Biosynthetic Pathway Engineering Strategies
Claudia Schmidt-Dannert
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
Search for more papers by this authorAlexander Pisarchik
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
Search for more papers by this authorClaudia Schmidt-Dannert
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
Search for more papers by this authorAlexander Pisarchik
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
Search for more papers by this authorProf. Dr. Stefan Lutz
Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
Search for more papers by this authorProf. Dr. Uwe T. Bornscheuer
Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
Search for more papers by this authorSummary
This chapter contains sections titled:
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Introduction
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Initial Pathway Design
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Optimization of the Precursor Supply
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Engineering of Control Loops
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Engineering of Alternative Precursor Routes
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Balancing Gene Expression Levels and Activities of Metabolic Enzymes
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Metabolic Network Integration and Optimization
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Engineering Pathways for the Production of Diverse Compounds
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Future Perspectives
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Abbreviations
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References
References
- Bailey, J.E. (1991) Toward a science of metabolic engineering. Science, 252, 1668–75.
- Nielsen, J. (2001) Metabolic engineering. Applied Microbiology and Biotechnology, 55, 263–83.
- Hibbert, E.G., Baganz, F., Hailes, H.C., Ward, J.M., Lye, G.J., Woodley, J.M. and Dalby, P.A. (2005) Directed evolution of biocatalytic processes. Biomolecular Engineering, 22, 11–19.
- Koffas, M. (2005) Evolutionary metabolic engineering. Metabolic Engineering, 7, 1–3.
- McDaniel, R. and Weiss, R. (2005) Advances in synthetic biology: on the path from prototypes to applications. Current Opinion in Biotechnology, 16, 476–83.
- Watts, K.T., Mijts, B.N. and Schmidt-Dannert, C. (2005) Current and emerging approaches for natural product biosynthesis in microbial cells. Advanced Synthesis and Catalysis, 347, 927–40.
- Tyo, K.E., Alper, H.S. and Stephanopoulos, G.N. (2007) Expanding the metabolic engineering toolbox: more options to engineer cells. Trends in Biotechnology, 25, 132–7.
- Sacchettini, J.C. and Poulter, C.D. (1997) Creating isoprenoid diversity. Science, 277, 1788–9.
- Fraga, B.M. (2006) Natural sesquiterpenoids. Natural Product Reports, 23, 943–72.
- Hanson, J.R. (2006) Diterpenoids. Natural Product Reports, 23, 875–85.
- Vershinin, A. (1999) Biological functions of carotenoids – diversity and evolution. Biofactors, 10, 99–104.
- Lee, P.C. and Schmidt-Dannert, C. (2002) Metabolic engineering towards biotechnological production of carotenoids in microorganisms. Applied Microbiology and Biotechnology, 60, 1–11.
- Klein-Marcuschamer, D., Ajikumar, P.K. and Stephanopoulos, G. (2007) Engineering microbial cell factories for biosynthesis of isoprenoid molecules: beyond lycopene. Trends in Biotechnology, 25, 417–24.
- Maury, J., Asadollahi, M.A., Moller, K., Clark, A. and Nielsen, J. (2005) Microbial isoprenoid production: an example of green chemistry through metabolic engineering. Advances in Biochemical Engineering/Biotechnology, 100, 19–51.
-
Sandmann, G.
(2002)
Combinatorial biosynthesis of carotenoids in a heterologous host: a powerful approach for the biosynthesis of novel structures.
ChemBioChem,
3,
629–35.
10.1002/1439-7633(20020703)3:7<629::AID-CBIC629>3.0.CO;2-5 CAS PubMed Web of Science® Google Scholar
- Fraser, P.D., Misawa, N., Linden, M., Yamano, S., Kobayashi, K. and Sandmann, G. (1992) Expression in Escherichia coli, purification, and reactivation of the recombinant Erwinia uredovora phytoene desaturase. The Journal of Biological Chemistry, 267, 19891–5.
- Cunningham, F., Chamovitz, D., Misawa, N., Gantt, E. and Hirschberg, J. (1993) Cloning and functional expression in Escherichia coli of a cyanobacterial gene for lycopene cyclase, the enzyme that catalyzes the biosynthesis of beta-carotene. FEBS Letters, 328, 130–8.
- Bauer, C., Bollivar, D. and Suzuki, J. (1993) Genetic analysis of photopigment biosynthesis in eubacteria – a guiding light for algae and plants. Journal of Bacteriology, 175, 3919–25.
- Armstrong, G. (1994) Eubacteria show their true colors: genetics of carotenoid pigment biosynthesis from microbes to plants. Journal of Bacteriology, 176, 4795–802.
- Ausich, R. (1994) Production of carotenoids by recombinant DNA technology. Pure and Applied Chemistry, 66, 1057–62.
- Hundle, B. Alberti, M., Nievelstein, V., Beyer, P., Kleinig, H., Armstrong, G., Burke, D. and Hearst, J. (1994) Functional assignment of Erwinia herbicola Eho10 carotenoid genes expressed in Escherichia coli. Molecular and General Genetics, 245, 406–16.
- Sandmann, G. (2003) Novel carotenoids genetically engineered in a heterologous host. Chemistry and Biology, 10, 478–9.
- Sandmann, G., Albrecht, M., Schnurr, G., Knorzer, O. and Boger, P. (1999) The biotechnological potential and design of novel carotenoids by gene combination in Escherichia coli. Trends in Biotechnology, 17, 233–7.
- Armstrong, G.A., Alberti, M., Leach, F. and Hearst, J.E. (1989) Nucleotide sequence, organization, and nature of the protein products of the carotenoid biosynthesis gene cluster of Rhodobacter capsulatus. Molecular and General Genetics, 216, 254–68.
- Misawa, N., Nakagawa, M., Kobayashi, K., Yamano, S., Izawa, Y., Nakamura, K. and Harashima, K. (1990) Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli. Journal of Bacteriology, 172, 6704–12.
- Ruther, A., Misawa, N., Boger, P. and Sandmann, G. (1997) Production of zeaxanthin in Escherichia coli transformed with different carotenogenic plasmids. Applied Microbiology and Biotechnology, 48, 162–7.
- Hausmann, A. and Sandmann, G. (2000) A single five-step desaturase is involved in the carotenoid biosynthesis pathway to beta-carotene and torulene in Neurospora crassa. Fungal Genetics and Biology, 30, 147–53.
- Ruiz-Hidalgo, M.Y., Benito, E., Sandmann, G. and Eslava, A. (1997) The phytoene dehydrogenase gene of Phycomyces: regulation of its expression by blue light and vitamin A. Molecular and General Genetics, 253, 734–44.
- Sandmann, G., Misawa, N., Wiedemann, M., Vittorioso, P., Carattoli, A., Morelli, G. and Macino, G. (1993) Functional identification of al-3 from Neurospora crassa as the gene for geranylgeranyl pyrophosphate synthase by complementation with crt genes, in vitro characterization of the gene product and mutant analysis. Journal of Photochemistry and Photobiology. B, Biology, 18, 245–51.
- Quinlan, R.F., Jaradat, T.T. and Wurtzel, E.T. (2007) Escherichia coli as a platform for functional expression of plant P450 carotene hydroxylases. Archives of Biochemistry and Biophysics, 458, 146–57.
- Pecker, I., Chamovitz, D., Linden, H., Sandmann, G. and Hirschberg, J. (1992) A single polypeptide catalyzing the conversion of phytoene to zeta-carotene is transcriptionally regulated during tomato fruit ripening. Proceedings of the National Academy of Sciences of the United States of America, 89, 4962–6.
- Pecker, I., Gabbay, R., Cunningham, F. and Hirschberg, J. (1996) Cloning and characterization of the cDNA for lycopene beta-cyclase from tomato reveals decrease in its expression during fruit ripening. Plant Molecular Biology, 30, 807–19.
- Cunningham, F., Pogson, B., Sun, Z., McDonald, K., DellaPenna, D. and Gantt, E. (1996) Functional analysis of the beta and epsilon lycopene cyclase enzymes of Arabidopsis reveals a mechanism for control of cyclic carotenoid formation. Plant Cell, 8, 1613–26.
- Tobias, A.V. and Arnold, F.H. (2006) Biosynthesis of novel carotenoid families based on unnatural carbon backbones: a model for diversification of natural product pathways. Biochimica et Biophysica Acta, 1761, 235–46.
- Cheng, Q. (2006) Structural diversity and functional novelty of new carotenoid biosynthesis genes. Journal of Industrial Microbiology and Biotechnology, 33, 552–9.
- Sandmann, G. (2003) Combinatorial biosynthesis of novel carotenoids in E. coli. Methods in Molecular Biology, 205, 303–14.
- Schmidt-Dannert, C. (2000) Engineering novel carotenoids in microorganisms. Current Opinion in Biotechnology, 11, 255–61.
- Schmidt-Dannert, C., Lee, P. and Mitjs, B. (2006) Creating carotenoid diversity in E. coli cells using combinatorial and directed evolution strategies. Phytochemistry Reviews, 5, 67–74.
- Lee, P.C., Momen, A.Z., Mijts, B.N. and Schmidt-Dannert, C. (2003) Biosynthesis of structurally novel carotenoids in Escherichia coli. Chemistry and Biology, 10, 453–62.
- Mijts, B.N., Lee, P.C. and Schmidt-Dannert, C. (2005) Identification of a carotenoid oxygenase synthesizing acyclic xanthophylls: Combinatorial biosynthesis and directed evolution. Chemistry and Biology, 12, 453–60.
- Albrecht, M., Takaichi, S., Steiger, S., Wang, Z.Y. and Sandmann, G. (2000) Novel hydroxycarotenoids with improved antioxidative properties produced by gene combination in Escherichia coli. Nature Biotechnology, 18, 843–6.
- Christianson, D.W. (2006) Structural biology and chemistry of the terpenoid cyclases. Chemical Reviews, 106, 3412–42.
- Chang, M.C. and Keasling, J.D. (2006) Production of isoprenoid pharmaceuticals by engineered microbes. Nature Chemical Biology, 2, 674–81.
- Ro, D.K., Paradise, E.M., Ouellet, M., Fisher, K.J., Newman, K.L., Ndungu, J.M., Ho, K.A., Eachus, R.A., Ham, T.S., Kirby, J. et al. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature, 440, 940–3.
- Martin, V.J., Pitera, D.J., Withers, S.T., Newman, J.D. and Keasling, J.D. (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nature Biotechnology, 21, 796–802.
- Huang, Q., Roessner, C.A., Croteau, R. and Scott, A.I. (2001) Engineering Escherichia coli for the synthesis of taxadiene, a key intermediate in the biosynthesis of taxol. Bioorganic and Medicinal Chemistry, 9, 2237–42.
- DeJong, J.M., Liu, Y.L., Bollon, A.P., Long, R.M., Jennewein, S., Williams, D. and Croteau, R.B. (2006) Genetic engineering of Taxol biosynthetic genes in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 93, 212–24.
- Cyr, A., Wilderman, P.R., Determan, M. and Peters, R.J. (2007) A modular approach for facile biosynthesis of labdane-related diterpenes. Journal of the American Chemical Society, 129, 6684–6.
- Lee, P.C., Mijts, B.N. and Schmidt-Dannert, C. (2004) Investigation of factors influencing production of the monocyclic carotenoid torulene in metabolically engineered Escherichia coli. Applied Microbiology and Biotechnology, 65, 538–46.
-
Johnson, E. and
Schroeder, W.
(1995)
Microbial carotenoids.
Advances in Biochemical Engineering/Biotechnology,
53,
119–78.
10.1007/BFb0102327 Google Scholar
- Shimada, H., Kondo, K., Fraser, P., Miura, Y., Saito, T. and Misawa, N. (1998) Increased carotenoid production by the food yeast Candida utilis through metabolic engineering of the isoprenoid pathway. Applied and Environmental Microbiology, 64, 2676–80.
- Verdoes, J.C., Sandmann, G., Visser, H., Diaz, M., van Mossel, M. and van Ooyen, A.J. (2003) Metabolic engineering of the carotenoid biosynthetic pathway in the yeast Xanthophyllomyces dendrorhous (Phaffia rhodozyma). Applied and Environmental Microbiology, 69, 3728–38.
- Yamano, S., Ishii, T., Nakagawa, M., Ikenaga, H. and Misawa, N. (1994) Metabolic engineering for production of beta-carotene and lycopene in Saccharomyces cerevisiae. Bioscience, Biotechnology and Biochemistry, 58, 1112–14.
- Miura, Y., Kondo, K., Saito, T., Shimada, H., Fraser, P. and Misawa, N. (1998) Production of the carotenoid lycopene, beta-carotene, and astaxanthin in the food yeast Candida utilis. Applied and Environmental Microbiology, 64, 1226–9.
-
Miura, Y.,
Kondo, K.,
Shimada, H.,
Saito, T.,
Nakamura, K. and
Misawa, N.
(1998)
Production of lycopene by the food yeast, Candida utilis that does not naturally synthesize carotenoid.
Biotechnology and Bioengineering,
58,
306–8.
10.1002/(SICI)1097-0290(19980420)58:2/3<306::AID-BIT29>3.0.CO;2-8 CAS PubMed Web of Science® Google Scholar
- Verwaal, R., Wang, J., Meijnen, J.P., Visser, H., Sandmann, G., van den Berg, J.A. and van Ooyen, A.J. (2007) High-level production of beta-carotene in Saccharomyces cerevisiae by successive transformation with carotenogenic genes from Xanthophyllomyces dendrorhous. Applied and Environmental Microbiology, 73, 4342–50.
- Harker, M. and Hirschberg, J. (1997) Biosynthesis of ketocarotenoids in transgenic cyanobacteria expressing the algal gene for beta-C-4-oxygenase, crtO. FEBS Letters, 404, 129–34.
- Garcia-Asua, G., Cogdell, R.J. and Hunter, C.N. (2002) Functional assembly of the foreign carotenoid lycopene into the photosynthetic apparatus of Rhodobacter sphaeroides, achieved by replacement of the native 3-step phytoene desaturase with its 4-step counterpart from Erwinia herbicola. Molecular Microbiology, 44, 233–44.
- Mukoyama, D., Takeyama, H., Kondo, Y. and Matsunaga, T. (2006) Astaxanthin formation in the marine photosynthetic bacterium Rhodovulum sulfidophilum expressing crtI, crtY, crtW and crtZ. FEMS Microbiology Letters, 265, 69–75.
- Ye, R.W., Yao, H., Stead, K., Wang, T., Tao, L., Cheng, Q., Sharpe, P.L., Suh, W., Nagel, E., Arcilla, D. et al. (2007) Construction of the astaxanthin biosynthetic pathway in a methanotrophic bacterium Methylomonas sp. strain 16a. Journal of Industrial Microbiology and Biotechnology, 34, 289–99.
- Tao, L., Wagner, L.W., Rouviere, P.E. and Cheng, Q. (2006) Metabolic engineering for synthesis of aryl carotenoids in Rhodococcus. Applied Microbiology and Biotechnology, 70, 222–8.
- Szczebara, F.M., Chandelier, C., Villeret, C., Masurel, A., Bourot, S., Duport, C., Blanchard, S., Groisillier, A., Testet, E., Costaglioli, P. et al. (2003) Total biosynthesis of hydrocortisone from a simple carbon source in yeast. Nature Biotechnology, 21, 143–9.
- Jennewein, S., Wildung, M.R., Chau, M., Walker, K. and Croteau, R. (2004) Random sequencing of an induced Taxus cell cDNA library for identification of clones involved in Taxol biosynthesis. Proceedings of the National Academy of Sciences of the United States of America, 101, 9149–54.
- Shiba, Y., Paradise, E.M., Kirby, J., Ro, D.K. and Keasling, J.D. (2007) Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metabolic Engineering, 9, 160–8.
- Newman, J.D., Marshall, J., Chang, M., Nowroozi, F., Paradise, E., Pitera, D., Newman, K.L. and Keasling, J.D. (2006) High-level production of amorpha-4,11-diene in a two-phase partitioning bioreactor of metabolically engineered Escherichia coli. Biotechnology and Bioengineering, 95, 684–91.
- Eisenreich, W., Bacher, A., Arigoni, D. and Rohdich, F. (2004) Biosynthesis of isoprenoids via the non-mevalonate pathway. Cellular and Molecular Life Sciences, 61, 1401–26.
- Rohmer, M. (2007) Diversity in isoprene unit biosynthesis: The methylerythritol phosphate pathway in bacteria and plastids. Pure and Applied Chemistry, 79, 739–51.
- Harker, M. and Bramley, P.M. (1999) Expression of prokaryotic 1-deoxy-D-xylulose-5-phosphatases in Escherichia coli increases carotenoid and ubiquinone biosynthesis. FEBS Letters, 448, 115–19.
- Matthews, P.D. and Wurtzel, E.T. (2000) Metabolic engineering of carotenoid accumulation in Escherichia coli by modulation of the isoprenoid precursor pool with expression of deoxyxylulose phosphate synthase. Applied Microbiology and Biotechnology, 53, 396–400.
- Jones, K.L., Kim, S.W. and Keasling, J.D. (2000) Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metabolic Engineering, 2, 328–38.
- Hahn, F.M., Hurlburt, A.P. and Poulter, C.D. (1999) Escherichia coli open reading frame 696 is idi, a nonessential gene encoding isopentenyl diphosphate isomerase. Journal of Bacteriology, 181, 4499–504.
- Kajiwara, S., Fraser, P.D., Kondo, K. and Misawa, N. (1997) Expression of an exogenous isopentenyl diphosphate isomerase gene enhances isoprenoid biosynthesis in Escherichia coli. The Biochemical Journal, 324 (Pt 2), 421–6.
-
Kim, S.W. and
Keasling, J.D.
(2001)
Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production.
Biotechnology and Bioengineering,
72,
408–15.
10.1002/1097-0290(20000220)72:4<408::AID-BIT1003>3.0.CO;2-H CAS PubMed Web of Science® Google Scholar
- Albrecht, M., Misawa, N. and Sandmann, G. (1999) Metabolic engineering of the terpenoid biosynthetic pathway of Escherichia coli for production of the carotenoids beta-carotene and zeaxanthin. Biotechnology Letters, 21, 791–5.
-
Wang, C.W.,
Oh, M.K. and
Liao, J.C.
(1999)
Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli.
Biotechnology and Bioengineering,
62,
235–41.
10.1002/(SICI)1097-0290(19990120)62:2<235::AID-BIT14>3.0.CO;2-U CAS PubMed Web of Science® Google Scholar
-
Pronk, J.T.,
Yde Steensma, H. and
Van Dijken, J.P.
(1996)
Pyruvate metabolism in Saccharomyces cerevisiae.
Yeast,
12,
1607–33.
10.1002/(SICI)1097-0061(199612)12:16<1607::AID-YEA70>3.0.CO;2-4 CAS PubMed Web of Science® Google Scholar
- Servouse, M. and Karst, F. (1986) Regulation of early enzymes of ergosterol biosynthesis in Saccharomyces cerevisiae. The Biochemical Journal, 240, 541–7.
- Dimster-Denk, D. and Rine, J. (1996) Transcriptional regulation of a sterol-biosynthetic enzyme by sterol levels in Saccharomyces cerevisiae. Molecular and Cellular Biology, 16, 3981–9.
- Dimster-Denk, D. et al. (1999) Comprehensive evaluation of isoprenoid biosynthesis regulation in Saccharomyces cerevisiae utilizing the Genome Reporter Matrix. Journal of Lipid Research, 40, 850–60.
- Osborne, T.F., Gil, G., Goldstein, J.L. and Brown, M.S. (1988) Operator constitutive mutation of 3-hydroxy-3-methylglutaryl coenzyme A reductase promoter abolishes protein binding to sterol regulatory element. The Journal of Biological Chemistry, 263, 3380–7.
- Smith, J.R., Osborne, T.F., Brown, M.S., Goldstein, J.L. and Gil, G. (1988) Multiple sterol regulatory elements in promoter for hamster 3-hydroxy-3-methylglutaryl-coenzyme A synthase. The Journal of Biological Chemistry, 263, 18480–7.
- Goldstein, J.L. and Brown, M.S. (1990) Regulation of the mevalonate pathway. Nature, 343, 425–30.
- Wang, X., Sato, R., Brown, M.S., Hua, X. and Goldstein, J.L. (1994) SREBP-1, a membrane-bound transcription factor released by sterol-regulated proteolysis. Cell, 77, 53–62.
- Hua, X., Yokoyama, C., Wu, J., Briggs, M.R., Brown, M.S., Goldstein, J.L. and Wang, X. (1993) SREBP-2, a second basic-helix-loop-helix-leucine zipper protein that stimulates transcription by binding to a sterol regulatory element. Proceedings of the National Academy of Sciences of the United States of America, 90, 11603–7.
- Veen, M. and Lang, C. (2004) Production of lipid compounds in the yeast Saccharomyces cerevisiae. Applied Microbiology and Biotechnology, 63, 635–46.
- Donald, K.A.G., Hampton, R.Y. and Fritz, I.B. (1997) Effects of overproduction of the catalytic domain of 3-hydroxy-3-methylglutaryl coenzyme A reductase on squalene synthesis in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 63, 3341–4.
- Polakowski, T., Stahl, U. and Lang, C. (1998) Overexpression of a cytosolic hydroxymethylglutaryl-CoA reductase leads to squalene accumulation in yeast. Applied Microbiology and Biotechnology, 49, 66–71.
- Shimada, H., Kondo, K., Fraser, P.D., Miura, Y., Saito, T. and Misawa, N. (1998) Increased carotenoid production by the food yeast Candida utilis through metabolic engineering of the isoprenoid pathway. Applied and Environmental Microbiology, 64, 2676–80.
- Jackson, B.E., Hart-Wells, E.A. and Matsuda, S.P. (2003) Metabolic engineering to produce sesquiterpenes in yeast. Organic Letters, 5, 1629–32.
- Szkopinska, A., Swiezewska, E. and Karst, F. (2000) The regulation of activity of main mevalonic acid pathway enzymes: farnesyl diphosphate synthase, 3-hydroxy-3-methylglutaryl-CoA reductase, and squalene synthase in yeast Saccharomyces cerevisiae. Biochemical and Biophysical Research Communications, 267, 473–7.
- Farmer, W.R. and Liao, J.C. (2001) Precursor balancing for metabolic engineering of lycopene production in Escherichia coli. Biotechnology Progress, 17, 57–61.
- Pitera, D.J., Paddon, C.J., Newman, J.D. and Keasling, J.D. (2007) Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metabolic Engineering, 9, 193–207.
- Yoon, S.H. et al. (2006) Enhanced lycopene production in Escherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate. Biotechnology and Bioengineering, 94, 1025–32.
- Vadali, R.V., Fu, Y., Bennett, G.N. and San, K.Y. (2005) Enhanced lycopene productivity by manipulation of carbon flow to isopentenyl diphosphate in Escherichia coli. Biotechnology Progress, 21, 1558–61.
- Tao, L., Jackson, R.E. and Cheng, Q. (2005) Directed evolution of copy number of a broad host range plasmid for metabolic engineering. Metabolic Engineering, 7, 10–17.
- Meynial-Salles, I., Cervin, M.A. and Soucaille, P. (2005) New tool for metabolic pathway engineering in Escherichia coli: one-step method to modulate expression of chromosomal genes. Applied and Environmental Microbiology, 71, 2140–4.
- Alper, H., Fischer, C., Nevoigt, E. and Stephanopoulos, G. (2005) Tuning genetic control through promoter engineering. Proceedings of the National Academy of Sciences of the United States of America, 102, 12678–83.
- Wang, C., Oh, M.K. and Liao, J.C. (2000) Directed evolution of metabolically engineered Escherichia coli for carotenoid production. Biotechnology Progress, 16, 922–6.
- Smolke, C.D., Martin, V.J. and Keasling, J.D. (2001) Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization. Metabolic Engineering, 3, 313–21.
- Kajiwara, S., Kakizono, T., Saito, T., Kondo, K., Ohtani, T., Nishio, N., Nagai, S. and Misawa, N. (1995) Isolation and functional identification of a novel cDNA for astaxanthin biosynthesis from Haematococcus pluvialis, and astaxanthin synthesis in Escherichia coli. Plant Molecular Biology, 29, 343–52.
- Misawa, N., Kajiwara, S., Kondo, K., Yokoyama, A., Satomi, Y., Saito, T., Miki, W. and Ohtani, T. (1995) Canthaxanthin biosynthesis by the conversion of methylene to keto groups in a hydrocarbon beta-carotene by a single-gene. Biochemical and Biophysical Research Communications, 209, 867–76.
- Martin, V.J., Yoshikuni, Y. and Keasling, J.D. (2001) The in vivo synthesis of plant sesquiterpenes by Escherichia coli. Biotechnology and Bioengineering, 75, 497–503.
- Zhang, Y., Perry, K., Vinci, V., Powell, K., Stemmer, W. and del Cardayre, S. (2002) Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature, 415, 644–6.
- Patnaik, R., Louie, S., Gavrilovic, V., Perry, K., Stemmer, W.P.C., Ryan, C.M. and del Cardayre, S. (2002) Genome shuffling of Lactobacillus for improved acid tolerance. Nature Biotechnology, 20, 707–12.
- Dai, M.H. and Copley, S.D. (2004) Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Applied and Environmental Microbiology, 70, 2391–7.
- Dai, M.H., Ziesman, S., Ratcliffe, T., Gill, R.T. and Copley, S.D. (2005) Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. Metabolic Engineering, 7, 45–52.
- Alper, H., Jin, Y.S., Moxley, J.F. and Stephanopoulos, G. (2005) Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metabolic Engineering, 7, 155–64.
- Alper, H., Miyaoku, K. and Stephanopoulos, G. (2006) Characterization of lycopene-overproducing E. coli strains in high cell density fermentations. Applied Microbiology and Biotechnology, 72, 968–74.
- Alper, H., Miyaoku, K. and Stephanopoulos, G. (2005) Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nature Biotechnology, 23, 612–16.
- Kang, M.J., Yoon, S.H., Lee, Y.M., Lee, S.H., Kim, J.E., Jung, K.H., Shin, Y.C. and Kim, S.W. (2005) Enhancement of lycopene production in Escherichia coli by optimization of the lycopene synthetic pathway. Journal of Microbiology and Biotechnology, 15, 880–6.
- Jin, Y.S. and Stephanopoulos, G. (2007) Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli. Metabolic Engineering, 9, 337–47.
- Alper, H. and Stephanopoulos, G. (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metabolic Engineering, 9, 258–67.
- Tsoi, C.J. and Khosla, C. (1995) Combinatorial biosynthesis of “unnatural” natural products: the polyketide example. Chemistry and Biology, 2, 355–62.
- Cane, D.E., Walsh, C.T. and Khosla, C. (1998) Harnessing the biosynthetic code: combinations, permutations, and mutations. Science, 282, 63–8.
- Khersonsky, O., Roodveldt, C. and Tawfik, D.S. (2006) Enzyme promiscuity: evolutionary and mechanistic aspects. Current Opinion in Chemical Biology, 10, 498–508.
- Fischbach, M.A. and Clardy, J. (2007) One pathway, many products. Nature Chemical Biology, 3, 353–5.
- Ohnuma, S., Nakazawa, T., Hemmi, H., Hallberg, A.M., Koyama, T., Ogura, K. and Nishino, T. (1996) Conversion from farnesyl diphosphate synthase to geranylgeranyl diphosphate synthase by random chemical mutagenesis. The Journal of Biological Chemistry, 271, 10087–95.
- Ohnuma, S., Hirooka, K., Hemmi, H., Ishida, C., Ohto, C. and Nishino, T. (1996) Conversion of product specificity of archaebacterial geranylgeranyl-diphosphate synthase. Identification of essential amino acid residues for chain length determination of prenyltransferase reaction. The Journal of Biological Chemistry, 271, 18831–7.
- Ohnuma, S., Hirooka, K., Tsuruoka, N., Yano, M., Ohto, C., Nakane, H. and Nishino, T. (1998) A pathway where polyprenyl diphosphate elongates in prenyltransferase. Insight into a common mechanism of chain length determination of prenyltransferases. The Journal of Biological Chemistry, 273, 26705–13.
- Ohnuma, S., Narita, K., Nakazawa, T., Ishida, C., Takeuchi, Y., Ohto, C. and Nishino, T. (1996) A role of the amino acid residue located on the fifth position before the first aspartate-rich motif of farnesyl diphosphate synthase on determination of the final product. The Journal of Biological Chemistry, 271, 30748–54.
- Tarshis, L.C., Proteau, P.J., Kellogg, B.A., Sacchettini, J.C. and Poulter, C.D. (1996) Regulation of product chain length by isoprenyl diphosphate synthases. Proceedings of the National Academy of Sciences of the United States of America, 93, 15018–23.
- Lee, P.C., Mijts, B.N., Petri, R., Watts, K.T. and Schmidt-Dannert, C. (2004) Alteration of product specificity of Aeropyrum pernix farnesylgeranyl diphosphate synthase (Fgs) by directed evolution. Protein Engineering, Design and Selection, 17, 771–7.
- Lee, P.C., Petri, R., Mijts, B.N., Watts, K.T. and Schmidt-Dannert, C. (2005) Directed evolution of Escherichia coli farnesyl diphosphate synthase (IspA) reveals novel structural determinants of chain length specificity. Metabolic Engineering, 7, 18–26.
- Umeno, D. and Arnold, F.H. (2003) A C35 carotenoid biosynthetic pathway. Applied and Environmental Microbiology, 69, 3573–9.
- Umeno, D. and Arnold, F.H. (2004) Evolution of a pathway to novel long-chain carotenoids. Journal of Bacteriology, 186, 1531–6.
- Umeno, D., Tobias, A.V. and Arnold, F.H. (2002) Evolution of the C30 carotenoid synthase CrtM for function in a C40 pathway. Journal of Bacteriology, 184, 6690–9.
- Raisig, A. and Sandmann, G. (2001) Functional properties of diapophytoene and related desaturases of C(30) and C(40) carotenoid biosynthetic pathways. Plant Molecular Biology, 1533, 164–70.
- Segura, M.J.R., Jackson, B.E. and Matsuda, S.P.T. (2003) Mutagenesis approaches to deduce structure-function relationships in terpene synthases. Natural Product Reports, 20, 304–17.
- Greenhagen, B.T., O'Maille, P.E., Noel, J.P. and Chappell, J. (2006) Identifying and manipulating structural determinates linking catalytic specificities in terpene synthases. Proceedings of the National Academy of Sciences of the United States of America, 103, 9826–31.
- Yoshikuni, Y., Martin, V.J.J., Ferrin, T.E. and Keasling, J.D. (2006) Engineering cotton (+)-delta-cadinene synthase to an altered function: Germacrene D-4-ol synthase. Chemistry and Biology, 13, 91–8.
- Yoshikuni, Y., Ferrin, T.E. and Keasling, J.D. (2006) Designed divergent evolution of enzyme function. Nature, 440, 1078–82.
- Schmidt-Dannert, C., Umeno, D. and Arnold, F.H. (2000) Molecular breeding of carotenoid biosynthetic pathways. Nature Biotechnology, 18, 750–3.
- Patil, K.R., Rocha, I., Forster, J. and Nielsen, J. (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics, 6, 308.
- Vemuri, G.N. and Aristidou, A.A. (2005) Metabolic engineering in the -omics era: elucidating and modulating regulatory networks. Microbiology and Molecular Biology Reviews, 69, 197–216.
- Chin, J.W. (2006) Programming and engineering biological networks. Current Opinion in Structural Biology, 16, 551–6.
- Endy, D. (2005) Foundations for engineering biology. Nature, 438, 449–53.
- Sprinzak, D. and Elowitz, M.B. (2005) Reconstruction of genetic circuits. Nature, 438, 443–8.
- McDaniel, R. and Weiss, R. (2005) Advances in synthetic biology: on the path from prototypes to applications. Current Opinion in Biotechnology, 16, 476–83.
- Smith, H.O., Hutchison, C.A.3rd , Pfannkoch, C. and Venter, J.C. (2003) Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proceedings of the National Academy of Sciences of the United States of America, 100, 15440–5.
- Posfai, G., Plunkett, G.3rd, , Feher, T., Frisch, D., Keil, G.M., Umenhoffer, K., Kolisnychenko, V., Stahl, B., Sharma, S.S., de Arruda, M. et al. (2006) Emergent properties of reduced-genome Escherichia coli. Science, 312, 1044–6.
- Glass, J.I., Assad-Garcia, N., Alperovich, N., Yooseph, S., Lewis, M.R., Maruf, M., Hutchison, C.A.3rd, , Smith, H.O. and Venter, J.C. (2006) Essential genes of a minimal bacterium. Proceedings of the National Academy of Sciences of the United States of America, 103, 425–30.