用比较基因组的方法分析植物病原细菌致病性相关基因
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摘要
本文对已完成全基因组测序的16个植物病原细菌基因组进行序列分析，推测出基因组中的致病基因并对其进行了功能分类。通过将这些致病基因与20个细菌(包括16个已完成全基因组测序的植物病原细菌)基因组中的基因进行BlastP分析，确定了这些植物病原细菌基因组中的菌株特有基因。如：土壤根癌杆菌菌株C58特有基因有19个，欧文氏菌马铃薯黑胫亚种SCR11043特有基因有11个，拉尔氏菌属的茄科青枯雷尔氏菌GMI1000的特有基因有10个，苛养木杆菌Temeculal特有基因有3个，苛养木杆菌9a5c特有基因有1个，甘蔗宿根矮化病菌CTCB07特有基因有8个，丁香假单胞杆菌菜豆致病变种1448A特有基因有8个，丁香假单胞杆菌马铃薯致病变种DC3000特有基因有3个，丁香假单胞杆菌的丁香致病变种B728a特有基因有2个，黄单胞菌番茄致病变种85-10特有基因有4个，黄单胞菌柑橘致病变种306特有基因有2个，黄单胞菌野油菜致病变种特有基因有4个，黄单胞菌水稻致病变种特有基因有2个。
对11个植物病原细菌基因组中编码Ⅲ型分泌系统的hrp基因簇进行比较分析，确定了不同属基因簇中的属特有基因。如：假单胞菌属特有基因有5个，欧文氏菌属有5个，拉尔氏菌属有4个，黄单胞菌属有3个。在这些属的特有基因中假单胞菌属的hrpA_1、欧文氏菌属的hrpA、拉尔氏菌属的hrpY、黄单胞菌属的hrpE均是编码Ⅲ型菌毛的基因。通过对这4个属hrp基因簇中同源的3个hrc基因构建系统进化树，发现树形相似，均是假单胞菌属和欧文氏菌属的基因在一个分支上，黄单胞菌属和拉尔氏菌属基因在另一个分支上。黄单胞菌属6个菌株的hrp基因簇在hrpE-hrcC之外的其余部分基因组成和序列比对有很大差异。丁香假单胞菌3个致病变种的hrp基因簇在hrcC-hrcU区域的组成有很大差异。
应用基因的原核表达技术，对丁香假单胞菌番茄致病变种DC3000的菌株特有基因PSPTO_4711的功能进行了初步分析，发现PSPTO_4711表达的活性蛋白对拟南芥有很强的毒性。
In this paper, 16 sequenced phytopathogenic bacteria complete genome were analysed, As a result the pathogenic genes were speculated and classified basic on their function analyse. The strain specific genes in these phytopathogenic genomes were identified through the pathogenic genes and the genes of 20 bacterial genomes that included 16 completed genome sequence of phytopathogenic bacteria by BlastP. The results showed that ther were: 19 specific genes in Agrobacterium tumefaciens C58; 11 specific genes in Erwinia carotovora subsp, atroseptica SCRI1043; 10 specific genes in Ralstonia solanacearum GMI1000; 1 specific gene in Xylella fastidiosa 9a5c; 3 specific genes in Xylella fastidiosa Temeculal; 8 specific genes in Leifsonia xyli subsp, xyli CTCB07; 7 specific genes in Pseudomonas syringae pv. phaseolicola 1448A; 3 specific genes in Pseudomonas syringae pv. tomato DC3000; 2 specific genes in Pseudomonas syringae pv. syringae B728a; 4 specific genes in Xanthomonas campestris pv. vesicatoria 85-10; 2 specific genes in Xanthomonas axonopodis pv. citri 306, 4 specific genes in Xanthomonas campestris pv. campestris, 2 specific genes in Xanthomonas oryzae pv. oryzae.
Hrp gene clusters encode the typeⅢsecreted system. Comparative analysis of hrp gene clusters in the 11 phytopathogenic bacterial was carried out to identify the genera specific genes in these phytopathogenic bacteria. The results that indicated: 5 specific genes in Pseudomonas, 5 specific genes in Erwinia, 5 specific genes in Ralstonia 4 genes, 5 specific genes in Xanthomonas. Among them, hrpA_1 gene in Pseudomonas, hrpA gene in Erwinia, hrpY gene in Ralstonia and hrpE gene in Xanthomonas all encode typeⅢpilus. Phylogenetic trees of 3 homologous hrc genes of Hrp gene clusters in 4. genera show that genes in Pseudomonas and Erwinia were all on one embranch; genes in Xanthomonas and Ralstonia were on other embranch. The composition and sequenced alignment out of the hrpE-hrcC area are very different in the hrp gene clusters of Xanthomonas. The compositions of hrcC-hrcU area are very different in the hrp gene clusters of the Pseudomonas syringae three pahtovarifies.
The function of the strain specific gene PSPTO_4711 in the Pseudomonas syringae pv. tomato DC3000 genome was preliminarily analyzed by prokaryotic expression. It was found that PSPTO_471 gene encodes a protein with virulence to Arabidopsis thaliana.
对11个植物病原细菌基因组中编码Ⅲ型分泌系统的hrp基因簇进行比较分析，确定了不同属基因簇中的属特有基因。如：假单胞菌属特有基因有5个，欧文氏菌属有5个，拉尔氏菌属有4个，黄单胞菌属有3个。在这些属的特有基因中假单胞菌属的hrpA_1、欧文氏菌属的hrpA、拉尔氏菌属的hrpY、黄单胞菌属的hrpE均是编码Ⅲ型菌毛的基因。通过对这4个属hrp基因簇中同源的3个hrc基因构建系统进化树，发现树形相似，均是假单胞菌属和欧文氏菌属的基因在一个分支上，黄单胞菌属和拉尔氏菌属基因在另一个分支上。黄单胞菌属6个菌株的hrp基因簇在hrpE-hrcC之外的其余部分基因组成和序列比对有很大差异。丁香假单胞菌3个致病变种的hrp基因簇在hrcC-hrcU区域的组成有很大差异。
应用基因的原核表达技术，对丁香假单胞菌番茄致病变种DC3000的菌株特有基因PSPTO_4711的功能进行了初步分析，发现PSPTO_4711表达的活性蛋白对拟南芥有很强的毒性。
In this paper, 16 sequenced phytopathogenic bacteria complete genome were analysed, As a result the pathogenic genes were speculated and classified basic on their function analyse. The strain specific genes in these phytopathogenic genomes were identified through the pathogenic genes and the genes of 20 bacterial genomes that included 16 completed genome sequence of phytopathogenic bacteria by BlastP. The results showed that ther were: 19 specific genes in Agrobacterium tumefaciens C58; 11 specific genes in Erwinia carotovora subsp, atroseptica SCRI1043; 10 specific genes in Ralstonia solanacearum GMI1000; 1 specific gene in Xylella fastidiosa 9a5c; 3 specific genes in Xylella fastidiosa Temeculal; 8 specific genes in Leifsonia xyli subsp, xyli CTCB07; 7 specific genes in Pseudomonas syringae pv. phaseolicola 1448A; 3 specific genes in Pseudomonas syringae pv. tomato DC3000; 2 specific genes in Pseudomonas syringae pv. syringae B728a; 4 specific genes in Xanthomonas campestris pv. vesicatoria 85-10; 2 specific genes in Xanthomonas axonopodis pv. citri 306, 4 specific genes in Xanthomonas campestris pv. campestris, 2 specific genes in Xanthomonas oryzae pv. oryzae.
Hrp gene clusters encode the typeⅢsecreted system. Comparative analysis of hrp gene clusters in the 11 phytopathogenic bacterial was carried out to identify the genera specific genes in these phytopathogenic bacteria. The results that indicated: 5 specific genes in Pseudomonas, 5 specific genes in Erwinia, 5 specific genes in Ralstonia 4 genes, 5 specific genes in Xanthomonas. Among them, hrpA_1 gene in Pseudomonas, hrpA gene in Erwinia, hrpY gene in Ralstonia and hrpE gene in Xanthomonas all encode typeⅢpilus. Phylogenetic trees of 3 homologous hrc genes of Hrp gene clusters in 4. genera show that genes in Pseudomonas and Erwinia were all on one embranch; genes in Xanthomonas and Ralstonia were on other embranch. The composition and sequenced alignment out of the hrpE-hrcC area are very different in the hrp gene clusters of Xanthomonas. The compositions of hrcC-hrcU area are very different in the hrp gene clusters of the Pseudomonas syringae three pahtovarifies.
The function of the strain specific gene PSPTO_4711 in the Pseudomonas syringae pv. tomato DC3000 genome was preliminarily analyzed by prokaryotic expression. It was found that PSPTO_471 gene encodes a protein with virulence to Arabidopsis thaliana.
引文
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