Dynamic modeling of metabolic and gene regulatory systems toward developing virtual microbes

Journal of Chemical Engineering of Japan

Volumn 47, Issue 1, 2014, Pages 1-9

  Kurata, Hiroyuki ^a   Maeda, Kazuhiro ^a   Matsuoka, Yu ^a  

^a KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Biochemical Network; Computer Simulation; Design; Dynamic Models

Indexed keywords

BIOCHEMICAL NETWORK; CRITICAL PROBLEMS; CULTURE CONDITIONS; GENETIC MODIFICATIONS; HIGH DIMENSIONALITY; PARAMETER UNCERTAINTY; REALISTIC PROJECTS; REGULATORY SYSTEMS;

BACTERIA; COMPUTER SIMULATION; DESIGN; DYNAMIC MODELS; METABOLISM;

COMPLEX NETWORKS;

EID: 84892734889     PISSN: 00219592     EISSN: None     Source Type: Journal    
DOI: 10.1252/jcej.13we152     Document Type: Review

References (71)

1. Asprey, S. P. and Y. Naka; "Mathematical Problems in Fitting Kinetic Models-Some New Perspectives, " J. Chem. Eng. Japan, 32, 328-337 (1999)
2. Ball, P.; "Synthetic Biology: Designs for Life, " Nature, 448, 32-33 (2007)
3. Banga, J. R.; "Optimization in Computational Systems Biology, " BMC Syst. Biol., 2, 47 (2008)
4. Banga, J. R. and E. Balsa-Canto; "Parameter Estimation and Optimal Experimental Design, " Essays Biochem., 45, 195-210 (2008)
5. Bates, D. G. and C. Cosentino; "Validation and Invalidation of Systems Biology Models Using Robustness Analysis, " IET Syst. Biol., 5, 229-244 (2011)
6. Bettenbrock, K., S. Fischer, A. Kremling, K. Jahreis, T. Sauter and E. D. Gilles; "A Quantitative Approach to Catabolite Repression in Escherichia coli, " J. Biol. Chem., 281, 2578-2584 (2006)
7. Bhalla, U. S. and R. Iyengar; "Emergent Properties of Networks of Biological Signaling Pathways, " Science, 283, 381-387 (1999)
8. Bhattacharjya, A. and S. Liang; "Power-Law Distributions in Some Random Boolean Networks, " Phys. Rev. Lett., 77, 1644-1647 (1996)
9. Bruggeman, F. J., F. C. Boogerd and H. V. Westerhoff; "The Multifarious Short-Term Regulation of Ammonium Assimilation of Escherichia coli: Dissection Using an in Silico Replica, " FEBS J., 272, 1965-1985 (2005)
10. Ceschia, S. and A. Schaerf; "Modeling and Solving the Dynamic Patient Admission Scheduling Problem under Uncertainty, " Artif. Intell. Med., 56, 199-205 (2012)
11. Chang, A., M. Scheer, A. Grote, I. Schomburg and D. Schomburg; "BRENDA, AMENDA and FRENDA the Enzyme Information System: New Content and Tools in 2009, " Nucleic Acids Res., 37(Database issue), D588-D592 (2009)
12. Chassagnole, C., N. Noisommit-Rizzi, J. W. Schmid, K. Mauch and M. Reuss; "Dynamic Modeling of the Central Carbon Metabolism of Escherichia coli, " Biotechnol. Bioeng., 79, 53-73 (2002)
13. Covert, M. W., C. H. Schilling, I. Famili, J. S. Edwards, E. Goryanin II, E. Selkov and B. O. Palsson; "Metabolic Modeling of Microbial Strains in Silico, " Trends Biochem. Sci., 26, 179-186 (2001)
14. Doucette, C. D., D. J. Schwab, N. S. Wingreen and J. D. Rabinowitz; "α-Ketoglutarate Coordinates Carbon and Nitrogen Utilization via Enzyme I Inhibition, " Nat. Chem. Biol., 7, 894-901 (2011)
15. Drubin, D. A., J. C. Way and P. A. Silver; "Designing Biological Systems, " Genes Dev., 21, 242-254 (2007)
16. Elowitz, M. and W. A. Lim; "Build Life to Understand It, " Nature, 468, 889-890 (2010)
17. Gama-Castro, S., V. Jimenez-Jacinto, M. Peralta-Gil, A. Santos-Zavaleta, M. I. Penaloza-Spinola, B. Contreras-Moreira, J. Segura-Salazar, L. Muniz-Rascado, I. Martinez-Flores, H. Salgado, C. Bonavides-Martinez, C. Abreu-Goodger, C. Rodriguez-Penagos, J. Miranda-Rios, E. Morett, E. Merino, A. M. Huerta, L. Trevino-Quintanilla and J. Collado-Vides; "RegulonDB (version 6.0): Gene Regulation Model of Escherichia coli K-12 beyond Transcription, Active (Experimental) Annotated Promoters and Textpresso Navigation, " Nucleic Acids Res., 36(Database issue), D120-D124 (2008)
18. Hakamada, K., T. Hanai, H. Honda and T. Kobayashi; "Preprocessing Method for Inferring Genetic Interaction from Gene Expression Data Using Boolean Algorithm, " J. Biosci. Bioeng., 98, 457-463 (2004)
19. Inoue, K., K. Maeda, Y. Kato, S. Tonami, S. Takagi and H. Kurata; "CADLIVE Optimizer: Web-Based Parameter Estimation for Dynamic Models, " Source Code Biol. Med., 7, 9 (2012)
20. Jaqaman, K. and G. Danuser; "Linking Data to Models: Data Regression, " Nat. Rev. Mol. Cell Biol., 7, 813-819 (2006)
21. Ji, X. and Y. Xu; "libSRES: a C Library for Stochastic Ranking Evolution Strategy for Parameter Estimation, " Bioinformatics, 22, 124-126 (2006)
22. Kadir, T. A., A. A. Mannan, A. M. Kierzek, J. McFadden and K. Shimizu; "Modeling and Simulation of the Main Metabolism in Escherichia coli and Its Several Single-Gene Knockout Mutants with Experimental Verification, " Microb. Cell Fact., 9, 88 (2010)
23. Kanehisa, M., S. Goto, S. Kawashima and A. Nakaya; "The KEGG Databases at GenomeNet, " Nucleic Acids Res., 30, 42-46 (2002)
24. Karr, J. R., J. C. Sanghvi, D. N. Macklin, M. V. Gutschow, J. M. Jacobs, B. Bolival Jr., N. Assad-Garcia, J. I. Glass and M. W. Covert; "A Whole-Cell Computational Model Predicts Phenotype from Genotype, " Cell, 150, 389-401 (2012)
25. Katsuda, T. and T. Maruyama; "Chemical-Kinetics Model for the Growth of a Multicellular Tumor Spheroid, " J. Chem. Eng. Japan, 42, 198-203 (2009)
26. Kauffman, S. A.; The Origin of Order, Self-Organization and Selection in Evolution, Oxford University Press, Oxford, U.S.A. (1993)
27. Kimura, S., K. Ide, A. Kashihara, M. Kano, M. Hatakeyama, R. Masui, N. Nakagawa, S. Yokoyama, S. Kuramitsu and A. Konagaya; "Inference of S-System Models of Genetic Networks Using a Cooperative Coevolutionary Algorithm, " Bioinformatics, 21, 1154-1163 (2005)
28. Koh, G., H. F. Teong, M. V. Clement, D. Hsu and P. S. Thiagarajan; "A Decompositional Approach to Parameter Estimation in Pathway Modeling: A Case Study of the Akt and MAPK Pathways and Their Crosstalk, " Bioinformatics, 22, e271-e280 (2006)
29. Kotte, O., J. B. Zaugg and M. Heinemann; "Bacterial Adaptation through Distributed Sensing of Metabolic Fluxes, " Mol. Syst. Biol., 6, 355 (2010)
30. Kremling, A. and E. D. Gilles; "The Organization of Metabolic Reaction Networks. II. Signal Processing in Hierarchical Structured Functional Units, " Metab. Eng., 3, 138-150 (2001)
31. Kremling, A., K. Jahreis, J. W. Lengeler and E. D. Gilles; "The Organization of Metabolic Reaction Networks: A Signal-Oriented Approach to Cellular Models, " Metab. Eng., 2, 190-200 (2000)
32. Kremling, A., K. Bettenbrock, B. Laube, K. Jahreis, J. W. Lengeler and E. D. Gilles; "The Organization of Metabolic Reaction Networks. III. Application for Diauxic Growth on Glucose and Lactose, " Metab. Eng., 3, 362-379 (2001)
33. Kurata, H., N. Matoba and N. Shimizu; "CADLIVE for Constructing a Large-Scale Biochemical Network Based on a Simulation-Directed Notation and Its Application to Yeast Cell Cycle, " Nucleic Acids Res., 31, 4071-4084 (2003)
34. Kurata, H., K. Masaki, Y. Sumida and R. Iwasaki; "CADLIVE Dynamic Simulator: Direct Link of Biochemical Networks to Dynamic Models, " Genome Res., 15, 590-600 (2005)
35. Kurata, H., T. Tanaka and F. Ohnishi; "Mathematical Identification of Critical Reactions in the Interlocked Feedback Model, " PLOS ONE, 2, e1103 (2007)
36. Le Novere, N., B. Bornstein, A. Broicher, M. Courtot, M. Donizelli, H. Dharuri, L. Li, H. Sauro, M. Schilstra, B. Shapiro, J. L. Snoep and M. Hucka; "BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems, " Nucleic Acids Res., 34(Database issue), D689-D691 (2006)
37. Li, C., M. Courtot, N. Le Novere and C. Laibe; "BioModels. net Web Services, a Free and Integrated Toolkit for Computational Modelling Software, " Brief. Bioinform., 11, 270-277 (2010)
38. Lillacci, G. and M. Khammash; "Parameter Estimation and Model Selection in Computational Biology, " PLOS Comput. Biol., 6, e1000696 (2010)
39. Liu, X., J. Jiang, O. Ajayi, X. Gu, D. Gilbert and R. Sinnott; "BioNessie(G)-A Grid Enabled Biochemical Networks Simulation Environment, " Stud. Health Technol. Inform., 138, 147-157 (2008)
40. Ma, H., F. C. Boogerd and I. Goryanin; "Modelling Nitrogen Assimilation of Escherichia coli at Low Ammonium Concentration, " J. Biotechnol., 144, 175-183 (2009)
41. Maeda, K. and H. Kurata; "Two-Phase Search (TPS) Method: Nonbiased and High-Speed Parameter Search for Dynamic Models of Biochemical Networks, " IPSJ Transaction on Bioinformatics, 2, 2-14 (2009)
42. Maeda, K. and H. Kurata; "Quasi-Multiparameter Sensitivity Measure for Robustness Analysis of Complex Biochemical Networks, " J. Theor. Biol., 272, 174-186 (2011)
43. Maeda, K., Y. Fukano, S. Yamamichi, D. Nitta and H. Kurata; "An Integrative and Practical Evolutionary Optimization for a Complex, Dynamic Model of Biological Networks, " Bioprocess Biosyst. Eng., 34, 433-446 (2011)
44. Maeda, K., H. Minamida, K. Yoshida and H. Kurata; "Flux Module Decomposition for Parameter Estimation in a Multiple-Feedback Loop Model of Biochemical Networks, " Bioprocess Biosyst. Eng., 36, 333-344 (2013)
45. Masaki, K., K. Maeda and H. Kurata; "Biological Design Principles of Complex Feedback Modules in the E. coli Ammonia Assimilation System, " Artif. Life, 18, 53-90 (2012)
46. Matsuno, H., Y. Tanaka, H. Aoshima, A. Doi, M. Matsui and S. Miyano; "Biopathways Representation and Simulation on Hybrid Functional Petri Net, " In Silico Biol., 3, 389-404 (2003)
47. Mendes, P. and D. Kell; "Non-Linear Optimization of Biochemical Pathways: Applications to Metabolic Engineering and Parameter Estimation, " Bioinformatics, 14, 869-883 (1998)
48. Moles, C. G., P. Mendes and J. R. Banga; "Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods, " Genome Res., 13, 2467-2474 (2003)
49. Murabito, E., K. Smallbone, J. Swinton, H. V. Westerhoff and R. Steuer; "A Probabilistic Approach to Identify Putative Drug Targets in Biochemical Networks, " J. R. Soc. Interface, 8, 880-895 (2011)
50. Nishio, Y., Y. Usuda, K. Matsui and H. Kurata; "Computer-Aided Rational Eesign of the Phosphotransferase System for Enhanced Glucose Uptake in Escherichia coli, " Mol. Syst. Biol., 4, 160 (2008)
51. Olivier, B. G. and J. L. Snoep; "Web-Based Kinetic Modelling Using JWS Online, " Bioinformatics, 20, 2143-2144 (2004)
52. Quinton-Tulloch, M. J., F. J. Bruggeman, J. L. Snoep and H. V. Westerhoff; "Trade-off of Dynamic Fragility but not of Robustness in Metabolic Pathways in Silico, " FEBS J., 280, 160-173 (2013)
53. Rizzi, M., M. Baltes, U. Theobald and M. Reuss; "In vivo Analysis of Metabolic Dynamics in Saccharomyces cerevisiae: II. Mathematical Model, " Biotechnol. Bioeng., 55, 592-608 (1997)
54. Rodriguez-Fernandez, M., J. A. Egea and J. R. Banga; "Novel Metaheuristic for Parameter Estimation in Nonlinear Dynamic Biological Systems, " BMC Bioinformatics, 7, 483 (2006)
55. Schacherer, F., C. Choi, U. Gotze, M. Krull, S. Pistor and E. Wingender; "The TRANSPATH Signal Transduction Database: A Knowledge Base on Signal Transduction Networks, " Bioinformatics, 17, 1053-1057 (2001)
56. Schmid, J. W., K. Mauch, M. Reuss, E. D. Gilles and A. Kremling; "Metabolic Design Based on a Coupled Gene Expression-Metabolic Network Model of Tryptophan Production in Escherichia coli, " Metab. Eng., 6, 364-377 (2004)
57. Schomburg, I., A. Chang and D. Schomburg; "BRENDA, Enzyme Data and Metabolic Information, " Nucleic Acids Res., 30, 47-49 (2002)
58. Schuster, S., T. Dandekar and D. A. Fell; "Detection of Elementary Flux Modes in Biochemical Networks: A Promising Tool for Pathway Analysis and Metabolic Engineering, " Trends Biotechnol., 17, 53-60 (1999)
59. Stelling, J., U. Sauer, Z. Szallasi, F. J. Doyle 3rd and J. Doyle; "Robustness of Cellular Functions, " Cell, 118, 675-685 (2004)
60. Sun, D.-Y. and C.-L. Chen; "An Algorithm for Optimizing the Unsteady Chemical Processes by Simulated Annealing, " J. Chem. Eng. Japan, 37, 711-722 (2004)
61. Takahashi, H., S. Tomida, T. Kobayashi and H. Honda; "Inference of Common Genetic Network Using Fuzzy Adaptive Resonance Theory Associated Matrix Method, " J. Biosci. Bioeng., 96, 154-160 (2003)
62. Transtrum, M. K. and P. Qiu; "Optimal Experiment Selection for Parameter Estimation in Biological Differential Equation Models, " BMC Bioinformatics, 13, 181 (2012)
63. Usuda, Y., Y. Nishio, S. Iwatani, S. J. Van Dien, A. Imaizumi, K. Shimbo, N. Kageyama, D. Iwahata, H. Miyano and K. Matsui; "Dynamic Modeling of Escherichia coli Metabolic and Regulatory Systems for Amino-Acid Production, " J. Biotechnol., 147, 17-30 (2010)
64. van Riel, N. A. and E. D. Sontag; "Parameter Estimation in Models Combining Signal Transduction and Metabolic Pathways: The Dependent Input Approach, " Syst. Biol., 153, 263-274 (2006), Stevenage
65. Vaseghi, S., A. Baumeister, M. Rizzi and M. Reuss; "In vivo Dynamics of the Pentose Phosphate Pathway in Saccharomyces cerevisiae, " Metab. Eng., 1, 128-140 (1999)
66. Voit, E. O. and J. Almeida; "Decoupling Dynamical Systems for Pathway Identification from Metabolic Profiles, " Bioinformatics, 20, 1670-1681 (2004)
67. Wagner, A.; "Circuit Topology and the Evolution of Robustness in Two-Gene Circadian Oscillators, " Proc. Natl. Acad. Sci. U.S.A., 102, 11775-11780 (2005)
68. Westerhoff, H. V., C. Winder, H. Messiha, E. Simeonidis, M. Adamczyk, M. Verma, F. J. Bruggeman and W. Dunn; "Systems Biology: The Elements and Principles of Life, " FEBS Lett., 583, 3882-3890 (2009)
69. Wittig, U., R. Kania, M. Golebiewski, M. Rey, L. Shi, L. Jong, E. Algaa, A. Weidemann, H. Sauer-Danzwith, S. Mir, O. Krebs, M. Bittkowski, E. Wetsch, I. Rojas and W. Muller; "SABIO-RK-Database for Biochemical Reaction Kinetics, " Nucleic Acids Res., 40(Database issue), D790-D796 (2012)
70. Yuan, J., C. D. Doucette, W. U. Fowler, X. J. Feng, M. Piazza, H. A. Rabitz, N. S. Wingreen and J. D. Rabinowitz; "Metabolomics-Driven Quantitative Analysis of Ammonia Assimilation in E. coli, " Mol. Syst. Biol., 5, 302 (2009)
71. Zi, Z. and E. Klipp; "SBML-PET: a Systems Biology Markup Language-Based Parameter Estimation Tool, " Bioinformatics, 22, 2704-2705 (2006)