Engineering microbial factories for synthesis of value-added products

Oxford University Press (OUP) - Tập 38 - Trang 873-890 - 2011
Jing Du1, Zengyi Shao1, Huimin Zhao1,2
1Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
2Departments of Chemistry and Biochemistry, Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA

Tóm tắt

Microorganisms have become an increasingly important platform for the production of drugs, chemicals, and biofuels from renewable resources. Advances in protein engineering, metabolic engineering, and synthetic biology enable redesigning microbial cellular networks and fine-tuning physiological capabilities, thus generating industrially viable strains for the production of natural and unnatural value-added compounds. In this review, we describe the recent progress on engineering microbial factories for synthesis of valued-added products including alkaloids, terpenoids, flavonoids, polyketides, non-ribosomal peptides, biofuels, and chemicals. Related topics on lignocellulose degradation, sugar utilization, and microbial tolerance improvement will also be discussed.

Tài liệu tham khảo

Ajikumar PK, Xiao WH, Tyo KE, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G (2010) Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 330:70–74 Alexander DC, Rock J, Gu JQ, Mascio C, Chu M, Brian P, Baltz RH (2011) Production of novel lipopeptide antibiotics related to A54145 by Streptomyces fradiae mutants blocked in biosynthesis of modified amino acids and assignment of lptJ, lptK and lptL gene functions. J Antibiot (Tokyo) 64:79–87 Allen RS, Millgate AG, Chitty JA, Thisleton J, Miller JA, Fist AJ, Gerlach WL, Larkin PJ (2004) RNAi-mediated replacement of morphine with the nonnarcotic alkaloid reticuline in opium poppy. Nat Biotechnol 22:1559–1566 Alper H, Stephanopoulos G (2009) Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential? Nat Rev Microbiol 7:715–723 Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJY, Hanai T, Liao JC (2008) Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng 10:305–311 Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–89 Atsumi S, Wu TY, Eckl EM, Hawkins SD, Buelter T, Liao JC (2010) Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes. Appl Microbiol Biotechnol 85:651–657 Austin MB, Bowman ME, Ferrer JL, Schroder J, Noel JP (2004) An aldol switch discovered in stilbene synthases mediates cyclization specificity of type III polyketide synthases. Chem Biol 11:1179–1194 Bajwa PK, Pinel D, Martin VJJ, Trevors JT, Lee H (2010) Strain improvement of the pentose-fermenting yeast Pichia stipitis by genome shuffling. J Microbiol Methods 81:179–186 Baltz RH (2010) Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters. J Ind Microbiol Biotechnol 37:759–772 Barnes HJ, Arlotto MP, Waterman MR (1991) Expression and enzymatic activity of recombinant cytochrome P450 17 alpha-hydroxylase in Escherichia coli. Proc Natl Acad Sci USA 88:5597–5601 Beller HR, Goh EB, Keasling JD (2010) Genes involved in long-chain alkene biosynthesis in Micrococcus luteus. Appl Environ Microbiol 76:1212–1223 Boghigian BA, Pfeifer BA (2008) Current status, strategies, and potential for the metabolic engineering of heterologous polyketides in Escherichia coli. Biotechnol Lett 30:1323–1330 Bonomo J, Warnecke T, Hume P, Marizcurrena A, Gill RT (2006) A comparative study of metabolic engineering anti-metabolite tolerance in Escherichia coli. Metab Eng 8:227–239 Bozell JJ, Petersen GR (2010) Technology development for the production of biobased products from biorefinery carbohydrates-the US Department of Energy’s “Top 10” revisited. Green Chem 12:539–554 Bull AT, Goodfellow M, Slater JH (1992) Biodiversity as a source of innovation in biotechnology. Annu Rev Microbiol 46:219–252 Burgess CM, Smid EJ, Dv Sinderen (2009) Bacterial vitamin B2, B11 and B12 overproduction: an overview. Int J Food Microbiol 133:1–7 Butler MS (2005) Natural products to drugs: natural product derived compounds in clinical trials. Nat Prod Rep 22:162–195 Cakar ZP, Seker UOS, Tamerler C, Sonderegger M, Sauer U (2005) Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res 5:569–578 Cane DE (2010) Programming of erythromycin biosynthesis by a modular polyketide synthase. J Biol Chem 285:27517–27523 Chang MC, Eachus RA, Trieu W, Ro DK, Keasling JD (2007) Engineering Escherichia coli for production of functionalized terpenoids using plant P450 s. Nat Chem Biol 3:274–277 Chang MC, Keasling JD (2006) Production of isoprenoid pharmaceuticals by engineered microbes. Nat Chem Biol 2:674–681 Chau M, Jennewein S, Walker K, Croteau R (2004) Taxol biosynthesis: molecular cloning and characterization of a cytochrome P450 taxoid 7 beta-hydroxylase. Chem Biol 11:663–672 Christ TN, Deweese KA, Woodyer RD (2010) Directed evolution toward improved production of l-ribose from ribitol. Comb Chem High Throughput Screen 13:302–308 Connor MR, Liao JC (2008) Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol. Appl Environ Microbiol 74:5769–5775 Davies J (1999) Millennium bugs. Trends Cell Biol 9:M2–M5 Demain AL (2006) From natural products discovery to commercialization: a success story. J Ind Microbiol Biotechnol 33:486–495 Den Haan R, Rose SH, Lynd LR, van Zyl WH (2007) Hydrolysis and fermentation of amorphous cellulose by recombinant Saccharomyces cerevisiae. Metab Eng 9:87–94 Dimster-Denk D, Thorsness MK, Rine J (1994) Feedback regulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase in Saccharomyces cerevisiae. Mol Biol Cell 5:655–665 Dong X, Quinn PJ, Wang X (2011) Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for the production of l-threonine. Biotechnol Adv 29:11–23 Du H, Huang Y, Tang Y (2010) Genetic and metabolic engineering of isoflavonoid biosynthesis. Appl Microbiol Biotechnol 86:1293–1312 Du J, Li SJ, Zhao H (2010) Discovery and characterization of novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis. Mol Biosyst 6:2150–2156 Engels B, Dahm P, Jennewein S (2008) Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards taxol (paclitaxel) production. Metab Eng 10:201–206 Fischbach MA, Walsh CT (2006) Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 106:3468–3496 Forkmann G, Martens S (2001) Metabolic engineering and applications of flavonoids. Curr Opin Biotechnol 12:155–160 Fujii N, Inui T, Iwasa K, Morishige T, Sato F (2007) Knockdown of berberine bridge enzyme by RNAi accumulates (S)-reticuline and activates a silent pathway in cultured California poppy cells. Transgenic Res 16:363–375 Galazka JM, Tian CG, Beeson WT, Martinez B, Glass NL, Cate JHD (2010) Cellodextrin transport in yeast for improved biofuel production. Science 330:84–86 Galbe M, Zacchi G (2002) A review of the production of ethanol from softwood. Appl Microbiol Biotechnol 59:618–628 Gao X, Wang P, Tang Y (2010) Engineered polyketide biosynthesis and biocatalysis in Escherichia coli. Appl Microbiol Biotechnol 88:1233–1242 Gershenzon J, Dudareva N (2007) The function of terpene natural products in the natural world. Nat Chem Biol 3:408–414 Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA III, Smith HO (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319:1215–1220 Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA III (2008) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci USA 105:20404–20409 Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA III, Smith HO, Venter JC (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52–56 Gonzalez R, Tao H, Purvis JE, York SW, Shanmugam KT, Ingram LO (2003) Gene array-based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: comparison of KO11 (parent) to LY01 (resistant mutant). Biotechnol Prog 19:612–623 Ha SJ, Galazka JM, Rin Kim S, Choi JH, Yang X, Seo JH, Louise Glass N, Cate JH, Jin YS (2010) Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation. Proc Natl Acad Sci USA Hahn-Hagerdal B, Karhumaa K, Fonseca C, Spencer-Martins I, Gorwa-Grauslund MF (2007) Towards industrial pentose-fermenting yeast strains. Appl Microbiol Biotechnol 74:937–953 Hanai T, Atsumi S, Liao JC (2007) Engineered synthetic pathway for isopropanol production in Escherichia coli. Appl Environ Microbiol 73:7814–7818 Hawkins KM, Smolke CD (2008) Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Nat Chem Biol 4:564–573 Hector RE, Qureshi N, Hughes SR, Cotta MA (2008) Expression of a heterologous xylose transporter in a Saccharomyces cerevisiae strain engineered to utilize xylose improves aerobic xylose consumption. Appl Microbiol Biotechnol 80:675–684 Hertweck C, Luzhetskyy A, Rebets Y, Bechthold A (2007) Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork. Nat Prod Rep 24:162–190 Hill J, Nelson E, Tilman D, Polasky S, Tiffany D (2006) Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. Proc Natl Acad Sci USA 103:11206–11210 Hong ME, Lee KS, Yu BJ, Sung YJ, Park SM, Koo HM, Kweon DH, Park JC, Jin YS (2010) Identification of gene targets eliciting improved alcohol tolerance in Saccharomyces cerevisiae through inverse metabolic engineering. J Biotechnol 149:52–59 Goodman J, Walsh V (2001) The story of taxol: nature and politics in the pursuit of an anti-cancer drug. Cambridge University Press, Cambridge Jiang XL, Meng X, Xian M (2009) Biosynthetic pathways for 3-hydroxypropionic acid production. Appl Microbiol Biotechnol 82:995–1003 Julsing MK, Koulman A, Woerdenbag HJ, Quax WJ, Kayser O (2006) Combinatorial biosynthesis of medicinal plant secondary metabolites. Biomol Eng 23:265–279 Katahira S, Ito M, Takema H, Fujita Y, Tanino T, Tanaka T, Fukuda H, Kondo A (2008) Improvement of ethanol productivity during xylose and glucose co-fermentation by xylose-assimilating S. cerevisiae via expression of glucose transporter Sut1. Enzyme Microb Technol 43:115–119 Katsuyama Y, Funa N, Miyahisa I, Horinouchi S (2007) Synthesis of unnatural flavonoids and stilbenes by exploiting the plant biosynthetic pathway in Escherichia coli. Chem Biol 14:613–621 Katsuyama Y, Hirose Y, Funa N, Ohnishi Y, Horinouchi S (2010) Precursor-directed biosynthesis of curcumin analogs in Escherichia coli. Biosci Biotechnol Biochem 74:641–645 Katsuyama Y, Matsuzawa M, Funa N, Horinouchi S (2008) Production of curcuminoids by Escherichia coli carrying an artificial biosynthesis pathway. Microbiology 154:2620–2628 Kemeny-Beke A, Aradi J, Damjanovich J, Beck Z, Facsko A, Berta A, Bodnar A (2006) Apoptotic response of uveal melanoma cells upon treatment with chelidonine, sanguinarine and chelerythrine. Cancer Lett 237:67–75 Kingston DG (2007) The shape of things to come: structural and synthetic studies of taxol and related compounds. Phytochemistry 68:1844–1854 Kong WJ, Wei J, Abidi P, Lin MH, Inaba S, Li C, Wang YL, Wang ZZ, Si SY, Pan HN, Wang SK, Wu JD, Wang Y, Li ZR, Liu JW, Jiang JD (2004) Berberine is a novel cholesterol-lowering drug working through a unique mechanism distinct from statins. Nat Med 10:1344–1351 Kotter P, Ciriacy M (1993) Xylose fermentation by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 38:776–783 Kwan CY, Achike FI (2002) Tetrandrine and related bis-benzylisoquinoline alkaloids from medicinal herbs: cardiovascular effects and mechanisms of action. Acta Pharmacol Sin 23:1057–1068 Lai JH (2002) Immunomodulatory effects and mechanisms of plant alkaloid tetrandrine in autoimmune diseases. Acta Pharmacol Sin 23:1093–1101 Leadbetter JR (2003) Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory. Curr Opin Microbiol 6:274–281 Leandro MJ, Goncalves P, Spencer-Martins I (2006) Two glucose/xylose transporter genes from the yeast Candida intermedia: first molecular characterization of a yeast xylose-H+ symporter. Biochem J 395:543–549 Lee SJ, Song H, Lee SY (2006) Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production. Biochem J 72:1939–1948 Lee SY, Kim HU, Park JH, Park JM, Kim TY (2009) Metabolic engineering of microorganisms: general strategies and drug production. Drug Discov Today 14:78–88 Leonard E, Koffas MA (2007) Engineering of artificial plant cytochrome P450 enzymes for synthesis of isoflavones by Escherichia coli. Appl Environ Microbiol 73:7246–7251 Leonard E, Lim KH, Saw PN, Koffas MA (2007) Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli. Appl Environ Microbiol 73:3877–3886 Leonard E, Nielsen D, Solomon K, Prather KJ (2008) Engineering microbes with synthetic biology frameworks. Trends Biotechnol 26:674–681 Leonard E, Runguphan W, O’Connor S, Prather KJ (2009) Opportunities in metabolic engineering to facilitate scalable alkaloid production. Nat Chem Biol 5:292–300 Leonard E, Yan Y, Fowler ZL, Li Z, Lim CG, Lim KH, Koffas MA (2008) Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Mol Pharm 5:257–265 Li SJ, Du J, Sun J, Galazka JM, Glass NL, Cate JHD, Yang XM, Zhao H (2010) Overcoming glucose repression in mixed sugar fermentation by co-expressing a cellobiose transporter and a beta-glucosidase in Saccharomyces cerevisiae. Mol BioSyst 6:2129–2132 Linger JG, Adney WS, Darzins A (2010) Heterologous expression and extracellular secretion of cellulolytic enzymes by Zymomonas mobilis. Appl Environ Microbiol 76:6360–6369 Lynd LR, Cushman JH, Nichols RJ, Wyman CE (1991) Fuel ethanol from cellulosic biomass. Science 251:1318–1323 Lynd LR, Laser MS, Brandsby D, Dale BE, Davison B, Hamilton R, Himmel M, Keller M, McMillan JD, Sheehan J, Wyman CE (2008) How biotech can transform biofuels. Nat Biotechnol 26:169–172 Lynd LR, van Zyl WH, McBride JE, Laser M (2005) Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotechnol 16:577–583 Matsushika A, Inoue H, Murakami K, Takimura O, Sawayama S (2009) Bioethanol production performance of five recombinant strains of laboratory and industrial xylose-fermenting Saccharomyces cerevisiae. Bioresour Technol 100:2392–2398 Mazumdar S, Clomburg JM, Gonzalez R (2010) Escherichia coli strains engineered for homofermentative production of d-lactic acid from glycerol. Appl Environ Microbiol 76:4327–4336 McDaniel R, Weiss R (2005) Advances in synthetic biology: on the path from prototypes to applications. Curr Opin Biotechnol 16:476–483 Menzella HG, Reeves CD (2007) Combinatorial biosynthesis for drug development. Curr Opin Microbiol 10:238–245 Minami H, Kim JS, Ikezawa N, Takemura T, Katayama T, Kumagai H, Sato F (2008) Microbial production of plant benzylisoquinoline alkaloids. Proc Natl Acad Sci USA 105:7393–7398 Miyahisa I, Funa N, Ohnishi Y, Martens S, Moriguchi T, Horinouchi S (2006) Combinatorial biosynthesis of flavones and flavonols in Escherichia coli. Appl Microbiol Biotechnol 71:53–58 Moon TS, Dueber JE, Shiue E, Prather KLJ (2010) Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab Eng 12:298–305 Moon TS, Yoon SH, Lanza AM, Roy-Mayhew JD, Prather KLJ (2009) Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl Environ Microbiol 75:589–595 Muntendam R, Melillo E, Ryden A, Kayser O (2009) Perspectives and limits of engineering the isoprenoid metabolism in heterologous hosts. Appl Microbiol Biotechnol 84:1003–1019 Mutka SC, Bondi SM, Carney JR, Da Silva NA, Kealey JT (2006) Metabolic pathway engineering for complex polyketide biosynthesis in Saccharomyces cerevisiae. FEMS Yeast Res 6:40–47 Mutka SC, Carney JR, Liu Y, Kennedy J (2006) Heterologous production of epothilone C and D in Escherichia coli. Biochemistry 45:1321–1330 Nair NU, Zhao H (2008) Evolution in reverse: engineering a d-xylose-specific xylose reductase. ChemBioChem 9:1213–1215 Nair NU, Zhao H (2010) Selective reduction of xylose to xylitol from a mixture of hemicellulosic sugars. Metab Eng 12:462–468 Nakamura CE, Whited GM (2003) Metabolic engineering for the microbial production of 1, 3-propanediol. Curr Opin Biotechnol 14:454–459 Nguyen KT, He X, Alexander DC, Li C, Gu JQ, Mascio C, Van Praagh A, Mortin L, Chu M, Silverman JA, Brian P, Baltz RH (2010) Genetically engineered lipopeptide antibiotics related to A54145 and daptomycin with improved properties. Antimicrob Agents Chemother 54:1404–1413 Nguyen KT, Ritz D, Gu JQ, Alexander D, Chu M, Miao V, Brian P, Baltz RH (2006) Combinatorial biosynthesis of novel antibiotics related to daptomycin. Proc Natl Acad Sci USA 103:17462–17467 Nicolaou KC, Yang Z, Liu JJ, Ueno H, Nantermet PG, Guy RK, Claiborne CF, Renaud J, Couladouros EA, Paulvannan K et al (1994) Total synthesis of taxol. Nature 367:630–634 Olano C, Mendez C, Salas JA (2009) Antitumor compounds from actinomycetes: from gene clusters to new derivatives by combinatorial biosynthesis. Nat Prod Rep 26:628–660 Olano C, Mendez C, Salas JA (2010) Post-PKS tailoring steps in natural product-producing actinomycetes from the perspective of combinatorial biosynthesis. Nat Prod Rep 27:571–616 Pfeifer BA, Admiraal SJ, Gramajo H, Cane DE, Khosla C (2001) Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 291:1790–1792 Holton RA, Biediger RJ, Boatman PD (1995) Taxol: science and applications. CRC, Boca Raton Raab AM, Gebhardt G, Bolotina N, Weuster-Botz D, Lang C (2010) Metabolic engineering of Saccharomyces cerevisiae for the biotechnological production of succinic acid. Metab Eng 12:518–525 Rao Z, Ma Z, Shen W, Fang H, Zhuge J, Wang X (2008) Engineered Saccharomyces cerevisiae that produces 1, 3-propanediol from d-glucose. J Appl Microbiol 105:1768–1776 Rathnasingh C, Raj SM, Jo JE, Park S (2009) Development and evaluation of efficient recombinant Escherichia coli strains for the production of 3-hydroxypropionic acid from glycerol. Biotechnol Bioeng 104:729–739 Ro DK, Ouellet M, Paradise EM, Burd H, Eng D, Paddon CJ, Newman JD, Keasling JD (2008) Induction of multiple pleiotropic drug resistance genes in yeast engineered to produce an increased level of anti-malarial drug precursor, artemisinic acid. BMC Biotechnol 8:83 Ro DK, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM, Ho KA, Eachus RA, Ham TS, Kirby J, Chang MC, Withers ST, Shiba Y, Sarpong R, Keasling JD (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440:940–943 Roberts SC (2007) Production and engineering of terpenoids in plant cell culture. Nat Chem Biol 3:387–395 Roca C, Haack MB, Olsson L (2004) Engineering of carbon catabolite repression in recombinant xylose fermenting Saccharomyces cerevisiae. Appl Microbiol Biotechnol 63:578–583 Runquist D, Fonseca C, Radstrom P, Spencer-Martins I, Hahn-Hagerdal B (2009) Expression of the Gxf1 transporter from Candida intermedia improves fermentation performance in recombinant xylose-utilizing Saccharomyces cerevisiae. Appl Microbiol Biotechnol 82:123–130 Runquist D, Hahn-Hagerdal B, Bettiga M (2010) Increased ethanol productivity in xylose-utilizing Saccharomyces cerevisiae via a randomly mutagenized xylose reductase. Appl Environ Microbiol 76:7796–7802 Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD (2010) Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl Environ Microbiol 76:1935–1945 Saha BC (2003) Hemicellulose bioconversion. J Ind Microbiol Biotechnol 30:279–291 Sanchez AM, Bennett GN, San KY (2005) Efficient succinic acid production from glucose through overexpression of pyruvate carboxylase in an Escherichia coli alcohol dehydrogenase and lactate dehydrogenase mutant. Biotechnol Prog 21:358–365 Sanchez C, Mendez C, Salas JA (2006) Engineering biosynthetic pathways to generate antitumor indolocarbazole derivatives. J Ind Microbiol Biotechnol 33:560–568 Sanchez C, Salas AP, Brana AF, Palomino M, Pineda-Lucena A, Carbajo RJ, Mendez C, Moris F, Salas JA (2009) Generation of potent and selective kinase inhibitors by combinatorial biosynthesis of glycosylated indolocarbazoles. Chem Commun (Camb):4118–4120 Sato F, Hashimoto T, Hachiya A, Tamura K, Choi KB, Morishige T, Fujimoto H, Yamada Y (2001) Metabolic engineering of plant alkaloid biosynthesis. Proc Natl Acad Sci USA 98:367–372 Sato F, Inui T, Takemura T (2007) Metabolic engineering in isoquinoline alkaloid biosynthesis. Curr Pharm Biotechnol 8:211–218 Schafer H, Wink M (2009) Medicinally important secondary metabolites in recombinant microorganisms or plants: progress in alkaloid biosynthesis. Biotechnol J 4:1684–1703 Schirmer A, Rude MA, Li XZ, Popova E, del Cardayre SB (2010) Microbial biosynthesis of alkanes. Science 329:559–562 Sevrioukova IF, Li H, Zhang H, Peterson JA, Poulos TL (1999) Structure of a cytochrome P450-redox partner electron-transfer complex. Proc Natl Acad Sci USA 96:1863–1868 Shao Z, Luo Y, Zhao H (2011) Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler. Mol BioSyst (in press) Shao Z, Zhao H, Zhao H (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37:e16 Sieber SA, Marahiel MA (2005) Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem Rev 105:715–738 Siewers V, Chen X, Huang L, Zhang J, Nielsen J (2009) Heterologous production of non-ribosomal peptide LLD-ACV in Saccharomyces cerevisiae. Metab Eng 11:391–397 Simkhada D, Kim E, Lee HC, Sohng JK (2009) Metabolic engineering of Escherichia coli for the biological synthesis of 7-O-xylosyl naringenin. Mol Cells 28:397–401 Singhvi M, Joshi D, Adsul M, Varma A, Gokhale D (2010) d-(-)-Lactic acid production from cellobiose and cellulose by Lactobacillus lactis mutant RM2-24. Green Chem 12:1106–1109 Staunton J, Weissman KJ (2001) Polyketide biosynthesis: a millennium review. Nat Prod Rep 18:380–416 Steen EJ, Chan R, Prasad N, Myers S, Petzold CJ, Redding A, Ouellet M, Keasling JD (2008) Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb Cell Fact 7:36–43 Steen EJ, Kang YS, Bokinsky G, Hu ZH, Schirmer A, McClure A, del Cardayre SB, Keasling JD (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559–562 Tang XM, Tan YS, Zhu H, Zhao K, Shen W (2009) Microbial conversion of glycerol to 1, 3-propanediol by an engineered strain of Escherichia coli. Appl Environ Microbiol 75:1628–1634 Tatarko M, Romeo T (2001) Disruption of a global regulatory gene to enhance central carbon flux into phenylalanine biosynthesis in Escherichia coli. Curr Microbiol 43:26–32 Tsai SL, Goyal G, Chen W (2010) Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production. Appl Environ Microbiol 76:7514–7520 Turnbull JJ, Nakajima J, Welford RW, Yamazaki M, Saito K, Schofield CJ (2004) Mechanistic studies on three 2-oxoglutarate-dependent oxygenases of flavonoid biosynthesis: anthocyanidin synthase, flavonol synthase, and flavanone 3β-hydroxylase. J Biol Chem 279:1206–1216 van Zyl WH, Lynd LR, den Haan R, McBride JE (2007) Consolidated bioprocessing for bioethanol production using Saccharomyces cerevisiae. In: Biofuels, vol 108. Advances in biochemical engineering/biotechnology. Springer, Berlin Heidelberg New York, pp 205–235 Walker GM (1998) Yeast physiology and biotechnology. Wiley, New York Wang Y, Boghigian BA, Pfeifer BA (2007) Improving heterologous polyketide production in Escherichia coli by overexpression of an S-adenosylmethionine synthetase gene. Appl Microbiol Biotechnol 77:367–373 Wani MC, Taylor HL, Wall ME, Coggon P, McPhail AT (1971) Plant antitumor agents. VI. The isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus brevifolia. J Am Chem Soc 93:2325–2327 Weisshaar B, Jenkins GI (1998) Phenylpropanoid biosynthesis and its regulation. Curr Opin Plant Biol 1:251–257 Weissman KJ, Leadlay PF (2005) Combinatorial biosynthesis of reduced polyketides. Nat Rev Microbiol 3:925–936 Wen F, Nair NU, Zhao H (2009) Protein engineering in designing tailored enzymes and microorganisms for biofuels production. Curr Opin Biotechnol 20:412–419 Wen F, Sun J, Zhao H (2010) Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl Environ Microbiol 76:1251–1260 Williams PA, Cosme J, Sridhar V, Johnson EF, McRee DE (2000) Microsomal cytochrome P450 2C5: comparison to microbial P450 s and unique features. J Inorg Biochem 81:183–190 Woodyer RD, Wymer NJ, Racine FM, Khan SN, Saha BC (2008) Efficient production of l-ribose with a recombinant Escherichia coli biocatalyst. Appl Environ Microbiol 74:2967–2975 Yakandawala N, Romeo T, Friesen AD, Madhyastha S (2008) Metabolic engineering of Escherichia coli to enhance phenylalanine production. Appl Microbiol Biotechnol 78:283–291 Yan Y, Huang L, Koffas MA (2007) Biosynthesis of 5-deoxyflavanones in microorganisms. Biotechnol J 2:1250–1262 Yan Y, Liao JC (2009) Engineering metabolic systems for production of advanced fuels. J Ind Microbiol Biotechnol 36:471–479 Yang SH, Pelletier DA, Lu TYS, Brown SD (2010) The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors. BMC Biotechnol 10:11 Zhang H, Boghigian BA, Pfeifer BA (2010) Investigating the role of native propionyl-CoA and methylmalonyl-CoA metabolism on heterologous polyketide production in Escherichia coli. Biotechnol Bioeng 105:567–573 Zhang W, Li Y, Tang Y (2008) Engineered biosynthesis of bacterial aromatic polyketides in Escherichia coli. Proc Natl Acad Sci USA 105:20683–20688 Zhang XM, Li Y, Zhuge B, Tang XM, Shen W, Rao ZM, Fang HY, Zhuge J (2006) Construction of a novel recombinant Escherichia coli strain capable of producing 1, 3-propanediol and optimization of fermentation parameters by statistical design. World J Microbiol Biotechnol 22:945–952 Zulak KG, Cornish A, Daskalchuk TE, Deyholos MK, Goodenowe DB, Gordon PM, Klassen D, Pelcher LE, Sensen CW, Facchini PJ (2007) Gene transcript and metabolite profiling of elicitor-induced opium poppy cell cultures reveals the coordinate regulation of primary and secondary metabolism. Planta 225:1085–1106