Genome-wide analyses of Escherichia coli gene expression responsive to the BaeSR two-component regulatory system

Abstract

The BaeSR two-component regulatory system controls expression of exporter genes conferring drug resistance in Escherichia coli (S. Nagakubo, K. Nishino, T. Hirata, and A. Yamaguchi, J. Bacteriol. 184:4161-4167, 2002; N. Baranova and H. Nikaido, J. Bacteriol. 184:4168-4176, 2002). To understand the whole picture of BaeSR regulation, a DNA microarray analysis of the effect of BaeR overproduction was performed. BaeR overproduction activated 59 genes related to two-component signal transduction, chemotactic responses, flagellar biosynthesis, maltose transport, and multidrug transport, and BaeR overproduction also repressed the expression of the ibpA and ibpB genes. All of the changes in the expression levels were also observed by quantitative real-time reverse transcription-PCR analysis. The expression levels of 15 of the 59 BaeR-activated genes were decreased by deletion of baeSR. Of 11 genes induced by indole (a putative inducer of the BaeSR system), 10 required the BaeSR system for induction. Combination of the expression data sets revealed a BaeR-binding site sequence motif, 5'-TTTTTCTCCATDATTGGC-3' (where D is G, A, or T). Several genes up-regulated by BaeR overproduction, including genes for maltose transport, chemotactic responses, and flagellar biosynthesis, required an intact PhoBR or CreBC two-component regulatory system for up-regulation. These data indicate that there is cross-regulation among the BaeSR, PhoBR, and CreBC two-component regulatory systems. Such a global analysis should reveal the regulatory network of the BaeSR system.

FIG. 1.

Gene clusters whose expression was increased by BaeR overproduction. The expression changes for genes detected by real-time qRT-PCR are indicated under the gene names. The numbers in parentheses indicate the expression level changes detected by microarray analysis. The kb (kilobase pair) data indicate the positions on E. coli chromosomal DNA, as annotated on the Colibri website (http://genolist.Pasteur.fr/Colibri/). baeR was overexpressed from the high-copy-number plasmid pUCbaeR. N.D., not determined.

FIG. 2.

Intersections of genomic data sets. The diagram summarizes the data for 59 genes whose expression levels were increased by BaeR overproduction and for which there were valid data for expression profiles of the baeSR mutant and wild type with the addition of indole. The expression levels of 15 of the 59 genes were decreased by deletion of baeSR, and 11 genes were identified as indole-regulated genes. The seven genes in the overlap of all three data sets were identified as components of the BaeSR regulon, as described in the text.

FIG. 3.

Consensus sequence in the upstream regions of BaeR-regulated genes. Consensus sequences were found in the upstream regions of mdtA, spy, acrD, and ycaC. The numbering is relative to the start codon of the genes.