Reconstruction and use of microbial metabolic networks: The core Escherichia coli metabolic model as an educational guide

EcoSal Plus

Volumn 4, Issue 1, 2010, Pages

  Orth, Jeffrey D ^a   Fleming, R M T ^a   Palsson, Bernhard O ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84927781592     PISSN: None     EISSN: 23246200     Source Type: Journal    
DOI: 10.1128/ecosalplus.10.2.1     Document Type: Article

References (197)

1. Palsson BØ. 2006. Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, New York, NY.
2. Varma A, Palsson BØ. 1993. Metabolic capabilities of Escherichia coli: I. Synthesis of biosynthetic precursors and cofactors. J Theor Biol 165:477-502.
3. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ. 2007. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA 104:1777-1782.
4. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. 2007. A genomescale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121.
5. Nogales J, Palsson BØ, Thiele I. 2008. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2:79.
6. Resendis-Antonio O, Reed JL, Encarnacion S, Collado-Vides J, Palsson BØ. 2007. Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. PLoS Comput. Biol. 3:1887-1895.
7. Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO. 2009. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7:129-143.
8. Price ND, Papin JA, Schilling CH, Palsson B. 2003. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21:162-169.
9. Pal C, Papp B, Lercher MJ. 2005. Horizontal gene transfer depends on gene content of the host. Bioinformatics 21(Suppl. 2):ii222-ii223.
10. Pal C, Papp B, Lercher MJ. 2005. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37:1372-1375.
11. Pal C, Papp B, Lercher MJ, Csermely P, Oliver SG, Hurst LD. 2006. Chance and necessity in the evolution of minimal metabolic networks. Nature 440:667-670.
12. Mahadevan R, Schilling CH. 2003. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 5:264-276.
13. Burgard AP, Nikolaev EV, Schilling CH, Maranas CD. 2004. Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res 14:301-312.
14. Barrett CL, Herring CD, Reed JL, Palsson BO. 2005. The global transcriptional regulatory network for metabolism in Escherichia coli attains few dominant functional states. Proc Natl Acad Sci USA 102:19103-19108.
15. Samal A, Jain S. 2008. The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response. BMC Syst Biol 2:21.
16. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. 2004. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427:839-843.
17. Edwards JS, Ibarra RU, Palsson BØ. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125-130.
18. Segre D, Vitkup D, Church GM. 2002. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99:15112-15117.
19. Shlomi T, Berkman O, Ruppin E. 2005. Regulatory on/offminimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 102:7695-7700.
20. Ibarra RU, Edwards JS, Palsson BØ. 2002. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420:186-189.
21. Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S. 2006. Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol 188:8259-8271.
22. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BØ. 2006. Systems approach to refining genome annotation. Proc Natl Acad Sci USA 103: 17480-17484.
23. Herrgard MJ, Fong SS, Palsson BØ. 2006. Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput Biol 2:e72.
24. Kumar VS, Maranas CD. 2009. GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol 5:e1000308.
25. Park JH, Lee KH, Kim TY, Lee SY. 2007. Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci USA 104:7797-7802.
26. Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO. 2005. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91:643-648.
27. Burgard AP, Pharkya P, Maranas CD. 2003. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84:647-657.
28. Patil KR, Rocha I, Forster J, Nielsen J. 2005. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6:308.
29. Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Bonavides-Martinez C, Ingraham J. 2007. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res 35:7577-7590.
30. Stein L. 2001. Genome annotation: from sequence to biology. Nat Rev Genet 2:493-503.
31. Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM. 2004. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res 32(Database issue):D311-D314.
32. Guldener U, Munsterkotter M, Kastenmuller G, Strack N, van Helden J, Lemer C, Richelles J, Wodak SJ, Garcia-Martinez J, Perez-Ortin JE, Michael H, Kaps A, Talla E, Dujon B, Andre B, Souciet JL, De Montigny J, Bon E, Gaillardin C, Mewes HW. 2005. CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res 33:D364-D368.
33. Maglott D, Ostell J, Pruitt KD, Tatusova T. 2005. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 33: D54-D58.
34. Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O. 2001. The comprehensive microbial resource. Nucleic Acids Res 29: 123-125.
35. Stoesser G, Tuli MA, Lopez R, Sterk P. 1999. The EMBL nucleotide sequence database. Nucleic Acids Res 27:18-24.
36. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Lykidis A, Mavromatis K, Ivanova N, Kyrpides NC. 2006. The integrated microbial genomes (IMG) system. Nucleic Acids Res 34: D344-D348.
37. Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27-30.
38. Chang A, Scheer M, Grote A, Schomburg I, Schomburg D. 2009. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res 37:D588-D592.
39. Bairoch A. 2000. The ENZYME database in 2000. Nucleic Acids Res 28:304-305.
40. Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD. 2004. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 32(Database issue):D438-D442.
41. DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A. 2007. Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 8:139.
42. Ren Q, Chen K, Paulsen IT. 2007. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 35:D274-D279.
43. Paley SM, Karp PD. 2002. Evaluation of computational metabolicpathway predictions for Helicobacter pylori. Bioinformatics 18:715-724.
44. Claudel-Renard C, Chevalet C, Faraut T, Kahn D. 2003. Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res 31:6633-6639.
45. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25-29.
46. Reed JL, Famili I, Thiele I, Palsson BØ. 2006. Towards multidimensional genome annotation. Nat Rev Genet 7:130-141.
47. Neidhardt FC, Curtis R III, Ingraham J, Lin ECC, Low KB, Magasanik B, ReznikoffWS, Riley M, Schaechter M, Umbarger HE (ed). 1996. Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. ASM Press, Washington, DC.
48. Edwards JS, Palsson BO. 2000. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97:5528-5533.
49. Varma A, Palsson BØ. 1993. Metabolic capabilities of Escherichia coli: II. Optimal growth patterns. J Theor Biol 165:503-522.
50. Varma A, Palsson BØ. 1994. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 60:3724-3731.
51. Duarte NC, Herrgard MJ, Palsson B. 2004. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14:1298-1309.
52. Breitling R, Vitkup D, Barrett MP. 2008. New surveyor tools for charting microbial metabolic maps. Nat Rev Microbiol 6:156-161.
53. Froman BE, Tait RC, Gottlieb LD. 1989. Isolation and characterization of the phosphoglucose isomerase gene from Escherichia coli. Mol Gen Genet 217:126-131.
54. Hua Q, Yang C, Baba T, Mori H, Shimizu K. 2003. Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J Bacteriol 185:7053-7067.
55. Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS. 2007. A predictive model for transcriptional control of physiology in a free living cell. Cell 131:1354-1365.
56. Herrgard MJ, Lee BS, Portnoy V, Palsson BØ. 2006. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. Genome Res 16:627-635.
57. Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. 2006. A systems approach to mapping DNA damage response pathways. Science 312:1054-1059.
58. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BØ. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429:92-96.
59. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. 2007. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5:e8.
60. Hu Z, Killion PJ, Iyer VR. 2007. Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39:683-687.
61. Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. 2003. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34:166-176.
62. Cho BK, Barrett CL, Knight EM, Park YS, Palsson BO. 2008. Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc Natl Acad Sci USA 105:19462-19467.
63. Cho BK, Knight EM, Barrett CL, Palsson BØ. 2008. Genomewide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res 18:900-910.
64. Cho BK, Knight EM, Palsson BØ. 2008. Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray. Methods Mol Biol 439:131-145.
65. Ideker TE, Thorsson V, Karp RM. 2000. Discovery of regulatory interactions through perturbation: inference and experimental design. Pacific Symp Biocomput 292:305-316.
66. Cho BK, Knight EM, Palsson BØ. 2006. Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. Microbiology 152:2207-2219.
67. Grainger DC, Aiba H, Hurd D, Browning DF, Busby SJ. 2007. Transcription factor distribution in Escherichia coli: studies with FNR protein. Nucleic Acids Res 35:269-278.
68. Shimada T, Ishihama A, Busby SJ, Grainger DC. 2008. The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res 36:3950-3955.
69. Covert MW, Schilling CH, Palsson B. 2001. Regulation of gene expression in flux balance models of metabolism. J Theor Biol 213:73-88.
70. Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BØ. 2006. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol 2:e101.
71. Gianchandani EP, Joyce AR, Palsson BO, Papin JA. 2009. Functional states of the genome-scale Escherichia coli transcriptional regulatory system. PLoS Comput Biol 5:e1000403.
72. Thiele I, Jamshidi N, Fleming RM, Palsson BO. 2009. Genomescale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol 5:e1000312.
73. Alberty RA. 2003. Thermodynamics of Biochemical Reactions. Massachusetts Institute of Technology, Cambridge, MA.
74. Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G III, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. 2006. Escherichia coli K-12: a cooperatively developed annotation snapshot-2005. Nucleic Acids Res 34:1-9.
75. Cunningham L, Guest JR. 1998. Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli. Microbiology 144(Pt 8):2113-2123.
76. Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD. 2005. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 33: D334-D337.
77. Stolz B, Huber M, Markovic-Housley Z, Erni B. 1993. The mannose transporter of Escherichia coli. Structure and function of the IIABMan subunit. J Biol Chem 268:27094-27099.
78. Reidl J, Boos W. 1991. The malX malY operon of Escherichia coli encodes a novel enzyme II of the phosphotransferase system recognizing glucose and maltose and an enzyme abolishing the endogenous induction of the maltose system. J Bacteriol 173:4862-4876.
79. Eberstadt M, Grdadolnik SG, Gemmecker G, Kessler H, Buhr A, Erni B. 1996. Solution structure of the IIB domain of the glucose transporter of Escherichia coli. Biochemistry 35:11286-11292.
80. Daldal F. 1984. Nucleotide sequence of gene pfkB encoding the minor phosphofructokinase of Escherichia coli K-12. Gene 28:337-342.
81. Rypniewski WR, Evans PR. 1989. Crystal structure of unliganded phosphofructokinase from Escherichia coli. J Mol Biol 207: 805-821.
82. Hines JK, Fromm HJ, Honzatko RB. 2006. Novel allosteric activation site in Escherichia coli fructose-1,6-bisphosphatase. J Biol Chem 281:18386-18393.
83. Alefounder PR, Baldwin SA, Perham RN, Short NJ. 1989. Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli. Biochem J 257:529-534.
84. Baldwin SA, Perham RN. 1978. Novel kinetic and structural properties of the class-I D-fructose 1,6-bisphosphate aldolase from Escherichia coli (Crookes' strain). Biochem J 169:643-652.
85. Thomson GJ, Howlett GJ, Ashcroft AE, Berry A. 1998. The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem J 331(Pt. 2):437-445.
86. Pichersky E, Gottlieb LD, Hess JF. 1984. Nucleotide sequence of the triose phosphate isomerase gene of Escherichia coli. Mol Gen Genet 195:314-320.
87. Branlant G, Branlant C. 1985. Nucleotide sequence of the Escherichia coli gap gene. Different evolutionary behavior of the NAD+-binding domain and of the catalytic domain of D-glyceraldehyde-3-phosphate dehydrogenase. Eur J Biochem 150:61-66.
88. Nellemann LJ, Holm F, Atlung T, Hansen FG. 1989. Cloning and characterization of the Escherichia coli phosphoglycerate kinase (pgk) gene. Gene 77:185-191.
89. Fraser HI, Kvaratskhelia M, White MF. 1999. The two analogous phosphoglycerate mutases of Escherichia coli. FEBS Lett 455: 344-348.
90. Kuhnel K, Luisi BF. 2001. Crystal structure of the Escherichia coli RNA degradosome component enolase. J Mol Biol 313:583-592.
91. Garrido-Pertierra A, Cooper RA. 1983. Evidence for two distinct pyruvate kinase genes in Escherichia coli K-12. FEBS Lett 162:420-422.
92. Muirhead H. 1990. Isoenzymes of pyruvate kinase. Biochem Soc Trans 18:193-196.
93. Josephson BL, Fraenkel DG. 1974. Sugar metabolism in transketolase mutants of Escherichia coli. J Bacteriol 118:1082-1089.
94. Josephson BL, Fraenkel DG. 1969. Transketolase mutants of Escherichia coli. J Bacteriol 100:1289-1295.
95. Peyru G, Fraenkel DG. 1968. Genetic mapping of loci for glucose-6-phosphate dehydrogenase, gluconate-6-phosphate dehydrogenase, and gluconate-6-phosphate dehydrase in Escherichia coli. J Bacteriol 95:1272-1278.
96. Thomason LC, Court DL, Datta AR, Khanna R, Rosner JL. 2004. Identification of the Escherichia coli K-12 ybhE gene as pgl, encoding 6-phosphogluconolactonase. J Bacteriol 186:8248-8253.
97. Veronese FM, Boccu E, Fontana A. 1976. Isolation and properties of 6-phosphogluconate dehydrogenase from Escherichia coli. Some comparisons with the thermophilic enzyme from Bacillus stearothermophilus. Biochemistry 15:4026-4033.
98. Essenberg MK, Cooper RA. 1975. Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles. Eur J Biochem 55:323-332.
99. Csonka LN, Fraenkel DG. 1977. Pathways of NADPH formation in Escherichia coli. J Biol Chem 252:3382-3391.
100. Melendez-Hevia E, Isidoro A. 1985. The game of the pentose phosphate cycle. J Theor Biol 117:251-263.
101. Iida A, Teshiba S, Mizobuchi K. 1993. Identification and characterization of the tktB gene encoding a second transketolase in Escherichia coli K-12. J Bacteriol 175:5375-5383.
102. Sprenger GA, Schorken U, Sprenger G, Sahm H. 1995. Transketolase A of Escherichia coli K12. Purification and properties of the enzyme from recombinant strains. Eur J Biochem 230:525-532.
103. Lyngstadaas A, Sprenger GA, Boye E. 1998. Impaired growth of an Escherichia coli rpe mutant lacking ribulose-5-phosphate epimerase activity. Biochim Biophys Acta 1381:319-330.
104. Reed LJ, Pettit FH, Eley MH, Hamilton L, Collins JH, Oliver RM. 1975. Reconstitution of the Escherichia coli pyruvate dehydrogenase complex. Proc Natl Acad Sci USA 72:3068-3072.
105. Nguyen NT, Maurus R, Stokell DJ, Ayed A, Duckworth HW, Brayer GD. 2001. Comparative analysis of folding and substrate binding sites between regulated hexameric type II citrate synthases and unregulated dimeric type I enzymes. Biochemistry 40:13177-13187.
106. Brock M, Maerker C, Schutz A, Volker U, Buckel W. 2002. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur J Biochem 269:6184-6194.
107. Prodromou C, Haynes MJ, Guest JR. 1991. The aconitase of Escherichia coli: purification of the enzyme and molecular cloning and map location of the gene (acn). J Gen. Microbiol. 137:2505-2515.
108. Burke WF, Johanson RA, Reeves HC. 1974. NADP+-specific isocitrate dehydrogenase of Escherichia coli. II. Subunit structure. Biochim Biophys Acta 351:333-340.
109. Perham RN, Packman LC. 1989. 2-Oxo acid dehydrogenase multienzyme complexes: domains, dynamics, and design. Ann N Y Acad Sci 573:1-20.
110. Bridger WA, Wolodko WT, Henning W, Upton C, Majumdar R, Williams SP. 1987. The subunits of succinyl-coenzyme A synthetase-function and assembly. Biochem Soc Symp 54:103-111.
111. Yankovskaya V, Horsefield R, Tornroth S, Luna-Chavez C, Miyoshi H, Leger C, Byrne B, Cecchini G, Iwata S. 2003. Architecture of succinate dehydrogenase and reactive oxygen species generation. Science 299:700-704.
112. Condon C, Cammack R, Patil DS, Owen P. 1985. The succinate dehydrogenase of Escherichia coli. Immunochemical resolution and biophysical characterization of a 4-subunit enzyme complex. J Biol Chem 260:9427-9434.
113. Bell PJ, Andrews SC, Sivak MN, Guest JR. 1989. Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12. J Bacteriol 171:3494-3503.
114. Flint DH. 1994. Initial kinetic and mechanistic characterization of Escherichia coli fumarase A. Arch Biochem Biophys 311:509-516.
115. Woods SA, Schwartzbach SD, Guest JR. 1988. Two biochemically distinct classes of fumarase in Escherichia coli. Biochim Biophys Acta 954:14-26.
116. Sutherland P, McAlister-Henn L. 1985. Isolation and expression of the Escherichia coli gene encoding malate dehydrogenase. J Bacteriol 163:1074-1079.
117. Cole ST, Condon C, Lemire BD, Weiner JH. 1985. Molecular biology, biochemistry and bioenergetics of fumarate reductase, a complex membrane-bound iron-sulfur flavoenzyme of Escherichia coli. Biochim Biophys Acta 811:381-403.
118. Iverson TM, Luna-Chavez C, Cecchini G, Rees DC. 1999. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284:1961-1966.
119. Hoyt JC, Robertson EF, Berlyn KA, Reeves HC. 1988. Escherichia coli isocitrate lyase: properties and comparisons. Biochim Biophys Acta 966:30-35.
120. Molina I, Pellicer MT, Badia J, Aguilar J, Baldoma L. 1994. Molecular characterization of Escherichia coli malate synthase G. Differentiation with the malate synthase A isoenzyme. Eur J Biochem 224:541-548.
121. Narindrasorasak S, Bridger WA. 1977. Phosphoenolpyruvate synthetase of Escherichia coli: molecular weight, subunit composition, and identification of phosphohistidine in phosphoenzyme intermediate. J Biol Chem 252:3121-3127.
122. Cooper RA, Kornberg HL. 1965. Net formation of phosphoenolpyruvate from pyruvate by Escherichia coli. Biochim Biophys Acta 104:618-620.
123. Hansen EJ, Juni E. 1975. Isolation of mutants of Escherichia coli lacking NAD-and NADP-linked malic. Biochem Biophys Res Commun 65:559-566.
124. Hansen EJ, Juni E. 1974. Two routes for synthesis of phosphoenolpyruvate from C4-dicarboxylic acids in Escherichia coli. Biochem Biophys Res Commun 59:1204-1210.
125. Iwakura M, Hattori J, Arita Y, Tokushige M, Katsuki H. 1979. Studies on regulatory functions of malic enzymes. VI. Purification and molecular properties of NADP-linked malic enzyme from Escherichia coli W. J Biochem 85:1355-1365.
126. Mahajan SK, Chu CC, Willis DK, Templin A, Clark AJ. 1990. Physical analysis of spontaneous and mutagen-induced mutants of Escherichia coli K-12 expressing DNA exonuclease VIII activity. Genetics 125:261-273.
127. Niersbach M, Kreuzaler F, Geerse RH, Postma PW, Hirsch HJ. 1992. Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase. Mol Gen Genet 231:332-336.
128. Delbaere LT, Sudom AM, Prasad L, Leduc Y, Goldie H. 2004. Structure/function studies of phosphoryl transfer by phosphoenolpyruvate carboxykinase. Biochim Biophys Acta 1697:271-278.
129. Kai Y, Matsumura H, Izui K. 2003. Phosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms. Arch Biochem Biophys 414:170-179.
130. Kornberg HL. 1966. Anaplerotic sequences and their role in metabolism. Essays Biochem 2:1-31.
131. Kornberg HL. 1965. The coordination of metabolic routes. Function and Structure in Microorganisms: Fifteenth Symposium of the Society for General Microbiology. University Press, London, United Kingdom.
132. Wilks JC, Slonczewski JL. 2007. pH of the cytoplasm and periplasm of Escherichia coli: rapid measurement by green fluorescent protein fluorimetry. J Bacteriol 189:5601-5607.
133. Unden G, Dunnwald P. 11 March 2008, posting date. The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics, The Aerobic and Anaerobic Respiratory Chain of Escherichia coli and Salmonella enterica: Enzymes and Energetics. In Böck A, Curtiss R III, Kaper JB, Karp PD, Neidhardt FC, Nyström T, Slauch JM, Squires CL, and Ussery D (ed), EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, DC.
134. Schneider D, Pohl T, Walter J, Dorner K, Kohlstadt M, Berger A, Spehr V, Friedrich T. 2008. Assembly of the Escherichia coli NADH:ubiquinone oxidoreductase (complex I). Biochim Biophys Acta 1777:735-739.
135. Spehr V, Schlitt A, Scheide D, Guenebaut V, Friedrich T. 1999. Overexpression of the Escherichia coli nuo-operon and isolation of the overproduced NADH:ubiquinone oxidoreductase (complex I). Biochemistry 38:16261-16267.
136. Kobayashi K, Tagawa S, Mogi T. 1999. Electron transfer process in cytochrome bd-type ubiquinol oxidase from Escherichia coli revealed by pulse radiolysis. Biochemistry 38:5913-5917.
137. Cain BD, Simoni RD. 1989. Proton translocation by the F1F0 ATPase of Escherichia coli. Mutagenic analysis of the a subunit. J Biol Chem 264:3292-3300.
138. Kasimoglu E, Park SJ, Malek J, Tseng CP, Gunsalus RP. 1996. Transcriptional regulation of the proton-translocating ATPase (atpIBEFHAGDC) operon of Escherichia coli: control by cell growth rate. J Bacteriol 178:5563-5567.
139. Berry MB, Bae E, Bilderback TR, Glaser M, Phillips GN Jr. 2006. Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase. Proteins 62:555-556.
140. Brune M, Schumann R, Wittinghofer F. 1985. Cloning and sequencing of the adenylate kinase gene (adk) of Escherichia coli. Nucleic Acids Res 13:7139-7151.
141. Bizouarn T, Fjellstrom O, Meuller J, Axelsson M, Bergkvist A, Johansson C, Goran Karlsson B, Rydstrom J. 2000. Proton translocating nicotinamide nucleotide transhydrogenase from E. coli. Mechanism of action deduced from its structural and catalytic properties. Biochim Biophys Acta 1457:211-228.
142. Sauer U, Canonaco F, Heri S, Perrenoud A, Fischer E. 2004. The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J Biol Chem 279:6613-6619.
143. Clark DP. 1989. The fermentation pathways of Escherichia coli. FEMS Microbiol Rev 5:223-234.
144. Dym O, Pratt EA, Ho C, Eisenberg D. 2000. The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. Proc Natl Acad Sci USA 97:9413-9418.
145. Jiang GR, Nikolova S, Clark DP. 2001. Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli. Microbiology 147:2437-2446.
146. Knappe J, Sawers G. 1990. A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli. FEMS Microbiol Rev 6:383-398.
147. Sawers G, Watson G. 1998. A glycyl radical solution: oxygendependent interconversion of pyruvate formate-lyase. Mol Microbiol 29:945-954.
148. Suzuki T. 1969. Phosphotransacetylase of Escherichia coli B, activation by pyruvate and inhibition by NADH and certain nucleotides. Biochim Biophys Acta 191:559-569.
149. Skarstedt MT, Silverstein E. 1976. Escherichia coli acetate kinase mechanism studied by net initial rate, equilibrium, and independent isotopic exchange kinetics. J Biol Chem 251:6775-6783.
150. Ferrandez A, Garcia JL, Diaz E. 1997. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl) propionate catabolic pathway of Escherichia coli K-12. J Bacteriol 179: 2573-2581.
151. Kessler D, Herth W, Knappe J. 1992. Ultrastructure and pyruvate formate-lyase radical quenching property of the multienzymic AdhE protein of Escherichia coli. J Biol Chem 267:18073-18079.
152. Yuan J, Fowler WU, Kimball E, Lu W, Rabinowitz JD. 2006. Kinetic flux profiling of nitrogen assimilation in Escherichia coli. Nat Chem Biol 2:529-530.
153. Wu LF, Mandrand-Berthelot MA. 1995. A family of homologous substrate-binding proteins with a broad range of substrate specificity and dissimilar biological functions. Biochimie 77:744-750.
154. Wallace B, Yang YJ, Hong JS, Lum D. 1990. Cloning and sequencing of a gene encoding a glutamate and aspartate carrier of Escherichia coli K-12. J Bacteriol 172:3214-3220.
155. Rhee SG, Ubom GA, Hunt JB, Chock PB. 1982. Catalytic cycle of the biosynthetic reaction catalyzed by adenylylated glutamine synthetase from Escherichia coli. J Biol Chem 257:289-297.
156. Fersht A. 1999. Structure and Mechanism in Protein Science: a Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman, New York, NY.
157. Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ. 2007. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protocols 2:727-738.
158. Feist AM, Palsson BØ. 2008. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotech 26:659-667.
159. Neidhardt FC, Umbarger HE. 1996. Chemical composition of Escherichia coli, p 13-16. In Neidhardt FC, Curtis R III, Ingraham J, Lin ECC, Low KB, Magasanik B, ReznikoffWS, Riley M, Schaechter M, and Umbarger HE (ed), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 1. ASM Press, Washington, DC.
160. Bledig SA, Ramseier TM, Saier MH Jr. 1996. Frur mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli. J Bacteriol 178:280-283.
161. Iuchi S, Lin EC. 1988. arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc Natl Acad Sci USA 85:1888-1892.
162. Sawers G. 1993. Specific transcriptional requirements for positive regulation of the anaerobically inducible pfloperon by ArcA and FNR. Mol Microbiol 10:737-747.
163. Park SJ, Chao G, Gunsalus RP. 1997. Aerobic regulation of the sucABCD genes of Escherichia coli, which encode alpha-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter. J Bacteriol 179:4138-4142.
164. Park SJ, Gunsalus RP. 1995. Oxygen, iron, carbon, and superoxide control of the fumarase fumA and fumC genes of Escherichia coli: role of the arcA, fnr, and soxR gene products. J Bacteriol 177: 6255-6562.
165. Tseng CP. 1997. Regulation of fumarase (fumB) gene expression in Escherichia coli in response to oxygen, iron and heme availability: role of the arcA, fur, and hemA gene products. FEMS Microbiol Lett 157:67-72.
166. Tseng CP, Albrecht J, Gunsalus RP. 1996. Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli. J Bacteriol 178:1094-1098.
167. Bongaerts J, Zoske S, Weidner U, Unden G. 1995. Transcriptional regulation of the proton translocating NADH dehydrogenase genes (nuoA-N) of Escherichia coli by electron acceptors, electron donors and gene regulators. Mol Microbiol 16:521-534.
168. Green J, Guest JR. 1994. Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors. Mol Microbiol 12:433-444.
169. Pellicer MT, Fernandez C, Badia J, Aguilar J, Lin EC, Baldom L. 1999. Cross-induction of glc and ace operons of Escherichia coli attributable to pathway intersection. Characterization of the glc promoter. J Biol Chem 274:1745-1752.
170. Davies SJ, Golby P, Omrani D, Broad SA, Harrington VL, Guest JR, Kelly DJ, Andrews SC. 1999. Inactivation and regulation of the aerobic C(4)-dicarboxylate transport (dctA) gene of Escherichia coli. J Bacteriol 181:5624-5635.
171. Okinaka RT, Dobrogosz WJ. 1967. Catabolite repression and pyruvate metabolism in Escherichia coli. J Bacteriol 93:1644-1650.
172. Saier MH, Jr. 1998. Multiple mechanisms controlling carbon metabolism in bacteria. Biotechnol Bioeng 58:170-174.
173. Botsford JL, Harman JG. 1992. Cyclic AMP in prokaryotes. Microbiol Rev 56:100-122.
174. Sawers G. 2001. A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon. Mol Microbiol 39:1285-1298.
175. Plumbridge J. 1998. Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS. Mol Microbiol 27:369-380.
176. Gui L, Sunnarborg A, LaPorte DC. 1996. Regulated expression of a repressor protein: FadR activates iclR. J Bacteriol 178:4704-4709.
177. Cortay JC, Negre D, Galinier A, Duclos B, Perriere G, Cozzone AJ. 1991. Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor. EMBO J 10:675-679.
178. Golby P, Davies S, Kelly DJ, Guest JR, Andrews SC. 1999. Identification and characterization of a two-component sensor-kinase and response-regulator system (DcuS-DcuR) controlling gene expression in response to C4-dicarboxylates in Escherichia coli. J Bacteriol 181:1238-1248.
179. Tanaka Y, Kimata K, Inada T, Tagami H, Aiba H. 1999. Negative regulation of the pts operon by Mlc: mechanism underlying glucose induction in Escherichia coli. Genes Cells 4:391-399.
180. Membrillo-Hernandez J, Lin EC. 1999. Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by fnr and RpoS. J Bacteriol 181:7571-7579.
181. Mikulskis A, Aristarkhov A, Lin EC. 1997. Regulation of expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by catabolite repressor activator protein Cra. J Bacteriol 179:7129-7134.
182. Negre D, Oudot C, Prost JF, Murakami K, Ishihama A, Cozzone AJ, Cortay JC. 1998. FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli. J Mol Biol 276:355-365.
183. Quail MA, Guest JR. 1995. Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhRaceEF-lpd operon of Escherichia coli. Mol Microbiol 15:519-529.
184. Lee J, Owens JT, Hwang I, Meares C, Kustu S. 2000. Phosphorylation-induced signal propagation in the response regulator ntrC. J Bacteriol 182:5188-5195.
185. Camarena L, Poggio S, Garcia N, Osorio A. 1998. Transcriptional repression of gdhA in Escherichia coli is mediated by the Nac protein. FEMS Microbiol Lett 167:51-56.
186. Harris RM, Webb DC, Howitt SM, Cox GB. 2001. Characterization of PitA and PitB from Escherichia coli. J Bacteriol 183:5008-5014.
187. Becker SA, Palsson BØ. 2008. Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 4: e1000082.
188. Reed JL, Vo TD, Schilling CH, Palsson BØ. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4:R54.1-R54.12.
189. Chen L, Vitkup D. 2006. Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol 7:R17.
190. Kharchenko P, Vitkup D, Church GM. 2004. Filling gaps in a metabolic network using expression information. Bioinformatics 20(Suppl. 1):I178-I185.
191. Loh KD, Gyaneshwar P, MarkenscoffPapadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, Kustu S. 2006. A previously undescribed pathway for pyrimidine catabolism. Proc Natl Acad Sci USA 103:5114-5119.
192. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, NeuwegerH, OlsenG, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691-5702.
193. Osterman A. 2006. A hidden metabolic pathway exposed. Proc Natl Acad Sci USA 103:5637-5638.
194. Barrett CL, Kim TY, Kim HU, Palsson BO, Lee SY. 2006. Systems biology as a foundation for genome-scale synthetic biology. Curr Opin Biotechnol 17:488-492.
195. Kim TH, Ren B. 2006. Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet 7:81-102.
196. Wade JT, Struhl K, Busby SJ, Grainger DC. 2007. Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization. Mol Microbiol 65:21-26.
197. Zhou D, Yang R. 2006. Global analysis of gene transcription regulation in prokaryotes. Cell Mol Life Sci 63:2260-2290.