# Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae

**Authors:** Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, Jay D. Keasling

PMC · DOI: 10.3390/metabo10080320 · Metabolites · 2020-08-06

## TL;DR

This paper reviews how promoters in yeast can be engineered to improve gene regulation for better metabolic engineering.

## Contribution

The paper provides a comprehensive review of recent advances in promoter architecture and engineering in S. cerevisiae.

## Key findings

- Native promoters in S. cerevisiae have limitations like poor dynamic range and orthogonality.
- Synthetic promoters can be engineered to overcome these limitations.
- Machine learning is emerging as a powerful tool for designing synthetic promoters.

## Abstract

Promoters play an essential role in the regulation of gene expression for fine-tuning genetic circuits and metabolic pathways in Saccharomyces cerevisiae (S. cerevisiae). However, native promoters in S. cerevisiae have several limitations which hinder their applications in metabolic engineering. These limitations include an inadequate number of well-characterized promoters, poor dynamic range, and insufficient orthogonality to endogenous regulations. Therefore, it is necessary to perform promoter engineering to create synthetic promoters with better properties. Here, we review recent advances related to promoter architecture, promoter engineering and synthetic promoter applications in S. cerevisiae. We also provide a perspective of future directions in this field with an emphasis on the recent advances of machine learning based promoter designs.

## Linked entities

- **Species:** Saccharomyces cerevisiae (taxon 4932)

## Full-text entities

- **Genes:** MIG1 (transcription factor MIG1) [NCBI Gene 852848] {aka CAT4, SSN1, TDS22}, REB1 (DNA-binding protein REB1) [NCBI Gene 852338] {aka EBF1, GRF2}, PHO2 (Pho2p) [NCBI Gene 851452] {aka BAS2, GRF10}, CYC1 (cytochrome c isoform 1) [NCBI Gene 853507], ARO9 (aromatic-amino-acid:2-oxoglutarate transaminase) [NCBI Gene 856539], FTH1 (ferritin heavy chain 1) [NCBI Gene 2495] {aka FHC, FTH, FTHL6, HFE5, NBIA9, PIG15}, COX5B (cytochrome c oxidase subunit 5B) [NCBI Gene 1329] {aka COXVB}, CA2 (carbonic anhydrase 2) [NCBI Gene 760] {aka CA-II, CAC, CAII, Car2, HEL-76, HEL-S-282}, PRDX5 (peroxiredoxin 5) [NCBI Gene 25824] {aka ACR1, AOEB166, B166, HEL-S-55, PLP, PMP20}, YHP1 (Yhp1p) [NCBI Gene 852062], MSN1 (Msn1p) [NCBI Gene 854033] {aka FUP1, HRB382, MSS10, PHD2}, GAL1 (galactokinase) [NCBI Gene 852308], RPS28A (40S ribosomal protein eS28 RPS28A) [NCBI Gene 854338] {aka RPS33A}, SPAG8 (sperm associated antigen 8) [NCBI Gene 26206] {aka BS-84, CILD28, CT142, HSD-1, SMP1, SPAG3}, CPA2 (carboxypeptidase A2) [NCBI Gene 1358], ZNF875 (zinc finger protein 875) [NCBI Gene 284459] {aka HKR1}, GAL4 (galactose-responsive transcription factor GAL4) [NCBI Gene 855828] {aka GAL81}, PPP4R3C (protein phosphatase 4 regulatory subunit 3C) [NCBI Gene 139420] {aka FLFL3P, PPP4R3CP, SMEK3P, smk1}, ATP2C1 (ATPase secretory pathway Ca2+ transporting 1) [NCBI Gene 27032] {aka ATP2C1A, BCPM, HHD, PMR1, SPCA1, hSPCA1}, ABF1 (DNA-binding protein ABF1) [NCBI Gene 853748] {aka BAF1, EBF2, OBF1, REB2, SBF1}, CYC1 (cytochrome c1) [NCBI Gene 1537] {aka MC3DN6, UQCR4}, XBP1 (X-box binding protein 1) [NCBI Gene 7494] {aka TREB-5, TREB5, XBP-1, XBP2}, KMT2B (lysine methyltransferase 2B) [NCBI Gene 9757] {aka CXXC10, DYT28, HRX2, MLL1B, MLL2, MLL4}, TEF1 (translation elongation factor EF-1 alpha) [NCBI Gene 856195], IME1 (transcription factor IME1) [NCBI Gene 853556], MSN2 (stress-responsive transcriptional activator MSN2) [NCBI Gene 855053], MCM1 (transcription factor MCM1) [NCBI Gene 855060] {aka FUN80}, CLB2 (B-type cyclin CLB2) [NCBI Gene 856236], ZNF569 (zinc finger protein 569) [NCBI Gene 148266] {aka ZAP1, ZNF, Zfp74}, MYRF (myelin regulatory factor) [NCBI Gene 745] {aka 11orf9, C11orf9, CUGS, MMERV, MRF, NNO1}, HIS3 (imidazoleglycerol-phosphate dehydratase HIS3) [NCBI Gene 854377] {aka HIS10, HIS8}, MATALPHA2 (homeodomain mating type protein alpha2) [NCBI Gene 850406] {aka ALPHA2}, YGP1 (Ygp1p) [NCBI Gene 855562], ARG1 (arginase 1) [NCBI Gene 383], RAP1 (DNA-binding transcription factor RAP1) [NCBI Gene 855505] {aka GRC4, GRF1, TBA1, TUF1}, GSX1 (GS homeobox 1) [NCBI Gene 219409] {aka GSH1, Gsh-1}, PCK1 (phosphoenolpyruvate carboxykinase 1) [NCBI Gene 5105] {aka PCKDC, PEPCK-C, PEPCK1, PEPCKC}, YAP1 (Yes1 associated transcriptional regulator) [NCBI Gene 10413] {aka COB1, YAP, YAP-1, YAP2, YAP65, YKI}, FUS1 (Fus1p) [NCBI Gene 850330], BAS1 (Bas1p) [NCBI Gene 853974], PRDM16 (PR/SET domain 16) [NCBI Gene 63976] {aka CMD1LL, KMT8F, LVNC8, MEL1, PFM13}, CCW14 (Ccw14p) [NCBI Gene 851107] {aka SSR1, YLR391W, YLR391W-A}, GAL3 (transcriptional regulator GAL3) [NCBI Gene 851572], COL2A1 (collagen type II alpha 1 chain) [NCBI Gene 1280] {aka ACG2, ANFH, ANFH1, AOM, COL11A3, EDMMD}, SOK2 (Sok2p) [NCBI Gene 855030], RAD3 (TFIIH/NER complex ATP-dependent 5'-3' DNA helicase subunit RAD3) [NCBI Gene 856918] {aka REM1}, SUM1 (Sum1p) [NCBI Gene 851905], PPT1 (palmitoyl-protein thioesterase 1) [NCBI Gene 5538] {aka CLN1, INCL, PPT}, GCN4 (amino acid starvation-responsive transcription factor GCN4) [NCBI Gene 856709] {aka AAS101, AAS3, ARG9}, PSMD9 (proteasome 26S subunit, non-ATPase 9) [NCBI Gene 5715] {aka Rpn4, p27}
- **Diseases:** hypoxic (MESH:D002534), toxicities (MESH:D064420)
- **Species:** Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Saccharomyces eubayanus (species) [taxon 1080349], Komagataella pastoris (species) [taxon 4922], Escherichia coli (E. coli, species) [taxon 562], Saccharomyces kudriavzevii (species) [taxon 114524], Bacillus subtilis (species) [taxon 1423]
- **Mutations:** A)4TAG

## Full text

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## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC7466126/full.md

## References

148 references — full list in the complete paper: https://tomesphere.com/paper/PMC7466126/full.md

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Source: https://tomesphere.com/paper/PMC7466126