Molecular mechanisms of plant growth-promotion by beneficial soil bacteria

植物的根部自然被各种细菌定植，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。这将导致农业管理战略，以支持高作物产量。******为了鉴定促进植物生长的新细菌基因，我们将促进植物生长的细菌丁香假单胞菌GR12-2与密切相关的丁香假单胞菌植物病原体的基因组序列进行了比较。我们将首先关注植物有益菌株特有的一组基因，这些基因被预测会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。这些编码的鞭毛糖基化酶可能在逃避植物防御中起作用，蛋白质包括功能未知的蛋白质分泌系统，生长素外排载体分泌信号分子吲哚乙酸（IAA），以及胞质外功能sigma因子具有不寻常的结构，在植物有益的假单胞菌中保守。这些基因在细菌生理和生态中的功能将在遗传和生化水平上得到表征。******IAA是由多种细菌产生的，它在促进植物生长中的作用是有充分记录的。它也是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。考虑到这种信号分子的重要性，了解它的产生是如何被调节的是至关重要的。我们已经确定，在土壤细菌中，IAA合成的关键酶吲哚丙酮酸脱羧酶的表达需要转录因子TyrR，并被芳香氨基酸上调和支链氨基酸下调。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应答转录因子来进一步表征IAA调控。这些氨基酸的调控，加上IAA在不同环境下原核生物中广泛产生，以及已知的生物合成酶广泛的底物特异性，表明IAA途径在细菌生理中具有重要作用，而不仅仅是植物相互作用。我们将确定支链氨基酸对吲哚丙酮酸脱羧酶的下调是否是优先考虑氮源利用和/或响应碳氮可用性失衡的机制。******这项研究将为五名研究生和几名本科生研究人员提供机会，以发展全基因组和目标基因/蛋白质水平的分子微生物学技能，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.