Mechanistic pathway modeling for industrial biotechnology: Challenging but worthwhile

Current Opinion in Biotechnology

Volumn 22, Issue 5, 2011, Pages 604-610

  Wiechert, Wolfgang ^a   Noack, Stephan ^a  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL NETWORK; BIOCHEMICAL PATHWAY; BIOPROCESS DEVELOPMENT; CENTRAL PROBLEMS; ENZYME INHIBITORS; INDUSTRIAL BIOTECHNOLOGY; MECHANISTIC MODELS; MECHANISTIC PATHWAYS; METABOLIC NETWORK; MODELING APPLICATIONS; NETWORK STRUCTURES; STEADY STATE; SYSTEMS BIOLOGY;

BIOTECHNOLOGY; STOICHIOMETRY;

REACTION KINETICS;

ENZYME ACTIVATOR; ENZYME INHIBITOR;

BIOTECHNOLOGY; CHEMICAL ANALYSIS; CHEMICAL REACTION; EXPERIMENT; GENOME; INDUSTRIAL BIOTECHNOLOGY; MECHANISTIC MODEL; METABOLISM; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM; REVIEW; STOICHIOMETRY; VALIDATION STUDY;

BIOTECHNOLOGY; ENZYMES; GENE EXPRESSION REGULATION; KINETICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY;

EID: 80053384558     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2011.01.001     Document Type: Review

References (57)

1. Demin O., Goryanin I. Kinetic Modeling in Systems Biology 2009, Chapman & Hall/CRC.
2. Richardson R.C., Stephan A. Mechanism and mechanical explanation in cell biology. Systems Biology-Philosophical Foundations 2007, Elsevier. F. Boogerd, F.J. Bruggeman, J.-H.S. Hofmeyr, H.V. Westerhoff (Eds.).
3. Jamshidi N., Palsson B.O. Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol 2008, 4:171.
4. Smallbone K., Simeonidis E., Swainston N., Mendes P. Towards a genome-scale kinetic model of cellular metabolism. BMC Syst Biol 2010, 4:6.
5. Li C., Donizelli M., Rodriguez N., Dharuri H., Endler L., Chelliah V., Li L., He E., Henry A., Stefan M.I., et al. BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010, 4:92.
6. van Gend C., Conradie R., du Preez F.B., Snoep J.L. Data and model integration using JWS Online. In Silico Biol 2007, 7:S27-35.
7. Klipp E., Liebermeister W., Helbig A., Kowald A., Schaber J. Systems biology standards-the community speaks. Nat Biotechnol 2007, 25:390-391.
8. Wiechert W., Noack S., Elsheikh A. Modeling languages for biochemical network simulation: reaction vs equation based approaches. Adv Biochem Eng Biotechnol 2010, 121:109-138.
9. Liebermeister W., Baur U., Klipp E. Biochemical network models simplified by balanced truncation. FEBS J 2005, 272:4034-4043.
10. Chassagnole C., Noisommit-Rizzi N., Schmid J.W., Mauch K., Reuss M. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 2002, 79:53-73.
11. Beard D.A., Qian H. Chemical Biophysics: Quantitative Analysis of Cellular Systems 2008, Cambridge University Press.
12. Soh K.C., Hatzimanikatis V. Network thermodynamics in the post-genomic era. Curr Opin Microbiol 2010, 13:350-357.
13. Petersen S., von Lieres E., Wiechert W., de Graaf A.A. A multi-scale approach for the predictive modeling of metabolic regulation. In Metabolic Engineering in a Post Genomic Era 2003, vol 10. Horizon Scientific Press.
14. Young J.D., Henne K.L., Morgan J.A., Konopka A.E., Ramkrishna D. Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control. Biotechnol Bioeng 2008, 100:542-559.
15. Schuetz R., Kuepfer L., Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 2007, 3:119.
16. Snoep J.L., Bruggeman F., Olivier B.G., Westerhoff H.V. Towards building the silicon cell: a modular approach. Biosystems 2006, 83:207-216.
17. Bevilacqua A., Wilkinson S.J., Dimelow R., Murabito E., Rehman S., Nardelli M., van Eunen K., Rossell S., Bruggeman F.J., Bluthgen N., et al. Vertical systems biology: from DNA to flux and back. SEB Exp Biol Ser 2008, 61:65-91.
18. Bettenbrock K., Fischer S., Kremling A., Jahreis K., Sauter T., Gilles E.D. A quantitative approach to catabolite repression in Escherichia coli. J Biol Chem 2006, 281:2578-2584.
19. Kotte O., Zaugg J.B., Heinemann M. Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 2010, 6.
20. Usuda Y., Nishio Y., Iwatani S., Van Dien S.J., Imaizumi A., Shimbo K., Kageyama N., Iwahata D., Miyano H., Matsui K. Dynamic modeling of Escherichia coli metabolic and regulatory systems for amino-acid production. J Biotechnol 2010, 147:17-30.
21. Nikolaev E.V. The elucidation of metabolic pathways and their improvements using stable optimization of large-scale kinetic models of cellular systems. Metab Eng 2010, 12:26-38.
22. Douma R.D., Verheijen P.J.T., de Laat W.T.A.M., Heijnen J.J., van Gulik W.M. Dynamic gene expression regulation model for growth and penicillin production in Penicillium chrysogenum. Biotechnol Bioeng 2010, 106:608-618.
23. Thiele I., Jamshidi N., Fleming R.M., Palsson B.O. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol 2009, 5:e1000312.
24. Polynikis A., Hogan S.J., di Bernardo M. Comparing different ODE modelling approaches for gene regulatory networks. J Theor Biol 2009, 261:511-530.
25. Hardiman T., Meinhold H., Hofmann J., Ewald J.C., Siemann-Herzberg M., Reuss M. Prediction of kinetic parameters from DNA-binding site sequences for modeling global transcription dynamics in Escherichia coli. Metab Eng 2010, 12:196-211.
26. Salis H.M., Mirsky E.A., Voigt C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 2009, 27:946-950.
27. Lindsley J.E., Rutter J. Whence cometh the allosterome?. Proc Natl Acad Sci U S A 2006, 103:10533-10535.
28. Wahl S.A., Haunschild M.D., Oldiges M., Wiechert W. Unravelling the regulatory structure of biochemical networks using stimulus response experiments and large-scale model selection. IEE Proc Syst Biol 2006, 153:275-285.
29. van Eunen K., Bouwman J., Daran-Lapujade P., Postmus J., Canelas A.B., Mensonides F.I.C., Orij R., Tuzun I., van den Brink J., Smits G.J., et al. Measuring enzyme activities under standardized in vivo-like conditions for systems biology. FEBS J 2010, 277:749-760.
30. Schaub J., Reuss M. In vivo dynamics of glycolysis in Escherichia coli shows need for growth-rate dependent metabolome analysis. Biotechnol Prog 2008, 24:1402-1407.
31. Ishii N., Tomita M. Multi-omics data-driven systems biology of E. coli. Systems Biology and Biotechnology of Escherichia coli 2009, 41-57. Springer. S.Y. Lee (Ed.).
32. Kim T.Y., Kim H.U., Lee S.Y. Data integration and analysis of biological networks. Curr Opin Biotechnol 2010, 21:78-84.
33. Gibon Y., Blaesing O.E., Hannemann J., Carillo P., Hohne M., Hendriks J.H., Palacios N., Cross J., Selbig J., Stitt M. A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. Plant Cell 2004, 16:3304-3325.
34. Lara A.R., Taymaz-Nikerel H., Mashego M.R., van Gulik W.M., Heijnen J.J., Ramirez O.T., van Winden W.A. Fast dynamic response of the fermentative metabolism of Escherichia coli to aerobic and anaerobic glucose pulses. Biotechnol Bioeng 2009, 104:1153-1161.
35. Wahl S.A., Noh K., Wiechert W. C-13 labeling experiments at metabolic nonstationary conditions: an exploratory study. BMC Bioinform 2008, 9:152.
36. Selivanov V.A., Puigjaner J., Sillero A., Centelles J.J., Ramos-Montoya A., Lee P.W., Cascante M. An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites. Bioinformatics 2004, 20:3387-3397.
37. Heijnen J.J. Approximative kinetic formats used in metabolic network modeling. Biotechnol Bioeng 2005, 91:534-545.
38. Machina A., Ponosov A., Voit E.O. Automated piecewise power-law modeling of biological systems. J Biotechnol 2010, 149:154-165.
39. Liebermeister W., Uhlendorf J., Klipp E. Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation. Bioinformatics 2010, 26:1528-1534.
40. Lee L.W., Yin L., Zhu X.M., Ao P. Generic enzymatic rate equation under living conditions. J Biol Syst 2007, 15:495-514.
41. Hadlich F., Noack S., Wiechert W. Translating biochemical network models between different kinetic formats. Metab Eng 2009, 11:87-100.
42. Drager A., Kronfeld M., Ziller M.J., Supper J., Planatscher H., Magnus J.B., Oldiges M., Kohlbacher O., Zell A. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst Biol 2009, 3:5.
43. Ederer M., Gilles E.D. Thermodynamic constraints in kinetic modeling: thermodynamic-kinetic modeling in comparison to other approaches. Eng Life Sci 2008, 8:467-476.
44. Nikerel I.E., van Winden W.A., van Gulik W.M., Heijnen J.J. A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics. BMC Bioinform 2006, 7.
45. Nikerel I.E., van Winden W.A., Verheijen P.J.T., Heijnen J.J. Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics. Metab Eng 2009, 11:20-30.
46. Degenring D., Froemel C., Dikta G., Takors R. Sensitivity analysis for the reduction of complex metabolism models. J Process Control 2004, 14:729-745.
47. Gutenkunst R.N., Waterfall J.J., Casey F.P., Brown K.S., Myers C.R., Sethna J.P. Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol 2007, 3:1871-1878.
48. Miskovic L., Hatzimanikatis V. Modeling of uncertainties in biochemical reactions. Biotechnol Bioeng 2011, 108:413-423.
49. Rizk M.L., Liao J.C. Ensemble modeling for aromatic production in Escherichia coli. PLoS ONE 2009, 4:e6903.
50. Joshi M., Seidel-Morgenstern A., Kremling A. Exploiting the bootstrap method for quantifying parameter confidence intervals in dynamical systems. Metab Eng 2006, 8:447-455.
51. Zavrel M., Schmidt T., Michalik C., Ansorge-Schumacher M., Marquardt W., Buchs J., Spiess A.C. Mechanistic kinetic model for symmetric carboligations using benzaldehyde lyase. Biotechnol Bioeng 2008, 101:27-38.
52. Schenkendorf R., Kremling A., Mangold M. Optimal experimental design with the sigma point method. IET Syst Biol 2009, 3:10-23.
53. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., Datsenko K.A., Tomita M., Wanner B.L., Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006, 2. 2006 0008.
54. Nevoigt E., Fischer C., Mucha O., Matthaus F., Stahl U., Stephanopoulos G. Engineering promoter regulation. Biotechnol Bioeng 2007, 96:550-558.
55. Noack S., Wahl A., Qeli E., Wiechert W. Visualizing regulatory interactions in metabolic networks. BMC Biol 2007, 5:46.
56. Teusink B., Passarge J., Reijenga C.A., Esgalhado E., van der Weijden C.C., Schepper M., Walsh M.C., Bakker B.M., van Dam K., Westerhoff H.V., et al. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 2000, 267:5313-5329.
57. McGuffee S.R., Elcock A.H. Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol 2010, 6:e1000694.