Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
BMC Microbiol. 2010 Mar 4;10:69. doi: 10.1186/1471-2180-10-69.
The genomes of numerous cellulolytic organisms have been recently sequenced or in the pipeline of being sequenced. Analyses of these genomes as well as the recently sequenced metagenomes in a systematic manner could possibly lead to discoveries of novel biomass-degradation systems in nature.
We have identified 4,679 and 49,099 free acting glycosyl hydrolases with or without carbohydrate binding domains, respectively, by scanning through all the proteins in the UniProt Knowledgebase and the JGI Metagenome database. Cellulosome components were observed only in bacterial genomes, and 166 cellulosome-dependent glycosyl hydrolases were identified. We observed, from our analysis data, unexpected wide distributions of two less well-studied bacterial glycosyl hydrolysis systems in which glycosyl hydrolases may bind to the cell surface directly rather than through linking to surface anchoring proteins, or cellulosome complexes may bind to the cell surface by novel mechanisms other than the other used SLH domains. In addition, we found that animal-gut metagenomes are substantially enriched with novel glycosyl hydrolases.
The identified biomass degradation systems through our large-scale search are organized into an easy-to-use database GASdb at http://csbl.bmb.uga.edu/~ffzhou/GASdb/, which should be useful to both experimental and computational biofuel researchers.
最近，许多纤维素分解生物的基因组已经被测序或正在测序过程中。对这些基因组以及最近测序的宏基因组进行系统分析，可能会发现自然界中新型生物质降解系统。
我们通过扫描 UniProt 知识库和 JGI 宏基因组数据库中的所有蛋白质，分别鉴定出 4679 个和 49099 个具有或不具有碳水化合物结合结构域的游离糖苷水解酶。纤维素酶组件仅在细菌基因组中观察到，鉴定出 166 个依赖纤维素酶的糖苷水解酶。从我们的分析数据中可以看出，两种研究较少的细菌糖苷水解系统分布广泛，出乎意料。在这些系统中，糖苷水解酶可能直接与细胞表面结合，而不是通过与表面锚定蛋白连接，或者纤维素酶复合物可能通过其他尚未使用的 SLH 结构域结合到细胞表面的新机制。此外，我们发现动物肠道宏基因组中富含新型糖苷水解酶。
通过大规模搜索鉴定的生物质降解系统已被组织成一个易于使用的数据库 GASdb，可在 http://csbl.bmb.uga.edu/~ffzhou/GASdb/ 上访问，这对于实验和计算生物燃料研究人员都将非常有用。
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