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

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.

[1]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[2]  J. Guest,et al.  Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli. , 1997, Microbiology.

[3]  E. Lin,et al.  Purification and phosphorylation of the Arc regulatory components of Escherichia coli , 1992, Journal of bacteriology.

[4]  J. Bongaerts,et al.  Transcriptional regulation of the proton translocating NADH dehydrogenase (nuoA‐N) of Escherichia coli by electron acceptors, electron donors and gene regulators , 1995, Molecular microbiology.

[5]  G. Church,et al.  A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. , 1998, Journal of molecular biology.

[6]  J. Cronan,et al.  Two-Carbon Compounds and Fatty Acids as Carbon Sources , 2005, EcoSal Plus.

[7]  Xueqiao Liu,et al.  Probing the ArcA-P Modulon of Escherichia coli by Whole Genome Transcriptional Analysis and Sequence Recognition Profiling* , 2004, Journal of Biological Chemistry.

[8]  D. Touati,et al.  Iron and oxygen regulation of Escherichia coli MnSOD expression: competition between the global regulators Fur and ArcA for binding to DNA , 1993, Molecular microbiology.

[9]  A. S. Lynch,et al.  Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters , 1996, Journal of bacteriology.

[10]  H. Schulz,et al.  Beta oxidation of fatty acids. , 1991, Biochimica et biophysica acta.

[11]  Juan Aguilar,et al.  Cross-induction of glc and ace Operons ofEscherichia coli Attributable to Pathway Intersection , 1999, The Journal of Biological Chemistry.

[12]  J. W. Campbell,et al.  A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic β‐oxidation pathway , 2003, Molecular microbiology.

[13]  E C Lin,et al.  A weight matrix for binding recognition by the redox‐response regulator ArcA‐P of Escherichia coli , 1999, Molecular microbiology.

[14]  P. Black Primary sequence of the Escherichia coli fadL gene encoding an outer membrane protein required for long-chain fatty acid transport , 1991, Journal of bacteriology.

[15]  S. Iuchi,et al.  Adaptation of Escherichia coli to respiratory conditions: Regulation of gene expression , 1991, Cell.

[16]  D. Georgellis,et al.  Identification of a quinone-sensitive redox switch in the ArcB sensor kinase. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[17]  A. Pramanik,et al.  Isolation of a multi-enzyme complex of fatty acid oxidation from Escherichia coli. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[18]  R. Haselbeck,et al.  Regulation of fatty acid transport in Escherichia coli: analysis by operon fusion , 1983, Journal of bacteriology.

[19]  Timothy M. Frayling,et al.  Combining genome and mouse knockout expression data to highlight binding sites for the transcription factor HNF1alpha , 2003, Silico Biol..

[20]  R. Gunsalus,et al.  Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon , 2000, Molecular microbiology.

[21]  M. Saier,et al.  The Transporter Classification (TC) System, 2002 , 2002, Critical reviews in biochemistry and molecular biology.

[22]  C. DiRusso,et al.  Characterization of FadR, a global transcriptional regulator of fatty acid metabolism in Escherichia coli. Interaction with the fadB promoter is prevented by long chain fatty acyl coenzyme A. , 1992, The Journal of biological chemistry.

[23]  J. W. Campbell,et al.  The Enigmatic Escherichia coli fadE Gene Is yafH , 2002, Journal of bacteriology.

[24]  W. D. Nunn A molecular view of fatty acid catabolism in Escherichia coli. , 1986, Microbiological reviews.

[25]  A. Pramanik,et al.  Five different enzymatic activities are associated with the multienzyme complex of fatty acid oxidation from Escherichia coli , 1979, Journal of bacteriology.

[26]  G. Sawers,et al.  Purification of ArcA and analysis of is specific interaction with the pfl promoter‐regulatory region , 1995, Molecular microbiology.

[27]  Markus J. Herrgård,et al.  Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.

[28]  A. S. Lynch,et al.  In vitro phosphorylation study of the arc two-component signal transduction system of Escherichia coli , 1997, Journal of bacteriology.

[29]  T. Mizuno,et al.  Phosphotransfer circuitry of the putative multi‐signal transducer, ArcB, of Escherichia coli: in vitro studies with mutants , 1995, Molecular microbiology.

[30]  S. Park,et al.  Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products , 1997, Journal of bacteriology.

[31]  P. Black,et al.  Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase. , 1992, The Journal of biological chemistry.

[32]  J. Cronan,et al.  The Escherichia coli fadK (ydiD) Gene Encodes an Anerobically Regulated Short Chain Acyl-CoA Synthetase* , 2004, Journal of Biological Chemistry.

[33]  K. Jensen The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels , 1993, Journal of bacteriology.

[34]  J. Aguilar,et al.  A mutational study of the ArcA-P binding sequences in the aldA promoter of Escherichia coli , 1999, Molecular and General Genetics MGG.

[35]  S. Ryu,et al.  Expression of ptsG Encoding the Major Glucose Transporter Is Regulated by ArcA in Escherichia coli* , 2004, Journal of Biological Chemistry.

[36]  E. Lin,et al.  Quinones as the Redox Signal for the Arc Two-Component System of Bacteria , 2001, Science.

[37]  T. Mizuno,et al.  Osmoregulation of the fatty acid receptor gene fadL in Escherichia coli , 1993, Molecular and General Genetics MGG.

[38]  J. Cronan,et al.  A new mechanism of transcriptional regulation: Release of an activator triggered by small molecule binding , 1992, Cell.

[39]  T. Rapoport,et al.  Crystal Structure of the Long-Chain Fatty Acid Transporter FadL , 2004, Science.

[40]  R. Gunsalus,et al.  Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB ) gene expression in Escherichia coli , 1997, Molecular microbiology.

[41]  E. Lin,et al.  arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[42]  T. Nyström,et al.  The fats of Escherichia coli during infancy and old age: regulation by global regulators, alarmones and lipid intermediates , 1998, Molecular microbiology.

[43]  G. Sawers,et al.  Signal transduction and bacterial conjugation: characterization of the role of ArcA in regulating conjugative transfer of the resistance plasmid R1. , 1998, Journal of molecular biology.

[44]  D. Georgellis,et al.  Co-regulation of lipoamide dehydrogenase and 2-oxoglutarate dehydrogenase synthesis in Escherichia coli: characterisation of an ArcA binding site in the lpd promoter. , 1998, FEMS microbiology letters.

[45]  T. Lamark,et al.  The complex bet promoters of Escherichia coli: regulation by oxygen (ArcA), choline (BetI), and osmotic stress , 1996, Journal of bacteriology.

[46]  C. Rock,et al.  Regulation of fatty acid biosynthesis in Escherichia coli. , 1993, Microbiological reviews.

[47]  S. Park,et al.  Regulation of malate dehydrogenase (mdh) gene expression in Escherichia coli in response to oxygen, carbon, and heme availability , 1995, Journal of bacteriology.

[48]  R. Utsumi,et al.  Functional Characterization in Vitro of All Two-component Signal Transduction Systems from Escherichia coli* , 2005, Journal of Biological Chemistry.

[49]  T. Mizuno,et al.  A novel device of bacterial signal transducers. , 1994, The EMBO journal.

[50]  E. Lin,et al.  Regulation of gene expression in fermentative and respiratory systems in Escherichia coli and related bacteria. , 1991, Annual review of genetics.

[51]  R. Heath,et al.  The FadR·DNA Complex , 2001, The Journal of Biological Chemistry.

[52]  S. Subrahmanyam,et al.  FadR, transcriptional co‐ordination of metabolic expediency , 1998, Molecular microbiology.

[53]  Bernhard O Palsson,et al.  PCR-based tandem epitope tagging system for Escherichia coli genome engineering. , 2006, BioTechniques.

[54]  P. Overath,et al.  Fatty Acid Degradation in Escherichia coli: Requirement of Cyclic Adenosine Monophosphate and Cyclic Adenosine Monophosphate Receptor Protein for Enzyme Synthesis , 1974, Journal of bacteriology.