Exploring post-transcriptional regulators in Acinetobacter baumannii

PROJECT SUMMARY Bacterial gene expression can be regulated at nearly every conceivable point across the central dogma of molecular biology where DNA is transcribed into RNA, which is in turn translated into proteins. Following transcription, mRNA transcripts are subject to regulation by so-called post-transcriptional regulators, which includes both RNA-binding proteins (RBPs) as well as short (50-500 nt), non-coding RNA transcripts, referred to as small RNAs, or sRNAs. The post-transcriptional regulation networks comprised by the sRNAs and associated RBPs are thought to allow bacteria to rapidly respond to changing environmental conditions by enhancing plasticity within gene expression networks. Research in my lab combines large-scale, genome-wide analyses facilitated by next generation sequencing approaches with classic bacterial genetics techniques. We utilize these approaches in a complimentary fashion; we leverage the sequencing results to inform the genetics experiments, and vice versa. Ultimately, we use the data to generate and test hypotheses about novel regulatory networks and regulatory mechanisms, with a particular focus on the RNA binding proteins, sRNAs and post- transcriptional regulatory networks in the gram-negative bacterium, Acinetobacter baumannii, a notorious opportunistic human pathogen. A. baumannii is a frequent cause of ventilator associated pneumonia, skin and soft tissue infections, and other hospital acquired infections. These organisms are amongst the most problematic species in the context of antibiotic resistance, where extensively drug resistant isolates present an urgent crisis to our healthcare system, especially considering that contemporary isolates also demonstrate increased virulence properties relative to ancestral strains. In this proposal, I present two major research projects in my laboratory, which address key concerns for understanding bacterial pathogens through the lens of understanding post-transcriptional regulation. Post-transcriptional regulatory networks remain largely unstudied in A. baumannii. We previously performed experiments to identify and characterize key RNA-RNA interactions and identified hundreds of RNA-RNA interactions, suggesting the existence of a robust post-transcriptional regulatory network in A. baumannii. In this proposal, we propose to systematically dissect relevant RNA-RNA interactions that are mediated by a key RNA binding protein, called Hfq, and further characterize how this essential protein integrates RNA-mediated regulation with cellular RNA processing enzymes. Collectively, the results of these studies will provide a comprehensive picture of the sRNA regulatory landscape in a significant bacterial pathogen and will enhance our understanding about the post-transcriptional regulatory network coordinates gene expression in the context of human disease.