Comparison of genome structures of vibrios, bacteria possessing two chromosomes

Abstract

Vibrios are gram-negative gamma-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.

FIG. 1.

Restriction fragments of the genomic DNA of KX-V237. (A and B) Genomic DNA of KX-V237 was digested with NotI (lanes 1 and 5), SfiI (lanes 2 and 6), or I-CeuI (lanes 3 and 7) and then analyzed by PFGE (A) or FIGE (B). Lane 4 contained λ HindIII molecular weight markers. (C) Size of each restriction fragment.

FIG. 2.

Physical map of the genome of V. parahaemolyticus KX-V237. The linkage of NotI fragments and the relative locations of SfiI and I-CeuI fragments are shown. In this study, we constructed the map of NotI restriction fragments. The SfiI or I-CeuI fragments are not linked by, for example, linking clones. This is why the arcs that indicate the SfiI or I-CeuI fragments have gaps. The positions of the SfiI or I-CeuI fragments were determined from the results of hybridization with the NotI-linking clones or probes for the genes indicated. The restriction fragments whose designations have a superscript (e.g., SD^b) are the fragments for which multiple fragments having indistinguishable sizes were found (Fig. 1); we could not identify which fragment was which.

FIG. 3.

Comparison of genetic maps of KX-V237 and AQ4673. The arrows on the large chromosomes indicate a putative genetic inversion between the two strains. Although I-CeuI digestion of the genomic DNA of KX-V237 and AQ4673 suggested the presence of 10 and 9 rrn operons, respectively, fewer rrn operons are indicated because a single NotI fragment can have more than one rrn operon.

FIG. 4.

Comparison of genetic maps of V. cholerae N16961 and V. parahaemolyticus KX-V237. The ORFs of N16961 corresponding to probes L1 to L27 and S1 to S15 are listed in Table 2.

FIG. 5.

Comparison of genetic maps of V. cholerae N16961 and V. parahaemolyticus KX-V237. The maps are in a linearized form, starting at the oriC sites of the N16961 genome.