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, 102 (8), 3004-9

Complete Genome Sequence of Vibrio Fischeri: A Symbiotic Bacterium With Pathogenic Congeners

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Complete Genome Sequence of Vibrio Fischeri: A Symbiotic Bacterium With Pathogenic Congeners

E G Ruby et al. Proc Natl Acad Sci U S A.

Abstract

Vibrio fischeri belongs to the Vibrionaceae, a large family of marine gamma-proteobacteria that includes several dozen species known to engage in a diversity of beneficial or pathogenic interactions with animal tissue. Among the small number of pathogenic Vibrio species that cause human diseases are Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus, the only members of the Vibrionaceae that have had their genome sequences reported. Nonpathogenic members of the genus Vibrio, including a number of beneficial symbionts, make up the majority of the Vibrionaceae, but none of these species has been similarly examined. Here we report the genome sequence of V. fischeri ES114, which enters into a mutualistic symbiosis in the light organ of the bobtail squid, Euprymna scolopes. Analysis of this sequence has revealed surprising parallels with V. cholerae and other pathogens.

Figures

Fig. 1.
Fig. 1.
Genome maps of Chr I (2.9 Mbp) and Chr II (1.3 Mbp) of V. fischeri ES114. (From the inside) Ring 1, rrn operons (red); tRNAs (green). Ring 2, “foreign” elements (black). Ring 3, type IV pilus loci (red). Circle 1, G+C content over a 200-kb window with 5-kb steps; red and blue denote G+C content higher and lower than average, respectively. Circle 2, homology on + and - strands to V. cholerae N16961 ORFs, determined by using FASTA; red, e value < -30; green, e value > -30. Circle 3, location in kilobases.
Fig. 2.
Fig. 2.
V. fischeri ES114 ORFs on the + and - strands, color-coded to functionality (see key).
Fig. 3.
Fig. 3.
Comparison of the V. cholerae CTX phage locus (A) with a homologous locus in V. fischeri ES114 (B). ORFs encoding the CTX genes ctxA and ctxB, and the second RS2 element downstream of the locus, are missing in V. fischeri. Identifiable attL and attR sites are indicated.
Fig. 4.
Fig. 4.
The TCP gene cluster in V. fischeri ES114 (green) and V. cholerae N16961 (red). V. fischeri has no identifiable homologs of aldA, tagA, toxT,or tcpJ, and the V. fischeri ORF labeled “hyp.” has no detectable similarity to V. cholerae tcpR.
Fig. 5.
Fig. 5.
G+C content of ORFs in and around the TCP gene clusters of V. fischeri ES114 (green) and V. cholerae N16961 (red) plotted against their relative linear position on the chromosome. The average G+C content of the two species' genomes are indicated by the colored dotted lines, and the arrow points to the locations of their TcpA pilin ORFs, around which the rest of the sequences have been aligned.

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