Bacterial XylRs and synthetic promoters function as genetically encoded xylose biosensors in Saccharomyces cerevisiae

Biotechnology Journal

Volumn 10, Issue 2, 2015, Pages 315-322

  Teo, Wei Suong ^a,b,c   Chang, Matthew Wook ^b,c  

^a Nanyang Technological University   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Biofuel; Saccharomyces cerevisiae; Synthetic biology; Synthetic promoter; Xylose biosensor

Indexed keywords

BIOFUELS; BIOSENSORS; GENE EXPRESSION; PROTEINS; SUGARS;

CLOSTRIDIUM DIFFICILE; CONSTITUTIVE EXPRESSIONS; LIGNOCELLULOSIC BIOMASS; LIGNOCELLULOSIC HYDROLYSATES; PROTEIN EXPRESSIONS; STRAIN OPTIMIZATION; SYNTHETIC BIOLOGY; SYNTHETIC PROMOTER;

YEAST;

BACTERIAL PROTEIN; BIOFUEL; ENHANCED GREEN FLUORESCENT PROTEIN; GLUCOSE; LIGNOCELLULOSE; PROTEIN XYLR; UNCLASSIFIED DRUG; XYLOSE; BACTERIAL DNA;

ARTICLE; BIOFUEL PRODUCTION; BIOMASS; BIOSENSOR; CARBON SOURCE; CONTROLLED STUDY; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; MOLECULAR CLONING; NONHUMAN; OPERATOR GENE; PEPTOCLOSTRIDIUM DIFFICILE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE; TETRAGENOCOCCUS HALOPHILUS; ENTEROCOCCACEAE; GENETIC ENGINEERING; GENETICS; LACTOBACILLUS; METABOLISM; PROCEDURES; SYNTHETIC BIOLOGY;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM DIFFICILE; LACTOBACILLUS PENTOSUS; SACCHAROMYCES CEREVISIAE; TETRAGENOCOCCUS;

BACTERIAL PROTEINS; CLONING, MOLECULAR; CLOSTRIDIUM DIFFICILE; DNA, BACTERIAL; ENTEROCOCCACEAE; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC ENGINEERING; LACTOBACILLUS; PROMOTER REGIONS, GENETIC; SACCHAROMYCES CEREVISIAE; SYNTHETIC BIOLOGY; XYLOSE;

EID: 84922625273     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201400159     Document Type: Article

References (45)

1. Peralta-Yahya, P. P., Zhang, F., del Cardayre, S. B., Keasling, J. D., Microbial engineering for the production of advanced biofuels. Nature 2012, 488, 320-328.
2. Tippmann, S., Chen, Y., Siewers, V., Nielsen, J., From flavors and pharmaceuticals to advanced biofuels: Production of isoprenoids in Saccharomyces cerevisiae. Biotechnol. J. 2013, 8, 1435-1444.
3. Hasunuma, T., Kondo, A., Development of yeast cell factories for consolidated bioprocessing of lignocellulose to bioethanol through cell surface engineering. Biotechnol. Adv. 2012, 30, 1207-1218.
4. Buschke, N., Schäfer, R., Becker, J., Wittmann, C., Metabolic engineering of industrial platform microorganisms for biorefinery applications - Optimization of substrate spectrum and process robustness by rational and evolutive strategies. Bioresource Technol. 2013, 135, 544-554.
5. Nevoigt, E., Progress in metabolic engineering of Saccharomyces cerevisiae. Microbiol. Molecular Biology Reviews 2008, 72, 379-412.
6. Cai, Z., Zhang, B., Li, Y., Engineering Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: Reflections and perspectives. Biotechnol. J. 2012, 7, 34-46.
7. Tanino, T., Hotta, A., Ito, T., Ishii, J. et al., Construction of a xylose-metabolizing yeast by genome integration of xylose isomerase gene and investigation of the effect of xylitol on fermentation. Appl. Microbiol. Biotechnol. 2010, 88, 1215-1221.
8. Kuyper, M., Harhangi, H. R., Stave, A. K., Winkler, A. A. et al., High-level functional expression of a fungal xylose isomerase: the key to efficient ethanolic fermentation of xylose by Saccharomyces cerevisiae? FEMS Yeast Res. 2003, 4, 69-78.
9. Zha, J., Hu, M., Shen, M., Li, B. et al., Balance of XYL1 and XYL2 expression in different yeast chassis for improved xylose fermentation. Frontiers Microbiol. 2012, 3, 335.
10. Kim, S. R., Park, Y.-C., Jin, Y.-S., Seo, J.-H., Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism. Biotechnol. Adv. 2013, 31, 851-861.
11. Wei, N., Quarterman, J., Kim, S. R., Cate, J. H. D., Jin, Y.-S., Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast. Nat. Commun. 2013, 4, 2580.
12. Kim, S. R., Ha, S.-J., Wei, N., Oh, E. J., Jin, Y.-S., Simultaneous co-fermentation of mixed sugars: a promising strategy for producing cellulosic ethanol. Trends Biotechnol. 2012, 30, 274-282.
13. Ha, S.-J., Galazka, J. M., Rin Kim, S., Choi, J.-H. et al., Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation. Proc. Natl. Acad. Sci. USA 2011, 108, 504-509.
14. Young, E. M., Tong, A., Bui, H., Spofford, C., Alper, H. S., Rewiring yeast sugar transporter preference through modifying a conserved protein motif. Proc. Natl. Acad. Sci. USA 2013, 111, 131-136.
15. Farwick, A., Bruder, S., Schadeweg, V., Oreb, M., Boles, E., Engineering of yeast hexose transporters to transport d-xylose without inhibition by d-glucose. Proc. Natl. Acad. Sci. USA 2014, 111, 5159-5164.
16. Schallmey, M., Frunzke, J., Eggeling, L., Marienhagen, J., Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors. Curr. Opin. Biotechnol. 2014, 26, 148-154.
17. Michener, J. K., Thodey, K., Liang, J. C., Smolke, C. D., Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab. Eng. 2012, 14, 212-222.
18. Zhang, F., Carothers, J. M., Keasling, J. D., Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol. 2012, 30, 354-359.
19. Seo, S. W., Yang, J., Min, B. E., Jang, S. et al., Synthetic biology: Tools to design microbes for the production of chemicals and fuels. Biotechnol. Adv. 2013, 31, 811-817.
20. Seo, S., Kim, S., Jung, G., Synthetic regulatory tools for microbial engineering. Biotechnol. Bioproc. E 2012, 17, 1-7.
21. Abatemarco, J., Hill, A., Alper, H. S., Expanding the metabolic engineering toolbox with directed evolution. Biotechnol. J. 2013, 8, 1397-1410.
22. Chaillou, S., Lokman, B. C., Leer, R. J., Posthuma, C. et al., Cloning, sequence analysis, and characterization of the genes involved in isoprimeverose metabolism in Lactobacillus pentosus. J. Bacteriol. 1998, 180, 2312-2320.
23. Takeda, Y., Takase, K., Yamato, I., Abe, K., Sequencing and characterization of the xyl Operon of a Gram-positive bacterium, Tetragenococcus halophila. Appl. Environ. Microbiol. 1998, 64, 2513-2519.
24. Nariya, H., Miyata, S., Kuwahara, T., Okabe, A., Development and characterization of a xylose-inducible gene expression system for Clostridium perfringens. Appl. Environ. Microbiol. 2011, 77, 8439-8441.
25. Teo, W. S., Hee, K. S., Chang, M. W., Bacterial FadR and synthetic promoters function as modular fatty acid sensor-regulators in Saccharomyces cerevisiae. Eng. Life Sci. 2013, 13, 456-463.
26. Teo, W. S., Chang, M. W., Development and characterization of AND-gate dynamic controllers with a modular synthetic GAL1 core promoter in Saccharomyces cerevisiae. Biotechnol. Bioeng. 2013, 111, 144-151.
27. Yamanishi, M., Ito, Y., Kintaka, R., Imamura, C. et al., A genome-wide activity assessment of terminator regions in Saccharomyces cerevisiae Provides a "Terminatome" Toolbox. ACS Synth. Biol. 2013, 2, 337-347.
28. Keren, L., Zackay, O., Lotan Pompan, M., Barenholz, U. et al., Promoters maintain their relative activity levels under different growth conditions. 2013, 9, 701.
29. Cameron, D. E., Bashor, C. J., Collins, J. J., A brief history of synthetic biology. Nat. Rev. Microbiol. 2014, 12, 381-390.
30. Dahl, M. K., Schmiedel, D., Hillen, W., Glucose and glucose-6-phosphate interaction with Xyl repressor proteins from Bacillus spp. may contribute to regulation of xylose utilization. J. Bacteriol. 1995, 177, 5467-5472.
31. Gu, Y., Ding, Y., Ren, C., Sun, Z. et al., Reconstruction of xylose utilization pathway and regulons in Firmicutes. BMC Genomics 2010, 11, 255.
32. Partow, S., Siewers, V., Bjørn, S., Nielsen, J., Maury, J., Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast 2010, 27, 955-964.
33. Vickers, C., Bydder, S., Zhou, Y., Nielsen, L., Dual gene expression cassette vectors with antibiotic selection markers for engineering in Saccharomyces cerevisiae. Microb. Cell Fact. 2013, 12, 1-11.
34. Sun, J., Shao, Z., Zhao, H., Nair, N. et al., Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae. Biotechnol. Bioeng. 2012, 109, 2082-2092.
35. Blount, B. A., Weenink, T., Vasylechko, S., Ellis, T., Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS One 2012, 7, e33279.
36. Angermayr, M., Oechsner, U., Bandlow, W., Reb1p-dependent DNA bending effects nucleosome positioning and constitutive transcription at the yeast profilin promoter. J. Biol. Chem. 2003, 278, 17918-17926.
37. 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.
38. Lo, T.-M., Teo, W. S., Ling, H., Chen, B. et al., Microbial engineering strategies to improve cell viability for biochemical production. Biotechnol. Adv. 2013, 31, 903-914.
39. Ling, H., Teo, W., Chen, B., Leong, S. S. J., Chang, M. W., Microbial tolerance engineering toward biochemical production: From lignocellulose to products. Curr. Opin. Biotechnol. 2014, 29, 99-106.
40. McIsaac, R. S., Oakes, B. L., Wang, X., Dummit, K. A. et al., Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast. Nucleic Acids Res. 2013, 41, e57.
41. McIsaac, R. S., Gibney, P. A., Chandran, S. S., Benjamin, K. R., Botstein, D., Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae. Nucleic Acids Res. 2014, 42, e48.
42. Ellis, T., Wang, X., Collins, J. J., Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol. 2009, 27, 465-471.
43. Murphy, K. F., Balázsi, G., Collins, J. J., Combinatorial promoter design for engineering noisy gene expression. Proc. Natl. Acad. Sci. USA 2007, 104, 12726-12731.
44. Blazeck, J., Alper, H. S., Promoter engineering: Recent advances in controlling transcription at the most fundamental level. Biotechnol. J. 2013, 8, 46-58.
45. Wang, C., Shen, Y., Hou, J., Suo, F., Bao, X., An assay for functional xylose transporters in Saccharomyces cerevisiae. Anal. Biochem. 2013, 442, 241-248.