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

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

Departments of ^*Biochemistry and ^‡Genetics, ^§Howard Hughes Medical Institute, Stanford University School of Medicine, and ^¶Department of Biological Sciences, Stanford University, Stanford, CA 94305; and ^†Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720

Contributed by Charles Yanofsky

Abstract

We investigated the global changes in mRNA abundance in Escherichia coli elicited by various perturbations of tryptophan metabolism. To do so we printed DNA microarrays containing 95% of all annotated E. coli ORFs. We determined the expression profile that is predominantly dictated by the activity of the tryptophan repressor. Only three operons, trp, mtr, and aroH, exhibited appreciable expression changes consistent with this profile. The quantitative changes we observed in mRNA levels for the five genes of the trp operon were consistent within a factor of 2, with expectations based on established Trp protein levels. Several operons known to be regulated by the TyrR protein, aroF-tyrA, aroL, aroP, and aroG, were down-regulated on addition of 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 effects of changes in tryptophan metabolism on intracellular mRNA pools, most prominent of which was the sensitivity of arginine biosynthetic operons to tryptophan starvation.

Footnotes

↵ ‖ To whom reprint requests should be addressed at: Department of Biological Sciences, Herrin Labs, 385 Serra Mall, Stanford University, Stanford, CA 94305-5020. E-mail: yanofsky{at}cmgm.stanford.edu.
Article published online before print: Proc. Natl. Acad. Sci. USA, 10.1073/pnas.220414297.
Article and publication date are at www.pnas.org/cgi/doi/10.1073/pnas.220414297