Lavín José L, Kiil Kristoffer, Resano Ohiana, Ussery David W, Oguiza José A
Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain.
BMC Genomics. 2007 Oct 31;8:397. doi: 10.1186/1471-2164-8-397.
Pseudomonas syringae is a widespread bacterial plant pathogen, and strains of P. syringae may be assigned to different pathovars based on host specificity among different plant species. The genomes of P. syringae pv. syringae (Psy) B728a, pv. tomato (Pto) DC3000 and pv. phaseolicola (Pph) 1448A have been recently sequenced providing a major resource for comparative genomic analysis. A mechanism commonly found in bacteria for signal transduction is the two-component system (TCS), which typically consists of a sensor histidine kinase (HK) and a response regulator (RR). P. syringae requires a complex array of TCS proteins to cope with diverse plant hosts, host responses, and environmental conditions.
Based on the genomic data, pattern searches with Hidden Markov Model (HMM) profiles have been used to identify putative HKs and RRs. The genomes of Psy B728a, Pto DC3000 and Pph 1448A were found to contain a large number of genes encoding TCS proteins, and a core of complete TCS proteins were shared between these genomes: 30 putative TCS clusters, 11 orphan HKs, 33 orphan RRs, and 16 hybrid HKs. A close analysis of the distribution of genes encoding TCS proteins revealed important differences in TCS proteins among the three P. syringae pathovars.
In this article we present a thorough analysis of the identification and distribution of TCS proteins among the sequenced genomes of P. syringae. We have identified differences in TCS proteins among the three P. syringae pathovars that may contribute to their diverse host ranges and association with plant hosts. The identification and analysis of the repertoire of TCS proteins in the genomes of P. syringae pathovars constitute a basis for future functional genomic studies of the signal transduction pathways in this important bacterial phytopathogen.
丁香假单胞菌是一种广泛存在的细菌性植物病原体，基于其对不同植物物种的宿主特异性，丁香假单胞菌菌株可被归为不同的致病变种。丁香假单胞菌丁香致病变种（Psy）B728a、番茄致病变种（Pto）DC3000和菜豆致病变种（Pph）1448A的基因组最近已被测序，为比较基因组分析提供了重要资源。细菌中常见的一种信号转导机制是双组分系统（TCS），它通常由一个传感组氨酸激酶（HK）和一个应答调节因子（RR）组成。丁香假单胞菌需要一系列复杂的TCS蛋白来应对不同的植物宿主、宿主反应和环境条件。
基于基因组数据，利用隐马尔可夫模型（HMM）轮廓进行模式搜索，以鉴定假定的HK和RR。发现Psy B728a、Pto DC3000和Pph 1448A的基因组包含大量编码TCS蛋白的基因，这些基因组之间共享一组完整的核心TCS蛋白：30个假定TCS簇、11个孤儿HK、33个孤儿RR和16个杂合HK。对编码TCS蛋白的基因分布进行的仔细分析揭示了三种丁香假单胞菌致病变种之间TCS蛋白的重要差异。
在本文中，我们对丁香假单胞菌测序基因组中TCS蛋白的鉴定和分布进行了全面分析。我们已经确定了三种丁香假单胞菌致病变种之间TCS蛋白的差异，这些差异可能有助于它们不同的宿主范围以及与植物宿主的关联。丁香假单胞菌致病变种基因组中TCS蛋白库的鉴定和分析，为该重要细菌性植物病原体信号转导途径的未来功能基因组学研究奠定了基础。
