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Microbiology 152 (2006), 2207-2219; DOI  10.1099/mic.0.28912-0
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Microbiology 152 (2006), 2207-2219; DOI  10.1099/mic.0.28912-0
© 2006 Society for General Microbiology

Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA

Byung-Kwan Cho{dagger}, Eric M. Knight{dagger} and Bernhard Ø. Palsson

Department of Bioengineering, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA

Correspondence
Bernhard Ø. Palsson
palsson{at}ucsd.edu

ArcA is a global transcription factor required for optimal growth of Escherichia coli during anaerobic growth. In this study, the role of ArcA on the transcriptional regulatory subnetwork of the fad regulon was investigated. Gene expression profiles of deletion mutants ({Delta}arcA, {Delta}fadR and {Delta}arcA/{Delta}fadR) indicated that (i) ArcA is a major transcription factor for the transcriptional regulation of fatty acid metabolism in the absence of oxygen, and (ii) ArcA and FadR cooperatively regulate the fad regulon under anaerobic conditions. To determine the direct interaction between ArcA and the promoters of the fad regulon genes, chromatin immunoprecipitation (ChIP) analysis was performed. ChIP analysis suggested that ArcA directly binds to the promoter regions of the fad regulon genes in vivo. An ArcA-binding motif was identified from known binding sequences and predicted putative binding sites in the promoter regions of the fad regulon genes. These results indicate that ArcA directly represses the expression of fad regulon genes during anaerobic growth.

Abbreviations: ArcA-P, ArcA-phosphate; ChIP, chromatin immunoprecipitation; CT, threshold cycle; EMSA, electrophoretic mobility shift assay; IP, immunoprecipitated; LCFA, long-chain fatty acid; PWM, position weight matrix; qPCR, quantitative PCR

The authors disclose a possible conflict of interest related to US Patent Application 20040072723.

{dagger}These authors contributed equally to this study.




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