bims-mitran Biomed News
on Mitochondrial translation
Issue of 2021–10–24
thirteen papers selected by
Andreas Kohler, Stockholm University
  1. An in vitro system to silence mitochondrial gene expression.
  2. Mitochondrial Translation Occurs Preferentially in the Peri-Nuclear Mitochondrial Network of Cultured Human Cells.
  3. Multi-Omics Approach to Mitochondrial DNA Damage in Human Muscle Fibers.
  4. Cell-Free Mitochondrial DNA as a Potential Biomarker for Astronauts' Health.
  5. Human Mitochondrial DNA: Particularities and Diseases.
  6. Research progress on the physiological function of mtDNA and its specific detection and therapy.
  7. Decreasing mitochondrial RNA polymerase activity reverses biased inheritance of hypersuppressive mtDNA.
  8. Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation.
  9. Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data.
  10. Association of snR190 snoRNA chaperone with early pre-60S particles is regulated by the RNA helicase Dbp7 in yeast.
  11. [mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts].
  12. The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering.
  13. The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly.
  1. Cell. 2021 Oct 11. pii: S0092-8674(21)01116-8. [Epub ahead of print]
    An in vitro system to silence mitochondrial gene expression.
    Luis Daniel Cruz-Zaragoza, Sven Dennerlein, Andreas Linden, Roya Yousefi, Elena Lavdovskaia, Abhishek Aich, Rebecca R Falk, Ridhima Gomkale, Thomas Schöndorf, Markus T Bohnsack, Ricarda Richter-Dennerlein, Henning Urlaub, Peter Rehling.
      The human mitochondrial genome encodes thirteen core subunits of the oxidative phosphorylation system, and defects in mitochondrial gene expression lead to severe neuromuscular disorders. However, the mechanisms of mitochondrial gene expression remain poorly understood due to a lack of experimental approaches to analyze these processes. Here, we present an in vitro system to silence translation in purified mitochondria. In vitro import of chemically synthesized precursor-morpholino hybrids allows us to target translation of individual mitochondrial mRNAs. By applying this approach, we conclude that the bicistronic, overlapping ATP8/ATP6 transcript is translated through a single ribosome/mRNA engagement. We show that recruitment of COX1 assembly factors to translating ribosomes depends on nascent chain formation. By defining mRNA-specific interactomes for COX1 and COX2, we reveal an unexpected function of the cytosolic oncofetal IGF2BP1, an RNA-binding protein, in mitochondrial translation. Our data provide insight into mitochondrial translation and innovative strategies to investigate mitochondrial gene expression.
    Keywords:  IGF2BP1; antisense; mitochondria; mitochondrial ribosome; morpholino; oxidative phosphorylation; translation
    DOI:  https://doi.org/10.1016/j.cell.2021.09.033
  2. Biology (Basel). 2021 Oct 15. pii: 1050. [Epub ahead of print]10(10):
    Mitochondrial Translation Occurs Preferentially in the Peri-Nuclear Mitochondrial Network of Cultured Human Cells.
    Christin A Albus, Rolando Berlinguer-Palmini, Caroline Hewison, Fiona McFarlane, Elisabeta-Ana Savu, Robert N Lightowlers, Zofia M Chrzanowska-Lightowlers, Matthew Zorkau.
      Human mitochondria are highly dynamic organelles, fusing and budding to maintain reticular networks throughout many cell types. Although extending to the extremities of the cell, the majority of the network is concentrated around the nucleus in most of the commonly cultured cell lines. This organelle harbours its own genome, mtDNA, with a different gene content to the nucleus, but the expression of which is critical for maintaining oxidative phosphorylation. Recent advances in click chemistry have allowed us to visualise sites of mitochondrial protein synthesis in intact cultured cells. We show that the majority of translation occurs in the peri-nuclear region of the network. Further analysis reveals that whilst there is a slight peri-nuclear enrichment in the levels of mitoribosomal protein and mitochondrial rRNA, it is not sufficient to explain this substantial heterogeneity in the distribution of translation. Finally, we also show that in contrast, a mitochondrial mRNA does not show such a distinct gradient in distribution. These data suggest that the relative lack of translation in the peripheral mitochondrial network is not due to an absence of mitoribosomes or an insufficient supply of the mt-mRNA transcripts.
    Keywords:  co-localisation; heterogeneity; mammalian; mitochondria; peri-nuclear; peripheral; protein synthesis
    DOI:  https://doi.org/10.3390/biology10101050
  3. Int J Mol Sci. 2021 Oct 14. pii: 11080. [Epub ahead of print]22(20):
    Multi-Omics Approach to Mitochondrial DNA Damage in Human Muscle Fibers.
    Matthias Elstner, Konrad Olszewski, Holger Prokisch, Thomas Klopstock, Marta Murgia.
      Mitochondrial DNA deletions affect energy metabolism at tissue-specific and cell-specific threshold levels, but the pathophysiological mechanisms determining cell fate remain poorly understood. Chronic progressive external ophthalmoplegia (CPEO) is caused by mtDNA deletions and characterized by a mosaic distribution of muscle fibers with defective cytochrome oxidase (COX) activity, interspersed among fibers with retained functional respiratory chain. We used diagnostic histochemistry to distinguish COX-negative from COX-positive fibers in nine muscle biopsies from CPEO patients and performed laser capture microdissection (LCM) coupled to genome-wide gene expression analysis. To gain molecular insight into the pathogenesis, we applied network and pathway analysis to highlight molecular differences of the COX-positive and COX-negative fiber transcriptome. We then integrated our results with proteomics data that we previously obtained comparing COX-positive and COX-negative fiber sections from three other patients. By virtue of the combination of LCM and a multi-omics approach, we here provide a comprehensive resource to tackle the pathogenic changes leading to progressive respiratory chain deficiency and disease in mitochondrial deletion syndromes. Our data show that COX-negative fibers upregulate transcripts involved in translational elongation and protein synthesis. Furthermore, based on functional annotation analysis, we find that mitochondrial transcripts are the most enriched among those with significantly different expression between COX-positive and COX-negative fibers, indicating that our unbiased large-scale approach resolves the core of the pathogenic changes. Further enrichments include transcripts encoding LIM domain proteins, ubiquitin ligases, proteins involved in RNA turnover, and, interestingly, cell cycle arrest and cell death. These pathways may thus have a functional association to the molecular pathogenesis of the disease. Overall, the transcriptome and proteome show a low degree of correlation in CPEO patients, suggesting a relevant contribution of post-transcriptional mechanisms in shaping this disease phenotype.
    Keywords:  disease models; mtDNA deletions; myopathy; proteomics; skeletal muscle; transcriptomics
    DOI:  https://doi.org/10.3390/ijms222011080
  4. J Am Heart Assoc. 2021 Oct 20. e022055
    Cell-Free Mitochondrial DNA as a Potential Biomarker for Astronauts' Health.
    Malik Bisserier, Santhanam Shanmughapriya, Amit Kumar Rai, Carolina Gonzalez, Agnieszka Brojakowska, Venkata Naga Srikanth Garikipati, Muniswamy Madesh, Paul J Mills, Kenneth Walsh, Arsen Arakelyan, Raj Kishore, Lahouaria Hadri, David A Goukassian.
      Background Space travel-associated stressors such as microgravity or radiation exposure have been reported in astronauts after short- and long-duration missions aboard the International Space Station. Despite risk mitigation strategies, adverse health effects remain a concern. Thus, there is a need to develop new diagnostic tools to facilitate early detection of physiological stress. Methods and Results We measured the levels of circulating cell-free mitochondrial DNA in blood plasma of 14 astronauts 10 days before launch, the day of landing, and 3 days after return. Our results revealed a significant increase of cell-free mitochondrial DNA in the plasma on the day of landing and 3 days after return with vast ~2 to 355-fold interastronaut variability. In addition, gene expression analysis of peripheral blood mononuclear cells revealed a significant increase in markers of inflammation, oxidative stress, and DNA damage. Conclusions Our study suggests that cell-free mitochondrial DNA abundance might be a biomarker of stress or immune response related to microgravity, radiation, and other environmental factors during space flight.
    Keywords:  astronaut; biomarker; cell‐free DNA; space medicine
    DOI:  https://doi.org/10.1161/JAHA.121.022055
  5. Biomedicines. 2021 Oct 01. pii: 1364. [Epub ahead of print]9(10):
    Human Mitochondrial DNA: Particularities and Diseases.
    Mouna Habbane, Julio Montoya, Taha Rhouda, Yousra Sbaoui, Driss Radallah, Sonia Emperador.
      Mitochondria are the cell's power site, transforming energy into a form that the cell can employ for necessary metabolic reactions. These organelles present their own DNA. Although it codes for a small number of genes, mutations in mtDNA are common. Molecular genetics diagnosis allows the analysis of DNA in several areas such as infectiology, oncology, human genetics and personalized medicine. Knowing that the mitochondrial DNA is subject to several mutations which have a direct impact on the metabolism of the mitochondrion leading to many diseases, it is therefore necessary to detect these mutations in the patients involved. To date numerous mitochondrial mutations have been described in humans, permitting confirmation of clinical diagnosis, in addition to a better management of the patients. Therefore, different techniques are employed to study the presence or absence of mitochondrial mutations. However, new mutations are discovered, and to determine if they are the cause of disease, different functional mitochondrial studies are undertaken using transmitochondrial cybrid cells that are constructed by fusion of platelets of the patient that presents the mutation, with rho osteosarcoma cell line. Moreover, the contribution of next generation sequencing allows sequencing of the entire human genome within a single day and should be considered in the diagnosis of mitochondrial mutations.
    Keywords:  mitochondrial diseases; molecular diagnosis; mtDNA; mutation
    DOI:  https://doi.org/10.3390/biomedicines9101364
  6. Chembiochem. 2021 Oct 18.
    Research progress on the physiological function of mtDNA and its specific detection and therapy.
    Congcong Zhang, Yufei Xue, Lan Wang, Qiong Wu, Bin Fang, Yu Shen, Hua Bai, Bo Peng, Naidi Yang, Lin Li.
      Mitochondrial DNA (mtDNA) is a mitochondrial genetic material, which is a circular double-stranded deoxyribonucleotide found in the mitochondria of cells. Despite the diminutive size of mitochondrial genome, mtDNA mutations are an important cause of mitochondrial diseases that are characterized by defects in oxidative phosphorylation. Mitochondrial diseases are involved in multiple systems, particularly in the organs that are highly dependent on aerobic metabolism. The diagnosis of mitochondrial disease is further complicated since mtDNA mutations can cause various clinical symptoms. To obtain more accurate diagnosis and treatment of mitochondrial diseases, the detection of mtDNA and the design of drugs acting on mtDNA are extremely important. Over the past few years, many probes and therapeutic drugs targeting mtDNA have been developed, making significant contributions to fundamental research including elucidation of the mechanisms of mitochondrial diseases at the genetic level. In this review, we summarize the structure, function, detection and their applications in mechanisms exploration and treatment of mtDNA mutation-related disorders. Noting that we specifically discuss how these probes and drugs for mtDNA are designed and developed. We hope that this review will provide readers with a comprehensive understanding of the importance of mtDNA, and promote the development of effective molecules for theragnosis of mtDNA mutation-related diseases.
    Keywords:  DNA targeting; Fluorescent probes; Mitochondrial DNA; mitochondrial dysfunction; mitochondrial therapy
    DOI:  https://doi.org/10.1002/cbic.202100474
  7. PLoS Genet. 2021 Oct 19. 17(10): e1009808
    Decreasing mitochondrial RNA polymerase activity reverses biased inheritance of hypersuppressive mtDNA.
    Daniel Corbi, Angelika Amon.
      Faithful inheritance of mitochondrial DNA (mtDNA) is crucial for cellular respiration/oxidative phosphorylation and mitochondrial membrane potential. However, how mtDNA is transmitted to progeny is not fully understood. We utilized hypersuppressive mtDNA, a class of respiratory deficient Saccharomyces cerevisiae mtDNA that is preferentially inherited over wild-type mtDNA (rho+), to uncover the factors governing mtDNA inheritance. We found that some regions of rho+ mtDNA persisted while others were lost after a specific hypersuppressive takeover indicating that hypersuppressive preferential inheritance may partially be due to active destruction of rho+ mtDNA. From a multicopy suppression screen, we found that overexpression of putative mitochondrial RNA exonuclease PET127 reduced biased inheritance of a subset of hypersuppressive genomes. This suppression required PET127 binding to the mitochondrial RNA polymerase RPO41 but not PET127 exonuclease activity. A temperature-sensitive allele of RPO41 improved rho+ mtDNA inheritance over a specific hypersuppressive mtDNA at semi-permissive temperatures revealing a previously unknown role for rho+ transcription in promoting hypersuppressive mtDNA inheritance.
    DOI:  https://doi.org/10.1371/journal.pgen.1009808
  8. EMBO J. 2021 Oct 20. e108299
    Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation.
    Yuhei Chadani, Nobuyuki Sugata, Tatsuya Niwa, Yosuke Ito, Shintaro Iwasaki, Hideki Taguchi.
      Continuous translation elongation, irrespective of amino acid sequences, is a prerequisite for living organisms to produce their proteomes. However, nascent polypeptide products bear an inherent risk of elongation abortion. For example, negatively charged sequences with occasional intermittent prolines, termed intrinsic ribosome destabilization (IRD) sequences, weaken the translating ribosomal complex, causing certain nascent chain sequences to prematurely terminate translation. Here, we show that most potential IRD sequences in the middle of open reading frames remain cryptic and do not interrupt translation, due to two features of the nascent polypeptide. Firstly, the nascent polypeptide itself spans the exit tunnel, and secondly, its bulky amino acid residues occupy the tunnel entrance region, thereby serving as a bridge and protecting the large and small ribosomal subunits from dissociation. Thus, nascent polypeptide products have an inbuilt ability to ensure elongation continuity.
    Keywords:  cell-free translation; nascent polypeptide chain; polypeptidyl-tRNA; ribosomal exit tunnel; ribosome
    DOI:  https://doi.org/10.15252/embj.2021108299
  9. Methods. 2021 Oct 18. pii: S1046-2023(21)00230-9. [Epub ahead of print]
    Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data.
    Gobet Cédric, Félix Naef.
      Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained difficult to measure. Recently, the development of ribosome profiling has enabled the inference of translation parameters through modelling, as this method informs on the ribosome position along the mRNA. Here, we present an automated, reproducible and portable computational pipeline to infer single-codon and codon-pair dwell times as well as gene flux from raw ribosome profiling sequencing data. As a case study, we applied our workflow to a publicly available yeast ribosome profiling dataset consisting of 57 independent gene knockouts related to RNA and tRNA modifications. We uncovered the effect of those modifications on translation elongation and codon selection during decoding. In particular, knocking out mod5 and trm7 increases codon-specific dwell times which indicates their potential tRNA targets, and effect of nucleotide modifications on ribosome decoding rate.
    DOI:  https://doi.org/10.1016/j.ymeth.2021.10.004
  10. Nat Commun. 2021 Oct 22. 12(1): 6153
    Association of snR190 snoRNA chaperone with early pre-60S particles is regulated by the RNA helicase Dbp7 in yeast.
    Mariam Jaafar, Julia Contreras, Carine Dominique, Sara Martín-Villanueva, Régine Capeyrou, Patrice Vitali, Olga Rodríguez-Galán, Carmen Velasco, Odile Humbert, Nicholas J Watkins, Eduardo Villalobo, Katherine E Bohnsack, Markus T Bohnsack, Yves Henry, Raghida Abou Merhi, Jesús de la Cruz, Anthony K Henras.
      Synthesis of eukaryotic ribosomes involves the assembly and maturation of precursor particles (pre-ribosomal particles) containing ribosomal RNA (rRNA) precursors, ribosomal proteins (RPs) and a plethora of assembly factors (AFs). Formation of the earliest precursors of the 60S ribosomal subunit (pre-60S r-particle) is among the least understood stages of ribosome biogenesis. It involves the Npa1 complex, a protein module suggested to play a key role in the early structuring of the pre-rRNA. Npa1 displays genetic interactions with the DExD-box protein Dbp7 and interacts physically with the snR190 box C/D snoRNA. We show here that snR190 functions as a snoRNA chaperone, which likely cooperates with the Npa1 complex to initiate compaction of the pre-rRNA in early pre-60S r-particles. We further show that Dbp7 regulates the dynamic base-pairing between snR190 and the pre-rRNA within the earliest pre-60S r-particles, thereby participating in structuring the peptidyl transferase center (PTC) of the large ribosomal subunit.
    DOI:  https://doi.org/10.1038/s41467-021-26207-w
  11. Mol Biol (Mosk). 2021 Sep-Oct;55(4):55(4): 796-828
    [mRNA Targeting, Transport and Local Translation in Eukaryotic Cells: From the Classical View to a Diversity of New Concepts].
    K A Lashkevich, S E Dmitriev.
      Spatial organization of protein biosynthesis in the eukaryotic cell has been studied for more than fifty years, thus many facts have already been included in textbooks. According to the classical view, mRNA transcripts encoding secreted and transmembrane proteins are translated by ribosomes associated with endoplasmic reticulum membranes, while soluble cytoplasmic proteins are synthesized on free polysomes. However, in the last few years, new data has emerged, revealing selective translation of mRNA on mitochondria and plastids, in proximity to peroxisomes and endosomes, in various granules and at the cytoskeleton (actin network, vimentin intermediate filaments, microtubules and centrosomes). There are also long-standing debates about the possibility of protein synthesis in the nucleus. Localized translation can be determined by targeting signals in the synthesized protein, nucleotide sequences in the mRNA itself, or both. With RNA-binding proteins, many transcripts can be assembled into specific RNA condensates and form RNP particles, which may be transported by molecular motors to the sites of active translation, form granules and provoke liquid-liquid phase separation in the cytoplasm, both under normal conditions and during cell stress. The translation of some mRNAs occurs in specialized "translation factories," assemblysomes, transperons and other structures necessary for the correct folding of proteins, interaction with functional partners and formation of oligomeric complexes. Intracellular localization of mRNA has a significant impact on the efficiency of its translation and presumably determines its response to cellular stress. Compartmentalization of mRNAs and the translation machinery also plays an important role in viral infections. Many viruses provoke the formation of specific intracellular structures, virus factories, for the production of their proteins. Here we review the current concepts of the molecular mechanisms of transport, selective localization and local translation of cellular and viral mRNAs, their effects on protein targeting and topogenesis, and on the regulation of protein biosynthesis in different compartments of the eukaryotic cell. Special attention is paid to new systems biology approaches, providing new cues to the study of localized translation.
    Keywords:  assemblysomes; endoplasmic reticulum; localized translation; mRNA transport; mitochondria; nuclear translation; stress granules; translation factories; viral factories
    DOI:  https://doi.org/10.31857/S002689842104008X
  12. Chem Sci. 2021 Sep 15. 12(35): 11851-11857
    The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering.
    Quyen V Vu, Yang Jiang, Mai Suan Li, Edward P O'Brien.
      Interactions between the ribosome and nascent chain can destabilize folded domains in the ribosome exit tunnel's vestibule, the last 3 nm of the exit tunnel where tertiary folding can occur. Here, we test if a contribution to this destabilization is a weakening of hydrophobic association, the driving force for protein folding. Using all-atom molecular dynamics simulations, we calculate the potential-of-mean force between two methane molecules along the center line of the ribosome exit tunnel and in bulk solution. Associated methanes, we find, are half as stable in the ribosome's vestibule as compared to bulk solution, demonstrating that the hydrophobic effect is weakened by the presence of the ribosome. This decreased stability arises from a decrease in the amount of water entropy gained upon the association of the methanes. And this decreased entropy gain originates from water molecules being more ordered in the vestibule as compared to bulk solution. Therefore, the hydrophobic effect is weaker in the vestibule because waters released from the first solvation shell of methanes upon association do not gain as much entropy in the vestibule as they do upon release in bulk solution. These findings mean that nascent proteins pass through a ribosome vestibule environment that can destabilize folded structures, which has the potential to influence co-translational protein folding pathways, energetics, and kinetics.
    DOI:  https://doi.org/10.1039/d1sc01008e
  13. Nat Commun. 2021 Oct 22. 12(1): 6152
    The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly.
    Gerald Ryan R Aquino, Philipp Hackert, Nicolai Krogh, Kuan-Ting Pan, Mariam Jaafar, Anthony K Henras, Henrik Nielsen, Henning Urlaub, Katherine E Bohnsack, Markus T Bohnsack.
      Early pre-60S ribosomal particles are poorly characterized, highly dynamic complexes that undergo extensive rRNA folding and compaction concomitant with assembly of ribosomal proteins and exchange of assembly factors. Pre-60S particles contain numerous RNA helicases, which are likely regulators of accurate and efficient formation of appropriate rRNA structures. Here we reveal binding of the RNA helicase Dbp7 to domain V/VI of early pre-60S particles in yeast and show that in the absence of this protein, dissociation of the Npa1 scaffolding complex, release of the snR190 folding chaperone, recruitment of the A3 cluster factors and binding of the ribosomal protein uL3 are impaired. uL3 is critical for formation of the peptidyltransferase center (PTC) and is responsible for stabilizing interactions between the 5' and 3' ends of the 25S, an essential pre-requisite for subsequent pre-60S maturation events. Highlighting the importance of pre-ribosome remodeling by Dbp7, our data suggest that in the absence of Dbp7 or its catalytic activity, early pre-ribosomal particles are targeted for degradation.
    DOI:  https://doi.org/10.1038/s41467-021-26208-9
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