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Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P

Peil, Lauri ; Starosta, Agata L ; Lassak, Jürgen ; Atkinson, Gemma C LU ; Virumäe, Kai ; Spitzer, Michaela ; Tenson, Tanel ; Jung, Kirsten ; Remme, Jaanus and Wilson, Daniel N (2013) In Proceedings of the National Academy of Sciences of the United States of America 110(38). p.15265-15270
Abstract

Ribosomes are the protein synthesizing factories of the cell, polymerizing polypeptide chains from their constituent amino acids. However, distinct combinations of amino acids, such as polyproline stretches, cannot be efficiently polymerized by ribosomes, leading to translational stalling. The stalled ribosomes are rescued by the translational elongation factor P (EF-P), which by stimulating peptide-bond formation allows translation to resume. Using metabolic stable isotope labeling and mass spectrometry, we demonstrate in vivo that EF-P is important for expression of not only polyproline-containing proteins, but also for specific subsets of proteins containing diprolyl motifs (XPP/PPX). Together with a systematic in vitro and in vivo... (More)

Ribosomes are the protein synthesizing factories of the cell, polymerizing polypeptide chains from their constituent amino acids. However, distinct combinations of amino acids, such as polyproline stretches, cannot be efficiently polymerized by ribosomes, leading to translational stalling. The stalled ribosomes are rescued by the translational elongation factor P (EF-P), which by stimulating peptide-bond formation allows translation to resume. Using metabolic stable isotope labeling and mass spectrometry, we demonstrate in vivo that EF-P is important for expression of not only polyproline-containing proteins, but also for specific subsets of proteins containing diprolyl motifs (XPP/PPX). Together with a systematic in vitro and in vivo analysis, we provide a distinct hierarchy of stalling triplets, ranging from strong stallers, such as PPP, DPP, and PPN to weak stallers, such as CPP, PPR, and PPH, all of which are substrates for EF-P. These findings provide mechanistic insight into how the characteristics of the specific amino acid substrates influence the fundamentals of peptide bond formation.

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author
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publishing date
type
Contribution to journal
publication status
published
keywords
Amino Acid Motifs/genetics, Chromatography, Liquid, Escherichia coli K12/metabolism, Humans, Peptide Elongation Factors/metabolism, Proline/metabolism, Protein Biosynthesis/physiology, Proteomics, Ribosomes/metabolism, Tandem Mass Spectrometry, beta-Galactosidase
in
Proceedings of the National Academy of Sciences of the United States of America
volume
110
issue
38
pages
15265 - 15270
publisher
National Academy of Sciences
external identifiers
  • pmid:24003132
  • scopus:84884335094
ISSN
1091-6490
DOI
10.1073/pnas.1310642110
language
English
LU publication?
no
id
20ef5131-8719-48d8-b439-78aff6c87c54
date added to LUP
2021-09-27 15:53:51
date last changed
2024-06-16 20:01:39
@article{20ef5131-8719-48d8-b439-78aff6c87c54,
  abstract     = {{<p>Ribosomes are the protein synthesizing factories of the cell, polymerizing polypeptide chains from their constituent amino acids. However, distinct combinations of amino acids, such as polyproline stretches, cannot be efficiently polymerized by ribosomes, leading to translational stalling. The stalled ribosomes are rescued by the translational elongation factor P (EF-P), which by stimulating peptide-bond formation allows translation to resume. Using metabolic stable isotope labeling and mass spectrometry, we demonstrate in vivo that EF-P is important for expression of not only polyproline-containing proteins, but also for specific subsets of proteins containing diprolyl motifs (XPP/PPX). Together with a systematic in vitro and in vivo analysis, we provide a distinct hierarchy of stalling triplets, ranging from strong stallers, such as PPP, DPP, and PPN to weak stallers, such as CPP, PPR, and PPH, all of which are substrates for EF-P. These findings provide mechanistic insight into how the characteristics of the specific amino acid substrates influence the fundamentals of peptide bond formation. </p>}},
  author       = {{Peil, Lauri and Starosta, Agata L and Lassak, Jürgen and Atkinson, Gemma C and Virumäe, Kai and Spitzer, Michaela and Tenson, Tanel and Jung, Kirsten and Remme, Jaanus and Wilson, Daniel N}},
  issn         = {{1091-6490}},
  keywords     = {{Amino Acid Motifs/genetics; Chromatography, Liquid; Escherichia coli K12/metabolism; Humans; Peptide Elongation Factors/metabolism; Proline/metabolism; Protein Biosynthesis/physiology; Proteomics; Ribosomes/metabolism; Tandem Mass Spectrometry; beta-Galactosidase}},
  language     = {{eng}},
  number       = {{38}},
  pages        = {{15265--15270}},
  publisher    = {{National Academy of Sciences}},
  series       = {{Proceedings of the National Academy of Sciences of the United States of America}},
  title        = {{Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P}},
  url          = {{http://dx.doi.org/10.1073/pnas.1310642110}},
  doi          = {{10.1073/pnas.1310642110}},
  volume       = {{110}},
  year         = {{2013}},
}