Phenotypic and Transcriptomic Characterization of Colonial Phase Variation in the Cholera Pathogen Reveals a Novel Smooth Biofilm-Defective Form

Abstract

Biofilm formation, through the production of Vibrio polysaccharide (VPS), greatly enhances the environmental fitness and pathogenic success of Vibrio cholerae. As a result of phase variation, V. cholerae can switch from a smooth form to rugose, whose cells produce excess VPS, resulting in highly structured biofilms and greater resistance to stress. To further characterize the reversible process of phase variation, we isolated three colonial lineages. Each lineage began with a smooth parent, N16961, and contained a rugose variant derived from the parent, N16961R, as well as a smooth revertant of the rugose, N16961SD. We found clear phenotypic and transcriptomic distinctions among all three variant forms. Namely, the N16961SD variants were biofilm-deficient unlike the other two variant types. However, despite their lack of biofilm, we found evidence of transcriptional up-regulation of genes encoding VPS components in the N16961SD variants that were consistent with elevated transcription levels observed in N16961R. Using RNA-seq, we identified other shared stress-adaptive transcriptomic signatures between the N16961R and N16961SD variants and found evidence that supports a role for certain central metabolic pathways in phase variation in V. cholerae. Whole genome sequencing identified mutations unique to the N16961SD variants which mapped to a gene encoding a protein containing a glycosyl hydrolase domain, VCA0254. Mutagenesis of VCA0254 in the N16961 parental background resulted in a significant increase in biofilm formation, suggesting that VPS may be a substrate for the glycosyl hydrolase. Therefore, we predict that VCA0254 may play a role in biofilm maintenance in this organism.