Talamantes Darrian, Biabini Nazmehr, Dang Hoang, Abdoun Kenza, Berlemont Renaud
Department of Biological Sciences, California State University, Long Beach, 1250 Bellflower Blvd., Long Beach, 90840-9502 USA.
Biotechnol Biofuels. 2016 Jun 29;9:133. doi: 10.1186/s13068-016-0538-6. eCollection 2016.
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.
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.
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.
靶向纤维素、木聚糖和几丁质的糖苷水解酶（GH）在已测序的细菌基因组中很常见。然而，对于多结构域和多活性糖苷水解酶的结构了解甚少。在这些酶中，组合的催化结构域协同作用，从而显示出整体提高的催化效率，这使得这些蛋白质对生物燃料技术产业具有很高的吸引力。
在这里，我们确定了来自11953个已测序细菌基因组的40946种靶向纤维素、木聚糖和几丁质的蛋白质的结构域组织。已知这些细菌能够或有潜力降解多糖，或者是新鉴定的潜在降解菌（如放线孢菌属、滨田氏菌属、孢囊杆菌属和小双孢菌属）。我们鉴定出的大多数蛋白质含有一个单一的催化结构域，该结构域通常与一个辅助非催化结构域相关联。关于多结构域蛋白质，我们发现许多细菌菌株具有独特的GH蛋白结构，并且大多数属的整体蛋白质组织并不保守。我们鉴定出217种具有至少两个针对纤维素、木聚糖和几丁质的GH结构域的多活性蛋白质。在这些蛋白质中，211种具有靶向相似或相关底物（即纤维素和木聚糖）的GH结构域，而只有6种蛋白质同时靶向纤维素和几丁质。52%的多活性GH是杂合GH。最后，GH6、-10、-44和-48结构域大多位于C末端；GH9、-11、-12和-18结构域大多位于N末端；而GH5结构域位于N末端或C末端。
我们在细菌基因组中鉴定出40946种靶向纤维素酶、几丁质酶和木聚糖酶的多结构域/多活性蛋白质，并提出了可能在生物燃料生产中发挥作用的碳水化合物加工新候选谱系和蛋白质结构。
