bims-mitran 2025-04-20 papers

Issue of 2025–04–20
six papers selected by
Andreas Kohler, Umeå University

Trends Biochem Sci. 2025 Apr 11. pii: S0968-0004(25)00056-8. [Epub ahead of print]

Emerging mechanisms of human mitochondrial translation regulation.

Michele Brischigliaro, Ahram Ahn, Seungwoo Hong, Flavia Fontanesi, Antoni Barrientos.

Mitochondrial translation regulation enables precise control over the synthesis of hydrophobic proteins encoded by the organellar genome, orchestrating their membrane insertion, accumulation, and assembly into oxidative phosphorylation (OXPHOS) complexes. Recent research highlights regulation across all translation stages (initiation, elongation, termination, and recycling) through a complex interplay of mRNA structures, specialized translation factors, and unique regulatory mechanisms that adjust protein levels for stoichiometric assembly. Key discoveries include mRNA-programmed ribosomal pausing, frameshifting, and termination-dependent re-initiation, which fine-tune protein synthesis and promote translation of overlapping open reading frames (ORFs) in bicistronic transcripts. In this review, we examine these advances, which are significantly enhancing our understanding of mitochondrial gene expression.

Keywords: RNA folding; mitochondrial translation; programmed ribosomal frameshifting; ribosome stalling; termination-reinitiation

DOI: https://doi.org/10.1016/j.tibs.2025.03.007

Nat Commun. 2025 Apr 17. 16(1): 3641

Coupling of ribosome biogenesis and translation initiation in human mitochondria.

Marleen Heinrichs, Anna Franziska Finke, Shintaro Aibara, Angelique Krempler, Angela Boshnakovska, Peter Rehling, Hauke S Hillen, Ricarda Richter-Dennerlein.

Biogenesis of mitoribosomes requires dedicated chaperones, RNA-modifying enzymes, and GTPases, and defects in mitoribosome assembly lead to severe mitochondriopathies in humans. Here, we characterize late-step assembly states of the small mitoribosomal subunit (mtSSU) by combining genetic perturbation and mutagenesis analysis with biochemical and structural approaches. Isolation of native mtSSU biogenesis intermediates via a FLAG-tagged variant of the GTPase MTG3 reveals three distinct assembly states, which show how factors cooperate to mature the 12S rRNA. In addition, we observe four distinct primed initiation mtSSU states with an incompletely matured rRNA, suggesting that biogenesis and translation initiation are not mutually exclusive processes but can occur simultaneously. Together, these results provide insights into mtSSU biogenesis and suggest a functional coupling between ribosome biogenesis and translation initiation in human mitochondria.

DOI: https://doi.org/10.1038/s41467-025-58827-x

Sci Adv. 2025 Apr 18. 11(16): eads6830

Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.

Adam Begeman, John A Smolka, Ahmad Shami, Tejashree Pradip Waingankar, Samantha C Lewis.

Protein- and RNA-rich bodies contribute to the spatial organization of gene expression in the cell and are also sites of quality control critical to cell fitness. In most eukaryotes, mitochondria harbor their own genome, and all steps of mitochondrial gene expression co-occur within a single compartment-the matrix. Here, we report that processed mitochondrial RNAs are consolidated into micrometer-scale translation hubs distal to mitochondrial DNA transcription and RNA processing sites in human cells. We find that, during stress, mitochondrial messenger and ribosomal RNA are sequestered in mesoscale bodies containing mitoribosome components, concurrent with suppression of active translation. Stress bodies are triggered by proteotoxic stress downstream of double-stranded RNA accumulation in cells lacking unwinding activity of the highly conserved helicase SUPV3L1/SUV3. We propose that the spatial organization of nascent polypeptide synthesis into discrete domains serves to throttle the flow of genetic information to support recovery of mitochondrial quality control.

DOI: https://doi.org/10.1126/sciadv.ads6830

Biochim Biophys Acta Mol Cell Res. 2025 Apr 15. pii: S0167-4889(25)00060-6. [Epub ahead of print] 119955

In vivo composition of the mitochondrial nucleoid in mice.

Rodolfo García-Villegas, Franka Odenthal, Yvonne Giannoula, Nina A Bonekamp, Inge Kühl, Chan Bae Park, Henrik Spåhr, Elisa Motori, Fredrik Levander, Nils-Göran Larsson.

Mitochondrial DNA (mtDNA) is compacted into dynamic structures called mitochondrial nucleoids (mt-nucleoids), with the mitochondrial transcription factor A (TFAM) as the core packaging protein. We generated bacterial artificial chromosome (BAC) transgenic mice expressing FLAG-tagged TFAM protein (Tfam-FLAGBAC mice) to investigate the mt-nucleoid composition in vivo. Importantly, we show that the TFAM-FLAG protein is functional and complements the absence of the wild-type TFAM protein in homozygous Tfam knockout mice. We performed immunoprecipitation experiments from different mouse tissues and identified 12 proteins as core mt-nucleoid components by proteomics analysis. Among these, eight proteins correspond to mtDNA replication and transcription factors, while the other four are involved in the mitoribosome assembly. In addition, we used the Tfam-FLAGBAC mice to identify ten proteins that may stabilize TFAM-FLAG upon depletion of the mitochondrial RNA polymerase despite the absence of mtDNA and induction of the LONP1 protease. Finally, we evaluated the changes in mt-nucleoids caused by very high levels of TFAM unraveling nine interactors that could counteract the high TFAM levels to maintain active mtDNA transcription. Altogether, we demonstrate that the Tfam-FLAGBAC mice are a valuable tool for investigating the mt-nucleoid composition in vivo.

Keywords: Mitochondrial nucleoid; Mitochondrial translation; TFAM; Transgenic mice; mtDNA expression

DOI: https://doi.org/10.1016/j.bbamcr.2025.119955

Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2417477122

The POLγ Y951N patient mutation disrupts the switch between DNA synthesis and proofreading, triggering mitochondrial DNA instability.

Josefin M E Forslund, Tran V H Nguyen, Vimal Parkash, Andreas Berner, Steffi Goffart, Jaakko L O Pohjoismäki, Paulina H Wanrooij, Erik Johansson, Sjoerd Wanrooij.

Mitochondrial DNA (mtDNA) stability, essential for cellular energy production, relies on DNA polymerase gamma (POLγ). Here, we show that the POLγ Y951N disease-causing mutation induces replication stalling and severe mtDNA depletion. However, unlike other POLγ disease-causing mutations, Y951N does not directly impair exonuclease activity and only mildly affects polymerase activity. Instead, we found that Y951N compromises the enzyme's ability to efficiently toggle between DNA synthesis and degradation, and is thus a patient-derived mutation with impaired polymerase-exonuclease switching. These findings provide insights into the intramolecular switch when POLγ proofreads the newly synthesized DNA strand and reveal a new mechanism for causing mitochondrial DNA instability.

Keywords: DNA polymerases; mitochondria; mitochondrial disease; mtDNA; mtDNA replication

DOI: https://doi.org/10.1073/pnas.2417477122