Literature DB >> 33505387

Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding.

Ekaterina Samatova1, Jan Daberger1, Marija Liutkute1, Marina V Rodnina1.   

Abstract

Protein homeostasis of bacterial cells is maintained by coordinated processes of protein production, folding, and degradation. Translational efficiency of a given mRNA depends on how often the ribosomes initiate synthesis of a new polypeptide and how quickly they read the coding sequence to produce a full-length protein. The pace of ribosomes along the mRNA is not uniform: periods of rapid synthesis are separated by pauses. Here, we summarize recent evidence on how ribosome pausing affects translational efficiency and protein folding. We discuss the factors that slow down translation elongation and affect the quality of the newly synthesized protein. Ribosome pausing emerges as important factor contributing to the regulatory programs that ensure the quality of the proteome and integrate the cellular and environmental cues into regulatory circuits of the cell.
Copyright © 2021 Samatova, Daberger, Liutkute and Rodnina.

Entities:  

Keywords:  cotranslational folding; nascent peptide; prokaryotes; ribosome pausing; tRNA; translation; translation efficiency

Year:  2021        PMID: 33505387      PMCID: PMC7829197          DOI: 10.3389/fmicb.2020.619430

Source DB:  PubMed          Journal:  Front Microbiol        ISSN: 1664-302X            Impact factor:   5.640


  174 in total

1.  Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events.

Authors:  Matthieu Chartier; Francis Gaudreault; Rafael Najmanovich
Journal:  Bioinformatics       Date:  2012-03-30       Impact factor: 6.937

Review 2.  Translation regulation via nascent polypeptide-mediated ribosome stalling.

Authors:  Daniel N Wilson; Stefan Arenz; Roland Beckmann
Journal:  Curr Opin Struct Biol       Date:  2016-02-07       Impact factor: 6.809

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Journal:  Nature       Date:  2008-03-09       Impact factor: 49.962

4.  Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell.

Authors:  Joana Pinto Vieira; Julien Racle; Vassily Hatzimanikatis
Journal:  Biophys J       Date:  2016-05-10       Impact factor: 4.033

5.  Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation.

Authors:  A A Komar; T Lesnik; C Reiss
Journal:  FEBS Lett       Date:  1999-12-03       Impact factor: 4.124

6.  EF-P is essential for rapid synthesis of proteins containing consecutive proline residues.

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Journal:  Science       Date:  2012-12-13       Impact factor: 47.728

Review 7.  Codon usage and tRNA content in unicellular and multicellular organisms.

Authors:  T Ikemura
Journal:  Mol Biol Evol       Date:  1985-01       Impact factor: 16.240

8.  Nascentome analysis uncovers futile protein synthesis in Escherichia coli.

Authors:  Koreaki Ito; Yuhei Chadani; Kenta Nakamori; Shinobu Chiba; Yoshinori Akiyama; Tatsuhiko Abo
Journal:  PLoS One       Date:  2011-12-05       Impact factor: 3.240

9.  Comparative context analysis of codon pairs on an ORFeome scale.

Authors:  Gabriela Moura; Miguel Pinheiro; Raquel Silva; Isabel Miranda; Vera Afreixo; Gaspar Dias; Adelaide Freitas; José L Oliveira; Manuel A S Santos
Journal:  Genome Biol       Date:  2005-02-15       Impact factor: 13.583

10.  The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.

Authors:  Khanh Dao Duc; Yun S Song
Journal:  PLoS Genet       Date:  2018-01-16       Impact factor: 5.917

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  14 in total

1.  Deep conservation of ribosome stall sites across RNA processing genes.

Authors:  Katarzyna Chyżyńska; Kornel Labun; Carl Jones; Sushma N Grellscheid; Eivind Valen
Journal:  NAR Genom Bioinform       Date:  2021-05-25

2.  Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance.

Authors:  Kaitlyn Tsai; Vanja Stojković; Lianet Noda-Garcia; Iris D Young; Alexander G Myasnikov; Jordan Kleinman; Ali Palla; Stephen N Floor; Adam Frost; James S Fraser; Dan S Tawfik; Danica Galonić Fujimori
Journal:  Elife       Date:  2022-01-11       Impact factor: 8.140

3.  Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel.

Authors:  Michal H Kolář; Gabor Nagy; John Kunkel; Sara M Vaiana; Lars V Bock; Helmut Grubmüller
Journal:  Nucleic Acids Res       Date:  2022-02-28       Impact factor: 16.971

4.  Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation.

Authors:  Yuhei Chadani; Nobuyuki Sugata; Tatsuya Niwa; Yosuke Ito; Shintaro Iwasaki; Hideki Taguchi
Journal:  EMBO J       Date:  2021-10-20       Impact factor: 11.598

5.  Co-translational folding of nascent polypeptides: Multi-layered mechanisms for the efficient biogenesis of functional proteins.

Authors:  Kevin Maciuba; Nandakumar Rajasekaran; Xiuqi Chen; Christian M Kaiser
Journal:  Bioessays       Date:  2021-05-13       Impact factor: 4.653

Review 6.  Ribosome Rescue Pathways in Bacteria.

Authors:  Claudia Müller; Caillan Crowe-McAuliffe; Daniel N Wilson
Journal:  Front Microbiol       Date:  2021-03-18       Impact factor: 5.640

Review 7.  Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors.

Authors:  Franziska Nadler; Elena Lavdovskaia; Ricarda Richter-Dennerlein
Journal:  RNA Biol       Date:  2021-12-31       Impact factor: 4.652

Review 8.  RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence.

Authors:  Laura Antoine; Roberto Bahena-Ceron; Heemee Devi Bunwaree; Martin Gobry; Victor Loegler; Pascale Romby; Stefano Marzi
Journal:  Genes (Basel)       Date:  2021-07-24       Impact factor: 4.096

9.  Protein Folding Interdiction Strategy for Therapeutic Drug Development in Viral Diseases: Ebola VP40 and Influenza A M1.

Authors:  Fernando Bergasa-Caceres; Herschel A Rabitz
Journal:  Int J Mol Sci       Date:  2022-03-31       Impact factor: 5.923

Review 10.  Bacterial Protein Homeostasis Disruption as a Therapeutic Intervention.

Authors:  Laleh Khodaparast; Guiqin Wu; Ladan Khodaparast; Béla Z Schmidt; Frederic Rousseau; Joost Schymkowitz
Journal:  Front Mol Biosci       Date:  2021-06-02
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