Small proteins and dual RNA regulators in Vibrio cholerae

Dual RNA regulators are a unique group of small regulatory RNAs (sRNAs) that merges base-pairing sRNA function with small protein (SP) encoding function of an mRNA. In the previous decades, the importance of sRNAs has been extensively studied ranging from stress responses, antibiotic tolerance, virulence, carbon metabolism, and intercellular communication. In contrast, only little is known about dual RNA regulators and SPs. The problem is mainly due to the small size of SPs (≤ 50 amino acids), poor annotation, and the lack of genetic screens aiming to characterize SPs in bacteria.

To address this problem in the major human pathogen Vibrio cholerae, we performed ribosome profiling to identify potential small open reading frames at the genome-wide level. These experiments revealed 75 potential sORFs in V. cholerae, of which we confirmed 44 for in vivo translation by GFP reporter and validated 21 by Western Blotting. Characterization of SPs led us to discover the V. cholerae dual RNA and protein (VcdRP) harboring the VcdP SP and the VcdR sRNA, which together synchronize carbon uptake and central metabolism in V. cholerae (1). Following the search for additional dual regulators pivotal during carbon utilization, we identified an additional dual RNA regulator in V. cholerae named VcsRP (V. cholerae carbon starvation dual RNA and Protein). The vcsRP gene encodes the VcsP SP and the VcsR sRNA, which is processed from 3" UTR by ribonuclease E. Expression of vcsRP is activated under carbon limitation and is repressed under glucose-rich conditions. Further, we obtained evidence showing that VcsR acts post-transcriptionally and in concert with Hfq to inhibit the expression of enzymes involved in galactose metabolism and oxidative phosphorylation.

Reference:

K. Venkat et al., A dual-function RNA balances carbon uptake and central metabolism in Vibrio cholerae. EMBO J 40, e108542 (2021).