A Vibrio parahaemolyticus transcriptome map captures conserved and specific regulators

Abstract

How bacterial sRNAs arise, evolve, and decay is poorly understood, despite their importance as posttranscriptional regulators. Here, we provide a high-resolution transcriptome map and curated sRNA set for the pathogen Vibrio parahaemolyticus. We identify over 100 sRNAs, including broadly conserved, lineage-specific, and previously unidentified transcripts, as well as dual-function (regulatory/coding) sRNAs. We show that broadly conserved VcrX represses chitin utilization genes and may regulate Vibrio Spot 42, which we also confirm is translated. We expand on FlaX regulation of polar flagella by demonstrating that it differentially activates/represses downstream flagellins across the genus, and identifying a potential FlaX sponge in only some clades. We further show that RyhB is translated in V. parahaemolyticus but not V. cholerae and encodes a Cys-rich small protein. Together, this provides a resource for Vibrio and foundation for comparative study of posttranscriptional regulation to understand how sRNAs and their networks evolve.