Access Type

Open Access Thesis

Date of Award

January 2017

Degree Type


Degree Name




First Advisor

Andrew Feig


Number of small RNA (sRNA) gene regulators have mounted in E. coli over the years whereas the number of validated protein partners has not changed considerably. Hfq has remained the only well studied global regulatory partner of sRNAs in E. coli. However, direct or indirect involvement of other protein partners has always been speculated. Study from Blasi lab has shown that CsdA, one of the five DEAD-box RNA helicases of E. coli, is required for the DsrA mediated upregulation of rpoS under cold stress condition. Previous study from our lab has identified two other DEAD-box RNA helicases, RhlB and RhlE, as potential protein partner of Hfq-sRNA mediated gene regulatory pathway. The work presented here was focused to investigate the plausible roles of RhlB and RhlE, DEAD-box helicases in Hfq-sRNA mediated regulatory pathways. In this study, using Hfq dependent sRNAs and their target mRNAs as substrates, we have shown that RhlB and RhlE both shows differential stimulation in substrate dependent manner; example: rA18 significantly simulates RhlE but fails to stimulate RhlB. Contrary to literature reports, significant ATPase activity has been observed for RhlB with several RNA substrates used in this study. However, consistent with literature reported observations, RhlE shows several folds higher stimulation of ATPase activity than the RhlB. Presence of Hfq has very little effects on the RhlE ATPase activity whereas the ATPase activity of RhlB was significantly modulated. While further investigation is needed, this study has shown that Hfq dependent sRNA and mRNA could significantly stimulate RhlB and RhlE, indicating towards the potential contribution of these helicases in-vivo.