Metabolic engineering of strains: from industrial-scale to lab-scale chemical production

Journal of Industrial Microbiology and Biotechnology

Volumn 42, Issue 3, 2015, Pages 423-436

  Sun, Jie ^a   Alper, Hal S ^a,b  

^a The University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACID; ALCOHOL DERIVATIVE; ALKANE DERIVATIVE; ALKENE DERIVATIVE; AMINO ACID DERIVATIVE; ANTIBIOTIC AGENT; FATTY ACID ESTER; ORGANIC COMPOUND; TERPENE DERIVATIVE; AMINO ACID;

ARTICLE; BACTERIAL STRAIN; ESCHERICHIA COLI; FUNGAL STRAIN; GENETIC ENGINEERING; INDUSTRIAL PRODUCTION; METABOLIC ENGINEERING; NONHUMAN; SACCHAROMYCES CEREVISIAE; SCALE UP; BIOSYNTHESIS; GENETICS; LABORATORY; METABOLISM; MICROBIOLOGY; PROCEDURES;

ACIDS; ALCOHOLS; AMINO ACIDS; ESCHERICHIA COLI; INDUSTRIAL MICROBIOLOGY; LABORATORIES; METABOLIC ENGINEERING; ORGANIC CHEMICALS; SACCHAROMYCES CEREVISIAE;

EID: 84925494179     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-014-1539-8     Document Type: Article

References (175)

1. Adrio JL, Demain AL (2010) Recombinant organisms for production of industrial products. Bioeng Bugs 1:116–131
2. Ajikumar PK, Xiao WH, Tyo KE et al (2010) Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 330:70–74
3. Akinterinwa O, Cirino PC (2011) Anaerobic obligatory xylitol production in Escherichia coli strains devoid of native fermentation pathways. Appl Environ Microbiol 77:706–709
4. Albertsen L, Chen Y, Bach LS et al (2011) Diversion of flux toward sesquiterpene production in Saccharomyces cerevisiae by fusion of host and heterologous enzymes. Appl Environ Microbiol 77:1033–1040
5. Alper H, Stephanopoulos G (2008) Uncovering the gene knockout landscape for improved lycopene production in E. coli. Appl Microbiol Biotechnol 78:801–810
6. Anastassiadis S, Morgunov IG, Kamzolova SV, Finogenova TV (2008) Citric acid production patent review. Recent Pat Biotechnol 2:107–123
7. Araki K, Ozeki T (2000) Amino acids. Kirk-Othmer Encyclopedia of Chemical Technology. Wiley, USA
8. Asadollahi MA, Maury J, Schalk M et al (2010) Enhancement of farnesyl diphosphate pool as direct precursor of sesquiterpenes through metabolic engineering of the mevalonate pathway in Saccharomyces cerevisiae. Biotechnol Bioeng 106:86–96
9. Ashok S, Sankaranarayanan M, Ko Y et al (2013) Production of 3-hydroxypropionic acid from glycerol by recombinant Klebsiella pneumoniae DeltadhaTDeltayqhD which can produce vitamin B(1)(2) naturally. Biotechnol Bioeng 110:511–524
10. Askenazi M, Driggers EM, Holtzman DA et al (2003) Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat Biotechnol 21:150–156
11. Atsumi S, Cann AF, Connor MR et al (2008) Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng 10:305–311
12. Atsumi S, Hanai T, Liao JC (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86-U13
13. Atsumi S, Liao JC (2008) Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli. Appl Environ Microbiol 74:7802–7808
14. Backman K, O’Connor MJ, Maruya A et al (1990) Genetic engineering of metabolic pathways applied to the production of phenylalanine. Ann NY Acad Sci 589:16–24
15. Baez A, Cho KM, Liao JC (2011) High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal. Appl Microbiol Biotechnol 90:1681–1690
16. Bailey JE (1991) Toward a science of metabolic engineering. Science 252:1668–1675
17. Bailey JE, Sburlati A, Hatzimanikatis V et al (1996) Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 52:109–121
18. Barkei JJ, Kevany BM, Felnagle EA, Thomas MG (2009) Investigations into viomycin biosynthesis by using heterologous production in Streptomyces lividans. Chembiochem 10:366–376
19. Becker J, Boles E (2003) A modified Saccharomyces cerevisiae strain that consumes l-arabinose and produces ethanol. Appl Environ Microbiol 69:4144–4150
20. Becker J, Zelder O, Hafner S et al (2011) From zero to hero: design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production. Metab Eng 13:159–168
21. Becker JV, Armstrong GO, van der Merwe MJ et al (2003) Metabolic engineering of Saccharomyces cerevisiae for the synthesis of the wine-related antioxidant resveratrol. FEMS Yeast Res 4:79–85
22. Blazeck J, Hill A, Liu L et al (2014) Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production. Nat Commun 5:3131
23. Blazeck J, Liu L, Knight R, Alper HS (2013) Heterologous production of pentane in the oleaginous yeast Yarrowia lipolytica. J Biotechnol 165:184–194
24. Blazeck J, Miller J, Pan A et al (2014) Metabolic engineering of Saccharomyces cerevisiae for itaconic acid production. Appl Microbiol Biotechnol. doi:10.1007/s00253-014-5895-0
25. Bond-Watts BB, Bellerose RJ, Chang MC (2011) Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat Chem Biol 7:222–227
26. Bramucci MG, Flint D, Miller ES et al (2013) Method for the production of 2-butanol. Google Patents. US8426174 B2
27. Brochado AR, Matos C, Moller BL et al (2010) Improved vanillin production in baker’s yeast through in silico design. Microb Cell Fact 9:84
28. Buschke N, Schafer R, Becker J, Wittmann C (2013) Metabolic engineering of industrial platform microorganisms for biorefinery applications-optimization of substrate spectrum and process robustness by rational and evolutive strategies. Bioresour Technol 135:544–554
29. Causey TB, Zhou S, Shanmugam KT, Ingram LO (2003) Engineering the metabolism of Escherichia coli W3110 for the conversion of sugar to redox-neutral and oxidized products: homoacetate production. Proc Natl Acad Sci USA 100:825–832
30. Chang MC, Eachus RA, Trieu W et al (2007) Engineering Escherichia coli for production of functionalized terpenoids using plant P450s. Nat Chem Biol 3:274–277
31. Chemler JA, Fowler ZL, McHugh KP, Koffas MA (2010) Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering. Metab Eng 12:96–104
32. Choi HS, Lee SY, Kim TY, Woo HM (2010) In silico identification of gene amplification targets for improvement of lycopene production. Appl Environ Microbiol 76:3097–3105
33. Choi JI, Lee SY, Han K (1998) Cloning of the Alcaligenes latus polyhydroxyalkanoate biosynthesis genes and use of these genes for enhanced production of Poly(3-hydroxybutyrate) in Escherichia coli. Appl Environ Microbiol 64:4897–4903
34. Clomburg JM, Gonzalez R (2011) Metabolic engineering of Escherichia coli for the production of 1,2-propanediol from glycerol. Biotechnol Bioeng 108:867–879
35. Coelho PS, Farrow MF, Smith MA (2014) De novo metabolic pathways for isoprene biosynthesis. Google Patents. WO2014066892 A1
36. Connor MR, Cann AF, Liao JC (2010) 3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation. Appl Microbiol Biotechnol 86:1155–1164
37. Crook NC, Schmitz AC, Alper HS (2014) Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering. ACS Synth Biol 3:307–313
38. Curran KA, Leavitt JM, Karim AS, Alper HS (2013) Metabolic engineering of muconic acid production in Saccharomyces cerevisiae. Metab Eng 15:55–66
39. Dai Z, Liu Y, Huang L, Zhang X (2012) Production of miltiradiene by metabolically engineered Saccharomyces cerevisiae. Biotechnol Bioeng 109:2845–2853
40. Debabov VG (2003) The threonine story. Adv Biochem Eng Biotechnol 79:113–136
41. 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
42. Deng Y, Fong SS (2011) Metabolic engineering of Thermobifida fusca for direct aerobic bioconversion of untreated lignocellulosic biomass to 1-propanol. Metab Eng 13:570–577
43. Dien BS, Nichols NN, Bothast RJ (2002) Fermentation of sugar mixtures using Escherichia coli catabolite repression mutants engineered for production of l-lactic acid. J Ind Microbiol Biotechnol 29:221–227
44. Ding BJ, Hofvander P, Wang HL et al (2014) A plant factory for moth pheromone production. Nat Commun 5:3353
45. Dunlop MJ, Dossani ZY, Szmidt HL et al (2011) Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol 7:487
46. Egel-Mitani M, Andersen AS, Diers II et al (2000) Yield improvement of heterologous peptides expressed in yps1-disrupted Saccharomyces cerevisiae strains. Enzyme Microb Technol 26:671–677
47. 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
48. Farhi M, Marhevka E, Masci T et al (2011) Harnessing yeast subcellular compartments for the production of plant terpenoids. Metab Eng 13:474–481
49. Farmer WR, Liao JC (2000) Improving lycopene production in Escherichia coli by engineering metabolic control. Nat Biotechnol 18:533–537
50. Feldman RMR, Gunawardena U, Urano J et al (2013) Yeast organism producing isobutanol at a high yield. Google Patents. US8455239 B2
51. Fong SS, Burgard AP, Herring CD et al (2005) In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 91:643–648
52. Formanek J, Mackie R, Blaschek HP (1997) Enhanced butanol production by Clostridium beijerinckii BA101 grown in semidefined P2 medium containing 6 percent maltodextrin or glucose. Appl Environ Microbiol 63:2306–2310
53. Fossati E, Ekins A, Narcross L et al (2014) Reconstitution of a 10-gene pathway for synthesis of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisiae. Nat Commun 5:3283
54. Gatenby AA, Patnaik R, Sariaslani FS et al (2008) Method for producing an l-tyrosine over-producing bacterial strain. Google Patent. EP1873249 A1
55. Gidijala L, Kiel JA, Douma RD et al (2009) An engineered yeast efficiently secreting penicillin. PLoS One 4:e8317
56. Grabar TB, Zhou S, Shanmugam KT et al (2006) Methylglyoxal bypass identified as source of chiral contamination in l(+) and d(-)-lactate fermentations by recombinant Escherichia coli. Biotechnol Lett 28:1527–1535
57. Hackel BJ, Huang D, Bubolz JC et al (2006) Production of soluble and active transferrin receptor-targeting single-chain antibody using Saccharomyces cerevisiae. Pharm Res 23:790–797
58. Hansen EH, Moller BL, Kock GR et al (2009) De novo biosynthesis of vanillin in fission yeast (Schizosaccharomyces pombe) and baker’s yeast (Saccharomyces cerevisiae). Appl Environ Microbiol 75:2765–2774
59. Hawkins KM, Smolke CD (2008) Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Nat Chem Biol 4:564–573
60. Inokuma K, Liao JC, Okamoto M, Hanai T (2010) Improvement of isopropanol production by metabolically engineered Escherichia coli using gas stripping. J Biosci Bioeng 110:696–701
61. Inui M, Suda M, Kimura S et al (2008) Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biotechnol 77:1305–1316
62. Ishida M, Kawashima H, Sato K et al (1994) Factors improving l-threonine production by a three l-threonine biosynthetic genes-amplified recombinant strain of Brevibacterium lactofermentum. Biosci Biotechnol Biochem 58:768–770
63. Jantama K, Zhang X, Moore JC et al (2008) Eliminating side products and increasing succinate yields in engineered strains of Escherichia coli C. Biotechnol Bioeng 101:881–893
64. Jeppsson M, Johansson B, Hahn-Hagerdal B, Gorwa-Grauslund MF (2002) Reduced oxidative pentose phosphate pathway flux in recombinant xylose-utilizing Saccharomyces cerevisiae strains improves the ethanol yield from xylose. Appl Environ Microbiol 68:1604–1609
65. Jin YS, Stephanopoulos G (2007) Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli. Metab Eng 9:337–347
66. Jung WS, Kang JH, Chu HS et al (2014) Elevated production of 3-hydroxypropionic acid by metabolic engineering of the glycerol metabolism in Escherichia coli. Metab Eng 23:116–122
67. Kalscheuer R, Stolting T, Steinbuchel A (2006) Microdiesel: Escherichia coli engineered for fuel production. Microbiology 152:2529–2536
68. Katsuyama Y, Funa N, Horinouchi S (2007) Precursor-directed biosynthesis of stilbene methyl ethers in Escherichia coli. Biotechnol J 2:1286–1293
69. Kaup B, Bringer-Meyer S, Sahm H (2005) d-Mannitol formation from d-glucose in a whole-cell biotransformation with recombinant Escherichia coli. Appl Microbiol Biotechnol 69:397–403
70. Kim Y, Ingram LO, Shanmugam KT (2007) Construction of an Escherichia coli K-12 mutant for homoethanologenic fermentation of glucose or xylose without foreign genes. Appl Environ Microbiol 73:1766–1771
71. Kind S, Neubauer S, Becker J et al (2014) From zero to hero—production of bio-based nylon from renewable resources using engineered Corynebacterium glutamicum. Metab Eng 25:113–123
72. Kirby J, Nishimoto M, Park JG et al (2010) Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae. Phytochemistry 71:1466–1473
73. Koivuranta KT, Ilmen M, Wiebe MG et al (2014) l-lactic acid production from d-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene. Microb Cell Fact 13:107
74. Kuyper M, Winkler AA, van Dijken JP, Pronk JT (2004) Minimal metabolic engineering of Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: a proof of principle. FEMS Yeast Res 4:655–664
75. Lee JY, Jang YS, Lee J et al (2009) Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production. Biotechnol J 4:1432–1440
76. Lee KH, Park JH, Kim TY et al (2007) Systems metabolic engineering of Escherichia coli for l-threonine production. Mol Syst Biol 3:149
77. Lee SJ, Song H, Lee SY (2006) Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production. Appl Environ Microbiol 72:1939–1948
78. Lee SM, Jellison T, Alper HS (2012) Directed evolution of xylose isomerase for improved xylose catabolism and fermentation in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol 78:5708–5716
79. Lee SM, Jellison T, Alper HS (2014) Systematic and evolutionary engineering of a xylose isomerase-based pathway in Saccharomyces cerevisiae for efficient conversion yields. Biotechnol Biofuels 7:122
80. Lee SY (1996) Plastic bacteria? Progress and prospects for polyhydroxyalkanoate production in bacteria. Trends Biotechnol 14:431–438
81. Lee W, Dasilva NA (2006) Application of sequential integration for metabolic engineering of 1,2-propanediol production in yeast. Metab Eng 8:58–65
82. Lemuth K, Steuer K, Albermann C (2011) Engineering of a plasmid-free Escherichia coli strain for improved in vivo biosynthesis of astaxanthin. Microb Cell Fact 10:29
83. Lenihan JR, Tsuruta H, Diola D et al (2008) Developing an industrial artemisinic acid fermentation process to support the cost-effective production of antimalarial artemisinin-based combination therapies. Biotechnol Prog 24:1026–1032
84. Lennen RM, Braden DJ, West RA et al (2010) A process for microbial hydrocarbon synthesis: overproduction of fatty acids in Escherichia coli and catalytic conversion to alkanes. Biotechnol Bioeng 106:193–202
85. 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
86. Leonard E, Yan Y, Fowler ZL et al (2008) Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Mol Pharm 5:257–265
87. Li ZJ, Shi ZY, Jian J et al (2010) Production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) from unrelated carbon sources by metabolically engineered Escherichia coli. Metab Eng 12:352–359
88. Lian J, Chao R, Zhao H (2014) Metabolic engineering of a Saccharomyces cerevisiae strain capable of simultaneously utilizing glucose and galactose to produce enantiopure (2R,3R)-butanediol. Metab Eng 23:92–99
89. Lim CG, Fowler ZL, Hueller T et al (2011) High-yield resveratrol production in engineered Escherichia coli. Appl Environ Microbiol 77:3451–3460
90. Lindberg P, Park S, Melis A (2010) Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism. Metab Eng 12:70–79
91. Lowin T, Raab U, Schroeder J et al (2005) Parvovirus B19 VP2-proteins produced in Saccharomyces cerevisiae: comparison with VP2-particles produced by baculovirus-derived vectors. J Vet Med B Infect Dis Vet Public Health 52:348–352
92. Malla S, Koffas MA, Kazlauskas RJ, Kim BG (2012) Production of 7-O-methyl aromadendrin, a medicinally valuable flavonoid, in Escherichia coli. Appl Environ Microbiol 78:684–694
93. Martin VJ, Pitera DJ, Withers ST et al (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21:796–802
94. Max B, Salgado JM, Rodriguez N et al (2010) Biotechnological production of citric acid. Braz J Microbiol 41:862–875
95. Mikkelsen MD, Buron LD, Salomonsen B et al (2012) Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform. Metab Eng 14:104–111
96. Minami H, Kim JS, Ikezawa N et al (2008) Microbial production of plant benzylisoquinoline alkaloids. Proc Natl Acad Sci USA. doi:10.1073/pnas.0802981105
97. Moon SY, Hong SH, Kim TY, Lee SY (2008) Metabolic engineering of Escherichia coli for the production of malic acid. Biochem Eng J 40:312–320
98. Moon TS, Yoon SH, Lanza AM et al (2009) Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl Environ Microbiol 75:589–595
99. Myers RL (2007) The 100 most important chemical compounds: a reference guide. Greenwood Press, USA
100. Nakamura CE, Whited GM (2003) Metabolic engineering for the microbial production of 1,3-propanediol. Curr Opin Biotechnol 14:454–459
101. Nakashima N, Akita H, Hoshino T (2014) Establishment of a novel gene expression method, BICES (biomass-inducible chromosome-based expression system), and its application to the production of 2,3-butanediol and acetoin. Metab Eng 25C:204–214
102. Niu W, Draths KM, Frost JW (2002) Benzene-free synthesis of adipic acid. Biotechnol Prog 18:201–211
103. Ohnishi J, Mitsuhashi S, Hayashi M et al (2002) A novel methodology employing Corynebacterium glutamicum genome information to generate a new l-lysine-producing mutant. Appl Microbiol Biotechnol 58:217–223
104. Ohta K, Beall DS, Mejia JP et al (1991) Genetic improvement of Escherichia coli for ethanol production: chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Appl Environ Microbiol 57:893–900
105. Okabe M, Lies D, Kanamasa S, Park EY (2009) Biotechnological production of itaconic acid and its biosynthesis in Aspergillus terreus. Appl Microbiol Biotechnol 84:597–606
106. Okino S, Noburyu R, Suda M et al (2008) An efficient succinic acid production process in a metabolically engineered Corynebacterium glutamicum strain. Appl Microbiol Biotechnol 81:459–464
107. Paddon CJ, Westfall PJ, Pitera DJ et al (2013) High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 496:528–532
108. Park JH, Jang YS, Lee JW, Lee SY (2011) Escherichia coli W as a new platform strain for the enhanced production of l-valine by systems metabolic engineering. Biotechnol Bioeng 108:1140–1147
109. Park JH, Kim TY, Lee KH, Lee SY (2011) Fed-batch culture of Escherichia coli for l-valine production based on in silico flux response analysis. Biotechnol Bioeng 108:934–946
110. Park JH, Lee KH, Kim TY, Lee SY (2007) Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci USA 104:7797–7802
111. Park SH, Kim HU, Kim TY et al (2014) Metabolic engineering of Corynebacterium glutamicum for l-arginine production. Nat Commun 5:4618
112. Peng X, Ranganathan S, Maranas CD, Koffas M (2011) An integrated computational and experimental study to increase the intra-cellular malonyl-CoA: application to flavanone synthesis. In: Bioengineering Conference (NEBEC), IEEE 37th Annual Northeast
113. Peralta-Yahya PP, Ouellet M, Chan R et al (2011) Identification and microbial production of a terpene-based advanced biofuel. Nat Commun 2:483
114. Pray T (2010) Biomass R&D Technical Advisory Committee: Drop-in fuels panel. Amyris, Aurora, Colorado US. Available http://www.biomassboard.gov/pdfs/biomass_tac_todd_pray_09_29_2010.pdf. Accessed 15 Aug 2014
115. Raab AM, Gebhardt G, Bolotina N et al (2010) Metabolic engineering of Saccharomyces cerevisiae for the biotechnological production of succinic acid. Metab Eng 12:518–525
116. Raj SM, Rathnasingh C, Jo JE, Park SH (2008) Production of 3-hydroxypropionic acid from glycerol by a novel recombinant Escherichia coli BL21 strain. Process Biochem 43:1440–1446
117. 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
118. Rathnasingh C, Raj SM, Lee Y et al (2012) Production of 3-hydroxypropionic acid via malonyl-CoA pathway using recombinant Escherichia coli strains. J Biotechnol 157:633–640
119. Renninger NS, McPhee DJ (2008) Petroleum component, fuel additive and microorganism produced isoprenoids; conversion of simple sugars, polysaccharides and/or nonfermentable carbon sources; diesel fuel, jet fuel, kerosene or gasoline replacements. Google Patent. US20080098645 A1
120. Ro DK, Ouellet M, Paradise EM et al (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
121. Ro DK, Paradise EM, Ouellet M et al (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440:940–943
122. Rodriguez E, Ward S, Fu H et al (2004) Engineered biosynthesis of 16-membered macrolides that require methoxymalonyl-ACP precursors in Streptomyces fradiae. Appl Microbiol Biotechnol 66:85–91
123. Rodriguez GM, Tashiro Y, Atsumi S (2014) Expanding ester biosynthesis in Escherichia coli. Nat Chem Biol 10:259–265
124. Sauer M, Branduardi P, Valli M, Porro D (2004) Production of l-ascorbic acid by metabolically engineered Saccharomyces cerevisiae and Zygosaccharomyces bailii. Appl Environ Microbiol 70:6086–6091
125. Schalk M, Pastore L, Mirata MA et al (2012) Toward a biosynthetic route to sclareol and amber odorants. J Am Chem Soc 134:18900–18903
126. Schirmer A, Rude MA, Li X et al (2010) Microbial biosynthesis of alkanes. Science 329:559–562
127. Shen CR, Lan EI, Dekishima Y et al (2011) Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl Environ Microbiol 77:2905–2915
128. Shen CR, Liao JC (2008) Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Metab Eng 10:312–320
129. Shigechi H, Koh J, Fujita Y et al (2004) Direct production of ethanol from raw corn starch via fermentation by use of a novel surface-engineered yeast strain codisplaying glucoamylase and alpha-amylase. Appl Environ Microbiol 70:5037–5040
130. Steen EJ, Chan R, Prasad N et al (2008) Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb Cell Fact 7:36
131. Steen EJ, Kang Y, Bokinsky G et al (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559–562
132. Sydor T, Schaffer S, Boles E (2010) Considerable increase in resveratrol production by recombinant industrial yeast strains with use of rich medium. Appl Environ Microbiol 76:3361–3363
133. Tang X, Tan Y, Zhu H et al (2009) Microbial conversion of glycerol to 1,3-propanediol by an engineered strain of Escherichia coli. Appl Environ Microbiol 75:1628–1634
134. 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
135. Tsuruta H, Paddon CJ, Eng D et al (2009) High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS One 4:e4489
136. Vai M, Brambilla L, Orlandi I et al (2000) Improved secretion of native human insulin-like growth factor 1 from gas1 mutant Saccharomyces cerevisiae cells. Appl Environ Microbiol 66:5477–5479
137. Van der Beek CP, Roels JA (1984) Penicillin production: biotechnology at its best. Antonie Van Leeuwenhoek 50:625–639
138. Van Dien S (2013) From the first drop to the first truckload: commercialization of microbial processes for renewable chemicals. Curr Opin Biotechnol 24:1061–1068
139. Van Maris AJ, Geertman JM, Vermeulen A et al (2004) Directed evolution of pyruvate decarboxylase-negative Saccharomyces cerevisiae, yielding a C2-independent, glucose-tolerant, and pyruvate-hyperproducing yeast. Appl Environ Microbiol 70:159–166
140. Vellanki RN, Komaravelli N, Tatineni R, Mangamoori LN (2007) Expression of hepatitis B surface antigen in Saccharomyces cerevisiae utilizing glyceraldeyhyde-3-phosphate dehydrogenase promoter of Pichia pastoris. Biotechnol Lett 29:313–318
141. Vemuri GN, Eiteman MA, Altman E (2002) Succinate production in dual-phase Escherichia coli fermentations depends on the time of transition from aerobic to anaerobic conditions. J Ind Microbiol Biotechnol 28:325–332
142. Verhoef S, Wierckx N, Westerhof RG et al (2009) Bioproduction of p-hydroxystyrene from glucose by the solvent-tolerant bacterium Pseudomonas putida S12 in a two-phase water-decanol fermentation. Appl Environ Microbiol 75:931–936
143. Verwaal R, Wang J, Meijnen JP et al (2007) High-level production of beta-carotene in Saccharomyces cerevisiae by successive transformation with carotenogenic genes from Xanthophyllomyces dendrorhous. Appl Environ Microbiol 73:4342–4350
144. Wang C, Yoon SH, Shah AA et al (2010) Farnesol production from Escherichia coli by harnessing the exogenous mevalonate pathway. Biotechnol Bioeng 107:421–429
145. Wang Y, Halls C, Zhang J et al (2011) Stepwise increase of resveratrol biosynthesis in yeast Saccharomyces cerevisiae by metabolic engineering. Metab Eng 13:455–463
146. Wang Y, Manow R, Finan C et al (2011) Adaptive evolution of nontransgenic Escherichia coli KC01 for improved ethanol tolerance and homoethanol fermentation from xylose. J Ind Microbiol Biotechnol 38:1371–1377
147. Wang Y, Yu O (2012) Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells. J Biotechnol 157:258–260
148. Watanabe K, Hotta K, Praseuth AP et al (2006) Total biosynthesis of antitumor nonribosomal peptides in Escherichia coli. Nat Chem Biol 2:423–428
149. 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
150. Werpy T, Petersen G (2004) Top value added chemicals from biomass: volume I—results of screening for potential candidates from sugars and synthesis gas. U.S. Department of Energy. Available http://www.osti.gov/scitech//servlets/purl/15008859-s6ri0N/native/. Accessed 15 Aug 2014
151. Westfall PJ, Pitera DJ, Lenihan JR et al (2012) Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci USA 109:E111–E118
152. Wu J, Liu P, Fan Y et al (2013) Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine. J Biotechnol 167:404–411
153. Xie X, Pashkov I, Gao X et al (2009) Rational improvement of simvastatin synthase solubility in Escherichia coli leads to higher whole-cell biocatalytic activity. Biotechnol Bioeng 102:20–28
154. Xu Y, Chu H, Gao C et al (2014) Systematic metabolic engineering of Escherichia coli for high-yield production of fuel bio-chemical 2,3-butanediol. Metab Eng 23:22–33
155. Yamada R, Yamakawa S, Tanaka T et al (2011) Direct and efficient ethanol production from high-yielding rice using a Saccharomyces cerevisiae strain that express amylases. Enzyme Microb Technol 48:393–396
156. Yang J, Xian M, Su S et al (2012) Enhancing production of bio-isoprene using hybrid MVA pathway and isoprene synthase in E. coli. PLoS One 7:e33509
157. Yim H, Haselbeck R, Niu W et al (2011) Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7:445–452
158. Yoon SH, Lee SH, Das A et al (2009) Combinatorial expression of bacterial whole mevalonate pathway for the production of beta-carotene in E. coli. J Biotechnol 140:218–226
159. Yu KO, Jung J, Kim SW et al (2012) Synthesis of FAEEs from glycerol in engineered Saccharomyces cerevisiae using endogenously produced ethanol by heterologous expression of an unspecific bacterial acyltransferase. Biotechnol Bioeng 109:110–115
160. Yu KO, Jung J, Ramzi AB et al (2012) Increased ethanol production from glycerol by Saccharomyces cerevisiae strains with enhanced stress tolerance from the overexpression of SAGA complex components. Enzyme Microb Technol 51:237–243
161. Yuzbashev TV, Yuzbasheva EY, Sobolevskaya TI et al (2010) Production of succinic acid at low pH by a recombinant strain of the aerobic yeast Yarrowia lipolytica. Biotechnol Bioeng 107:673–682
162. Zaslaver A, Bren A, Ronen M et al (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3:623–628
163. Zhang H, Wang Y, Wu J et al (2010) Complete biosynthesis of erythromycin A and designed analogs using E. coli as a heterologous host. Chem Biol 17:1232–1240
164. Zhang W, Li Y, Tang Y (2008) Engineered biosynthesis of bacterial aromatic polyketides in Escherichia coli. Proc Natl Acad Sci USA 105:20683–20688
165. Zhang X, Jantama K, Moore JC et al (2007) Production of l-alanine by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 77:355–366
166. Zhang X, Wang X, Shanmugam KT, Ingram LO (2011) l-malate production by metabolically engineered Escherichia coli. Appl Environ Microbiol 77:427–434
167. Zhang X, Zhang R, Bao T et al (2014) The rebalanced pathway significantly enhances acetoin production by disruption of acetoin reductase gene and moderate-expression of a new water-forming NADH oxidase in Bacillus subtilis. Metab Eng 23:34–41
168. Zhang Y, Li SZ, Li J et al (2006) Using unnatural protein fusions to engineer resveratrol biosynthesis in yeast and mammalian cells. J Am Chem Soc 128:13030–13031
169. Zhao Y, Yang J, Qin B et al (2011) Biosynthesis of isoprene in Escherichia coli via methylerythritol phosphate (MEP) pathway. Appl Microbiol Biotechnol 90:1915–1922
170. Zhao ZJ, Zou C, Zhu YX et al (2011) Development of l-tryptophan production strains by defined genetic modification in Escherichia coli. J Ind Microbiol Biotechnol 38:1921–1929
171. Zhou B, Martin GJ, Pamment NB (2008) Increased phenotypic stability and ethanol tolerance of recombinant Escherichia coli KO11 when immobilized in continuous fluidized bed culture. Biotechnol Bioeng 100:627–633
172. Zhou L, Zuo ZR, Chen XZ et al (2011) Evaluation of genetic manipulation strategies on d-lactate production by Escherichia coli. Curr Microbiol 62:981–989
173. Zhou S, Shanmugam KT, Ingram LO (2003) Functional replacement of the Escherichia colid-(-)-lactate dehydrogenase gene (ldhA) with the l-(+)-lactate dehydrogenase gene (ldhL) from Pediococcus acidilactici. Appl Environ Microbiol 69:2237–2244
174. Zhou YJ, Gao W, Rong Q et al (2012) Modular pathway engineering of diterpenoid synthases and the mevalonic acid pathway for miltiradiene production. J Am Chem Soc 134:3234–3241
175. Zhu Y, Eiteman MA, Altman R, Altman E (2008) High glycolytic flux improves pyruvate production by a metabolically engineered Escherichia coli strain. Appl Environ Microbiol 74:6649–6655