Transcriptome Analysis Reveals Genes Commonly Induced by Botrytis cinerea Infection, Cold, Drought and Oxidative Stresses in Arabidopsis

Signaling pathways controlling biotic and abiotic stress responses may interact synergistically or antagonistically. To identify the similarities and differences among responses to diverse stresses, we analyzed previously published microarray data on the transcriptomic responses of Arabidopsis to infection with Botrytis cinerea (a biotic stress), and to cold, drought, and oxidative stresses (abiotic stresses). Our analyses showed that at early stages after B. cinerea inoculation, 1498 genes were up-regulated (B. cinerea up-regulated genes; BUGs) and 1138 genes were down-regulated (B. cinerea down-regulated genes; BDGs). We showed a unique program of gene expression was activated in response each biotic and abiotic stress, but that some genes were similarly induced or repressed by all of the tested stresses. Of the identified BUGs, 25%, 6% and 12% were also induced by cold, drought and oxidative stress, respectively; whereas 33%, 7% and 5.5% of the BDGs were also down-regulated by the same abiotic stresses. Coexpression and protein-protein interaction network analyses revealed a dynamic range in the expression levels of genes encoding regulatory proteins. Analysis of gene expression in response to electrophilic oxylipins suggested that these compounds are involved in mediating responses to B. cinerea infection and abiotic stress through TGA transcription factors. Our results suggest an overlap among genes involved in the responses to biotic and abiotic stresses in Arabidopsis. Changes in the transcript levels of genes encoding components of the cyclopentenone signaling pathway in response to biotic and abiotic stresses suggest that the oxylipin signal transduction pathway plays a role in plant defense. Identifying genes that are commonly expressed in response to environmental stresses, and further analyzing the functions of their encoded products, will increase our understanding of the plant stress response. This information could identify targets for genetic modification to improve plant resistance to multiple stresses.调控生物与非生物胁迫响应的信号通路，可能存在协同或拮抗交互作用。为明确不同胁迫响应间的异同，我们分析了已发表的微阵列（microarray）数据集，该数据集涵盖拟南芥（Arabidopsis）受灰葡萄孢菌（Botrytis cinerea，一种生物胁迫）侵染，以及遭受低温、干旱与氧化胁迫（abiotic stresses）时的转录组响应。分析结果显示，在灰葡萄孢菌接种后的早期阶段，共有1498个基因被上调（命名为灰葡萄孢菌上调基因，BUGs），1138个基因被下调（命名为灰葡萄孢菌下调基因，BDGs）。研究发现，拟南芥针对每种生物及非生物胁迫均激活一套独特的基因表达程序，但同时也存在部分基因可被所有受试胁迫诱导或抑制。在所鉴定的BUGs中，分别有25%、6%和12%的基因同时可被低温、干旱和氧化胁迫诱导；而在BDGs中，分别有33%、7%和5.5%的基因可被上述相同的非生物胁迫下调。共表达与蛋白质-蛋白质相互作用（protein-protein interaction）网络分析揭示了调控蛋白编码基因表达水平的动态变化范围。针对亲电性氧脂素（electrophilic oxylipins）的基因表达分析表明，这类化合物可通过TGA转录因子（TGA transcription factors）介导拟南芥对灰葡萄孢菌侵染与非生物胁迫的响应。本研究结果表明，拟南芥中参与生物与非生物胁迫响应的基因存在重叠。环戊烯酮信号通路（cyclopentenone signaling pathway）组分编码基因的转录水平在生物与非生物胁迫下发生改变，提示氧脂素信号转导通路在植物防御中发挥重要作用。鉴定响应环境胁迫的共表达基因，并进一步解析其编码产物的功能，将有助于加深我们对植物胁迫响应机制的理解。此类信息可用于筛选遗传改造靶点，以提升植物对多种胁迫的抗性。