Metabolic engineering of Saccharomyces cerevisiae for the synthesis of valuable chemicals

References

• Gao S, Lyu Y, Zeng W, et al. Efficient biosynthesis of (2 S)-naringenin from p -coumaric acid in Saccharomyces cerevisiae. J Agric Food Chem. 2020;68(4):1015–1021.
   PubMed Web of Science ®Google Scholar
• Baloch MA, Mahmood N, Zhang JW. Effect of natural resources, renewable energy and economic development on CO2 emissions in BRICS countries. Sci Total Environ. 2019;678:632–638.
   PubMed Web of Science ®Google Scholar
• Davy AM, Kildegaard HF, Andersen MR. Cell factory engineering. Cell Syst. 2017;4(3):262–275.
   PubMed Web of Science ®Google Scholar
• European Commission. A sustainable bioeconomy for Europe: strengthening the connection between economy, society and the environment. European Union. 2018. https://ec.europa.eu/research/bioeconomy/pdf/ec_bioeconomy_strategy_2018.pdf#view=fit&pagemode=none
   Google Scholar
• Shi W, Li J, Chen Y, et al. Enhancement of C6–C10 fatty acid ethyl esters production in Saccharomyces cerevisiae CA by metabolic engineering. LWT-Food Sci Technol. 2021;145:111496.
   Web of Science ®Google Scholar
• Wang L, Li B, Wang S, et al. Improving multiple stress-tolerance of a flocculating industrial Saccharomyces cerevisiae strain by random mutagenesis and hybridization. Process Biochem. 2021;102:275–285.
   Web of Science ®Google Scholar
• Wei Y, Bergenholm D, Gossing M, et al. Expression of cocoa genes in Saccharomyces cerevisiae improves cocoa butter production. Microb Cell Fact. 2018;17(1):11.
   PubMedGoogle Scholar
• Żolądek T, Boguta M, Putrament A. Nuclear suppressors of the mitochondrial mutation oxi1-V25 in Saccharomyces cerevisiae-I. The phenotypes of some suppressors. Curr Genet. 1985;9(6):427–433.
   Web of Science ®Google Scholar
• Ren J-Y, Liu G, Chen Y-F, et al. Enhanced production of ethyl lactate in Saccharomyces cerevisiae by genetic modification. J Agric Food Chem. 2020;68(47):13863–13870.
   PubMed Web of Science ®Google Scholar
• Auesukaree C. Molecular mechanisms of the yeast adaptive response and tolerance to stresses encountered during ethanol fermentation. J Biosci Bioeng. 2017;124(2):133–142.
   PubMed Web of Science ®Google Scholar
• Burphan T, Tatip S, Limcharoensuk T, et al. Enhancement of ethanol production in very high gravity fermentation by reducing fermentation-induced oxidative stress in Saccharomyces cerevisiae. Sci Rep. 2018;8(1):13069.
   PubMedGoogle Scholar
• Hu K, Jin G, Mei W, et al. Increase of medium-chain fatty acid ethyl ester content in mixed H. uvarum/S. cerevisiae fermentation leads to wine fruity aroma enhancement. Food Chem. 2018;239:495–501.
   PubMed Web of Science ®Google Scholar
• Jang WD, Kim GB, Kim Y, et al. Applications of artificial intelligence to enzyme and pathway design for metabolic engineering. Curr Opin Biotechnol. 2022;73:101–107. http://www.sciencedirect.com/science/article/pii/S0958166921001361.
   PubMed Web of Science ®Google Scholar
• Teixeira P, Ferreira R, Zhou Y, et al. Dynamic regulation of fatty acid pools for improved production of fatty alcohols in Saccharomyces cerevisiae. Microb Cell Fact. 2017;16(1):45.
   PubMedGoogle Scholar
• Shi S, Wang Z, Shen L, et al. Synthetic biology: a new frontier in food production. Trends Biotechnol. 2022;40(7):781–803.
   PubMed Web of Science ®Google Scholar
• Baptista SL, Costa CE, Cunha JT, et al. Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates. Biotechnol Adv. 2021;47:107697.
   PubMed Web of Science ®Google Scholar
• Kulagina N, Besseau S, Godon C, et al. Yeasts as biopharmaceutical production platforms. Front Microbiol. 2021;2:733492.
   Google Scholar
• Qiu Z, Jiang R. Improving Saccharomyces cerevisiae ethanol production and tolerance via RNA polymerase II subunit Rpb7. Biotechnol Biofuels. 2017;10(1):125.
   PubMedGoogle Scholar
• Niu Y, Wu L, Shen Y, et al. Coexpression of β-xylosidase and xylose isomerase in Saccharomyces cerevisiae improves the efficiency of saccharification and fermentation from xylo-oligosaccharides. Cellulose. 2019;26(13-14):7923–7937.
   Web of Science ®Google Scholar
• Shi X, Zou Y, Chen Y, et al. Overexpression of THI4 and HAP4 improves glucose metabolism and ethanol production in Saccharomyces cerevisiae. Front Microbiol. 2018;9:1444.
   PubMed Web of Science ®Google Scholar
• Zahoor A, Messerschmidt K, Boecker S, et al. ATPase-based implementation of enforced ATP wasting in Saccharomyces cerevisiae for improved ethanol production. Biotechnol Biofuels. 2020;13(1):185.
   PubMed Web of Science ®Google Scholar
• Liu K, Yuan X, Liang L, et al. Using CRISPR/Cas9 for multiplex genome engineering to optimize the ethanol metabolic pathway in Saccharomyces cerevisiae. Biochem Eng J. 2019;145:120–126.
   Web of Science ®Google Scholar
• Wu R, Chen D, Cao S, et al. Enhanced ethanol production from sugarcane molasses by industrially engineered Saccharomyces cerevisiae via replacement of the PHO4 gene. RSC Adv. 2020;10(4):2267–2276.
   PubMed Web of Science ®Google Scholar
• Cunha JT, Soares PO, Romaní A, et al. Xylose fermentation efficiency of industrial Saccharomyces cerevisiae yeast with separate or combined xylose reductase/xylitol dehydrogenase and xylose isomerase pathways. Biotechnol Biofuels. 2019;12:20.
   PubMed Web of Science ®Google Scholar
• Zhang C, Xue Q, Hou J, et al. In-depth two-stage transcriptional reprogramming and evolutionary engineering of Saccharomyces cerevisiae for efficient bioethanol production from cylose with scetate. J Agric Food Chem. 2019;67(43):12002–12012.
   PubMed Web of Science ®Google Scholar
• Zhu L, Li P, Sun T, et al. Overexpression of SFA1 in engineered Saccharomyces cerevisiae to increase xylose utilization and ethanol production from different lignocellulose hydrolysates. Bioresour Technol. 2020;313:123724.
   PubMed Web of Science ®Google Scholar
• Fraser MP, Cass GR, Simoneit B, et al. Air quality model evaluation data for organics: 5 C6-C22 nonpolar and semipolar aromatic compounds. Environ. Sci. Technol. 1998;32(12):1760–1770.
   Web of Science ®Google Scholar
• Ribeiro SR, Carvalho CD, Cavaleiro C, et al. A novel insight on an ancient aromatic plant: the rosemary (rosmarinus officinalis L.). Trends Food Sci Tech. 2015;45(2):355–368.
   Web of Science ®Google Scholar
• Fossati E, Ekins A, Narcross L, et al. Reconstitution of a 10-gene pathway for synthesis of the plant alkaloid dihydrosanguinarine in Saccharomyces cerevisiae. Nat Commun. 2014;5:3283.
   PubMed Web of Science ®Google Scholar
• Pyne ME, Kevvai K, Grewal PS, et al. A yeast platform for high-level synthesis of tetrahydroisoquinoline alkaloids. Nat Commun. 2020;11(1):3337.
   PubMed Web of Science ®Google Scholar
• Dickey RM, Forti AM, Kunjapur AM. Advances in engineering microbial biosynthesis of aromatic compounds and related compounds. Bioresour Bioprocess. 2021;8(1):1–17.
   Web of Science ®Google Scholar
• Suástegui M, Guo W, Feng X, et al. Investigating strain dependency in the production of aromatic compounds in Saccharomyces cerevisiae. Biotechnol Bioeng. 2016;113(12):2676–2685.
   PubMed Web of Science ®Google Scholar
• Liu Q, Yu T, Li X, et al. Rewiring carbon metabolism in yeast for high level production of aromatic chemicals. Nat Commun. 2019;10(1):4976.
   PubMedGoogle Scholar
• Borja GM, Rodriguez A, Campbell K, et al. Metabolic engineering and transcriptomic analysis of Saccharomyces cerevisiae producing p-coumaric acid from xylose. Microb Cell Fact. 2019;18(1):191.
   PubMed Web of Science ®Google Scholar
• Hassan J, Kaleem I, Rasool A, et al. Engineered Saccharomyces cerevisiae for the de novo synthesis of the aroma compound longifolene. Chem Eng Sci. 2020;226:115799.
   Web of Science ®Google Scholar
• Zhu L, Wang J, Xu S, et al. Improved aromatic alcohol production by strengthening the shikimate pathway in Saccharomyces cerevisiae. Process Biochem. 2021;103:18–30.
   Web of Science ®Google Scholar
• Kuivanen J, Kannisto M, Mojzita D, et al. Engineering of Saccharomyces cerevisiae for anthranilate and methyl anthranilate production. Microb Cell Fact. 2021;20(1):34.
   PubMed Web of Science ®Google Scholar
• Sun Z, Meng H, Li J, et al. Identification of novel knockout targets for improving terpenoids biosynthesis in Saccharomyces cerevisiae. PLoS One. 2014;9(11):e112615.
   PubMed Web of Science ®Google Scholar
• Zhang W, Cai Y, Chen X, et al. Optimized extraction based on the terpenoids of heterotrigona itama propolis and their antioxidative and anti-inflammatory activities. J Food Biochem. 2020;44(8):e13296.
   PubMed Web of Science ®Google Scholar
• Li X, Wang Z, Zhang G, et al. Improving lycopene production in Saccharomyces cerevisiae through optimizing pathway and chassis metabolism. Chem Eng Sci. 2019;193:364–369.
   Web of Science ®Google Scholar
• Singh N, Yadav SS, Kumar S, et al. A review on traditional uses, phytochemistry, pharmacology, and clinical research of dietary spice cuminum cyminum. L. Phytother Res. 2021;35(9):5007–5030.
   PubMed Web of Science ®Google Scholar
• Cainelli G, Cardillo G. Some aspects of the stereospecific synthesis of terpenoids by means of isoprene units. Accounts. Chem Res. 1981;14:89–94 https://doi.org/10.1021/ar00063a005.
   Web of Science ®Google Scholar
• Kemper K, Hirte M, Reinbold M, et al. Opportunities and challenges for the sustainable production of structurally complex diterpenoids in recombinant microbial systems. Beilstein J Org Chem. 2017;13:845–854.
   PubMed Web of Science ®Google Scholar
• Peng B, Nielsen LK, Kampranis SC, et al. Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiae. Metab Eng. 2018;47:83–93.
   PubMed Web of Science ®Google Scholar
• Cheng S, Liu X, Jiang G, et al. Orthogonal engineering of biosynthetic pathway for efficient production of limonene in Saccharomyces cerevisiae. ACS Synth Biol. 2019;8(5):968–975.
   PubMed Web of Science ®Google Scholar
• Jiang G, Yao M, Wang Y, et al. A “push-pull-restrain” strategy to improve citronellol production in Saccharomyces cerevisiae. Metab Eng. 2021;66:51–59.
   PubMed Web of Science ®Google Scholar
• Guo Y, Li F, Zhao J, et al. Diverting mevalonate pathway metabolic flux leakage in Saccharomyces cerevisiae for monoterpene geraniol production from cane molasses. Biochem. Eng J. 2022;181:108398.
   Web of Science ®Google Scholar
• Yee DA, DeNicola AB, Billingsley JM, et al. Engineered mitochondrial production of monoterpenes in Saccharomyces cerevisiae. Metab Eng. 2019;55:76–84.
   PubMed Web of Science ®Google Scholar
• Schilmiller AL, Schauvinhold I, Larson M, et al. Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate. Proc Natl Acad Sci U S A. 2009;106(26):10865–10870.
   PubMed Web of Science ®Google Scholar
• Zhang C, Ju H, Lu C, et al. High-titer production of 13R-manoyl oxide in metabolically engineered Saccharomyces cerevisiae. Microb Cell Fact. 2019;18(1):73.
   PubMedGoogle Scholar
• Kim J, Baidoo EEK, Amer B, et al. Engineering Saccharomyces cerevisiae for isoprenol production. Metab Eng. 2021;64:154–166.
   PubMed Web of Science ®Google Scholar
• Han J, Seo SH, Song J, et al. High-level recombinant production of squalene using selected Saccharomyces cerevisiae strains. J Ind Microbiol Biotechnol. 2018;45(4):239–251.
   PubMed Web of Science ®Google Scholar
• Wei L, Kwak S, Liu J, et al. Improved squalene production through increasing lipid contents in Saccharomyces cerevisiae. Biotechnol Bioeng. 2018;115(7):1793–1800.
   PubMed Web of Science ®Google Scholar
• Zhao F, Bai P, Nan W, et al. A modular engineering strategy for high‐level production of protopanaxadiol from ethanol by Saccharomyces cerevisiae. AIChE J. 2019;65(3):866–874.
   Web of Science ®Google Scholar
• Gao H, Zhao H, Hu T, et al. Metabolic engineering of Saccharomyces cerevisiae for high-level friedelin via genetic manipulation. Front Bioeng Biotech. 2022;10:805429.
   PubMed Web of Science ®Google Scholar
• Ma B, Liu M, Li Z, et al. Significantly enhanced production of patchoulol in metabolically engineered Saccharomyces cerevisiae. J Agric Food Chem. 2019;67(31):8590–8598.
   PubMed Web of Science ®Google Scholar
• Chen H, Zhu C, Zhu M, et al. High production of valencene in Saccharomyces cerevisiae through metabolic engineering. Microb Cell Fact. 2019;18(1):195.
   PubMed Web of Science ®Google Scholar
• Meng X, Liu H, Xu W, et al. Metabolic engineering Saccharomyces cerevisiae for de novo production of the sesquiterpenoid (+)-nootkatone. Microb Cell Fact. 2020;19(1):21.
   PubMed Web of Science ®Google Scholar
• Ma T, Shi B, Ye Z, et al. Lipid engineering combined with systematic metabolic engineering of Saccharomyces cerevisiae for high-yield production of lycopene. Metab Eng. 2019;52:134–142.
   PubMed Web of Science ®Google Scholar
• Fathi Z, Tramontin LRR, Ebrahimipour G, et al. Metabolic engineering of Saccharomyces cerevisiae for production of β-carotene from hydrophobic substrates. Fems Yeast Res. 2021;21:foaa068.
   PubMed Web of Science ®Google Scholar
• Bu X, Lin J, Duan C, et al. Dual regulation of lipid droplet-triacylglycerol metabolism and ERG9 expression for improved β-carotene production in Saccharomyces cerevisiae. Microb Cell Fact. 2022;21(1):3.
   PubMed Web of Science ®Google Scholar
• Su B, Lai P, Yang F, et al. Engineering a balanced acetyl voenzyme a metabolism in Saccharomyces cerevisiae for lycopene production through rational and evolutionary engineering. J Agric Food Chem. 2022;70(13):4019–4029.
   PubMed Web of Science ®Google Scholar
• Muro E, Atilla GGE, Eggert US. Lipids in cell biology: how can we understand them better? Mol Biol Cell. 2014;25(12):1819–1823.
   PubMed Web of Science ®Google Scholar
• Eriksen DT, Hamedirad M, Yuan Y, et al. Orthogonal fatty acid biosynthetic pathway improves fatty acid ethyl ester production in Saccharomyces cerevisiae. ACS Synth Biol. 2015;4(7):808–814.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Su M, Qin N, et al. Expressing a cytosolic pyruvate dehydrogenase complex to increase free fatty acid production in Saccharomyces cerevisiae. Microb Cell Fact. 2020;19(1):226.
   PubMed Web of Science ®Google Scholar
• You S, Joo YC, Kang D, et al. Enhancing fatty acid production of Saccharomyces cerevisiae as an animal feed supplement. J Agric Food Chem. 2017;65(50):11029–11035.
   PubMed Web of Science ®Google Scholar
• Faergeman NJ, Black PN, Zhao XD, et al. The Acyl-CoA synthetases encoded within FAA1 andFAA4 in Saccharomyces cerevisiae function as components of the fatty acid transport system linking import, activation, and intracellular utilization. J Biol Chem. 2001;276(40):37051–37059.
   PubMed Web of Science ®Google Scholar
• Liu J, Zhang C, Lu W. Biosynthesis of long-chain ω-hydroxy fatty acids by engineered Saccharomyces cerevisiae. J Agric Food Chem. 2019;67(16):4545–4552.
   PubMed Web of Science ®Google Scholar
• Kim DH, Kim IJ, Yun EJ, et al. Metabolic engineering of Saccharomyces cerevisiae by using the CRISPR-Cas9 system for enhanced fatty acid production. Process Biochem. 2018;73:23–28.
   Web of Science ®Google Scholar
• Peng H, He L, Haritos VS. Metabolic engineering of lipid pathways in Saccharomyces cerevisiae and staged bioprocess for enhanced lipid production and cellular physiology. J Ind Microbiol Biotechnol. 2018;45(8):707–717.
   PubMed Web of Science ®Google Scholar
• Arhar S, Gogg FG, Ogrizović M, et al. Engineering of Saccharomyces cerevisiae for the accumulation of high amounts of triacylglycerol. Microb Cell Fact. 2021;20(1):147.
   PubMed Web of Science ®Google Scholar
• Saerens SMG, Verstrepen KJ, Van Laere SDM, et al. The Saccharomyces cerevisiae EHT1 and EEB1 genes encode novel enzymes with medium-chain fatty acid ethyl ester synthesis and hydrolysis capacity. J Biol Chem. 2006;281(7):4446–4456.
   PubMed Web of Science ®Google Scholar
• Dong J, Wang P, Fu X, et al. Increase ethyl acetate production in Saccharomyces cerevisiae by genetic engineering of ethyl acetate metabolic pathway. J Ind Microbiol Biotechnol. 2019;46(6):801–808.
   PubMed Web of Science ®Google Scholar
• Bermejo DV, Ibáñez E, Reglero G, et al. Effect of cosolvents (ethyl lactate, ethyl acetate and ethanol) on the supercritical CO2 extraction of caffeine from green tea. J Supercrit Fluid. 2016;107:507–512.
   Web of Science ®Google Scholar
• Ma Y, Deng Q, Du Y, et al. Biosynthetic pathway for ethyl butyrate production in Saccharomyces cerevisiae. J Agric Food Chem. 2020;68(14):4252–4260.
   PubMed Web of Science ®Google Scholar
• Yin H, Hu T, Zhuang Y, et al. Metabolic engineering of Saccharomyces cerevisiae for high-level production of gastrodin from glucose. Microb Cell Fact. 2020;19(1):218.
   PubMed Web of Science ®Google Scholar
• Babaei M, Borja ZGM, Chen X, et al. Metabolic engineering of Saccharomyces cerevisiae for rosmarinic acid production. ACS Synth Biol. 2020;9(8):1978–1988.
   PubMed Web of Science ®Google Scholar
• Xu Y, Geng L, Zhang Y, et al. De novo biosynthesis of salvianolic acid B in Saccharomyces cerevisiae engineered with the rosmarinic acid biosynthetic pathway. J Agric Food Chem. 2022;70(7):2290–2302.
   PubMed Web of Science ®Google Scholar
• Li Y, Mao J, Liu Q, et al. De novo biosynthesis of caffeic acid from glucose by engineered Saccharomyces cerevisiae. ACS Synth Biol. 2020;9(4):756–765.
   PubMed Web of Science ®Google Scholar
• Zhou P, Yue C, Shen B, et al. Metabolic engineering of Saccharomyces cerevisiae for enhanced production of caffeic acid. Appl Microbiol Biotechnol. 2021;105(14-15):5809–5819.
   PubMed Web of Science ®Google Scholar
• Lyu X, Zhao G, Ng KR, et al. Metabolic engineering of Saccharomyces cerevisiae for de novo production of kaempferol. J Agric Food Chem. 2019;67(19):5596–5606.
   PubMed Web of Science ®Google Scholar
• Zhang R, Tan Y, Cui Y, et al. Lignin valorization for protocatechuic acid production in engineered Saccharomyces cerevisiae. Green Chem. 2021;23(17):6515–6526.
   Web of Science ®Google Scholar
• Gao JQ, Li YX, Yu W, et al. Rescuing yeast from cell death enables overproduction of fatty acids from sole methanol. Nat Metab. 2022;4(7):932–943.
   PubMedGoogle Scholar
• Matias M, Silvestre S, Falcão A, et al. Gastrodia elata and epilepsy: rationale and therapeutic potential. Phytomedicine. 2016;23(12):1511–1526.
   PubMed Web of Science ®Google Scholar
• Herbst E, Lee A, Tang Y, et al. Heterologous catalysis of the final steps of tetracycline biosynthesis by Saccharomyces cerevisiae. ACS Chem Biol. 2021;16(8):1425–1434.
   PubMed Web of Science ®Google Scholar
• Ignea C, Pontini M, Maffei ME, et al. Engineering monoterpene production in yeast using a synthetic dominant negative geranyl diphosphate synthase. ACS Synth Biol. 2014;3(5):298–306.
   PubMed Web of Science ®Google Scholar
• Peng BY, Plan MR, Chrysanthopoulos P, et al. A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae. Metab Eng. 2017;39:209–219.
   PubMed Web of Science ®Google Scholar
• Hu Y, Zhou Y, Bao J, et al. Metabolic engineering of Saccharomyces cerevisiae for production of germacrene A, a precursor of beta-elemene. J Ind Microbiol Biotechnol. 2017;44(7):1065–1072.
   PubMed Web of Science ®Google Scholar
• Sun ZJ, Lian JZ, Li Z, et al. Combined biosynthetic pathway engineering and storage Pool expansion for High-Level production of ergosterol in industrial Saccharomyces cerevisiae. Front Bioeng Biotech. 2021;9:681666.
   PubMed Web of Science ®Google Scholar
• Kim JE, Jang IS, Son SH, et al. Tailoring the Saccharomyces cerevisiae endoplasmic reticulum for functional assembly of terpene synthesis pathway. Metab Eng. 2019;56:50–59.
   PubMed Web of Science ®Google Scholar
• Hu Z, Lin L, Li H, et al. Engineering Saccharomyces cerevisiae for production of the valuable monoterpene d- limonene during chinese baijiu fermentation. J Ind Microbiol Biotechnol. 2020;47(6-7):511–523.
   PubMed Web of Science ®Google Scholar
• Muñiz CS, Bisquert R, Puig S, et al. Overproduction of hydroxytyrosol in Saccharomyces cerevisiae by heterologous overexpression of the Escherichia coli 4-hydroxyphenylacetate 3-monooxygenase. Food Chem. 2020;308:125646.
   PubMed Web of Science ®Google Scholar
• Ignea C, Trikka FA, Nikolaidis AK, et al. Efficient diterpene production in yeast by engineering ERG20p into a geranylgeranyl diphosphate synthase. Metab Eng. 2015;27:65–75.
   PubMed Web of Science ®Google Scholar
• Yuan SF, Yi X, Johnston TG, et al. De novo resveratrol production through modular engineering of an Escherichia coli–Saccharomyces cerevisiae co-culture[J]. Microb Cell Fact. 2020;19(1):1–12. 10.1186/s12934-020-01401-5.
   PubMed Web of Science ®Google Scholar