The intrinsically disordered AR2 microdomain of RNase E binds mRNA translation initiation regions

ABSTRACT: RNA decay is central to gene regulation and ensures that once genes are expressed, they have a finite lifespan. In Escherichia coli, bulk degradation is carried out by the RNA degradosome, a multi-protein complex that is scaffolded by the endoribonuclease RNase E. RNase E recognises RNA substrates through at least four RNA-binding sites that feed RNA to the catalytic centre. The ribonuclease consists of a structured N-terminal domain that contains the catalytic site, and an intrinsically disordered C-terminal domain that contains two unstructured RNA-binding sites termed RBD and AR2. The intrinsically disordered domain provides a major pathway for RNA recruitment to the catalytic centre, including mRNAs targeted by regulatory small RNAs (sRNAs). To understand how sRNA-mRNA pairs are recognised by the intrinsically disordered C-terminal domain we have engineered protease cleavage sites that separate the AR2 microdomain from RNase E and performed UV-crosslinking and sequencing (termed split-CRAC). We find that the AR2 binding site recognises AUAA motifs within mRNA translation initiation regions (RBS and start codons) and is depleted of sRNA interactions. We demonstrate that the AUAA motif is required for sRNA regulation of the highly abundant murein lipoprotein, Lpp, and that mRNAs with an AR2 motif tend to be more stable and more highly expressed.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE317719 | GEO | 2026/08/11

REPOSITORIES: GEO