Molecular Analyses of Plant Root-Microbe Interaction

植物的根提供机械支持，并从土壤中吸收水分和养分;然而，根也帮助植物与土壤环境相互作用。植物的生存和生产力在很大程度上取决于根系感知和响应土壤中生物和非生物因素的能力。在根际（延伸到根周围几毫米的土壤区域）中与植物根相互作用的一组生物是细菌，这组生物由致病和有益形式组成。根际中的细菌影响植物根的生理学和植物的整体健康。因此，有可能通过选择性地增加有益细菌的数量和减少根际病原体来改善植物健康和生产力。为了实现这一目标，对介导根-细菌相互作用的细菌和植物因子的清楚理解是至关重要的。我的研究重点是了解介导根微生物相互作用的植物因素。我们要问的问题之一是：是否存在允许有益细菌选择性地在根部定植的植物基因？为此，我们使用植物模型拟南芥和细菌假单胞菌注射器pv番茄DC 3000 [Pst DC 3000]（病原体）和恶臭假单胞菌（有益的）。在以前的发现基金资助的支持下，我们已经鉴定出了表现出两种截然不同的定殖模式的拟南芥单基因突变体; 1.支持病原体Pst DC 3000生长并减少有益细菌恶臭假单胞菌定殖的突变体，2.促进恶臭假单胞菌定殖并降低Pst DC 3000生长的突变体。计算机模拟分析和支持的初步结果表明，由这些基因编码的蛋白质与一些其他拟南芥蛋白质相互作用，最终导致差异根定植表型。拟议的研究计划将使用在以前的发现项目中确定的拟南芥突变体来开发一种系统生物学方法，以了解根与微生物相互作用的分子基础。本研究的目的是：1）研究根定殖表型改变的突变体的蛋白质组; 2）表征在病原菌和有益菌暴露时影响根-微生物相互作用的基因的时空表达; 3）研究植物根-微生物相互作用中的蛋白质-蛋白质相互作用; 4）研究响应于接种Pst DC 3000和恶臭假单胞菌的突变体植物的全代谢组的差异，并与野生型植物的全代谢组进行比较5）整合转录组，蛋白质组学和代谢组学数据，以更好地了解介导植物根-微生物相互作用的生理网络。这项研究计划将为目前对根际植物-微生物相互作用的理解增加相当多的新知识。根-微生物相互作用的遗传基础的结果将解开促进植物与有益细菌相互作用同时减少其与病原体的关联的分子网络。在这项研究计划中确定的基因将有助于开发“设计师”作物品种，这些品种具有增强的能力，可以将有益微生物招募到根部和根际。开发这种作物品种将大大减少化肥、农药和水等农业投入的使用，最终促进可持续农业。

Plant roots offer mechanical support and absorb water and nutrients from the soil; however, roots also help plants interact with the soil environment. Plants’ survival and productivity largely depends on the ability of the root system to sense and respond to biotic and abiotic factors in the soil. One group of organisms that interact with plant root in the rhizosphere (the soil zone extending to a few millimeters immediately surrounding the root) is bacteria, a group consisting of both pathogenic and beneficial forms. Bacteria in the rhizosphere influence physiology of the plant roots and overall health of the plant. Thus, there is potential to improve plant health and productivity by selectively increasing the population of beneficial bacteria and reducing pathogens in the rhizosphere. To achieve this objective a clear understanding of the bacterial and plant factors that mediates root-bacteria interaction is critical. My research focuses on understanding plant factors that mediate root-microbe interaction. One of the questions we are asking is: are there plant genes that allow selective colonization of roots by beneficial bacteria? To this end we are using the plant model Arabidospsis thaliana and bacteria Pseudomonas syringe pv tomato DC3000 [Pst DC3000] (pathogen) and Pseudomonas putida (beneficial). With the support from the previous Discovery grant funding we have identified Arabidopsis single gene mutants that exhibited two contrasting colonization pattern; 1. mutants that support growth of the pathogen Pst DC3000 and reduced colonization of the beneficial bacteria P. putida, 2. mutants that promote colonization by P. putida and reduced the growth of Pst DC3000. In silico analysis and supporting preliminary results suggest that the proteins encoded by these genes interact with a number of other Arabidopsis proteins that ultimately cause the differential root-colonization phenotype. The proposed research program will use the Arabidopsis mutant identified in the previous Discovery project to develop a systems biology approach to understand the molecular basis of root-microbe interaction. The objective of this research program are 1) to study the proteome of the mutants that are altered in root-colonization phenotype 2) to characterize the spatiotemporal expression of genes that affect root-microbe interaction identified in the previous project when exposed to pathogenic and the beneficial bacteria 3) to study plant protein-protein interaction in root-microbe interaction 4)to study the difference in the whole metabolome of the mutant plants in response to inoculation with the Pst DC3000 and P. putida and to compare with that of the wild type plant 5) integrating the transcriptomic, proteomic and metabolomics data to better understand the physiological networks that mediate plant root-microbe interaction. This proposed research program will add considerable new knowledge to the current understanding of rhizosphere plant-microbe interactions. The results of the genetic basis of root-microbe interaction will unravel molecular networks that promote plants’ interaction with beneficial bacteria while diminishing its association with pathogens. The genes identified in this research program will aid in the development of ‘designer’ crop varieties that have the enhanced ability to recruit beneficial microbes on to the root and rhizosphere . Development of such crop varieties will significantly reduce the use of agricultural inputs like fertilizer, pesticides and water ultimately promoting sustainable agriculture.