Metabolomic analysis of indolepyruvate decarboxylase pathway derivatives in the rhizobacterium Enterobacter cloacae

The plant growth-promoting capabilities of some rhizobacteria have been attributed in part to production of the signaling molecule indoleacetic acid (IAA) based on the reduction of plant growth-stimulation by mutants with disruptions in the ipdC gene encoding indolepyruvate decarboxylase, a key enzyme in the IAA biosynthetic pathway. However, indolepyruvate decarboxylases have relaxed substrate specificity, and therefore the pathway catalyzed by this enzyme may produce other plant bioactive signaling molecules in addition to IAA directly or indirectly via connected pathways. The aim of this study was to identify the indolepyruvate pathway-dependent metabolites produced by the plant-beneficial soil bacterium Enterobacter cloacae cultured in media containing tryptophan and phenylalanine, which are required for expression of indolepyruvate decarboxylase. Using an untargeted metabolomics approach and an ipdC mutant, indolepyruvate decarboxylase-dependent changes to the metabolic profile were measured and linked to tryptophan, phenylalanine, fatty acid, and glucosinolate metabolism. In addition to IAA, other indolepyruvate decarboxylase-dependent metabolites identified in this study could serve as signaling molecules, or their precursors, that mediate bacteria-host or bacteria-bacteria interactions.