Developmental strategies and regulation of cell-free enzyme system for ethanol production: a molecular prospective

Applied Microbiology and Biotechnology

Volumn 98, Issue 23, 2014, Pages 9561-9578

  Khattak, Waleed Ahmad ^a   Ullah, Muhammad Wajid ^a   Ul Islam, Mazhar ^a   Khan, Shaukat ^a   Kim, Minah ^a   Kim, Yeji ^a   Park, Joong Kon ^a  

^a Kyungpook National University   (South Korea)

Author keywords

Cell free enzyme system; Conventional fermentation; Ethanol; Glycolytic and fermentation enzymes; Whole cell system

Indexed keywords

CELLS; ENZYME IMMOBILIZATION; ETHANOL; FERMENTATION; PLANNING;

CELL-FREE; CELL-FREE EXTRACTS; DEVELOPMENT AND OPERATIONS; ETHANOL PRODUCTION; IMMOBILIZATION TECHNIQUE; INNOVATIVE TECHNOLOGY; METABOLIC CHANNELING; WHOLE CELL;

CELL IMMOBILIZATION;

ENZYME ACTIVITY; ETHANOL; FERMENTATION; GENE EXPRESSION; METABOLISM; MOLECULAR ANALYSIS;

ALCOHOL; DRUG MIXTURE; ENZYME; IMMOBILIZED ENZYME;

DRUG MIXTURE; ENZYMOLOGY; FERMENTATION; GENETIC TRANSCRIPTION; GLYCOLYSIS; ISOLATION AND PURIFICATION; METABOLISM; PROTEIN SYNTHESIS; SACCHAROMYCES CEREVISIAE;

COMPLEX MIXTURES; ENZYMES; ENZYMES, IMMOBILIZED; ETHANOL; FERMENTATION; GLYCOLYSIS; PROTEIN BIOSYNTHESIS; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

EID: 84911435849     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-014-6154-0     Document Type: Review

References (170)

1. Agapakis CM, Ducat DC, Boyle PM, Wintermute EH, Way JC, Silver PA (2010) Insulation of a synthetic hydrogen metabolism circuit in bacteria. J Biol Eng 4:3. doi:10.1186/1754-1611-4-3
2. Aguilera A, Zimmermann FK (1986) Isolation and molecular analysis of the phosphoglucose isomerase structural gene of Saccharomyces cerevisiae. Mol Gen Genet 202:83–89. doi:10.1007/BF00330521
3. Allain EJ (2007) Cell-free ethanol production: the future of fuel ethanol? J Chem Technol Biotechnol 82:117–120. doi:10.1002/jctb.1649
4. Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314:1565–1568. doi:10.1126/science.1131969
5. Arnaud JP, Lacroix C, Choplin L (1992) Effect of agitation rate on cell release rate and metabolism during continuous fermentation with entrapped growing. Biotechnol Tech 6:265–270. doi:10.1007/BF02439356
6. Ayeni AO, Omoleye JA, Mudliar S, Hymore FK, Pandey RA (2014) Utilization of lignocellulosic waste for ethanol production: enzymatic digestibility and fermentation of pretreated shea tree sawdust. Korean J Chem Eng 31:1180–1186. doi:10.1007/s11814-014-0026-2
7. Bai FW, Anderson WA, Moo-Young M (2008) Ethanol fermentation technologies from sugar and starch feedstocks. Biotechnol Adv 26:89–105. doi:10.1016/j.biotechadv.2007.09.002
8. Bartrons R, Van Schaftingen E, Vissers S, Hers HG (1982) The stimulation of yeast phosphofructokinase by fructose 2,6-bisphosphate. FEBS Lett 143:137–140. doi:10.1016/0014-5793(82)80290-1
9. Bauler P, Huber G, Leyh T, McCammon J (2010) Channeling by proximity: the catalytic advantages of active site colocalization using Brownian dynamics. J Phys Chem 1:1332–1335. doi:10.1021/jz1002007
10. Berg JM, Tymoczko JL, Stryer L (2010) Biochemistry. W.H Freeman and Company, New York
11. Betancor L, Berne C, Luckarift HR, Spain JC (2006) Coimmobilization of a redox enzyme and a cofactor regeneration system. Chem Commun 14:3640–3642. doi:10.1039/b604689d
12. Bischof JC, Padanilam J, Holmes WH, Ezzell RM, Lee RC, Tompkins RG, Yarmush ML, Toner M (1995) Dynamics of cell membrane permeability changes at supraphysiological temperatures. Biophys J 68:2608–2614. doi:10.1016/S0006-3495(95)80445-5
13. Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF (2012) Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci USA 109:478–483. doi:10.1073/pnas.1108557109
14. Breddam K, Beenfeldt T (1991) Acceleration of yeast autolysis by chemical methods for production of intracellular enzymes. Appl Microbiol Biotechnol 35:323–329. doi:10.1007/BF00172720
15. Buchner E (1897) Alkoholische Gährung ohne Hefezellen. Ber Dtsch Chem Ges 30:117–124. doi:10.1002/cber.189703001215
16. Buchner E (1966) “Cell Free Fermentation" Nobel Lectures. Chemistry 1901–1921:99–122
17. Bulow L, Ljungcrantz P, Mosbach K (1985) Preparation of a soluble bifunctional enzyme by gene fusion. Nat Biotech 3:821–823. doi:10.1038/nbt0985-821
18. Calhoun KA, Swartz JR (2005) Energizing cell-free protein synthesis with glucose metabolism. Biotechnol Bioeng 90:606–613. doi:10.1002/bit.20449
19. Calhoun KA, Swartz JR (2006) Total amino acid stabilization during cell-free protein synthesis reactions. J Biotechnol 123:193–203. doi:10.1016/j.jbiotec.2005.11.011
20. Carere J, Baker P, Seah SY (2011) Investigating the molecular determinants for substrate channeling in BphI-BphJ, an aldolase-dehydrogenase complex from the polychlorinated biphenyls degradation pathway. Biochemistry 50:8407–8416. doi:10.1021/bi200960j
21. Chambers A, Tsang JS, Stanway C, Kingsman AJ, Kingsman SM (1989) Transcriptional control of the Saccharomyces cerevisiae PGK gene by RAP1. Mol Cell Biol 9:5516–5524. doi:10.1128/MCB.9.12.5516
22. Chapple C, Ladish M, Meilan R (2007) Loosening lignin’s grip on biofuel production. Nat Biotechnol 25:746–748. doi:10.1038/nbt0707-746
23. Chen AH, Silver PA (2012) Designing biological compartmentalization. Trends Cell Biol 22:662–670. doi:10.1016/j.tcb.2012.07.002
24. Chen Z, Jandt U, Rappert S, Zeng A-P (2013) Proteindesign fuer die Entwicklung von industriellen Mikroorganismen. BIOspektrum 19:99–101. doi:10.1007/s12268-013-0276-2
25. Ciriacy M, Breitenbach I (1979) Physiological effects of seven different blocks in glycolysis in Saccharomyces cerevisiae. J Bacteriol 139:152–160
26. Clifton D, Weinstock SB, Fraenkel DG (1978) Glycolysis mutants in Saccharomyces cerevisiae. Genetics 88:1–11
27. Compagno C, Brambilla L, Capitanio D, Boschi F, Ranzi BM, Porro D (2001) Alterations of the glucose metabolism in a triose phosphate isomerase-negative Saccharomyces cerevisiae mutant. Yeast 18:663–670. doi:10.1002/yea.715
28. Conrado RJ, Varner JD, DeLisa MP (2008) Engineering the spatial organization of metabolic enzymes: mimicking nature’s synergy. Curr Opin Biotechnol 19:492–499. doi:10.1016/j.copbio.2008.07.006
29. Delneri D, Gardner DCJ, Bruschi CV, Oliver SG (1999) Disruption of seven hypothetical aryl alcohol dehydrogenase genes from Saccharomyces cerevisiae and construction of a multiple knockout strain. Yeast 15:1681–1698. doi:10.1002/(SICI)1097-0061(199911)15:15<1681::AID-YEA486>3.0.CO;2-A
30. Denis CL, Ferguson J, Young ET (1983) mRNA levels for the fermentative alcohol dehydrogenase of Saccharomyces cerevisiae decrease upon growth on a non fermentable carbon source. J Biol Chem 258:1165–1171, PMID: 6337132
31. Dickinson JR, Schweizer M (2004) Metabolism and molecular physiology of Saccharomyces cerevisiae. CRC Press, London
32. Dickinson JR, Harrison SJ, Dickinson JA, Hewlins MJ (2000) An investigation of the metabolism of isoleucine to active amyl alcohol in Saccharomyces cerevisiae. J Biol Chem 275:10937–10942. doi:10.1074/jbc.275.15.10937
33. Doi RH, Kosugi A (2004) Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nat Rev Microbiol 2:541–551. doi:10.1038/nrmicro925
34. Dunn MF (2012) Allosteric regulation of substrate channeling and catalysis in the tryptophan synthase bienzyme complex. Arch Biochem Biophys 519:154–166. doi:10.1016/j.abb.2012.01.016
35. Edwards MC, Doran-Peterson J (2012) Pectin-rich biomass as feedstock for fuel ethanol production. Appl Microbiol Biotechnol 95:565–575. doi:10.1007/s00253-012-4173-2
36. Elçin YM (1995) Encapsulation of urease enzyme in xanthan-alginate spheres. Biomaterials 16:1157–1161. doi:10.1016/0142-9612(95)93580-7
37. El-Mansi E, Bryce CF, Demain AL, Allman A (2006) Fermentation microbiology and biotechnology. CRC Press, London
38. Entian K-D (1997) Sugar phosphorylation in yeast. In: Zimmermann FK and Entian K-D (ed) Yeast sugar metabolism. Biochemistry, Genetics, Biotechnology, and Applications. Technomic, Lancaster, pp 67–79
39. Fan LH, Zhang ZJ, Yu XY, Xue YX, Wang MW, Tan TW (2013) In vitro assembly of minicellulosomes with two scaffoldins on the yeast cell surface for cellulose saccharification and bioethanol production. Process Biochem 48:430–437. doi:10.1016/j.procbio.2013.01.012
40. Forster AC, Church GM (2007) Synthetic biology projects in vitro. Genome Res 17:1–6. doi:10.1101/gr.5776007
41. Fothergill-Gilmore LA, Watson HC (1990) Phosphoglycerate mutases. Biochem Soc Trans 18:190–193, PMID: 2165930
42. Frank RA, Titman CM, Pratap JV, Luisi BF, Perham RN (2004) A molecular switch and proton wire synchronize the active sites in thiamine enzymes. Science 306:872–876. doi:10.1126/science.1101030
43. Ge X, Green VS, Zhang N, Sivakumar G, Xu J (2012) Eastern gamagrass as an alternative cellulosic feedstock for bioethanol production. Process Biochem 47:335–339. doi:10.1016/j.procbio.2011.11.008
44. Gehrmann W, Elsner M (2011) A specific fluorescence probe for hydrogen peroxide detection in peroxisomes. Free Radic Res 45:501–506. doi:10.3109/10715762.2011.560148
45. Gitai Z (2005) The new bacterial cell biology: moving parts and subcellular architecture. Cell 120:577–586. doi:10.1016/j.cell.2005.02.026
46. Goldberg S (2008) Mechanical/physical methods of cell disruption and tissue homogenization. Methods Mol Biol 424:3–22. doi:10.1007/978-1-60327-064-9_1
47. Gong Z, Shen H, Wang Q, Yang X, Xie H, Zhao ZK (2013) Efficient conversion of biomass into lipids by using the simultaneous saccharification and enhanced lipid production process. Biotechnol Biofuels 6:36. doi:10.1186/1754-6834-6-36
48. Green JBA, Wright APH, Cheung WY, Lancashire WE, Hartley BS (1988) The structure and regulation of phosphoglucose isomerase in Saccharomyces cerevisiae. Mol Gen Genet 215:100–106. doi:10.1007/BF00331310
49. Griffiths AD, Tawfik DS (2003) Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization. EMBOJ 22:24–35. doi:10.1093/emboj/cdg014
50. Griffiths LJ, Anyim M, Doffman SR, Wilks M, Millar MR, Agrawal SG (2006) Comparison of DNA extraction methods for Aspergillus fumigatus using real-time PCR. J Med Microbiol 55:1187–1191. doi:10.1099/jmm. 0.46510-0
51. Gu Y, Shrivastava IH, Amara SG, Bahar I (2009) Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter. Proc Natl Acad Sci USA 106:2589–2594. doi:10.1073/pnas.0812299106
52. Haeckel R, Hess B, Lauterborn W, Wuster KH (1968) Purification and allosteric properties of yeast pyruvate kinase. Hoppe-Seyler’s Z. Physiol Chem 349:699–714, PMID: 4386962
53. Hakobyan D, Nazaryan K (2010) Molecular dynamics study of interaction and substrate channeling between neuron-specific enolase and B-type phosphoglycerate mutase. Proteins Struct Funct Bioinforma 78:1691–1704. doi:10.1002/prot.22686
54. Han M, Kang KE, Kim Y, Choi G-W (2013) High efficiency bioethanol production from barley straw using a continuous pretreatment reactor. Process Biochem 48:488–495. doi:10.1016/j.procbio.2013.01.007
55. Hasunuma T, Akihiko K (2012) Consolidated bioprocessing and simultaneous saccharification and fermentation of lignocellulose to ethanol with thermotolerant yeast strains. Process Biochem 47:1287–1294. doi:10.1016/j.procbio.2012.05.004
56. He M-X, Qin H, Yin X, Ruan Z-Y, Tan F-R, Wu B, Shui Z-X, Dai L-C, Hu Q-C (2014) Direct ethanol production from dextran industrial waste water by Zymomonas mobilis. Korean J Chem Eng. doi:10.1007/s11814-014-0108-1
57. Heinisch JJ, von Borstel RC, Rodicio R (1991) Sequence and localization of the gene encoding yeast phosphoglycerate mutase. Cur Genet 20:167–171. doi:10.1007/BF00312781
58. Heinisch JJ, Muller S, Schluter E, Jacoby J, Rodicio R (1998) Investigation of two yeast genes encoding putative isoenzymes of phosphoglycerate mutase. Yeast 14:203–213. doi:10.1002/(SICI)1097-0061(199802)14:3<203::AID-YEA205>3.0.CO;2-8
59. Herrero P, Galindez J, Ruiz N, Martinez-Campa C, Moreno F (1995) Transcriptional regulation of the Saccharomyces cerevisiae HXK1, HXK2 and GLK1 genes. Yeast 11:137–144. doi:10.1002/yea.320110205
60. Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26:1155–1160. doi:10.1038/nbt1492
61. Hess B, Haeckel R, Brand K (1966) FDP-activation of yeast pyruvate kinase. Biochem Bioph Res Co 24:824–831. doi:10.1016/0006-291X(66)90322-6
62. Hildebrand A, Schlacta T, Warmack R, Kasuga T, Fan Z (2013) Engineering Escherichia coli for improved ethanol production from gluconate. J Biotechnol 168:101–106. doi:10.1016/j.jbiotec.2013.07.033
63. Hitzeman RA, Hagie FE, Hayflick JS, Chen CY, Seeburg PH, Derynck R (1982) The primary structure of the Saccharomyces cerevisiae gene for 3-phosphoglycerate kinase. Nucleic Acids Res 10:7791–7808. doi:10.1093/nar/10.23.7791
64. Hodgman CE, Jewett MC (2012) Cell-free synthetic biology: thinking outside the cell. Metab Eng 14:261–269. doi:10.1016/j.ymben.2011.09.002
65. Hohmann S, Mager WH (2003) Yeast stress responses. Springer, New York
66. Holland JP, Holland MJ (1980) Structural comparison of two nontandemly repeated yeast glyceraldehyde-3-phosphate dehydrogenase genes. J Biol Chem 255:2596–2605, PMID: 6244283
67. Holland MJ, Holland JP, Thill GP, Jackson KA (1981) The primary structures of two yeast enolase genes. Homology between the 5ʹ noncoding flanking regions of yeast enolase and glyceraldehyde-3-phosphate dehydrogenase genes. J Biol Chem 256:1385–1395, PMID: 6256394
68. Jandt U, You C, Zhang YH-P, Zeng A-P (2013) Compartmentalization and metabolic channeling for multienzymatic biosynthesis: practical strategies and modeling approaches. Adv Biochem Eng Biotechnol 137:41–65. doi:10.1007/10_2013_221
69. Jeon BY, Park DH (2010) Improvement of ethanol production by electrochemical redox coupling of Zymomonas mobilis and Saccharomyces cerevisiae. J Microbiol Biotechnol 20:94–100. doi:10.4014/jmb.0904.04029
70. Jewett MC, Calhoun KA, Voloshin A, Wuu JJ, Swartz JR (2008) An integrated cell-free metabolic platform for protein production and synthetic biology. Mol Syst Biol 4:220. doi:10.1038/msb.2008.57
71. Johansson TB, Kelly H, Reddy AKN, Williams RH (1993) Renewable fuels and electricity for a growing world economy—defining and achieving the potential. In: Johansson TB, Kelly H, Reddy AKN, Williams RH (eds) Renewable energy: sources for fuels and electricity. Island Press, Washington, DC, pp 1–71
72. Kádár Z, Szengyel Z, Réczey K (2004) Simultaneous saccharification and fermentation (SSF) of industrial wastes for the production of ethanol. Ind Crop Prod 20:103–110. doi:10.1016/j.indcrop.2003.12.015
73. Kawasaki G, Fraenkel DG (1982) Cloning of yeast glycolysis genes by complementation. Biochem Bioph Res Co 108:1107–1122. doi:10.1016/0006-291X(82)92114-3
74. Kellermann E, Seeboth PG, Hollenberg CP (1986) Analysis of the primary structure and promoter function of a pyruvate decarboxylase gene (PDC1) from Saccharomyces cerevisiae. Nucleic Acids Res 14:8963–8977. doi:10.1093/nar/14.22.8963
75. Khattak WA, Ul-Islam M, Park JK (2012) Prospects of reusable endogenous hydrolyzing enzymes in bioethanol production by simultaneous saccharification and fermentation. Korean J Chem Eng 29:1467–1482. doi:10.1007/s11814-012-0174-1
76. Khattak WA, Kang M, Ul-Islam M, Park JK (2013a) Partial purification of saccharifying and cell wall-hydrolyzing enzymes from malt in waste from beer fermentation broth. Bioprocess Biosyst Eng 36:737–347. doi:10.1007/s00449-013-0899-1
77. Khattak WA, Khan T, Ha JH, Ul-Islam M, Kang MK, Park JK (2013b) Enhanced production of bioethanol from waste of beer fermentation broth at high temperature through consecutive batch strategy by simultaneous saccharification and fermentation. Enzyme Microb Technol 53:322–330. doi:10.1016/j.enzmictec.2013.07.004
78. Khattak WA, Ul-Islam M, Ullah MW, Yu B, Khan S, Park JK (2014) Yeast cell-free enzyme system for bioethanol production at elevated temperature. Process Biochem 49:357–364. doi:10.1016/j.procbio.2013.12.019
79. Kim TW, Chokhawala H, Hess M, Dana CM, Baer Z, Sczyrba A, Rubin EM, Blanch HW, Clark DS (2011) High-throughput in vitro glycoside hydrolase (HIGH) screening for enzyme discovery. Angew Chem Int Ed Engl 50:11215–11218. doi:10.1002/anie.201104685
80. Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA (2009) Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol 392:319–333. doi:10.1016/j.jmb.2009.03.056
81. Kopperschläger G, Heinisch JJ (1997). Phosphofructokinase. In: Zimmermann FK and Entian K-D (ed) Yeast sugar metabolism. Biochemistry, Genetics, Biotechnology, and Applications, Technomic, Lancaster, PA. pp 97–118.
82. Kourkoutas Y, Bekatorou A, Banatb IM, Marchant R, Koutinas AA (2004) Immobilization technologies and support materials suitable in alcohol beverages production: a review. Food Microbiol 2:377–397. doi:10.1016/j.fm.2003.10.005
83. Lam KS, Wassink JWDG (1990) Enzymatic digestion of spent yeast cells for nutrient recycling in inulase production. J Ind Microbiol 6:207–210. doi:10.1007/BF01577697
84. Le Borgne S (2012) Genetic engineering of industrial strains of Saccharomyces cerevisiae. Methods Mol Biol 824:451–465. doi:10.1007/978-1-61779-433-9_24
85. Liu D, Zeng X-A, Sun D-W, Han Z (2013) Disruption and protein release by ultrasonication of yeast cells. Innov Food Sci Emerg 18:132–137. doi:10.1016/j.ifset.2013.02.006
86. Ljungcrantz P, Carlsson H, Mansson MO, Buckel P, Mosbach K, Bulow L (1989) Construction of an artificial bifunctional enzyme, beta-galactosidase/galactose dehydrogenase, exhibiting efficient galactose channeling. Biochemistry 28:8786–8792. doi:10.1021/bi00448a016
87. Lobo Z (1984) Saccharomyces cerevisiae aldolase mutants. J Bacteriol 160:222–226
88. Lobo Z, Maitra PK (1977) Resistance to 2-deoxyglucose in yeast: a direct selection of mutants lacking glucose-phosphorylating enzymes. Mol Gen Genet 157:297–300. doi:10.1007/BF00268666
89. Lodish H, Berk A, Zipursky SL, P Matsudaira, Baltimore D, James Darnell (2000) Molecular cell biology. 4th Edition. New York: W. H. Freeman. Section 5.2, Purification of cells and their parts
90. Lu C (2011) Butanol production from lignocellulosic feedstocks by acetone-butanol-ethanol fermentation with integrated product recovery. The Ohio State University, Dissertation
91. Lu G, Dobritzsch D, Baumann S, Schneider G, Konig S (2000) The structural basis of substrate activation in yeast pyruvate decarboxylase. A crystallographic and kinetic study. Eur J Biochem 267:861–868. doi:10.1046/j.1432-1327.2000.01070.x
92. Madin K, Sawasaki T, Ogasawara T, Endo Y (2000) A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes. Proc Natl Acad Sci USA 97:559–564. doi:10.1073/pnas.97.2.559
93. Mager WH, Winderickx J (2005) Yeast as a model for medical and medicinal research. Trends Pharmacol Sci 26:265–273. doi:10.1016/j.tips.2005.03.004
94. Mai NL, Kim SH, Ha SH, Shin HS, Koo Y-M (2013) Selective recovery of acetone-butanol-ethanol from aqueous mixture by pervaporation. Korean J Chem Eng 30:1804–1809. doi:10.1007/s11814-013-0116-6
95. Maitra PK, Lobo Z (1977) Yeast pyruvate kinase: a mutant from catalytically insensitive to fructose 1,6-bisphosphate. Eur J Biochem 78:353–360. doi:10.1111/j.1432-1033.1977.tb11747.x
96. Malilas W, Kang SW, Kim SB, Yoo HY, Chulalaksananukul W, Kim SW (2013) Lipase from Penicillium camembertii KCCM 11268: optimization of solid state fermentation and application to biodiesel production. Korean J Chem Eng 30:405–512. doi:10.1007/s11814-012-0132-y
97. Mansson MO, Siegbahn N, Mosbach K (1983) Site-to-site directed immobilization of enzymes with bis-NAD analogues. Proc Natl Acad Sci USA 80:1487–1491. doi:10.1073/pnas.80.6.1487
98. Martz E (1966) A centrifuge for rapid concentration of large fragile cells without extensive lysis. J Protozool 13:380–382. doi:10.1111/j.1550-7408.1966.tb01924.x
99. Mateo C, Chmura A, Rustler S, van Rantwijk F, Stolz A, Sheldon RA (2006) Synthesis of enantiomerically pure (S)-mandelic acid using an oxynitrilase–nitrilase bienzymatic cascade: a nitrilase surprisingly shows nitrile hydratase activity. Tetrahedron: Asymmetry 17:320–323. doi:10.1016/j.tetasy.2006.01.020
100. McAlister L, Holland MJ (1982) Targeted deletion of a yeast enolase structural gene Identification and isolation of yeast enolase isozymes. J Biol Chem 257:7181–7188, PMID: 6282834
101. McAlister L, Holland MZ (1985) Differential expression of the three yeast glyceraldehyde-3-phosphate dehydrogenase genes. J Biol Chem 260:15019–15027. doi:10.1371/journal.pgen.1003871
102. McLain AL, Szweda PA, Szweda LI (2011) Ketoglutarate dehydrogenase: a mitochondrial redox sensor. Free Radic Res 45(1):29–36. doi:10.3109/10715762.2010.534163
103. Melzoch K, Rychtera M, Hábová V (1994) Effect of immobilization upon the properties and behaviour of Saccharomyces cerevisiae cells. J Biotechnol 32:59–65. doi:10.1016/0168-1656(94)90120-1
104. Meynial SI, Forchhammer N, Croux C, Girbal L, Soucaille P (2007) Evolution of a Saccharomyces cerevisiae metabolic pathway in Escherichia coli. Metab Eng 9:152–159. doi:10.1016/j.ymben.2006.09.002
105. Moehlenbrock MJ, Toby TK, Waheed A, Minteer SD (2010) Metabolon catalyzed pyruvate/air biofuel cell. J Am Chem Soc 132:6288–6289. doi:10.1021/ja101326b
106. Moore PA, Sagliocco FA, Wood RM, Brown AJP (1991) Yeast glycolytic mRNAs are differentially regulated. Mol Cell Biol 11:5330–5337. doi:10.1128/MCB.11.10.5330
107. Morris CN, Ainsworth S, Kinderlerer J (1986) The regulatory properties of yeast pyruvate kinase. Effect of fructose 1,6-bisphosphate. Biochem J 234:691–698
108. Murtas G, Kuruma Y, Bianchini P, Diaspro A, Luisi PL (2007) Protein synthesis in liposomes with a minimal set of enzymes. Biochem Biophys Res Commun 363:12–17. doi:10.1016/j.bbrc.2007.07.201
109. Najafpour G, Younesi H, Ismail KSK (2004) Ethanol fermentation in an immobilized cell reactor using Saccharomyces cerevisiae. Bioresour Technol 92:251–260. doi:10.1016/j.biortech.2003.09.009
110. Nishizawa M, Araki R, Teranishi Y (1989) Identification of an upstream activating sequence and an upstream repressible sequence of the pyruvate kinase gene of the yeast Saccharomyces cerevisiae. Mol Cell Biol 9:442–451. doi:10.1128/MCB.9.2.442
111. Norton S, D’Amore T (1994) Physiological effects of yeast cell immobilization: applications for brewing. Enzym Microb Tech 16:365–375. doi:10.1007/s10482-013-9978-1
112. Pancholi V (2001) Multifunctional alpha-enolase: its role in diseases. Cell Mol Life Sci 58:902–920, PMID: 11497239
113. Panesar PS, Marwaha SS, Kumar H (2010) Enzymes in food processing: fundamentals and potential applications. IK International Publishing House, New Delhi, p 11
114. Panke S, Held M, Wubbolts M (2004) Trends and innovations in industrial biocatalysis for the production of fine chemicals. Curr Opin Biotechnol 15:272–279. doi:10.1016/j.copbio.2004.06.011
115. Park N, Um SH, Funabashi H, Xu J, Luo D (2009) A cell-free protein-producing gel. Nat Mater 8:432–437. doi:10.1038/nmat2419
116. Parsons JB, Frank S, Bhella D, Liang M, Prentice MB, Mulvihill DP, Warren MJ (2010) Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement. Mol Cell 38:305–315. doi:10.1016/j.molcel.2010.04.008
117. Prasad S, Singh A, Joshi HC (2007) Ethanol as an alternative fuel from agricultural, industrial and urban residues. Resour Conserv Recy 50:1–39. doi:10.1016/j.resconrec.2006.05.007
118. Prasetyo PJ, Park EY (2013) Waste paper sludge as a potential biomass for bio-ethanol production. Korean J Chem Eng 30:253–261. doi:10.1007/s11814-013-0003-1
119. Prevost H, Divies C (1987) Fresh fermented cheese production with continuous pre-fermented milk by a mixed culture of mesophilic lactic streptococci entrapped in Ca-alginate. Biotechnol Lett 9:789–794. doi:10.1007/BF01028285
120. Prevost H, Divies C (1992) Cream fermentation by a mixed culture of lactococci entrapped in two-layer calcium alginate gel beads. Biotechnol Lett 14:583–588
121. Ratanapongleka K (2010) Recovery of biological products in aqueous two phase systems. Int J Chem Eng App 1:191–198. doi:10.1002/jsfa.3956
122. Ravikumar R, Ranganathan BV, Chathoth KN, Gobikrishnan S (2013) Innovative and intensified technology for the biological pretreatment of agro waste for ethanol production. Korean J Chem Eng 30:1051–1057. doi:10.1007/s11814-012-0215-9
123. Rodriguez A, De La Cera T, Herrero P, Moreno F (2001) The hexokinase 2 protein regulates the expression of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae. Biochem J 355:625–631, PMID: 11311123
124. Rollin JA, Tam KT, Zhang Y-HP (2013) New biotechnology paradigm: cell-free biosystems for biomanufacturing. Green Chem 5:1708–1719. doi:10.1039/C3GC40625C
125. Rupp S (2013) Next-generation bioproduction systems: cell-free conversion concepts for industrial biotechnology. Eng Life Sci 13:19–25. doi:10.1002/elsc.201100237
126. Rutter WJ (1960) Aldolase. In: Boyer PD, Lardy HA, Myrbach K (eds) The enzymes 5. Academic, New York, pp 341–366
127. Sampson EM, Bobik TA (2008) Microcompartments for B12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate. J Bacteriol 190:2966–2971. doi:10.1128/JB.01925-07
128. Santangelo GM, Tornow J (1990) Efficient transcription of the glycolytic gene ADH1 and three translational component genes requires the GCR1 product, which can act through TUF/GRF/RAP binding sites. Method Mol Cell Biol 10:859–862. doi:10.1128/MCB.10.2.859
129. Saptoro A, Herng MTH, Teng ELW (2014) Oxygen transfer to cassava starch solutions in an aerated, well-mixed bioreactor: experimental and mass transfer studies. Korean J Chem Eng. doi:10.1007/s11814-013-0251-0
130. Scott EW, Baker HV (1993) Concerted action of the transcriptional activators REB1, RAP1, and GCR1 in the high-level expression of the glycolytic gene TPI. Method Mol Cell Biol 13:543–550. doi:10.1128/MCB.13.1.543
131. Seeboth PG, Bohnsack K, Hollenberg CP (1990) pdc1(0) mutants of Saccharomyces cerevisiae give evidence for an additional structural PDC gene: cloning of PDC5, a gene homologous to PDC1. J Bacteriol 172:678–685
132. Selwood T, Jaffe EK (2011) Dynamic dissociating homo-oligomers and the control of protein function. Arch Biochem Biophys 519:131–143. doi:10.1016/j.abb.2011.11.020
133. Sergienko EA, Jordan F (2002) New model for activation of yeast pyruvate decarboxylase by substrate consistent with the alternating sites mechanism: demonstration of the existence of two active forms of the enzyme. Biochemistry 41:3952–3967. doi:10.1021/bi011860a
134. Shapouri H, James D, Michael W (2002) The energy balance of corn ethanol: an update. United States Department of Agriculture, Report No, 55
135. Sheng J, Huang L, Zhu X, Cai J, Zhinan X (2014) Reconstitution of the peptidoglycan cytoplasmic precursor biosynthetic pathway in cell-free system and rapid screening of antisense oligonucleotides for Mur enzymes. Appl Microbiol Biotechnol 98:1785–1794. doi:10.1007/s00253-013-5467-8
136. Sheu TY, Marshall RT (1993) Microentrapment of lactobacilli in calcium alginate gels. J Food Sci 58:557–561. doi:10.1111/j.1365-2621.1993.tb04323.x
137. Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19:751–755. doi:10.1038/90802
138. Shimono K, Goto M, Kikukawa T, Miyauchi S, Shirouzu M, Kamo N, Yokoyama S (2009) Production of functional bacteriorhodopsin by an Escherichia coli cell-free protein synthesis system supplemented with steroid detergent and lipid. Protein Sci 18:2160–2171. doi:10.1002/pro.230
139. Shirsat SP, Dawande SD, Kakade SS (2013) Simulation and optimization of extractive distillation sequence with pre-separator. Korean J Chem Eng 30:2163–2169. doi:10.1007/s11814-013-0175-8
140. Simpson RJ (2011) Disruption of cultured cells by nitrogen cavitation. Cold Spring Harb Protoc. doi:10.1101/pdb.prot5513
141. Singer MA, Lindquist S (1998) Multiple effects of trehalose on protein folding in vitro and in vivo. Mol Cell 1:639–648. doi:10.1016/S1097-2765(00)80064-7
142. Steenson LR, Klaenhammer TR, Swaisgood HE (1987) Calcium alginate-immobilized cultures of lactic streptococci are protected from attack by lytic bacteriophage. J Dairy Sci 70:1121–1127. doi:10.3168/jds.S0022-0302(87)80121-2
143. Takamitsu I, Izumida H, Akagi Y, Sakamoto M (1993) Continuous ethanol fermentation in molasses medium using Zymomonas mobilis immobilized in photo-cross linkable resin gels. J Ferment Bioeng 75:32–35. doi:10.1016/0922-338X(93)90174-7
144. Taskova RM, Zorn H, Krings U, Bouws H, Berger RG (2006) A comparison of cell wall disruption techniques for the isolation of intracellular metabolites from Pleurotus and Lepista sp. J Biosci 61:347–350
145. Tekamp-Olson P, Najarian R, Burke RL (1988) The isolation, characterization and nucleotide sequence of the phosphoglucoisomerase gene of Saccharomyces cerevisiae. Gene 73:153–161. doi:10.1016/0378-1119(88)90321-6
146. ter Schure EG, Flikweert MT, van Dijken JP, Pronk JT, Verrips CT (1998) Pyruvate decarboxylase catalyzes decarboxylation of branched-chain 2-oxo acids but is not essential for fusel alcohol production by Saccharomyces cerevisiae. Appl Environ Microb 64:1303–1307
147. Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, Snoep JL (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
148. Tran L, Broadhurst RW, Tosin M, Cavalli A, Weissman KJ (2010) Insights into protein–protein and enzyme-substrate interactions in modular polyketide synthases. Chem Biol 17:705–716. doi:10.1016/j.chembiol.2010.05.017
149. Trott A, Morano KA (2003) The yeast response to heat shock. In: Hohmann S, Mager WH (eds) Yeast Stress Responses. Springer, NewYork, pp 71–119
150. Ullah MW, Khattak WA, Ul-Islam M, Khan S, Park JK (2014) Bio-ethanol production through simultaneous saccharification and fermentation using an encapsulated reconstituted cell-free enzyme system. Biochem Eng J 91:110–119. doi:10.1016/j.bej.2014.08.006
151. van Dijken JP, Weusthuis RA, Pronk JT (1993) Kinetics of growth and sugar consumption in yeasts. A Van Leeuw 63:343–352. doi:10.1007/BF00871229
152. van Dongen S, Nallani M, Cornelissen J, Nolte R, van Hest J (2009) A three-enzyme cascade reaction through positional assembly of enzymes in a polymersome nanoreactor. Chemistry 15:1107–1114. doi:10.1002/chem.200802114
153. Vijayakrishnan S, Kelly S, Gilbert R, Callow P, Bhella D, Forsyth T, Lindsay J, Byron O (2010) Solution structure and characterisation of the human pyruvate dehydrogenase complex core assembly. J Mol Biol 399:71–93. doi:10.1016/j.jmb.2010.03.043
154. Walsh RB, Kawasaki G, Fraenkel DG (1983) Cloning of genes that complement yeast hexokinase and glucokinase mutants. J Bacteriol 154:1002–1004
155. Wang F-S, Li C-C, Lin Y-S, Lee W-C (2013) Enhanced ethanol production by continuous fermentation in a two-tank system with cell recycling. Process Biochem 48:1425–1428. doi:10.1016/j.procbio.2013.06.023
156. Welch P, Scopes RK (1985) Studies on cell-free metabolism: ethanol production by a yeast glycolytic system reconstituted from purified enzymes. J Biotechnol 2:257–273. doi:10.1016/0168-1656(85)90029-X
157. Wernick DG, Liao JC (2013) Protein-based biorefining: metabolic engineeringfor production of chemicals and fuel with regeneration of nitrogen fertilizers. Appl Microbiol Biotechnol 97:1397–1406. doi:10.1007/s00253-012-4605-z
158. Wilner OI, Weizmann Y, Gill R, Lioubashevski O, Freeman R, Willner I (2009) Enzyme cascades activated on topologically programmed DNA scaffolds. Nat Nanotechnol 4:249–254. doi:10.1038/nnano.2009.50
159. Won KY, Kim YS, Oh KK (2012) Comparison of bio-ethanol production of simultaneoussaccharification and fermentation and separation hydrolysis and fermentationfrom cellulose-rich barley straw. Korean J Chem Eng 29:1341–1346. doi:10.1007/s11814-012-0019-y
160. Xu J, Taylor KB (1993) Characterization of ethanol production from xylose and xylitol by a cell-free Pachysolen tannophilus system. Appl Environ Microbiol 59:231–235
161. Yeng ALY, Ab Kadir MS, Ghazali HM, Abd Rahman RNZR (2013) A comparative study of extraction techniques for maximum recovery of glutamate decarboxylase (GAD) from Aspergillus oryzae NSK. BMC Res Notes 6:526. doi:10.1186/1756-0500-6-526
162. Ylitervo P, Franzén CJ, Taherzadeh MJ (2011) Ethanol production at elevated temperatures using encapsulation of yeast. J Biotechnol 156:22–29. doi:10.1016/j.jbiotec.2011.07.018
163. You C, Zhang YHP (2012) Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling. ACS Synth Biol 2:102–110. doi:10.1021/sb300068g
164. You C, Zhang YH (2013) Cell-free biosystems for biomanufacturing. Adv Biochem Eng Biotechnol 131:89–119. doi:10.1007/10_2012_159
165. You C, Myung S, Zhang YHP (2012) Facilitated substrate channeling in a self-assembled trifunctional enzyme complex. Angew Chem Int Edit 51:8787–8790. doi:10.1002/anie.201202441
166. Zaks A (2001) Industrial biocatalysis. Curr Opin Chem Biol 5:130–136. doi:10.1016/S1367-5931(00)00181-2
167. Zhang Y-HP (2009) A sweet out-of-the-box solution to the hydrogen economy: Is the sugar-powered car science fiction? Energy Environ Sci 2:272–282. doi:10.1039/B818694D
168. Zhang Y-HP (2010) Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: challenges and opportunities. Biotechnol Bioeng 105:663–677. doi:10.1002/bit.22630
169. Zhang YH, Lynd LR (2004) Toward an aggregated understanding of enzymatic hydrolysis of cellulose: noncomplexed cellulase systems. Biotechnol Bioeng 88:797–824. doi:10.1002/bit.20282
170. Zhu Z, Tam TK, Zhang Y-HP (2013) Cell-free biosystems in the production of electricity and bioenergy. Adv Biochem Eng Biotechnol 137:125–152. doi:10.1007/10_2013_201