Natural diversity of cellulases, xylanases, and chitinases in bacteria

Abstract

Background: Glycoside hydrolases (GH) targeting cellulose, xylan, and chitin are common in the bacterial genomes that have been sequenced. Little is known, however, about the architecture of multi-domain and multi-activity glycoside hydrolases. In these enzymes, combined catalytic domains act synergistically and thus display overall improved catalytic efficiency, making these proteins of high interest for the biofuel technology industry.

Results: Here, we identify the domain organization in 40,946 proteins targeting cellulose, xylan, and chitin derived from 11,953 sequenced bacterial genomes. These bacteria are known to be capable, or to have the potential, to degrade polysaccharides, or are newly identified potential degraders (e.g., Actinospica, Hamadaea, Cystobacter, and Microbispora). Most of the proteins we identified contain a single catalytic domain that is frequently associated with an accessory non-catalytic domain. Regarding multi-domain proteins, we found that many bacterial strains have unique GH protein architectures and that the overall protein organization is not conserved across most genera. We identified 217 multi-activity proteins with at least two GH domains for cellulose, xylan, and chitin. Of these proteins, 211 have GH domains targeting similar or associated substrates (i.e., cellulose and xylan), whereas only six proteins target both cellulose and chitin. Fifty-two percent of multi-activity GHs are hetero-GHs. Finally, GH6, -10, -44 and -48 domains were mostly C-terminal; GH9, -11, -12, and -18 were mostly N-terminal; and GH5 domains were either N- or C-terminal.

Conclusion: We identified 40,946 multi-domain/multi-activity proteins targeting cellulase, chitinase, and xylanase in bacterial genomes and proposed new candidate lineages and protein architectures for carbohydrate processing that may play a role in biofuel production.

Keywords: Biofuel; CAZy; Carbohydrate; Cellulase; Chitinases; GH; Glycoside hydrolase; Polysaccharide; Xylanase.

Fig. 1

Frequency of GHs targeting cellulose, xylan, and chitin per sequenced genome (number of analyzed genomes in parentheses), a in bacterial genera and b species

Fig. 2

Architecture of 59 proteins with GH domains targeting cellulose, xylan, and chitin in Actinospica robiniae DSM44927 (phylum Actinobacteria). There are no genomic sequences of close relatives to A. robiniae

Fig. 3

Example of clustering of 10 strains from the genus Caldicellulosiruptor, according to (a) the distribution of proteins with GH domains for cellulose, xylan, chitin, and accessory non-catalytic domains, and (b) the distribution of GH domains for cellulose, xylan, and chitin. Color key: number of identified protein (a) and GH domain (b) in each analyzed genome. c Significant correlations between the A and B clustering analyses for bacterial genera with at least 10 sequenced genomes

Fig. 4

Architecture of multi-activity GHs (i.e., MA-GHs) targeting cellulose:xylan and cellulose:chitin