Natural Promoters and Promoter Engineering Strategies for Metabolic Regulation in Saccharomyces Cerevisiae

Overview

Journal J Ind Microbiol Biotechnol

Publisher Oxford University Press

Specialty Biotechnology

Date 2023 Jan 12

PMID 36633543

Authors

Shifan He

Zhanwei Zhang

Wenyu Lu

Affiliations

Soon will be listed here.

Abstract

Sharomyces cerevisiae is currently one of the most important foreign gene expression systems. S. cerevisiae is an excellent host for high-value metabolite cell factories due to its advantages of simplicity, safety, and nontoxicity. A promoter, as one of the basic elements of gene transcription, plays an important role in regulating gene expression and optimizing metabolic pathways. Promoters control the direction and intensity of transcription, and the application of promoters with different intensities and performances will largely determine the effect of gene expression and ultimately affect the experimental results. Due to its significant role, there have been many studies on promoters for decades. While some studies have explored and analyzed new promoters with different functions, more studies have focused on artificially modifying promoters to meet their own scientific needs. Thus, this article reviews current research on promoter engineering techniques and related natural promoters in S. cerevisiae. First, we introduce the basic structure of promoters and the classification of natural promoters. Then, the classification of various promoter strategies is reviewed. Finally, by grouping related articles together using various strategies, this review anticipates the future development direction of promoter engineering.

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References

Lee K, DaSilva N . Evaluation of the Saccharomyces cerevisiae ADH2 promoter for protein synthesis. Yeast. 2005; 22(6):431-40. DOI: 10.1002/yea.1221. View

Rajkumar A, Liu G, Bergenholm D, Arsovska D, Kristensen M, Nielsen J . Engineering of synthetic, stress-responsive yeast promoters. Nucleic Acids Res. 2016; 44(17):e136. PMC: 5041464. DOI: 10.1093/nar/gkw553. View

Feng X, Marchisio M . Promoter Engineering before and during the Synthetic Biology Era. Biology (Basel). 2021; 10(6). PMC: 8229000. DOI: 10.3390/biology10060504. View

Gari E, Piedrafita L, Aldea M, Herrero E . A set of vectors with a tetracycline-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae. Yeast. 1997; 13(9):837-48. DOI: 10.1002/(SICI)1097-0061(199707)13:9<837::AID-YEA145>3.0.CO;2-T. View

Deng J, Wu Y, Zheng Z, Chen N, Luo X, Tang H . A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae. Microb Cell Fact. 2021; 20(1):202. PMC: 8522093. DOI: 10.1186/s12934-021-01691-3. View

Xi L, Fondufe-Mittendorf Y, Xia L, Flatow J, Widom J, Wang J . Predicting nucleosome positioning using a duration Hidden Markov Model. BMC Bioinformatics. 2010; 11:346. PMC: 2900280. DOI: 10.1186/1471-2105-11-346. View

Schnepf M, Ludwig C, Bandilla P, Ceolin S, Unnerstall U, Jung C . Sensitive Automated Measurement of Histone-DNA Affinities in Nucleosomes. iScience. 2020; 23(2):100824. PMC: 6994541. DOI: 10.1016/j.isci.2020.100824. View

Stagoj M, Comino A, Komel R . Fluorescence based assay of GAL system in yeast Saccharomyces cerevisiae. FEMS Microbiol Lett. 2005; 244(1):105-10. DOI: 10.1016/j.femsle.2005.01.041. View

Mannan A, Liu D, Zhang F, Oyarzun D . Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors. ACS Synth Biol. 2017; 6(10):1851-1859. DOI: 10.1021/acssynbio.7b00172. View

10.

Bassel J, Mortimer R . Genetic order of the galactose structural genes in Saccharomyces cerevisiae. J Bacteriol. 1971; 108(1):179-83. PMC: 247048. DOI: 10.1128/jb.108.1.179-183.1971. View

11.

Gueldener U, Heinisch J, Koehler G, Voss D, Hegemann J . A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res. 2002; 30(6):e23. PMC: 101367. DOI: 10.1093/nar/30.6.e23. View

12.

Wimalarathna R, Pan P, Shen C . Chromatin repositioning activity and transcription machinery are both recruited by Ace1p in yeast CUP1 activation. Biochem Biophys Res Commun. 2012; 422(4):658-63. DOI: 10.1016/j.bbrc.2012.05.047. View

13.

Myburgh M, Rose S, Viljoen-Bloom M . Evaluating and engineering Saccharomyces cerevisiae promoters for increased amylase expression and bioethanol production from raw starch. FEMS Yeast Res. 2020; 20(6). DOI: 10.1093/femsyr/foaa047. View

14.

Yoshimatsu T, Nagawa F . Effect of artificially inserted intron on gene expression in Saccharomyces cerevisiae. DNA Cell Biol. 1994; 13(1):51-8. DOI: 10.1089/dna.1994.13.51. View

15.

Nevoigt E, Fischer C, Mucha O, Matthaus F, Stahl U, Stephanopoulos G . Engineering promoter regulation. Biotechnol Bioeng. 2006; 96(3):550-8. DOI: 10.1002/bit.21129. View

16.

Li Y, Chen G, Liu W . Multiple metabolic signals influence GAL gene activation by modulating the interaction of Gal80p with the transcriptional activator Gal4p. Mol Microbiol. 2010; 78(2):414-28. DOI: 10.1111/j.1365-2958.2010.07343.x. View

17.

Rajkumar A, Ozdemir E, Lis A, Schneider K, Qin J, Jensen M . Engineered Reversal of Function in Glycolytic Yeast Promoters. ACS Synth Biol. 2019; 8(6):1462-1468. DOI: 10.1021/acssynbio.9b00027. View

18.

Kim J, Jang I, Sung B, Kim S, Lee J . Rerouting of NADPH synthetic pathways for increased protopanaxadiol production in Saccharomyces cerevisiae. Sci Rep. 2018; 8(1):15820. PMC: 6202386. DOI: 10.1038/s41598-018-34210-3. View

19.

Ricci-Tam C, Ben-Zion I, Wang J, Palme J, Li A, Savir Y . Decoupling transcription factor expression and activity enables dimmer switch gene regulation. Science. 2021; 372(6539):292-295. PMC: 8173539. DOI: 10.1126/science.aba7582. View

20.

Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, Lotan-Pompan M . Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet. 2012; 44(7):743-50. DOI: 10.1038/ng.2305. View