A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures

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.

Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria

“…R6 is one of the GGDEF domain containing receptors (VC2224 in V. cholerae O1 El Tor). The differential expression of this gene was one of the causes for the phase variation between the rugose and smooth forms of this strain (25). Furthermore, VC2224 was the only gene involved in c-di-GMP homeostasis that was expressed in vitro and repressed in the intestine during mouse infection (26).…”

Diverse Horizontally-Acquired Gene Clusters Confer Sucrose Utilization to Different Lineages of the Marine Pathogen Photobacterium damselae subsp. damselae

“…The mechanisms underlying this phenotype await further and promising studies in Pdd. Interestingly, a recent study pointed out that the V. cholerae VCA0653 gene encoding the sucrose-specific PTS component ScrA, was 30-fold downregulated on the phase variation switch from wild-type-colony phenotype to a rugose-colony phenotype, associated with advanced biofilm architecture [64]. This suggests that the ability to utilize sucrose would impair biofilm formation, and thus transition to a rugose phenotype correlates with a strong downregulation of sucrose uptake.…”