茎瘤固氮根瘤菌趋化系统基因的比较基因组学分析及相关蛋白序列分析

Comparative genomic and protein sequence analyses of the chemotaxis system of Azorhizobium caulinodans

摘要:

[目的] 茎瘤固氮根瘤菌既可以与毛萼田菁共生固氮，又可以自生或作为内生菌在其他植物体内固氮。由于其具有3种生活状态及固氮能力，其感受外界信号的趋化系统应当更为复杂多样。目前对茎瘤固氮根瘤菌的趋化通路研究很少，因此我们将茎瘤固氮根瘤菌的趋化系统与其他已有研究的菌株相比较。[方法] 基于NCBI蛋白数据库，利用BLAST程序对菌株ORS571及已公布全基因组序列的α变形菌门的其他菌种进行趋化基因簇的比较分析；基于Pfam蛋白数据库，利用HMMER3程序对甲基化受体蛋白序列进行比较分析。[结果] 分析结果表明茎瘤固氮根瘤菌中有1条主要的趋化基因簇，其中所编码的甲基化酶CheR为非五肽依赖型；此外，该菌还具有43个甲基化受体蛋白基因，所编码的受体蛋白保守区段均由38个七肽单位组成。[结论] 通过比较基因组学的分析可知茎瘤固氮根瘤菌与其他菌属相比趋化系统具有高度同源性，但同时存在自身的独特性，这一结论能够使我们更好的了解茎瘤固氮根瘤菌利用趋化系统适应环境的过程。

Abstract:

[Objective] Azorhizobium caulinodans ORS571 can fix nitrogen not only as a free-living organism and an associative-symbiotic bacterium by colonizing the root surface of non-leguminous plants, but also as a symbiotic bacterium by interacting with leguminous plant Sesbania rostrata. Due to its ability to grow and fix nitrogen under three conditions, A. caulinodans uses sophisticated chemotaxis signal transduction systems to transform environmental cues into corresponding behavioral responses. Chemotaxis appears crucial for the growth of A. caulinodansin complicated environment and the construction of associative relationship with the plant. However, little is known about the chemotactic pathway of A. caulinodans. Thus, our study aimed to compare the chemotaxis-like genes of A. caulinodans with those of well-studied species.[Methods] NCBI protein BLAST was used for searching sequence similarity with default parameter values against the genomes of A. caulinodans. HMMER3, based on Pfam database, was used for comparative analyses of methyl-accepting chemotaxis protein (MCP).[Results] There was a major chemotaxis cluster in A. caulinodans and the CheR methylated MCPs independently of pentapeptide motif. There were 43 MCP homologs containing diverse signal-sensing architectures in A. caulinodans. In addition, cytoplasmic domains of these MCPs were all composed of 38 heptad repeats.[Conclusion] Despite the extremely high homology presented between the chemotactic system of A. caulinodans and those of well-studied species, A. caulinodans shows its own unique characteristics. The classification of these chemotactic pathways by comparative genomics enables us to better understand how A. caulinodansresponds to changes in environment via exquisite signal transductions in chemotaxis system.