Molecular mechanisms of plant growth-promotion by beneficial soil bacteria

植物的根部自然会被各种细菌定居，这些细菌可以增强植物的健康。我的研究计划的总体目标是了解有益的土壤细菌促进植物生长的分子机制。这将导致制定农业管理战略，以支持作物高产。 为了寻找有助于植物生长促进的新的细菌基因，我们比较了植物生长促进细菌紫丁香假单胞菌GR12-2的基因组序列和与其密切相关的紫丁香科植物病原菌的基因组序列。我们首先将重点放在植物有益菌株特有的基因子集上，这些基因被预测为编码在细菌细胞表面发挥功能的蛋白质，因此有可能与宿主植物相互作用。它们编码鞭毛糖基化的酶，这些酶可能在逃避植物防御中发挥作用，蛋白质包括未知功能的蛋白质分泌系统，生长素外流载体分泌信号分子吲哚乙酸(IAA)，以及具有特殊结构的胞外功能sigma因子，其结构在对植物有益的假单胞菌中是保守的。这些基因在细菌的生理和生态中的功能将在遗传和生化水平上进行表征。 IAA是由多种细菌产生的，它在促进植物生长方面的作用是有据可查的。它也是一些植物病原体产生的毒力因子，是一种抗菌代谢产物，也是细菌应激反应的调节因子。鉴于这种信号分子的重要性，了解它的生产是如何调控的至关重要。我们已经确定，吲哚丙酮酸脱羧酶是土壤细菌合成IAA的关键酶，它的表达需要转录因子TyrR，并受芳香氨基酸的上调和支链氨基酸的下调。我们将通过鉴定直接或间接控制吲哚丙酮酸脱羧酶表达的支链氨基酸反应转录因子来进一步表征IAA的调控。这些氨基酸的调节，加上IAA在不同环境中原核生物中的广泛产生，以及已知的广泛的底物合成酶的特异性，表明IAA途径在植物相互作用之外的细菌生理中具有重要的作用。我们将确定支链氨基酸下调吲哚丙酮酸脱羧酶是否是优先利用氮源和/或回应碳和氮可利用性失衡的机制。 这项研究将为五名研究生和几名本科生研究人员提供在全基因组和目标基因/蛋白质水平上发展分子微生物学技能的机会，并与生物信息学、有机化学和蛋白质结构方面的专家合作。

The roots of plants are naturally colonized by diverse bacteria that enhance plant health. The overall aim of my research program is to understand the molecular mechanisms by which beneficial soil bacteria promote the growth of plants. This will lead to agricultural management strategies to support high crop yields. To identify novel bacterial genes that contribute to plant growth-promotion, we compared the genome sequence of the plant growth-promoting bacterium Pseudomonas syringae GR12-2 to those of closely related P. syringae phytopathogens. We will initially focus on a subset of genes that are unique to the plant beneficial strain and are predicted to encode proteins that function at the bacterial cell surface and therefore have potential to interact with host plants. These encode enzymes for flagella glycosylation that may function in evasion of plant defenses, proteins that comprise a protein secretion system of unknown function, an auxin efflux carrier for secretion of the signaling molecule indoleacetic acid (IAA), and an extracytoplasmic function sigma factor with an unusual structure that is conserved among plant-beneficial pseudomonads. The function of these genes in the physiology and ecology of the bacterium will be characterized at the genetic and biochemical levels. IAA is produced by diverse bacteria, and its role in plant growth-promotion is well documented. It is also a virulence factor produced by some plant pathogens, an antimicrobial metabolite, and a regulator of bacterial stress responses. Given the importance of this signaling molecule, it is critical to understand how its production is regulated. We have determined that expression of indolepyruvate decarboxylase, a key enzyme in IAA synthesis in a soil bacterium, requires the transcription factor TyrR and is upregulated by aromatic amino acids and downregulated by branched-chain amino acids. We will further characterize IAA regulation by identifying the branched-chain amino acid-responsive transcription factors that directly or indirectly control expression of indolepyruvate decarboxylase. Regulation by these amino acids, together with the widespread production of IAA among prokaryotes in diverse environments, and the known broad substrate specificity of the biosynthetic enzymes, suggests that IAA pathways have an important role in bacterial physiology, beyond plant interactions. We will determine if downregulation of indolepyruvate decarboxylase by branched-chain amino acids is a mechanism to prioritize nitrogen source utilization and/or respond to imbalances in carbon and nitrogen availability. This research will provide opportunities for five graduate and several undergraduate student researchers to develop skills in molecular microbiology at the whole genome and targeted gene/protein levels and to collaborate with experts in bioinformatics, organic chemistry, and protein structure.