Role of polynucleotide phosphorylase in sRNA function in Escherichia coli

In Escherichia coli, many small noncoding regulatory RNAs (sRNAs) post-transcriptionally regulate gene expression by base-pairing to mRNAs in a process that is mediated by the RNA chaperone Hfq. Binding of the sRNA to the mRNA can lead to increased or decreased mRNA stability and/or translation. It...

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Bibliographic Details
Published in:RNA (Cambridge) 2011-06, Vol.17 (6), p.1172-1189
Main Authors: De Lay, Nicholas, Gottesman, Susan
Format: Article
Language:English
Subjects:
Endoribonucleases - genetics
Endoribonucleases - metabolism
Escherichia coli
Escherichia coli - enzymology
Escherichia coli - genetics
Escherichia coli - metabolism
Gene Expression Regulation, Bacterial
Host Factor 1 Protein - genetics
Host Factor 1 Protein - metabolism
Polyribonucleotide Nucleotidyltransferase - genetics
Polyribonucleotide Nucleotidyltransferase - metabolism
RNA Stability - genetics
RNA, Bacterial - genetics
RNA, Bacterial - metabolism
RNA, Messenger - metabolism
RNA, Small Untranslated - metabolism
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Summary:In Escherichia coli, many small noncoding regulatory RNAs (sRNAs) post-transcriptionally regulate gene expression by base-pairing to mRNAs in a process that is mediated by the RNA chaperone Hfq. Binding of the sRNA to the mRNA can lead to increased or decreased mRNA stability and/or translation. It is not known if proteins other than Hfq are necessary for this process. In order to identify additional genes required for the post-transcriptional regulation of gene expression by Hfq-dependent sRNAs, we developed a novel combined genetic selection and screen for mutants defective in sRNA regulation. In our combined genetic selection and screen, we isolated hfq mutants and mutants in pnp, encoding polynucleotide phosphorylase (PNPase). We show that loss-of-function mutations in pnp result in a decreased stability of several sRNAs including RyhB, SgrS, and CyaR and also decrease both the negative and positive regulation by sRNAs. The defect in stability of CyaR and in negative and positive regulation are suppressed by deletion mutations in RNase E. Altogether, our results suggest that the lack of sRNA-mediated regulation in the absence of an active form of PNPase is due to the rapid turnover of sRNA resulting from an increase in RNase E activity and/or an increase in access of other ribonucleases to sRNAs.
ISSN:1355-8382
1469-9001
DOI:10.1261/rna.2531211