Poster abstracts

Poster number 20 submitted by Samantha Grecco

The effect of the small RNA RyhB on the structure of its mRNA targets

Samantha M. Grecco (Department of Biochemistry and Molecular Biology, Beckman Scholar, Schreyer Honors College, Pennsylvania State University, University Park, Pennsylvania, USA), Janie K. Frandsen (Department of Chemistry, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA), Philip C. Bevilacqua (Department of Biochemistry and Molecular Biology, Department of Chemistry, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA)

Abstract:
There are many ways that Escherichia coli combats environmental stressors, one such mechanism is gene regulation by small non-coding RNAs (sRNA). sRNAs are post-transcriptional regulators that base pair with mRNA targets to change the expression of the encoded gene. RyhB is a sRNA that is expressed under iron-limiting conditions and regulates the iron sparing response by shifting the limited iron present to essential proteins and downregulating nonessential iron utilizing proteins.1 However, the majority of RyhB targets have not been characterized and the role of RNA structure in the sRNA-mRNA interactions is unknown. It is hypothesized that the target mRNA secondary structure influences the ability of RhyB to interact and that the interaction may induce a structural rearrangement that alters gene expression. In this study, we used data from six-genome-wide analyses1 to select putative RyhB targets for in vivo RNA structure probing analysis to determine the effect of RyhB on the structure of its target mRNAs. The uncharacterized mRNA targets of RyhB that were identified in four or more of the genome-wide studies were then further analyzed using the IntaRNA2 and RNAstructure3 programs. Target mRNAs that showed the potential for both a strong interaction with RyhB and a relatively unstructured binding site with a high probability of structural rearrangement upon RyhB binding were chosen for further analysis. Four putative RyhB targets were selected: the positively regulated genes, cirA and fliA, and the negatively regulated genes, sufAB and frdA. This research will provide a deeper understanding of the regulatory system in E. coli, which could help combat pathogenic infections and antibiotic resistance.

References:
1. Chareyre, S., Mandin, P. (2018) Bacterial Iron Homeostasis Regulation by sRNAs, Microbiol. Spectr. 6(2), 267-281.
2. Mann, M., Wright, P. R., and Backofen, R. (2017) IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions, Nucleic Acids Research, 45(W1), W435–W439
3. Reuter, J. S., and Mathews, D. H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis, BMC Bioinformatics 11,129.

Keywords: sRNA, Ecoli