EFFECTORSEARCH:病原菌基因组中三型分泌系统效应蛋白的预测

摘要

病原菌为了生存和侵入寄主细胞,经过漫长的进化形成了多种可介导大分子转运的分子机制,细菌Ⅲ型分泌系统(T3SS)是其中最重要的一种.T3SS又被称为“细菌注射器”,病原菌利用此系统可以将效应蛋白注射到靶细胞中.近年来发现,T3SS不仅存在于在人类、动物、甚至植物的多种致病菌中,在其它环境下的细菌中也存在.本文介绍了一种最新的生物信息学预测工具(EFFECTORSEARCH),可用于在微生物基因组中预测T3SS的基因,并且在本文中着重介绍了其在丁香假单胞菌(Pseudomonas syringae)基因组中T3SS基因的预测结果.%Many gram-negative bacteria use the type Ⅲ secretion system (T3SS) to inject virulence proteins (effectors) directly into host cells.These effectors play a central role in pathogen interactions,and their molecular structures are highly variable.Previous researchers have used particular motifs common to all effectors in order to identify a full suite of candidate effectors of T3SS in the genome of Pseudomonas syringae.Here,we present a program called EFFECTORSEARCH that synthesizes and extends previous work by allowing users to identify candidate effectors based on any combination of the following five criteria:protein length,proximity to the hrp promoter,n-terminal region,similarity to known effectors,and dissimilarity to housekeeping genes.We demonstrate the utility of the program in allowing users either to search broadly for candidates or to restrict attention to the candidates with the highest confidence in their assignment.