bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2024–07–21
eight papers selected by
Edmond Chan, Queen’s University, School of Medicine
  1. The human mitochondrial mRNA structurome reveals mechanisms of gene expression.
  2. RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for degradation and cytosolic release.
  3. Supernumerary proteins of the human mitochondrial ribosomal small subunit are integral for assembly and translation.
  4. ATAD1 prevents clogging of TOM and damage caused by un-imported mitochondrial proteins.
  5. Mfn2-dependent fusion pathway of PE-enriched micron-sized vesicles.
  6. Mitochondrial antioxidants abate SARS-COV-2 pathology in mice.
  7. The actin binding protein profilin 1 localizes inside mitochondria and is critical for their function.
  8. Nup358 restricts ER-mitochondria connectivity by modulating mTORC2/Akt/GSK3β signalling.
  1. Science. 2024 Jul 19. 385(6706): eadm9238
    The human mitochondrial mRNA structurome reveals mechanisms of gene expression.
    J Conor Moran, Amir Brivanlou, Michele Brischigliaro, Flavia Fontanesi, Silvi Rouskin, Antoni Barrientos.
      The human mitochondrial genome encodes crucial oxidative phosphorylation system proteins, pivotal for aerobic energy transduction. They are translated from nine monocistronic and two bicistronic transcripts whose native structures remain unexplored, posing a gap in understanding mitochondrial gene expression. In this work, we devised the mitochondrial dimethyl sulfate mutational profiling with sequencing (mitoDMS-MaPseq) method and applied detection of RNA folding ensembles using expectation-maximization (DREEM) clustering to unravel the native mitochondrial messenger RNA (mt-mRNA) structurome in wild-type (WT) and leucine-rich pentatricopeptide repeat-containing protein (LRPPRC)-deficient cells. Our findings elucidate LRPPRC's role as a holdase contributing to maintaining mt-mRNA folding and efficient translation. mt-mRNA structural insights in WT mitochondria, coupled with metabolic labeling, unveil potential mRNA-programmed translational pausing and a distinct programmed ribosomal frameshifting mechanism. Our data define a critical layer of mitochondrial gene expression regulation. These mt-mRNA folding maps provide a reference for studying mt-mRNA structures in diverse physiological and pathological contexts.
    DOI:  https://doi.org/10.1126/science.adm9238
  2. Mol Cell. 2024 Jul 11. pii: S1097-2765(24)00530-6. [Epub ahead of print]
    RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for degradation and cytosolic release.
    Sujin Kim, Stephanie Tan, Jayoung Ku, Tria Asri Widowati, Doyeong Ku, Keonyong Lee, Kwontae You, Yoosik Kim.
      Mitochondria are essential regulators of innate immunity. They generate long mitochondrial double-stranded RNAs (mt-dsRNAs) and release them into the cytosol to trigger an immune response under pathological stress conditions. Yet the regulation of these self-immunogenic RNAs remains largely unknown. Here, we employ CRISPR screening on mitochondrial RNA (mtRNA)-binding proteins and identify NOP2/Sun RNA methyltransferase 4 (NSUN4) as a key regulator of mt-dsRNA expression in human cells. We find that NSUN4 induces 5-methylcytosine (m5C) modification on mtRNAs, especially on the termini of light-strand long noncoding RNAs. These m5C-modified RNAs are recognized by complement C1q-binding protein (C1QBP), which recruits polyribonucleotide nucleotidyltransferase to facilitate RNA turnover. Suppression of NSUN4 or C1QBP results in increased mt-dsRNA expression, while C1QBP deficiency also leads to increased cytosolic mt-dsRNAs and subsequent immune activation. Collectively, our study unveils the mechanism underlying the selective degradation of light-strand mtRNAs and establishes a molecular mark for mtRNA decay and cytosolic release.
    Keywords:  5-methylcytosine RNA modification; CRISPR screening; RNA stability; RNA-binding protein; innate immunity; mitochondrial double-stranded RNA
    DOI:  https://doi.org/10.1016/j.molcel.2024.06.023
  3. iScience. 2024 Jul 19. 27(7): 110185
    Supernumerary proteins of the human mitochondrial ribosomal small subunit are integral for assembly and translation.
    Taru Hilander, Ryan Awadhpersad, Geoffray Monteuuis, Krystyna L Broda, Max Pohjanpelto, Elizabeth Pyman, Sachin Kumar Singh, Tuula A Nyman, Isabelle Crevel, Robert W Taylor, Ann Saada, Diego Balboa, Brendan J Battersby, Christopher B Jackson, Christopher J Carroll.
      Mitochondrial ribosomes (mitoribosomes) have undergone substantial evolutionary structural remodeling accompanied by loss of ribosomal RNA, while acquiring unique protein subunits located on the periphery. We generated CRISPR-mediated knockouts of all 14 unique (mitochondria-specific/supernumerary) human mitoribosomal proteins (snMRPs) in the small subunit to study the effect on mitoribosome assembly and protein synthesis, each leading to a unique mitoribosome assembly defect with variable impact on mitochondrial protein synthesis. Surprisingly, the stability of mS37 was reduced in all our snMRP knockouts of the small and large ribosomal subunits and patient-derived lines with mitoribosome assembly defects. A redox-regulated CX9C motif in mS37 was essential for protein stability, suggesting a potential mechanism to regulate mitochondrial protein synthesis. Together, our findings support a modular assembly of the human mitochondrial small ribosomal subunit mediated by essential supernumerary subunits and identify a redox regulatory role involving mS37 in mitochondrial protein synthesis in health and disease.
    Keywords:  biochemistry; biological sciences; cell biology; molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2024.110185
  4. Cell Rep. 2024 Jul 17. pii: S2211-1247(24)00802-7. [Epub ahead of print]43(8): 114473
    ATAD1 prevents clogging of TOM and damage caused by un-imported mitochondrial proteins.
    John Kim, Madeleine Goldstein, Lauren Zecchel, Ryan Ghorayeb, Christopher A Maxwell, Hilla Weidberg.
      Mitochondria require the constant import of nuclear-encoded proteins for proper functioning. Impaired protein import not only depletes mitochondria of essential factors but also leads to toxic accumulation of un-imported proteins outside the organelle. Here, we investigate the consequences of impaired mitochondrial protein import in human cells. We demonstrate that un-imported proteins can clog the mitochondrial translocase of the outer membrane (TOM). ATAD1, a mitochondrial ATPase, removes clogged proteins from TOM to clear the entry gate into the mitochondria. ATAD1 interacts with both TOM and stalled proteins, and its knockout results in extensive accumulation of mitochondrial precursors as well as decreased protein import. Increased ATAD1 expression contributes to improved fitness of cells with inefficient mitochondrial protein import. Overall, we demonstrate the importance of the ATAD1 quality control pathway in surveilling protein import and its contribution to cellular health.
    Keywords:  AAA ATPase; ATAD1; CP: Cell biology; CP: Metabolism; TOM clogging; mitochondrial protein import; mitochondrial stress; protein quality control; proteotoxicity
    DOI:  https://doi.org/10.1016/j.celrep.2024.114473
  5. Proc Natl Acad Sci U S A. 2024 Jul 23. 121(30): e2313609121
    Mfn2-dependent fusion pathway of PE-enriched micron-sized vesicles.
    Daniel A Peñalva, Ajay K Monnappa, Paolo Natale, Iván López-Montero.
      Mitofusins (Mfn1 and Mfn2) are the mitochondrial outer-membrane fusion proteins in mammals and belong to the dynamin superfamily of multidomain GTPases. Recent structural studies of truncated variants lacking alpha helical transmembrane domains suggested that Mfns dimerize to promote the approximation and the fusion of the mitochondrial outer membranes upon the hydrolysis of guanine 5'-triphosphate disodium salt (GTP). However, next to the presence of GTP, the fusion activity seems to require multiple regulatory factors that control the dynamics and kinetics of mitochondrial fusion through the formation of Mfn1-Mfn2 heterodimers. Here, we purified and reconstituted the full-length murine Mfn2 protein into giant unilamellar vesicles (GUVs) with different lipid compositions. The incubation with GTP resulted in the fusion of Mfn2-GUVs. High-speed video-microscopy showed that the Mfn2-dependent membrane fusion pathway progressed through a zipper mechanism where the formation and growth of an adhesion patch eventually led to the formation of a membrane opening at the rim of the septum. The presence of physiological concentration (up to 30 mol%) of dioleoyl-phosphatidylethanolamine (DOPE) was shown to be a requisite to observe GTP-induced Mfn2-dependent fusion. Our observations show that Mfn2 alone can promote the fusion of micron-sized DOPE-enriched vesicles without the requirement of regulatory cofactors, such as membrane curvature, or the assistance of other proteins.
    Keywords:  giant unilamellar vesicles; membrane fusion; mitochondrial dynamics; mitofusin 2
    DOI:  https://doi.org/10.1073/pnas.2313609121
  6. Proc Natl Acad Sci U S A. 2024 Jul 23. 121(30): e2321972121
    Mitochondrial antioxidants abate SARS-COV-2 pathology in mice.
    Joseph W Guarnieri, Timothy Lie, Yentli E Soto Albrecht, Peter Hewin, Kellie A Jurado, Gabrielle A Widjaja, Yi Zhu, Meagan J McManus, Todd J Kilbaugh, Kelsey Keith, Prasanth Potluri, Deanne Taylor, Alessia Angelin, Deborah G Murdock, Douglas C Wallace.
      Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection inhibits mitochondrial oxidative phosphorylation (OXPHOS) and elevates mitochondrial reactive oxygen species (ROS, mROS) which activates hypoxia-inducible factor-1alpha (HIF-1α), shifting metabolism toward glycolysis to drive viral biogenesis but also causing the release of mitochondrial DNA (mtDNA) and activation of innate immunity. To determine whether mitochondrially targeted antioxidants could mitigate these viral effects, we challenged mice expressing human angiotensin-converting enzyme 2 (ACE2) with SARS-CoV-2 and intervened using transgenic and pharmacological mitochondrially targeted catalytic antioxidants. Transgenic expression of mitochondrially targeted catalase (mCAT) or systemic treatment with EUK8 decreased weight loss, clinical severity, and circulating levels of mtDNA; as well as reduced lung levels of HIF-1α, viral proteins, and inflammatory cytokines. RNA-sequencing of infected lungs revealed that mCAT and Eukarion 8 (EUK8) up-regulated OXPHOS gene expression and down-regulated HIF-1α and its target genes as well as innate immune gene expression. These data demonstrate that SARS-CoV-2 pathology can be mitigated by catalytically reducing mROS, potentially providing a unique host-directed pharmacological therapy for COVID-19 which is not subject to viral mutational resistance.
    Keywords:  EUK8; SARS-CoV-2; antioxidant therapy; mCAT; mitochondria
    DOI:  https://doi.org/10.1073/pnas.2321972121
  7. EMBO Rep. 2024 Jul 18.
    The actin binding protein profilin 1 localizes inside mitochondria and is critical for their function.
    Tracy-Ann Read, Bruno A Cisterna, Kristen Skruber, Samah Ahmadieh, Tatiana M Liu, Josefine A Vitriol, Yang Shi, Joseph B Black, Mitchell T Butler, Halli L Lindamood, Austin Eyt Lefebvre, Alena Cherezova, Daria V Ilatovskaya, James E Bear, Neal L Weintraub, Eric A Vitriol.
      The monomer-binding protein profilin 1 (PFN1) plays a crucial role in actin polymerization. However, mutations in PFN1 are also linked to hereditary amyotrophic lateral sclerosis, resulting in a broad range of cellular pathologies which cannot be explained by its primary function as a cytosolic actin assembly factor. This implies that there are important, undiscovered roles for PFN1 in cellular physiology. Here we screened knockout cells for novel phenotypes associated with PFN1 loss of function and discovered that mitophagy was significantly upregulated. Indeed, despite successful autophagosome formation, fusion with the lysosome, and activation of additional mitochondrial quality control pathways, PFN1 knockout cells accumulate depolarized, dysmorphic mitochondria with altered metabolic properties. Surprisingly, we also discovered that PFN1 is present inside mitochondria and provide evidence that mitochondrial defects associated with PFN1 loss are not caused by reduced actin polymerization in the cytosol. These findings suggest a previously unrecognized role for PFN1 in maintaining mitochondrial integrity and highlight new pathogenic mechanisms that can result from PFN1 dysregulation.
    Keywords:  Actin; Mitochondria; Mitochondrial-derived Vesicles; Mitophagy; Profilin
    DOI:  https://doi.org/10.1038/s44319-024-00209-3
  8. EMBO Rep. 2024 Jul 18.
    Nup358 restricts ER-mitochondria connectivity by modulating mTORC2/Akt/GSK3β signalling.
    Misha Kalarikkal, Rimpi Saikia, Lizanne Oliveira, Yashashree Bhorkar, Akshay Lonare, Pallavi Varshney, Prathamesh Dhamale, Amitabha Majumdar, Jomon Joseph.
      ER-mitochondria contact sites (ERMCSs) regulate processes, including calcium homoeostasis, energy metabolism and autophagy. Previously, it was shown that during growth factor signalling, mTORC2/Akt gets recruited to and stabilizes ERMCSs. Independent studies showed that GSK3β, a well-known Akt substrate, reduces ER-mitochondria connectivity by disrupting the VAPB-PTPIP51 tethering complex. However, the mechanisms that regulate ERMCSs are incompletely understood. Here we find that annulate lamellae (AL), relatively unexplored subdomains of ER enriched with a subset of nucleoporins, are present at ERMCSs. Depletion of Nup358, an AL-resident nucleoporin, results in enhanced mTORC2/Akt activation, GSK3β inhibition and increased ERMCSs. Depletion of Rictor, a mTORC2-specific subunit, or exogenous expression of GSK3β, was sufficient to reverse the ERMCS-phenotype in Nup358-deficient cells. We show that growth factor-mediated activation of mTORC2 requires the VAPB-PTPIP51 complex, whereas, Nup358's association with this tether restricts mTORC2/Akt signalling and ER-mitochondria connectivity. Expression of a Nup358 fragment that is sufficient for interaction with the VAPB-PTPIP51 complex suppresses mTORC2/Akt activation and disrupts ERMCSs. Collectively, our study uncovers a novel role for Nup358 in controlling ERMCSs by modulating the mTORC2/Akt/GSK3β axis.
    Keywords:  Annulate Lamellae; ER-mitochondria Contact Sites; GSK3β; Nucleoporins; mTORC2
    DOI:  https://doi.org/10.1038/s44319-024-00204-8
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