用生物信息学方法预测猪链球菌2型05ZYH33株的脂蛋白

Putative lipoproteins of Streptococcus suis type 2 identified by bioinformatic genome analysis

摘要:

【目的】鉴别已公布基因组序列的SS2 05ZYH33株的脂蛋白（Lpp）。【方法】首先从Genbank获取由SS2 05ZYH33基因组推测的蛋白质氨基酸序列， 然后利用Lpp预测软件PrositeScan和DOLOP预测05ZYH33株的Lpp，采用SignalP 3.0 HMM、PrediSi、Phobius、LipoP-HMM和TMHMM version2.0分析预测的Lpp的信号肽，然后经“多数票决法”确定Lpp；最后利用InterProScan和BlastP服务器对鉴定的Lpp进行功能分析。【结果】鉴定出34种Lpp，占SS2致病株05ZYH33蛋白质组的1.555%。结构与功能分析结果表明，最大的一类Lpp是ABC运输蛋白的底物结合蛋白，共有16种，其中YP_001197586、YP_001197918、YP_001198449、YP_001199435、YP_001197482、YP_001199452和YP_001198914等7种基因可与其他成分组成完整的ABC运输蛋白操纵子，这些Lpp在SS2获取糖、氨基酸和金属离子等营养物质方面具有重要作用。YP_001197698与无乳链球菌的黏附素Lmb和化脓链球菌的黏附素Lbp及YP_001198710与肺炎链球菌的SlrA高度同源，推测它们与黏附功能有关，为SS2新的毒力因子；其他Lpp包括酶、参与蛋白质折叠过程的Lpp及功能未知的Lpp。【结论】这些资料提示Lpp在SS2的生理和致病性方面具有重要作用。

Abstract:

[Objective] To identify putative lipoproteins of Streptococcus suis serotype 2 (SS2). [Methods] First, I used the ScanProsite feature of Prosite and the website Database Of bacterial LipOProteins(DOLOP) to identify putative lipopro-teins in the recently published genome of SS2 strains 05ZYH33, then validated the identified putative lipoproteins to ex-clude the false positive by a ‘majority vote’ approach following analysis with standard tools for signal peptide verification. Finally, putative functions were attributed to individual lipoproteins by reference to the identification of conserved do-mains of InterPro. Homologous proteins were identified by unfiltered BlastP homology searches (including conserved domain detection). [Results] Among the 38 identified putative lipoproteins, 34 were validated as lipoprotein and 4 as false positive lipoproteins. The largest functional category (16/34, 44%) of lipoproteins was that predicted to comprise of sub-strate binding proteins of ATP-binding cassette transport systems. Other roles included lipoproteins that participated in adhesion (YP_001197698 and YP_001198710), protein export and folding. [Conclusion] Lipoproteins contributed to the physiology of SS2 and influenced its virulence.