Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility

Significance Bacteria rely on RNA-binding and RNA-remodeling proteins to regulate gene expression posttranscriptionally. RNA-dependent nucleoside-triphosphatases of the DEAH/RHA family constitute important posttranscriptional gene regulatory proteins in bacteria, but their molecular mechanisms are presently poorly understood. Here, we show that the DEAH/RHA protein, HrpA, fromEscherichia coli is an RNA helicase and that its helicase activity is required to modulate bacterial survival under diverse antibiotics treatments. HrpA crystal structures in different functional states, cross-linking/mass spectrometry, and structure-guided functional analyses indicate that alternative interdomain contacts facilitate large-scale domain movements that are required for RNA binding, translocation, and unwinding. Our findings portray HrpA as a molecular ratchet that translocates single-stranded RNA through a central orifice, thereby displacing a complementary strand.