The Effect of the Small RNA RyhB on the Structure of its mRNA Targets

Open Access
- Author:
- Grecco, Samantha
- Area of Honors:
- Biochemistry and Molecular Biology
- Degree:
- Bachelor of Science
- Document Type:
- Thesis
- Thesis Supervisors:
- Philip C Bevilacqua, Thesis Supervisor
Ying Gu, Thesis Honors Advisor - Keywords:
- sRNA
RyhB
gene expression profiling
in vivo chemical structure probing
pulldown assay
antibiotic resistance
structure-function relationship - Abstract:
- When Escherichia coli experiences environmental stressors, such as iron starvation, it initiates a regulatory response to maintain homeostasis. One such type of regulation is by mediating the efficiency of mRNA translation using small non-coding RNAs (sRNA), 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. 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. Four putative RyhB targets (cirA, fliA, sufAB, frdA) were selected that showed the potential for both a strong interaction with RyhB and a relatively unstructured binding site or have a high probability of structural rearrangement upon RyhB binding. Gene expression profiling and in vivo structure probing was used to analyze how RyhB regulates the levels and expression of the four putative mRNA targets. This research will provide a deeper understanding of the regulatory system in E. coli, which could help combat pathogenic infections and antibiotic resistance.