Toward large-scale modeling of the microbial cell for computer simulation

Journal of Biotechnology

Volumn 113, Issue 1-3, 2004, Pages 281-294

  Ishii, Nobuyoshi ^a   Robert, Martin ^a   Nakayama, Yoichi ^a   Kanai, Akio ^a   Tomita, Masaru ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

Bioinformatics; Computer simulation; Mathematical model; Metabolic engineering; Metabolome; Systems biology

Indexed keywords

BIOINFORMATICS; PHARMACEUTICAL INDUSTRY; SYSTEMS BIOLOGY;

COMPUTER SIMULATION; MATHEMATICAL MODELS; METABOLISM; MICROORGANISMS; PROTEINS;

CELLS;

BIOINFORMATICS; BIOMEDICINE; CELL COMPOSITION; CELL METABOLISM; COMPUTER SIMULATION; CONFERENCE PAPER; DATA ANALYSIS; MATHEMATICAL MODEL; MEDICAL RESEARCH; MEDICINE; METABOLIC ENGINEERING; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS;

BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ESCHERICHIA COLI; MODELS, BIOLOGICAL;

EID: 4544227574     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2004.04.038     Document Type: Conference Paper

References (100)

1. A. Aharoni, C.H. Ric de Vos, H.A. Verhoeven, C.A. Maliepaard, G. Kruppa, R. Bino, and D.B. Goodenowe Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry OMICS 6 2002 217 234
2. S. Aiba, and M. Matsuoka Identification of metabolic model: citrate production from glucose by Candida lipolytica Biotechnol. Bioeng. 21 1979 1373 1386
3. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucl. Acids Res. 25 1997 3389 3402
4. F. Alvarez-Vasquez, C. Gonzalez-Alcon, and N.V. Torres Metabolism of citric acid production by Aspergillus niger: model definition, steady-state analysis and constrained optimization of citric acid production rate Biotechnol. Bioeng. 70 2000 82 108
5. A. Anderko, and M.M. Lencka Computation of electrical conductivity of multicomponent aqueous systems in wide concentration and temperature ranges Ind. Eng. Chem. Res. 36 1997 1932 1943
6. J.E. Bailey Toward a science of metabolic engineering Science 252 1991 1668 1674
7. B.A. Barshop, R.F. Wrenn, and C. Frieden Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM - a flexible portable system Anal. Biochem. 130 1983 134 145
8. H.W. Blanch Microbial growth kinetics Chem. Eng. Commun. 8 1981 181 211
9. B. Boeckmann, A. Bairoch, R. Apweiler, M.C. Blatter, A. Estreicher, E. Gasteiger, M.J. Martin, K. Michoud, C. O'Donovan, I. Phan, S. Pilbout, and M. Schneider The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucl. Acids Res. 31 2003 365 370
10. J.I. Castrillo, A. Hayes, S. Mohammed, S.J. Gaskell, and S.G. Oliver An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry Phytochemistry 62 2003 929 937
11. C. Chassagnole, B. Rais, E. Quentin, D.A. Fell, and J.P. Mazat An integrated study of threonine-pathway enzyme kinetics in Escherichia coli Biochem. J. 356 2001 415 423
12. C. Chassagnole, N. Noisommit-Rizzi, J.W. Schmid, K. Mauch, and M. Reuss Dynamic modeling of the central carbon metabolism of Escherichia coli Biotechnol. Bioeng. 79 2002 53 73
13. A. Cornish-Vowden, and J.H. Hofmeyr MetaModel: a program for modeling and control analysis of metabolic pathways on the IBM PC and compatibles Comput. Appl. Biosci. 7 1991 89 93
14. M.W. Covert, and B.O. Palsson Transcriptional regulation in constraints-based metabolic models of Escherichia coli J. Biol. Chem. 277 2002 28058 28064
15. K. Dairaku, E. Izumoto, H. Morikawa, S. Shioya, and T. Takamatsu Optimal quality control of Baler's yeast fed-batch culture using population dynamics Biotechnol. Bioeng. 24 1982 2661 2674
16. A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg Improved microbial gene identification with GLIMMER Nucl. Acids Res. 27 1999 4636 4641
17. M.M. Domach, S.K. Leung, R.E. Cahn, G.G. Cocks, and M.L. Shuler Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A Biotechnol. Bioeng. 26 1984 203 216
18. J.S. Edwards, and B.O. Palsson Systems properties of the Haemophilus influenzae Rd metabolic genotype J. Biol. Chem. 274 1999 17410 17416
19. J.S. Edwards, and B.O. Palsson The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities Proc. Natl. Acad. Sci. U.S.A. 97 2000 5528 5533
20. M. Ehlde, and G. Zacchi MIST: a user-friendly metabolic simulator Comput. Appl. Biosci. 11 1995 201 207
21. M.B. Elowitz, A.J. Levine, E.D. Siggia, and P.S. Swain Stochastic gene expression in a single cell Science 297 2002 1183 1186
22. L.B. Evans, and R.P. Field Bioprocess simulation: a new tool for process development Biotechnology 6 1988 200 203
23. J. Forster, I. Famili, P. Fu, B.O. Palsson, and J. Nielsen Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network Genome Res. 13 2003 244 253
24. L.L. Furge, and F.P. Guengerich Explanation of pre-steady-state kinetics and decreased burst amplitude of HIV-1 reverse transcriptase at sites of modified DNA bases with an additional, nonproductive enzyme-DNA-nucleotide complex Biochemistry 38 1999 4818 4825
25. T.D. Garvey, P. Lincoln, C.J. Pedersen, D. Martin, and M. Johnson BioSPICE: access to the most current computational tools for biologists OMICS 7 2003 411 420
26. E. Gasteiger, A. Gattiker, C. Hoogland, I. Ivanyi, R.D. Appel, and A. Bairoch ExPASy: the proteomics server for in-depth protein knowledge and analysis Nucl. Acids Res. 31 2003 3784 3788
27. E.D. Gilles Network theory for chemical processes Chem. Eng. Technol. 21 1998 121 132
28. D.T. Gillespie Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81 1977 2340 2361
29. M. Ginkel, A. Kremling, T. Nutsch, R. Rehner, and E.D. Gilles Modular modeling of cellular systems with ProMoT/Diva Bioinformatics 19 2003 1169 1176
30. I. Goryanin, T.C. Hodgman, and E. Selkov Mathematical simulation and analysis of cellular metabolism and regulation Bioinformatics 15 1999 749 758
31. S. Goto, Y. Okuno, M. Hattori, T. Nishioka, and M. Kanehisa LIGAND: database of chemical compounds and reactions in biological pathways Nucl. Acids Res. 30 2002 402 404
32. W. Gujer, M. Henze, T. Mino, and M.C.M. Loosdrecht Activated Sludge Model No. 3 Wat. Sci. Technol. 39 1999 183 193
33. M.A. Henson Dynamic modeling of microbial cell populations Curr. Opin. Biotechnol. 14 2003 460 467
34. B. Hernandez-Bermejo, V. Fairen, and A. Sorribas Power-law modeling based on least-squares minimization criteria Math. Biosci. 161 1999 83 94
35. M.H. Hoefnagel, M.J. Starrenburg, D.E. Martens, J. Hugenholtz, M. Kleerebezem, I.I. Van Swam, R. Bongers, H.V. Westerhoff, and J.L. Snoep Metabolic engineering of lactic acid bacteria, the combined approach: kinetic modelling, metabolic control and experimental analysis Microbiology 148 2002 1003 1013
36. C.G. Hocker Applying bifurcation theory to enzyme kinetics Methods Enzymol. 240 1994 781 816
37. M. Hucka, A. Finney, H.M. Sauro, H. Bolouri, J. Doyle, and H. Kitano The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology Pac. Symp. Biocomput. 2002 450 461
38. M. Hucka, A. Finney, H.M. Sauro, H. Bolouri, J.C. Doyle, H. Kitano, A.P. Arkin, B.J. Bornstein, D. Bray, A. Cornish-Bowden, A.A. Cuellar, S. Dronov, E.D. Gilles, M. Ginkel, V. Gor, I.I. Goryanin, W.J. Hedley, T.C. Hodgman, J.H. Hofmeyr, P.J. Hunter, N.S. Juty, J.L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L.M. Loew, D. Lucio, P. Mendes, E. Minch, E.D. Mjolsness, Y. Nakayama, M.R. Nelson, P.F. Nielsen, T. Sakurada, J.C. Schaff, B.E. Shapiro, T.S. Shimizu, H.D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang SBML Forum The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 19 2003 524 531
39. F. Hynne, S. Dano, and P.G. Sorensen Full-scale model of glycolysis in Saccharomyces cerevisiae Biophys. Chem. 94 2001 121 163
40. T. Ideker, T. Galitski, and L. Hood A new approach to decoding life: systems biology Annu. Rev. Genomics Hum. Genet. 2 2001 343 372
41. T. Ideker, V. Thorsson, J.A. Ranish, R. Christmas, J. Buhler, J.K. Eng, R. Bumgarner, D.R. Goodlett, R. Aebersold, and L. Hood Integrated genomic and proteomic analyses of a systematically perturbed metabolic network Science 292 2001 929 934
42. International Human Genome Sequencing Consortium, 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
43. J.W. Jeong, J. Snay, and M.M. Attai A mathematical model for examining growth and sporulation process of Bacillus subtilis Biotechnol. Bioeng. 35 1990 160 184
44. M. Kanehisa, S. Goto, S. Kawashima, and A. Nakaya The KEGG databases at GenomeNet Nucl. Acids Res. 30 2002 42 46
45. P.D. Karp, M. Riley, M. Saier, I.T. Paulsen, S.M. Paley, and A. Pellegrini-Toole The EcoCyc and MetaCyc databases Nucl. Acids Res. 28 2000 56 59
46. A. Khibnik, Y. Kuznetsov, V. Levitin, and E. Nikolaev Continuation techniques and interactive software for bifurcation analysis of ODEs and iterated maps Physica D 62 1993 164 168
47. A.M. Kierzek STOCKS: STOChastic kinetic simulations of biochemical systems with Gillespie algorithm Bioinformatics 18 2002 470 481
48. H. Kitano Perspectives on systems biology New Generation Comput. 18 2000 199 216
49. F. Kose, W. Weckwerth, T. Linke, and O. Fiehn Visualizing plant metabolomic correlation networks using clique-metabolite matrices Bioinformatics 17 2001 1198 1208
50. M. Kramer, J. Bongaerts, R. Bovenberg, S. Kremer, U. Muller, S. Orf, M. Wubbolts, and L. Raeven Metabolic engineering for microbial production of shikimic acid Metab. Eng. 5 2003 277 283
51. D.Y. Lee, H. Yun, S. Park, and S.Y. Lee MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis Bioinformatics 19 2003 2144 2146
52. L.M. Loew, and J.C. Schaff The virtual cell: a software environment for computational cell biology Trends Biotech. 19 2001 401 406
53. J. Makinia, M. Swinarski, and E. Dobiegala Experiences with computer simulation at two large wastewater treatment plants in northern Poland Wat. Sci. Technol. 45 2002 209 218
54. C.A. Mannella, D.R. Pfeiffer, P.C. Bradshaw, I.I. Moraru, B. Slepchenko, L.M. Loew, C.E. Hsieh, K. Buttle, and M. Marko Topology of the mitochondrial inner membrane: dynamics and bioenergetic implications IUBMB Life 52 2001 93 100
55. P. Mendes GEPASI: a software package for modeling the dynamics, steady states and control of biochemical and other systems Comput. Appl. Biosci. 1993 563 571
56. Mohl, K.D., Spieker, A., Kohler, R., Gilles, E.D., Zeitz, M., 1997. DIVA - A Simulation Environment for Chemical Engineering Applications. ICCS Collect. Vol. Sci. Pap. Donetsk State Techn. University, Ukraine.
57. J. Monod The growth of bacterial cultures Ann. Rev. Microbiol. 3 1949 371 394
58. N.L. Novere, and T.S. Shimizu StochSim: modeling of stochastic biomolecular processes Bioinformatics 17 2001 575 576
59. H. Ogata, S. Goto, K. Sato, W. Fujibuchi, H. Bono, and M. Kanehisa KEGG: Kyoto encyclopedia of genes and genomes Nucl. Acids Res. 27 1999 29 34
60. R. Overbeek, N. Larsen, G.D. Pusch, M. D'Souza, E. Selkov Jr., N. Kyrpides, M. Fonstein, N. Maltsev, and E. Selkov WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction Nucl. Acids Res. 28 2000 123 125
61. D. Petrides BioPro designer: an advanced computing environment for modeling and design biochemical processes Comput. Chem. Eng. 18 1994 S621 S625
62. L.R. Petzold Automatic selection of methods for solving stiff and nonstiff systems of ordinary differential equations SIAM J. Sci. Statist. Comput. 4 1983 136 148
63. J. Pramanik, and J.D. Keasling Stoichiometric model of Escherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements Biotechnol. Bioeng. 56 1997 398 421
64. J. Pramanik, and J.D. Keasling Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model Biotechnol. Bioeng. 60 1998 230 238
65. N.D. Price, J.A. Papin, C.H. Schilling, and B.O. Palsson Genome-scale microbial in silico models: the constraints-based approach Trends Biotechnol. 21 2003 162 169
66. J.L. Reed, and B.O. Palsson Thirteen years of building constraint-based in silico models of Escherichia coli J. Bacteriol. 185 2003 2692 2699
67. M. Rizzi, M. Baltes, U. Theobald, and M. Reuss In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae II. Mathematical model Biotechnol. Bioeng. 55 1997 592 608
68. J.M. Rohwer, P.W. Postma, B.N. Kholodenko, and H.V. Westerhoff Implications of macromolecular crowding for signal transduction and metabolite channeling Proc. Natl. Acad. Sci. U.S.A. 95 1998 10547 10552
69. H.M. Sauro SCAMP: a general-purpose simulator and metabolic control analysis program Comput. Appl. Biosci. 9 1993 441 450
70. S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin Interpolated Markov models for eukaryotic gene finding Genomics 59 1999 24 31
71. C.H. Schilling, J.S. Edwards, and B.O. Palsson Toward metabolic phenomics: analysis of genomic data using flux balances Biotechnol. Prog. 15 1999 288 295
72. C.H. Schilling, M.W. Covert, I. Famili, G.M. Church, J.S. Edwards, and B.O. Palsson Genome-scale metabolic model of Helicobacter pylori 26695 J. Bacteriol. 184 2002 4582 4593
73. I. Schomburg, A. Chang, O. Hofmann, C. Ebeling, F. Ehrentreich, and D. Schomburg BRENDA: a resource for enzyme data and metabolic information Trends Biochem. Sci. 27 2002 54 56
74. E. Selkov, S. Basmanova, T. Gaasterland, I. Goryanin, Y. Gretchkin, N. Maltsev, V. Nenashev, R. Overbeek, E. Panyushkina, L. Pronevitch, E. Selkov Jr., and I. Yunus The metabolic pathway collection from EMP: the enzymes and metabolic pathways database Nucl. Acids Res. 24 1996 26 28
75. T.S. Shimizu, and D. Bray Modelling the bacterial chemotaxis receptor complex Novartis Found Symp. 247 2002 162 177
76. F. Shiraishi, and M.A. Savageau The tricarboxylic acid cycle in Dictyostelium discoideum I. Formulation of alternative kinetic representations J. Biol. Chem. 267 1992 22912 22918
77. B.M. Slepchenko, J.C. Schaff, I. Macara, and L.M. Loew Quantitative cell biology with the virtual cell Trends Cell Biol. 13 2003 570 576
78. T. Soga, Y. Ueno, H. Naraoka, Y. Ohashi, M. Tomita, and T. Nishioka Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry Anal. Chem. 74 2002 2233 2239
79. T. Soga, Y. Ueno, H. Naraoka, K. Matsuda, M. Tomita, and T. Nishioka Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions Anal. Chem. 74 2002 6224 6229
80. T. Soga, Y. Ohashi, Y. Ueno, H. Naraoka, M. Tomita, and T. Nishioka Quantitative metabolome analysis using capillary electrophoresis Mass spectrometry J. Proteome Res. 2 2003 488 494
81. G. Stephanopoulos, and J.J. Vallino Network rigidity and metabolic engineering in metabolite overproduction Science 252 1991 1675 1681
82. G. Stoesser, W. Baker, A. van den Broek, M. Garcia-Pastor, C. Kanz, T. Kulikova, R. Leinonen, Q. Lin, V. Lombard, R. Lopez, R. Mancuso, F. Nardone, P. Stoehr, M.A. Tuli, K. Tzouvara, and R. Vaughan The EMBL nucleotide sequence database: major new developments Nucl. Acids Res. 31 2003 17 22
83. W.R. Strohl Biochemical engineering of natural product biosynthesis pathways Metab. Eng. 3 2001 4 14
84. K. Takahashi, K. Yugi, K. Hashimoto, Y. Yamada, C. Pickett, and M. Tomita Computational challenges in cell simulation IEEE Intell. Syst. 17 2002 64 71
85. K. Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta, A. Shiozawa, F. Miyoshi, Y. Naito, Y. Nakayama, and M. Tomita E-Cell 2: multi-platform E-Cell simulation system Bioinformatics 19 2003 1727 1729
86. K. Takahashi, K. Kaizu, B. Hu, and M. Tomita A multi-algorithm, multi-timescale method for cell simulation Bioinformatics 20 2004 538 546
87. R.L. Tatusov, D.A. Natale, I.V. Garkavtsev, T.A. Tatusova, U.T. Shankavaram, B.S. Rao, B. Kiryutin, M.Y. Galperin, N.D. Fedorova, and E.V. Koonin The COG database: new developments in phylogenetic classification of proteins from complete genomes Nucl. Acids Res. 29 2001 22 28
88. U. Theobald, W. Mailinger, M. Baltes, M. Rizzi, and M. Reuss In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae I. Experimental observations Biotechnol. Bioeng. 55 1997 305 316
89. J. Thykaer, and J. Nielsen Metabolic engineering of beta-lactam production Metab. Eng. 5 2003 56 69
90. M. Tomita, K. Hashimoto, K. Takahashi, T.S. Shimizu, Y. Matsuzaki, F. Miyoshi, K. Saito, S. Tanida, K. Yugi, J.C. Venter, and C.A. Hutchison 3rd E-CELL: software environment for whole-cell simulation Bioinformatics 15 1999 72 84
91. M. Tomita Whole-cell simulation: a grand challenge of the 21st century Trends Biotechnol. 19 2001 205 210
92. M. Tomita Towards computer aided design (CAD) of useful microorganisms Bioinformatics 17 2001 1091 1092
93. J.D. Varner Large-scale prediction of phenotype: concept Biotechnol. Bioeng. 69 2000 664 678
94. S. Vaseghi, A. Baumeister, M. Rizzi, and M. Reuss In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae Metab. Eng. 1 1999 128 140
95. C. Venter The sequence of the human genome Science 291 2001 1304 1351
96. J. Villadsen, and M.L. Michelesen Solution of Differential Equation Models by Polynomial Approximation 1978 Prentice-Hall Englewood Cliffs
97. R. Weinberg, and M. Berkus Computer stimulation of a living cell I. Int. J. Biomed. Comput. 2 1971 95 120
98. R. Weinberg, and M. Berkus Computer simulation of a living cell II. Int. J. Biomed. Comput. 2 1971 167 188
99. W. Wiechert Modeling and simulation: tools for metabolic engineering J. Biotechnol. 94 2002 37 63
100. B.P. Zeigler, and R. Weinberg System theoretic analysis of models: computer simulation of a living cell J. Theor. Biol. 29 1970 35 56