bims-mirnam Biomed News
on Mitochondrial RNA metabolism
Issue of 2026–04–12
six papers selected by
Hana Antonicka, McGill University



  1. Nat Commun. 2026 Apr 04.
      Mitochondrial translation is essential for cellular function, and its dysregulation is associated with mitochondrial disorders and cancer. However, the mechanisms by which human mitochondrial ribosomes initiate translation remain poorly understood, particularly because mitochondrial mRNAs generally lack the 5' untranslated regions that guide translation initiation in bacterial and cytoplasmic systems. Using real-time single-molecule fluorescence measurements, biochemical assays, and cryo-EM analysis, we show that human mitochondrial translation initiation occurs through two parallel pathways. In one pathway, leaderless mRNA first loads onto the 28S small subunit, followed by recruitment of the 39S large subunit to form the 55S initiation complex. In the second pathway, a preassembled 55S monosome directly loads onto leaderless mRNA. Both pathways require recruitment of mtIF2 and fMet-tRNAMet before mRNA binding. However, the monosome-loading pathway tolerates non-formylated Met-tRNAMet and is suppressed by mtIF3. Together, these findings define the heterogeneous pathways of human mitochondrial translation initiation on leaderless mRNAs.
    DOI:  https://doi.org/10.1038/s41467-026-71535-4
  2. PLoS One. 2026 ;21(4): e0337155
      AlkB homolog 1 (ALKBH1) is a member of the AlkB family of Fe(II) and α-ketoglutarate (α-KG)-dependent dioxygenases, known for its enzymatic activity on various nucleic acid substrates. Its reported targets include N1-methyladenosine (m1A), N6-methyladenosine (m6A), N3-methylcytidine (m3C), and 5-methylcytosine (m5C) in RNA, as well as N6-methyladenine (N6-mA, 6mA) in DNA and the histone protein H2A. Moreover, dysregulation or dysfunction of ALKBH1 has been implicated in a broad spectrum of human diseases. In order to shed further light on the substrate scope and role of ALKBH1, we used quantitative mass spectrometry to assess its activity in vitro and in human cell lines. To study ALKBH1 activity on defined substrates in vitro, we enzymatically generated tRNAs specifically carrying the m3C32 (tRNA-ThrUGU and tRNA-SerUCN) and i6A37 (tRNA-SerUCN) modifications. Here we show that ALKBH1 reduces m3C, m1A and m5C in vitro in total extracts of tRNAs, but has no impact on rRNA modifications in human cell lines. However, upon overexpression or siRNA-mediated knock-down of ALKBH1 in human cell lines no impact on the modification of total tRNA extracts or specifically enriched RNAs could be observed. In addition, varying the glucose and fetal bovine serum (FBS) concentration in the growth medium of HEK293T cells, in combination with ALKBH1 siRNA-mediated knock-down, also shows no impact on tRNA methylation. Based on our data, we conclude that in human cells lines grown under optimal conditions ALKBH1 does not play an important role in the demethylation of tRNAs.
    DOI:  https://doi.org/10.1371/journal.pone.0337155
  3. Proc Natl Acad Sci U S A. 2026 Apr 14. 123(15): e2523913123
      In eukaryotic cells, mitochondria form networks that range from highly fused interconnected structures to fragmented populations of individual organelles that undergo transient interactions. These structures can be described as temporal networks of physical units, whose dynamic topology is determined by fusion, fission, and motion of the mitochondria through intracellular space. The heterogeneity of the mitochondrial population is governed by diffusive transport and interunit exchange of proteins, lipids, ions, and RNA within these networks. We present a unifying framework for the dispersion of material within temporal networks of spatially embedded units that span across a broad connectivity range. Specifically, we consider filling of the networks with a locally produced but globally consumed material, demonstrating that the steady-state content is determined by the balance of timescales for spatial encounter between clusters, local fusion, fission, and diffusive transport within a cluster. As the connectivity increases, filling behavior transitions from three-dimensional spread through a "social network" limited by cluster interactions to low-dimensional transport through a largely stationary "physical network" limited by material diffusivity. We extract parameters for mitochondrial networks in three human cell lines, demonstrating that different cells can access both the social and the physical network regimes. These results provide a quantitative basis for predicting the homogenization of biomolecules through a mitochondrial population. Our framework unifies a variety of temporal network structures into an overarching theory for transport through populations of interacting and interconnected units.
    Keywords:  intracellular transport; mitochondria; networks; organelle dynamics; temporal networks
    DOI:  https://doi.org/10.1073/pnas.2523913123
  4. bioRxiv. 2026 Mar 31. pii: 2026.03.13.711628. [Epub ahead of print]
       Motivation: Crosslinking and immunoprecipitation (CLIP) methods remain the gold stan-dard for characterizing RNA binding protein (RBP) behavior. As a result, many researchers rely on CLIP to assess how treatments targeting RBPs alter binding patterns and regulatory activity. However, current tools for differential RBP binding analysis lack core features required for rigorous statistical inference, including proper normalization and appropriate handling of replicate experiments. Furthermore, existing approaches cannot adequately separate expression driven effects from true changes in RBP binding, complicating interpretation of differential analyses. Addressing these limitations is essential for producing reproducible and informative analyses of differential RBP binding.
    Results: Here we present Flipper, an application purpose built for the analysis of differential RBP binding. Flipper introduces several innovations that adapt the DESeq2 framework for robust differential analysis of eCLIP count data. These include integration of input controls to account for expression driven binding shifts, hierarchical normalization strategies that adjust for technical variation without confounding signal to noise ratios, and improved post-differential analysis tools. We demonstrate that Flipper exhibits high specificity when applied to real differential eCLIP data while also providing deeper biological insights. In addition, analyses of both real and simulated data indicate that Flipper achieves superior sensitivity and precision compared with existing approaches. Together, these results highlight Flipper as a robust and generalizable framework for differential RBP binding analysis.
    DOI:  https://doi.org/10.64898/2026.03.13.711628
  5. Nat Commun. 2026 Apr 09.
      Mitochondrial transfer RNA (mt-tRNA) modification determines organelle translation and function. GTPBP3 and MTO1 catalyze 5-taurinomethyluridine (τm5U) modification at wobble uridine of five mt-tRNAs. τm5U hypomodification causes mitochondrial encephalomyopathy, but the underlying pathogenesis and intervention strategy due to GTPBP3 mutations are lacking. In this study, we identify two genetic variants (c.689 A > C (p.Q230P) and c.1120 A > G (p.N374D)) of GTPBP3 in a Chinese proband with metabolic disorders and multisystem dysfunction. Mechanistically, Q230P and N374D mutations induce protein multimerization/aggregation, protease degradation, decreased GTPase activity, and tRNA modification to varying degrees, affecting mitochondrial translation, respiration, dynamics, and function. Homozygous N374D mutations in mice cause embryonic lethality; homozygous E230P or compound heterozygous E230P/N374D knock-in mice develop cardiac and muscular dysfunction due to altered mitochondrial translation. Mitochondrial dysfunction and pathology are efficiently reversed by virus-mediated GTPBP3 expression in cells and animals. This study provides valuable insights into the etiology of and promising intervention strategies for GTPBP3-related diseases.
    DOI:  https://doi.org/10.1038/s41467-026-71750-z
  6. J Mol Biol. 2026 Apr 07. pii: S0022-2836(26)00168-3. [Epub ahead of print] 169795
      RNApdbee 3.0 (publicly available athttps://rnapdbee.cs.put.poznan.pl/) offers an advanced pipeline for comprehensive RNA structural annotation, integrating 2D and 3D data to build detailed nucleotide interaction networks. It classifies base pairs as canonical or noncanonical using the Leontis-Westhof and Saenger schemes and identifies stacking, base-ribose, base-phosphate, and base-triple interactions. The tool handles incomplete or modified residues, marking missing nucleotides and distinguishing noncanonical base pairs for accurate and effective visualization. Results are provided in standard formats - namely, extended dot-bracket notation, BPSEQ, and CT - and in detailed graphical visualizations. RNApdbee decomposes 2D structures into stems, loops, and single strands and offers flexible pseudoknot encoding. Its unified framework addresses inconsistencies across structural data formats by standardizing all inputs to PDBx/mmCIF and integrating seven widely used annotation tools. Finally, RNApdbee ensures reliable, format-independent, and comprehensive RNA structural annotation and interpretation.
    Keywords:  2D structure visualization; RNA 2D structure annotation; RNA 3D structure processing; base-pair identification; consensus 2D structure
    DOI:  https://doi.org/10.1016/j.jmb.2026.169795