Lycopene overproduction in Saccharomyces cerevisiae through combining pathway engineering with host engineering

Microbial Cell Factories

Volumn 15, Issue 1, 2016, Pages

  Chen, Yan ^a   Xiao, Wenhai ^a   Wang, Ying ^a   Liu, Hong ^a   Li, Xia ^a   Yuan, Yingjin ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

Heterologous pathway; Lycopene; Metabolic engineering; Saccharomyces cerevisiae; Synthetic biology

Indexed keywords

ACETIC ACID; ACETYL COENZYME A; CAROTENOID; FARNESYL TRANS TRANSFERASE; FUNGAL ENZYME; LYCOPENE; PHYTOENE DESATURASE; PHYTOENE SYNTHASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR INO2; UNCLASSIFIED DRUG; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BIOREACTOR; BIOSYNTHESIS; BLAKESLEA TRISPORA; CONTROLLED STUDY; ENZYME ENGINEERING; FED BATCH FERMENTATION; FUNGAL STRAIN; GENE LOCUS; MATING TYPE; NONHUMAN; SACCHAROMYCES CEREVISIAE; ENZYMOLOGY; GENETICS; METABOLIC ENGINEERING; METABOLISM;

BIOSYNTHETIC PATHWAYS; CAROTENOIDS; METABOLIC ENGINEERING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84975247455     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-016-0509-4     Document Type: Article

References (54)

1. Alper H, Jin YS, Moxley JF, Stephanopoulos G. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng. 2005;7(3):155-64.
2. Alper H, Miyaoku K, Stephanopoulos G. Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol. 2005;23(5):612-6.
3. Brochado AR, Patil KR. Model-guided identification of gene deletion targets for metabolic engineering in Saccharomyces cerevisiae. Methods Mol Biol. 2014;1152:281-94.
4. Jin YS, Stephanopoulos G. Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli. Metab Eng. 2007;9(4):337-47.
5. Trikka FA, Nikolaidis A, Athanasakoglou A, Andreadelli A, Ignea C, Kotta K, Argiriou A, Kampranis SC, Makris AM. Iterative carotenogenic screens identify combinations of yeast gene deletions that enhance sclareol production. Microb Cell Fact. 2015;14:60.
6. Ajikumar PK, Xiao WH, Tyo KE, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science. 2010;330(6000):70-4.
7. Chen Y, Daviet L, Schalk M, Siewers V, Nielsen J. Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism. Metab Eng. 2013;15:48-54.
8. Lv X, Xie W, Lu W, Guo F, Gu J, Yu H, Ye L. Enhanced isoprene biosynthesis in Saccharomyces cerevisiae by engineering of the native acetyl-CoA and mevalonic acid pathways with a push-pull-restrain strategy. J Biotechnol. 2014;186:128-36.
9. Ma T, Deng Z, Liu T. Microbial production strategies and applications of lycopene and other terpenoids. World J Microbiol Biotechnol. 2016;32(1):15.
10. Özaydin B, Burd H, Lee TS, Keasling JD. Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production. Metab Eng. 2013;15:174-83.
11. Swidah R, Wang H, Reid PJ, Ahmed HZ, Pisanelli AM, Persaud KC, Grant CM, Ashe MP. Butanol production in S. cerevisiae via a synthetic ABE pathway is enhanced by specific metabolic engineering and butanol resistance. Biotechnol Biofuels. 2015;8:97.
12. Sies H, Stahl W. Lycopene: antioxidant and biological effects and its bioavailability in the human. Proc Soc Exp Biol Med. 1998;218:121-4.
13. Giovannucci E, Ascherio A, Rimm EB, Stampfer MJ, Colditz GA, Willett WC. Intake of carotenoids and retinol in relation to risk of prostate cancer. J Natl Cancer Inst. 1995;87(23):1767-76.
14. Ray BL, Raetz CR. The biosynthesis of gram-negative endotoxin. A novel kinase in Escherichia coli membranes that incorporates the 4'-phosphate of lipid A. J Biol Chem. 1987;262(3):1122-8.
15. Mantzouridou F, Tsimidou MZ. Lycopene formation in Blakeslea trispora. Chemical aspects of a bioprocess. Trends Food Sci Technol. 2008;19(7):363-71.
16. Xie W, Lv X, Ye L, Zhou P, Yu H. Construction of lycopene-overproducing Saccharomyces cerevisiae by combining directed evolution and metabolic engineering. Metab Eng. 2015;30:69-78.
17. Kim YS, Lee JH, Kim NH, Yeom SJ, Kim SW, Oh DK. Increase of lycopene production by supplementing auxiliary carbon sources in metabolically engineered Escherichia coli. Appl Microbiol Biotechnol. 2011;90(2):489-97.
18. Zhu F, Lu L, Fu S, Zhong X, Hu M, Deng Z, Liu T. Targeted engineering and scale up of lycopene overproduction in Escherichia coli. Process Biochem. 2015;50(3):341-6.
19. Donald KA, Hampton RY, Fritz IB. Effects of overproduction of the catalytic domain of 3-hydroxy-3-methylglutaryl coenzyme A reductase on squalene synthesis in Saccharomyces cerevisiae. Appl Environ Microbiol. 1997;63:3341-4.
20. Gietz RD, Schiestl RH. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat Protoc. 2007;2(1):31-4.
21. Longtine MS, McKenzie IIIA, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998;14(10):953-61.
22. Lian J, Si T, Nair NU, Zhao H. Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains. Metab Eng. 2014;24:139-49.
23. Cao YX, Xiao WH, Liu D, Zhang JL, Ding MZ, Yuan YJ. Biosynthesis of odd-chain fatty alcohols in Escherichia coli. Metab Eng. 2015;29:113-23.
24. Xie W, Liu M, Lv X, Lu W, Gu J, Yu H. Construction of a controllable beta-carotene biosynthetic pathway by decentralized assembly strategy in Saccharomyces cerevisiae. Biotechnol Bioeng. 2014;111(1):125-33.
25. Britton G. General carotenoid methods. Methods Enzymol. 1985;111(4):113-49.
26. Zhao J, Li Q, Sun T, Zhu X, Xu H, Tang J, Zhang X, Ma Y. Engineering central metabolic modules of Escherichia coli for improving beta-carotene production. Metab Eng. 2013;17:42-50.
27. Westfall PJ, Pitera DJ, Lenihan JR, Eng D, Woolard FX, Regentin R, Horning T, Tsuruta H, Melis DJ, Owens A, et al. Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. Proc Natl Acad Sci USA. 2012;109(3):E111-8.
28. Thomas KC, Hynes SH, Ingledew WM. Influence of medium buffering capacity on inhibition of Saccharomyces cerevisiae growth by acetic and lactic acids. Appl Environ Microbiol. 2002;68(4):1616-23.
29. Chang JJ, Thia C, Lin HY, Liu HL, Ho FJ, Wu JT, Shih MC, Li WH, Huang CC. Integrating an algal β-carotene hydroxylase gene into a designed carotenoid-biosynthesis pathway increases carotenoid production in yeast. Bioresour Technol. 2015;184:2-8.
30. Ding MZ, Yan HF, Li LF, Zhai F, Shang LQ, Yin Z, Yuan YJ. Biosynthesis of Taxadiene in Saccharomyces cerevisiae: selection of geranylgeranyl diphosphate synthase directed by a computer-aided docking strategy. PLoS ONE. 2014;9(10):e109348.
31. Greene JJ. Host cell compatibility in protein expression. Methods Mol Biol. 2004;267:3-14.
32. Sarria S, Wong B, Garcia Martin H, Keasling JD, Peralta-Yahya P. Microbial synthesis of pinene. ACS Synth Biol. 2014;3(7):466-75.
33. Misawa N, Shimada H. Metabolic engineering for the production of carotenoids in non-carotenogenic bacteria and yeasts. J Biotechnol. 1997;59(3):169-81.
34. Mata-Gomez LC, Montanez JC, Mendez-Zavala A, Aguilar CN. Biotechnological production of carotenoids by yeasts: an overview. Microb Cell Fact. 2014;13:12.
35. Verwaal R, Wang J, Meijnen JP, Visser H, Sandmann G, van den Berg JA, van Ooyen AJ. High-level production of beta-carotene in Saccharomyces cerevisiae by successive transformation with carotenogenic genes from Xanthophyllomyces dendrorhous. Appl Environ Microbiol. 2007;73(13):4342-50.
36. Yoon SH, Kim JE, Lee SH, Park HM, Choi MS, Kim JY, Lee SH, Shin YC, Keasling JD, Kim SW. Engineering the lycopene synthetic pathway in E. coli by comparison of the carotenoid genes of Pantoea agglomerans and Pantoea ananatis. Appl Microbiol Biotechnol. 2007;74(1):131-9.
37. Sun J, Sun XX, Tang PW, Yuan QP. Molecular cloning and functional expression of two key carotene synthetic genes derived from Blakeslea trispora into E. coli for increased β-carotene production. Biotechnol Lett. 2012;34(11):2077-82.
38. Wang CW, Oh MK, Liao JC. Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli. Biotechnol Bioeng. 1999;62(2):235-41.
39. Ohnuma SI, Suzuki M, Nishino T. Archaebacterial ether-linked lipid biosynthetic gene. Expression cloning, sequencing, and characterization of geranylgeranyl-diphosphate synthase. J Biol Chem. 1994;269(20):14792-7.
40. Dai Z, Liu Y, Huang L, Zhang X. Production of miltiradiene by metabolically engineered Saccharomyces cerevisiae. Biotechnol Bioeng. 2012;109(11):2845-53.
41. Engels B, Dahm P, Jennewein S. Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production. Metab Eng. 2008;10(3-4):201-6.
42. Gruszecki WI, Strzalka K. Carotenoids as modulators of lipid membrane physical properties. Biochim Biophys Acta. 2005;1740(2):108-15.
43. Verwaal R, Jiang Y, Wang J, Daran JM, Sandmann G, van den Berg JA, van Ooyen AJ. Heterologous carotenoid production in Saccharomyces cerevisiae induces the pleiotropic drug resistance stress response. Yeast. 2010;27(12):983-98.
44. Ohto C, Muramatsu M, Obata S, Sakuradani E, Shimizu S. Overexpression of the gene encoding HMG-CoA reductase in Saccharomyces cerevisiae for production of prenyl alcohols. Appl Microbiol Biotechnol. 2009;82(5):837-45.
45. Jackson BE, Hart-Wells EA, Matsuda SP. Metabolic engineering to produce sesquiterpenes in yeast. Org Lett. 2003;5(10):1629-32.
46. Anderegg RJ, Betz R, Carr SA, Crabb JW, Duntze W. Structure of Saccharomyces cerevisiae mating hormone a-factor. Identification of S-farnesyl cysteine as a structural component. J Biol Chem. 1988;263(34):18236-40.
47. Rico J, Pardo E, Orejas M. Enhanced production of a plant monoterpene by overexpression of the 3-hydroxy-3-methylglutaryl coenzyme A reductase catalytic domain in Saccharomyces cerevisiae. Appl Environ Microbiol. 2010;76(19):6449-54.
48. Szappanos B, Kovács K, Szamecz B, Honti F, Costanzo M, Baryshnikova A, Gelius-Dietrich G, Lercher MJ, Jelasity M, Myers CL, et al. An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet. 2011;43(7):656-62.
49. Li BZ, Cheng JS, Ding MZ, Yuan YJ. Transcriptome analysis of differential responses of diploid and haploid yeast to ethanol stress. J Biotechnol. 2010;148(4):194-203.
50. Villa-Garcia MJ, Choi MS, Hinz FI, Gaspar ML, Jesch SA, Henry SA. Genome-wide screen for inositol auxotrophy in Saccharomyces cerevisiae implicates lipid metabolism in stress response signaling. Mol Genet Genomics. 2011;285(2):125-49.
51. Ling H, Chen B, Kang A, Lee JM, Chang MW. Transcriptome response to alkane biofuels in Saccharomyces cerevisiae: identification of efflux pumps involved in alkane tolerance. Biotechnol Biofuels. 2013;6(1):95.
52. Chumnanpuen P, Nookaew I, Nielsen J. Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast. BMC Syst Biol. 2013;7(Suppl 3):S7.
53. Vemuri GN, Eiteman MA, McEwen JE, Olsson L, Nielsen J. Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 2007;104(7):2402-7.
54. Zhang C, Chen X, Zou R, Zhou K, Stephanopoulos G, Too HP. Combining genotype improvement and statistical media optimization for isoprenoid production in E. coli. PLoS ONE. 2013;8(10):e75164.