Global post-transcriptional regulators in Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen found ubiquitously in both natural and manmade environments. Central to its ability to grow in different environments is the organism’s coordinated deployment of virulence factors, metabolic responses, and other genetically-encoded adaptations controlled at the levels of transcription and translation. Using a modified ChIP-seq approach, I demonstrate that three P. aeruginosa post-transcriptional regulators, Hfq, Crc, and RsmA, are able to function in a co-transcriptional manner. These regulators are associated with hundreds of nascent transcripts, including those not previously known to be targeted by these proteins. I validate several of these novel targets and show that they are controlled by these post-transcriptional regulators at the level of translation. These results suggest that functioning co-transcriptionally may be a widespread regulatory mechanism of RNA-binding proteins in bacteria, where transcription and translation are coupled events. Small noncoding RNAs (sRNAs) are another class of post-transcriptional regulator. Although P. aeruginosa is predicted to encode several hundred sRNAs, relatively few have been functionally characterized. Here I describe TrrC, a novel sRNA in P. aeruginosa that positively regulates cupA fimbrial gene expression. I present evidence suggesting that TrrC directly targets the H-NS family member MvaU to counter the latter’s silencing effect on the cupA genes. Together, this thesis describes a facile approach to study the co-transcriptional activities of RNA-binding proteins in bacteria and expands on current understandings of how post-transcriptional regulators function in these organisms.