TfoX-based genetic mapping identifies Vibrio fischeri strain-level differences and reveals a common lineage of laboratory strains.

TitleTfoX-based genetic mapping identifies Vibrio fischeri strain-level differences and reveals a common lineage of laboratory strains.
Publication TypeJournal Article
Year of Publication2015
AuthorsBrooks, JF, Gyllborg, MC, Kocher, AA, Markey, LEH, Mandel, MJ
JournalJ Bacteriol
Volume197
Issue6
Pagination1065-74
Date Published2015/03/31
ISSN1098-5530
KeywordsAliivibrio fischeri, Animals, Bacterial Proteins, Carrier State, Chromosome Mapping, Chromosomes, Bacterial, Decapodiformes, DNA, Bacterial, Gene Expression Regulation, Bacterial, Genetic Markers, Trans-Activators
Abstract

Bacterial strain variation exists in natural populations of bacteria and can be generated experimentally through directed or random mutation. The advent of rapid and cost-efficient whole-genome sequencing has facilitated strain-level genotyping. Even with modern tools, however, it often remains a challenge to map specific traits to individual genetic loci, especially for traits that cannot be selected under culture conditions (e.g., colonization level or pathogenicity). Using a combination of classical and modern approaches, we analyzed strain-level variation in Vibrio fischeri and identified the basis by which some strains lack the ability to utilize glycerol as a carbon source. We proceeded to reconstruct the lineage of the commonly used V. fischeri laboratory strains. Compared to the wild-type ES114 strain, we identify in ES114-L a 9.9-kb deletion with endpoints in tadB2 and glpF; restoration of the missing portion of glpF restores the wild-type phenotype. The widely used strains ESR1, JRM100, and JRM200 contain the same deletion, and ES114-L is likely a previously unrecognized intermediate strain in the construction of many ES114 derivatives. ES114-L does not exhibit a defect in competitive squid colonization but ESR1 does, demonstrating that glycerol utilization is not required for early squid colonization. Our genetic mapping approach capitalizes on the recently discovered chitin-based transformation pathway, which is conserved in the Vibrionaceae; therefore, the specific approach used is likely to be useful for mapping genetic traits in other Vibrio species.

DOI10.1128/JB.02347-14
Alternate JournalJ Bacteriol
PubMed ID25561715
PubMed Central IDPMC4336346
Grant ListR25 GM079300 / GM / NIGMS NIH HHS / United States
R25 GM086262 / GM / NIGMS NIH HHS / United States
T32 GM008061 / GM / NIGMS NIH HHS / United States
GM08061 / GM / NIGMS NIH HHS / United States