A Quantitative Approach to Catabolite Repression in Escherichia coli*

A dynamic mathematical model was developed to describe the uptake of various carbohydrates (glucose, lactose, glycerol, sucrose, and galactose) in Escherichia coli. For validation a number of isogenic strains with defined mutations were used. By considering metabolic reactions as well as signal transduction processes influencing the relevant pathways, we were able to describe quantitatively the phenomenon of catabolite repression in E. coli. We verified model predictions by measuring time courses of several extra- and intracellular components such as glycolytic intermediates, EII-ACrr phosphorylation level, both LacZ and PtsG concentrations, and total cAMP concentrations under various growth conditions. The entire data base consists of 18 experiments performed with nine different strains. The model describes the expression of 17 key enzymes, 38 enzymatic reactions, and the dynamic behavior of more than 50 metabolites. The different phenomena affecting the phosphorylation level of EIIACrr, the key regulation molecule for inducer exclusion and catabolite repression in enteric bacteria, can now be explained quantitatively.

[1]  S. Ryu,et al.  Purification of Mlc and Analysis of Its Effects on thepts Expression in Escherichia coli * , 1999, The Journal of Biological Chemistry.

[2]  Nihon Hassei Seibutsu Gakkai,et al.  Genes to cells , 1996 .

[3]  P. Postma,et al.  Phosphoenolpyruvate:carbohydrate phosphotransferase system of bacteria. , 1985, Microbiological reviews.

[4]  E. Gilles,et al.  The organization of metabolic reaction networks. III. Application for diauxic growth on glucose and lactose. , 2001, Metabolic engineering.

[5]  J. Lengeler,et al.  Plasmid‐mediated sucrose metabolism in Escherichia coli K12: mapping of the scr genes of pUR400 , 1988, Molecular microbiology.

[6]  Regulation of glycerol kinase by enzyme IIIGlc of the phosphoenolpyruvate:carbohydrate phosphotransferase system , 1986, Journal of bacteriology.

[7]  T. Inada,et al.  Down regulation of cAMP production by cAMP receptor protein in Escherichia coli: an assessment of the contributions of transcriptional and posttranscriptional control of adenylate cyclase , 1996, Molecular and General Genetics MGG.

[8]  B. Erni,et al.  The glucose transporter of Escherichia coli. Mutants with impaired translocation activity that retain phosphorylation activity. , 1992, The Journal of biological chemistry.

[9]  M. Saier,et al.  Regulation of genes coding for enzyme constituents of the bacterial phosphotransferase system , 1980, Journal of bacteriology.

[10]  H. Aiba,et al.  A novel regulatory role of glucose transporter of Escherichia coli: membrane sequestration of a global repressor Mlc , 2000, The EMBO journal.

[11]  W. Epstein,et al.  Phosphorylation of D-glucose in Escherichia coli mutants defective in glucosephosphotransferase, mannosephosphotransferase, and glucokinase , 1975, Journal of bacteriology.

[12]  H. Takahashi,et al.  Inducer exclusion in Escherichia coli by non‐PTS substrates: the role of the PEP to pyruvate ratio in determining the phosphorylation state of enzyme IIAGlc , 1998, Molecular microbiology.

[13]  B. Palsson,et al.  Transcriptional regulation in constraints-based metabolic models of Escherichia coli Covert , 2002 .

[14]  T. Inada,et al.  A global repressor (Mlc) is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli , 1998, Molecular microbiology.

[15]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[16]  Andreas Kremling,et al.  Modular Modeling of Cellular Systems with ProMoT/Diva , 2003, Bioinform..

[17]  J. Knabe.  Methoden der enzymatischen Analyse, 3. Auflage. Herausgeb. v. H. U. Bergmeyer, LXXXI, 2353 Seiten in 2 Bänden. Preis DM 460,–, Verlag Chemie, Weinheim/Bergstr., 1974 , 1974 .

[18]  H. Westerhoff,et al.  Understanding Glucose Transport by the Bacterial Phosphoenolpyruvate:Glycose Phosphotransferase System on the Basis of Kinetic Measurements in Vitro * , 2000, The Journal of Biological Chemistry.

[19]  H. Aiba,et al.  A lowered concentration of cAMP receptor protein caused by glucose is an important determinant for catabolite repression in Escherichia coli , 1993, Molecular microbiology.

[20]  P. Postma,et al.  CRP down-regulates adenylate cyclase activity by reducing the level of phosphorylated IIAGlc, the glucose-specific phosphotransferase protein, in Escherichia coli , 1998, Molecular and General Genetics MGG.

[21]  J. Lengeler,et al.  Glucose Transporter Mutants of Escherichia coli K-12 with Changes in Substrate Recognition of IICBGlc and Induction Behavior of theptsG Gene , 2000, Journal of bacteriology.

[22]  U. Alon,et al.  Detailed map of a cis-regulatory input function , 2003, Proceedings of the National Academy of Sciences of the United States of America.

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

[24]  J. Keasling,et al.  Mathematical Model of the lac Operon: Inducer Exclusion, Catabolite Repression, and Diauxic Growth on Glucose and Lactose , 1997, Biotechnology progress.

[25]  T. Inada,et al.  Mechanism responsible for glucose–lactose diauxie in Escherichia coli: challenge to the cAMP model , 1996, Genes to cells : devoted to molecular & cellular mechanisms.

[26]  E. Gilles,et al.  Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism. , 2004, Bio Systems.

[27]  W. Boos,et al.  Signal transduction between a membrane‐bound transporter, PtsG, and a soluble transcription factor, Mlc, of Escherichia coli , 2000, The EMBO journal.

[28]  Reinhold Brückner,et al.  Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. , 2002, FEMS microbiology letters.

[29]  Dongwoo Shin,et al.  The Escherichia coli glucose transporter enzyme IICBGlc recruits the global repressor Mlc , 2001, The EMBO journal.

[30]  E. Gilles,et al.  The organization of metabolic reaction networks. II. Signal processing in hierarchical structured functional units. , 2001, Metabolic engineering.

[31]  R. Schmitt,et al.  Plasmid-mediated uptake and metabolism of sucrose by Escherichia coli K-12 , 1982, Journal of bacteriology.

[32]  Norman D. Meadow,et al.  Reverse Genetics of Escherichia coliGlycerol Kinase Allosteric Regulation and Glucose Control of Glycerol Utilization In Vivo , 2001, Journal of bacteriology.

[33]  H. Westerhoff,et al.  Limits to inducer exclusion: inhibition of the bacterial phosphotransferase system by glycerol kinase , 1998, Molecular microbiology.

[34]  R. A. Roehl,et al.  Genetic locus, distant from ptsM, affecting enzyme IIA/IIB function in Escherichia coli K-12 , 1980, Journal of bacteriology.

[35]  J. Plumbridge,et al.  Expression of ptsG, the gene for the major glucose PTS transporter in Escherichia coli, is repressed by Mlc and induced by growth on glucose , 1998, Molecular microbiology.

[36]  H. Bergmeyer.  Methoden der enzymatischen Analyse , 1962 .

[37]  August Böck,et al.  Phosphoglucose isomerase from Escherischia coli K10: Purification, properties and formation under aerobic and anaerobic condition , 1980, Archives of Microbiology.

[38]  T. Larson,et al.  Structures of the promoter and operator of the glpD gene encoding aerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12 , 1988, Journal of bacteriology.

[39]  E. Gilles,et al.  Modeling and experimental validation of the signal transduction via the Escherichia coli sucrose phospho transferase system. , 2004, Journal of biotechnology.

[40]  B. Erni,et al.  Glucose permease of Escherichia coli. The effect of cysteine to serine mutations on the function, stability, and regulation of transport and phosphorylation. , 1988, The Journal of biological chemistry.

[41]  T. Inada,et al.  Negative regulation of the pts operon by Mlc: mechanism underlying glucose induction in Escherichia coli , 1999, Genes to cells : devoted to molecular & cellular mechanisms.

[42]  J. Weiner,et al.  Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. , 1978, The Journal of biological chemistry.

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

[44]  A Danchin,et al.  The ptsH, ptsI, and crr genes of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system: a complex operon with several modes of transcription , 1988, Journal of bacteriology.

[45]  E D Gilles,et al.  Modeling of inducer exclusion and catabolite repression based on a PTS-dependent sucrose and non-PTS-dependent glycerol transport systems in Escherichia coli K-12 and its experimental verification. , 2001, Journal of biotechnology.

[46]  V. Muronetz,et al.  Interaction between d‐glyceraldehyde‐3‐phosphate dehydrogenase and 3‐phosphoglycerate kinase and its functional consequences , 1992, FEBS letters.

[47]  C. Chassagnole,et al.  Dynamic modeling of the central carbon metabolism of Escherichia coli. , 2002, Biotechnology and bioengineering.

[48]  W. Boos,et al.  Analysis of the Interaction between the Global Regulator Mlc and EIIBGlc of the Glucose-specific Phosphotransferase System in Escherichia coli * , 2003, The Journal of Biological Chemistry.

[49]  S J Remington,et al.  Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase , 1993, Science.

[50]  J. Adler,et al.  Galactokinase from Escherichia coli , 1963 .

[51]  A. Pardee,et al.  The initial kinetics of enzyme induction. , 1961, Biochimica et biophysica acta.

[52]  J. Lengeler,et al.  CTnscr94, a conjugative transposon found in enterobacteria , 1997, Journal of bacteriology.

[53]  H. Buc,et al.  Kinetics of the allosteric interactions of phosphofructokinase from Escherichia coli. , 1968, Journal of molecular biology.

[54]  E. Lin,et al.  Replacement of a Phosphoenolpyruvate-dependent Phosphotransferase by a Nicotinamide Adenine Dinucleotide-linked Dehydrogenase for the Utilization of Mannitol , 1967, Journal of bacteriology.

[55]  J. Plumbridge,et al.  Regulation of gene expression in the PTS in Escherichia coli: the role and interactions of Mlc. , 2002, Current opinion in microbiology.