RNA-RNA interactome approaches provide in vivo 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 messenger RNAs (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 amino acid substitutions 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

SUBMITTER: Luo X 

PROVIDER: S-EPMC12700109 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature