Abstract
BackgroundGlycoside 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.ResultsHere, 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.ConclusionWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0538-6) contains supplementary material, which is available to authorized users.
Highlights
Glycoside hydrolases (GH) targeting cellulose, xylan, and chitin are common in the bacterial genomes that have been sequenced
To identify bacteria with a high potential for cellulose, xylan, and chitin processing, we first investigated the average frequency of GH domains for cellulose, xylan, and chitin per genome, at the genus and species levels (Fig. 1)
We identified several lineages that had not been previously known to be cellulose, xylan, and chitin degraders, but contained GHs that target these carbohydrates
Summary
Glycoside hydrolases (GH) targeting cellulose, xylan, and chitin are common in the bacterial genomes that have been sequenced. About the architecture of multi-domain and multi-activity glycoside hydrolases In these enzymes, combined catalytic domains act synergistically and display overall improved catalytic efficiency, making these proteins of high interest for the biofuel technology industry. Plant-derived cellulose and xylan represent the major source of carbon in terrestrial ecosystems, whereas chitin is the most abundant source of carbon in marine ecosystems. The deconstruction of these polysaccharides by GH is key to the global earth carbon cycle [2], mammal nutrition [3], and is the primary target of several industries (e.g., biofuel production) [4]. There are some GH families that do not target-specific substrates (e.g., GH16)
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