bims-mirnam Biomed News
on Mitochondrial RNA metabolism
Issue of 2026–03–29
nine papers selected by
Hana Antonicka, McGill University
  1. DCTPP1 orchestrates dCTP pool dynamics and mtDNA stability in quiescent cells.
  2. Transplantation of Saccharomyces cerevisiae Rmd9p peptide into mammalian mitochondrial IF2 substitutes for the IF1 function in Escherichia coli.
  3. No Correlation Between Interferon Signaling and Cytosolic Mitochondrial DNA/RNA Leakage in Cultured Skin Fibroblasts of Patients With Mitochondrial Diseases.
  4. Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications.
  5. Organelle-anchored translation factories: the roles of neuronal RBP condensates in organizing local protein synthesis in neurological diseases.
  6. R-loops processing by human apurinic/apyrimidinic endonuclease APE1.
  7. Expanding the Phenotype of TUFM-Related Combined Oxidative Phosphorylation Deficiency 4.
  8. RNA G-quadruplexes mediate cooperativity in HNRNPH binding and splicing regulation.
  9. Quantitative analysis of oligonucleotide delivery into isolated mitochondria: a proof-of-concept method.
  1. Cell Death Dis. 2026 Mar 26.
    DCTPP1 orchestrates dCTP pool dynamics and mtDNA stability in quiescent cells.
    Belén Fernández, Guiomar Pérez-Moreno, Blanca Martínez-Arribas, Antonio E Vidal, Luis Miguel Ruiz-Pérez, Dolores González-Pacanowska.
      Defects in nucleotide metabolism and imbalances in deoxynucleotide triphosphate (dNTP) pools are associated with several human diseases, including cancer and mitochondrial disorders. In non-replicative cells, while DNA synthesis is reduced, a continuous supply of nucleotides is essential to sustain mitochondrial DNA (mtDNA) replication and repair. Human all-α dCTP pyrophosphatase 1 (DCTPP1), a nucleotido hydrolase with high specificity for dCTP, plays a critical role in maintaining nucleotide homeostasis, however its participation in mtDNA stability remains unexplored. In this study we performed a detailed analysis of pyrimidine metabolism enzymes in non-dividing cells. We found that during quiescence, DCTPP1 is predominantly localized to mitochondria. Depletion of the enzyme leads to upregulation of the de novo thymidylate synthesis pathway and expansion of both the dCTP and dGTP pools, highlighting its pivotal role in regulating the dNTP balance. To explore the potential therapeutic relevance of these observations, we used an in vitro model of mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), a rare mitochondrial disorder caused by thymidine phosphorylase (TP) deficiency and characterized by dCTP depletion and mtDNA loss. Long-term thymidine overloading in quiescent cells (a model mimicking TP deficiency) led to reduced dCTP levels and the depletion of mtDNA, effects that were reversed upon DCTPP1 knockdown. Hence, reduced DCTPP1 levels restored dCTP availability and increased mtDNA copy number. These findings suggest that DCTPP1 plays a critical role in regulating mitochondrial dNTP pools and that down-regulation of the enzyme may serve as a compensatory mechanism in disorders marked by secondary dCTP depletion. DCTPP1 may therefore represent a promising therapeutic target for mitochondrial DNA depletion syndromes such as MNGIE.
    DOI:  https://doi.org/10.1038/s41419-026-08632-1
  2. Microbiology (Reading). 2026 Mar;172(3):
    Transplantation of Saccharomyces cerevisiae Rmd9p peptide into mammalian mitochondrial IF2 substitutes for the IF1 function in Escherichia coli.
    Jitendra Singh, Amit Kumar Sahu, Umesh Varshney.
      Mitochondrial translation machinery exhibits similarities with the bacterial translation apparatus. Of the three bacterial translation initiation factors (IF1, IF2 and IF3), two (IF2 and IF3) have homologues in mitochondria (mtIF2 and mtIF3). A high conservation of decoding nucleotides in the ribosomal A-site suggests relevance of IF1-like proteins in mitochondria. The mitochondrial translation machineries have evolved with different solutions for the IF1 function. However, in Saccharomyces cerevisiae, the identity of such a protein remains unknown. Here, based on sequence alignment with human mtIF2, we deduced that Rmd9p may contribute to an IF1-like function in S. cerevisiae. Our genetic analyses show that Rmd9p is required for mitochondrial translation. In addition, we show that a sequence from Rmd9p, pivotal for its mitochondrial function, when inserted into mtIF2, substitutes for both the IF2 and IF1 functions in an established model of Escherichia coli. Interestingly, while the mutations at the critical residues in the Rmd9p peptide compromise the IF1 function, the mutant peptide is still able to support E. coli growth, suggesting that the structure (rather than the precise sequence) of the IF1-like insert domain in mitochondrial IF2 plays a major role in the recognition of the decoding nucleotides in the ribosomal A-site.
    Keywords:   mitochondrial IF2; translation initiation factors; IF1; Rmd9p
    DOI:  https://doi.org/10.1099/mic.0.001689
  3. Eur J Immunol. 2026 Apr;56(4): e70176
    No Correlation Between Interferon Signaling and Cytosolic Mitochondrial DNA/RNA Leakage in Cultured Skin Fibroblasts of Patients With Mitochondrial Diseases.
    Manon Marchais, Alessandra Pennisi, Alexandre Pierga, Alice Lepelley, Nicolas Cagnard, Christine Bole, Patrick Nitschke, Mohamed Hamici, Frédéric Rieux-Laucat, Manuel Schiff, Arnold Munnich, Agnès Rötig.
      Mitochondria have long been known to be involved in the regulation of innate immune response. We questioned whether cultured skin fibroblasts of patients suffering from mitochondrial diseases are valuable biological resources for the study of interferon signaling. Expression of interferon-stimulated genes was measured in control cells supplemented with interferon and in cultured fibroblasts of patients carrying pathogenic variants in mitochondrial disease-causing genes. Control fibroblasts showed a strong expression of interferon-stimulated genes in response to interferon, but only 43% of patients' fibroblasts displayed increased interferon stimulated genes scores. Cytosolic mitochondrial DNA and RNA were quantified by immunofluorescence and confocal microscopy. No correlation between elevated interferon response and cytosolic mitochondrial DNA or RNA release could be established. We found that cultured skin fibroblasts represent a valuable biological resource for the investigation of interferon signaling, but that abnormal interferon signaling is not always observed in patients with mitochondrial diseases. At variance to gene silencing in control fibroblasts, the lack of correlation between elevated interferon response and cytosolic mitochondrial DNA or RNA leakage in patients' fibroblasts questions the relevance of cellular models as illustrators of pathological situations in humans.
    DOI:  https://doi.org/10.1002/eji.70176
  4. Nat Commun. 2026 Mar 23.
    Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications.
    Yuru Wang, Kinga Pajdzik, Yutao Zhao, Chang Ye, Talbot Stone, Li-Sheng Zhang, Wen Zhang, Mahdi Assari, Wenxin Zhao, Caraline Sepich-Poore, Qing Dai, Ke Wang, Minkui Luo, Tao Pan, Chuan He.
      Pseudouridine (Ψ) is one of the most abundant chemical modifications and plays important roles in RNA function. Advances in our understanding of Ψ have been hindered by a limit of robust methods to precisely and sensitively map their distributions in cellular RNAs. Here, we present ELAP-seq (Enzymatic Labeling and Pull-down for Sequencing) for Ψ detection, which leverages a naturally occurring N1-methyl pseudouridine methyltransferase from Methanocaldococcus jannaschii (Mj1640). This enzyme promiscuously converts Ψ to N1-methyl-Ψ (m1Ψ) or installs a propargyl group at the same location in vitro under a mild condition, exhibiting high sensitivity and specificity, and is also functional inside cells. ELAP-seq enriches Ψ-containing RNA fragments and enables single-nucleotide-resolution Ψ detection with markedly enhanced signal-to-noise ratio and reduced sequencing and computational demands. Using ELAP-seq, we identify thousands of candidate Ψ sites in human HeLa and HEK 293 T transcriptomes, validating many previously identified sites as well as reporting additional ones. This versatile enzymatic platform expands the toolkit for sensitive labeling and detection of Ψ, advancing the study of RNA modification biology.
    DOI:  https://doi.org/10.1038/s41467-026-70597-8
  5. Protein Cell. 2026 Mar 25. pii: pwag026. [Epub ahead of print]
    Organelle-anchored translation factories: the roles of neuronal RBP condensates in organizing local protein synthesis in neurological diseases.
    Semin Park, Hari Lim, Jin-A Lee.
      Neurons face a fundamental proteostasis challenge: synapses and axons located far from the soma must rapidly remodel their proteome during activity, stress, and development. While local protein synthesis has long been recognized as essential for meeting these demands, classical models largely focused on ribonucleoprotein (RNP) granules as autonomous carriers of translationally silent mRNAs, treating membranous organelles as parallel logistics or metabolic systems. Recent work overturns this view, revealing that endosomes, lysosomes, axonal endoplasmic reticulum, mitochondria, and their contact sites actively function as mobile translation platforms. In this review, we propose an RBP-centered framework in which phase-separated condensates physically tether specific mRNA cohorts to organelle surfaces, coupling mRNA transport, translational control, and organelle dynamics into a unified network. By organizing recent discoveries into functional modules-long-range transport, localized translation, and stress buffering-this neuron-focused framework identifies organelle-anchored translation factories as a unifying principle of synaptic proteostasis and a broadly applicable design paradigm for highly polarized cells.
    Keywords:  RNA-binding proteins; neuronal local translation; organelle-anchored translation; ribonucleoprotein granules
    DOI:  https://doi.org/10.1093/procel/pwag026
  6. Biochimie. 2026 Mar 25. pii: S0300-9084(26)00077-5. [Epub ahead of print]
    R-loops processing by human apurinic/apyrimidinic endonuclease APE1.
    Anastasia A Gavrilova, Anastasia M Yakovleva, Elena S Mikushina, Mariya I Meschaninova, Darya S Novopashina, Nikita A Kuznetsov, Aleksandra A Kuznetsova.
      R-loops are three-stranded nucleic acid structures that arise during transcription and play important roles in genome regulation, but their unscheduled accumulation can lead to genomic instability. Apurinic/apyrimidinic endonuclease 1 (APE1) is a multifunctional enzyme mainly involved in base excision DNA repair. However, APE1, being both nuclear and cytoplasmic enzyme, could be also considered as important participant of RNA metabolism through their endo- and exoribonuclease as well as RNase H activities. This study investigates the ability of APE1 to process R-loop structures through its various enzymatic activities in vitro. We demonstrate that APE1 exhibits RNase H activity on DNA:RNA hybrids within R-loops, with efficiency decreasing as hybrid length increases beyond 16 nucleotides. Additionally, APE1 cleaves abasic sites in both RNA and DNA strands of R-loops via its AP-endonuclease activity. Notably, an abasic site in the RNA strand is efficiently processed followed by robust 3'-5' exoribonuclease degradation, while an abasic site in the DNA strand is cleaved less efficiently and strongly inhibits RNase H activity. This functional versatility reinforces the importance of APE1 in nucleic acid metabolism, offering new insights into its biological significance beyond traditional DNA repair pathways.
    Keywords:  AP-endonuclease activity; R-loops; RNase H activity; human apurinic/apyrimidinic endonuclease 1 APE1; multifunctional enzymes
    DOI:  https://doi.org/10.1016/j.biochi.2026.03.012
  7. Am J Med Genet A. 2026 Mar 22.
    Expanding the Phenotype of TUFM-Related Combined Oxidative Phosphorylation Deficiency 4.
    Noémie Villeneuve-Cloutier, Jodi Warman-Chardon, Danielle K Bourque.
      Combined oxidative phosphorylation deficiency 4 (COXPD4) is a rare mitochondrial condition caused by biallelic deleterious variants in the nuclear-encoded gene TUFM. To date, most individuals with COXPD4 have presented with encephalopathy, hypotonia, and abnormal brain imaging. Many of the reported individuals died in infancy. We aim to expand the clinical and biochemical phenotype of COXPD4 by reporting on an adult with this condition. Our proband has a homozygous TUFM c.1025T>G, p.(Val342Gly) variant. He has sensorineural hearing loss, hyperlactatemia with mild illness, and reduced activity in mitochondrial complexes I, III, and IV on endomyocardial biopsy. He presents with hypertrophic cardiomyopathy and chronic kidney failure, which have not previously been reported in this condition. Our findings suggest not all individuals with COXPD4 present with significant neurological involvement and highlight the importance of considering COXPD4 as part of the differential diagnosis of hypertrophic cardiomyopathy.
    Keywords:   TUFM ; cardiomyopathy; combined oxidative phosphorylation deficiency 4; lactic acidosis; mitochondrial disorder
    DOI:  https://doi.org/10.1002/ajmg.a.70136
  8. bioRxiv. 2026 Mar 03. pii: 2026.03.03.709289. [Epub ahead of print]
    RNA G-quadruplexes mediate cooperativity in HNRNPH binding and splicing regulation.
    Kerstin Tretow, Mario Keller, Mikhail Mesitov, Miona Corovic, Mirko Brueggemann, Jonas Busam, Farica Zhuang, Nadine Koertel, Nicolas Melchior, Anke Busch, Simon Braun, Nadja Hellmann, Heike Haenel, Pol Basenius, Susanne Strand, Yoseph Barash, Stefan Legewie, Friederike Schmid, Julian Koenig, Kathi Zarnack.
      Alternative splicing, regulated by RNA-binding proteins (RBPs), enables the generation of diverse transcript isoforms critical for cellular function. However, how RNA secondary structure impacts RBP binding and function remains poorly understood. Here, we unravel how RNA G-quadruplexes (rG4s) facilitate cooperativity in splicing regulation by the RBP heterogeneous nuclear ribonucleoprotein H (HNRNPH). Through high-throughput in vivo and in vitro studies combined with theoretical modeling, we dissect how rG4s mediate cooperative HNRNPH binding to RNA, ultimately modulating the splicing of hundreds of exons. rG4 unfolding by HNRNPH exposes multiple G-rich binding sites, thereby establishing indirect cooperativity, which is further amplified to achieve switch-like splicing regulation. HNRNPH-mediated regulation is evident in breast cancer patients, with tumors showing rG4-disrupting variants and global HNRNPH alterations, driving distinct splicing patterns that distinguish tumor subtypes. Overall, our findings offer valuable insights into the mechanistic role of RNA secondary structures in cooperative RBP binding and splicing regulation and highlight the clinical relevance of HNRNPH-dependent splicing in cancer.
    DOI:  https://doi.org/10.64898/2026.03.03.709289
  9. Biotechniques. 2026 Jan-Dec;78(1-12):78(1-12): 1-11
    Quantitative analysis of oligonucleotide delivery into isolated mitochondria: a proof-of-concept method.
    Joshua McHale, Veronica Bazzani, Abdechakour Elkihel, Jing Wu, Ling Peng, Carlo Vascotto.
      Mitochondria, with their own DNA, Represent a potential target for nucleic acid-based precision therapies. However, effective delivery of therapeutic oligonucleotides remains challenging due to the dual mitochondrial membranes and the localization of mitochondrial DNA within nucleoid complexes in the matrix. To understand the delivery process and assess the delivery efficiency of potential vectors, such as dendrimers, it is essential to effectively quantify the oligonucleotides that are successfully delivered to and remain within mitochondria. Currently, there are only limited yet inconvenient methods available for this purpose. Here, we describe a method for quantifying the delivery of fluorescent oligonucleotide cargos in isolated mitochondria using a microfiltration apparatus for reliable fluorescent analysis. By working within a range of dilutions, we are able to safeguard the concentration limits. The quantification protocol also enables the visualization of specific localization within mitochondria, allowing for the determination of whether delivery can occur across both membranes. This is particularly useful, as it offers a key insight into improving vectors as they must deliver the cargoes within the mitochondrial matrix. We validate this method in this proof-of-concept study, providing biological data to assess the difference between two amphiphilic dendrimer vectors for oligonucleotide delivery in mitochondria.
    Keywords:  Oligonucleotide delivery; dendrimers; microfiltration; mitochondria; subcellular localization
    DOI:  https://doi.org/10.1080/07366205.2026.2635461
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