Research Projects

Escherichia coli is a widely studied bacteria, but the functions of many non-protein coding RNAs (non-coding RNAs) remain unknown. Regulatory non-coding RNAs play a crucial role in physiological, adaptation, and immunological processes of bacteria. They can be cis-regulating or trans-regulating, and can have multiple classes of partners. studying non-coding RNAs provides insights into bacterial physiology, virulence, and is useful for developing applications like CRIsPR. This project aims to systematically study non-coding RNAs in E. coli using bioinformatics, in vitro, in cell, and in vivo techniques. Phylogenetic distribution of identified non-coding RNAs will be used to arrive at secondary structures through covariation analysis. RNA of interest will be tagged with fluorogenic RNA Mango tag, which is an excellent toolbox for RNA studies, including RNA-Protein purification and analysis. Tagged RNAs will be expressed through plasmids in deletion strains of E. coli, and RNAP complexes will be immunoprecipitated and analyzed with mass-spectrometry to identify RNA binding partners. Expression profiles of RNA of interest and its native promoter system will be studied under different stress conditions. The wild type and deletion strain will be introduced into mouse models to study the effect of the RNA of interest on E. coli virulence.