Abstract
BackgroundIn a process known as phase variation, the marine bacterium and cholera pathogen Vibrio cholerae alternately expresses smooth or rugose colonial phenotypes, the latter being associated with advanced biofilm architecture and greater resistance to ecological stress. To define phase variation at the transcriptomic level in pandemic V. cholerae O1 El Tor strain N16961, we compared the RNA-seq-derived transcriptomes among the smooth parent N16961, its rugose derivative (N16961R) and a smooth form obtained directly from the rugose at high frequencies consistent with phase variation (N16961SD).ResultsDifferentially regulated genes which clustered into co-expression groups were identified for specific cellular functions, including acetate metabolism, gluconeogenesis, and anaerobic respiration, suggesting an important link between these processes and biofilm formation in this species. Principal component analysis separated the transcriptome of N16961SD from the other phase variants. Although N16961SD was defective in biofilm formation, transcription of its biofilm-related vps and rbm gene clusters was nevertheless elevated as judged by both RNA-seq and RT-qPCR analyses. This transcriptome signature was shared with N16961R, as were others involving two-component signal transduction, chemotaxis, and c-di-GMP synthesis functions.ConclusionsPrecise turnarounds in gene expression did not accompany reversible phase transitions (i.e., smooth to rugose to smooth) in the cholera pathogen. Transcriptomic signatures consisting of up-regulated genes involved in biofilm formation, environmental sensing and persistence, chemotaxis, and signal transduction, which were shared by N16961R and N16961SD variants, may implicate a stress adaptation in the pathogen that facilitates transition of the N16961SD smooth form back to rugosity should environmental conditions dictate.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3233-x) contains supplementary material, which is available to authorized users.
Highlights
In a process known as phase variation, the marine bacterium and cholera pathogen Vibrio cholerae alternately expresses smooth or rugose colonial phenotypes, the latter being associated with advanced biofilm architecture and greater resistance to ecological stress
The two vps gene clusters are separated by an intergenic region that contains the rbm genes, which encode biofilm matrix proteins unique to V. cholerae [15]
Isolation and phenotypic characterization of colonial phase variants Starting with three well-isolated smooth colonies of the parental strain N16961, independent broth cultures were passaged daily with occasional plating for individual colonies
Summary
In a process known as phase variation, the marine bacterium and cholera pathogen Vibrio cholerae alternately expresses smooth or rugose colonial phenotypes, the latter being associated with advanced biofilm architecture and greater resistance to ecological stress. Epidemic strains undergo a reversible phase variation event between smooth and rugose colonial morphotypes at a frequency apparently greater than that of non-epidemic clinical and environmental strains [2]. Characterization of non-polar vps deletion mutants revealed that most of the vps genes are required for the production of corrugated colonies, pellicles, and biofilms [14]. The two vps gene clusters are separated by an intergenic region that contains the rbm genes, which encode biofilm matrix proteins unique to V. cholerae [15]. Bap, encoded by the unlinked VC1888 gene, is a homolog of one of the Rbm proteins and is required for V. cholerae biofilm stability [14, 15]
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