SCAN:Important factors in small RNA degradation: contrasting roles of PNPase and Hfq in the regulation of non-coding RNAs

ITQB SCAN Seminar

Title: Important factors in small RNA degradation: contrasting roles of PNPase and Hfq in the regulation of non-coding RNAs

Speaker: José Andrade

From: Control of Gene Expression Laboratory

Abstract:

Bacterial small RNAs (sRNAs) are extremely labile when are not associated with the RNA chaperone Hfq. This protein is homologous to Sm and Sm-like proteins involved in RNA processing in eukaryotes and it facilitates the sRNA-mRNA pairing. Although critical for sRNA stabilization and function, the mechanism by which Hfq protects sRNAs has been elusive.
In this work, we have found that the 3'-5' exonuclease polynucleotide phosphorylase (PNPase) is a major factor involved in the rapid degradation of small RNAs, especially when they are not bound to Hfq. The levels of several regulatory RNAs are drastically increased upon PNPase inactivation in Hfq cells. The Hfq-mediated protection of the 3'end was thus shown to be critical for the sRNA stability and in the absence of Hfq, all sRNAs are slightly shorter than their full-length species as result of 3'-end trimming. The turnover of Hfq-free small RNAs is growth phase regulated and the PNPase degradative activity is particularly important in stationary-phase. Indeed, the exonuclease PNPase makes a greater contribution than the endonuclease RNase E, commonly believed to be the main enzyme in the decay of sRNAs. Our data also suggests that when the sRNA is not associated with Hfq, the degradation occurs mainly in a target-independent pathway in which RNase III has a reduced impact.
Overall, our data re-evaluates the degradation mechanisms of Hfq-free small RNAs. In fact, the small RNA degradation by PNPase and the counter 3´end protection offered by Hfq seems far more common than was previously envisaged.