bims-mirnam Biomed News
on Mitochondrial RNA metabolism
Issue of 2025–11–16
nineteen papers selected by
Hana Antonicka, McGill University
  1. Mitochondrial DNA Replication and Disease: A Historical Perspective on Molecular Insights and Therapeutic Advances.
  2. Serine tRNAs compete to regulate the mRNA translation of serine-sensitive codons.
  3. Lost in Translation: When the Rules Do Not Apply.
  4. Monitoring the complexity and dynamics of mitochondrial translation.
  5. SLC25A11 Is Associated with KDM2A-Dependent Reduction in rRNA Transcription Induced by Aminooxyacetic Acid.
  6. Mitochondrial Calcium Channels and MAM Interaction in Calcium Homeostasis Dysregulation in Parkinson's Disease.
  7. Mitochondrial gene phylogenetic incongruencies are linked to chromosomal position and function.
  8. GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins.
  9. Characterization of Novel POLG Mutations in Mitochondrial Encephalomyopathy: Pathogenic Validation and Comprehensive Genetic Profiling.
  10. MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics.
  11. TFAM Loss Induces Oxidative Stress and Divergent Phenotypes in Glioblastoma Metabolic Subtypes.
  12. Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP.
  13. The function of Mak16 in ribosome biogenesis depends on its [4Fe-4S] cluster.
  14. Alternative start codon selection shapes mitochondrial function and rare human diseases.
  15. The METTL Family as Regulators of Methylation and Therapeutic Targets in Cardiovascular Diseases.
  16. RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing.
  17. Development of programmable RNA imaging with RNA-guided GFP via click chemistry.
  18. The bottleneck for maternal transmission of mtDNA is linked to purifying selection by autophagy.
  19. Mitochondrial NAD+-mediated mitophagy alleviates type I interferon response to the cytosolic mitochondrial dna.
  1. Int J Mol Sci. 2025 Oct 22. pii: 10275. [Epub ahead of print]26(21):
    Mitochondrial DNA Replication and Disease: A Historical Perspective on Molecular Insights and Therapeutic Advances.
    Shruti Somai, Chioma H Aloh, Dillon E King, William C Copeland.
      Mitochondria are vital for cellular energy production, as these organelles generate most of the cellular energy required for various metabolic processes. Mitochondria contain their own circular DNA, which is present in multiple copies and is exclusively maternally inherited. Cellular energy in the form of adenosine 5'-triphosphate is produced via oxidative phosphorylation and involves the coordinated expression of genes encoded by both the nuclear and mitochondrial genomes. Mitochondrial DNA itself is replicated by a dedicated set of nuclear-encoded proteins composed of the DNA polymerase gamma, the Twinkle helicase, the mitochondrial single-stranded DNA binding protein, as well as several accessory factors. Mutations in these genes, as well as in the genes involved in nucleotide metabolism, are associated with a spectrum of mitochondrial disorders that can affect individuals from infancy to old age. Additionally, mitochondrial disease can arise as a result of point mutations, deletions, or depletion in the mitochondrial DNA or in genes involved in mitochondrial transcription, replication, maintenance, and repair. Although a cure for mitochondrial diseases is currently elusive, several treatment options have been explored. In this review, we explore the molecular insights of the core mitochondrial replisome proteins that have aided our understanding of mitochondrial diseases and influenced current therapies.
    Keywords:  DNA polymerase γ; PolG; PolG2; Twinkle; mitochondria; mitochondrial diseases; mtDNA; mtDNA replication; mtSSB
    DOI:  https://doi.org/10.3390/ijms262110275
  2. Sci Adv. 2025 Nov 14. 11(46): eady4521
    Serine tRNAs compete to regulate the mRNA translation of serine-sensitive codons.
    Veronica Costiniti, Wyatt C Tran, Nandhini Rajesh Babu, Evgeny Kanshin, Beatrix Ueberheide, Alec C Kimmelman, Robert S Banh.
      Differential mRNA translation efficiency (mTE) of codons is important in regulating protein synthesis and cellular states and can change in response to amino acid availability. While the mTE of codons is canonically associated with their corresponding transfer RNA (tRNA) isoacceptors, its regulation by amino acids in mammalian cells remains unexplored. We found that ELAC2, a 3' tRNA maturation endonuclease, decreases the mTE of UC[C/U] serine (Ser) codons in response to Ser limitation. Ablation of ELAC2 restored UC[C/U] mTE but reduced the mTE of AG[U/C] Ser codons. Among the tRNASer isoacceptors, tRNASer(GCU) decreased the most in ELAC2-deficient cells. Unexpectedly, tRNASer(GCU) delivery restored AG[U/C] mTE and reduced UC[C/U] mTE in ELAC2-deficient cells. Last, we deciphered the effects of Ser-sensitive codons on mRNA translation and the human proteome. Our study revealed that in response to Ser limitation, regulation of tRNASer(GCU) levels fine-tune the mTE of UC[C/U] or AG[U/C] Ser-sensitive codons and shapes the proteome.
    DOI:  https://doi.org/10.1126/sciadv.ady4521
  3. Wiley Interdiscip Rev RNA. 2025 Nov-Dec;16(6):16(6): e70029
    Lost in Translation: When the Rules Do Not Apply.
    Shu Jun Lin, Esperanza Rosas, Gabriele Fuchs, Hannah K Shorrock.
      Eukaryotic gene expression is strictly controlled and regulated during translation. For eukaryotic mRNAs, canonical cap-dependent translation is the preferred pathway to synthesize proteins and starts with the recruitment of eukaryotic initation factors and the ribosome to the 5' m7G cap structure of the mRNA, followed by ribosome scanning and AUG recognition. Canonical translation can however be impaired during cellular responses to certain environmental factors, including stress, viral infection, and hypoxia. In response to these conditions, cells shut down the canonical translation initiation pathway and utilize alternative translation initiation mechanisms some of which are heavily dependent on RNA secondary structures. One such non-canonical initiation mechanism is mediated through Internal Ribosome Entry Sites (IRESs), found in viral and cellular mRNAs, which directly recruit the ribosome and do not require all translation initiation factors. Repeat-associated non-AUG (RAN) translation is another form of non-canonical translation initiation shown to heavily rely on RNA structure: this mode of translation initiation is relevant in the context of a subset of neurological diseases. This review focuses on the role of RNA structure in noncanonical translation initiation mechanisms, with a focus on IRES-mediated and RAN translation. This article is categorized under: Translation > Mechanisms Translation > Regulation RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
    Keywords:  IRES; RAN translation; RNA structure; repeat expansion disease; translation
    DOI:  https://doi.org/10.1002/wrna.70029
  4. Mol Cell. 2025 Nov 12. pii: S1097-2765(25)00863-9. [Epub ahead of print]
    Monitoring the complexity and dynamics of mitochondrial translation.
    Taisei Wakigawa, Mari Mito, Yushin Ando, Haruna Yamashiro, Kotaro Tomuro, Haruna Tani, Kazuhito Tomizawa, Takeshi Chujo, Asuteka Nagao, Takeo Suzuki, Osamu Nureki, Fan-Yan Wei, Yuichi Shichino, Yuzuru Itoh, Tsutomu Suzuki, Shintaro Iwasaki.
      Since mitochondrial translation leads to the synthesis of the essential oxidative phosphorylation (OXPHOS) subunits, exhaustive and quantitative delineation of mitoribosome traversal is needed. Here, we developed a variety of high-resolution mitochondrial ribosome profiling derivatives and revealed the intricate regulation of mammalian mitochondrial translation. Harnessing a translation inhibitor, retapamulin, our approach assessed the stoichiometry and kinetics of mitochondrial translation flux, such as the number of mitoribosomes on a transcript, the elongation rate, and the initiation rate. We also surveyed the impacts of modifications at the anticodon stem loop in mitochondrial tRNAs (mt-tRNAs), including all possible modifications at the 34th position, in cells deleting the corresponding enzymes and derived from patients, as well as in mouse tissues. Moreover, a retapamulin-assisted derivative and mito-disome profiling revealed mitochondrial translation initiation factor (mtIF) 3-mediated translation initiation from internal open reading frames (ORFs) and programmed mitoribosome collision sites across the mitochondrial transcriptome. Our work provides a useful platform for investigating protein synthesis within the energy powerhouse of the cell.
    Keywords:  MELAS; Ribo-Seq; disome; kinetics; mitochondria; mitoribosomes; mtIF3; ribosome profiling; tRNA modification; translation
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.022
  5. Cells. 2025 Oct 22. pii: 1655. [Epub ahead of print]14(21):
    SLC25A11 Is Associated with KDM2A-Dependent Reduction in rRNA Transcription Induced by Aminooxyacetic Acid.
    Yuji Tanaka, Nagisa Miyazawa, Yuuki Toba.
      The malate-aspartate shuttle (MAS) is an NADH shuttle that transports cytoplasmic reducing equivalents to the mitochondria for producing energy. We previously demonstrated that K-demethylase 2A (KDM2A), a jmjC-type histone demethylase, decreases ribosomal RNA (rRNA) transcription via demethylation of H3K36me2 in the rRNA gene promoter region in response to energy reduction in MCF-7 cells. However, whether MAS inhibition is involved in KDM2A activity has not been investigated. In this study, we demonstrate that aminooxyacetic acid (AOA), which inhibits aspartate transaminase (AST/GOT) in MAS, decreased intracellular ATP levels and reduced rRNA transcription via KDM2A-dependent reduction in H3K36me2 levels in the rRNA gene promoter in MCF-7 cells. On the other hand, N-phenylmaleimide (NPM), which inhibits the mitochondrial αKG/malate carrier SLC25A11 in MAS, also decreased intracellular ATP levels but did not induce KDM2A activity. Additionally, NPM pretreatment or knockdown of SLC25A11 inhibited AOA-induced KDM2A activity. Dimethyl αKG, a cell-permeable αKG, restored KDM2A activity inhibited by NPM-pretreatment in AOA-treated cells. These results demonstrate that AOA and NPM have different abilities to induce a decrease in rRNA transcription via KDM2A. Furthermore, the αKG/malate carrier SLC25A11 is associated with KDM2A-dependent reduction in rRNA transcription via demethylation under MAS inhibition.
    Keywords:  K-demethylase 2A (KDM2A); SLC25A11; malate–aspartate shuttle (MAS); ribosomal RNA (rRNA)
    DOI:  https://doi.org/10.3390/cells14211655
  6. Neurochem Res. 2025 Nov 15. 50(6): 361
    Mitochondrial Calcium Channels and MAM Interaction in Calcium Homeostasis Dysregulation in Parkinson's Disease.
    Bingjie Han, Jie Bai.
      Parkinson's disease (PD), the second most common neurodegenerative disorder worldwide, currently lacks effective treatment options due to its complex pathogenesis. Growing evidence in recent years demonstrates that intracellular Calcium (Ca²⁺) homeostasis disruption plays a critical role in PD development and progression. Ca²⁺ imbalance not only causes Ca²⁺-dependent synaptic dysfunction and impaired neuronal plasticity but also leads to progressive neuronal loss, collectively forming the core pathological characteristics of PD neurodegeneration. Notably, mitochondrial Ca²⁺ imbalance has been identified as a key pathogenic factor in PD. As vital intracellular Ca²⁺ regulators, dysfunctional mitochondria can induce abnormal opening of the mitochondrial permeability transition pore (mPTP), triggering apoptotic cascades. Furthermore, mitochondrial Ca²⁺ overload disrupts oxidative phosphorylation, resulting in excessive reactive oxygen species production that exacerbates neuronal damage. Recent studies reveal the essential role of mitochondria-endoplasmic reticulum interactions in maintaining Ca²⁺ homeostasis, with these organelles forming structurally and functionally integrated connections through mitochondrial ER-associated membrane (MAM) to cooperatively regulate Ca²⁺ ion dynamics. This review describes the molecular mechanisms of mitochondrial Ca²⁺ imbalance in PD pathogenesis and summarizes the potential of mitochondrial channels and MAM-associated proteins as PD therapeutic targets. By thoroughly analyzing these targets mechanisms, we aim to provide a theoretical foundation for developing novel PD treatment strategies based on Ca²⁺ homeostasis regulation. These findings not only expand our understanding of PD pathogenesis but also point toward developing targeted neuroprotective therapies.
    Keywords:  Calcium homeostasis; Mitochondria; Mitochondrial endoplasmic reticulum-associated membrane; Parkinson’s disease
    DOI:  https://doi.org/10.1007/s11064-025-04591-9
  7. Genome Biol Evol. 2025 Nov 10. pii: evaf209. [Epub ahead of print]
    Mitochondrial gene phylogenetic incongruencies are linked to chromosomal position and function.
    Rob DeSalle, Michael Tessler.
      Mitochondrial DNA has been one of the key workhorses of evolutionary studies. Hence understanding the dynamics of DNA sequence change in this tiny genome (15 to 20 kilobases) is of utmost importance. However, we are unaware of large studies examining how the functionality and chromosomal positioning of mitochondrial genes may impact their phylogenetic patterning. To examine this, we assembled a large database of animal mitochondrial genomes (> 10,000 total individuals over 89 taxonomic groups) and compared their phylogenetics, functionality, and location on the mitochondrial genome (heavy and light strand in vertebrates or J and N strand in other animals and distance from origin of replication). We found that many genes show unique evolutionary patterns, often directly tied to chromosomal location or gene function (e.g. NADH dehydrogenases or ribosomal RNA genes [rRNA]). We also found rampant phylogenetic incongruence among the linked genes of the mitochondria in most of the taxonomic groups we examined. These results suggest mitochondrial genomes have accrued complex evolutionary patterns. The accumulated incongruence can influence phylogenetic inference in evolutionary studies, making mitochondrial gene choice for phylogenetics critical. The phenomena we show here should also be examined in other organelle and even nuclear gene studies.
    Keywords:  Mitochondrial genes; incongruence; light strand; mutational bias
    DOI:  https://doi.org/10.1093/gbe/evaf209
  8. Nucleic Acids Res. 2025 Oct 28. pii: gkaf1169. [Epub ahead of print]53(20):
    GRASP: a modular toolkit for building synthetic pentatricopeptide repeat RNA-binding proteins.
    Michael Dennis, Su Yi Low, Amy Viljoen, Anuradha Pullakhandam, Catherine Colas des Francs-Small, Leni Campbell-Clause, Charles S Bond, Ian Small, Farley M Kwok van der Giezen.
      Pentatricopeptide repeat (PPR) proteins are eukaryotic RNA-binding proteins with multiple roles in mitochondrial and chloroplast transcript processing. PPR proteins are naturally modular and hold great potential for development into tools for RNA processing or controlling RNA folding or expression. However, construction of synthetic PPR (sPPR) proteins is challenging due to their highly repetitive sequences. Here, we present the GRASP kit for assembly of sPPR proteins. Utilizing the S-variant of PPR motifs, we designed a library of 42 plasmids which can be combined to assemble sPPR proteins with 9, 14, or 19 motifs to target any RNA sequence of the same length. The GRASP kit enables rapid design and construction of PPR proteins of any desired specificity and is compatible with the MoClo assembly standard. To demonstrate the capabilities of GRASP, we assembled a sPPR-RNA-editing protein and variants with altered sequence specificity. We tested the functionality of 31 sPPR protein variants against a set of 46 RNA targets and used RNA sequencing to determine levels of RNA editing. The variations in editing provide a wealth of insights into PPR-RNA interactions. The GRASP kit provides a foundation for further development of sPPR protein technologies.
    DOI:  https://doi.org/10.1093/nar/gkaf1169
  9. Brain Behav. 2025 Nov;15(11): e71045
    Characterization of Novel POLG Mutations in Mitochondrial Encephalomyopathy: Pathogenic Validation and Comprehensive Genetic Profiling.
    Fanjing Zhou, Jiang Chen, Tingzheng Zhang, Fengnan Niu, Jinglong Hu, Yun Xu, Meijuan Zhang.
       INTRODUCTION/AIMS: Mitochondrial encephalomyopathies are multisystem disorders caused by defects in mitochondrial DNA (mtDNA) or nuclear DNA (nDNA). Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis (SANDO) syndrome is a rare manifestation, often associated with POLG mutations. This study identifies a novel POLG mutation in a SANDO patient, validates its pathogenicity, and analyzes the molecular genetics of 61 reported POLG-SANDO cases.
    METHODS: After obtaining informed consent, the proband underwent neurological examination, electromyography, muscle/nerve biopsies (histochemical/ultrastructural analyses), and genetic testing (whole-exome sequencing, mtDNA analysis). Pathogenicity of identified POLG variants was assessed in Cas9-mediated primary neuronal models expressing mutant proteins by measuring reactive oxygen species (ROS) levels and mtDNA copy number (qRT-PCR, ND1/APP ratio). Literature searches (PubMed, CNKI, Wanfang, and ClinVar) identified reported POLG mutations and clinical features in SANDO.
    RESULTS: Clinical and biopsy findings confirmed SANDO syndrome. Genetic analysis revealed compound heterozygous POLG mutations: a novel c.3297G>C (p.W1099C) and a known c.1774C>T (p.L592F). Neurons expressing either mutant exhibited elevated ROS levels (p < 0.05) and reduced mtDNA copy number compared with controls. Literature synthesis identified over 30 SANDO-associated POLG mutations, with p.A467T (31.2%) and p.W748S (22.1%) being the most frequent. The mean age of onset was 31.6 years.
    CONCLUSIONS: We identify a novel pathogenic POLG variant (p.W1099C) causing mitochondrial dysfunction via impaired mtDNA maintenance, expanding the SANDO genetic spectrum. Functional studies confirmed both mutations induce mitochondrial dysfunction (elevated ROS and decreased mtDNA Copy Number), validating their pathogenicity. The compiled mutation profile aids diagnosis of this phenotypically heterogeneous, frequently misdiagnosed disorder.
    Keywords:  POLG mutation; SANDO; mitochondrial encephalomyopathy
    DOI:  https://doi.org/10.1002/brb3.71045
  10. Genomics Proteomics Bioinformatics. 2025 Nov 14. pii: qzaf106. [Epub ahead of print]
    MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics.
    Yicen Zhou, Shanxin Lyu, Shiau Wei Liew, Xi Mou, Ian Hoffecker, Jian Yan, Yu Li, Chun Kit Kwok, Jilin Zhang.
      RNA structures are essential building blocks of functional RNA molecules. Profiling secondary structures in vivo and in real time remains challenging because RNAs exhibit dynamic structures and complex conformations. Besides the canonical stem-loop secondary structure, non-canonical structure RNA G-quadruplex (rG4) has attracted interest for its potential as a drug target. Early studies have demonstrated that RNAs can form distinct secondary structures. However, how distinct RNA structures, formed from the same RNA sequences, function within the transcriptome is poorly understood, and factors driving and regulating structure transitions remain to be investigated. Inspired by an HOXB9 segment able to form multiple structures, we found that many RNA segments across the transcriptome exhibit multi-faceted structure-forming potential. In the case of HOXB9, we demonstrate that N6-methyladenosine (m6A) modification influences RNA structure and binding to RNA-binding proteins (RBPs). Therefore, we collected RNA modification sites naturally occurring within the putative G-quadruplex-forming sequences (PQSs) of transcripts and developed MoRNiNG, a database for RNA modifications in natural rG4. MoRNiNG is structured with reliability tiers determined by the resolution of RNA modification sites and is designed to accommodate various large datasets. We experimentally validated the influence of m6A, 5-methylcytosine (m5C), and adenosine to inosine (A-to-I) editing on rG4-forming sequences, providing evidence to support the modification switch concept. The diversity and transition of secondary structures from the same RNA segment offer valuable insights into the regulation of RNA structure dynamics. MoRNiNG is freely accessible at https://www.cityu.edu.hk/bms/morning.
    Keywords:  Conformation dynamics; RNA G-quadruplex; RNA modification; RNA secondary structure; RNA-binding protein
    DOI:  https://doi.org/10.1093/gpbjnl/qzaf106
  11. Int J Mol Sci. 2025 Oct 27. pii: 10446. [Epub ahead of print]26(21):
    TFAM Loss Induces Oxidative Stress and Divergent Phenotypes in Glioblastoma Metabolic Subtypes.
    Stella G Cavalcante, Roseli da S Soares, Miyuki Uno, Maria J F Alves, Ricardo C Cintra, Paula R Sola, Christiane Y Ozaki, Antonio M Lerário, Sueli M Oba-Shinjo, Suely K N Marie.
      Mitochondrial transcription factor A (TFAM) is essential for mitochondrial DNA (mtDNA) maintenance and function, but its role in glioblastoma (GBM) remains largely unexplored. Analysis of patient astrocytomas and TCGA datasets has revealed progressive TFAM downregulation with increasing malignancy, with the lowest expression in glycolytic/plurimetabolic (GPM) subtypes. Functional and transcriptomic profiling of mesenchymal GBM cell lines showed that TFAM silencing in GPM-type U87MG cells enhanced proliferation, S-phase entry, reactive oxygen species (ROS) production, and adhesion, while reducing motility. These changes were correlated with upregulation of LDHC and TRAF2 and downregulation of androgen receptor-linked motility genes and LOXL2. By contrast, TFAM loss in mitochondrial (MTC)-type A172 cells caused minimal phenotypic alterations, associated with elevated SOD1 expression and activation of antioxidant, mitochondrial membrane, and survival pathways, alongside suppression of oxidative phosphorylation and vesicle-trafficking genes. TFAM overexpression reduced proliferation in U87MG but had a limited impact on A172 cells. Taken together, these findings establish TFAM as a subtype-specific regulator of GBM cell proliferation, redox balance, and motility. TFAM loss drives a proliferative, ROS-sensitive phenotype in GPM-type cells, while eliciting adaptive, stress-resilient programs in MTC-type cells. This study identifies TFAM and downstream effectors, TRAF2 and LOXL2, as potential therapeutic targets, supporting the development of metabolic subtype-tailored strategies for GBM treatment.
    Keywords:  GBM; TFAM; mitochondrial dysfunction; redox balance
    DOI:  https://doi.org/10.3390/ijms262110446
  12. Genomics Proteomics Bioinformatics. 2025 Nov 05. pii: qzaf098. [Epub ahead of print]
    Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP.
    Yuanxin Wang, Jiajia Wang, Yanyan Li, Peng Zhang, Zhonglong Wang, Shuai Liu, Yiwei Niu, Yirong Shi, Sijia Zhang, Tingrui Song, Tao Xu, Shunmin He.
      Dysfunctional mitochondria are implicated in various diseases, however comprehensive characterization of mitochondrial DNA (mtDNA) in the Chinese population remains limited. Here, we conducted a systematic analysis of mtDNA from 7331 samples, comprising 4129 Chinese samples (NyuWa) and 3202 samples from the 1000 Genomes Project (1KGP). We identified 7216 distinct high-quality mtDNA variants, classified them into 22 macro-haplogroups, and detected 1466 distinct nuclear mitochondrial DNA segments (NUMTs). Among these, 88 mtDNA variants and 642 NUMTs were specific to NyuWa. Genome-wide association analyses revealed significant correlations between 12 mtDNA variants and 199 nuclear DNA (nDNA) variants. Our findings demonstrated that all individuals in both NyuWa and 1KGP harbored common NUMTs, while one-fifth possessed ultra-rare NUMTs that tended to insert into nuclear gene regions. Notably, rare NUMTs in the NyuWa cohort showed significant enrichment of nuclear breakpoints in long interspersed nuclear elements (LINEs) compared to 1KGP. Overall, this study provides the first comprehensive profile of NUMTs in the Chinese population and establishes the most extensive resource of Chinese mtDNA variants and NUMTs based on high-depth whole genome sequencing (WGS) to date, providing valuable reference resources for genetic research on mtDNA-related diseases.
    Keywords:  Mitochondrial DNA; NUMTs; Whole genome sequencing; mtDNA variants; mtDNA-nDNA variant association
    DOI:  https://doi.org/10.1093/gpbjnl/qzaf098
  13. Proc Natl Acad Sci U S A. 2025 Nov 18. 122(46): e2513844122
    The function of Mak16 in ribosome biogenesis depends on its [4Fe-4S] cluster.
    Nadine Duppe, Lukas Knauer, Marc Hagebölling, Lena Langner, Martin Stümpfig, Volker Schünemann, Antonio J Pierik, Daili J Netz.
      Mak16 and its interacting partner Rpf1 play a critical role at an early step in the maturation of the ribosomal 60S subunit of eukaryotes, as revealed by cryoelectron microscopy structures. While these studies suggested no metal participation or the presence of a Zn2+ ion in Mak16, we identify a previously unexplored iron-sulfur (Fe/S) cluster in yeast Mak16 through both in vivo and in vitro methods. We demonstrate a functional link between mitochondrial and cytosolic Fe/S protein biogenesis and ribosome assembly, highlighting an overlooked aspect of 60S ribosomal biogenesis. Characterization of human and yeast Mak16 revealed a redox-active [4Fe-4S]2+/1+ cluster with a midpoint potential below -500 mV. Oxidative stress destabilizes Mak16 and disrupts its interaction with Rpf1 in vivo, while in vitro H2O2 causes [3Fe-4S]1+ cluster formation. Our findings also reveal that upon binding to rRNA expansion segment 7 the redox properties of the nearby Fe/S cluster largely remain unchanged. However, disruption of Fe/S cluster coordination destabilized Mak16, impaired the Mak16-Rpf1 complex formation and decreased the 25S rRNA level. The critical role of Fe/S proteins in eukaryotic DNA replication and repair, mitoribosomal function, and maturation has now been extended to nuclear ribosomal assembly. Relying on a vulnerable cofactor comes at a cost, as cluster loss can severely disrupt essential cellular processes. The inherent biosynthetic complexity and instability of the Fe/S cluster of Mak16 allows it to function as sensor for redox imbalance, creating the possibility to regulate cellular homeostasis under stress.
    Keywords:  iron–sulfur; metallocofactor; ribosome biogenesis
    DOI:  https://doi.org/10.1073/pnas.2513844122
  14. Mol Cell. 2025 Nov 07. pii: S1097-2765(25)00854-8. [Epub ahead of print]
    Alternative start codon selection shapes mitochondrial function and rare human diseases.
    Jimmy Ly, Matteo Di Bernardo, Yi Fei Tao, Ekaterina Khalizeva, Christopher J Giuliano, Sebastian Lourido, Mark D Fleming, Iain M Cheeseman.
      Rare genetic diseases collectively affect millions of individuals. A common target of many rare diseases is the mitochondria, intracellular organelles that originated through endosymbiosis. Eukaryotic cells require related proteins to function both within the mitochondria and in the host cell. By analyzing N-terminal protein isoforms generated through alternative start codon selection, we identify hundreds of differentially localized isoform pairs, including dual-localized isoforms that are essential for both mitochondrial and host cell function. Subsets of dual mitochondria-localized isoforms emerged during early eukaryotic evolution, coinciding with mitochondrial endosymbiosis. Importantly, we identify dozens of rare disease alleles that affect these alternative protein variants with unique molecular and clinical consequences. Alternative start codon selection can bypass pathogenic nonsense and frameshift mutations, thereby selectively eliminating specific isoforms, which we term isoform-selective alleles (ISAs). Together, our findings illuminate the evolutionary and pathological relevance of alternative translation, offering insights into the molecular basis of rare human diseases.
    Keywords:  TRNT1; alternative N-terminal isoforms; alternative translation; mitochondria; proteomic diversity; rare diseases; start codon selection; translation initiation
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.013
  15. Eur J Pharmacol. 2025 Nov 06. pii: S0014-2999(25)01098-2. [Epub ahead of print] 178344
    The METTL Family as Regulators of Methylation and Therapeutic Targets in Cardiovascular Diseases.
    Xiangyu Gao, Hui Wang, Hongyu Zhang, Jinkun Zhan, Zhongqiu Liu, Yuanyuan Cheng.
      Cardiovascular diseases (CVDs) remain the leading cause of global mortality, highlighting the urgent need for innovative therapeutic strategies. Methyltransferase-like proteins (METTLs), which harbor conserved S-adenosylmethionine (SAM)-binding and catalytic domains, dynamically regulate the functions of RNA, DNA, and proteins through diverse methylation modifications (e.g., N6-methyladenosine [m6A], N7-methylguanosine [m7G], 3-methylcytidine/4-methylcytidine [m3C/m4C], N6-methyladenine [6mA]). These modifications play pivotal roles in fundamental cellular processes such as proliferation, apoptosis, inflammation, and metabolism, and their dysregulation is directly implicated in CVD pathogenesis. This review compiles compelling evidence that connects aberrant METTL expression and activity to major CVDs such as myocardial infarction, maladaptive cardiac remodeling, atherosclerosis, and arrhythmias. We detail how METTLs influence myocardial injury/repair, fibrosis, vascular dysfunction, and electrophysiological homeostasis by altering RNA stability, translation efficiency, and signaling cascades. Additionally, we critically assess the emerging translational potential of METTL members as diagnostic/prognostic biomarkers and inhibitor development strategies. By clarifying the complex mechanisms of METTL-mediated epitranscriptomic and epigenetic regulation, this work lays the groundwork for advancing precision medicine approaches in CVD prevention and treatment.
    Keywords:  METTL family; biomarker; cardiovascular diseases; methylation modifications; therapeutic target
    DOI:  https://doi.org/10.1016/j.ejphar.2025.178344
  16. Nucleic Acids Res. 2025 Nov 06. pii: gkaf1144. [Epub ahead of print]
    RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing.
    Zhuobin Lin, Xiaoqiong Bao, Luowanyue Zhang, Yuantai Huang, Huiqin Li, Wei Liu, Jian Ren, Zhixiang Zuo, Kunhua Hu.
      Transcriptome profiling of RNA modifications is essential for uncovering and characterizing novel post-transcriptional regulatory mechanisms. However, most of the known RNA modifications remain poorly explored due to technological limitations. Nanopore direct RNA sequencing (DRS) provides an advantageous solution for transcriptome-wide RNA modification profiling, enabling simultaneous identification of any modification type in native RNA, with full-length coverage and single-molecule resolution. We developed RMPore (https://rmpore.renlab.cn/), a comprehensive database of single-molecule RNA modifications detected from 958 DRS samples across 34 species. We constructed a practical analytical pipeline integrating 20 detection tools and categorized all detected sites into three confidence levels (high, medium, and low) based on the prediction thresholds and reproducibility of tools, datasets, and other technologies, identifying a total of 65 025 784 modification sites spanning 25 modification types. To further investigate the characteristics of these modification sites and elucidate the regulatory relationships among different modification types, we performed single-molecule advanced analyses of correlated sites and haplotype-biased sites. Meanwhile, we also incorporated extensive molecular event annotations of modification sites in RMPore, including splicing events, RNA-binding protein interactions, RNA-RNA interactions, and circular RNAs. We expect that RMPore will advance single-molecule epitranscriptomics research, bridging critical gaps in the field of RNA modification research.
    DOI:  https://doi.org/10.1093/nar/gkaf1144
  17. Nucleic Acids Res. 2025 Oct 28. pii: gkaf1147. [Epub ahead of print]53(20):
    Development of programmable RNA imaging with RNA-guided GFP via click chemistry.
    Jun Nakamura, Miyako Shiraishi, Junpei Yamamoto, Keiichiro Suzuki.
      The CRISPR-Cas system revolutionized molecular biology by guiding Cas proteins to target nucleic acid sequences using customizable guide RNAs, offering unparalleled precision and versatility. Inspired by this innovation, we developed RNA-guided green fluorescent protein (RGG), a simple and programmable platform for targeting nucleic acid. Using a streamlined click chemistry approach, known for its high efficiency and specificity, we conjugated dibenzocyclooctyne (DBCO)-modified guide nucleic acids, designed to complement target sequences, with azide-exposed proteins to construct RGG. Systematic optimization identified 30-nt RNA with 3'-DBCO modifications as the most effective configuration for RGG, enabling precise visualization of nuclear-localized RNAs, including NEAT1 and Satellite III RNA, in living cells. This establishes RGG as a customizable and efficient system for RNA imaging and molecular analysis, underscoring the potential of direct conjugation between guide nucleic acids and proteins to enable precise nucleic acid recognition and dynamic molecular modification in living cells.
    DOI:  https://doi.org/10.1093/nar/gkaf1147
  18. Sci Adv. 2025 Nov 14. 11(46): eaea4660
    The bottleneck for maternal transmission of mtDNA is linked to purifying selection by autophagy.
    Laura S Kremer, Zoe Golder, Tom Barton-Owen, Polyxeni Papadea, Camilla Koolmeister, Patrick F Chinnery, Nils-Göran Larsson.
      Mammalian mitochondrial DNA (mtDNA) inheritance differs fundamentally from nuclear inheritance owing to exclusive maternal transmission, high mutation rate, and lack of recombination. Two key mechanisms shape this inheritance: the bottleneck, which drives stochastic transmission of maternal mtDNA variants, and purifying selection, which actively removes mutant mtDNA. Whether these mechanisms interact has been unresolved. To address this question, we generated a series of mouse models with random mtDNA mutations alongside alleles altering mtDNA copy number or decreasing autophagy. We demonstrate that tightening the mtDNA bottleneck increases heteroplasmic variance between individuals, causing lower mutational burden and nonsynonymous-to-synonymous ratios. In contrast, reduced autophagy weakens purifying selection, leading to decreased interoffspring heteroplasmic variance and increased mutational burden with higher nonsynonymous-to-synonymous ratios. These findings provide experimental evidence that the mtDNA bottleneck size modulates the efficacy of purifying selection. Our findings yield fundamental insights into the processes governing mammalian mtDNA transmission with direct implications for the origin and propagation of mtDNA mutations causing human disease.
    DOI:  https://doi.org/10.1126/sciadv.aea4660
  19. Autophagy. 2025 Nov 13.
    Mitochondrial NAD+-mediated mitophagy alleviates type I interferon response to the cytosolic mitochondrial dna.
    Tian Lan, Dantong Shang, Lan Lin, Haoyu Wang, Juan Zou, Mengxin Hu, Hanhua Cheng, Rongjia Zhou.
      Mitochondrial nicotinamide adenine dinucleotide (NAD+) plays a central role in energy metabolism, yet its roles and mechanisms in mitophagy and innate immunity remain poorly understood. In this study, we identify mitochondrial NAD+ depletion that causes mitophagy dysfunction and inflammation. We find that depletion of mitochondrial NAD+ owing to deficiency of the mitochondrial NAD+ transporter SLC25A51 impairs BNIP3-mediated mitophagy. Loss of mitochondrial NAD+ inhibits SIRT3-mediated deacetylation of FOXO3, leading to transcriptional downregulation of BNIP3 and subsequent disruption of MAP1LC3B/LC3B recruitment. Notably, mitochondrial NAD+ depletion promotes mitochondrial DNA (mtDNA) release from mitochondria to the cytosol upon oxidative stress, thereby exacerbating the type I interferon response to free cytosolic mtDNA via activation of the CGAS-STING1 signaling pathway. Our findings reveal a novel mechanistic link among mitochondrial NAD+, mitophagy, and mtDNA-induced inflammation by genetic manipulation of cell lines, highlighting mitochondrial NAD+ as a potential therapeutic target for mitigating sterile inflammation triggered by free cytosolic mtDNA. Thus, the study provides new insights into the crosstalk among mitochondrial homeostasis, inflammation, and innate immunity.
    Keywords:  Cytosolic mtDNA; SLC25A51; inflammation; innate immunity; mitochondrial NAD+; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2025.2589909
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