A Systems Biology-aided Investigation of Pathogen-mediated Manipulation of Sugar Metabolism in Arabidopsis

植物-微生物病理系统构成了一个非常复杂的生物网络，其中来自病原体和宿主的分子参与者都在争夺主导地位。特殊的病原体进化出了一套称为效应子的分子，可以调节宿主细胞生理学并支持寄生。在过去的几十年里，大量文献记录了诱导有效免疫反应和破坏效应介导的宿主防御的分子机制。然而，一个尚未解决的关键问题是病原体如何改变细胞代谢，包括操纵源库关系来获取营养。这个跨学科项目通过整合生物学和快速发展的计算机科学领域，显着超出了湿实验室技术的范围，以促进研究、教育和基于社区的科学参与。将寻求对效应器介导的扰动以从中央液泡动员糖的机制理解。阐明病原体感染如何调节全局转录动态并改变生物信息流是首要关注点。同样重要的是，代谢、激素、昼夜节律和免疫信号通路之间的串扰，包括来自致病性和非致病性细菌菌株的信号，也将被揭示。该项目位于阿拉巴马州的中心地带，是一所全国公认的多元化大学，其范围延伸到教育领域，因为高级基因组学课程的学生将获得相关生物信息学分析的经验，PI 领导的 BioTeach 项目中的城市高中教师将接触到当今的基因创新，而热心的招聘工作将寻求吸引邻近的 HBCU 少数族裔学生。该提案的中心框架是了解植物病原体如何通过其效应器的毒力活性，与之前单一病原体：一种蛋白质分析方法的限制维度相比，呈现出实质性的进步。具体来说，该项目重点关注病原体效应子 HopD1，它与一组宿主蛋白发生物理相互作用，形成一个功能模块，称为“液泡转化酶 (Vac-INV) 模块”。我们将研究 HopD1 扰乱 Vac-INV 模块以动员中央液泡中储存的糖，同时减缓质外体糖吸收到宿主细胞中的机制。还将研究 HopD1 通过干扰保守的水通道蛋白介导的气孔调节机制来抑制免疫反应。基于Vac-INV依赖转录回路的计算机模拟，还将构建植物-病原体相互作用中的高分辨率全局动态转录调控网络。该项目已经开发了一个基于网络的界面 OOCEAN，用于启动子和生物信息学分析，将继续扩展其在快速发展的系统生物学领域的实用性。基于新型网络生物学的分析将有助于广泛了解单个效应器如何同时针对植物免疫和代谢的不同分支以获得病原体的优势。这项工作还将产生一个可应用于与植物防御和新陈代谢有关的其他重要问题的系统。总的来说，这个系统级项目将巩固对效应子-宿主相互作用、效应子介导的扰动以及随后的动态转录调控的全球理解。

The plant-microbe pathosystem constitutes a very complex biological network in which the molecular players from both the pathogen and the host engage in a battle for dominance. Specialized pathogens have evolved suites of molecules called effectors that modulate host cell physiology and support parasitism. Over the past decades, a plethora of literature has documented the molecular mechanisms that underlie the induction of effective immune responses and subversion of effector-mediated host defenses. However, a key unresolved question is how pathogens alter cellular metabolism, including manipulation of the source-sink relationships, to acquire nutrients. This interdisciplinary project extends significantly beyond wet-lab techniques by integrating both biology and the rapidly evolving field of computer science for the advancement of research, education, and community-based scientific engagement. Mechanistic understanding of effector-mediated perturbations to mobilize sugars from the central vacuole will be pursued. Elucidating how pathogen infection modulates the global transcriptional dynamics and alters the flow of biological information is of prime focus. Equally paramount, cross-talk between metabolic, hormonal, circadian and immune signaling pathways, involving signals from pathogenic and non-pathogenic bacterial strains, will be revealed. Situated in the heart of Alabama, at a nationally recognized university for diversity, this project's scope extends into educational avenues as students in advanced level genomics courses will gain experience with relevant bioinformatic analyses, urban high school teachers in the PI's-led BioTeach program will gain exposure to the genetic innovations of today, and zealous recruiting efforts will seek to engage neighboring HBCU-minority students.The central framework of this proposal, understanding how plant pathogens acquire sugars through the virulence activities of their effectors, presents a substantial advancement over the previously limiting dimensions of a one pathogen: one protein analysis approach. Specifically, this project is focused on a pathogen effector, HopD1, that physically interacts with a set of host proteins forming a functional module, termed 'vacuolar invertase (Vac-INV) module.' The mechanisms by which HopD1 perturbs the Vac-INV module to mobilize sugars stored in the central vacuole while slowing down the resorption of apoplastic sugars into the host cell will be investigated. HopD1's immune response suppression through interference of a conserved aquaporin-mediated stomatal regulation mechanism will also be investigated. Based on the in silico modeling of Vac-INV?dependent transcriptional circuits, a high resolution global dynamic transcriptional regulatory network in plant-pathogen interactions will also also constructed. Having already developed a web-based interface, OOCEAN, for promoter and bioinformatics analyses, this project will continue to extend its utility in the fast-evolving world of Systems Biology. Novel network biology-based analyses will help obtain a broad understanding of how single effectors simultaneously target different branches of plant immunity and metabolism for the pathogen's advantage. This work will also result in a system that can be applied to other important questions pertaining to plant defense and metabolism as well. Collectively, this systems-level project will solidify global understanding of effector-host interactions, effector-mediated perturbations, and subsequently, dynamic transcriptional regulation.