A Cooperative PNPase-Hfq-RNA Carrier Complex Facilitates Bacterial Riboregulation

Abstract

Polynucleotide phosphorylase (PNPase) is an ancient exoribonuclease conserved in the course of evolution, and is found in species ranging from bacteria to humans. Paradoxically, Escherichia coli PNPase can act as a chaperone for small regulatory RNAs (sRNAs),with pleiotropic consequences for gene regulation, but the mechanism of this phenomenon has remained unclear. We present structures of the ternary assembly formed by PNPase, the RNA chaperone Hfq and sRNA, and show that this complex boosts sRNA stability in vitro. Comparison of the carrier complex structure with the structures of PNPase in the apo state and with bound substrate poised for degradation reveals how the RNA is rerouted away from the enzyme active site through interactions with Hfq and the KH and S1 RNA binding domains of PNPase. Together, these data explain how PNPase is repurposed to protect sRNAs from cellular ribonucleases such as RNase E, and could aid RNA presentation to facilitate regulatory actions on target genes.