Research

RNA-protein interactions are critical for gene regulation and the adaptation to stress in all organisms. Our research addresses the molecular mechanisms of how small (s)RNAs in bacteria collaborate with proteins such as Hfq to regulate messenger RNA translation and stability. We have recently developed an in vivo assay to harness the power of molecular genetics to discover and characterize RNA-protein interactions inside of E. coli cells. We have used this assay to learn more about how the E. coli RNA chaperone protein Hfq binds to its regulatory sRNAs. Students in the lab are adapting this assay to new interactions to explore the diversity of how small RNAs interact with their protein collaborators across bacteria that cause human diseases, and will quantitatively dissect these interactions using complementary biochemical tools.

Examples of projects students are working on include:

• Expanding the types of protein-RNA interactions we can detect in the assay.

• Optimizing components of the B3H assay (including the protein and RNAs components, and the bacterial reporter strain) to improve signal of detection.

• Screening for mutations in the bacterial RNA chaperone “Hfq” that alter its interactions with small RNAs and other cellular binding proteins (some of this is in collaboration with Biochem 314 lab)

• When we find interesting mutations, we will analyze their effect on the thermodynamics and kinetics of sRNA binding in vitro and study their functional consequences in vivo.