Comparison of Genome Structures of Vibrios, Bacteria Possessing Two Chromosomes

Abstract

Vibrios are gram-negative ␥-proteobacteria which are ubiquitous in marine and estuarine environments. Recently, we demonstrated that some, if not all, Vibrio species have two circular chromosomes. The whole genome sequence of Vibrio cholerae N16961 has been reported. In this study, we constructed a physical and genetic map of the genome of Kanagawa phenomenon-positive Vibrio parahaemolyticus strain KX-V237 and compared it with those of V. parahaemolyticus AQ4673 and V. cholerae N16961. The genome of KX-V237 comprised two circular chromosomes (3.3 and 1.9 Mb), similar to the structure of the AQ4673 genome. The relative positions of the genes on the genomes were well conserved in the two strains, but a large inversion on the large chromosomes, probably symmetric around the replication origin, was suggested. Although the sizes of the large chromosomes of KX-V237 and V. cholerae N16961 were similar, the sizes of the small chromosomes were very different. Unlike N16961, the superintegron of KX-V237 was located on the large chromosome. Comparison of the genetic maps of the chromosomes of KX-V237 and V. cholerae N16961 revealed that most of the open reading frames (ORFs) present on the large chromosome of the V. cholerae strain had homologues on the large chromosome of the V. parahaemolyticus strain and that most of the ORFs on the small chromosome of N16961 were present on the small chromosome of KX-V237. The difference in the orders of the ORFs on the chromosomes of N16961 and KX-V237 implies that numerous and frequent genetic exchanges have occurred intrachromosomally rather than interchromosomally.

Biodiversity of Vibrios

“…Several lines of evidence support this hypothesis, e.g., the presence of an integron (an element often found on plasmids) (257). In V. parahaemolyticus and V. vulnificus, an integron is present on the chromosome 1, suggesting that the position of integrons does not provide evidence for the megaplasmid hypothesis (67,251,374). Other researchers argue that the small chromosome may have arisen by excision from a single, large ancestral genome (418).…”

“…Most of the intrachromosomal rearrangements, particularly in chromosome 1, may have occurred without changing the relative distance from the replication origin (251,374). Such symmetrical rearrangements have been observed in other bacterial chromosomes (105,239,364).…”

“…The relative position of the conserved genes in V. cholerae and V. parahaemolyticus demonstrates that extensive genome rearrangements have occurred within, and between, the two chromosomes (251,374). Most of the intrachromosomal rearrangements, particularly in chromosome 1, may have occurred without changing the relative distance from the replication origin (251,374).…”

“…A comparison of the genomes of V. cholerae and V. parahaemolyticus revealed that although chromosome 1 does not differ greatly in size between the two genomes (3.0 and 3.3 Mb respectively), chromosome 2 is much larger in V. parahaemolyticus than in V. cholerae (1.9 and 1.1 Mb, respectively) (251,374). Examination of more species from the Vibrionaceae also demonstrated that while the sizes of chromosome 1 do not differ greatly, those of chromosome 2 are variable (T. Iida et al, unpublished data).…”

“…The super-integron spanned 126 kb and harbored 179 cassettes of mainly unassigned function (162). To date, super-integrons have been identified in several Vibrio species, including V. cholerae (335), V. parahaemolyticus (374), and V. vulnificus (357). A comparison of the super-integrons of V. cholerae and V. parahaemolyticus revealed that the contents of the gene cassettes differed substantially between the two (251).…”