Nicholas R. De Lay, PhD

Education

Postdoctoral Fellow

National Institutes of Health

Ph.D.

University of Illinois at Urbana-Champaign, 2007

Areas of Interest

Research Interests

Molecular mechanisms by which small regulatory RNAs (sRNAs) regulate gene expression in Gram-negative bacteria.

Small regulatory RNAs (sRNAs) that control gene expression by base-pairing with target mRNAs are found in all three domains of life. In many, if not all Gram-negative bacterial species including Escherichia coli, a large class of these sRNAs bind to an RNA chaperone called Hfq. Hfq stabilizes the sRNA and facilitates pairing to a short complementary sequence in a target mRNA. Pairing of the sRNA to the mRNA results in an increase or decrease in the synthesis, life span, or translation of the mRNA depending on the nature of their interactions. Disrupting sRNA-mediated gene regulation in bacteria by deleting hfq results in defects in growth and/or virulence and an increased sensitivity to antibiotics. These results suggest that proteins critical for Hfq-dependent sRNA-mediated regulation may be good targets for antibiotics. The identification of new molecular targets of antibiotics is of growing importance given the rising occurrence of multi-drug resistance among Gram-negative bacterial pathogens.

One focus of the research in my laboratory is on identifying and characterizing the key proteins involved in sRNA-mediated regulation using E. coli as the model system. This research will lead to a greater understanding of the process of sRNA-mediated regulation and to the identification of novel targets for antibiotics. Using a genetic approach, I have identified and begun to characterize additional factors required for Hfq-dependent sRNA-mediated gene regulation including polynucleotide phosphorylase (PNPase) and poly(A) polymerase (PAPI). The findings of this work have resulted in a new model for Hfq-dependent sRNA-mediated regulation. In this model, both Hfq and PNPase bind to separate sites on the sRNA, protecting the sRNA from degradation. This complex then facilitates pairing of the sRNA with a target mRNA. In many cases, this causes cleavage of the sRNA and mRNA target by RNase E. Our work has also shown that PNPase and PAPI have an important role in the subsequent decay of mRNA fragments generated by cleavage of sRNA targets by RNase E.

Some of the questions raised by this model that we want to address are: How does PNPase block the degradation of sRNAs? What keeps PNPase itself from using its exoribonuclease activity to degrade sRNAs? Does PNPase play additional roles in sRNA-mediated regulation? Are there additional proteins involved in sRNA-mediated regulation and what steps are they involved in?

Function of sRNAs and RNA binding proteins in controlling Streptococcus pneumoniae pathogenesis.

My laboratory is also interested in uncovering the molecular mechanisms by which sRNAs and RNA binding proteins transform S. pneumoniae physiology and virulence. By deciphering how these RNA binding proteins and sRNAs fit into regulatory pathways, i.e., how and when they are expressed, what genes these regulators control, and how that regulation leads to changes in gene expression, not only are we able to glean novel insights into how bacteria sense and adapt to its environment, stresses, and host interactions, but we can discover for the first time new regulatory pathways, new signals sensed by bacteria, new players involved in particular biological processes, and how different physiological processes occur.

Publications

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