RNA-RNA Interactome Approaches Provide <i>in vivo</i> Evidence for a Critical Role of the Hfq Rim Face in sRNA-mRNA Pairing.

ABSTRACT: Most bacterial small regulatory RNAs (sRNAs) modulate gene expression by forming complementary base pairs with target mRNAs, dependent upon the RNA chaperone Hfq. Hfq has three RNA-binding faces (proximal, rim, and distal), facilitating simultaneous binding of sRNAs and target mRNAs. Here, we systematically examined the functional impact of point mutations in the RNA binding faces on in vivo pairing, using the RNA Interaction by Ligation and Sequencing (RIL-seq) approach. The distal and proximal Hfq binding face mutants retained substantial numbers of RNA-RNA interactions (significant chimera counts or S-chimeras). However, the rim face mutant R16A showed a near-complete loss of S-chimeras, although Hfq R16A retained partial RNA binding activity as well as partial regulatory activity. Intr

SUBMITTER: Luo X 

PROVIDER: S-EPMC12262471 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature