Deves Valentin, D'Halluin Alexandre, Gilet Laëtitia, Condon Ciarán, Braun Frédérique
Expression Génétique Microbienne (EGM), UMR8261 CNRS-Université Paris Cité Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
Nucleic Acids Res. 2025 Aug 27;53(16). doi: 10.1093/nar/gkaf843.
The ribosome-associated endoribonuclease 1 (Rae1) cleaves messenger RNAs (mRNAs) in a translation-dependent manner. Here, we identify a new Rae1 target, the fliY mRNA, which is cleaved by Rae1 in the absence of the elongation factor P. The Rae1 site was mapped 12 nucleotides upstream of the second proline codon of an SPP stalling motif in fliY. Remarkably, Rae1 cleavages also occur 12 nucleotides upstream of the stop codon within two validated Rae1 mRNA targets, bmrX and spyA (S1025). Shifting the stop codon relative to the Rae1 cutting site abolished Rae1 sensitivity of bmrX and spyA mRNAs. We show that ribosome pausing occurs at the spyA stop codon, confirming its crucial role, and positioning the Rae1 cleavage at the tail end of the stalled ribosome, rather than in the A-site as previously proposed. These findings reveal a compelling novel mechanism by which Rae1 mediates mRNA cleavage in coordination with immobile ribosomes.
核糖体相关的核糖核酸内切酶1（Rae1）以依赖翻译的方式切割信使核糖核酸（mRNA）。在此，我们鉴定出一个新的Rae1靶标——fliY mRNA，它在缺乏延伸因子P的情况下被Rae1切割。Rae1切割位点位于fliY中一个SPP停滞基序的第二个脯氨酸密码子上游12个核苷酸处。值得注意的是，在两个经过验证的Rae1 mRNA靶标bmrX和spyA（S1025）中，Rae1切割也发生在终止密码子上游12个核苷酸处。相对于Rae1切割位点移动终止密码子会消除bmrX和spyA mRNA对Rae1的敏感性。我们表明核糖体在spyA终止密码子处发生停顿，证实了其关键作用，并将Rae1切割定位在停滞核糖体的尾端，而不是如先前提出的位于A位点。这些发现揭示了一种引人注目的新机制，通过该机制Rae1与固定的核糖体协同介导mRNA切割。
