates the mitochondrial matrix proteome and protein targeting routes.
    Yury S Bykov, Solene Zuttion, Dunya Edilbi, Marina Polozova, Johanna Arnold, Sergey Malitsky, Maxim Itkin, Bruno Senger, Ofir Klein, Yeynit Asraf, Hadar Meyer, Hubert D Becker, Roza Kucharczyk, Maya Schuldiner.
      The majority of mitochondrial proteins are encoded in the nuclear genome. Many of them lack clear targeting signals. Therefore, what constitutes the entire mitochondrial proteome is still unclear. We here build on our previously developed bi-genomic (BiG) split-GFP assay (Bader et al., 2020) to solidify the list of matrix and inner membrane mitochondrial proteins. The assay relies on one fragment (GFP1-10) encoded in the mitochondrial DNA enabling specific visualization of only the proteins tagged with a smaller fragment, GFP11, and localized to the mitochondrial matrix or the inner membrane. We used the SWAp-Tag (SWAT) strategy to tag every protein with GFP11 and mated them with the BiG GFP strain. Imaging the collection in six different conditions allowed us to visualize almost 400 mitochondrial proteins, 50 of which were never visualized in mitochondria before, and many are poorly studied dually localized proteins. We use structure-function analysis to characterize the dually localized protein Gpp1, revealing an upstream start codon that generates a mitochondrial targeting signal and explore its unique function. We also show how this data can be applied to study mitochondrial inner membrane protein topology and sorting. This work brings us closer to finalizing the mitochondrial proteome and the freely distributed library of GFP11-tagged strains will be a useful resource to study protein localization, biogenesis, and interactions.
    Keywords:  S. cerevisiae; automated microscopy; biochemistry; cell biology; chemical biology; dual localization; mitochondria; mitochondrial proteome; protein targeting; yeast genetics
    DOI:  https://doi.org/10.7554/eLife.98889
  4. RNA. 2025 Dec 15. pii: rna.080654.125. [Epub ahead of print]
    How Tailored Ribo-Seq Methods Probe Unique Translation Events.
    James Marks, Sezen Meydan.
      Ribosome profiling (Ribo-seq) is a next-generation, high-resolution sequencing technique that captures ribosome-protected mRNA fragments to map ribosome positions across the transcriptome. This method serves as a powerful proxy for global translational activity by revealing where ribosomes engage with mRNAs. Recent advances have expanded the utility of Ribo-seq to resolve distinct ribosome populations, including initiating ribosomes, small subunits, collided ribosomes, mitochondrial ribosomes, and those associated with specific translation factors or localized to subcellular compartments. These methodological advances have significantly broadened the scope of Ribo-seq, enabling new insights into the molecular mechanisms that govern translation across diverse eukaryotic systems. In this mini-review, we highlight key innovations in Ribo-seq technology and discuss how they have deepened our understanding of the spatial, temporal, and regulatory dimensions of translational control.
    Keywords:  Ribo-seq; next-generation sequencing; ribosome; ribosome profiling; translation regulation
    DOI:  https://doi.org/10.1261/rna.080654.125
  5. Biochem (Lond). 2025 Sep 02. 47(4): 3-7
    Reprogramming ribosomes during viral protein synthesis.
    Jemma Betts, Chris H Hill, Ian Brierley.
      It is estimated that ~1031 viruses exist on planet earth, and all are entirely dependent on host cell ribosomes for viral mRNA translation. Ribosomes, the engines of protein synthesis, can be regarded as the 'compilers' of life-responsible for interpreting the genetic instruction set in a consistent way and creating protein molecules with executive functions, each of which contributes towards the phenotype of the cell. Even subtle changes in how the ribosome normally operates can have dramatic consequences, as illustrated by the lethality of many antibiotics that target the protein synthesis machinery. For viruses, millions of years of evolutionary pressure have led to every possible avenue being explored to optimise the encoding of information within a (typically) small genome. This has led to the emergence of mechanisms to reprogram translation in a variety of ways, collectively termed 'recoding'. For example, elongating ribosomes can be induced to shift reading frame and access overlapping coding sequences or to continue elongating through a stop codon. Here, we review the discovery of these phenomena, explore the role of RNA structures in these processes, and outline mechanistic questions that remain unanswered.
    DOI:  https://doi.org/10.1042/bio_2025_136
  6. Front Cell Infect Microbiol. 2025 ;15 1714998
    Pathogen-induced mitochondrial dysfunction: mechanistic insights, immune crosstalk, and therapeutic opportunities.
    Yang Yang, Yuanyuan Zeng, Zeyi Liu, Jian-An Huang.
      Mitochondria have emerged as multifunctional organelles central to cellular metabolism, innate immunity, and cell fate determination. Increasing evidence demonstrates that pathogens-including viruses, bacteria, fungi, and parasites-target mitochondria to modulate host immune responses and metabolic reprogramming. Disruption of mitochondrial dynamics, excessive reactive oxygen species (ROS) generation, mitochondrial DNA (mtDNA) release, and altered mitophagy represent key hallmarks of pathogen-induced mitochondrial dysfunction. These processes not only compromise cellular bioenergetics but also influence immune signaling cascades, such as cGAS-STING and NLRP3 inflammasome pathways, thereby shaping infection outcomes. This review synthesizes the latest findings on how distinct pathogen classes orchestrate mitochondrial damage and explores their implications for infection biology and immune regulation. Furthermore, we highlight emerging mitochondria-targeted therapeutic strategies and future research directions aimed at mitigating infection-induced mitochondrial pathology.
    Keywords:  host defense; infection; mitochondria; mitochondrial dynamics; pathogens
    DOI:  https://doi.org/10.3389/fcimb.2025.1714998
  7. ACS Chem Biol. 2025 Dec 16.
    fpocketR: A Platform for Identification and Analysis of Ligand-Binding Pockets in RNA.
    Seth D Veenbaas, Simon Felder, Kevin M Weeks.
      Small molecules that bind specific sites in RNAs hold promise for altering RNA function, manipulating gene expression, and expanding the scope of druggable targets beyond proteins. Identifying binding sites in RNA that can engage ligands with good physicochemical properties remains a significant challenge. fpocketR is a software and framework for identifying, characterizing, and visualizing ligand-binding sites in RNA. fpocketR was optimized, through a comprehensive analysis of currently available RNA-ligand complexes, to identify pockets in RNAs able to bind small molecules possessing favorable properties, generally termed drug-like. Here, we demonstrate multiple, complex, uses of fpocketR to analyze RNA-ligand interactions and novel pockets in small and large RNAs, to assess ensembles of RNA structure models, to identify pockets in dynamic RNA systems, and to evaluate the shapes of RNA pockets. fpocketR performs best with RNA structures visualized at atomistic resolution but also provides useful information with lower resolution structures and computational models. fpocketR is a powerful, ligand-agnostic tool for discovery and analysis of targetable pockets in RNA molecules.
    DOI:  https://doi.org/10.1021/acschembio.5c00805
  8. RNA. 2025 Dec 18. pii: rna.080858.125. [Epub ahead of print]
    High-stoichiometry m6A sites are evolutionarily conserved.
    Hamish Nc Pike, Schraga Schwartz.
      N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in eukaryotes, yet whether m6A sites are functionally important or represent neutral byproducts remains unclear. Previous evolutionary analyses failed to detect consistent conservation signatures at m6A sites, and report conflicting patterns of conservation across genic regions, such as the coding sequence (CDS) and untranslated regions (UTRs). To reconcile these inconsistencies and definitively determine whether m6A sites are under selection, we develop novel motif-level conservation metrics that incorporate knowledge of m6A biogenesis to distinguish m6A-specific selection from other confounding sources. We analyze ~500,000 candidate sites with quantitative, single-nucleotide resolution m6A measurements across a phylogeny spanning 447 mammalian species. After controlling for proximity to exon-junctions, we observe a clear, dose-dependent relationship between m6A stoichiometry and evolutionary conservation in both CDS and UTRs. Highly methylated sites (>60%) exhibit significantly increased conservation compared to lowly methylated sites - with an effect size approximately one-third of the typical CDS-UTR difference - providing definitive evidence of purifying selection and supporting a model where highly modified sites contribute functionally to gene regulation. We establish a methodological framework for evolutionary analysis of RNA modifications, highlighting the necessity of quantitative measurements, comprehensive phylogenetic sampling, and careful consideration of modification biogenesis.
    Keywords:  Epitranscriptome; Evolution; Phylogenetic analysis; Purifying selection; RNA methylation
    DOI:  https://doi.org/10.1261/rna.080858.125
  9. Nat Commun. 2025 Dec 15. 16(1): 10992
    Mitochondrial RNA cytosolic leakage drives the SASP.
    Stella Victorelli, Madeline Eppard, Hélène Martini, Seung-Hwa Woo, Stacia P A Everts, Gung Lee, Nicholas Pirius, Nuan Han, Eugene Y Liang, Ana Catarina Franco, Yeaeun Han, Dominik Saul, Eva Nóvoa, Rubén Nogueiras, Patrick L Splinter, Steven P O'Hara, Olivia Morgenthaler, Lucía Valenzuela-Pérez, Hyun Se Kim Lee, Diana Jurk, Nicholas F LaRusso, Petra Hirsova, João F Passos.
      Senescent cells secrete proinflammatory factors known as the senescence-associated secretory phenotype (SASP), contributing to tissue dysfunction and aging. Mitochondrial dysfunction is a key feature of senescence, influencing SASP via mitochondrial DNA (mtDNA) release and cGAS/STING pathway activation. Here, we demonstrate that mitochondrial RNA (mtRNA) also accumulates in the cytosol of senescent cells, activating RNA sensors RIG-I and MDA5, leading to MAVS aggregation and SASP induction. Inhibition of these RNA sensors significantly reduces SASP factors. Furthermore, BAX and BAK play a key role in mtRNA leakage during senescence, and their deletion diminishes SASP expression in vitro and in a mouse model of Metabolic Dysfunction-Associated Steatohepatitis (MASH). These findings highlight mtRNA's role in SASP regulation and its potential as a therapeutic target for mitigating age-related inflammation.
    DOI:  https://doi.org/10.1038/s41467-025-66159-z
  10. bioRxiv. 2025 Nov 25. pii: 2025.11.23.690051. [Epub ahead of print]
    RAPMS 2.0 Improves Specificity and Throughput for Proteomic Identification of RNA Binding Proteins.
    D Honson, W Deng, M Blanco, J Sha, K Plath, J A Wohlschlegl, M Guttman, D Majumdar.
      RNA-protein complexes are critical factors in development, homeostasis, and disease. RNA proteomics methods are essential for characterizing these complexes but suffer from high levels of background, which hinders identification of ribonucleoprotein (RNP) components. Here, we present RNA Antisense Purification followed by Mass Spectrometry 2.0 (RAP-MS 2.0), an updated version our original RAP-MS protocol with innovations in bead preparation, RNA capture, and peptide purification. RAP-MS 2.0 has lower background than our original protocol, and allows lysate to be reused to capture multiple RNAs. We demonstrate that RAP-MS 2.0 recapitulates known RNPs for 7SL, 7SK, RMRP, U1, U2, U6, U7, and Xist. Additionally, we use RAP-MS 2.0 to identify novel RNA-protein interactions between Xist and TREX components and U1 with FET family transcriptional regulators.
    DOI:  https://doi.org/10.1101/2025.11.23.690051
  11. Nat Biotechnol. 2025 Dec 18.
    Engineered base editors with reduced bystander editing through directed evolution.
    Ramiro M Perrotta, Svenja Vinke, Raphaël Ferreira, Michaël Moret, Ahmed Mahas, Anush Chiappino-Pepe, Lisa M Riedmayr, Anna-Thérèse Mehra, Louisa S Lehmann, George M Church.
      Base editors enable precise genome modification but are constrained by bystander edits that limit their applicability. Existing strategies to enhance precision often compromise efficiency and remain highly sequence dependent. Here we present a parallel engineering approach that optimizes both guide RNAs and the deaminase enzyme to minimize bystander editing without sacrificing activity. We designed a library of 3'-extended guide RNAs and identified context-dependent variants that improved specificity. Using a precision-driven phage-assisted evolution system and protein language models, we evolved adenine base editor variants two- to threefold more precise than adenine base editor ABE8e while maintaining high efficiency across a library of thousands of human pathogenic contexts in vitro. Our findings establish a scalable framework for precision engineering of base editors, addressing a major challenge in genome editing.
    DOI:  https://doi.org/10.1038/s41587-025-02937-w
  12. EMBO Mol Med. 2025 Dec 19.
    Mutant CHCHD10 disrupts cytochrome c oxidation and activates mitochondrial retrograde signaling.
    Márcio Augusto Campos-Ribeiro, Erminia Donnarumma, Hendrik Nolte, Paul Cobine, Elodie Vimont, Dusanka Milenkovic, Juan Diego Hernandez-Camacho, Francina Langa-Vives, Etienne Kornobis, Esthel Pénard, Sonny Yde, Thomas Langer, Véronique Paquis-Flucklinger, Timothy Wai.
      Mutations in CHCHD10, a mitochondrial intermembrane space (IMS) protein implicated in proteostasis and cristae maintenance, cause mitochondrial disease. Knock-in mice modeling the human CHCHD10S59L variant associated with ALS-FTD develop a mitochondrial cardiomyopathy driven by CHCHD10 aggregation and activation of the mitochondrial integrated stress response (mtISR). We show that cardiac dysfunction is associated with dual defects originating at the onset of disease: (1) bioenergetic failure linked to impaired mitochondrial copper homeostasis and cytochrome c oxidation, and (2) maladaptive mtISR signaling via the OMA1-DELE1-HRI axis. Using protease-inactive Oma1E324Q/E324Q knock-in mice, we show that blunting mtISR in Chchd10S55L/+ mice delays cardiomyopathy onset without rescuing CHCHD10 insolubility, cristae defects or OXPHOS impairment. Proteomic profiling of insoluble mitochondrial proteins in Chchd10S55L/+ mice reveals widespread disruptions of mitochondrial proteostasis, including IMS proteins involved in cytochrome c biogenesis. Defective respiration in mutant mitochondria is rescued by the addition of cytochrome c, pinpointing IMS proteostasis disruption as a key pathogenic mechanism. Thus, mutant CHCHD10 insolubility compromises metabolic resilience by impairing bioenergetics and stress adaptation, offering new perspectives for the development of therapeutic targets.
    Keywords:  CHCHD10; Cardiomyopathy; Cytochrome c; Mitochondrial Disease; OMA1
    DOI:  https://doi.org/10.1038/s44321-025-00358-5
  13. Mol Cell. 2025 Dec 18. pii: S1097-2765(25)00939-6. [Epub ahead of print]85(24): 4587-4601.e7
    The TIM22 carrier translocase supports cell proliferation by facilitating mitochondrial iron uptake for Fe-S biogenesis.
    Shuai Liu, Qingyu Li, Mengye Cao, Zefang Bimo Zhao, Cong Liu, Zhuoran Zhen, Jiankun Ren, Chengyang Liu, Danyang Ruan, Luna Zhang, Wenjuan Zhang, Hao Gong, Xiaolong Liu, Xuejie Zhang, Deng Pan, Weijun Pan, Jiajun Zhu.
      Mitochondria host a number of reductive biosynthetic pathways and rely on extensive metabolite exchanges with the cytosol to support cellular anabolic metabolism. Mitochondrial iron-sulfur cluster (Fe-S) biogenesis is essential for multiple cellular functions, and its disruption causes various inborn genetic diseases. How mammalian cells regulate Fe-S biogenesis remains incompletely understood. Here, mitochondria-focused CRISPR screening and DepMap-based gene co-essentiality analysis consistently reveal that components of the carrier translocase of the inner mitochondrial membrane (TIM22) complex, including TIMM29, are selectively required for Fe-S biogenesis. Mechanistically, loss of TIM22 complex function reduced iron transporter presence on mitochondria, thereby impairing iron uptake from the cytosol. Reconstituting mitochondrial iron level was sufficient to restore Fe-S biogenesis and proliferation of TIMM29-deficient cells or rescue the embryonic development of timm29-deficient zebrafish. Thus, a primary function of the TIM22 carrier translocase is to facilitate transporter-mediated iron uptake required for Fe-S biogenesis, underscoring a biosynthetic role of mitochondria in cellular anabolism.
    Keywords:  TIM22 carrier translocase; cellular metabolism; iron-sulfur cluster; mitochondria
    DOI:  https://doi.org/10.1016/j.molcel.2025.11.022
  14. Nat Commun. 2025 Dec 13.
    Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation.
    Johann J Roske, Giulia Paris, Akanksha Goyal, Marina Rodnina, Nikolay Zenkin, Katarzyna J Bandyra, Ben F Luisi.
      In many bacterial species, transcription and translation can be coupled physically, with potential impact on the rates and efficiency of gene expression. Here, we present structural evidence from cryo-EM demonstrating that a bacterial RNA polymerase that is paused proximally to the promoter can associate with the pioneering 30S translation initiation complex (30S IC). These findings suggest that the physical link between transcription and translation can be established prior to commitment to protein synthesis. Although the mRNA is embedded in this 'early expressome' complex, it can nonetheless interact with small regulatory RNA (sRNA) and be targeted for cleavage in the protein-coding region by the RNA degradosome assembly in vitro. The potential tagging of transcripts with sRNA during pioneering and subsequent stages of translation initiation, when the 30S IC is at the 5' end of a polyribosome, may in principle contribute to efficient and rapid termination of gene expression in response to regulatory signals.
    DOI:  https://doi.org/10.1038/s41467-025-67330-2
  15. Cell Death Dis. 2025 Dec 18.
    NSUNs-driven dysregulation: the next frontier in targeted cancer therapy?
    Yingqi Zhao, Yuying Zhang, Haonan Zhou, Lei Zhang, Jinyu Guo, Yue Tan, Ting Wu, Yi Peng, Ying Che, Zhanlei Pei, Jun Li, Boshi Fu, Minjie Wei, Gang Wu, Xiaoyun Hu, Huizhe Wu.
      Epitranscriptomic modifications represent a fundamental regulatory layer in cancer biology, with RNA methylation emerging as a pivotal mechanism governing transcriptomic dynamics. Among these, 5-methylcytosine (m5C) RNA methylation-a ubiquitous and conserved epitranscriptomic mark-has been identified across diverse RNA species, including mRNAs, rRNAs, tRNAs, and mitochondrial RNAs. Notably, the RNA m5C "writers"-enzymes responsible for installing this modification onto target RNAs-have emerged as central regulators of tumorigenesis, with NSUN (NOP2/Sun RNA methyltransferase) proteins playing a particularly pivotal role. We synthesize current knowledge of the cellular localization, substrate specificity, and biological functions of m5C-modifying enzymes, focusing predominantly on the NSUN family in the cancer context. We first dissect the spatiotemporal regulation patterns of NSUN proteins-from their nuclear roles in pre-mRNA processing to cytoplasmic functions in mRNA decay and translation-and their conserved methyltransferase domains that dictate target RNA recognition. This review further explores the molecular mechanisms by which NSUN proteins govern tumor progression, metastasis, and therapeutic responses, emphasizing their dual roles in both initiating oncogenic programs and maintaining cancer cell plasticity. Finally, we discuss the translational implications of targeting NSUN-mediated m5C pathways, highlighting small-molecule inhibitors designed against NSUN substrate specificity, combinatorial strategies with conventional chemotherapy or immunotherapy, and the promise of epitranscriptomic diagnostics and prognostic based on NSUN expression signatures. By positioning NSUN proteins as integral nodes in the RNA epigenomic network, this synthesis not only deepens our understanding of cancer pathogenesis but also identifies novel epitranscriptomic targets for precision oncology.
    DOI:  https://doi.org/10.1038/s41419-025-08269-6
  16. Forensic Sci Int. 2025 Dec 12. pii: S0379-0738(25)00414-1. [Epub ahead of print]379 112770
    An efficient preprocessing workflow tailored for mitochondrial genome assembly from fragmented DNA.
    Yongheng Zhou, Peng Gao, Shuhui Yang, Yanchun Xu.
      Mitochondrial DNA (mtDNA), characterised by its high copy number, structural stability, and maternal inheritance, is a critical genetic marker in forensic genetics, species identification, and conservation studies. Accurate mtDNA genome assembly is essential for these applications. However, DNA from typical wildlife and historical sources - such as museum specimens, keratinised tissues, environmental samples, and ancient remains - is often highly fragmented and damaged, limiting assembly efficiency and accuracy. Here, we developed a preprocessing workflow (MTAK) specifically designed to improve mtDNA assembly from degraded DNA. MTAK integrates two core steps: (1) extraction of homologous reads via reference-sequence alignment and (2) targeted processing of severely damaged 5' and 3' terminal bases. The workflow was evaluated on 24 degraded samples of varying quality. MTAK substantially enhanced assembly completeness and accuracy, particularly in samples with extensive DNA damage, while reducing computational time by over tenfold and minimising resource consumption. An interaction model was implemented to guide optimal sequencing depth for efficient assembly. This approach is compatible with most existing assembly tools and significantly improves mtDNA recovery from challenging historical and wildlife samples.
    Keywords:  DNA damage; Fragmented DNA; Mitochondrial assembly; Pre-processing workflow
    DOI:  https://doi.org/10.1016/j.forsciint.2025.112770
  17. Cell Cycle. 2025 Dec 15. 1-26
    Beyond translation: systematic insight of the multifaceted roles of GARS1 in cellular biology and disease.
    Gabriela Coronel Vargas, Erika Iervasi, Kateryna Tkachenko, Deianira Bellitto, Matteo Raineri, Tiziana Bachetti, Camillo Rosano.
      Human glycyl-tRNA synthetase (GARS), encoded by the GARS1 gene, is a key protein within the aminoacyl-tRNA synthetases family, responsible for catalyzing the attachment of glycine to its corresponding tRNA during protein synthesis. While aminoacyl-tRNA synthetases are primarily known for their role in translation, emerging evidence indicates that they also have non-canonical functions in physiological and pathological processes, including metabolism, angiogenesis, immune responses, and inflammation. This review integrates glycyl-tRNA synthetase evolutionary origins, isoform biology, structure function relationships, immune roles, and cellular stress evidence across bladder, prostate, breast, colorectal, and hepatocellular tumors. Unlike prior papers about GARS, we (i) distinguish cytosolic vs mitochondrial GARS isoforms and their detection pitfalls; (ii) synthesize non-canonical mechanisms (neddylation interfaces, extracellular vesicles-mediated C-ter and N-ter peptides, CDH6-dependent signaling); and (iii) provide a comparative reliability map across cancers, identifying urinary bladder cancer as the most substantiated indication with convergent transcriptomic, proteomic, metabolic, and preliminary translational evidence. Current literature is dominated by correlative and in-vitro studies, and prospective clinical validation is scarce. GARS is a promising but incompletely defined oncologic and immunobiologic node; targeted, standardized, and clinically anchored studies are now feasible and necessary.
    Keywords:  Aminoacyl-tRNA synthetases; cellular signaling; gars deregulation; non-canonical functions; oncology targets
    DOI:  https://doi.org/10.1080/15384101.2025.2594015
  18. J Biol Chem. 2025 Dec 15. pii: S0021-9258(25)02910-2. [Epub ahead of print] 111058
    MRPL47 Deficiency Drives Mitochondrial Dysfunction via ROS-p38-p21 Signaling in Non-Small Cell Lung Cancer.
    Nikita Bhandari, Yengkhom Ghanapriya Devi, Disha Acharya, Vinita Bhat, Annesha Chatterjee, Shweta Yalshetti, Sharathchandra Arandkar, Bal Krishna Chaube, Sudhanshu Shukla.
      Mitoribosomes are pivotal for cellular energy metabolism through the synthesis of proteins essential for the oxidative phosphorylation (OXPHOS) system. Although mitoribosomal dysregulation has been implicated in cancer, the genomic landscape of mitoribosomal proteins (MRPs) in non-small cell lung cancer (NSCLC) remains largely uncharacterized. In this study, we conducted a comprehensive analysis of expression, copy number variations, and mutations of MRPs using data from TCGA-NSCLC patients. This screen identified MRPL47 as a significantly amplified and overexpressed mitoribosomal gene in NSCLC. Validation across three independent datasets (n=1513) confirmed MRPL47 as a robust and independent prognostic marker for poor survival. Functionally, MRPL47 inhibition significantly reduced NSCLC cell proliferation and migration. Intriguingly, MRPL47 depletion selectively impaired the translation of a subset of mitochondrial proteins, rather than causing a global defect, leading to impaired assembly of electron transport chain Complexes I and III. This resulted in a defective OXPHOS system, characterized by decreased ATP synthesis and elevated mitochondrial reactive oxygen species (ROS) levels. Transcriptomic analysis revealed a significant downregulation of E2F pathway activity in MRPL47-knockdown cells, with MRPL47 expression correlating with E2F target gene expression at both RNA and protein levels. Mechanistically, MRPL47 knockdown induced ROS accumulation, which promoted p38 phosphorylation and subsequent upregulation of p21. Increased p21, in turn, led to Rb hypophosphorylation, thereby inhibiting E2F activity and inducing G1 cell cycle arrest and senescence. Altogether, these findings establish that MRPL47 is amplified and overexpressed in NSCLC, functions as a strong prognostic predictor, and critically promotes tumor progression by modulating mitochondrial function and the ROS-p38-p21-Rb-E2F signaling axis.
    Keywords:  CDKN1A (Cyclin-Dependent Kinase Inhibitor 1A); Cellular Senescence; Mitogen-Activated Protein Kinase (MAPK); Mitoribosome; Oxidative Phosphorylation (OXPHOS); Reactive Oxygen Species (ROS)
    DOI:  https://doi.org/10.1016/j.jbc.2025.111058
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