Molecular evolution in plant pathogens and mutualistic bacteria

所有生物都存在于一个物种之间相互依存的复杂网络中，包括捕食者-猎物、寄生、互惠和共生关系。这些相互作用反过来又塑造了自然系统和作物物种的生态群落。除了病原体与宿主的相互作用外，植物还与土壤微生物发展了互利的相互作用，通过这种相互作用，它们可以更好地获得养分，并可能减轻微生物病原体的影响。了解促进病原微生物和有益微生物相互作用的机制可以对作物管理策略和农业实践产生直接影响。该提案研究将使用比较基因组学方法研究植物-微生物相互作用，并通过RNA测序和蛋白质组学分析进行增强。有益菌和致病菌都将被调查，共生和致病性之间的联系将被探讨。这项研究直接建立在McConkey实验室以前的工作基础上，该实验室结合了计算和湿实验室技术来研究蛋白质的功能、结构、进化和相互作用。由于病原体造成的农作物损失是世界范围内持续存在的问题，并对健康、社会以及地方和国家经济产生广泛影响。相反，有益细菌已被证明可以促进植物生长和生产，并可以显着减少植物病原体的影响。更好地了解病原菌和有益菌与植物的相互作用将对作物管理和病原菌控制策略产生直接影响。特别是，病原体控制策略可以有针对性地对特定病原体产生最大影响，同时减少对有益土壤细菌的影响。为了有效地做到这一点，我们需要深入了解植物，病原体和有益细菌之间的相互作用。这项研究将有助于提供这些知识，重要的是可以确定控制植物病原体的新分子靶点。新的致病机制的鉴定可以反过来导致新的，有针对性的病原体管理策略。正如我们最近对人类病原体的研究所示（多克塞和McConkey，2013），可以使用比较基因组学策略发现许多高度特异性的致病机制。我们将把类似的方法应用于植物病原体和有益细菌，以鉴定介导植物-细菌相互作用的蛋白质。为了补充基于基因组学的分析，还将使用高通量蛋白质组学和RNA测序来识别病原体和有益细菌的细菌效应蛋白。

All organisms exist within a complex network of interdependencies between species, including predator-prey, parasitic, mutualistic and symbiotic relationships. These interactions in turn shape ecological communities for both natural systems and crop species. In addition to pathogen-host interactions, plants have developed mutually beneficial interactions with soil microbes, through which they can gain improved access to nutrients and potentially lessen the impact of microbial pathogens. An understanding of the mechanisms facilitating interactions with both pathogenic and beneficial microbes can have a direct impact on crop management strategies and agricultural practices. The proposal research will investigate plant-microbial interactions using a comparative genomics approach, augmented by RNA sequencing and proteomics analysis. Both beneficial and pathogenic bacteria will be investigated, and links between symbiosis and pathogenicity will be explored. The proposed research builds directly upon previous work in the McConkey lab, which has combined computational and wet-lab techniques to investigate protein function, structure, evolution, and interaction. Loss of agricultural crops due to pathogens is an ongoing problem worldwide, and has broad impacts on health, society, and local and national economies. Conversely, beneficial bacteria have been shown to enhance plant growth and production, and can markedly reduce the impact of plant pathogens. Better understanding the interactions of pathogenic and beneficial bacteria with plants will have direct impacts on crop management and pathogen control strategies. In particular, pathogen control strategies can be targeted to have maximum impact on specific pathogens, while having a reduced impact on beneficial soil bacteria. To do this effectively, we require an in-depth understanding on the interactions between plants, pathogens, and beneficial bacteria. The research proposed in this grant will help provide this knowledge, and importantly may identify new molecular targets for controlling plant pathogens. Identification of novel mechanisms of pathogenicity can in turn lead to novel, targeted strategies for pathogen management. As our recent study on human pathogens has shown (Doxey and McConkey, 2013), there are numerous highly specific mechanisms of pathogenicity that can be uncovered using comparative genomics strategies. We will apply similar methodology to plant pathogens and beneficial bacteria to identify proteins that mediate plant-bacterial interactions. To complement genomics based analyses, high-throughput proteomics and RNA-sequencing will also be used to identify bacterial effector proteins for both pathogens and beneficial bacteria.