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Comparative Study
. 2008 Jan;74(1):44-51.
doi: 10.1128/AEM.01412-07. Epub 2007 Oct 12.

Conservation of the chitin utilization pathway in the Vibrionaceae

Dana E Hunt  1 , Dirk Gevers, Nisha M Vahora, Martin F Polz
Affiliations
Comparative Study

Conservation of the chitin utilization pathway in the Vibrionaceae

Dana E Hunt et al. Appl Environ Microbiol. 2008 Jan.

Abstract

Vibrionaceae are regarded as important marine chitin degraders, and attachment to chitin regulates important biological functions; yet, the degree of chitin pathway conservation in Vibrionaceae is unknown. Here, a core chitin degradation pathway is proposed based on comparison of 19 Vibrio and Photobacterium genomes with a detailed metabolic map assembled for V. cholerae from published biochemical, genomic, and transcriptomic results. Further, to assess whether chitin degradation is a conserved property of Vibrionaceae, a set of 54 strains from 32 taxa were tested for the ability to grow on various forms of chitin. All strains grew on N-acetylglucosamine (GlcNAc), the monomer of chitin. The majority of isolates grew on alpha (crab shell) and beta (squid pen) chitin and contained chitinase A (chiA) genes. chiA sequencing and phylogenetic analysis suggest that this gene is a good indicator of chitin metabolism but appears subject to horizontal gene transfer and duplication. Overall, chitin metabolism appears to be a core function of Vibrionaceae, but individual pathway components exhibit dynamic evolutionary histories.

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Figures

FIG. 1.
FIG. 1.
Schematic of the chitin catabolic cascade in V. cholerae. Enzymes and transporters are given gene identifiers from V. cholerae N16961 when possible. The boxes around gene identifiers denote how functions were predicted: gray shading, biochemical evidence in the vibrios; thick outline, microarray expression data (27); thin lines, bioinformatic prediction only; and dashed lines, predicted functions based on experimental evidence. (Expanded from reference with permission of the publisher.)
FIG. 2.
FIG. 2.
Distribution of predicted chitin pathway genes among Vibrionaceae genomes. The phylogenetic relationship is based on maximum-likelihood analysis of a concatenation of 100 shared genes. Numbers at nodes represent values based on 100 bootstrap replicates. Each of the columns corresponds to a chitin metabolism-related gene family, with the family name indicating the predicted function and the number indicating the reaction or transport mechanism identifier from Fig. 1, with a representative gene designation in parentheses. The number within the box indicates the number of copies of that gene family in the corresponding genome, which is further indicated by light-gray shading for one gene copy or dark-gray shading for two or more gene copies. An asterisk indicates a complete genome sequence.
FIG. 3.
FIG. 3.
Phylogenetic relationships of partial chiA gene sequences from Vibrionaceae and related organisms based on maximum-likelihood analysis. Numbers shown at nodes represent values based on 100 bootstrap replicates; only nodes with values of >80 are shown. Branch length to the outgroup is truncated, as indicated by the arrow. GenBank accession numbers are given for previously sequenced genes. Gray boxes indicate potential LGT events. Round circles indicate the two copies of chiA family genes in Photobacteria.
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