Small RNAs (sRNAs) have been propelled to the forefront of genetic research as their diverse roles in regulation of cellular processes have been recognized. sRNAs are crucial for development in higher organisms;in bacteria, sRNAs regulate responses to many environmental stresses. Bacterial sRNAs that require the RNA chaperone Hfq regulate the translation or stability of mRNA targets by base pairing-dependent mechanisms. The Hfq-dependent sRNA SgrS is essential in E. coli for the response to glucose- phosphate stress. SgrS represents a new paradigm for sRNA regulators in bacteria. Other characterized Hfq-dependent sRNAs are non-coding and function solely via base pairing with and regulating target mRNAs (riboregulation). SgrS performs riboregulation on mRNA targets, and additionally encodes a novel protein, SgrT. This proposal focuses on the riboregulation function of SgrS, which our preliminary data indicates is more evolutionarily conserved than the protein coding function. Preliminary microarray experiments identified 10 candidate SgrS target mRNAs and we provide further evidence that 3 of these are directly up- or down-regulated by base pairing with SgrS. Analysis of SgrS homologs and their putative targets suggests that SgrS:mRNA interactions are better conserved for some targets than others. Since regulation of multiple targets by a single sRNA is a common theme for both bacterial and eukaryotic sRNA regulators, we propose to use SgrS as a model to examine how regulation of multiple targets with different base pairing characteristics and affinities is coordinated. Experiments in Aim 1, will define the SgrS target regulon.
In Aim 2, a high- throughput RNA footprinting approach will be used to map sRNA:mRNA interactions for all E. coli SgrS:mRNA targets and some homologous SgrS:mRNA pairs with predicted unique base pairing characteristics. These studies will demonstrate direct interactions between SgrS and its targets and define the molecular determinants of these interactions.
In Aim 3, we will determine whether there is a mechanism for SgrS to prioritize regulation of targets when SgrS levels are limiting (i.e., establish a hierarchy). We will then alter base pairing interactions by mutagenesis and determine how these alterations affect the regulatory hierarchy.

Public Health Relevance

Since sRNAs from organisms from bacteria to humans are believed to regulate multiple targets by base pairing-dependent mechanisms, these studies are broadly relevant because they will enhance our understanding of basic characteristics of sRNA- mediated regulation. Studies of SgrS in particular are important since SgrS is the first member of a novel class of bifunctional sRNA regulators and therefore serves as a model for other similar sRNAs that will be identified in the future. Project Narrative Since sRNAs from organisms from bacteria to humans are believed to regulate multiple targets by base pairing-dependent mechanisms, these studies are broadly relevant because they will enhance our understanding of basic characteristics of sRNA- mediated regulation. Studies of SgrS in particular are important since SgrS is the first member of a novel class of bifunctional sRNA regulators and therefore serves as a model for other similar sRNAs that will be identified in the future.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM092830-05
Application #
8708113
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Reddy, Michael K
Project Start
2010-08-01
Project End
2015-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
5
Fiscal Year
2014
Total Cost
$292,553
Indirect Cost
$104,453
Name
University of Illinois Urbana-Champaign
Department
Microbiology/Immun/Virology
Type
Schools of Arts and Sciences
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Balasubramanian, Divya; Ragunathan, Preethi T; Fei, Jingyi et al. (2016) A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli. mSystems 1:
Bobrovskyy, Maksym; Vanderpool, Carin K (2016) Diverse mechanisms of post-transcriptional repression by the small RNA regulator of glucose-phosphate stress. Mol Microbiol 99:254-73
Whitaker, Rachel J; Vanderpool, Carin K (2016) CRISPR-Cas Gatekeeper: Slow on the Uptake but Gets the Job Done. Cell Host Microbe 19:135-7
Fei, Jingyi; Singh, Digvijay; Zhang, Qiucen et al. (2015) RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA. Science 347:1371-4
Papenfort, Kai; Vanderpool, Carin K (2015) Target activation by regulatory RNAs in bacteria. FEMS Microbiol Rev 39:362-78
Bobrovskyy, Maksym; Vanderpool, Carin K (2014) The small RNA SgrS: roles in metabolism and pathogenesis of enteric bacteria. Front Cell Infect Microbiol 4:61
Balasubramanian, Divya; Vanderpool, Carin K (2013) New developments in post-transcriptional regulation of operons by small RNAs. RNA Biol 10:337-41
Papenfort, Kai; Sun, Yan; Miyakoshi, Masatoshi et al. (2013) Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell 153:426-37
Balasubramanian, Divya; Vanderpool, Carin K (2013) Deciphering the interplay between two independent functions of the small RNA regulator SgrS in Salmonella. J Bacteriol 195:4620-30
McClure, Ryan; Balasubramanian, Divya; Sun, Yan et al. (2013) Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res 41:e140

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