细菌生物被膜核心胞外多糖靶向水解酶的生物信息挖掘

Bioinformatics data mining of hydrolases targeting core extracellular polysaccharides in bacterial biofilm

摘要:

【目的】胞外多糖是生物被膜不可或缺的重要成分，在细菌致病和耐药过程中发挥着重要作用。运用酶制剂针对生物被膜的核心胞外多糖进行靶向清除，能够从根本上破坏细菌生物被膜的核心骨架，有助于战胜细菌生物被膜导致的危害。【方法】本研究针对常见致病菌生物被膜核心胞外多糖Pel、Psl、褐藻胶、N-乙酰氨基葡萄糖(Poly-β(1,6)-N-acetyl-d-glucosamine, PNAG)和纤维素，基于NCBI数据库中丰富的基因序列信息，筛选靶向生物被膜核心胞外多糖的水解酶，进一步运用phyre2、SWISS-MODEL等生物信息工具，分析了这些水解酶的理化性质、遗传进化、功能域及三维结构。【结果】筛选获得了153个靶向生物被膜核心胞外多糖的水解酶及其序列信息。其中，靶向Pel胞外多糖的水解酶共30个，属于糖苷水解酶114家族(glycoside-hydrolase family GH114)；靶向Psl胞外多糖的水解酶共25个，属于糖苷水解酶超家族(glyco_hydro super family)；靶向褐藻胶胞外多糖的水解酶共33个，属于褐藻胶裂解酶超家族(AlgLyase superfamily)；靶向PNAG胞外多糖的水解酶共30个，属于糖苷水解酶13家族(glycoside-hydrolase family GH13)；靶向纤维素胞外多糖的水解酶共35个，属于糖苷水解酶8家族(glycosyl hydrolases family GH8)。【结论】这些水解酶菌具备靶向瓦解生物被膜核心胞外多糖的潜力，亟待进一步开发与应用。本研究提供了迄今为止最为全面的生物被膜核心胞外多糖水解酶序列组成及生物信息，为生物被膜的精准预防和靶向控制奠定扎实的数据基础。

关键词:水解酶;生物被膜;胞外多糖;生物信息学分析

Abstract:

[Objective] Extracellular polysaccharides, indispensable components of biofilm, play a role in bacterial pathogenicity and antibiotic resistance. Targeted elimination of the core extracellular polysaccharides of biofilm by enzyme preparations can fundamentally destroy the core skeleton of the biofilm and help overcome the harm caused by biofilm. [Methods] On the basis of the rich gene sequence information in the NCBI database, we screened the hydrolases targeting the extracellular polysaccharides Pel, Psl, algin, Poly-β(1,6)-N-acetyl-d-glucosamine (PNAG), and cellulose in the biofilm. Further, we employed the bioinformatics tools such as phyre2 and SWISS-MODEL to analyze the physical and chemical properties, genetic evolution, functional domains, and three-dimensional structures of these hydrolases. [Results] A total of 153 hydrolases targeting extracellular polysaccharides in biofilm were screened out and their sequence information was obtained. Among them, 30, 25, 33, 30, and 35 hydrolases targeted Pel, Psl, algin, PANG, and cellulose, respectively, which belonged to the glycoside-hydrolase family GH114, Glyco_hydro superfamily, AlgLyase superfamily, glycoside-hydrolase family GH13, and glycosyl hydrolase family GH8.[Conclusion] These hydrolases have the potential to cleavage the core extracellular polysaccharides in biofilm and need to be further developed and applied. This study provides the most comprehensive sequence and biological information of hydrolases targeting core extracellular polysaccharides in biofilms so far, laying a solid data foundation for precise prevention and targeted control of biofilms.

Key words:hydrolase;biofilm;extracellular polysaccharide;bioinformatics analysis