DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli

We investigated the global changes in mRNA abundance in Escherichia coli el icited by various perturbations of tryptophan metabolism. To do so we print ed DNA microarrays containing 95% of all annotated E. coli ORFs. We determi ned the expression profile that is predominantly dictated by the activity o f the tryptophan repressor. Only three operons, trp, mtr, and aroH, exhibit ed appreciable expression changes consistent with this profile. The quantit ative changes we observed in mRNA levels for the five genes of the frp oper on were consistent within a factor of 2, with expectations based on establi shed Trp protein levels. Several operons known to be regulated by the TyrR protein, aroF-tyrA, aroL, aroP, and aroG. were down-regulated on addition o f tryptophan. TyrR can be activated by any one of the:three aromatic amino acids. Only one operon. tnaAB, was significantly activated by the presence of tryptophan in the medium. We uncovered a plethora of likely indirect eff ects of changes in tryptophan metabolism on intracellular mRNA pools, most prominent of which was the sensitivity of arginine biosynthetic operons to tryptophan starvation.