Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria

Shree P. Pandey, Jonathan A. Winkler, Hu Li, Diogo M. Camacho, James J. Collins, Graham C. Walker

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Background: Conceptual parallels exist between bacterial and eukaryotic small-RNA (sRNA) pathways, yet relatively little is known about which protein may recognize and recruit bacterial sRNAs to interact with targets. In eukaryotes, Argonaute (AGO) proteins discharge such functions. The highly conserved bacterial YbeY RNase has structural similarities to the MID domain of AGOs. A limited study had indicated that in Sinorhizobium meliloti the YbeY ortholog regulates the accumulation of sRNAs as well as the target mRNAs, raising the possibility that YbeY may play a previously unrecognized role in bacterial sRNA regulation.Results: We have applied a multipronged approach of loss-of-function studies, genome-wide mRNA and sRNA expression profiling, pathway analysis, target prediction, literature mining and network analysis to unravel YbeY-dependent molecular responses of E. coli exposed to hydroxyurea (HU). Loss of ybeY function, which results in a marked resistance to HU, had global affects on sRNA-mediated gene expression. Of 54 detectable E. coli sRNAs in our microarray analysis, 30 sRNAs showed a differential expression upon HU stress, of which 28 sRNAs displayed a YbeY-dependent change in expression. These included 12 Hfq-dependent and 16 Hfq-independent sRNAs. We successfully identified at least 57 experimentally inferred sRNA-mRNA relationships. Further applying a 'context likelihood of relatedness' algorithm, we reverse engineered the YbeY-dependent Hfq-dependent sRNA-mRNA network as well as YbeY-dependent Hfq-independent sRNA-mRNA network.Conclusion: YbeY extensively modulates Hfq-dependent and independent sRNA-mRNA interactions. YbeY-dependent sRNAs have central roles in modulating cellular response to HU stress.

Original languageEnglish (US)
Article number121
JournalBMC Genomics
Volume15
Issue number1
DOIs
StatePublished - Feb 11 2014

Fingerprint

Ribonucleases
RNA
Hydroxyurea
Bacteria
Messenger RNA
Argonaute Proteins
Bacterial RNA
Escherichia coli
Sinorhizobium meliloti
Microarray Analysis
Eukaryota
Genome
Gene Expression
Proteins

Keywords

  • E. coli
  • Hfq
  • Hydroxyurea
  • Small-RNA
  • Stress adaptation
  • YbeY

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Medicine(all)

Cite this

Pandey, S. P., Winkler, J. A., Li, H., Camacho, D. M., Collins, J. J., & Walker, G. C. (2014). Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics, 15(1), [121]. https://doi.org/10.1186/1471-2164-15-121

Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. / Pandey, Shree P.; Winkler, Jonathan A.; Li, Hu; Camacho, Diogo M.; Collins, James J.; Walker, Graham C.

In: BMC Genomics, Vol. 15, No. 1, 121, 11.02.2014.

Research output: Contribution to journalArticle

Pandey, Shree P. ; Winkler, Jonathan A. ; Li, Hu ; Camacho, Diogo M. ; Collins, James J. ; Walker, Graham C. / Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. In: BMC Genomics. 2014 ; Vol. 15, No. 1.
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AU - Collins, James J.

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