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Updated: Sep 9, 2025

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The endoribonuclease Rae1 from Bacillus subtilis cleaves mRNA upstream of stalled ribosomes

Valentin Deves1, Alexandre D'Halluin1, Laëtitia Gilet1

  • 1Expression Génétique Microbienne (EGM), UMR8261 CNRS-Université Paris Cité Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.

Nucleic Acids Research
|September 3, 2025
PubMed

Insights

Ribosome-associated endoribonuclease 1 (Rae1) cleaves mRNAs near stalled ribosomes. This study identifies Rae1

Area of Science:

  • Molecular Biology
  • RNA Biology
  • Biochemistry

Background:

  • The ribosome-associated endoribonuclease 1 (Rae1) is known to degrade messenger RNAs (mRNAs) during translation.
  • The precise mechanism and location of Rae1 cleavage sites on target mRNAs remain incompletely understood.

Purpose of the Study:

  • To identify novel Rae1 mRNA targets and elucidate the mechanism of Rae1-mediated mRNA cleavage.
  • To investigate the role of ribosome stalling and specific mRNA sequences in directing Rae1 activity.

Main Methods:

  • Identification of Rae1 target mRNAs, including fliY, bmrX, and spyA.
  • Mapping of Rae1 cleavage sites using genetic and biochemical approaches.
  • Analysis of ribosome pausing at stop codons and its correlation with Rae1 cleavage.

Main Results:

  • Identified fliY mRNA as a novel target of Rae1, cleaved even without elongation factor P.
  • Mapped Rae1 cleavage sites 12 nucleotides upstream of stop codons in bmrX and spyA mRNAs.
  • Demonstrated that ribosome stalling at stop codons is crucial for Rae1 targeting and cleavage at the tail end of the stalled ribosome.

Conclusions:

  • Rae1-mediated mRNA cleavage is coordinated with ribosome stalling at specific mRNA sequences.
  • The cleavage site is positioned at the tail end of stalled ribosomes, challenging previous models.
  • This reveals a novel mechanism for Rae1 in regulating gene expression through translation-dependent mRNA degradation.

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