Towards the engineering of in vitro systems

Journal of the Royal Society Interface

Volumn 6, Issue SUPPL. 4, 2009, Pages

  Hold, Christoph ^a   Panke, Sven ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Enzymatic reaction network; Glycolysis; In vitro systems

Indexed keywords

BIOLOGICAL SYSTEMS; ENZYME KINETICS; PATHOLOGY;

DESIGN PARAMETERS; ENZYMATIC REACTION; ENZYMATIC REACTION NETWORK; GLYCOLYSIS; IN VITRO SYSTEMS; IN-VITRO; LIVING CELL; LIVING SYSTEMS; PARAMETER SPACES; RATIONAL DESIGN; SIMPLE SYSTEM; STEPPING STONE; SYNTHETIC BIOLOGY; TIME INVARIANTS;

REACTION KINETICS;

DNA FRAGMENT; ENZYME;

BIOENGINEERING; BIOLOGY; DNA SYNTHESIS; ENZYME KINETICS; ENZYME MECHANISM; ESCHERICHIA COLI; GLYCOLYSIS; IN VITRO STUDY; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NONHUMAN; REVIEW; SACCHAROMYCES CEREVISIAE; SYNTHETIC BIOLOGY;

EID: 67650660306     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2009.0110.focus     Document Type: Review

References (106)

1. Adler, J., Hazelbauer, G. L. & Dahl, M. M. 1973 Chemotaxis toward sugars in Escherichia coli. J. Bacteriol. 115, 824-847.
2. Alber, T., Banner, D. W., Bloomer, A. C., Petsko, G. A., Phillips, D., Rivers, P. S. & Wilson, I. A. 1981 On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase. Phil. Trans. R. Soc. Lond. B Biol. Sci. 293, 159-171. (doi:10.1098/rstb.1981.0069)
3. Albert, M. A., Haanstra, J. R., Hannaert, V., Van Roy, J., Opperdoes, F. R., Bakker, B. M. & Michels, P. A. 2005 Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei. J. Biol. Chem. 280, 28 306-28 315. (doi:10.1074/jbc. M502403200)
4. Anderson, J. C., Clarke, E. J., Arkin, A. P. & Voigt, C. A. 2006 Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355, 619-627. (doi:10.1016/j.jmb.2005.10.076)
5. Arnold, S., Siemann-Herzberg, M., Schmid, J. & Reuss, M. 2005 Model-based inference of gene expression dynamics from sequence information. Adv. Biochem. Eng. Biotechnol. 100, 89-179. (doi:10.1007/b136414)
6. Baldwin, S. A. & Perham, R. N. 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. (Pubitemid 8281769)
7. Bali, M. & Thomas, S. R. 2001 A modelling study of feedforward activation in human erythrocyte glycolysis. C R Acad. Sci. III 324, 185-199.
8. Bhartiya, S., Rawool, S. & Venkatesh, K. V. 2003 Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design. Eur. J. Biochem. 270, 2644-2651. (doi:10.1046/j.1432-1033.2003.03641.x)
9. Blangy, D., Buc, H. & Monod, J. 1968 Kinetics of the allosteric interactions of phosphofructokinase from Escherichia coli. J. Mol. Biol. 31, 13-35. (doi:10.1016/ 0022-2836(68))
10. Buchholz, A., Takors, R. & Wandrey, C. 2001 Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques. Anal. Biochem. 295, 129-137. (doi:10.1006/abio.2001.5183)
11. Bulik, S., Grimbs, S., Huthmacher, C., Selbig, J. & Holzhutter, H. G. 2009 Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws - a promising method for speeding up the kinetic modelling of complex metabolic networks. FEBS J. 276, 410-424. (doi:10.1111/j.1742- 4658.2008.06784.x)
12. Buziol, S., Bashir, I., Baumeister, A., Claassen,W., Noisommit- Rizzi, N., Mailinger, W. & Reuss, M. 2002 New bioreactorcoupled rapid stopped-flow sampling technique for measurements of metabolite dynamics on a subsecond time scale. Biotechnol. Bioeng. 80, 632-636. (doi:10.1002/bit. 10427)
13. Caldara, M., Dupont, G., Leroy, F., Goldbeter, A., De Vuyst, L. & Cunin, R. 2008 Arginine biosynthesis in Escherichia coli: experimental perturbation and mathematical modeling. J. Biol. Chem. 283, 6347-6358. (doi:10.1074/jbc. M705884200)
14. Chalhoub, E., Hanson, R. W. & Belovich, J. M. 2007 A computer model of gluconeogenesis and lipid metabolism in the perfused liver. Am. J. Physiol. Endocrinol. Metab. 293, E1676-E1686. (doi:10.1152/ajpendo.00161.2007)
15. Chance, B. 1964 Rapid mixing and sampling techniques in biochemistry. Pennsylvania University. Eldridge Reeves Johnson Foundation for Medical Physics. Colloquia. New York, NY: Academic Press.
16. Chassagnole, C., Rais, B., Quentin, E., Fell, D. A. & Mazat, J. P. 2001 An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. Biochem. J. 356, 415-423. (doi:10.1042/0264-6021:3560415) (Pubitemid 32532352)
17. Chassagnole, C., Noisommit-Rizzi, N., Schmid, J. W., Mauch, K. & Reuss, M. 2002 Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng. 79, 53-73. (doi:10.1002/bit.10288)
18. Chin, J. W. 2006 Modular approaches to expanding the functions of living matter. Nat. Chem. Biol. 2, 304-311. (doi:10.1038/nchembio789)
19. Clarke, S. 2003 Aging as war between chemical and biochemical processes: protein methylation and the recognition of age-damaged proteins for repair. Ageing Res. Rev. 2, 263-285. (doi:10.1016/S1568-1637(03)00011-4)
20. Conant, G. C. &Wolfe, K. H. 2007 Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol. Syst. Biol. 3, 129. (doi:10.1038/msb4100170)
21. D'Alessio, G. & Josse, J. 1971 Glyceraldehyde phosphate dehydrogenase of Escherichia coli. Structural and catalytic properties. J. Biol. Chem. 246, 4326-4333.
22. de Koning, W. & van Dam, K. 1992 A method for the determination of changes of glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH. Anal. Biochem. 204, 118-123. (doi:10.1016/0003- 2697(92)90149-2)
23. Draeger, A., Kronfeld, M., Ziller, M. J., Supper, J., Planatscher, H., Magnus, J. B., Oldiges, M., Kohlbacher, O. & Zell, A. 2009 Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst. Biol. 3, 5. (doi:10.1186/1752-0509-3-5)
24. Duee, E., Olivier-Deyris, L., Fanchon, E., Corbier, C., Branlant, G. & Dideberg, O. 1996 Comparison of the structures of wild-type and a N313T mutant of Escherichia coli glyceraldehyde 3-phosphate dehydrogenases: implication for NAD binding and cooperativity. J. Mol. Biol. 257, 814-838. (doi:10.1006/jmbi.1996.0204)
25. Fraser, H. I., Kvaratskhelia, M. & White, M. F. 1999 The two analogous phosphoglycerate mutases of Escherichia coli. FEBS Lett. 455, 344-348. (doi:10.1016/S0014- 5793(99)00910-2) (Pubitemid 29333064)
26. Gibson, D. G. et al. 2008 Complete chemical synthesis, assembly, and cloning of a Mcyoplasma genitalium genome. Science 319, 1215-1220. (doi:10.1126/science.1151721)
27. Hadlich, F., Noack, S. & Wiechert, W. 2009 Translating biochemical network models between different kinetic formats. Metab. Eng. 11, 87-100. (doi:10.1016/j.ymben. 2008.10.002)
28. Hardiman, T., Lemuth, K., Keller, M. A., Reuss, M.& Siemann- Herzberg, M. 2007 Topology of the global regulatory network of carbon limitation in Escherichia coli. J. Biotechnol. 132, 359-374. (doi:10.1016/j.jbiotec.2007. 08.029)
29. Harrison, D. E. & Maitra, P. K. 1969 Control of respiration and metabolism in growing Klebsiella aerogenes. The role of adenine nucleotides. Biochem. J. 112, 647-656.
30. Heinrich, R. & Rapoport, T. A. 1974 A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42, 89-95. (doi: 10.1111/j.1432-1033.1974.tb03318.x)
31. Helfert, S., Estevez, A. M., Bakker, B., Michels, P. & Clayton, C. 2001 Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei. Biochem. J. 357, 117-125. (doi:10.1042/0264-6021:3570117) (Pubitemid 32642909)
32. Hill, A. V. 1910 The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J. Physiol. 40, iv-vii.
33. Hill, A. V. 1913 The combinations of haemoglobin with oxygen and with carbon monoxide. I. Biochem. J. 7, 471-480.
34. Hynne, F., Dano, S. & Sorensen, P. G. 2001 Full-scale model of glycolysis in Saccharomyces cerevisiae. Biophys. Chem. 94, 121-163. (doi:10.1016/S0301-4622(01)00229-0)
35. Jewett, M. C., Calhoun, K. A., Voloshin, A., Wuu, J. J. & Swartz, J. R. 2008 An integrated cell-free metabolic platform for protein production and synthetic biology. Mol. Syst. Biol. 4, 220. (doi:10.1038/msb.2008.57)
36. Kacser, H. & Burns, J. A. 1973 The control of flux. Symp. Soc. Exp. Biol. 27, 65-104.
37. Karp, P. D. et al. 2005 Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33, 6083-6089. (doi:10.1093/nar/gki892)
38. Karp, P. D. et al. 2007 Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 35, 7577-7590. (doi:10.1093/nar/gkm740)
39. Keasling, J. D. 2008 Synthetic biology for synthetic chemistry. ACS Chem. Biol. 3, 64-76. (doi:10.1021/cb7002434)
40. Koshland Jr, D. E., Némethy, G. & Filmer, D. 1966 Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5, 365-385. (doi:10.1021/bi00865a047)
41. Kotlarz, D. & Buc, H. 1982 Phosphofructokinases from Escherichia coli. Methods Enzymol. 90, 60-70. (doi: 10.1016/S0076-6879(82)90107-0)
42. Kotlarz, D., Garreau, H. & Buc, H. 1975 Regulation of the amount and of the activity of phosphofructokinases and pyruvate kinases in Escherichia coli. Biochim. Biophys. Acta 381, 257-268.
43. Kresnowati, M. T., van Winden, W. A. & Heijnen, J. J. 2005 Determination of elasticities, concentration and flux control coefficients from transient metabolite data using linlog kinetics. Metab. Eng. 7, 142-153. (doi:10.1016/j. ymben.2004.12.002)
44. Kuhnel, K. & Luisi, B. F. 2001 Crystal structure of the Escherichia coli RNA degradosome component enolase. J. Mol. Biol. 313, 583-592. (doi:10.1006/jmbi.2001.5065)
45. Kundig, W., Ghosh, S. & Roseman, S. 1964 Phosphate bound to histidine in a protein as an intermediate in a novel phospho- transferase system. Proc. Natl Acad. Sci. USA 52, 1067-1074. (doi:10.1073/pnas.52.4.1067)
46. Lambeth, M. J. & Kushmerick, M. J. 2002 A computational model for glycogenolysis in skeletal muscle. Ann. Biomed. Eng. 30, 808-827. (doi:10.1114/1.1492813)
47. Le Novere, N. et al. 2006 BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689-D691. (doi:10.1093/nar/gkj092)
48. Leslie, A. G. & Wonacott, A. J. 1983 Coenzyme binding in crystals of glyceraldehyde-3-phosphate dehydrogenase. J. Mol. Biol. 165, 375-391. (doi:10.1016/S0022- 2836(83)80262-9)
49. Liebermeister, W. & Klipp, E. 2006 Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor. Biol. Med. Model 3, 41. (doi:10.1186/ 1742-4682-3-41)
50. Lunin, V. V., Li, Y., Schrag, J. D., Iannuzzi, P., Cygler, M. & Matte, A. 2004 Crystal structures of Escherichia coli ATPdependent glucokinase and its complex with glucose. J. Bacteriol. 186, 6915-6927. (doi:10.1128/JB.186. 20. 6915-6927.2004) (Pubitemid 38380920)
51. Maharjan, R. P. & Ferenci, T. 2003 Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. Anal. Biochem. 313, 145-154.
52. Maier, K., Hofmann, U., Reuss, M. & Mauch, K. 2008 Identification of metabolic fluxes in hepatic cells from transient 13C-labeling experiments: Part II. Flux estimation. Biotechnol. Bioeng. 100, 355-370. (doi:10.1002/ bit.21746)
53. Marchisio, M. A. & Stelling, J. 2008 Computational design of synthetic gene circuits with composable parts. Bioinformatics 24, 1903-1910. (doi:10.1093/bioinformatics/btn330)
54. Markus, M., Plesser, T., Boiteux, A., Hess, B. & Malcovati, M. 1980 Analysis of progress curves. Rate law of pyruvate kinase type I from Escherichia coli. Biochem. J. 189, 421-433.
55. Mashego, M. R., Rumbold, K., De Mey, M., Vandamme, E., Soetaert, W. & Heijnen, J. J. 2007 Microbial metabolomics: past, present and future methodologies. Biotechnol. Lett. 29, 1-16. (doi:10.1007/s10529-006-9218-0)
56. Meyer, A. J., Pellaux, R. & Panke, S. 2007 Bioengineering novel in vitro metabolic pathways using synthetic biology. Curr. Opin. Microbiol. 10, 246-253. (doi:10.1016/j.mib. 2007.05.009)
57. Meyer, D., Schneider-Fresenius, C., Horlacher, R., Peist, R. & Boos, W. 1997 Molecular characterization of glucokinase from Escherichia coli K-12. J. Bacteriol. 179, 1298-1306. (Pubitemid 27076595)
58. Michaelis, L. & Menten, M. L. 1913 The kinetics of the inversion effect. Biochem. Z. 49, 333-369.
59. Monod, J. 1947 The phenomenon of enzymatic adaptation and its bearings on problems of genetics and cellular differentiation. Growth 11, 223-289.
60. Monod, J., Changeux, J. P. & Jacob, F. 1963 Allosteric proteins and cellular control systems. J. Mol. Biol. 6, 306-329.
61. Monod, J., Wyman, J. & Changeux, J. P. 1965 On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12, 88-118.
62. Nahalka, J., Liu, Z. Y., Chen, X. & Wang, P. G. 2003 Superbeads: immobilization in 'sweet' chemistry. Chem. Eur. J. 9, 373-377. (doi:10.1002/chem.200390038)
63. Nakamura, C. E. & Whited, G. M. 2003 Metabolic engineering for the microbial production of 1,3-propanediol. Curr. Opin. Biotechnol. 14, 454-459. (doi:10.1016/j.copbio. 2003.08.005)
64. Neidhardt, F. C. (ed.) 1996 Escherichia coli and Salmonella. Washington, DC: ASM Press.
65. Novick, A. & Szilard, L. 1950 Experiments with the chemostat on spontaneous mutations of bacteria. Proc. Natl Acad. Sci. USA 36, 708-719. (doi:10.1073/pnas.36.12.708)
66. Ogawa, T., Mori, H., Tomita, M. & Yoshino, M. 2007 Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli. Res. Microbiol. 158, 159-163. (doi:10.1016/j.resmic.2006.11.003)
67. Popova, S. V. & Sel'kov, E. E. 1975 Generalization of the model by Monod, Wyman and Changeux for the case of a reversible monosubtrate reaction SR,TP. FEBS Lett. 53, 269-273. (doi:10.1016/0014-5793(75)80034-2)
68. Popova, S. V. & Sel'kov, E. E. 1976 Generalization of the Monod-Wyman-Changeux model for the case of multisubstrate reactions. Mol. Biol. (Mosk.) 10, 1116-1126.
69. Postma, P. W., Lengeler, J. W. & Jacobson, G. R. 1993 Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol. Rev. 57, 543-594.
70. Rais, B., Chassagnole, C., Letellier, T., Fell, D. A. & Mazat, J. P. 2001 Threonine synthesis from aspartate in Escherichia coli cell-free extracts: pathway dynamics. Biochem. J. 356, 425-432. (doi:10.1042/0264- 6021:3560425) (Pubitemid 32532353)
71. Richter, O., Betz, A. & Giersch, C. 1975 The response of oscillating glycolysis to perturbations in the NADH/NAD system: a comparison between experiments and a computer model. Biosystems 7, 137-146. (doi:10.1016/0303- 2647(75)90051-9)
72. Rizzi, M., Baltes, M., Theobald, U. & Reuss, M. 1997 In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. Biotechnol. Bioeng. 55, 592-608. (doi:10.1002/(SICI)1097-0290(19970820)55: 4<592::AID-BIT2>3.0.CO;2-C)
73. Rose, I. A., O'Connell, E. L. & Mehler, A. H. 1965 Mechanism of the aldolase reaction. J. Biol. Chem. 240, 1758-1765.
74. Savageau, M. A. 1995 Enzyme kinetics in vitro and in vivo: Michaelis - Menten revisited. In Cell chemistry and physiology, vol.4, pp. 93-146. Stamford, CT: JAI Press Inc.
75. Schaefer, U., Boos, W., Takors, R. & Weuster-Botz, D. 1999 Automated sampling device for monitoring intracellular metabolite dynamics. Anal. Biochem. 270, 88-96. (doi:10.1006/abio.1999.4048)
76. Schaub, J., Schiesling, C., Reuss, M. & Dauner, M. 2006 Integrated sampling procedure for metabolome analysis. Biotechnol. Prog. 22, 1434-1442. (doi:10.1021/bp050381q)
77. Schauer, M., Heinrich, R. & Rapoport, S.M. 1981 Mathematische Modellierung der Glykolyse und des Adeninnukleotidstoffwechsels menschlicher Erythrozyten. I. Reaktionskinetische Ansatze, Analyse des in vivo-Zustandes und Bestimmung der Anfangsbedingungen fur die in vitro-Experimente. Acta Biol.Med. Ger. 40, 1659-1682.
78. Schierbeck, B. & Larsson-Raznikiewicz, M. 1979 Product inhibition studies of yeast phosphoglycerate kinase evaluating properties of multiple substrate binding sites. Biochim. Biophys. Acta 568, 195-204.
79. Schmidt, P. P., Travers, F. & Barman, T. 1995 Transient and equilibrium kinetic studies on yeast 3-phosphoglycerate kinase. Evidence that an intermediate containing 1,3-bisphosphoglycerate accumulates in the steady state. Biochemistry 34, 824-832. (doi:10.1021/bi00003a016)
80. Schreyer, R. & Bock, A. 1980 Phosphoglucose isomerase from Escherischia coli K 10: purification, properties and formation under aerobic and anaerobic condition. Arch. Microbiol. 127, 289-298. (doi:10.1007/BF00427206)
81. Schuetz, R., Kuepfer, L. & Sauer, U. 2007 Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol. 3, 119. (doi: 10.1038/msb4100162)
82. Segel, I. H. 1975 Enzyme kinetics behavior and analysis of rapid equilibrium and steady-state enzyme systems. New York: Wiley.
83. Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K. & Ueda, T. 2001 Cell-free translation reconstituted with purified components. Nat. Biotechnol. 18, 751-755. (doi:10.1038/90802)
84. Shimizu, Y., Kuruma,Y., Ying, B.-W., Umekage, S. & Ueda, T. 2006 Cell-free translation systems for protein engineering. FEBS J. 273, 4133-4140. (doi:10.1111/j.1742-4658.2006. 05431.x) (Pubitemid 44326494)
85. Streichert, F. & Ulmer, H. 2005 JavaEvA - a Java framework for evolutionary algorithms. Tübingen: Centre for Bioinformatics Tü bingen, University of Tübingen.
86. Suarez, M., Tortosa, P., Carrera, J. & Jaramillo, A. 2008 Pareto optimization in computational protein design with multiple objectives. J. Comput. Chem. 29, 2704-2711. (doi:10.1002/jcc.20981)
87. Tchieu, J. H., Norris, V., Edwards, J. S. & Saier Jr, M. H. 2001 The complete phosphotranferase system in Escherichia coli. J. Mol. Microbiol. Biotechnol. 3, 329-346.
88. Teusink, B. et al. 2000 Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur. J. Biochem. 267, 5313-5329. (doi:10.1046/j.1432-1327.2000.01527.x)
89. Theobald, U., Mailinger, W., Reuss, M. & Rizzi, M. 1993 In vivo analysis of glucose-induced fast changes in yeast adenine nucleotide pool applying a rapid sampling technique. Anal. Biochem. 214, 31-37. (doi:10.1006/ abio.1993.1452)
90. Theobald, U., Mailinger,W., Baltes, M., Rizzi, M. & Reuss, M. 1997 In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. I. Experimental observations. Biotechnol. Bioeng. 55, 305-316. (doi:10.1002/(SICI) 1097- 0290(19970720)55:2,305::AID-BIT8.3.0.CO;2-M)
91. Thomson, G. J., Howlett, G. J., Ashcroft, A. E. & Berry, A. 1998 The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem. J. 331, 437-445. (Pubitemid 28182157)
92. Tian, J., Gong, H., Sheng, N., Zhou, X., Gulari, E., Gao, X. & Church, G. 2004 Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432, 1050-1054. (doi:10.1038/nature03151) (Pubitemid 38693463)
93. Vaseghi, S., Baumeister, A., Rizzi, M. & Reuss, M. 1999 In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. Metab. Eng. 1, 128-140. (doi: 10.1006/mben.1998.0110)
94. Vaz, A. & Vicente, L. 2007 A particle swarm pattern search method for bound constrained global optimization. J. Global Optim. 39, 197-219. (doi:10.1007/s10898-007-9133-5) (Pubitemid 47373392)
95. Visser, D. & Heijnen, J. J. 2003 Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. Metab. Eng. 5, 164-176. (doi:10.1016/S1096- 7176(03)00025-9)
96. Visser, D. et al. 2002 Rapid sampling for analysis of in vivo kinetics using the BioScope: a system for continuouspulse experiments. Biotechnol. Bioeng. 79, 674-681. (doi:10.1002/bit.10328)
97. Visser, D., Schmid, J.W., Mauch, K., Reuss, M. & Heijnen, J. J. 2004 Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics. Metab. Eng. 6, 378-390. (doi:10.1016/j.ymben.2004.07.001)
98. Wang, L., Xie, J. & Schultz, P. G. 2006 Expanding the genetic code. Annu. Rev. Biophys. Biomol. Struct. 35, 225-249. (doi:10.1146/annurev.biophys. 35.101105.121507)
99. Waygood, E. B. & Sanwal, B. D. 1974 The control of pyruvate kinases of Escherichia coli. I. Physicochemical and regulatory properties of the enzyme activated by fructose 1,6-diphosphate. J. Biol. Chem. 249, 265-274.
100. Waygood, E. B., Rayman, M. K. & Sanwal, B. D. 1975 The control of pyruvate kinases of Escherichia coli. II. Effectors and regulatory properties of the enzyme activated by ribose 5-phosphate. Can. J. Biochem. 53, 444-454.
101. Weuster-Botz, D. 1997 Sampling tube device for monitoring intracellular metabolite dynamics. Anal. Biochem. 246, 225-233. (doi:10.1006/abio.1997.2009)
102. Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M. & Goodacre, R. 2008 Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal. Chem. 80, 2939-2948. (doi:10.1021/ ac7023409)
103. Wurm, F. 2004 Production of recombinant protein therapeutics in cultivated mammalian cells. Nat. Biotechnol. 22, 1393-1398. (doi:10.1038/ nbt1026)
104. Yang, C. R., Shapiro, B. E., Hung, S. P., Mjolsness, E. D. & Hatfield, G. W. 2005 A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12. J. Biol. Chem. 280, 11 224-11 232. (doi:10.1074/jbc.M411471200)
105. Yokobayashi, Y., Weiss, R. & Arnold, F. H. 2002 Directed evolution of a genetic circuit. Proc. Natl Acad. Sci. USA 99, 16 587-16 591. (doi:10.1073/pnas. 252535999)
106. Zgiby, S. M., Thomson, G. J., Qamar, S. & Berry, A. 2000 Exploring substrate binding and discrimination in fructose1, 6-bisphosphate and tagatose 1,6-bisphosphate aldolases. Eur. J. Biochem. 267, 1858-1868. (doi: 10.1046/j.1432-1327.2000.01191.x)