bims-mitran Biomed News
on Mitochondrial Translation
Issue of 2021‒08‒15
six papers selected by
Andreas Kohler
  1. Ribosome Biogenesis in Archaea.
  2. Quality Control Mechanisms in Bacterial Translation.
  3. Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression.
  4. Structures of tmRNA and SmpB as they transit through the ribosome.
  5. Translational autoregulation of the S. cerevisiae high-affinity polyamine transporter Hol1.
  6. Simultaneous ribosome profiling of hundreds of microbes from the human microbiome.
  1. Front Microbiol. 2021 ;12 686977
    Ribosome Biogenesis in Archaea.
    Paola Londei, Sébastien Ferreira-Cerca.
      Making ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding the genetic information contained in messenger RNAs into proteins, their biogenesis shows an intriguing degree of variability across the tree of life. In this review, we summarize our knowledge on the least understood ribosome biogenesis pathway: the archaeal one. Furthermore, we highlight some evolutionary conserved and divergent molecular features of making ribosomes across the tree of life.
    Keywords:  RNA modifications; archaea; ribosomal RNA; ribosomal proteins; ribosome; ribosome biogenesis
    DOI:  https://doi.org/10.3389/fmicb.2021.686977
  2. Acta Naturae. 2021 Apr-Jun;13(2):13(2): 32-44
    Quality Control Mechanisms in Bacterial Translation.
    A S Zarechenskaia, P V Sergiev, I A Osterman.
      Ribosome stalling during translation significantly reduces cell viability, because cells have to spend resources on the synthesis of new ribosomes. Therefore, all bacteria have developed various mechanisms of ribosome rescue. Usually, the release of ribosomes is preceded by hydrolysis of the tRNA-peptide bond, but, in some cases, the ribosome can continue translation thanks to the activity of certain factors. This review describes the mechanisms of ribosome rescue thanks to trans-translation and the activity of the ArfA, ArfB, BrfA, ArfT, HflX, and RqcP/H factors, as well as continuation of translation via the action of EF-P, EF-4, and EttA. Despite the ability of some systems to duplicate each other, most of them have their unique functional role, related to the quality control of bacterial translation in certain abnormalities caused by mutations, stress cultivation conditions, or antibiotics.
    Keywords:  bacteria; quality control; termination; trans-translation; translation
    DOI:  https://doi.org/10.32607/actanaturae.11401
  3. Elife. 2021 Aug 12. pii: e70619. [Epub ahead of print]10
    Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression.
    Isao Masuda, Jae-Yeon Hwang, Thomas Christian, Sunita Maharjan, Fuad Mohammad, Howard Gamper, Allen R Buskirk, Ya-MIng Hou.
      N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E. coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the affected codons leave the A site. Enzyme- and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the stringent response that is typically induced by deficiency of amino acids. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.
    Keywords:  E. coli; infectious disease; microbiology
    DOI:  https://doi.org/10.7554/eLife.70619
  4. Nat Commun. 2021 Aug 13. 12(1): 4909
    Structures of tmRNA and SmpB as they transit through the ribosome.
    Charlotte Guyomar, Gaetano D'Urso, Sophie Chat, Emmanuel Giudice, Reynald Gillet.
      In bacteria, trans-translation is the main rescue system, freeing ribosomes stalled on defective messenger RNAs. This mechanism is driven by small protein B (SmpB) and transfer-messenger RNA (tmRNA), a hybrid RNA known to have both a tRNA-like and an mRNA-like domain. Here we present four cryo-EM structures of the ribosome during trans-translation at resolutions from 3.0 to 3.4 Å. These include the high-resolution structure of the whole pre-accommodated state, as well as structures of the accommodated state, the translocated state, and a translocation intermediate. Together, they shed light on the movements of the tmRNA-SmpB complex in the ribosome, from its delivery by the elongation factor EF-Tu to its passage through the ribosomal A and P sites after the opening of the B1 bridges. Additionally, we describe the interactions between the tmRNA-SmpB complex and the ribosome. These explain why the process does not interfere with canonical translation.
    DOI:  https://doi.org/10.1038/s41467-021-24881-4
  5. Mol Cell. 2021 Jul 30. pii: S1097-2765(21)00589-X. [Epub ahead of print]
    Translational autoregulation of the S. cerevisiae high-affinity polyamine transporter Hol1.
    Arya Vindu, Byung-Sik Shin, Kevin Choi, Eric T Christenson, Ivaylo P Ivanov, Chune Cao, Anirban Banerjee, Thomas E Dever.
      Polyamines, small organic polycations, are essential for cell viability, and their physiological levels are homeostatically maintained by post-transcriptional regulation of key biosynthetic enzymes. In addition to de novo synthesis, cells can also take up polyamines; however, identifying cellular polyamine transporters has been challenging. Here we show that the S. cerevisiae HOL1 mRNA is under translational control by polyamines, and we reveal that the encoded membrane transporter Hol1 is a high-affinity polyamine transporter and is required for yeast growth under limiting polyamine conditions. Moreover, we show that polyamine inhibition of the translation factor eIF5A impairs translation termination at a Pro-Ser-stop motif in a conserved upstream open reading frame on the HOL1 mRNA to repress Hol1 synthesis under conditions of elevated polyamines. Our findings reveal that polyamine transport, like polyamine biosynthesis, is under translational autoregulation by polyamines in yeast, highlighting the extensive control cells impose on polyamine levels.
    Keywords:  HOL1; eIF5A; polyamine; spermidine; translation termination; translational control; transporter; uORF
    DOI:  https://doi.org/10.1016/j.molcel.2021.07.020
  6. Nat Protoc. 2021 Aug 11.
    Simultaneous ribosome profiling of hundreds of microbes from the human microbiome.
    Brayon J Fremin, Cosmos Nicolaou, Ami S Bhatt.
      Ribosome profiling enables sequencing of ribosome-bound fragments of RNA, revealing which transcripts are being translated as well as the position of ribosomes along mRNAs. Although ribosome profiling has been applied to cultured bacterial isolates, its application to uncultured, mixed communities has been challenging. We present MetaRibo-Seq, a protocol that enables the application of ribosome profiling directly to the human fecal microbiome. MetaRibo-Seq is a benchmarked method that includes several modifications to existing ribosome profiling protocols, specifically addressing challenges involving fecal sample storage, purity and input requirements. We also provide a computational workflow to quality control and trim reads, de novo assemble a reference metagenome with metagenomic reads, align MetaRibo-Seq reads to the reference, and assess MetaRibo-Seq library quality ( https://github.com/bhattlab/bhattlab_workflows/tree/master/metariboseq ). This MetaRibo-Seq protocol enables researchers in standard molecular biology laboratories to study translation in the fecal microbiome in ~5 d.
    DOI:  https://doi.org/10.1038/s41596-021-00592-4
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