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Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT

Takada, Hiraku ; Fujiwara, Keigo ; Atkinson, Gemma C LU ; Chiba, Shinobu and Hauryliuk, Vasili LU orcid (2024) In Nucleic Acids Research p.1-13
Abstract

Efficiency of protein synthesis on the ribosome is strongly affected by the amino acid composition of the assembled amino acid chain. Challenging sequences include proline-rich motifs as well as highly positively and negatively charged amino acid stretches. Members of the F subfamily of ABC ATPases (ABCFs) have been long hypothesised to promote translation of such problematic motifs. In this study we have applied genetics and reporter-based assays to characterise the four housekeeping ABCF ATPases of Bacillus subtilis: YdiF, YfmM, YfmR/Uup and YkpA/YbiT. We show that YfmR cooperates with the translation factor EF-P that promotes translation of Pro-rich motifs. Simultaneous loss of both YfmR and EF-P results in a dramatic growth defect.... (More)

Efficiency of protein synthesis on the ribosome is strongly affected by the amino acid composition of the assembled amino acid chain. Challenging sequences include proline-rich motifs as well as highly positively and negatively charged amino acid stretches. Members of the F subfamily of ABC ATPases (ABCFs) have been long hypothesised to promote translation of such problematic motifs. In this study we have applied genetics and reporter-based assays to characterise the four housekeeping ABCF ATPases of Bacillus subtilis: YdiF, YfmM, YfmR/Uup and YkpA/YbiT. We show that YfmR cooperates with the translation factor EF-P that promotes translation of Pro-rich motifs. Simultaneous loss of both YfmR and EF-P results in a dramatic growth defect. Surprisingly, this growth defect can be largely suppressed though overexpression of an EF-P variant lacking the otherwise crucial 5-amino-pentanolylated residue K32. Using in vivo reporter assays, we show that overexpression of YfmR can alleviate ribosomal stalling on Asp-Pro motifs. Finally, we demonstrate that YkpA/YbiT promotes translation of positively and negatively charged motifs but is inactive in resolving ribosomal stalls on proline-rich stretches. Collectively, our results provide insights into the function of ABCF translation factors in modulating protein synthesis in B. subtilis.

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author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
epub
subject
in
Nucleic Acids Research
article number
gkae556
pages
1 - 13
publisher
Oxford University Press
external identifiers
  • pmid:38943426
ISSN
1362-4962
DOI
10.1093/nar/gkae556
language
English
LU publication?
yes
additional info
© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.
id
d0b367bc-7b2e-423f-a437-93051d6d1462
date added to LUP
2024-07-02 20:47:42
date last changed
2024-07-03 10:17:02
@article{d0b367bc-7b2e-423f-a437-93051d6d1462,
  abstract     = {{<p>Efficiency of protein synthesis on the ribosome is strongly affected by the amino acid composition of the assembled amino acid chain. Challenging sequences include proline-rich motifs as well as highly positively and negatively charged amino acid stretches. Members of the F subfamily of ABC ATPases (ABCFs) have been long hypothesised to promote translation of such problematic motifs. In this study we have applied genetics and reporter-based assays to characterise the four housekeeping ABCF ATPases of Bacillus subtilis: YdiF, YfmM, YfmR/Uup and YkpA/YbiT. We show that YfmR cooperates with the translation factor EF-P that promotes translation of Pro-rich motifs. Simultaneous loss of both YfmR and EF-P results in a dramatic growth defect. Surprisingly, this growth defect can be largely suppressed though overexpression of an EF-P variant lacking the otherwise crucial 5-amino-pentanolylated residue K32. Using in vivo reporter assays, we show that overexpression of YfmR can alleviate ribosomal stalling on Asp-Pro motifs. Finally, we demonstrate that YkpA/YbiT promotes translation of positively and negatively charged motifs but is inactive in resolving ribosomal stalls on proline-rich stretches. Collectively, our results provide insights into the function of ABCF translation factors in modulating protein synthesis in B. subtilis.</p>}},
  author       = {{Takada, Hiraku and Fujiwara, Keigo and Atkinson, Gemma C and Chiba, Shinobu and Hauryliuk, Vasili}},
  issn         = {{1362-4962}},
  language     = {{eng}},
  month        = {{06}},
  pages        = {{1--13}},
  publisher    = {{Oxford University Press}},
  series       = {{Nucleic Acids Research}},
  title        = {{Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT}},
  url          = {{http://dx.doi.org/10.1093/nar/gkae556}},
  doi          = {{10.1093/nar/gkae556}},
  year         = {{2024}},
}