Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae

Biotechnology and Bioengineering

Volumn 109, Issue 8, 2012, Pages 2082-2092

  Sun, Jie ^a,b   Shao, Zengyi ^a   Zhao, Hua ^a   Nair, Nikhil ^a   Wen, Fei ^a   Xu, Jian He ^b   Zhao, Huimin ^a  

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

^b EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Consolidated bioprocessing; Synthetic biology; Xylanases; Yeast promoters; Zeaxanthin

Indexed keywords

CONSOLIDATED BIOPROCESSING; SYNTHETIC BIOLOGY; XYLANASES; YEAST PROMOTERS; ZEAXANTHIN;

BIOCHEMISTRY; CLONING; DEGRADATION; GENES; GLUCOSE;

YEAST;

GLUCOSE; GREEN FLUORESCENT PROTEIN; OXYGEN; XYLAN; XYLOSE; ZEAXANTHIN;

ADH1P GFP ADH1T GENE; ARTICLE; BIODEGRADATION; BIOENGINEERING; BIOSYNTHESIS; DNA SEQUENCE; ENO2P GFP ENO2T GENE; FBA1P GFP FBA1T GENE; FED BATCH FERMENTATION; FLUORESCENCE; GENE CASSETTE; GLUCOSE UTILIZATION; GPDP GFP GPDT GENE; GPM1P GFP GPM1T GENE; HXT7P GFP HXT7T GENE; MOLECULAR CLONING; NONHUMAN; PDC1P GFP PDC1T GENE; PGI1P GFP PGI1T GENE; PGK1P GFP PGK1T GENE; PROMOTER REGION; PYK1P GFP PYK1T GENE; SACCHAROMYCES CEREVISIAE; TDH2P GFP TDH2T GENE; TEF1P GFP TEF1T GENE; TEF2P GFP TEF2T GENE; TPI1P GFP TPI1T GENE;

ARTIFICIAL GENE FUSION; BIOTECHNOLOGY; GENE EXPRESSION; GENES, REPORTER; GREEN FLUORESCENT PROTEINS; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; PROMOTER REGIONS, GENETIC; SACCHAROMYCES CEREVISIAE; XANTHOPHYLLS;

SACCHAROMYCES CEREVISIAE;

EID: 84862817382     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.24481     Document Type: Article

References (67)

1. Ajikumar PK, Xiao WH, Tyo KEJ, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G. 2010. Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 330: 70-74.
2. Alper H, Fischer C, Nevoigt E, Stephanopoulos G. 2005. Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102: 12678-12683.
3. Bitter GA, Egan KM. 1984. Expression of heterologous genes in Saccharomyces cerevisiae from vectors utilizing the glyceraldehyde-3-phosphate dehydrogenase gene promoter. Gene 32: 263-274.
4. Cartwright CP, Li Y, Zhut YS. 1994. Use of β-lactamase as a secreted reporter of promoter function in yeast. Yeast 10: 497-508.
5. Chemler JA, Yan Y, Koffas MA. 2006. Biosynthesis of isoprenoids, polyunsaturated fatty acids and flavonoids in Saccharomyces cerevisiae. Microb Cell Fact 5: 20.
6. Costa V, Moradas-Ferreira P. 2001. Oxidative stress and signal transduction in Saccharomyces cerevisiae: Insights into ageing, apoptosis and diseases. Mol Aspects Med 22: 217-246.
7. Daniel Gietz R, Woods RA. 2002. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Method Enzymol 350: 87-96.
8. Dekker RFH. 1983. Bioconversion of hemicellulose: Aspects of hemicellulase production by Trichoderma reesei QM 9414 and enzymic saccharification of hemicellulose. Biotechnol Bioeng 25: 1127-1146.
9. Den Haan R, Mcbride JE, La Grange DC, Lynd LR, van Zyl WH. 2007a. Functional expression of cellobiohydrolases in Saccharomyces cerevisiae towards one-step conversion of cellulose to ethanol. Enzyme Microb Technol 40: 1291-1299.
10. Den Haan R, Rose SH, Lynd LR, van Zyl WH. 2007b. Hydrolysis and fermentation of amorphous cellulose by recombinant Saccharomyces cerevisiae. Metab Eng 9: 87-94.
11. Denis CL, Ferguson J, Young ET. 1983. mRNA levels for the fermentative alcohol dehydrogenase of Saccharomyces cerevisiae decrease upon growth on a nonfermentable carbon source. J Biol Chem 258: 1165-1171.
12. Diderich JA, Schepper M, van Hoek P, Luttik MA, van Dijken JP, Pronk JT, Klaassen P, Boelens HF, de Mattos MJ, van Dam K, Kruckeberg AL. 1999. Glucose uptake kinetics and transcription of HXT genes in chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 274: 15350-15359.
13. Dodd D, Cann IK. 2009. Enzymatic deconstruction of xylan for biofuel production. Glob Change Biol Bioenergy 1: 2-17.
14. Ellis T, Wang X, Collins JJ. 2009. Diversity-based, model-guided construction of synthetic gene networks with prediced functions. Nat Biotechnol 27: 465-471.
15. Engels B, Dahm P, Jennewein S. 2008. Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards taxol (paclitaxel) production. Metab Eng 10: 201-206.
16. Fernandes S, Murray P. 2010. Metabolic engineering for improved microbial pentose fermentation. Bioeng Bugs 1: 424-428.
17. Fujita Y, Ito J, Ueda M, Fukuda H, Kondo A. 2004. Synergistic saccharification, and direct fermentation to ethanol, of amorphous cellulose by use of an engineered yeast strain codisplaying three types of cellulolytic enzyme. Appl Environ Microbiol 70: 1207-1212.
18. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
19. Gatignol A, Dassain M, Tiraby G. 1990. Cloning of Saccharomyces cerevisiae promoters using a probe vector based on phleomycin resistance. Gene 91: 35-41.
20. Ha SJ, Galazka JM, Kim SR, Choi JH, Yang XM, Seo JH, Glass NL, Cate JHD, Jin YS. 2011. Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation. Proc Natl Acad Sci USA 108: 504-509.
21. Hahn-Hagerdal B, Karhumaa K, Fonseca C, Spencer-Martins I, Gorwa-Grauslund MF. 2007. Towards industrial pentose-fermenting yeast strains. Appl Microbiol Biotechnol 74: 937-953.
22. Hammer K, Mijakovic I, Jensen PR. 2006. Synthetic promoter libraries-tuning of gene expression. Trends Biotechnol 24: 53-55.
23. Hartner FS, Ruth C, Langenegger D, Johnson SN, Hyka P, Lin-Cereghino GP, Lin-Cereghino J, Kovar K, Cregg JM, Glieder A. 2008. Promoter library designed for fine-tuned gene expression in Pichia pastoris. Nucleic Acids Res 36: e76.
24. Hauf J, Zimmermann FK, Muller S. 2000. Simultaneous genomic overexpression of seven glycolytic enzymes in the yeast Saccharomyces cerevisiae. Enzyme Microb Technol 26: 688-698.
25. Hawkins KM, Smolke CD. 2008. Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Nat Chem Biol 4: 564-573.
26. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77: 51-59.
27. Holland MJ, Holland JP. 1978. Isolation and identification of yeast messenger ribonucleic acids coding for enolase, glyceraldehyde-3-phosphate dehydrogenase, and phosphoglycerate kinase. Biochemistry 17: 4900-4907.
28. Jensen PR, Hammer K. 1998. Artificial promoters for metabolic optimization. Biotechnol Bioeng 58: 191-195.
29. Jin YS, Ni H, Laplaza JM, Jeffries TW. 2003. Optimal growth and ethanol production from xylose by recombinant Saccharomyces cerevisiae require moderate D-xylulokinase activity. Appl Environ Microbiol 69: 495-503.
30. Kotter P, Ciriacy M. 1993. Xylose fermentation by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 38: 776-783.
31. Krahulec S, Petschacher B, Wallner M, Longus K, Klimacek M, Nidetzky B. 2010. Fermentation of mixed glucose-xylose substrates by engineered strains of Saccharomyces cerevisiae: Role of the coenzyme specificity of xylose reductase, and effect of glucose on xylose utilization. Microb Cell Fact 9: 16.
32. Kwast KE, Lai LC, Menda N, James DT III, Aref S, Burke PV. 2002. Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: Functional roles of Rox1p and other factors in mediating the anoxic response. J Bacteriol 184: 250-265.
33. Lai LC, Kosorukoff AL, Burke PV, Kwast KE. 2005. Dynamical remodeling of the transcriptome during short-term anaerobiosis in Saccharomyces cerevisiae: Differential response and role of Msn2 and/or Msn4 and other factors in galactose and glucose media. Mol Cell Biol 25: 4075-4091.
34. Li S, Du J, Sun J, Galazka JM, Glass NL, Cate JH, Yang X, Zhao H. 2010. Overcoming glucose repression in mixed sugar fermentation by co-expressing a cellobiose transporter and a beta-glucosidase in Saccharomyces cerevisiae. Mol Biosyst 6: 2129-2132.
35. Liu C, Zhao Y, Wang Y. 2006. Artemisinin: Current state and perspectives for biotechnological production of an antimalarial drug. Appl Microbiol Biotechnol 72: 11-20.
36. Lu CF, Jeffries T. 2007. Shuffling of promoters for mutiple genes to optimize xylose fermentation in an engineered Saccharomyces cerevisiae strain. Appl Environ Microbiol 73: 6072-6077.
37. Lynd LR, van Zyl WH, McBride JE, Laser M. 2005. Consolidated bioprocessing of cellulosic biomass: An update. Curr Opin Biotechnol 16: 577-583.
38. Ma H, Kunes S, Schatz PJ, Botstein D. 1987. Plasmid construction by homologous recombination in yeast. Gene 58: 201-216.
39. Martens C, Krett B, Laybourn PJ. 2001. RNA polymerase II and TBP occupy the repressed CYC1 promoter. Mol Microbiol 40: 1009-1019.
40. Minami H, Kim JS, Ikezawa N, Takemura T, Katayama T, Kumagai H, Sato F. 2008. Microbial production of plant benzylisoquinoline alkaloids. Proc Natl Acad Sci USA 105: 7393-7398.
41. Misawa N, Shimada H. 1997. Metabolic engineering for the production of carotenoids in non-carotenogenic bacteria and yeasts. J Biotechnol 59: 169-181.
42. Misawa N, Nakagawa M, Kobayashi K, Yamano S, Izawa Y, Nakamura K, Harashima K. 1990. Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli. J Bacteriol 172: 6704-6712.
43. Moskvina E, Schuller C, Maurer CT, Mager WH, Ruis H. 1998. A search in the genome of Saccharomyces cerevisiae for genes regulated via stress response elements. Yeast 14: 1041-1050.
44. Mumberg D, Muller R, Funk M. 1995. Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 156: 119-122.
45. Nevoigt E, Kohnke J, Fischer CR, Alper H, Stahl U, Stephanopoulos G. 2006. Engineering of promoter replacement cassettes for fine-tuning of gene expression in Saccharomyces cerevisiae. Appl Environ Microbiol 72: 5266-5273.
46. Ogden JE, Stanway C, Kim S, Mellor J, Kingsman AJ, Kingsman SM. 1986. Efficient expression of the Saccharomyces cerevisiae PGK gene depends on an upstream activation sequence but does not require TATA sequences. Mol Cell Biol 6: 4335-4343.
47. Partow S, Siewers V, Bjorn S, Nielsen J, Maury J. 2010. Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast 27: 955-964.
48. Poutanen K, Puls J. 1988. Characteristics of Trichoderma reesei β-xylosidase and its use in the hydrolysis of solubilized xylans. Appl Microbiol Biotechnol 28: 425-432.
49. Reifenberger E, Boles E, Ciriacy M. 1997. Kinetic characterization of individual hexose transporters of Saccharomyces cerevisiae and their relation to the triggering mechanisms of glucose repression. Eur J Biochem 245: 324-333.
50. Ro DK, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM, Ho KA, Eachus RA, Ham TS, Kirby J, Chang MCY, Withers ST, Shiba Y, Sarpong R, Keasling JD. 2006. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440: 940-943.
51. Runquist D, Fonseca C, Radstrom P, Spencer-Martins I, Hahn-Hagerdal B. 2009. Expression of the Gxf1 transporter from Candida intermedia improves fermentation performance in recombinant xylose-utilizing Saccharomyces cerevisiae. Appl Microbiol Biotechnol 82: 123-130.
52. Ruohonen L, Aalto MK, Keranen S. 1995. Modifications to the ADH1 promoter of Saccharomyces cerevisiae for efficient production of heterologous proteins. J Biotechnol 39: 193-203.
53. Saha BC. 2003. Hemicellulose bioconversion. J Ind Microbiol Biotechnol 30: 279-291.
54. Schefe J, Lehmann K, Buschmann I, Unger T, Funke-Kaiser H. 2006. Quantitative real-time RT-PCR data analysis: Current concepts and the novel "gene expression's CT difference" formula. J Mol Med 84: 901-910.
55. Schirmaier F, Philippsen P. 1984. Identification of two genes coding for the translation elongation factor EF-1 alpha of Saccharomyces cerevisiae. EMBO J 3: 3311-3315.
56. Shao Z, Zhao H, Zhao H. 2009. DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37: e16.
57. Shimada T, Makinoshima H, Ogawa Y, Miki T, Maeda M, Ishihama A. 2004. Classification and strength measurement of stationary-phase promoters by use of a newly developed promoter cloning vector. J Bacteriol 186: 7112-7122.
58. Siewers V, Chen X, Huang L, Zhang J, Nielsen J. 2009. Heterologous production of non-ribosomal peptide LLD-ACV in Saccharomyces cerevisiae. Metab Eng 11: 391-397.
59. Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, Del Cardayre SB, Keasling JD. 2010. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463: 559-562.
60. Szczebara FM, Chandelier C, Villeret C, Masurel A, Bourot S, Duport C, Blanchard S, Groisillier A, Testet E, Costaglioli P, Cauet G, Degryse E, Balbuena D, Winter J, Achstetter T, Spagnoli R, Pompon D, Dumas B. 2003. Total biosynthesis of hydrocortisone from a simple carbon source in yeast. Nat Biotechnol 21: 143-149.
61. Teste MA, Duquenne M, François JM, Parrou JL. 2009. Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol Biol 10: 99.
62. Tsai SL, Goyal G, Chen W. 2010. Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production. Appl Environ Microbiol 76: 7514-7520.
63. van Peij NNME, Brinkmann J, Vru{ogonek}anská M, Visser J, de Graaff LH. 1997. β-Xylosidase activity, encoded by xlnD, is essential for complete hydrolysis of xylan by Aspergillus niger but not for induction of the xylanolytic enzyme spectrum. Eur J Biochem 245: 164-173.
64. van Zyl WH, Lynd LR, den Haan R, McBride JE. 2007. Consolidated bioprocessing for bioethanol production using Saccharomyces cerevisiae. Biofuels 108: 205-235.
65. Wen F, Sun J, Zhao H. 2010. Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl Environ Microbiol 76: 1251-1260.
66. West RW, Chen SM, Putz H. 1987. GAL1/GAL10 divergent promoter region of Saccharomyces cerevisiae contains negative control elements in addition to functionally separate and possibly overlapping upstream activating sequences. Genes Dev 1: 1118-1131.
67. Xu Q, Singh A, Himmel ME. 2009. Perspectives and new directions for the production of bioethanol using consolidated bioprocessing of lignocellulose. Curr Opin Biotechnol 20: 364-371.