Poly(A) polymerase is required for RyhB sRNA stability and function in Escherichia coli

Dhriti Sinha, Lisa M. Matz, Todd A. Cameron, Nicholas R. de Lay

Research output: Contribution to journalArticlepeer-review

Abstract

Small regulatory RNAs (sRNAs) are an important class of bacterial post-transcriptional regulators that control numerous physiological processes, including stress responses. In Gram-negative bacteria including Escherichia coli, the RNA chaperone Hfq binds many sRNAs and facilitates pairing to target transcripts, resulting in changes in mRNA transcription, translation, or stability. Here, we report that poly(A) polymerase (PAP I), which promotes RNA degradation by exoribonucleases through the addition of poly(A) tails, has a crucial role in the regulation of gene expression by Hfq-dependent sRNAs. Specifically, we show that deletion of pcnB, encoding PAP I, paradoxically resulted in an increased turnover of certain Hfq-dependent sRNAs, including RyhB. RyhB instability in the pcnB deletion strain was suppressed by mutations in hfq or ryhB that disrupt pairing of RyhB with target RNAs, by mutations in the 3 ′′ external transcribed spacer of the glyW-cysT-leuZ transcript (3 ′′ ETS LeuZ ) involved in pairing with RyhB, or an internal deletion in rne, which encodes the endoribonuclease RNase E. Finally, the reduced stability of RyhB in the pcnB deletion strain resulted in impaired regulation of some of its target mRNAs, specifically sodB and sdhCDAB. Altogether our data support a model where PAP I plays a critical role in ensuring the efficient decay of the 3 ′′ ETS LeuZ . In the absence of PAP I, the 3 ′′ ETS LeuZ transcripts accumulate, bind Hfq, and pair with RyhB, resulting in its depletion via RNase E-mediated decay. This ultimately leads to a defect in RyhB function in a PAP I deficient strain.

Original languageEnglish (US)
Pages (from-to)1496-1511
Number of pages16
JournalRNA
Volume24
Issue number11
DOIs
StatePublished - Nov 2018
Externally publishedYes

Keywords

  • Hfq
  • PcnB
  • Poly(A) polymerase
  • RNase E
  • Small RNAs

ASJC Scopus subject areas

  • Molecular Biology

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