In vitro reconstitution guide for targeted synthetic metabolism of chemicals, nutraceuticals and drug precursors

Synthetic and Systems Biotechnology

Volumn 1, Issue 1, 2016, Pages 25-33

  Tan, Gao Yi ^a   Zhu, Faying ^a   Deng, Zixin ^a,b   Liu, Tiangang ^a,b  

^a WUHAN UNIVERSITY   (China)

^b Wuhan Institute of Biotechnology   (China)

Author keywords

Fatty acid; In vitro reconstitution; Polyketide; Targeted engineering; Terpene

Indexed keywords

ASTAXANTHIN; BIODIESEL; CHEMICAL AGENT; DRUG; DRUG PRECURSOR; FARNESENE; FATTY ACID; FATTY ACID DERIVATIVE; FATTY ALCOHOL; LYCOPENE; NUTRACEUTICAL; POLYKETIDE; TERPENOID; UNCLASSIFIED DRUG;

ARTICLE; BIOSYNTHESIS; COENZYME; ENZYME ANALYSIS; ENZYME SUBSTRATE; ESCHERICHIA COLI; IN VITRO RECONSTITUTION; IN VITRO STUDY; IN VIVO STUDY; METABOLIC ENGINEERING; MICROBIAL METABOLISM; NONHUMAN; PRACTICE GUIDELINE; SACCHAROMYCES CEREVISIAE; STEADY STATE; SYNTHETIC BIOLOGY; TARGETED ENGINEERING;

EID: 85019538487     PISSN: None     EISSN: 2405805X     Source Type: Journal    
DOI: 10.1016/j.synbio.2016.02.003     Document Type: Review

References (98)

1. Quin MB, Schmidt-Dannert C. Designer microbes for biosynthesis. Curr Opin Biotechnol 2014;29:55-61.
2. Latif H, Zeidan AA, Nielsen AT, Zengler K. Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms. Curr Opin Biotechnol 2014;27:79-87.
3. Liu T, Khosla C. A balancing act for Taxol precursor pathways in E. coli. Science 2010;330:44-5.
4. Rabinovitch-Deere CA, Oliver JWK, Rodriguez GM, Atsumi S. Synthetic biology and metabolic engineering approaches to produce biofuels. Chem Rev 2013;113:4611-32.
5. Rollin JA, Tam TK, Zhang YHP. New biotechnology paradigm: cell-free biosystems for biomanufacturing. Green Chem 2013;15:1708-19.
6. Lee GN, Na J. The impact of synthetic biology. ACS Synth Biol 2013;2:210-2.
7. Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branchedchain higher alcohols as biofuels. Nature 2008;451:86-9.
8. Liu T, Khosla C. Genetic engineering of Escherichia coli for biofuel production. Annu Rev Genet 2010;44:53-69.
9. Borodina I, Nielsen J. Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. Biotechnol J 2014;9:609-20.
10. Martin VJJ, Piteral DJ, Withers ST, Newman JD, Keasling JD. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 2003;21:796-802.
11. Paddon CJ, Keasling JD. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 2014;12:355-67.
12. Cameron DE, Bashor CJ, Collins JJ. A brief history of synthetic biology. Nat Rev Microbiol 2014;12:381-90.
13. Paddon CJ,Westfall PJ, Pitera DJ, Benjamin K, Fisher K, McPhee D, et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 2013;496:528-32.
14. Hien TT, White NJ. Qinghaosu. Lancet 1993;341:603-8.
15. Hale V, Keasling JD, Renninger N, Diagana TT. Microbially derived artemisinin: a biotechnology solution to the global problem of access to affordable antimalarial drugs. Am J Trop Med Hyg 2007;77:198-202.
16. Tan G, Deng Z, Liu T. Recent advances in the elucidation of enzymatic function in natural product biosynthesis [version 1; referees: 2 approved]. F1000Res 2015;4(F1000 Faculty Rev):1399.
17. Service RF. Modified yeast produce opiates from sugar. Science 2015;349:677.
18. Galanie S, Thodey K, Trenchard IJ, Filsinger Interrante M, Smolke CD. Complete biosynthesis of opioids in yeast. Science 2015;349:1095-100.
19. Bayer TS. Grand Challenge Commentary: transforming biosynthesis into an information science. Nat Chem Biol 2010;6:859-61.
20. Van Noorden R. Demand for malaria drug soars. Nature 2010;466:672-3.
21. Ajikumar PK, Xiao WH, Tyo KEJ,Wang Y, Simeon F, Leonard E, et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 2010;330:70-4.
22. Zhang M, Eddy C, Deanda K, Finkelstein M, Picataggio S. Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science 1995;267:240-3.
23. Jetten MSM, Sinskey AJ. Recent advances in the physiology and genetics of amino acid-producing bacteria. Crit Rev Biotechnol 1995;15:73-103.
24. Yukimune Y, Tabata H, Higashi Y, Hara Y. Methyl jasmonate-induced overproduction of paclitaxel and baccatin III in Taxus cell suspension cultures. Nat Biotechnol 1996;14:1129-32.
25. Lee SY, Jang YS, Lee JY, Lee J, Park JH, Im JA, et al. Enhanced butanol production obtained by reinforcing the direct butanol-forming route in Clostridium acetobutylicum. mBio 2012;3.
26. Tan X, Yao L, Gao Q, Wang W, Qi F, Lu X. Photosynthesis driven conversion of carbon dioxide to fatty alcohols and hydrocarbons in cyanobacteria. Metab Eng 2011;13:169-76.
27. Peralta-Yahya PP, Ouellet M, Chan R, Mukhopadhyay A, Keasling JD, Lee TS. Identification and microbial production of a terpene-based advanced biofuel. Nat Commun 2011;2.
28. Jin YS, Alper H, Yang YT, Stephanopoulos G. Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach. Appl Environ Microbiol 2005;71:8249-56.
29. Fujita Y, Matsuoka H, Hirooka K. Regulation of fatty acid metabolism in bacteria. Mol Microbiol 2007;66:829-39.
30. White SW, Zheng J, Zhang YM, Rock CO. The structural biology of type II fatty acid biosynthesis. Annu Rev Biochem 2005;74:791-831.
31. Rock CO, Jackowski S. Forty years of bacterial fatty acid synthesis. Biochem Biophys Res Commun 2002;292:1155-66.
32. Davis MS, Solbiati J, Cronan JE Jr. Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J Biol Chem 2000;275:28593-8.
33. Heath RJ, Rock CO. Inhibition of ß-ketoacyl-acyl carrier protein synthase III (FabH) by acyl-acyl carrier protein in Escherichia coli. J Biol Chem 1996;271:10996-1000.
34. Heath RJ, Rock CO. Regulation of fatty acid elongation and initiation by acyl-acyl carrier protein in Escherichia coli. J Biol Chem 1996;271:1833-6.
35. Magnuson K, Jackowski S, Rock CO, Cronan JE Jr. Regulation of fatty acid biosynthesis in Escherichia coli. Microbiol Rev 1993;57:522-42.
36. Liu T, Vora H, Khosla C. Quantitative analysis and engineering of fatty acid biosynthesis in E. coli. Metab Eng 2010;12:378-86.
37. Yu X, Liu T, Zhu F, Khosla C. In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli. Proc Natl Acad Sci U S A 2011;108:18643-8.
38. Jackowski S, Murphy CM, Cronan JE Jr, Rock CO. Acetoacetyl-acyl carrier protein synthase. A target for the antibiotic thiolactomycin. J Biol Chem 1989;264:7624-9.
39. Lennarz W, Light R, Bloch K. A fatty acid synthetase from E. coli. PNAS 1962;48:840-6.
40. Silbert DF, Vagelos PR. Fatty acid mutant of E. coli lacking a beta-hydroxydecanoyl thioester dehydrase. Proc Natl Acad Sci U S A 1967;58:1579-86.
41. Hockenberry AJ, Jewett MC. Synthetic in vitro circuits. Curr Opin Chem Biol 2012;16:253-9.
42. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988;239:487-91.
43. Losick R. In vitro transcription. Annu Rev Biochem 1972;41:409-46.
44. Zhu F, Lu L, Fu S, Zhong X, Hu M, Deng Z, et al. Targeted engineering and scale up of lycopene overproduction in Escherichia coli. Process Biochem 2015;50:341-6.
45. Blazeck J, Alper HS. Promoter engineering: recent advances in controlling transcription at the most fundamental level. Biotechnol J 2013;8:46-58.
46. Liu Q, Wu K, Cheng Y, Lu L, Xiao E, Zhang Y, et al. Engineering an iterative polyketide pathway in Escherichia coli results in single-form alkene and alkane overproduction. Metab Eng 2015;28:82-90.
47. Siegl T, Tokovenko B, Myronovskyi M, Luzhetskyy A. Design, construction and characterisation of a synthetic promoter library for fine-tuned gene expression in actinomycetes. Metab Eng 2013;19:98-106.
48. Wang W, Li X,Wang J, Xiang S, Feng X, Yang K. An engineered strong promoter for streptomycetes. Appl Environ Microbiol 2013;79:4484-92.
49. Bai C, Zhang Y, Zhao X, Hu Y, Xiang S, Miao J, et al. Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces. Proc Natl Acad Sci U S A 2015;112:12181-6.
50. You C, Zhang XZ, Zhang YHP. Simple cloning via direct transformation of PCR product (DNA multimer) to Escherichia coli and Bacillus subtilis. Appl Environ Microbiol 2012;78:1593-5.
51. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 2009;6:343-5.
52. Li L, Zhao Y, Ruan L, Yang S, Ge M, Jiang W, et al. A stepwise increase in pristinamycin II biosynthesis by Streptomyces pristinaespiralis through combinatorial metabolic engineering. Metab Eng 2015;29:12-25.
53. Noskov VN, Karas BJ, Young L, Chuang RY, Gibson DG, Lin YC, et al. Assembly of large, high G+C bacterial DNA fragments in yeast. ACS Synth Biol 2012;1:267-73.
54. Zeng H, Wen S, Xu W, He Z, Zhai G, Liu Y, et al. Highly efficient editing of the actinorhodin polyketide chain length factor gene in Streptomyces coelicolor M145 using CRISPR/Cas9-CodA(sm) combined system. Appl Microbiol Biotechnol 2015;99:10575-85.
55. Liu Y, Tao W, Wen S, Li Z, Yang A, Deng Z, et al. In vitro CRISPR/Cas9 system for efficient targeted DNA editing. mBio 2015;6.
56. Cobb RE, Wang Y, Zhao H. High-Efficiency Multiplex genome editing of Streptomyces species using an engineered CRISPR/Cas system. ACS Synth Biol 2015;4:723-8.
57. Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams PD, et al. Targeted proteomics formetabolic pathway optimization: application to terpene production. Metab Eng 2011;13:194-203.
58. Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams PD, et al. Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics 2012;12:1289-99.
59. Tao H, Zhang Y, Cao X, Deng Z, Liu T. Absolute quantification of proteins in the fatty acid biosynthetic pathway using protein standard absolute quantification. Synth Sys Biotechnol 2016; doi: 10.1016/j.synbio.2016.01.001.
60. Zhang H,Wang Y, Pfeifer BA. Bacterial hosts for natural product production. Mol Pharm 2008;5:212-25.
61. Kalscheuer R, Luftmann H. Steinbüchel A. Synthesis of novel lipids in Saccharomyces cerevisiae by heterologous expression of an unspecific bacterial acyltransferase. Appl Environ Microbiol 2004;70:7119-25.
62. Guo D, Zhu J, Deng Z, Liu T. Metabolic engineering of Escherichia coli for production of fatty acid short-chain esters through combination of the fatty acid and 2-keto acid pathways. Metab Eng 2014;22:69-75.
63. Tao H, Guo D, Zhang Y, Deng Z, Liu T. Metabolic engineering of microbes for branched-chain biodiesel production with low-temperature property. Biotechnol Biofuels 2015;8:1-11.
64. Matsuda F, Ishii J, Kondo T, Ida K, Tezuka H, Kondo A. Increased isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance. Microb Cell Fact 2013;12.
65. Chen X, Nielsen KF, Borodina I, Kielland-Brandt MC, Karhumaa K. Increased isobutanol production in Saccharomyces cerevisiae by overexpression of genes in valine metabolism. Biotechnol Biofuels 2011;4.
66. Li X, Guo D, Cheng Y, Zhu F, Deng Z, Liu T. Overproduction of fatty acids in engineered Saccharomyces cerevisiae. Biotechnol Bioeng 2014;111:1841-52.
67. Stephanopoulos G. Challenges in engineering microbes for biofuels production. Science 2007;315:801-4.
68. Fortman JL, Chhabra S, Mukhopadhyay A, Chou H, Lee TS, Steen E, et al. Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol 2008;26:375-81.
69. Domergue F, Vishwanath SJ, Joubès J, Ono J, Lee JA, Bourdon M, et al. Three Arabidopsis fatty Acyl-coenzyme a reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition. Plant Physiol 2010;153:1539-54.
70. Teerawanichpan P, Qiu X. Fatty acyl-coA reductase and wax synthase from euglena gracilis in the biosynthesis of medium-chain wax esters. Lipids 2010;45:263-73.
71. Metz JG, Pollard MR, Anderson L, Hayes TR, Lassner MW. Purification of a jojoba embryo fatty acyl-coenzyme A reductase and expression of its cDNA in high erucic acid rapeseed. Plant Physiol 2000;122:635-44.
72. Reiser S, Somerville C. Isolation of mutants of Acinetobacter calcoaceticus deficient in wax ester synthesis and complementation of one mutation with a gene encoding a fatty acyl coenzyme A reductase. J Bacteriol 1997;179: 2969-75.
73. Schirmer A, Rude MA, Li X, Popova E, Del Cardayre SB. Microbial biosynthesis of alkanes. Science 2010;329:559-62.
74. Liu R, Zhu F, Lu L, Fu A, Lu J, Deng Z, et al. Metabolic engineering of fatty acyl-ACP reductase-dependent pathway to improve fatty alcohol production in Escherichia coli. Metab Eng 2014;22:10-21.
75. Hounsome N, Hounsome B, Tomos D, Edwards-Jones G. Plant metabolites and nutritional quality of vegetables. J Food Sci 2008;73:R48-65.
76. Phillips MA, León P, Boronat A, Rodríguez-Concepción M. The plastidial MEP pathway: unified nomenclature and resources. Trends Plant Sci 2008;13:619-23.
77. Rohmer M, Knani M, Simonin P, Sutter B, Sahm H. Isoprenoid biosynthesis in bacteria: a novel pathway for the early steps leading to isopentenyl diphosphate. Biochem J 1993;295:517-24.
78. Peralta-Yahya PP, Zhang F, Del Cardayre SB, Keasling JD. Microbial engineering for the production of advanced biofuels. Nature 2012;488:320-8.
79. Farmer WR, Liao JC. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat Biotechnol 2000;18:533-7.
80. Zhu F, Zhong X, Hu M, Lu L, Deng Z, Liu T. In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli. Biotechnol Bioeng 2014;111:1396-405.
81. Polakowski T, Stahl U, Lang C. Overexpression of a cytosolic hydroxymethylglutaryl-CoA reductase leads to squalene accumulation in yeast. Appl Microbiol Biotechnol 1998;49:66-71.
82. Pechous S, Whitaker B. Cloning and functional expression of an (E,E)-a-farnesene synthase cDNA from peel tissue of apple fruit. Planta 2004;219:84-94.
83. Ma T, Zhou Y, Li X, Zhu F, Cheng Y, Liu Y, et al. Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli. Biotechnol J 2015;doi:10.1002/biot.201400827.
84. Sies H, Stahl W. Lycopene: antioxidant and biological effects and its bioavailability in the human. Proc Soc Exp Biol Med 1998;218:121-4.
85. Karakaya S, Yilmaz N. Lycopene content and antioxidant activity of fresh and processed tomatoes and in vitro bioavailability of lycopene. J Sci Food Agric 2007;87:2342-7.
86. Takeoka GR, Dao L, Flessa S, Gillespie DM, JewellWT, Huebner B, et al. Processing effects on lycopene content and antioxidant activity of tomatoes. J Agric Food Chem 2001;49:3713-7.
87. Herzog A, Siler U, Spitzer V, Seifert N, Denelavas A, Hunziker PB, et al. Lycopene reduced gene expression of steroid targets and inflammatory markers in normal rat prostate. FASEB J 2005;19:272-4.
88. Higuera-Ciapara I, Félix-Valenzuela L, Goycoolea FM. Astaxanthin: a review of its chemistry and applications. Crit Rev Food Sci Nutr 2006;46:185-96.
89. Guerin M, Huntley ME, Olaizola M. Haematococcus astaxanthin: applications for human health and nutrition. Trends Biotechnol 2003;21:210-6.
90. Cronan JE, Thomas J. Bacterial fatty acid synthesis and its relationships with polyketide synthetic pathways. In: Methods in Enzymology. 2009. p. 395-433 [Chapter 17].
91. Smith S, Tsai SC. The type I fatty acid and polyketide synthases: a tale of two megasynthases. Nat Prod Rep 2007;24:1041-72.
92. Fischbach MA, Walsh CT. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic machinery, and mechanisms. Chem Rev 2006;106:3468-96.
93. Howard TP, Middelhaufe S, Moore K, Edner C, Kolak DM, Taylor GN, et al. Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli. Proc Natl Acad Sci U S A 2013;110:7636-41.
94. Choi YJ, Lee SY. Microbial production of short-chain alkanes. Nature 2013;502:571-4.
95. Rude MA, Baron TS, Brubaker S, Alibhai M, Del Cardayre SB, Schirmer A. Terminal olefin (1-alkene) biosynthesis by a novel P450 fatty acid decarboxylase from Jeotgalicoccus species. Appl Environ Microbiol 2011;77:1718-27.
96. Sukovich DJ, Seffernick JL, Richman JE, Gralnick JA, Wackett LP. Widespread head-to-head hydrocarbon biosynthesis in bacteria and role of OleA. Appl Environ Microbiol 2010;76:3850-62.
97. Beller HR, Goh EB, Keasling JD. Genes involved in long-chain alkene biosynthesis in micrococcus Luteus. Appl Environ Microbiol 2010;76:1212-23.
98. Ajikumar PK, XiaoW-H, Tyo KEJ,Wang Y, Simeon F, Leonard E, et al. Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 2010;330:70-4.