EasyClone-MarkerFree: A vector toolkit for marker-less integration of genes into Saccharomyces cerevisiae via CRISPR-Cas9

Biotechnology Journal

Volumn 11, Issue 8, 2016, Pages 1110-1117

  Jessop Fabre, Mathew M ^a   Jakočiūnas, Tadas ^a   Stovicek, Vratislav ^a   Dai, Zongjie ^b   Jensen, Michael K ^a   Keasling, Jay D ^a,c,d,e   Borodina, Irina ^a  

^a Chalmers University of Technology   (Denmark)

^b CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^c JOINT BIOENERGY INSTITUTE   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e University of California at Berkeley   (United States)

Author keywords

3 hydroxypropionic acid; CRISPR Cas9; Metabolic engineering; Saccharomyces cerevisiae

Indexed keywords

GENES; INDUSTRIAL CHEMICALS; INTEGRATION; METABOLIC ENGINEERING; RECOMBINANT PROTEINS; VECTORS;

3-HYDROXYPROPIONIC ACID; CHROMOSOMAL LOCATION; CRISPR-CAS9; EXPRESSION CASSETTE; GENOME ENGINEERING; INDUSTRIAL STRAIN; OVER-EXPRESSION; PYRUVATE DEHYDROGENASE COMPLEX;

YEAST;

ACETYL COENZYME A; GUIDE RNA; HYDRACRYLIC ACID; PYRUVATE DEHYDROGENASE;

ARTICLE; CHROMOSOMAL LOCALIZATION; CRISPR CAS SYSTEM; CYTOSOL; DIPLOIDY; FUNGAL GENE; GENE CASSETTE; GENE EXPRESSION; GENE INSERTION; GENE LOCUS; GENE OVEREXPRESSION; GENE VECTOR; GENETIC ENGINEERING; GENOME; HAPLOIDY; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

EID: 84979746885     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201600147     Document Type: Article

References (34)

1. Botstein, D., Chervitz, S. A., Cherry, J. M., Yeast as a model organism. Science 1997, 277, 1259–1260.
2. Borodina, I., Nielsen, J., Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. Biotechnol. J. 2014, 9, 609–620.
3. Jensen, M. K., Keasling, J. D., Recent applications of synthetic biology tools for yeast metabolic engineering. FEMS Yeast Res. 2015, 15, DOI: 10.1111/1567-1364.12185.
4. Schiestl, R. H., Petes, T. D., Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 1991, 88, 7585–7589.
5. Jensen, N. B., Strucko, T., Kildegaard, K. R., David, F. et al., EasyClone: Method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae. FEMS Yeast Res. 2014, 14, 238–248.
6. Stovicek, V., Borja, G. M., Forster, J., Borodina, I., EasyClone 2.0: Expanded toolkit of integrative vectors for stable gene expression in industrial Saccharomyces cerevisiae strains. J. Ind. Microbiol. Biotechnol. 2015, 42, 1519–1531.
7. Pronk, J. T., Auxotrophic yeast strains in fundamental and applied research. Appl. Environ. Microbiol. 2002, 68, 2095–2100.
8. Alam, M. T., Zelezniak, A., Mülleder, M., Shliaha, P. et al., The metabolic background is a global player in Saccharomyces gene expression epistasis. Nat. Microbiol. 2016, 1, 1–10.
9. Storici, F., Durham, C. L., Gordenin, D. A., Resnick, M. A., Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast. Proc. Natl. Acad. Sci. USA 2003, 100, 14994–14999.
10. Wingler, L. M., Cornish, V. W., Reiterative recombination for the in vivo assembly of libraries of multigene pathways. Proc. Natl. Acad. Sci. USA 2011, 108, 15135–15140.
11. Kuijpers, N. G., Chroumpi, S., Vos, T., Solis-Escalante, D. et al., One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae. FEMS Yeast Res. 2013, 13, 769–781.
12. Kuijpers, N. G., Solis-Escalante, D., Bosman, L., van den Broek, M. et al., A versatile, efficient strategy for assembly of multi-fragment expression vectors in Saccharomyces cerevisiae using 60 bp synthetic recombination sequences. Microb. Cell Fact. 2013, 12, 47.
13. DiCarlo, J. E., Norville, J. E., Mali, P., Rios, X. et al., Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013, 41, 4336–4343.
14. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337, 816–821.
15. Jakočiūnas, T., Bonde, I., Herrgård, M. J., Harrison, S. J. et al., Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab. Eng. 2015, 28, 213–222.
16. Jakočiūnas, T., Rajkumar, A. S., Zhang, J., Arsovska, D. et al. CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae. ACS Synth. Biol. 2015, 4, 1226–1234.
17. Stovicek, V., Borodina, I., Forster, J., CRISPR–Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains. Metab. Eng. Commun. 2015, 2, 13–22.
18. Ronda, C., Maury, J., Jakočiūnas, T., Jacobsen, S. A. et al., CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae. Microb. Cell Fact. 2015, 14, 97.
19. Mans, R., van Rossum, H. M., Wijsman, M., Backx, A. et al. CRISPR/Cas9: A molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae. FEMS Yeast Res. 2015, 15, DOI: 10.1093/femsyr/fov004.
20. Laughery, M. F., Hunter, T., Brown, A., Hoopes, J. et al. New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae. Yeast 2015, 32, 711–720.
21. Horwitz, A. A., Walter, J. M., Schubert, M. G., Kung, S. H. et al., Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR-Cas. Cell Systems 2015, 1, 88–96.
22. Jakočiūnas, T., Jensen, M. K., Keasling, K. D., CRISPR/Cas9 advances engineering of microbial cell factories. Metab. Eng. 2016, 34, 44–59.
23. Mikkelsen, M. D., Buron, L. D., Salomonsen, B., Olsen, C. E. et al., Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform. Metab. Eng. 2012, 14, 104–111.
24. Delneri, D., Tomlin, G. C., Wixon,, J. L., Hutter, A. et al., Exploring redundancy in the yeast genome: An improved strategy for use of the cre-loxP system. Gene. 2000, 252, 127–135.
25. Solis-Escalante, D., Kuijpers, N. G. A., van der Linden, F. H., Pronk, J. T. et al., Efficient simultaneous excision of multiple selectable marker cassettes using I-SceI-induced double-strand DNA breaks in Saccharomyces cerevisiae. FEMS Yeast Res. 2014, 14, 741–754.
26. Nour-Eldin, H. H., Geu-Flores, F., Halkier, B. A., USER cloning and USER fusion: The ideal cloning techniques for small and big laboratories. Methods Mol. Biol. 2010, 643, 185–200.
27. Gietz, R. D., Schiestl, R. H., High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2007, 2, 31–34.
28. Borodina, I., Kildegaard, K. R., Jensen, N. B., Blicher, T. H. et al., Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via beta-alanine. Metab. Eng. 2015, 27, 57–64.
29. Li, M., Borodina, I., Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae. FEMS Yeast Res. 2014, DOI: 10.1111/1567-1364.12213.
30. Kozak, B. U., van Rossum, H. M., Luttik, M. A., Akeroyd, M. et al., Engineering acetyl coenzyme A supply: Functional expression of a bacterial pyruvate dehydrogenase complex in the cytosol of Saccharomyces cerevisiae. MBio 2014, 5, e01696–e01614.
31. Shiba, Y., Paradise, E. M., Kirby, J., Ro, D. K., Keasling, J. D., Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metab. Eng. 2007, 9, 160–168.
32. Chen, Y., Bao, J., Il-Kwon, K., Siewers, V., Nielsen, J., Coupled incremental precursor and co-factor supply improves 3-hydroxypropionic acid production in Saccharomyces cerevisiae. Metab. Eng. 2014, 22, 104–109.
33. Jensen, N. B., Borodina, I., Chen, Y., Maury, J. et al., Microbial production of 3-hydroxypropionic acid. WO-Patent 198831 A1, 2014.
34. Kildegaard, K. R., Wang, Z., Chen, Y., Nielsen, J., Borodina, I., Production of 3-hydroxypropionic acid from glucose and xylose by metabolically engineered Saccharomyces cerevisiae. Metab. Eng. Comm. 2015, 2, 132–136.