Coordinated transcription factor and promoter engineering to establish strong expression elements in Saccharomyces cerevisiae

Biotechnology Journal

Volumn 11, Issue 7, 2016, Pages 866-876

  Leavitt, John M ^a   Tong, Alice ^a,b   Tong, Joyce ^a,b   Pattie, Jonathan ^a,b   Alper, Hal S ^a,b  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b The University of Texas at Austin   (United States)

Author keywords

Aro80; Circuits; Hybrid promoters; Inducible; Saccharomyces cerevisiae; traits; trans acting factors

Indexed keywords

AMINO ACIDS; NETWORKS (CIRCUITS); TRANSCRIPTION; TRANSCRIPTION FACTORS; YEAST;

ARO80; HYBRID PROMOTER; INDUCIBLE; TRAITS; TRANS ACTINGS;

GENE EXPRESSION;

TRANSCRIPTION FACTOR;

ARTICLE; CONTROLLED STUDY; FLOW CYTOMETRY; GENE EXPRESSION; GENE EXPRESSION SYSTEM; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ENGINEERING; SACCHAROMYCES CEREVISIAE;

EID: 84977514814     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201600029     Document Type: Article

References (41)

1. Leavitt, J. M., Alper, H. S, Advances and current limitations in transcript-level control of gene expression. Curr. Opin. Biotechnol. 2015, 34, 98–104.
2. Salis, H. M., Mirsky, E., Voigt, C. A., Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27, 946–950.
3. Kushwaha, M., Salis, H. M., A portable expression resource for engineering cross-species genetic circuits and pathways. Nat. Commun. 2015, 6, 7832.
4. Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M. et al., Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Mol. Syst. Biol. 2014, 10, 731–731.
5. Biggs, B. W., De Paepe, B., Santos, C. N. S., De Mey, M. et al., Multivariate modular metabolic engineering for pathway and strain optimization. Curr. Opin. Biotechnol. 2014, 29, 156–162.
6. Prindle, A., Selimkhanov, J., Li, H., Razinkov, I. et al., Rapid and tunable post-translational coupling of genetic circuits. Nature 2014, 508, 387–391.
7. Wang, B., Barahona, M., Buck, M., Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks. Nucleic Acids Res. 2014, 42, 9484–9492.
8. Liu, L., Redden, H., Alper, H. S., Frontiers of yeast metabolic engineering: Diversifying beyond ethanol and Saccharomyces. Curr. Opin. Biotechnol. 2013, 24, 1023–1030.
9. Sun, J., Alper, H., Metabolic engineering of strains: From industrial-scale to lab-scale chemical production. J. Ind. Microbiol. Biotechnol. 2015, 42, 423–436.
10. Curran, K., Alper, H. S., Expanding the chemical palate of cells by combining systems biology and metabolic engineering. Metab. Eng. 2012, 14, 289–297.
11. Blazeck, J., Garg, R., Reed, B., Alper, H. S., Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters. Biotechnol. Bioeng. 2012, 109, 2884–2895.
12. Curran, K., Crook, N., Karim, A., Gupta, A. et al., Design of synthetic yeast promoters via tuning of nucleosome architecture. Nat. Commun. 2014, 5, 4002.
13. Curran, K., Karim, A. S., Gupta, A., Alper, H. S., Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications. Metab. Eng. 2013, 19, 88–97.
14. Levo, M., Segal, E., In pursuit of design principles of regulatory sequences. Nat. Rev. Genet. 2014, 15, 453–468.
15. Levo, M., Zalckvar, E., Sharon, E., Dantas Machado, A. C. et al., Unraveling determinants of transcription factor binding outside the core binding site. Genome Res. 2015.
16. Teo, W. S., Chang, M. W., Bacterial XylRs and synthetic promoters function as genetically encoded xylose biosensors in Saccharomyces cerevisiae. Biotechnol. J. 2015, 10, 315–322.
17. Zhang, M., Wang, F., Li, S., Wang, Y. et al., TALE: A tale of genome editing. Prog. Biophys. Mol. Biol. 2014, 114, 25–32.
18. Farzadfard, F., Perli, S. D., Lu, T. K., Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas. ACS Synth. Biol. 2013, 2, 604–613.
19. Ottoz, D. S. M., Rudolf, F., Stelling, J., Inducible, tightly regulated and growth condition-independent transcription factor in Saccharomyces cerevisiae. Nucleic Acids Res. 2014, 42, e130.
20. Dobrin, A., Saxena, P., Fussenegger, M., Synthetic biology: Applying biological circuits beyond novel therapies. Integrative Biology 2016, 8, 409–430.
21. Da Silva, N. A., Srikrishnan, S., Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae. FEMS Yeast Research 2012, 12, 197–214.
22. Wimalarathna, R. N., Pan, P. Y., Shen, C.-H., Co-dependent recruitment of Ino80p and Snf2p is required for yeast CUP1 activation. Biochem. Cell Biol. 2013, 92, 69–75.
23. Korber, P., Barbaric, S., The yeast PHO5 promoter:From single locus to systems biology of a paradigm for gene regulation through chromatin. Nucleic Acids Res. 2014, 42, 10888–10902.
24. Iraqui, I., Vissers, S., André, B., Urrestarazu, A., Transcriptional Induction by Aromatic Amino Acids in Saccharomyces cerevisiae. Mol. Cell. Biol. 1999, 19, 3360–3371.
25. Solow, S. P., Sengbusch, J., Laird, M. W., Heterologous protein production from the inducible MET25 promoter in Saccharomyces cerevisiae. Biotechnol. Progr. 2005, 21, 617–620.
26. Weinhandl, K., Winkler, M., Glieder, A., Camattari, A., Carbon source dependent promoters in yeasts. Microb. Cell Fact. 2014, 13, 1–17.
27. Li, Q., Zhao, X.-Q, Chang, A. K., Zhang, Q.-M., Bai, F.-W., Ethanol-induced yeast flocculation directed by the promoter of TPS1 encoding trehalose-6-phosphate synthase 1 for efficient ethanol production. Metab. Eng. 2012, 14, 1–8.
28. Williams, T. C., Averesch, N. J. H., Winter, G., Plan, M. R. et al., Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae. Metab. Eng. 2015, 29, 124–134.
29. Lee, K., Hahn, J.-S., Interplay of Aro80 and GATA activators in regulation of genes for catabolism of aromatic amino acids in Saccharomyces cerevisiae. Mol. Microbiol. 2013, 88, 1120–1134.
30. Lee, K., Sung, C., Kim, B.-G., Hahn, J.-S., Activation of Aro80 transcription factor by heat-induced aromatic amino acid influx in Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. 2013, 438, 43–47.
31. Kim, S., Lee, K., Bae, S.-J., Hahn, J.-S., Promoters inducible by aromatic amino acids and1 γ-aminobutyrate (GABA) for metabolic engineering applications in Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 2015, 99, 2705–2714.
32. Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C. et al., Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 2009, 6, 343–345.
33. Gibson, D. G., Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Research 2009, 37, 6984–6990.
34. Gietz, R. D., Schiestl, R. H., High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2007, 2, 31–34.
35. Teste, M.-A., Duquenne, M., François, J. M., Parrou, J.-L., Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol. Biol. 2009, 10, 1–15.
36. Williams, T. C., Nielsen, L. K., Vickers, C. E., Engineered quorum sensing using pheromone-mediated cell-to-cell communication in Saccharomyces cerevisiae. ACS Synth. Biol. 2013, 2, 136–149.
37. Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P. et al., The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic Acids Res. 2014, 42, D161–D166.
38. Mumberg, D., Müller, R., Funk, M., Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 1995, 156, 119–122.
39. Blazeck, J., Liu, L., Redden, H., Alper, H., Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl. Environ. Microbiol. 2011, 77, 7905–7914.
40. Redden, H., Alper, H. S., The development and characterization of synthetic minimal yeast promoters. Nat. Commun. 2015, 6, 7810.
41. Siuti, P., Yazbek, J., Lu, T. K., Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 2013, 31, 448–452.