Molecular mechanisms of plant growth-promotion by beneficial soil bacteria

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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.