Seo Young-Su, Sriariyanun Malinee, Wang Li, Pfeiff Janice, Phetsom Jirapa, Lin Ye, Jung Ki-Hong, Chou Hui Hsien, Bogdanove Adam, Ronald Pamela
Department of Plant Pathology, University of California, Davis, CA 95616, USA.
BMC Microbiol. 2008 Jun 18;8:99. doi: 10.1186/1471-2180-8-99.
Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) are bacterial pathogens of the worldwide staple and grass model, rice. Xoo and Xoc are closely related but Xoo invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and Xoc colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on hrp genes for type III secretion to infect their host. We constructed a 50-70 mer oligonucleotide microarray based on available genome data for Xoo and Xoc and compared gene expression in Xoo strains PXO99A and Xoc strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce hrp genes in Xoo strain T7174.
Three biological replicates of the microarray experiment to compare global gene expression in representative strains of Xoo and Xoc grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of Xoo and 39 genes of Xoc were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for Xoo and Xoc selected for validation. The differentially expressed genes represent 17 functional categories.
We describe here the construction and validation of a two-genome microarray for the two pathovars of X. oryzae. Microarray analysis revealed that using representative strains, a greater number of Xoo genes than Xoc genes are differentially expressed in XOM2 relative to PSB, and that these include hrp genes and other genes important in interactions with rice. An exception was the rax genes, which are required for production of the host resistance elicitor AvrXa21, and which were expressed constitutively in both pathovars.
水稻白叶枯病菌（Xanthomonas oryzae pv. oryzae，Xoo）和水稻条斑病菌（X. oryzae pv. oryzicola，Xoc）是全球主要粮食作物水稻以及禾本科模式植物的细菌性病原菌。Xoo和Xoc亲缘关系密切，但Xoo侵入水稻维管束组织引发白叶枯病，该病在世界许多地区的水稻种植中危害严重，而Xoc定殖于叶肉薄壁组织引发条斑病，这是一种日益重要的病害。两种病原菌均依赖hrp基因进行Ⅲ型分泌以感染寄主。我们基于Xoo和Xoc的可用基因组数据构建了一个50 - 70个核苷酸的寡核苷酸微阵列，并比较了Xoo菌株PXO99A和Xoc菌株BLS256在丰富培养基PSB与XOM2（一种先前报道可诱导Xoo菌株T7174中hrp基因表达的基本培养基）中生长时的基因表达情况。
进行了三次生物重复的微阵列实验，以比较Xoo和Xoc代表性菌株在PSB与XOM2中生长时的全局基因表达。非特异性错误率以及生物重复间和重复点间的相关系数表明微阵列数据具有可靠性。Xoo的247个基因和Xoc的39个基因在两种培养基中差异表达，错误发现率为5%，最小倍数变化为1.75。半定量RT - PCR分析证实了为验证所选的Xoo和Xoc各16个基因的差异表达。差异表达的基因代表17个功能类别。
我们在此描述了一种针对水稻黄单胞菌两个致病变种的双基因组微阵列的构建与验证。微阵列分析表明，使用代表性菌株时，相对于PSB，在XOM2中差异表达的Xoo基因数量多于Xoc基因，其中包括hrp基因以及其他在与水稻互作中重要的基因。一个例外是rax基因，它是寄主抗性激发子AvrXa21产生所必需的，并且在两个致病变种中均组成型表达。
