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

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.