Access Type

Open Access Dissertation

Date of Award

January 2013

Degree Type


Degree Name




First Advisor

Andrew L. Feig


Regulatory RNAs (sRNAs) are essential for bacteria to thrive in diverse environments and they also play a key role in virulence [11]. Trans-sRNAs affect the stability and/or translation of their target mRNAs through complementary base-pairing. The base-pairing interaction is not perfect and requires the action of an RNA binding protein, Hfq. Hfq facilitates these RNA-RNA interactions by stabilizing duplex formation, aiding in structural rearrangements, increasing the rate of structural opening, and/or by increasing the rate of annealing [18-21]. Hfq has two well characterized binding surfaces: the proximal surface, which binds AU rich stretches typical of sRNAs, and the distal surface, which binds (ARN)x motifs typically found in target mRNAs [30, 33, 36]. Studies on Hfq-RNA interactions have focused largely on sRNAs until the more recent discovery of an (ARN)x motif within the 5'UTR of target mRNAs[36, 37]. The importance of this motif in facilitating Hfq-mRNA binding and its requirement for regulation of a couple well known target mRNAs led us to further characterize the motif in the work described in this thesis. We performed bioinformatic and in vitro analyses to investigate the prevalence, location, structural contexts, and Hfq-binding of (ARN)x motifs in known target mRNAs. We found that the known targets contain single stranded (ARN)x sequences in their 5'UTRs that bind to Hfq. Two predominant structural contexts of the single stranded (ARN)x motifs became clear: they were either flanked by stem loop structures or within a loop of an internal bulge, multi-branch junction or hairpin. The key features of the motifs were then used as a bioinformatic tool on a genome wide scale to identify mRNAs that might bind to Hfq. We found that 21% of mRNAs have a suitable (ARN)x motif and therefore likely bind to Hfq. Messages that bind to Hfq may be novel sRNA targets so we investigated this possibility using an in vivo reporter assay and found that 63% of the mRNAs tested are regulated by a specific sRNA. The novel targets are involved in pathways including iron salvage, biofilm formation, and amino acid metabolism. Overall, we defined key features of (ARN)x motifs and were able to use those to predict novel target mRNAs in E. coli. This approach is efficient, effective and adaptable other bacterial species.