Structural and biophysical insights into the unique RNase YicC

Abstract

RNA cleavage and processing are highly conserved regulatory mechanisms across bacteria. We recently discovered a novel family of RNases called YicC, conserved across all bacteria but unrelated to known RNase families. The cryo-EM structure of RNA bound to Escherichia coli YicC endonuclease suggested a clamshell-like ribonuclease mechanism for cleavage, although its exact mechanism and function remain elusive. Here, we report new cryo-EM structures that provide snapshots of the closing of the complex and also capture a surprising dimeric-RNA:protein complex. We further characterize the RNA cleavage targets in solution using nuclear magnetic resonance (NMR) spectroscopy, and use all-atom molecular dynamics (MD) simulations to study Mg2+ binding. Our findings suggest that the YicC family can bind RNA hairpin structures and dimeric conformations with appropriate sequence and structural constraints, with cleavage driven strongly by Mg2+ ion localization. This study therefore provides overall insight into the novel cleavage mechanism of the highly conserved family of YicC-like endoribonucleases.