In silico evaluation of a complex multi-enzymatic system using one-pot and modular approaches: Application to the high-yield production of hydrogen from a synthetic metabolic pathway

Chemical Engineering Science

Volumn 87, Issue , 2013, Pages 183-193

  Ardao, Inés ^a   Zeng, An Ping ^a  

^a HAMBURG UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Biochemical engineering; Mathematical modeling; Multi enzymatic system; Multi objective optimization; Reaction engineering; Simulation

Indexed keywords

BIOCHEMICAL ENGINEERING; ENZYMES; INDUSTRIAL CHEMICALS; MATHEMATICAL MODELS; METABOLISM; MULTIOBJECTIVE OPTIMIZATION; PRODUCTIVITY;

DOWN-STREAM; HIGH YIELD; HYDROGENASES; HYPERTHERMOPHILIC; IN-SILICO; METABOLIC PATHWAYS; MODULAR APPROACH; MODULAR PROCESS; MULTI OBJECTIVE OPTIMIZATIONS (MOO); MULTI-ENZYMATIC SYSTEM; ONE POT; ONE POT PROCESS; PRODUCTION OF HYDROGEN; REACTION ENGINEERING; SIMULATION;

HYDROGEN PRODUCTION;

EID: 84868496357     PISSN: 00092509     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ces.2012.10.005     Document Type: Article

References (59)

1. Bae H.-S., Lee S.-G., Hong S.-P., Kwak M.-S., Esaki N., Soda K., Sung M.-H. Production of aromatic d-amino acids from α-keto acids and ammonia by coupling of four enzyme reactions. J. Mol. Catal. B: Enzym. 1999, 6:241-247.
2. Bryant F.O., Adams M.W. Characterization of hydrogenase from the hyperthermophilic archaebacterium, Pyrococcus furiosus. J. Biol. Chem. 1989, 264:5070-5079.
3. 2O mixtures and a novel approach to protein crystallization. Molecules 2010, 15:793-803.
4. Cornish-Bowden A. Fundamentals of Enzyme Kinetics 2004, Portland Press.
5. Chenault H., Whitesides G. Regeneration of nicotinamide cofactors for use in organic synthesis. Appl. Biochem. Biotechnol. 1987, 14:147-197.
6. Deb K. Multi-Objective Optimization Using Evolutionary Algorithms 2001, John Wiley & Sons.
7. Dilipkumar M., Rajasimman M., Rajamohan N. Application of statistical design for the production of inulinase by Streptomyces sp. using pressmud. Front. Chem. Sci. Eng. 2011, 5:463-470.
8. Domagk G.F., Chilla R. Glucose-6-phosphate dehydrogenase from Candida utilis. Methods Enzymol. 1975, 41:205-208.
9. Essenberg M.K., Cooper R.A. Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles. Eur. J. Biochem. 1975, 55:323-332.
10. Fahey R.C., Kolb E., Harris J.I. Triose phosphate isomerase from Bacillus stearothermophilus. Biochem. J. 1971, 124:77P.
11. Fessner W.-D., Walter C. "Artificial metabolisms" for the asymmetric one-pot synthesis of branched-chain saccharides. Angew. Chem. Int. Ed. 1992, 31:614-616.
12. Findrik Z., Vasić-Rački D. Biotransformation of d-methionine into l-methionine in the cascade of four enzymes. Biotechnol. Bioeng. 2007, 98:956-967.
13. Findrik Z., Vasić-Rački D. Mathematical modelling of amino acid resolution catalyzed by l-amino acid oxidases from Crotalus adamanteus and Crotalus atrox. Process Biochem. 2008, 43:1186-1194.
14. Findrik Z., Vasić-Rački D. Overview on reactions with multi-enzyme systems. Chem. Biochem. Eng. Q. 2009, 23:545-553.
15. Gijsen H.J.M., Qiao L., Fitz W., Wong C.-H. Recent advances in the chemoenzymatic synthesis of carbohydrates and carbohydrate mimetics. Chem. Rev. 1996, 96:443-474.
16. Hasmann F.A., Gurpilhares D.B., Roberto I.C., Converti A., Pessoa A. New combined kinetic and thermodynamic approach to model glucose-6-phosphate dehydrogenase activity and stability. Enzyme Microb. Technol. 2007, 40:849-858.
17. Havel J., Link H., Hofinger M., Franco-Lara E., Weuster-Botz D. Comparison of genetic algorithms for experimental multi-objective optimization on the example of medium design for cyanobacteria. Biotechnol. J. 2006, 1:549-555.
18. Ishii N., Suga Y., Hagiya A., Watanabe H., Mori H., Yoshino M., Tomita M. Dynamic simulation of an in vitro multi-enzyme system. FEBS Lett. 2007, 581:413-420.
19. Jung C.-H., Hartman F.C., Lu T.-Y.S., Larimer F.W. d-ribose-5-phosphate isomerase from spinach: heterologous overexpression, purification, characterization, and site-directed mutagenesis of the recombinant enzyme. Arch. Biochem. Biophys. 2000, 373:409-417.
20. Khu S.T., Madsen H. Multiobjective calibration with Pareto preference ordering: an application to rainfall-runoff model calibration. Water Resour. Res. 2005, 41:W03004.
21. Kochetov G.A. Transketolase from yeast, rat liver, and pig liver. Methods Enzymol. 1982, 90:209-223.
22. Kourtoglou E., Mamma D., Topakas E., Christakopoulos P. Purification, characterization and mass spectrometric sequencing of transaldolase from Fusarium oxysporum. Process Biochem. 2008, 43:1094-1101.
23. Krietsch W.K.G. Triosephosphate isomerase from rabbit liver. Methods Enzymol. 1975, 41:438-442.
24. Levenspiel O. Chemical Reaction Engineering 1962, John Wiley & Sons.
25. Mertens R., Greiner L., Van Den Ban E.C.D., Haaker H.B.C.M., Liese A. Practical applications of hydrogenase I from Pyrococcus furiosus for NADPH generation and regeneration. J. Mol. Catal. B: Enzym. 2003, 24-25:39-52.
26. Morse D.E., Horecker B. The mechanism of action of aldolases. Adv. Enzymol. Relat. Areas Mol. Biol. 1968, 31:125-181.
27. Murata T., Ishibuchi H. MOGA: multi-objective genetic algorithms. Proc. 2nd IEEE Int. Conf. Evol. Comput. 1995, 1:289-294.
28. Myung S., Wang Y., Zhang Y.H.P. Fructose-1,6-bisphosphatase from a hyper-thermophilic bacterium Thermotoga maritima: characterization, metabolite stability, and its implications. Process Biochem. 2010, 45:1882-1887.
29. Nosoh Y. Glucose-6-phosphate isomerase from Bacillus stearothermophilus. Methods Enzymol. 1975, 41:383-387.
30. Philippov P.P., Shestakova I.K., Tikhomirova N.K., Kochetov G.A. Characterization and properties of pig liver transketolase. Biochim. Biophys. Acta, Enzymol. 1980, 613:359-369.
31. 2 removal system for electrochemical analysis under ambient air: application in an amperometric nitrate biosensor. Anal. Chem. 2012, 84:2141-2146.
32. Reichenbecher M., Lottspeich F., Bronnenmeier K. Purification and properties of a cellobiose phosphorylase (CepA) and a cellodextrin phosphorylase (CepB) from the cellulolytic thermophile Clostridium stercorarium. Eur. J. Biochem. 1997, 247:262-267.
33. Roessner C.A., Scott A.I. Achieving natural product synthesis and diversity via catalytic networking ex vivo. Chem. Biol. 1996, 3:325-330.
34. Ryan J.D., Fish R.H., Clark D.S. Engineering cytochrome P450 enzymes for improved activity towards biomimetic 1,4-NADH cofactors. ChemBioChem. 2008, 9:2579-2582.
35. Santacoloma P.A., Sin G.r., Gernaey K.V., Woodley J.M. Multienzyme-catalyzed processes: next-generation biocatalysis. Org. Process Res. Dev. 2010, 15:203-212.
36. Sarkar D., Modak J.M. Pareto-optimal solutions for multi-objective optimization of fed-batch bioreactors using nondominated sorting genetic algorithm. Chem. Eng. Sci. 2005, 60:481-492.
37. Scott W.A., Abramsky T. 6-phosphogluconate dehydrogenase from Neurospora crassa. Methods Enzymol. 1975, 41:227-231.
38. Soldatkin O.O., Peshkova V.M., Dzyadevych S.V., Soldatkin A.P., Jaffrezic-Renault N., El'skaya A.V. Novel sucrose three-enzyme conductometric biosensor. Mater. Sci. Eng., C 2008, 28:959-964.
39. Srere P.A., Mattiasson B., Mosbach K. An immobilized three-enzyme system: a model for microenvironmental compartmentation in mitochondria. Proc. Nat. Acad. Sci. 1973, 70:2534-2538.
40. The Enzymes 1972, 7:259-280.
41. van Haaster D.J., Silva P.J., Hagedoorn P.-L., Jongejan J.A., Hagen W.R. Reinvestigation of the steady-state kinetics and physiological function of the soluble NiFe-hydrogenase I of Pyrococcus furiosus. J. Bacteriol. 2008, 190:1584-1587.
42. Wang Y., Huang W., Sathitsuksanoh N., Zhu Z., Zhang Y.-H.P. Biohydrogenation from biomass sugar mediated by in vitro synthetic enzymatic pathways. Chem. Biol. 2011, 18:372-380.
43. Wang Y., Zhang Y.H.P. A highly active phosphoglucomutase from Clostridium thermocellum: cloning, purification, characterization and enhanced thermostability. J. Appl. Microbiol. 2010, 108:39-46.
44. Wichmann R., Vasic-Racki D. Cofactor Regeneration at the Lab Scale 2005, Springer, Berlin/Heidelberg.
45. Wong C.-H., Whitesides G. Enzymes in Synthetic Organic Chemistry 1994, Pergamon.
46. Wood T. Purification and properties of d-ribulose-5-phosphate 3-epimerase from calf liver. Biochim. Biophys. Acta, Enzymol. 1979, 570:352-362.
47. Woodward J., Orr M., Cordray K., Greenbaum E. Biotechnology: enzymatic production of biohydrogen. Nature 2000, 405:1014-1015.
48. Wu J.T., Wu L.H., Knight J.A. Stability of NADPH: effect of various factors on the kinetics of degradation. Clin. Chem. 1986, 32:314-319.
49. Ye X., Wang Y., Hopkins R.C., Adams M.W.W., Evans B.R., Mielenz J.R., Zhang Y.-H.P. Spontaneous high-yield production of hydrogen from cellulosic materials and water catalyzed by enzyme cocktails. ChemSusChem 2009, 2:149-152.
50. Yoon R.-Y., Yeom S.-J., Park C.-S., Oh D.-K. Substrate specificity of a glucose-6-phosphate isomerase from Pyrococcus furiosus for monosaccharides. Appl. Microbiol. Biotechnol. 2009, 83:295-303.
51. Yun H., Yang Y.-H., Cho B.-K., Hwang B.-Y., Kim B.-G. Simultaneous synthesis of enantiomerically pure (R)-1-phenylethanol and (R)-α-methylbenzylamine from racemic α-methylbenzylamine using ω-transaminase/alcohol dehydrogenase/glucose dehydrogenase coupling reaction. Biotechnol. Lett. 2003, 25:809-814.
52. Zeng A.-P. Meeting report: new biotechnological production systems. Biotechnol. J. 2011, 6:907-908.
53. Zhang Y.-H.P. Using extremophile enzymes to generate hydrogen for electricity. Microbe 2009, 4:560-565.
54. Zhang Y.-H.P. Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: challenges and opportunities. Biotechnol. Bioeng. 2010, 105:663-677.
55. Zhang Y.-H.P. Renewable carbohydrates are a potential high density hydrogen carrier. Int. J. Hydrogen Energy 2010, 35:10334-10342.
56. Zhang Y.-H.P. Substrate channeling and enzyme complexes for biotechnological applications. Biotechnol. Adv. 2011, 29:715-725.
57. Zhang Y.-H.P. Simpler is better: high-yield and potential low-cost biofuels production through cell-free synthetic pathway biotransformation (SyPaB). ACS Catal. 2011, 1:998-1009.
58. Zhang Y.-H.P., Evans B.R., Mielenz J.R., Hopkins R.C., Adams M.W.W. High-yield hydrogen production from starch and water by a synthetic enzymatic pathway. PLoS One 2007, 2:e456.
59. Zhou Y.H., Titchener-Hooker N.J. The application of a Pareto optimisation method in the design of an integrated bioprocess. Bioprocess. Biosyst. Eng. 2003, 25:349-355.