title: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA.
authors.forename: Darrian
authors.initials: D
authors.lastname: Talamantes
authors.affiliation: Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA.
authors.forename: Nazmehr
authors.initials: N
authors.lastname: Biabini
authors.affiliation: Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA.
authors.forename: Hoang
authors.initials: H
authors.lastname: Dang
authors.affiliation: Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA.
authors.forename: Kenza
authors.initials: K
authors.lastname: Abdoun
authors.affiliation: Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA.
authors.forename: Renaud
authors.initials: R
authors.lastname: Berlemont
keywords: Biofuel; CAZy; Carbohydrate; Cellulase; Chitinases; GH; Glycoside hydrolase; Polysaccharide; Xylanase