Transcriptional control of amino acid and nucleotide metabolism in Escherichia coli.

Abstract

Transcriptional regulation and control modulates levels of proteins via the expression of specialized group of genes, and is one of the primary mechanisms by which bacteria respond to changes in external and internal conditions During growth and division, cells spend significant amounts of resources, including carbon and energy, on biosynthesis of protein and nucleic acids. The biosynthesis of their precursors, amino acids and nucleotides, is controlled in large part by transcriptional regulation. The structure of the regulatory network in the model bacterium Escherichia coli was investigated by studying responses to systematic perturbations to existing metabolic pools. It was found that responses to individual perturbations were pathway specific and could propagate locally to other related pathways and globally to distant parts of cell metabolism and physiology. Local motifs of regulation, feedback, feed-forward and branched, were proposed for precursor utilization. Globally propagated responses were partitioned into those associated with growth and biosynthesis and those associated with stress and catabolism. Pathway specific gene expression was found to be coherent and was used to assign putative functions to unclassified or unrelated genes.

A method of analyzing transcriptional responses in the framework of gene sets (pre-classified sets of genes based on functional or other relationships) in single conditions was modified and adapted to analyze transcriptional responses to individual perturbations. The method (Gene Set Analysis) performs efficiently in characterizing expected responses to experimental perturbations.

The interactions of the anti-folate drug trimethoprim with nucleotide catabolism pathways are elucidated with the aim to understand the control of nucleotide metabolism and to uncover ways to potentiate drug activity. The pyrimidine salvage pathway, and the gene products catalyzing it ( deoR targets), are identified as targets to perturb nucleotide pools and exacerbate the effects of trimethoprim.

The phenomenon of cell death following the starvation of an essential metabolite, dTTP, was studied using complementary approaches of transcriptional profiling and chromosomal damage mapping to understand the bactericidal nature of thymine starvation known as "thymine-less death". Loss of gene copy number in the proximity of origin of replication was observed and it was proposed as the primary cause of cell death under those conditions.