Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli.
Broad-acting transcription factors (TFs) in bacteria form regulons. Here, we present a 4-step method to fully reconstruct the leucine-responsive protein (Lrp) regulon in Escherichia coli K-12 MG 1655 that regulates nitrogen metabolism. Step 1 is composed of obtaining high-resolution ChIP-chip data for Lrp, the RNA polymerase and expression profiles under multiple environmental conditions. We identified 138 unique and reproducible Lrp-binding regions and classified their binding state under different conditions. In the second step, the analysis of these data revealed 6 distinct regulatory modes for individual ORFs. In the third step, we used the functional assignment of the regulated ORFs to reconstruct 4 types of regulatory network motifs around the metabolites that are affected by the corresponding gene products. In the fourth step, we determined how leucine, as a signaling molecule, shifts the regulatory motifs for particular metabolites. The physiological structure that emerges shows the regulatory motifs for different amino acid fall into the traditional classification of amino acid families, thus elucidating the structure and physiological functions of the Lrp-regulon. The same procedure can be applied to other broad-acting TFs, opening the way to full bottom-up reconstruction of the transcriptional regulatory network in bacterial cells.
Cho
Byung-Kwan
BK
Department of Bioengineering, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0412, USA.
Barrett
Christian L
CL
Knight
Eric M
EM
Park
Young Seoub
YS
Palsson
Bernhard Ø
BØ
D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism; D025461:Feedback, Physiological; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D016680:Genome, Bacterial; D023281:Genomics; D007930:Leucine / Q000493:pharmacokinetics; D051756:Leucine-Responsive Regulatory Protein / Q000235:genetics* / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012329:RNA, Bacterial / Q000235:genetics; D014158:Transcription, Genetic
D029968:Escherichia coli Proteins; C497278:Lrp protein, E coli; D012329:RNA, Bacterial; D051756:Leucine-Responsive Regulatory Protein; D007930:Leucine; D009584:Nitrogen