Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in Saccharomyces cerevisiae

Biotechnology and Bioengineering

Volumn 113, Issue 1, 2016, Pages 206-215

  Wang, Meng ^a   Li, Sijin ^a   Zhao, Huimin ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

Directed evolution; Gene circuit; Metabolite sensing regulation; Synthetic biology

Indexed keywords

BIOLOGY; BIOMOLECULES; GENES; METABOLITES; THROUGHPUT; TRANSCRIPTION; YEAST;

BACTERIAL TRANSCRIPTION; DIRECTED EVOLUTION; EVOLUTIONARY ENGINEERING; GENE CIRCUITS; HIGH THROUGHPUT SCREENING METHODS; HIGH-THROUGHPUT PHENOTYPING; INTRACELLULAR METABOLITES; SYNTHETIC BIOLOGY;

CELL ENGINEERING;

CARRIER PROTEIN; XYLOSE;

GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLIC ENGINEERING; METABOLISM; SACCHAROMYCES CEREVISIAE;

GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; MEMBRANE TRANSPORT PROTEINS; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; SACCHAROMYCES CEREVISIAE; XYLOSE;

EID: 84947923934     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.25676     Document Type: Article

References (50)

1. Ang J, Harris E, Hussey BJ, Kil R, McMillen DR. 2013. Tuning response curves for synthetic biology. ACS Synth Biol 2:547-567.
2. Auslander S, Fussenegger M. 2013. From gene switches to mammalian designer cells: Present and future prospects. Trends Biotechnol 31:155-168.
3. Bao Z, Xiao H, Liang J, Zhang L, Xiong X, Sun N, Si T, Zhao H. 2014. Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. ACS Synth Biol 4:585-594.
4. Bettiga M, Bengtsson O, Hahn-Hagerdal B, Gorwa-Grauslund MF. 2009. Arabinose and xylose fermentation by recombinant Saccharomyces cerevisiae expressing a fungal pentose utilization pathway. Microb Cell Fact 8:40.
5. Blake WJ, KAErn M, Cantor CR, Collins JJ. 2003. Noise in eukaryotic gene expression. Nature 422:633-637.
6. Carlson M. 1999. Glucose repression in yeast. Curr Opin Microbiol 2:202-207.
7. Carr PA, Church GM. 2009. Genome engineering. Nat Biotechnol 27:1151-1162.
8. Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I. 2013. RegTransBase-a database of regulatory sequences and interactions based on literature: A resource for investigating transcriptional regulation in prokaryotes. BMC Genomics 14:213.
9. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819-823.
10. Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD. 2013. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 31:1039-1046.
11. Du J, Li S, Zhao H. 2010. Discovery and characterization of novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis. Mol Biosyst 6:2150-2156.
12. Du J, Yuan Y, Si T, Lian J, Zhao H. 2012. Customized optimization of metabolic pathways by combinatorial transcriptional engineering. Nucleic Acids Res 40:e142.
13. Ellis JM, Wolfgang MJ. 2012. A genetically encoded metabolite sensor for malonyl-CoA. Chem Biol 19:1333-1339.
14. Esvelt KM, Wang HH. 2013. Genome-scale engineering for systems and synthetic biology. Mol Syst Biol 9:641.
15. Farwick A, Bruder S, Schadeweg V, Oreb M, Boles E. 2014. Engineering of yeast hexose transporters to transport D-xylose without inhibition by D-glucose. Proc Natl Acad Sci USA 111:5159-5164.
16. Gartner D, Degenkolb J, Ripperger JA, Allmansberger R, Hillen W. 1992. Regulation of the Bacillus subtilis W23 xylose utilization operon: Interaction of the Xyl repressor with the xyl operator and the inducer xylose. Mol Gen Genet 232:415-422.
17. Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA III, Smith HO. 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343-345.
18. Hahn S, Young ET. 2011. Transcriptional regulation in Saccharomyces cerevisiae: Transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics 189:705-736.
19. Hasunuma T, Okazaki F, Okai N, Hara KY, Ishii J, Kondo A. 2013. A review of enzymes and microbes for lignocellulosic biorefinery and the possibility of their application to consolidated bioprocessing technology. Bioresour Technol 135:513-522.
20. Hsu PD, Lander ES, Zhang F. 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157:1262-1278.
21. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK. 2013. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31:227-229.
22. Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ. 2012. A synthetic biology framework for programming eukaryotic transcription functions. Cell 150:647-658.
23. Leemhuis H, Kelly RM, Dijkhuizen L. 2009. Directed evolution of enzymes: Library screening strategies. IUBMB Life 61:222-228.
24. Lokman BC, Heerikhuisen M, Leer RJ, van den Broek A, Borsboom Y, Chaillou S, Postma PW, Pouwels PH. 1997. Regulation of expression of the Lactobacillus pentosus xylAB operon. J Bacteriol 179:5391-5397.
25. Maya D, Quintero MJ, de la Cruz Munoz-Centeno M, Chavez S. 2008. Systems for applied gene control in Saccharomyces cerevisiae. Biotechnol Lett 30:979-987.
26. Murphy KF, Balazsi G, Collins JJ. 2007. Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci USA 104:12726-12731.
27. Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY. 2013. Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol 31:170-174.
28. Nevozhay D, Zal T, Balazsi G. 2013. Transferring a synthetic gene circuit from yeast to mammalian cells. Nat Commun 4:1451.
29. Rodicio R, Heinisch JJ, Hollenberg CP. 1993. Transcriptional control of yeast phosphoglycerate mutase-encoding gene. Gene 125:125-133.
30. Scheler A, Hillen W. 1994. Regulation of xylose utilization in Bacillus licheniformis: Xyl repressor-xyl-operator interaction studied by DNA modification protection and interference. Mol Microbiol 13:505-512.
31. Segal DJ, Meckler JF. 2013. Genome engineering at the dawn of the golden age. Annu Rev Genomics Hum Genet 14:135-158.
32. Shao Z, Zhao H. 2009. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37:e16.
33. Si T, Luo Y, Bao Z, Zhao H. 2014. RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering. ACS Synth Biol 4:283-291.
34. Sizemore C, Wieland B, Gotz F, Hillen W. 1992. Regulation of Staphylococcus xylosus xylose utilization genes at the molecular level. J Bacteriol 174:3042-3048.
35. Stephanopoulos G. 2007. Challenges in engineering microbes for biofuels production. Science 315:801-804.
36. Sun J, Shao Z, Zhao H, Nair N, Wen F, Xu JH. 2012. Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae. Biotechnol Bioeng 109:2082-2092.
37. Sun N, Bao Z, Xiong X, Zhao H. 2014. SunnyTALEN: A second-generation TALEN system for human genome editing. Biotechnol Bioeng 111:683-691.
38. Sun N, Zhao H. 2013. Transcription activator-like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing. Biotechnol Bioeng 110:1811-1821.
39. Templeton GW, Moorhead GB. 2004. A renaissance of metabolite sensing and signaling: From modular domains to riboswitches. Plant Cell 16:2252-2257.
40. Teo WS, Chang MW. 2015. Bacterial XylRs and synthetic promoters function as genetically encoded xylose biosensors in Saccharomyces cerevisiae. Biotechnol J 10:315-322.
41. Teo WS, Hee KS, Chang MW. 2013. Bacterial FadR and synthetic promoters function as modular fatty acid sensor- regulators in Saccharomyces cerevisiae. Eng Life Sci 13:456-463.
42. Trumbly RJ. 1992. Glucose repression in the yeast Saccharomyces cerevisiae. Mol Microbiol 6:15-21.
43. Umeyama T, Okada S, Ito T. 2013. Synthetic gene circuit-mediated monitoring of endogenous metabolites: Identification of GAL11 as a novel multicopy enhancer of S-adenosylmethionine level in yeast. ACS Synth Biol 2:425-430.
44. Wagner JC, Platt RJ, Goldfless SJ, Zhang F, Niles JC. 2014. Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum. Nat Methods 11:915-918.
45. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. 2009. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:894-898.
46. Young EM, Comer AD, Huang H, Alper HS. 2012. A molecular transporter engineering approach to improving xylose catabolism in Saccharomyces cerevisiae. Metab Eng 14:401-411.
47. Young EM, Tong A, Bui H, Spofford C, Alper HS. 2014. Rewiring yeast sugar transporter preference through modifying a conserved protein motif. Proc Natl Acad Sci USA 111:131-136.
48. Zhang F, Carothers JM, Keasling JD. 2012. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30:354-359.
49. Zhang F, Keasling J. 2011. Biosensors and their applications in microbial metabolic engineering. Trends Microbiol 19:323-329.
50. Zhang F, Rodriguez S, Keasling JD. 2011. Metabolic engineering of microbial pathways for advanced biofuels production. Curr Opin Biotechnol 22:775-783.