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A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis

Takada, Hiraku ; Paternoga, Helge ; Fujiwara, Keigo ; Nakamoto, Jose A LU orcid ; Park, Esther N ; Dimitrova-Paternoga, Lyudmila ; Beckert, Bertrand ; Saarma, Merilin ; Tenson, Tanel and Buskirk, Allen R , et al. (2024) In Nucleic Acids Research p.1-17
Abstract

Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of... (More)

Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of S4-domain-containing protein RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC by facilitating the addition of poly-alanine tails to truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species YlmH plays a central role in the RQC.

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organization
publishing date
type
Contribution to journal
publication status
epub
subject
in
Nucleic Acids Research
article number
gkae399
pages
1 - 17
publisher
Oxford University Press
external identifiers
  • pmid:38811035
ISSN
1362-4962
DOI
10.1093/nar/gkae399
language
English
LU publication?
yes
additional info
© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.
id
011e6754-ba49-4eb6-a66c-e728376d40f9
date added to LUP
2024-05-31 16:12:18
date last changed
2024-06-03 08:22:47
@article{011e6754-ba49-4eb6-a66c-e728376d40f9,
  abstract     = {{<p>Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of S4-domain-containing protein RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC by facilitating the addition of poly-alanine tails to truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species YlmH plays a central role in the RQC.</p>}},
  author       = {{Takada, Hiraku and Paternoga, Helge and Fujiwara, Keigo and Nakamoto, Jose A and Park, Esther N and Dimitrova-Paternoga, Lyudmila and Beckert, Bertrand and Saarma, Merilin and Tenson, Tanel and Buskirk, Allen R and Atkinson, Gemma C and Chiba, Shinobu and Wilson, Daniel N and Hauryliuk, Vasili}},
  issn         = {{1362-4962}},
  language     = {{eng}},
  month        = {{05}},
  pages        = {{1--17}},
  publisher    = {{Oxford University Press}},
  series       = {{Nucleic Acids Research}},
  title        = {{A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis}},
  url          = {{http://dx.doi.org/10.1093/nar/gkae399}},
  doi          = {{10.1093/nar/gkae399}},
  year         = {{2024}},
}