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Related Experiment Video

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Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses
11:19

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Published on: February 25, 2011

ArfA recruits RF2 into stalled ribosomes.

Yoshihiro Shimizu1

  • 1Laboratory for Cell-Free Protein Synthesis, Quantitative Biology Center (QBiC), RIKEN, 2-2-3, Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. yshimizu@riken.jp

Journal of Molecular Biology
|August 28, 2012
PubMed
Summary

The ribosome rescue factors YaeJ and alternative ribosome rescue factor A (ArfA) aid stalled ribosome release in E. coli. ArfA requires release factor 2 (RF2), which it recruits to the ribosome.

Area of Science:

  • Molecular Biology
  • Bacterial Protein Synthesis
  • Ribosome Rescue Mechanisms

Background:

  • Ribosome stalling during translation poses a threat to cellular function.
  • Escherichia coli utilizes multiple systems, including YaeJ and ArfA, to rescue stalled ribosomes.
  • The tmRNA-trans-translation system is a well-established ribosome rescue pathway.

Purpose of the Study:

  • To investigate the distinct mechanisms of YaeJ and ArfA in rescuing stalled ribosomes.
  • To elucidate the role of release factor 2 (RF2) in ArfA-mediated ribosome rescue.
  • To compare the efficiency and length-dependence of YaeJ and ArfA pathways.

Main Methods:

  • Utilized a reconstituted cell-free protein synthesis system.
  • Examined ribosome recycling from mRNA lacking in-frame stop codons.

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  • Assessed the requirement of RF2 for ArfA-dependent ribosome rescue.

    • Main Results:

    • YaeJ alone effectively recycled stalled ribosomes.
    • ArfA-mediated rescue required the presence of RF2, which ArfA recruits to the ribosome's A site.
    • ArfA efficiency decreased with increasing mRNA length downstream of the A site, while YaeJ function remained robust.

    Conclusions:

    • YaeJ and ArfA represent distinct ribosome rescue pathways with differing dependencies and efficiencies.
    • ArfA actively recruits RF2 to facilitate peptidyl-tRNA hydrolysis, a key step in ribosome rescue.
    • The differential length-dependence suggests distinct in vivo roles for YaeJ and ArfA in managing translation stress.