Metabolomic analysis of derivatives of the pathways catalyzed by indolepyruvate decarboxylase and an uncharacterized aldo-keto reductase in a soil and enteric bacterium

Abstract

Enterobacter cloacae UW5 is a common enteric commensal and soil bacterium whose plant growth-promoting capabilities have been attributed to production of the signaling molecule indoleacetic acid (IAA). Mutants with deletions in the ipdC gene encoding indolepyruvate decarboxylase, a key enzyme in the IAA biosynthetic pathway no longer promote plant growth. However, indolepyruvate decarboxylases are promiscuous, and therefore the indolepyruvate pathway may produce other plant bioactive signaling molecules in addition to IAA. Moreover, ipdC is upregulated in the presence of both tryptophan (a pathway precursor) and phenylalanine (not known to be metabolized by the indolepyruvate pathway in E. cloacae). One of the aims of this study was to identify the indolepyruvate pathway-dependent metabolites produced by E. cloacae cultured in tryptophan and phenylalanine media. Expression of ipdC and an adjacent gene (akr) predicted to encode an aldo-keto reductase (AKR) are regulated by the transcription factor TyrR. Because the genes are co-regulated, I hypothesized that the pathways catalyzed by the two enzymes may be connected. Therefore, a second aim of this study was to identify metabolites in the AKR pathway, in particular those shared with the indolepyruvate pathway. Using an untargeted metabolomics approach, and ipdC and akr mutants, indolepyruvate decarboxylase-dependent changes to the metabolic profile were measured and putatively linked to tryptophan, phenylalanine, glucosinolate, sphingolipid, and linoleic acid metabolism. Additionally, 137 putative metabolites in the AKR pathway were uncovered, and pyruvate metabolism was discovered to be a potential link between the two enzymatic pathways. Many indolepyruvate-dependent changes to E. cloacae metabolism identified in this study could serve as signaling molecules or their precursors, thus shedding light on the ecological role of the indolepyruvate pathway as a potential mediator of bacteria-host or bacteria-bacteria interactions beyond its known role in IAA biosynthesis.