Synthetic metabolic engineering-a novel, simple technology for designing a chimeric metabolic pathway

Microbial Cell Factories

Volumn 11, Issue , 2012, Pages

  Ye, Xiaoting ^a   Honda, Kohsuke ^a,b   Sakai, Takaaki ^a   Okano, Kenji ^a   Omasa, Takeshi ^a,c   Hirota, Ryuichi ^d   Kuroda, Akio ^d   Ohtake, Hisao ^a  

^a OSAKA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c UNIVERSITY OF TOKUSHIMA   (Japan)

^d HIROSHIMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; LACTATE DEHYDROGENASE;

ARTICLE; ESCHERICHIA COLI; METABOLIC ENGINEERING; NONHUMAN; PYROCOCCUS HORIKOSHII; STOICHIOMETRY; SYNTHETIC BIOLOGY; SYNTHETIC METABOLIC ENGINEERING; THERMOCOCCUS KODAKARENSIS; THERMUS THERMOPHILUS;

ADENOSINE TRIPHOSPHATE; ESCHERICHIA COLI; GLUCOSE; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASES; HYDROGEN-ION CONCENTRATION; LACTIC ACID; MALATE DEHYDROGENASE; METABOLIC ENGINEERING; PHOSPHOGLYCERATE MUTASE; PYROCOCCUS; TEMPERATURE; THERMOCOCCUS; THERMUS THERMOPHILUS;

PYROCOCCUS HORIKOSHII; THERMOCOCCUS KODAKARENSIS; THERMUS; THERMUS THERMOPHILUS;

EID: 84865800305     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-11-120     Document Type: Article

References (42)

1. Rohlin L, Oh MK, Liao JC. Microbial pathway engineering for industrial processes: evolution, combinatorial biosynthesis and rational design. Curr Opin Microbiol 2001, 4:330-335. 10.1016/S1369-5274(00)00213-7, 11378488.
2. Stephanopoulos G. Challenges in engineering microbes for biofuels production. Science 2007, 315:801-804. 10.1126/science.1139612, 17289987.
3. Stephanopoulos G, Sinskey AJ. Metabolic engineering-methodologies and future prospects. Trends Biotechnol 1993, 11:392-396. 10.1016/0167-7799(93)90099-U, 7764086.
4. Kwok R. Five hard truths for synthetic biology. Nature 2010, 463:288-290. 10.1038/463288a, 20090726.
5. Zhang YHP. Production of biocommodities and bioelectricity by cell-free synthetic enzymatic pathway biotransformations: challenges and opportunities. Biotechnol Bioeng 2010, 105:663-677.
6. Hodgman CE, Jewett MC. Cell-free synthetic biology: thinking outside the cell. Metab Eng 2012, 14:261-269. 10.1016/j.ymben.2011.09.002, 21946161.
7. Welch P, Scopes RK. Studies on cell-free metabolism: Ethanol production by a yeast glycolytic system reconstituted from purified enzymes. J Biotechnol 1985, 2:257-273.
8. Algar EM, Scopes RK. Studies on cell-free metabolism: Ethanol production by extracts of Zymomonas mobilis. J Biotechnol 1985, 2:275-287.
9. Demirjian DC, Morís-Varas F, Cassidy CS. Enzymes from extremophiles. Curr Opin Chem Biol 2001, 5:144-151. 10.1016/S1367-5931(00)00183-6, 11282340.
10. Niehaus F, Bertoldo C, Kähler M, Antranikian G. Extremophiles as a source of novel enzymes for industrial application. Appl Microbiol Biotechnol 1999, 51:711-729. 10.1007/s002530051456, 10422220.
11. Honda K, Maya S, Omasa T, Hirota R, Kuroda A, Ohtake H. Production of 2-deoxyribose 5-phosphate from fructose to demonstrate a potential of artificial bio-synthetic pathway using thermophilic enzymes. J Biotechnol 2010, 148:204-207. 10.1016/j.jbiotec.2010.06.008, 20547190.
12. Sato M, Masuda Y, Kirimura K, Kino K. Thermostable ATP regeneration system using polyphosphate kinase from Thermosynechococcus elongatus BP-1 for D-amino acid dipeptide synthesis. J Biosci Bioeng 2007, 103:179-184. 10.1263/jbb.103.179, 17368402.
13. Iwamoto S, Motomura K, Shinoda Y, Urata M, Kato J, Takiguchi N, Ohtake H, Hirota R, Kuroda A. Use of an Escherichia coli recombinant producing thermostable polyphosphate kinase as an ATP regenerator to produce fructose 1,6-diphosphate. Appl Environ Microbiol 2007, 73:5676-5678. 10.1128/AEM.00278-07, 2042086, 17616610.
14. Wang Y, Zhang YHP. Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration. Microb Cell Fact 2009, 8:30. 10.1186/1475-2859-8-30, 2701922, 19497097.
15. Yao S, Mikkelsen MJ. Metabolic engineering to improve ethanol production in Thermoanaerobacter mathranii. Appl Microbiol Biotechnol 2010, 88:199-208. 10.1007/s00253-010-2703-3, 20552355.
16. Wichmann R, Vasic-Racki D. Cofactor regeneration at the lab scale. Adv Biochem Eng Biotechnol 2005, 92:225-260.
17. Verhees CH, Kengen SW, Tuininga JE, Schut GJ, Adams MW, de Vos WM, van der Oost J. The unique features of glycolytic pathways in Archaea. Biochem J 2003, 375:231-246. 10.1042/BJ20021472, 1223704, 12921536.
18. Dandekar T, Schuster S, Snel B, Huynen M, Bork P. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem J 1999, 343:115-124. 10.1042/0264-6021:3430115, 1220531, 10493919.
19. Kengen SWM, Tuininga JE, de Bok FAM, Stams AJM, de Vos WM. Purification and characterization of a novel ADP-dependent glucokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 1995, 270:30453-30457. 10.1074/jbc.270.51.30453, 8530474.
20. Tuininga JE, Verhees CH, van der Oost J, Kengen SW, Stams AJ, de Vos WM. Molecular and biochemical characterization of the ADP-dependent phosphofructokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 1999, 274:21023-21028. 10.1074/jbc.274.30.21023, 10409652.
21. Mukund S, Adams MW. Glyceraldehyde-3-phosphate ferredoxin oxidoreductase, a novel tungsten-containing enzyme with a potential glycolytic role in the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 1995, 270:8389-8392. 10.1074/jbc.270.15.8389, 7721730.
22. Brunner NA, Brinkmann H, Siebers B, Hensel R. NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. The first identified archaeal member of the aldehyde dehydrogenase superfamily is a glycolytic enzyme with unusual regulatory properties. J Biol Chem 1998, 273:6149-6156. 10.1074/jbc.273.11.6149, 9497334.
23. Ettema TJ, Ahmed H, Geerling AC, van der Oost J, Siebers B. The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway. Extremophiles 2007, 12:75-88.
24. Matsubara K, Yokooji Y, Atomi H, Imanaka T. Biochemical and genetic characterization of the three metabolic routes in Thermococcus kodakarensis linking glyceraldehyde 3-phosphate and 3-phosphoglycerate. Mol Microbiol 2011, 81:1300-1312. 10.1111/j.1365-2958.2011.07762.x, 21736643.
25. Dumbrepatil A, Adsul M, Chaudhari S, Khire J, Gokhale D. Utilization of molasses sugar for lactic acid production by Lactobacillus delbrueckii subsp. delbrueckiimutant Uc-3 in batch fermentation. Appl Environ Microbial 2008, 74:333-335.
26. Joglekar HG, Rahman I, Babu S, Kulkarni BD, Joshi A. Comparative assessment of downstream processing options for lactic acid. Sep Purif Tech 2006, 52:1-17.
27. Kim YH, Moon SH. Lactic acid recovery from fermentation broth using one-stage electrodialysis. J Chem Technol 2001, 76:169-178.
28. Wu JT, Wu LH, Knight JA. Stability of NADPH: effect of various factors on the kinetics of degradation. Clin Chem 1986, 32:314-319.
29. González JM, Masuchi Y, Robb FT, Ammerman JW, Maeder DL, Yanagibayashi M, Tamaoka J, Kato C. Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles 1998, 2:123-130. 10.1007/s007920050051, 9672687.
30. Oshima T, Imahori K. Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a nonsporulating thermophilic bacterium from a Japanese Thermal Spa. Int J Syst Bacteriol 1974, 24:102-112.
31. Johnsen U, Schönheit P. Characterization of cofactor-dependent and cofactor-independent phosphoglycerate mutases from Archaea. Extremophiles 2007, 11:647-657. 10.1007/s00792-007-0094-x, 17576516.
32. Garvie EI. Bacterial lactate dehydrogenases. Microbiol Rev 1980, 44:106-139. 373236, 6997721.
33. Yokoyama S, Matsuo Y, Hirota H, Kigawa T, Shirouzu M, Kuroda Y, Kurumizaka H, Kawaguchi S, Ito Y, Shibata T, Kainosho M, Nishimura Y, Inoue Y, Kuramitsu S. Structural genomics projects in Japan. Nat Struct Biol 2000, 7:943-945.
34. Itoh A, Ohashi Y, Soga T, Mori H, Nishioka T, Tomita M. Application of capillary electrophoresis-mass spectrometry to synthetic in vitro glycolysis studies. Electrophoresis 2004, 25:1996-2002. 10.1002/elps.200305905, 15237399.
35. Meadow ND, Fox DK, Roseman S. The bacterial phosphoenolpyruvate: glycose phosphotransferase system. Annu Rev Biochem 1990, 59:497-542. 10.1146/annurev.bi.59.070190.002433, 2197982.
36. Postma PW, Lengeler JW, Jacobson GR. Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol Rev 1993, 57:543-594. 372926, 8246840.
37. Lee JW, Kim TY, Jang YS, Choi S, Lee SY. Systems metabolic engineering for chemicals and materials. Trends Biotechnol 2011, 29:370-378. 10.1016/j.tibtech.2011.04.001, 21561673.
38. Valverde F, Losada M, Serrano A. Engineering a central metabolic pathway: glycolysis with no net phosphorylation in an Escherichia coli gap mutant complemented with a plant GapN gene. FEBS Lett 1999, 449:153-158. 10.1016/S0014-5793(99)00430-5, 10338122.
39. Ansell RJ, Lowe CR. Artificial redox coenzymes: Biomimetic analogues of NAD+. Appl Microbiol Biotechnol 1999, 51:703-710.
40. Ryan JD, Fish RH, Clark DS. Engineering cytochrome P450 enzymes for improved activity towards biomimetic 1,4-NADH cofactors. Chem Bio Chem 2008, 9:2579-2582.
41. Tuesink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, Snoep JL. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 2000, 267:5313-5329. 10.1046/j.1432-1327.2000.01527.x, 10951190.
42. Conrado RJ, Varner JD, DeLisa MP. Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy. Curr Opin Biotechnol 2008, 19:492-499. 10.1016/j.copbio.2008.07.006, 18725290.