The aromatic amino acid responsive TyrR transcription factor of Enterobacter cloacae UW5 : its role in regulation of indole-3-acetic acid biosynthesis and the identification of an expanded regulon using RNA-sequencing

Abstract

The control of transcription is an important process in all living cells. In the bacterial family Enterobacteriaceae, the transcription factor TyrR controls genes for aromatic amino acid uptake and biosynthesis. In this thesis, I explore the control of genes by TyrR in Enterobacter cloacae UW5, a soil bacterium commonly associated with plant roots that confer beneficial effects on its host and is also an inhabitant of human intestinal microflora and an opportunistic pathogen. Chapter 1 provides a general introduction to bacterial activities in the plant rhizosphere and transcriptional regulation, especially by TyrR. In Chapter 2, I investigated the regulation of two divergently transcribed genes, ipdC and akr, by TyrR. The ipdC gene encodes indolepyruvate decarboxylase for the production of the plant growth hormone indole-3-acetic acid, which plays an important role in the plant beneficial behavior of E. cloacae. TyrR is required for activation of ipdC by binding a single DNA element upstream of the promoter. All three aromatic amino acids act as cofactors for TyrR to induce ipdC expression. Expression of akr, encoding a putative aldo-keto reductase, was repressed by TyrR independently of aromatic amino acids and involved TyrR binding an atypical DNA site within the promoter. In Chapter 3, I assembled the E. cloacae UW5 genome sequence, which revealed genes and pathways that contribute to its plant-associated lifestyle and served as a reference for mapping RNA-sequencing data. In Chapter 4, I delineated the TyrR regulon by comparing transcription profiles in wild-type and tyrR mutant strains of E. cloacae generated through RNA-sequencing. Broad changes in gene expression were identified and several new TyrR members confirmed, including dmpM encoding a methyltransferase that is highly upregulated by tyrosine and phenylalanine, and cpxP and cpxR, which encode components of the envelope stress response. Additionally, pathways for aromatic metabolism, anaerobic respiration, and motility were altered in the tyrR mutant. Chapter 5 summarizes this research that suggests that the E. cloacae TyrR regulon has expanded from that of E. coli to include genes for survival in the diverse environments that this bacterium inhabits and illustrates the expansion and plasticity of transcription factor regulons.