伴放线放线杆菌中幽门螺杆菌毒力相关基因的生物信息学分析

Bioinformatic analysis of H.pylori cytotoxin related genes in A.actinomycetemcomitans

目的:应用生物信息学方法分析幽门螺杆菌(Hp)毒力岛基因和空泡毒素基因在伴放线放线杆菌(Aa)中的存在及序列的变化。方法:用ncbi genbank数据库、蛋白同源性比对(blastP和tblastn)、极大似然法构建进化树和计算序列多态性研究Aa中是否含有Hp的毒力岛基因及空泡毒素基因,分析其相应的序列变异特征。结果:在Aa菌株中含有4个Hp毒力岛基因的同源基因,cagE、cagX、cagY和cagBeta。与其他种属菌株相比,Aa的cagE与Hp有较近的亲缘关系,且Aa菌株含有cagE基因的比列较高;基因多态性分析发现,cagE在两个物种中均有较低的Tajima’s D值(负值),两者的Pi值存在明显差异(P<0.01)。结论:Aa中含有Hp的部分毒力岛基因,其中cagE在两个物种中有较近的亲缘关系,且受到了负向选择的作用。

Objective:To compare the cytotoxin related genes in A.actinomycetemcomitans(Aa)and H.pylori(Hp)using bioinformatics methods.Methods:The ncbi genbank database,blastP and tblastn,maximum likelihood for phylogenetic tree construction in MEGA and gene polymorphism analysis were used to study the possible orthologs and their sequence characters of Hp cagPAI genes and vacA in Aa.Results:There were 4 cytotoxin related ortholog genes,cagE,cagX,cagY and cagBeta in both Aa and Hp.Whose orthologs were all located in cagPAI region in Hp.The protein sequence of cagE in Aa was similar to that in Hp and more commonly found in Aa compared to other strains from genbank.Polymorphism analysis showed that both Aa and Hp cagE genes had very low(minus)Tajima’s D values,but significant different in their Pi value(P<0.01).Conclusion:Aa has 4 cytotoxin related ortholog genes which are found in Hp.cagE genes in Aa may has closer relationship to Hp than those in other strains,and may be under negative selection in both strains.