Detection and Transformation of Genome Segments That Differ within a Coastal Population of Vibrio cholerae Strains

Abstract

Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae strains comprise a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain N16961 as conserved, variably present, or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose and diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. The transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through the acquisition of new sequences by horizontal gene transfer or by the loss of preexisting DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.

Identification of a Chitin-Induced Small RNA That Regulates Translation of thetfoXGene, Encoding a Positive Regulator of Natural Competence in Vibrio cholerae

“…Blokesch and Schoolnik demonstrated that the whole O1-specific antigen gene cluster of V. cholerae O1 El Tor can be exchanged by the O37-or O139-antigen gene cluster through chitin-induced natural competence (4). In addition, the cholera toxin prophage (65) and clusters of metabolic genes (43) can be transferred in the same manner. Recently, other Vibrio species, Vibrio vulnificus, Vibrio fischeri, and Vibrio parahaemolyticus, were shown to be naturally transformable upon exposure to chitin (8,17,50).…”

Microbial Surface Colonization and Biofilm Development in Marine Environments

“…In addition, vibrios are common producers of auxins such as indole-3-acetic acid (544), likely playing a role in stimulating the activity (such as mucus exudation) of marine algae and the formation of vibrio-alga associations (545). Surface association not only increases vibrio survival and fitness but also increases opportunities for vibrio intraspecies and interspecies exchanges of genes, including those for the utilization of unusual substrates and for virulence (15,(546)(547)(548)(549). Such exchanges are supported by surface-induced natural competence and likely involve plasmids, phages, transposons, integrons/gene cassettes, and perhaps other horizontal gene transfer mechanisms (550)(551)(552).…”

TfoX-Based Genetic Mapping Identifies Vibrio fischeri Strain-Level Differences and Reveals a Common Lineage of Laboratory Strains

“…A previous use of the pathway has been to facilitate defined mutagenesis in multiple Vibrio species, and it was shown that in the presence of chitin V. cholerae strains could undergo a serogroup conversion, which requires the exchange of an ϳ42-kb fragment of DNA (22)(23)(24)41). In another study it was shown that chitin-based transformation led to transmission of large genomic fragments in V. cholerae, with an average size of 22.7 kb (25). We observe similarly large fragments in V. fischeri, and we demonstrate the novel application of the use of TfoX-induced transformation for genetic mapping.…”

“…The last decade has revealed that Vibrio spp. are naturally transformable in the presence of chitin, and that large fragments of DNA (Ͼ20 kb) can be exchanged in nature or in the laboratory upon induction of the transformation regulatory cascade (21)(22)(23)(24)(25). The availability of transformation in V. fischeri, coupled with other genetic tools under development in the laboratory, presented an opportunity to develop a generalized system for genetic mapping in V. fischeri.…”