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Open Access Highly Accessed Research article

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

Shree P Pandey1*, Jonathan A Winkler2, Hu Li24, Diogo M Camacho2, James J Collins2 and Graham C Walker3*

Author Affiliations

1 Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, Nadia, West Bengal 741252, India

2 Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Howard Hughes Medical Institute, Boston University, Boston, MA, USA

3 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02315, USA

4 Current address: Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA

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BMC Genomics 2014, 15:121  doi:10.1186/1471-2164-15-121

Published: 11 February 2014

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.

Keywords:
YbeY; Small-RNA; Hfq; Hydroxyurea; Stress adaptation; E. coli