MULTI-LAYERED RNA-SEQ APPROACH REVEALS RNA-MEDIATED REGULATION OF QUORUM SENSING IN PSEUDOMONAS AERUGINOSA

Maya Shamir ¹ Maureen Thomason ² Daniel Dar ¹ Ofir Cohen ³ Peter E. Greenberg ² Rotem Sorek ¹

¹Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
²Department of Microbiology, University of Washington, Seattle, Washington, USA
³Department of Medical Oncology, Dana-Farber Cancer Institute, Broad Institute of Harvard and MIT, Boston, Massachusetts, USA

Quorum sensing is a highly regulated cell–cell communication phenomenon that coordinates bacterial behaviors on a community level, such as swarming, sporulation and virulence. A well-established model organism in the quorum sensing field is Pseudomonas aeruginosa, which is a major pathogen in the diseased microbiome of cystic fibrosis patients. In P. aeruginosa, over 300 genes are controlled by acyl-homoserine lactones (AHLs) mediated quorum sensing, yet many aspects of this regulation remain unknown. We sought to better understand the involvement of RNA-based regulation in P. aeruginosa quorum-sensing circuits by characterizing the dynamic transcriptome-wide response to AHLs. A multi-layered approach, comprised of quantitative RNA-seq and global mapping of transcription start sites and termination sites on a single nucleotide resolution, revealed a set of previously unknown sRNAs that are up-regulated upon exposure to AHLs. Remarkably, one of these sRNAs is located within the 5’ UTR of the AHL synthase gene, rhlI, suggesting a novel RNA-based regulation of this major quorum sensing gene. Indeed, mutations in the putative rhlI ribo-regulator resulted in complete abolishment of AHL synthesis by RhlI, thus representing a new RNA-mediated regulation layer in the P. aeruginosa quorum sensing network.