Arabidopsis 2010: Expression Profiling of Plant Disease Resistance Pathways

植物通过多种信号通路对病原体的攻击作出反应，其中包括大量的调控基因和效应基因。在过去的几年中，通过对拟南芥的遗传分析，已经鉴定出许多与防御相关的基因。重要的是，拟南芥表现出其他植物中存在的所有主要防御反应。虽然已经确定了相对大量的拟南芥防御相关基因，但目前在开发植物与病原体相互作用的整体解释模型方面的进展受到两个主要实验障碍的限制。首先，大多数用于表征病原体-宿主相互作用的表型测试没有足够的区分能力来将防御相关基因分配到特定的信号反应途径。为了克服这一限制，将对适当选择的拟南芥防御相关突变体（包括双突变体和三重突变体）进行大规模转录物分析。将遗传上位分析与基因组技术相结合，应该会导致更详细的模型的发展，以了解各种防御相关基因如何在对抗病原体攻击中发挥作用和相互作用。第二个限制理解植物防御反应的因素是，使用传统方法根本不可能分析当前大量数据。在不久的将来将产生大量的微阵列数据，使这个问题更加复杂。此外，由于没有采用标准化的实验条件，来自不同实验室的数据不能直接比较。为了帮助减轻与大型数据集分析相关的问题，将创建一个可通过网络访问的复杂的植物-微生物相互作用数据库（PMIDB），为实验数据提供一个公共存储库和标准化格式。该项目的具体目标是：1)利用转录谱分析鉴定拟南芥防御相关基因，构建富含防御相关基因的定制微阵列（病理阵列）（目前鉴定的基因列表可在http://genetics.mgh.harvard.edu/ausubelweb/nsf2010/NSF_2010.html上找到）。这些定制的病理阵列将以象征性的成本提供给拟南芥群落，期望使用这些病理阵列产生的实验结果将被存储在pmidb中。2)使用来自Aim 1和拟南芥防御相关突变体的病理阵列来定义由防御途径激活引起的表达特征。3)建立可访问的植物-微生物相互作用数据库（PMIDB）。该数据库可在http://genetics.mgh.harvard.edu/ausubelweb/nsf2010/NSF_2010.html上访问，将在未来四年内开发，将包含用于分析宿主防御反应的标准化实验程序，所有致病相关突变体及其表型的列表，与各种序列数据库链接的防御相关基因列表，以及不同植物-病原体相互作用和不同防御相关突变体的表达谱。这个2010年的项目为应用基因组方法进行植物防御机制的遗传分析提供了一个独特的机会。了解植物防御机制不仅对基础科学研究有重要意义，而且对农业发展和环境保护也有重要意义。

Plants respond to pathogen attack through a variety of signaling pathways consisting of a large number of regulatory as well as effector genes. During the past several years, many defense-related genes have been identified through genetic analysis conducted in Arabidopsis thaliana. Importantly, Arabidopsis exhibits all of the major kinds of defense responses present in other plants. Although a relatively large number of Arabidopsis defense-related genes have been identified, progress in developing overall explanatory models of plant-pathogen interactions is currently limited by two major experimental roadblocks. First, most of the phenotypic tests that have been used to characterize pathogen-host interactions do not have sufficient discriminatory power to assign defense-related genes to specific signal response pathways. To circumvent this limitation, large-scale transcript profiling analyses will be carried out on appropriately selected Arabidopsis defense-related mutants, including double and triple mutants. Combining genetic epistasis analysis with genomic technologies should lead to the development of a much more detailed model of how the various defense-related genes function and interact in combating pathogen attack. The second factor limiting the understanding of the plant defense response is that it is simply not possible to analyze the overwhelming volume of current data using conventional methods. The large volume of microarray data that will be generated in the near future compounds this problem. Moreover, data from different laboratories are not directly comparable because standardized experimental conditions are not employed. To help mitigate the problems associated with the analysis of large data sets, a sophisticated web-accessible plant-microbe interaction database (PMIDB) will be created to provide a common repository and standardized format for experimental data. The specific aims of the project are to:1) Use transcript-profiling analysis to identify Arabidopsis defense-related genes and construct a custom microarray (pathoarray) enriched for defense-related genes (A list the genes identified so far can be found at http://genetics.mgh.harvard.edu/ausubelweb/nsf2010/NSF_2010.html). These custom pathoarrays will be made available to the Arabidopsis community at a nominal cost with the expectation that the experimental results generated using these pathoarrays will be deposited in PMIDB.2) Use the pathoarrays from Aim 1 and Arabidopsis defense-related mutants to define the expression signatures resulting from the activation of defense pathways. 3) Create a web-accessible plant-microbe interaction database (PMIDB). This database, which will be accessible at http://genetics.mgh.harvard.edu/ausubelweb/nsf2010/NSF_2010.html, will be developed during the next four years and will contain standardized experimental procedures for analyzing host defense responses, a list of all the pathogenesis-related mutants and their phenotypes, a list of defense-related genes with links to various sequence databases, and expression profiles of different plant-pathogen interactions and different defense-related mutants. This 2010 Project provides a unique opportunity for applying genomic approaches to genetic analysis of plant defense mechanisms. Understanding the mechanisms of plant defense is of interest not only to basic science but also to development of agriculture and protection of the environment.