Application of Selection and Optimization of Promoter in Metabolic Engineering of Saccharomyces cerevisiae

doi:10.13560/j.cnki.biotech.bull.1985.2017-0909

Abstract

Abstract: Saccharomyces cerevisiae，the simplest eukaryote，is widely used in the life science as a model organism. So far，the majority of the natural products were extracted directly from organism，which has been gradually replaced by the approaches of synthetic biology duo to its inefficiency and consuming a lot of biological resources. Modifying its metabolic pathways and adding heterometabolic pathways of S. cerevisiae for target natural products has been an efficient approach of acquiring resources. The direct synthesis of target metabolites has become the research hot spot in synthetic biology and metabolic engineering of S. cerevisiae through optimizing and transforming the exogenous gene promoter，regulating the expression level of the exogenous gene in the host，and coordinating the metabolic pathways of hosts. Here we had a detailed introduction on the structures and types of promoters as well optimizing methods of expression in the process of synthetizing natural products from the constructed S. cerevisiae，which may provide a reference for relevant researchers to use S. cerevisiae as chassis cells in synthetic biology.

Key words: Saccharomyces cerevisiae, promoter, synthetic biology, metabolic engineering

WANG Ke-wen ,YIN Xue, WANG Yu ,LI Yu-hua. Application of Selection and Optimization of Promoter in Metabolic Engineering of Saccharomyces cerevisiae[J]. Biotechnology Bulletin, 2018, 34(6): 38-47.

References

[1] Galanie S, Thodey K, Trenchard IJ, et al. Complete biosynthesis of opioids in yeast[J] . Science, 2015, 349（6252）：1095.
[2] Li M, Kildegaard KR, Chen Y, et al. De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae[J] . Metab Eng, 2015, 32：1-11.
[3] Zhou K, Qiao K, Edgar S, et al. Distributing a metabolic pathway among a microbial consortium enhances production of natural products[J] . Nature Biotechnology, 2015, 33（4）：377-383.
[4] 许静, 徐俊. 海洋共附生微生物天然产物生物合成基因研究进展[J] . 微生物学报, 2008, 48（7）：975-979.
[5] 王勇. 新本草计划——基于合成生物学的药用植物活性代谢物研究[J] . 生物工程学报, 2017, 33（3）：478-485.
[6] Jiang H, Wood KV, Morgan JA. Metabolic engineering of the phenylpropanoid pathway in Saccharomyces cerevisiae[J] . Appl Environ Microbiol, 2005, 71（6）：2962-2969.
[7] Kannan K, Gibson DG. Yeast genome, by design[J] . Science, 2017, 355（6329）：1024.
[8] Galanie S, Thodey K, Trenchard IJ, et al. Complete biosynthesis of opioids in yeast[J] . Science, 2015, 349（6252）：1095-1100.
[9] Dai Z, Liu Y, Zhang X, et al. Metabolic engineering of Saccharomyces cerevisiae for production of ginsenosides[J] . Metabolic Engineer-ing, 2013, 20（5）：146-156.
[10] Xie W, Liu M, et al. Construction of a controllable β-carotene bio-synthetic pathway by decentralized assembly strategy in Saccharo-myces cerevisiae[J] . Biotechnol Bioeng, 2014, 1：125-133.
[11] Westfall PJ, Pitera DJ, Lenihan JR, et al. Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin[J] . Proc Natl Acad Sci USA, 2012, 109（3）：111-118.
[12] Leonard E, et al. Investigation of two distinct flavone synthases for plant-specific flavone biosynthesis in Saccharomyces cerevisiae[J] . Appl Environ Microbiol, 2005, 71（12）：8241.
[13] Medina VG, Almering MJH, Maris AJAV, et al. Elimination of glycerol production in anaerobic cultures of a Saccharomyces cerevisiae strain engineered to use acetic acid as an electron acceptor[J] . Appl Environ Microbiol, 2010, 76（1）：190-195.
[14] Chen X, Nielsen KF, Borodina I, et al. Increased isobutanol production in Saccharomyces cerevisiae by overexpression of genes in valine metabolism[J] . Biotechnol Biofuels, 2011, 4（1）：21.
[15] Yu KO, Ju J, Kim SW, et al. Synthesis of faees from glycerol in engineered Saccharomyces cerevisiae using endogenously produced ethanol by heterologous expression of an unspecific bacterial acyltransferase[J] . Biotechnol Bioeng, 2012, 1：110-115.
[16] Peraltayahya PP, Ouellet M, Chan R, et al. Identification and microbial production of a terpene-based advanced biofuel[J] . Nature Communications, 2011, 2（1）：483.
[17] Sauer M, Branduardi P, Valli M, et al. Production of l-ascorbic acid by metabolically engineered Saccharomyces cerevisiae and Zygosaccharomyces bailii[J] . Appl Environ Microbiol, 2004, 70（10）：6086-6091.
[18] Raab AM, Gebhardt G, Bolotina N, et al. Metabolic engineering of Saccharomyces cerevisiae for the biotechnological production of succinic acid[J] . Metab Eng, 2010, 12（6）：518-525.
[19] Maris AJAV, Geertman JMA, Vermeulen A, et al. Directed evolution of pyruvate decarboxylase-negative Saccharomyces cerevisiae, yielding a c2-independent, glucose-tolerant, and pyruvate-hyperproducing yeast[J] . Appl Environ Microbiol, 2004, 70（1）：159-166.
[20] Zhao L, Wang J, Zhou J, et al[modification of carbon flux in Sacchromyces cerevisiae to improve l-lactic acid production] [J] . Acta Microbiologica Sinica, 2011, 51（1）：50.
[21] Blazeck J, Alper HS. Promoter engineering：Recent advances in controlling transcription at the most fundamental level[J] . Biotechnol J, 2013, 8（1）：46-58.
[22] Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast tata box-containing genes[J] . Cell, 2004, 116（5）：699-709.
[23] Rando OJ, Winston F. Chromatin and transcription in yeast[J] . Genetics, 2012, 190（2）：351.
[24] Redden H, Alper HS. The development and characterization of synthetic minimal yeast promoters[J] . Nature Communications, 2015, 6：7810.
[25] Giniger E, et al. Specific DNA binding of gal4, a positive regulatory protein of yeast[J] . Cell, 1985, 40（4）：767-774.
[26] Hahn S, Young ET. Transcriptional regulation in Saccharomyces cerevisiae：Transcription factor regulation and function, mechani-sms of initiation, and roles of activators and coactivators[J] . Genetics, 2011, 189（3）：705-736.
[27] Partow S, Siewers V, Bj?rn S, et al. Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae[J] . Yeast, 2010, 27（11）：955-964.
[28] Wang D, Wang L, Hou L, et al. Metabolic engineering of Saccharomyces cerevisiae for accumulating pyruvic acid[J] . Annals of Microbiology, 2015, 65（4）：2323-2331.
[29] Sun J, Shao Z, Zhao H, et al. Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae[J] . Biotechnol Bioeng, 2012, 8：2082.
[30] Blount BA, Weenink T, et al. Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology[J] . PLoS One, 2012, 7（3）：e33279.
[31] Monfort A, Finger S, Sanz P, et al. Evaluation of different promoters for the efficient production of heterologous proteins in baker’s yeast[J] . Biotechnology Letters, 1999, 21（3）：225-229.
[32] Hubmann G, et al. Natural and modified promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae[J] . Methods Mol Biol, 2014, 1152：17-42.
[33] Emmerstorfer A, et al. Over-expression of ice2 stabilizes cytochro-me p450 reductase in Saccharomyces cerevisiae and pichia pastoris[J] . Biotechnol J, 2015, 10（4）：623-635.
[34] Zacharioudakis I, et al. Bimodal expression of yeast gal genes is controlled by a long non-coding rna and a bifunctional galactoki-nase[J] . Biochem Biophys Res Commun, 2017, 1：63-69.
[35] Horák J. Regulations of sugar transporters：Insights from yeast[J] . Current Genetics, 2013, 59（1-2）：1-31.
[36] Ro DK, Paradise EM, Ouellet M, et al. Production of the antimala-rial drug precursor artemisinic acid in engineered yeast[J] . Nature, 2006, 440（7086）：940.
[37] Yan X, Fan Y, Wei W, et al. Production of bioactive ginsenoside compound k in metabolically engineered yeast[J] . Cell Research, 2014, 24（6）：770-773.
[38] Bahieldin A, et al. Efficient production of lycopene in Saccharom-yces cerevisiae by expression of synthetic crt genes from a plasmid harboring the adh2 promoter[J] . Plasmid, 2014, 72：18.
[39] Lee KK, Da SN, Kealey JT. Determination of the extent of phosphopantetheinylation of polyketide synthases expressed in escherichia coli and Saccharomyces cerevisiae[J] . Analytical Biochemistry, 2009, 394（1）：75-80.
[40] Bernal DAN. Metabolic Engineering of Saccharomyces cerevisiae for the production of aromatic componds[D] . Brisbane: School of Chemistry and Molecular Biosciences, University of Queensland, 2012.
[41] Kim SI, Ha BS, et al. Evaluation of copper-inducible fungal laccase promoter in foreign gene expression in pichia pastoris[J] . Biotechnol Bioprocess Engineering, 2016, 1：53-59.
[42] Gross A, R?del G, Ostermann K. Application of the yeast pherom-one system for controlled cell-cell communication and signal ampl-ification[J] . Lett Appl Microbiol, 2011, 5：521-526.
[43] Ammerer G. Identification, purification, and cloning of a polypeptide（prtf/grm）that binds to mating-specific promoter elements in yeast[J] . Genes Dev, 1990, 4（2）：299-312.
[44] Gancedo JM, Flores CL, Gancedo C. The repressor rgt1 and the camp-dependent protein kinases control the expression of the suc2 gene in Saccharomyces cerevisiae[J] . BBA-General Subjects, 2015, 1850（7）：1362-1367.
[45] Silva NAD, Srikrishnan S. Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae[J] . Fems Yeast Research, 2012, 12（2）：197-214.
[46] Poor CB, Wegner SV, Li H, et al. Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator aft2[J] . Proc Natl Acad Sci USA, 2014, 111（11）：4043-4048.
[47] Zhu Y, Sun J, Zhu Y, et al. Endogenic oxidative stress response contributes to glutathione over-accumulation in mutant Saccharomyces cerevisiae y518[J] . Appl Microbiol Biotechnol, 2015, 99（17）：7069-7078.
[48] Noble J, Sanchez I, Blondin B. Identification of new Saccharomyces cerevisiae variants of the met2 and skp2 genes controlling the sulfur assimilation pathway and the production of undesirable sulfur compounds during alcoholic fermentation[J] . Microbial Cell Factories, 2015, 14（1）：68.
[49] Anton C, Zanolari B, Arcones I, et al. Involvement of the exomer complex in the polarized transport of ena1 required for Saccharomyces cerevisiae survival against toxic cations[J] . Molecular Biology of the Cell, 2017, mbc. E17-09-0549.
[50] Zhang C, Li Z, Zhang X, et al. Transcriptomic profiling of chemical exposure reveals roles of yap1 in protecting yeast cells from oxidative and other types of stresses[J] . Yeast, 2016, 33（1）：5-19.
[51] Martínez JL, Liu L, Petranovic D, et al. Engineering the oxygen sensing regulation results in an enhanced recombinant human hemoglobin production by Saccharomyces cerevisiae[J] . Biotechnol Bioeng, 2015, 112（1）：181.
[52] Hubmann G, Thevelein JM, Nevoigt E. Natural and modified promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae[M] . Springer New York, 2014.
[53] Williams TC, Averesch NJH, Winter G, et al. Quorum-sensing linked rna interference for dynamic metabolic pathway control in Saccharomyces cerevisiae[J] . Metab Eng, 2015, 29：124.
[54] Gueldener U, Heinisch J, Koehler GJ, et al. A second set of loxp marker cassettes for cre-mediated multiple gene knockouts in budding yeast[J] . Nucleic Acids Res, 2002, 30（6）：e23.
[55] Redden H, Morse N, et al. The synthetic biology toolbox for tuning gene expression in yeast[J] . FEMS Yeast Res, 2014, 1：1-10.
[56] Nevoigt E, Kohnke J, et al. Engineering of promoter replacement cassettes for fine-tuning of gene expression in Saccharomyces cerevisiae[J] . Appl Environ Microbiol, 2006, 8：5266-5273.
[57] Nevoigt E, Fischer C, Mucha O, et al. Engineering promoter regulation[J] . Biotechnol Bioeng, 2007, 96（3）：550-558.
[58] 张旭, 王晶晶, 刘建平. 基于启动子和宿主改造的酿酒酵母表达系统优化研究[J] . 中国生物工程杂志, 2015（1）：61-66.
[59] Jensen PR, Hammer K. Artificial promoters for metabolic optimization[J] . Biotechnol Bioeng, 2015, 58（2-3）：191-195.
[60] Johnson AN, Weil PA. Identification of a transcriptional activation domain in yeast repressor activator protein 1（rap1）using an altered DNA-binding specificity variant[J] . Journal of Biological Chemistry, 2017, 292（14）：5705-5723.
[61] Jeppsson M, Johansson B, Jensen PR, et al. The level of glucose-6-phosphate dehydrogenase activity strongly influences xylose fermentation and inhibitor sensitivity in recombinant Saccharomyces cerevisiae strains[J] . Yeast, 2003, 20（15）：1263.
[62] Rich MS, Payen C, et al. Comprehensive analysis of the sul1 prom-oter of Saccharomyces cerevisiae[J] . Genetics, 2016, 1：191.
[63] Blazeck J, Garg R, Reed B, et al. Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters[J] . Biotechnol Bioeng, 2012, 109（11）：2884-2895.
[64] Ruohonen L, Penttil? M, Ker?nen S. Optimization of bacillus alpha-amylase production by Saccharomyces cerevisiae[J] . Yeast, 1991, 7（4）：337-346.
[65] Ruohonen L, Aalto MK, Ker?nen S. Modifications to the adh1 promoter of Saccharomyces cerevisiae for efficient production of heterologous proteins[J] . J Biotechnol, 1995, 3：193-203.
[66] Denis CL, Ferguson J, Young ET. Mrna levels for the fermentative alcohol dehydrogenase of Saccharomyces cerevisiae decrease upon growth on a nonfermentable carbon source[J] . Journal of Biological Chemistry, 1983, 258（2）：1165-1171.
[67] Wang S, Cheng G, Joshua C, et al. Furfural tolerance and detoxification mechanism in candida tropicalis[J] . Biotechnol Biofuels, 2016, 9（1）：250.
[68] Kim S, Lee K, Bae SJ, et al. Promoters inducible by aromatic amino acids and γ-aminobutyrate（gaba）for metabolic engineering applications in Saccharomyces cerevisiae[J] . Appl Microbiol Biotechnol, 2015, 99（6）：2705-2714.
[69] Leavitt JM, Tong A, Tong J, et al. Coordinated transcription factor and promoter engineering to establish strong expression elements in Saccharomyces cerevisiae[J] . Biotechnol J, 2016, 11（7）：866.
[70] Malakar P, Venkatesh KV. Gal regulon of Saccharomyces cerevisiae performs optimally to maximize growth on galactose[J] . Fems Yeast Research, 2014, 14（2）：346-356.
[71] 唐瑞琪, 熊亮, 白凤武, 等. 酿酒酵母人工杂合启动子与天然启动子活性比较[J] . 生物技术通报, 2017（1）：120-128.
[72] Garí E, Piedrafita L, Aldea M, et al. A set of vectors with a tetracyc-line-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae[J] . Yeast, 2010, 13（9）：837-848.
[73] Wawiórka L, Molestak E, Szajwaj M, et al. The multiplication of ribosomal p-stalk proteins contributes to the fidelity of translation[J] . Mol Cell Biol, 2017, 37（17）. Plie00060-17.
[74] Revankar SG, Fu J, et al. Cloning and characterization of the lanos-terol 14α-demethylase（erg11）gene in cryptococcus neoformans[J] . Biochem Biophys Res Commun, 2004, 324（2）：719-728.
[75] Blount BA, Weenink T, Ellis T. Construction of synthetic regulatory networks in yeast[J] . Febs Letters, 2012, 586（15）：2112.
[76] Bellí G, Garí E, Piedrafita L, et al. An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast[J] . Nucleic Acids Res, 1998, 26（4）：942-947.
[77] Shimizu-Sato S, Huq E, Tepperman JM, Quail PH. A light-switchable gene promoter system[J] . Nature Biotechnology, 2002, 20（10）：1041-1044.
[78] Mcisaac RS, Gibney PA, Chandran SS, et al. Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae[J] . Nucleic Acids Res, 2014, 6：e48.
[79] Hector RE, Mertens JA. A synthetic hybrid promoter for xylose-regulated control of gene expression in Saccharomyces yeasts[J] . Molecular Biotechnology, 2017, 59（1）：24-33.
[80] 高义平, 赵和, 吕孟雨, 等. 易错PCR研究进展及应用[J] . 核农学报, 2013, 27（5）：607-612.
[81] Jeppsson M, Johansson B, Jensen PR, et al. The level of glucose-6-phosphate dehydrogenase activity strongly influences xylose fermentation and inhibitor sensitivity in recombinant Saccharomyces cerevisiae strains[J] . Yeast, 2003, 20（15）：1263-1272.
[82] Wang S, Cheng G, Joshua C, et al. Furfural tolerance and detoxification mechanism incandida tropicalis[J] . Biotechnol Biofuels, 2016, 9（1）：250.
[83] 余君涵, 马雯雯, 王智文, 等. 人工合成启动子文库研究进展[J] . 微生物学通报, 2016, 43（1）：198-204.
[84] Zong Y, Zhang HM, Cheng L, et al. Insulated transcriptional elements enable precise design of genetic circuits[J] . Nature Communications, 2017, 8（1）：52.
[85] Rohlhill J, Sandoval NR, Papoutsakis ET. Sort-seq approach to engineering a formaldehyde-inducible promoter for dynamically regulated escherichia coli growth on methanol[J] . Acs Synthetic Biology, 2017, 6（8）：1584-1595.