A chitin-binding domain in a marine bacterial chitinase and other microbial chitinases: implications for the ecology and evolution of 1,4-β-glycanases

Abstract

To examine the ecology and evolution of microbial chitinases, especially the chitin-binding domain, one of the chitinase genes (&A) from the marine bacterium Vibrio harveyi was analysed. The deduced amino acid sequence of ChiA is not very similar overall to other proteins, except for two regions, the putative catalytic and chitin-binding domains. Among all bacterial chitinases sequenced to date, there is no relationship between percentage similarity of catalytic domains and chitin-binding domains in pairwise comparisons, suggesting that these two domains have evolved separately. The chitinbinding domain appears to be evolutionarily conserved among many bacterial chitinases and is also somewhat similar to cellulose-binding domains found in microbial cellulases and xylanases. To investigate the role of the chitin-binding domain, clones producing versions of ChiA with or without this domain were examined. One version with the domain (ChiAl) bound to and hydrolysed chitin, whereas a truncated ChiA without the putative chitin-binding domain (ChiA2) did not bind to chitin, but it could hydrolyse chitin, although not as well. ChiAl diffused more slowly in agarose containing colloidal chitin than ChiA2, but diffusion of the two proteins in agarose without colloidal chitin was similar. These results indicate that the chitin-binding domain helps determine the movement of chitinase along IV-acetylglucosamine strands and within environments containing chitin.

Nutrient regime regulates complex transcriptional start site usage within a Pseudoalteromonas chitinase gene cluster

“…Different chitin-binding domains enable attachment to various types of chitin (Svitil and Kirchman, 1998). Svitil and Kirchman (1998) found that endochitinase activity from the V. harveyi chiA gene increased upon removal of the chitin-binding domain, as this changed the enzyme's accessibility to glycosidic bonds within a chitin strand.…”

“…Different chitin-binding domains enable attachment to various types of chitin (Svitil and Kirchman, 1998). Svitil and Kirchman (1998) found that endochitinase activity from the V. harveyi chiA gene increased upon removal of the chitin-binding domain, as this changed the enzyme's accessibility to glycosidic bonds within a chitin strand. In B. circulans, when the chiA1 chitin-binding domain was cloned separately from the gene in which it is located and expressed, the ChiA1 domain protein maintained its structure and function (Ikegami et al, 2000).…”

“…The presence or absence of a chitin-binding domain affects chitinolytic activity (Svitil and Kirchman, 1998). Different chitin-binding domains enable attachment to various types of chitin (Svitil and Kirchman, 1998).…”

Bacterial chitinases and chitin-binding proteins as virulence factors

“…CBM2 domains are found in bacterial family 18 chitinases, while CBM5/12s are frequently found in both family 18 and 19 chitinases, as well as in some CBPs (CAZy, 2013;Punta et al, 2012;Karlsson & Stenlid, 2009). Functional studies on chitin-binding properties of CBM2 and CBM5/12 have mainly focused on the role of the latter, but both domains have been shown to enhance substrate affinity and increase catalytic efficiency of chitinases (Watanabe et al, 1994;Hashimoto et al, 2000;Svitil & Kirchman, 1998;Nakamura et al, 2008), in a manner likely dependent on certain conserved surface-exposed aromatic residues (Morimoto et al, 1997).…”

“…Based on sequence analyses the GH family 18 enzymes have been separated into different groups (Karlsson & Stenlid, 2009;Svitil & Kirchman, 1998;Watanabe et al, 1993). This classification illuminates the phylogenetic relationships between catalytic domains, but has so far not offered insights regarding distinct roles of biological significance.…”