Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli

ABSTRACT Cra (catabolite repressor activator) is a global regulator of the genes for carbon metabolism in Escherichia coli. To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX (systematic evolution of ligands by exponential enrichment) system. Surprisingly, a total of 164 binding sites were identified for Cra, 144 (88%) of which were newly identified. The majority of known targets were included in the SELEX chip pattern. The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra. These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra. The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid (TCA) cycle and aerobic respiration. Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism.

[1]  A. Ishihama.  Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks. , 2010, FEMS microbiology reviews.

[2]  Akira Ishihama,et al.  A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions , 2010, Nucleic acids research.

[3]  A. Ishihama,et al.  Two Modes of Autoregulation of the murR Repressor in Escherichia coli , 2009, Bioscience, biotechnology, and biochemistry.

[4]  A. Ishihama.  The Nucleoid: an Overview , 2009, EcoSal Plus.

[5]  A. Ishihama,et al.  Involvement of the Leucine Response Transcription Factor LeuO in Regulation of the Genes for Sulfa Drug Efflux , 2009, Journal of bacteriology.

[6]  A. Joachimiak,et al.  Structural and Biochemical Characterization of the Type II Fructose-1,6-bisphosphatase GlpX from Escherichia coli* , 2009, Journal of Biological Chemistry.

[7]  S. Kędracka-Krok,et al.  cAMP Receptor Protein from Escherichia coli as a Model of Signal Transduction in Proteins – A Review , 2008, Journal of Molecular Microbiology and Biotechnology.

[8]  M. Reuss,et al.  Global Transcription and Metabolic Flux Analysis of Escherichia coli in Glucose-Limited Fed-Batch Cultivations , 2008, Applied and Environmental Microbiology.

[9]  U. Sauer,et al.  Cyclic AMP-Dependent Catabolite Repression Is the Dominant Control Mechanism of Metabolic Fluxes under Glucose Limitation in Escherichia coli , 2008, Journal of bacteriology.

[10]  Julio Collado-Vides,et al.  RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation , 2007, Nucleic Acids Res..

[11]  A. Ishihama,et al.  RutR is the uracil/thymine‐sensing master regulator of a set of genes for synthesis and degradation of pyrimidines , 2007, Molecular microbiology.

[12]  Akira Ishihama,et al.  PdhR (Pyruvate Dehydrogenase Complex Regulator) Controls the Respiratory Electron Transport System in Escherichia coli , 2007, Journal of bacteriology.

[13]  C. K. Vanderpool,et al.  Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress. , 2007, Current opinion in microbiology.

[14]  Liran Carmel,et al.  Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like Phosphatase Family* , 2006, Journal of Biological Chemistry.

[15]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[16]  J. Snoep,et al.  Glycolysis and Flux Control , 2005, EcoSal Plus.

[17]  Akira Ishihama,et al.  Systematic search for the Cra‐binding promoters using genomic SELEX system , 2005, Genes to cells : devoted to molecular & cellular mechanisms.

[18]  W. Boos,et al.  Hexose/Pentose and Hexitol/Pentitol Metabolism , 2005, EcoSal Plus.

[19]  Milton H. Saier,et al.  Functional Interactions between the Carbon and Iron Utilization Regulators, Crp and Fur, in Escherichia coli , 2005, Journal of bacteriology.

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

[21]  S. Gottesman,et al.  Involvement of a novel transcriptional activator and small RNA in post‐transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system , 2004, Molecular microbiology.

[22]  J. Preiss,et al.  ADP-Glucose Pyrophosphorylase, a Regulatory Enzyme for Bacterial Glycogen Synthesis , 2003, Microbiology and Molecular Biology Reviews.

[23]  Akira Ishihama,et al.  Two different modes of transcription repression of the Escherichia coli acetate operon by IclR , 2002, Molecular microbiology.

[24]  T. Larson,et al.  Purification and Characterization ofglpX-Encoded Fructose 1,6-Bisphosphatase, a New Enzyme of the Glycerol 3-Phosphate Regulon of Escherichia coli , 2000, Journal of bacteriology.

[25]  M. Saier,et al.  Multiple mechanisms controlling carbon metabolism in bacteria. , 1998, Biotechnology and bioengineering.

[26]  A. Ishihama,et al.  FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli. , 1998, Journal of molecular biology.

[27]  A. Horswill,et al.  Propionate catabolism in Salmonella typhimurium LT2: two divergently transcribed units comprise the prp locus at 8.5 centisomes, prpR encodes a member of the sigma-54 family of activators, and the prpBCDE genes constitute an operon , 1997, Journal of bacteriology.

[28]  R. Horlacher,et al.  Molecular characterization of glucokinase from Escherichia coli K-12 , 1997, Journal of bacteriology.

[29]  M. Saier,et al.  Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli , 1996, Current Microbiology.

[30]  T. Ramseier.  Cra and the control of carbon flux via metabolic pathways. , 1996, Research in microbiology.

[31]  C Geourjon,et al.  Definition of a consensus DNA‐binding site for the Escherichia coli pleiotropic regulatory protein, FruR , 1996, Molecular microbiology.

[32]  M. Saier,et al.  The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli , 1995, Molecular microbiology.

[33]  Michael A. Quail,et al.  Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR–aceEF–Ipd operon of Escherichia coli , 1995, Molecular microbiology.

[34]  M H Saier,et al.  In vitro binding of the pleiotropic transcriptional regulatory protein, FruR, to the fru, pps, ace, pts and icd operons of Escherichia coli and Salmonella typhimurium. , 1993, Journal of molecular biology.

[35]  S. Teshiba,et al.  Identification and characterization of the tktB gene encoding a second transketolase in Escherichia coli K-12 , 1993, Journal of bacteriology.

[36]  B. Erni,et al.  Membrane topology of the glucose transporter of Escherichia coli. , 1993, The Journal of biological chemistry.

[37]  A. Ishihama,et al.  Protein-protein communication within the transcription apparatus , 1993, Journal of bacteriology.

[38]  A. Ishihama.  Role of the RNA polymerase α subunit in transcription activation , 1992, Molecular microbiology.

[39]  R. E. Wolf,et al.  Molecular characterization of the Escherichia coli K-12 zwf gene encoding glucose 6-phosphate dehydrogenase , 1991, Journal of bacteriology.

[40]  R. Geerse,et al.  The repressor of the PEP: Fructose phosphotransferase system is required for the transcription of the pps gene of Escherichia coli , 1989, Molecular and General Genetics MGG.

[41]  J. Preiss,et al.  Genetic regulation of glycogen biosynthesis in Escherichia coli: in vitro effects of cyclic AMP and guanosine 5'-diphosphate 3'-diphosphate and analysis of in vivo transcripts , 1989, Journal of bacteriology.

[42]  M H Saier,et al.  Altered transcriptional patterns affecting several metabolic pathways in strains of Salmonella typhimurium which overexpress the fructose regulon , 1989, Journal of bacteriology.

[43]  F. Daldal.  Molecular cloning of the gene for phosphofructokinase-2 of Escherichia coli and the nature of a mutation, pfkB1, causing a high level of the enzyme. , 1983, Journal of molecular biology.

[44]  B. Hess,et al.  Analysis of progress curves. Interaction of pyruvate kinase from Escherichia coli with fructose 1,6-bisphosphate and calcium ions. , 1983, The Biochemical journal.

[45]  W. A. Bridger,et al.  The kinetic properties of phosphoenolpyruvate carboxykinase of Escherichia coli. , 1980, Canadian journal of biochemistry.

[46]  H. Kornberg,et al.  The direct synthesis of phosphoenolpyruvate from pyruvate by Escherichia coli , 1967, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[47]  J. Katz,et al.  The labeling of pentose phosphate from glucose-14C and estimation of the rates of transaldolase, transketolase, the contribution of the pentose cycle, and ribose phosphate synthesis. , 1967, Biochemistry.

[48]  B. Horecker,et al.  Fructose-1,6-Diphosphatase and Acid Hexose Phosphatase of Escherichia coli , 1965, Journal of bacteriology.

[49]  A. Ishihama,et al.  University of Birmingham The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions , 2008 .

[50]  U. Sauer,et al.  Impact of Global Transcriptional Regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on Glucose Catabolism in Escherichia coli , 2005, Journal of bacteriology.

[51]  G R Jacobson,et al.  Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. , 1993, Microbiological reviews.

[52]  H. Buc,et al.  Transcriptional regulation by cAMP and its receptor protein. , 1993, Annual review of biochemistry.

[53]  G. Valentini,et al.  AMP- and fructose 1,6-bisphosphate-activated pyruvate kinases from Escherichia coli. , 1982, Methods in enzymology.

[54]  A. Cornish-Bowden.  Analysis of Progress Curves , 1976 .

[55]  Jeffrey H. Miller.  Experiments in molecular genetics , 1972 .