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TitleDiverse mechanisms of translation arrest by a Clostridia ribosome stalling peptide CliM.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateMay 18, 2026
AuthorsMayu Yoshida / Felix Gersteuer / Ole Berendes / Keigo Fujiwara / Haaris A Safdari / Helge Paternoga / Hiraku Takada / Nozomu Obana / Helmut Grubmüller / Lars V Bock / Daniel N Wilson / Shinobu Chiba /
PubMed AbstractRibosome arrest peptides undergo programmed translational stalling in response to changes in the cellular environment to feedback-regulate gene expression. CliM, an arrest peptide in Clostridia, is ...Ribosome arrest peptides undergo programmed translational stalling in response to changes in the cellular environment to feedback-regulate gene expression. CliM, an arrest peptide in Clostridia, is encoded upstream of the YidC membrane protein insertase gene, but its function and mechanism remain unclear. Here we show that CliM monitors YidC activity to maintain adequate cellular YidC capacity. Interestingly, Clostridium kluyveri CliM induces elongation arrest at multiple sense codons, whereas Clostridioides difficile CliM causes termination arrest. Cryo-EM-based structural and mutational analyses demonstrate that C. difficile CliM adopts multiple α-helices within the nascent polypeptide exit tunnel, where it forms extensive arrest-essential interactions with the ribosome. The residue immediately N-terminal to the stalling site contributes to arrest by sterically interfering with full accommodation of the release factor or aminoacyl-tRNA in the A-site. Molecular dynamics simulations suggest that membrane insertion of CliM induces sequential unwinding of these α-helical structures and relocation of the penultimate residue, thereby triggering arrest release. These findings provide a unified mechanistic framework that explains the distinct arrest behaviors of CliM homologs.
External linksNat Commun / PubMed:42151144 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 2.8 Å
Structure data

50855

9fy1

EMDB-50855, PDB-9fy1:
Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in the A-site
Method: EM (single particle) / Resolution: 2.3 Å

50856

9fy2

EMDB-50856, PDB-9fy2:
Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-site
Method: EM (single particle) / Resolution: 2.3 Å

50858

9fy3

EMDB-50858, PDB-9fy3:
Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-site
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • bacillus subtilis subsp. subtilis str. 168 (bacteria)
  • clostridioides difficile 630 (bacteria)
KeywordsRIBOSOME / Arrest peptide / Stalled ribosome complex / Bacillus subtilis / ApcF

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