The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens

The pathogen Agrobacterium tumefaciens infects a broad range of plants, introducing the T-DNA into their genome. Contrary to all known bacterial phyto-pathogens, Agrobacterium lacks the hypersensitive response-inducing HRP genes although it introduces numerous proteins into the plant cell through a type IV secretion system. To understand the timing and extent of the plant transcriptional response to this unusual pathogen, we used an Arabidopsis 26-thousand gene oligonucleotide microarray. We inoculated Arabidopsis cell cultures with an oncogenic strain of Agrobacterium and analyzed four biological replicates to identify two robust sets of regulated genes, one induced and the other suppressed. In both cases, the response was distinct at 48 hours after infection, but not at 24 hours or earlier. The induced set includes genes encoding known defense proteins, the repressed set is enriched with genes characteristic of cell proliferation even though a growth arrest was not visible in the inoculated cultures. The analysis of the repressed genes revealed that the conserved upstream regulatory elements Frankiebox (a.k.a. “site II”) and Telobox are associated with the suppression of gene expression. The regulated gene sets should be useful in dissecting the signaling pathways in this plant-pathogen interaction. Keywords: Time-course of Agrobacterium infection Time-course of Agrobacterium-inoculated Arabidopsis cell cultures. Four biological replicates of mock- and Agrobacterium-inoculated samples collected at 4h, 12h, 24h and 48h after inoculation were compared to a reference RNA in a oligonucleotide array.

根癌农杆菌（Agrobacterium tumefaciens）作为一类植物病原菌，可侵染广泛的寄主植物，并将其T-DNA整合进入植物基因组中。与所有已报道的植物病原细菌不同，根癌农杆菌虽可通过IV型分泌系统向植物细胞内转运大量蛋白质，却缺失过敏反应诱导HRP基因。为解析植物对该特殊病原菌的转录响应时序与响应范围，本研究采用包含26000个拟南芥（Arabidopsis）基因的寡核苷酸微阵列开展实验。我们使用致癌型根癌农杆菌菌株侵染拟南芥细胞培养物，并通过四次生物学重复实验，筛选得到两组稳定的差异表达基因集：一组为诱导上调基因集，另一组为抑制下调基因集。两组基因的表达变化均在侵染后48小时呈现显著差异，而在24小时及更早时间点无明显变化。上调基因集包含编码已知防卫蛋白的基因；而下调基因集则富集细胞增殖相关特征基因，尽管在受侵染的细胞培养物中未观察到生长停滞现象。对下调基因的分析显示，保守的上游调控元件Frankiebox（亦称"site II"）与Telobox与基因表达抑制存在关联。上述差异表达基因集将有助于解析该植物-病原菌互作过程中的信号通路机制。关键词：根癌农杆菌侵染时序；根癌农杆菌侵染的拟南芥细胞培养物时序。本研究在接种后4小时、12小时、24小时及48小时分别采集Mock对照与根癌农杆菌侵染的样本，共四次生物学重复，通过寡核苷酸微阵列将其与参考RNA进行杂交比较。