DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae

Abstract

Here we determine the complete genomic sequence of the gram negative, gamma-Proteobacterium Vibrio cholerae El Tor N16961 to be 4,033,460 base pairs (bp). The genome consists of two circular chromosomes of 2,961,146 bp and 1,072,314 bp that together encode 3,885 open reading frames. The vast majority of recognizable genes for essential cell functions (such as DNA replication, transcription, translation and cell-wall biosynthesis) and pathogenicity (for example, toxins, surface antigens and adhesins) are located on the large chromosome. In contrast, the small chromosome contains a larger fraction (59%) of hypothetical genes compared with the large chromosome (42%), and also contains many more genes that appear to have origins other than the gamma-Proteobacteria. The small chromosome also carries a gene capture system (the integron island) and host 'addiction' genes that are typically found on plasmids; thus, the small chromosome may have originally been a megaplasmid that was captured by an ancestral Vibrio species. The V. cholerae genomic sequence provides a starting point for understanding how a free-living, environmental organism emerged to become a significant human bacterial pathogen.

Figure 1. Linear representation of the V. cholerae chromosomes.

The location of the predicted coding regions, colour-coded by biological role, RNA genes, tRNAs, other RNAs, Rho-independent terminators and Vibrio cholerae repeats (VCRs) are indicated (see the larger, printable PDF file (2622K). Arrows represent the direction of transcription for each predicted coding region. Numbers next to the tRNAs represent the number of tRNAs at a locus. Numbers next to GES represent the number of membrane-spanning domains predicted by the Goldman, Engleman and Steitz scale calculated by TopPred for that protein. Gene names are available at the TIGR web site (www.tigr.org) and as Supplementary Information .

Figure 2. Circular representation of the V. cholerae genome.

The two chromosomes, large and small, are depicted. From the outside inward: the first and second circles show predicted protein-coding regions on the plus and minus strand, by role, according to the colour code in Fig. 1 (unknown and hypothetical proteins are in black). The third circle shows recently duplicated genes on the same chromosome (black) and on different chromosomes (green). The fourth circle shows transposon-related (black), phage-related (blue), VCRs (pink) and pathogenesis genes (red). The fifth circle shows regions with significant χ² values for trinucleotide composition in a 2,000-bp window. The sixth circle shows percentage G+C in relation to mean G+C for the chromosome.The seventh and eighth circles are tRNAs and rRNAs, respectively.

Figure 3. Overview of metabolism and transport in V. cholerae.

Pathways for energy production and the metabolism of organic compounds, acids and aldehydes are shown. Transporters are grouped by substrate specificity: cations (green), anions (red), carbohydrates (yellow), nucleosides, purines and pyrimidines (purple), amino acids/peptides/amines (dark blue) and other (light blue). Question marks associated with transporters indicate a putative gene, uncertainty in substrate specificity, or direction of transport. Permeases are represented as ovals; ABC transporters are shown as composite figures of ovals, diamonds and circles; porins are represented as three ovals; the large-conductance mechanosensitive channel is shown as a gated cylinder; other cylinders represent outer membrane transporters or receptors; and all other transporters are drawn as rectangles. Export or import of solutes is designated by the direction of the arrow through the transporter. If a precise substrate could not be determined for a transporter, no gene name was assigned and a more general common name reflecting the type of substrate being transported was used. Gene location on the two chromosomes, for both transporters and metabolic steps, is indicated by arrow colour: all genes located on the large chromosome (black); all genes located on the small chromosome (blue); all genes needed for the complete pathway on one chromosome, but a duplicate copy of one or more genes on the other chromosome (purple); required genes on both chromosomes (red); complete pathway on both chromosomes (green). (Complete pathways, except for glycerol, are found on the large chromosome.) Gene numbers on the two chromosomes are in parentheses and follow the colour scheme for gene location. Substrates underlined and capitalized can be used as energy sources. PRPP, phosphoribosyl-pyrophosphate; PEP, phosphoenolpyruvate; PTS, phosphoenolpyruvate-dependant phosphotransferase system; ATP, adenosine triphosphate; ADP, adenosine diphosphate; MCP, methyl-accepting chaemotaxis protein; NAG, N-acetylglucosamine; G3P, glycerol-3-phosphate; glyc, glycerol; NMN, nicotinamide mononucleotide. Asterisk, because V. cholerae does not use cellobiose, we expect this PTS system to be involved in chitobiose transport.

Figure 4. Percentage of total Vibrio cholerae open reading frames (ORFs) in biological roles compared with other γ-Proteobacteria.

These were V. cholerae, chromosome 1 (blue); V. cholerae, chromosome 2 (red); Escherichia coli (yellow); Haemophilus influenzae (pale blue). Significant partitioning (P < 0.01) of biological roles between V. cholerae chromosomes is indicated with an asterisk, as determined with a χ² analysis. 1, Hypothetical contains both conserved hypothetical proteins and hypothetical proteins, and is at 1/10 scale compared with other roles.

Figure 5. Comparison of the V. cholerae ORFs with those of other completely sequenced genomes.

The sequence of all proteins from each completed genome were retrieved from NCBI, TIGR and the Caenorhabditis elegans (wormpep16) databases. All V. cholerae ORFs (large chromosome, blue; small chromosome, red) were searched against all other genomes with FASTA3. The number of V. cholerae ORFs with greatest similarity (E ≤ 10^-5) are shown in proportion to the total number of ORFs in that genome. There were no ORFs that were most similar to a Mycoplasma pneumoniae ORF.

Figure 6. Phylogenetic tree of methyl-accepting chemotactic proteins (MCP) homologues in completed genomes.

Homologues of MCP were identified by FASTA3 searches of all available complete genomes. Amino-acid sequences of the proteins were aligned using CLUSTALW, and a neighbour-joining phylogenetic tree was generated from the alignment using the PAUP* program (using a PAM-based distance calculation). Hypervariable regions of the alignment and positions with gaps in many of the sequences were excluded from the analysis. Nodes with significant bootstrap values are indicated: two asterisks, >70%; asterisk, 40–70%.