Molecular mechanisms of plant growth-promotion by beneficial soil bacteria

植物的根部自然地被各种细菌定殖，从而增强植物的健康。我的研究计划的总体目标是了解有益土壤细菌促进植物生长的分子机制。这将导致支持作物高产的农业管理战略。 为了鉴定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假单胞菌GR 12 -2与密切相关的假单胞菌植物病原体的基因组序列。我们将首先关注植物有益菌株所特有的一组基因，这些基因被预测编码在细菌细胞表面起作用的蛋白质，因此有可能与宿主植物相互作用。这些编码酶鞭毛糖基化，可能在逃避植物防御功能，蛋白质，包括未知功能的蛋白质分泌系统，生长素外排载体分泌的信号分子吲哚乙酸（IAA），和细胞质外功能σ因子与一个不寻常的结构，是保守的植物有益的假单胞菌。这些基因在细菌生理学和生态学中的功能将在遗传和生物化学水平上表征。 IAA是由多种细菌产生的，它在植物生长促进中的作用是有据可查的。它也是由一些植物病原体产生的毒力因子、抗菌代谢物和细菌应激反应的调节剂。鉴于这种信号分子的重要性，了解其生产是如何调节的至关重要。我们已经确定，吲哚丙酮酸脱羧酶，在土壤细菌中的IAA合成的关键酶的表达，需要转录因子TyrR和上调芳香族氨基酸和下调支链氨基酸。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响应性转录因子来进一步表征IAA调控。这些氨基酸的调节，以及原核生物在不同环境中广泛产生IAA，以及已知的生物合成酶的广泛底物特异性，表明IAA途径在细菌生理学中具有重要作用，超出了植物相互作用。我们将确定是否下调吲哚丙酮酸脱羧酶的支链氨基酸是一种机制，优先考虑氮源的利用和/或响应碳和氮的可用性不平衡。 这项研究将为五名研究生和几名本科生研究人员提供机会，在全基因组和靶基因/蛋白质水平上培养分子微生物学技能，并与生物信息学，有机化学和蛋白质结构专家合作。

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.