bims-mitran Biomed News
on Mitochondrial translation
Issue of 2021–09–19
eight papers selected by
Andreas Kohler, Stockholm University
  1. Cristae-dependent quality control of the mitochondrial genome.
  2. A role for mitochondrial DNA in cellular proteostasis.
  3. Analysis of codon-specific translation by ribosome profiling.
  4. A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability.
  5. Investigating the consequences of mRNA modifications on protein synthesis using in vitro translation assays.
  6. Efficient fractionation and analysis of ribosome assembly intermediates in human cells.
  7. Structural basis of human transcription-DNA repair coupling.
  8. Increased fidelity of protein synthesis extends lifespan.
  1. Sci Adv. 2021 Sep 03. 7(36): eabi8886
    Cristae-dependent quality control of the mitochondrial genome.
    Christopher Jakubke, Rodaria Roussou, Andreas Maiser, Christina Schug, Felix Thoma, David Bunk, David Hörl, Heinrich Leonhardt, Peter Walter, Till Klecker, Christof Osman.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/sciadv.abi8886
  2. Nat Rev Genet. 2021 Sep 13.
    A role for mitochondrial DNA in cellular proteostasis.
    Caroline Barranco.
      
    DOI:  https://doi.org/10.1038/s41576-021-00418-9
  3. Methods Enzymol. 2021 ;pii: S0076-6879(21)00284-6. [Epub ahead of print]658 191-223
    Analysis of codon-specific translation by ribosome profiling.
    Yeji Kim, Cristian Eggers, Ekaterina Shvetsova, Leon Kleemann, Olga Sin, Sebastian A Leidel.
      Chemical modifications of RNA molecules can affect translation in multiple ways. Therefore, it is critical to understand how their absence changes cellular translation dynamics and in particular codon-specific translation. In this chapter, we discuss the application of ribosome profiling to analyze changes in codon-specific translation and differential translation in Saccharomyces cerevisiae and human cells.
    Keywords:  Codon-specific translation; RNA modification; Ribosome profiling; tRNA
    DOI:  https://doi.org/10.1016/bs.mie.2021.06.025
  4. Elife. 2021 09 15. pii: e71611. [Epub ahead of print]10
    A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability.
    Michele Felletti, Cédric Romilly, E Gerhart H Wagner, Kristina Jonas.
      The ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes; nevertheless, the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability in Caulobacter crescentus. By performing a detailed biochemical and genetic analysis of the dnaA mRNA, we identified a sequence downstream of the dnaA start codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, is critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that translation regulation by nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.
    Keywords:  DNA replication; E. coli; bacteria; chromosomes; gene expression; infectious disease; mRNA; microbiology; ribosome; starvation; translation
    DOI:  https://doi.org/10.7554/eLife.71611
  5. Methods Enzymol. 2021 ;pii: S0076-6879(21)00270-6. [Epub ahead of print]658 379-406
    Investigating the consequences of mRNA modifications on protein synthesis using in vitro translation assays.
    Jeremy G Monroe, Tyler J Smith, Kristin S Koutmou.
      The ribosome translates the information stored in the genetic code into functional proteins. In this process messenger RNAs (mRNAs) serve as templates for the ribosome, ensuring that amino acids are linked together in the correct order. Chemical modifications to mRNA nucleosides have the potential to influence the rate and accuracy of protein synthesis. Here, we present an in vitro Escherichia coli translation system utilizing highly purified components to directly investigate the impact of mRNA modifications on the speed and accuracy of the ribosome. This system can be used to gain insights into how individual chemical modifications influence translation on the molecular level. While the fully reconstituted system described in this chapter requires a lengthy time investment to prepare experimental materials, it is highly verstaile and enables the systematic assessment of how single variables influence protein synthesis by the ribosome.
    Keywords:  Fidelity; In vitro translation; Miscoding; RNA modification; Ribosome purification; mRNA modification; tRNA purification
    DOI:  https://doi.org/10.1016/bs.mie.2021.06.011
  6. RNA Biol. 2021 Sep 17. 1-16
    Efficient fractionation and analysis of ribosome assembly intermediates in human cells.
    Blanca Nieto, Sonia G Gaspar, Russell T Sapio, Laura Clavaín, Xosé R Bustelo, Dimitri G Pestov, Mercedes Dosil.
      Biochemical studies of the human ribosome synthesis pathway have been hindered by technical difficulties in obtaining intact preribosomal complexes from internal regions of the nucleolus. Here we provide a detailed description of an extraction method that enables efficient detection, isolation, and characterization of nucleolar preribosomes containing large pre-rRNA species. The three-step Preribosome Sequential Extraction (PSE) protocol preserves the integrity of early preribosomal complexes and yields preparations amenable to biochemical analyses from low amounts of starting material. We validate this procedure through the detection of specific trans-acting factors and pre-rRNAs in the extracted preribosomes using affinity matrix pull-downs and sedimentation assays. In addition, we describe the application of the PSE method for monitoring cellular levels of ribosome-free 5S RNP complexes as an indicator of ribosome biogenesis stress. Our optimized experimental procedures will facilitate studies of human ribosome biogenesis in normal, mutant and stressed-cell scenarios, including the characterization of candidate ribosome biogenesis factors, preribosome interactors under specific physiological conditions or effects of drugs on ribosome maturation.
    Keywords:  Human ribosome synthesis; pre-rRNA maturation; preribosomes; ribosome assembly
    DOI:  https://doi.org/10.1080/15476286.2021.1965754
  7. Nature. 2021 Sep 15.
    Structural basis of human transcription-DNA repair coupling.
    Goran Kokic, Felix R Wagner, Aleksandar Chernev, Henning Urlaub, Patrick Cramer.
      Transcription-coupled DNA repair removes bulky DNA lesions from the genome1,2 and protects cells against ultraviolet (UV) irradiation3. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4CSA and UV-stimulated scaffold protein A (UVSSA)3. Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published3,4 data, the structures provide a model for transcription-repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, ECTCR, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4CSA spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4CSA lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA.
    DOI:  https://doi.org/10.1038/s41586-021-03906-4
  8. Cell Metab. 2021 Sep 08. pii: S1550-4131(21)00417-4. [Epub ahead of print]
    Increased fidelity of protein synthesis extends lifespan.
    Victoria Eugenia Martinez-Miguel, Celia Lujan, Tristan Espie-Caullet, Daniel Martinez-Martinez, Saul Moore, Cassandra Backes, Suam Gonzalez, Evgeniy R Galimov, André E X Brown, Mario Halic, Kazunori Tomita, Charalampos Rallis, Tobias von der Haar, Filipe Cabreiro, Ivana Bjedov.
      Loss of proteostasis is a fundamental process driving aging. Proteostasis is affected by the accuracy of translation, yet the physiological consequence of having fewer protein synthesis errors during multi-cellular organismal aging is poorly understood. Our phylogenetic analysis of RPS23, a key protein in the ribosomal decoding center, uncovered a lysine residue almost universally conserved across all domains of life, which is replaced by an arginine in a small number of hyperthermophilic archaea. When introduced into eukaryotic RPS23 homologs, this mutation leads to accurate translation, as well as heat shock resistance and longer life, in yeast, worms, and flies. Furthermore, we show that anti-aging drugs such as rapamycin, Torin1, and trametinib reduce translation errors, and that rapamycin extends further organismal longevity in RPS23 hyperaccuracy mutants. This implies a unified mode of action for diverse pharmacological anti-aging therapies. These findings pave the way for identifying novel translation accuracy interventions to improve aging.
    Keywords:  RPS23; aging; archaea; mTOR; protein synthesis; proteostasis; ribosome; translation; translation accuracy; translation fidelity
    DOI:  https://doi.org/10.1016/j.cmet.2021.08.017
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