铜绿假单胞菌YfiB蛋白的生物信息学分析  

Bioinformatic analysis of the YfiB protein of Pseudomonas aeruginosa

作　　者：鲍佳佳 李倩[1] 孙铭艳[2] 吴倩倩 赵雪 陶元勇[2] BAO Jia-jia;LI Qian;SUN Ming-yan;WU Qian-qian;ZHAO Xue;TAO Yuan-yong(Department of Laboratory Medicine,Weifang Medical University,Weifang,Shandong261053,China;Laboratory,Weifang Medical University Hospital)

机构地区：[1]潍坊医学院医学检验学院,山东潍坊261053 [2]潍坊医学院附属医院检验科

出　　处：《中国病原生物学杂志》2021年第4期406-410,共5页Journal of Pathogen Biology

基　　金：国家自然科学基金项目(No.81802054);潍坊市科技发展计划项目(医学类No.2019YX019)。

摘　　要：目的采用多种生物预测软件分析铜绿假单胞菌YfiB蛋白及其编码基因结构和生物学功能。方法由NCBI数据库获取YfiB蛋白的基因组信息,经ORF Finger软件预测基因ORF区;ProtParam、SOSUI、ExPASy-ProtScale、SignalP 4.1 Server和TargetP-2.0 Server软件分析YfiB蛋白理化性质、亲疏水性和信号肽;TMHMM Server v.2.0、NetPhos 3.1 Server、BLAST软件对跨膜区域、磷酸化位点和保守结构域分析;采用SOPMA、COILS、SWISS-MODEL、ABCpred、SYFPEITHI和STRING预测软件分析YfiB蛋白结构、抗原表位及相互作用蛋白。结果 YfiB基因序列长507 bp,存在3个开放阅读框架,编码168个氨基酸。YfiB蛋白分子式为C_(802)H_(1311)N_(241)O_(245)S_(5),相对分子质量为18.41×10^(3),脂族指数92.38,PI为7.89,为不稳定亲水性蛋白。含有1个信号肽,14个磷酸化修饰位点,无跨膜区域。二级结构中占比较高的是无规则卷曲和α-螺旋,分别为42.26%和33.93%。预测YfiB蛋白含有8个B细胞表位、12个限制性CTL表位和6个限制性Th表位,10种蛋白可能与其相互作用。结论生物信息学方法预测YfiB蛋白存在多个B、T细胞表位,可为铜绿假单胞菌YfiBNR信号系统促进相关生物膜形成的功能机制研究提供参考。Objective To use biological prediction software to analyze the structure and biological functions of the YfiB gene of Pseudomonas aeruginosa encoding the YfiB protein. Methods Genetic information on the YfiB protein was obtained from NCBI, and the ORF region of the gene was predicted using ORF Finger. The software ProtParam, SOSUI, ExPASy-ProtScale, SignalP 4.1 Server, and TargetP-2.0 Server were used to analyze the signal peptides, hydrophilicity and hydrophobicity, and physicochemical properties of the YfiB protein. The software TMHMM Server v. 2.0, NetPhos 3.1 Server, and BLAST were used to analyze its transmembrane regions, phosphorylation sites, and conserved domains. The predictive software SOPMA, COILS, SWISS-MODEL, ABCpred, SYFPEITHI, and STRING were used to analyze the structure, epitopes, and interacting proteins of the YfiB protein. Results The YfiB gene sequence is 507 bp in length, it encodes 168 amino acids, and it contains three ORFs. The molecular formula for the YfiB protein is C_(802)H_(1311)N_(241)O_(245)S_(5), its relative molecular mass is 18.41×10^(3), its aliphatic index is 92.38, and its theoretical isoelectric point is 7.89. It is an unstable hydrophilic protein. It contains a signal peptide at amino acids 1-26, 14 phosphorylation modification sites, and no transmembrane regions. Random coils accounted for 42.26% of the protein’s secondary structure and α-helices accounted for 33.93%. The YfiB protein contains 8 B-cell epitopes, 12 CTL cell epitopes, and 6 Th-cell epitopes, and 10 proteins may interact with it. Conclusion Bioinformatics predicted the existence of multiple B and T-cell epitopes in the YfiB protein. This finding may provide a reference for research on the functional mechanism of YfiBNR signaling in P. aeruginosa to promote the formation of biofilm.

关 键 词：铜绿假单胞菌 YfiB蛋白 生物膜 生物信息学 

分 类 号：R378.991[医药卫生—病原生物学]