Wicket: A Versatile Tool for the Integration and Optimization of Exogenous Pathways in Saccharomyces cerevisiae

ACS Synthetic Biology

Volumn 7, Issue 3, 2018, Pages 782-788

  Hou, Sha ^a   Qin, Qin ^a   Dai, Junbiao ^a,b  

^a TSINGHUA UNIVERSITY   (China)

^b SHENZHEN INSTITUTES OF ADVANCED TECHNOLOGY   (China)

Author keywords

cocktail integration; CRISPR Cas; multicopy integration; pathway optimization; Saccharomyces cerevisiae; tandem duplication

Indexed keywords

BETA CAROTENE;

ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; CRISPR-CAS9 SYSTEM; FUNGAL STRAIN; GENE EDITING; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; STABLE EXPRESSION; CRISPR CAS SYSTEM; GENETIC ENGINEERING; GENETICS; MUTAGENESIS; PROCEDURES;

CRISPR-CAS SYSTEMS; GENETIC ENGINEERING; MUTAGENESIS; SACCHAROMYCES CEREVISIAE;

EID: 85044055636     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.7b00391     Document Type: Article

References (30)

1. Mahdavi, H., Ulrich, A. C., and Liu, Y. (2012) Metal removal from oil sands tailings pond water by indigenous micro-alga. Chemosphere 89, 350-354, 10.1016/j.chemosphere.2012.04.041
2. Pinjing, H., Liming, S., Zhiwen, Y., and Guojian, L. (2001) Removal of hydrogen sulfide and methyl mercaptan by a packed tower with immobilized micro-organism beads. Water Sci. Technol. J. Int. Assoc. Water Pollut. Res. 44, 327-333
3. Fletcher, E., Krivoruchko, A., and Nielsen, J. (2016) Industrial systems biology and its impact on synthetic biology of yeast cell factories. Biotechnol. Bioeng. 113, 1164-1170, 10.1002/bit.25870
4. Hong, K.-K. and Nielsen, J. (2012) Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries. Cell. Mol. Life Sci. 69, 2671-2690, 10.1007/s00018-012-0945-1
5. Kim, I.-K., Roldao, A., Siewers, V., and Nielsen, J. (2012) A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res. 12, 228-248, 10.1111/j.1567-1364.2011.00779.x
6. Jensen, N. B., Strucko, T., Kildegaard, K. R., David, F., Maury, J., Mortensen, U. H., Forster, J., Nielsen, J., and Borodina, I. (2014) EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae. FEMS Yeast Res. 14, 238-248, 10.1111/1567-1364.12118
7. Ryan, O. W., Skerker, J. M., Maurer, M. J., Li, X., Tsai, J. C., Poddar, S., Lee, M. E., DeLoache, W., Dueber, J. E., Arkin, A. P., and Cate, J. H. (2014) Selection of chromosomal DNA libraries using a multiplex CRISPR system. eLife 3, 03703 10.7554/eLife.03703
8. Eckert-Boulet, N., Pedersen, M. L., Krogh, B. O., and Lisby, M. (2012) Optimization of ordered plasmid assembly by gap repair in Saccharomyces cerevisiae. Yeast 29, 323-334, 10.1002/yea.2912
9. Maury, J., Germann, S. M., Jacobsen, S. A. B., Jensen, N. B., Kildegaard, K. R., Herrgard, M. J., Schneider, K., Koza, A., Forster, J., Nielsen, J., and Borodina, I. (2016) EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae. PLoS One 11, e0150394, 10.1371/journal.pone.0150394
10. Mitchell, L. A., Chuang, J., Agmon, N., Khunsriraksakul, C., Phillips, N. A., Cai, Y., Truong, D. M., Veerakumar, A., Wang, Y., Mayorga, M., Blomquist, P., Sadda, P., Trueheart, J., and Boeke, J. D. (2015) Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae. Nucleic Acids Res. 43, 6620-6630, 10.1093/nar/gkv466
11. Guo, Y., Dong, J., Zhou, T., Auxillos, J., Li, T., Zhang, W., Wang, L., Shen, Y., Luo, Y., Zheng, Y., Lin, J., Chen, G.-Q., Wu, Q., Cai, Y., and Dai, J. (2015) YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae. Nucleic Acids Res. 43, e88, 10.1093/nar/gkv464
12. Lee, M. E., Aswani, A., Han, A. S., Tomlin, C. J., and Dueber, J. E. (2013) Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay. Nucleic Acids Res. 41, 10668-10678, 10.1093/nar/gkt809
13. Lopes, T. S., Klootwijk, J., Veenstra, A. E., van der Aar, P. C., van Heerikhuizen, H., Raué, H. A., and Planta, R. J. (1989) High-copy-number integration into the ribosomal DNA of Saccharomyces cerevisiae: a new vector for high-level expression. Gene 79, 199-206, 10.1016/0378-1119(89)90202-3
14. Shi, S., Liang, Y., Zhang, M. M., Ang, E. L., and Zhao, H. (2016) A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metab. Eng. 33, 19-27, 10.1016/j.ymben.2015.10.011
15. Zhou, P., Ye, L., Xie, W., Lv, X., and Yu, H. (2015) Highly efficient biosynthesis of astaxanthin in Saccharomyces cerevisiae by integration and tuning of algal crtZ and bkt. Appl. Microbiol. Biotechnol. 99, 8419-8428, 10.1007/s00253-015-6791-y
16. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., and Zhang, F. (2013) Multiplex Genome Engineering Using CRISPR/Cas Systems. Science 339, 819-823, 10.1126/science.1231143
17. Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L., and Church, G. M. (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833-838, 10.1038/nbt.2675
18. DiCarlo, J. E., Norville, J. E., Mali, P., Rios, X., Aach, J., and Church, G. M. (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 41, 4336-4343, 10.1093/nar/gkt135
19. Ronda, C., Maury, J., Jakočiunas, T., Jacobsen, S. A. B., Germann, S. M., Harrison, S. J., Borodina, I., Keasling, J. D., Jensen, M. K., and Nielsen, A. T. (2015) CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae. Microb. Cell Fact. 14, 97, 10.1186/s12934-015-0288-3
20. Walter, J. M., Chandran, S. S., and Horwitz, A. A. (2016) CRISPR-Cas-Assisted Multiplexing (CAM): Simple Same-Day Multi-Locus Engineering in Yeast. J. Cell. Physiol. 231, 2563-2569, 10.1002/jcp.25375
21. Bao, Z., Xiao, H., Liang, J., Zhang, L., Xiong, X., Sun, N., Si, T., and Zhao, H. (2015) Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. ACS Synth. Biol. 4, 585-594, 10.1021/sb500255k
22. Verwaal, R., Wang, J., Meijnen, J.-P., Visser, H., Sandmann, G., van den Berg, J. A., and van Ooyen, A. J. J. (2007) High-Level Production of Beta-Carotene in Saccharomyces cerevisiae by Successive Transformation with Carotenogenic Genes from Xanthophyllomyces dendrorhous. Appl. Environ. Microbiol. 73, 4342-4350, 10.1128/AEM.02759-06
23. Xie, W., Ye, L., Lv, X., Xu, H., and Yu, H. (2015) Sequential control of biosynthetic pathways for balanced utilization of metabolic intermediates in Saccharomyces cerevisiae. Metab. Eng. 28, 8-18, 10.1016/j.ymben.2014.11.007
24. Yamano, S., Ishii, T., Nakagawa, M., Ikenaga, H., and Misawa, N. (1994) Metabolic Engineering for Production of β-Carotene and Lycopene in Saccharomyces cerevisiae. Biosci., Biotechnol., Biochem. 58, 1112-1114, 10.1271/bbb.58.1112
25. Oliveira, C., Teixeira, J. A., Lima, N., Da Silva, N. A., and Domingues, L. (2007) Development of stable flocculent Saccharomyces cerevisiae strain for continuous Aspergillus niger β-galactosidase production. J. Biosci. Bioeng. 103, 318-324, 10.1263/jbb.103.318
26. Yamada, R., Taniguchi, N., Tanaka, T., Ogino, C., Fukuda, H., and Kondo, A. (2010) Cocktail δ-integration: a novel method to construct cellulolytic enzyme expression ratio-optimized yeast strains. Microb. Cell Fact. 9, 32, 10.1186/1475-2859-9-32
27. Kato, H., Matsuda, F., Yamada, R., Nagata, K., Shirai, T., Hasunuma, T., and Kondo, A. (2013) Cocktail δ-integration of xylose assimilation genes for efficient ethanol production from xylose in Saccharomyces cerevisiae. J. Biosci. Bioeng. 116, 333-336, 10.1016/j.jbiosc.2013.03.020
28. Liu, H., Wei, Z., Dominguez, A., Li, Y., Wang, X., and Qi, L. S. (2015) CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics 31, 3676-3678, 10.1093/bioinformatics/btv423
29. Rozen, S. and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. Clifton NJ. 132, 365-386
30. Teste, M.-A., Duquenne, M., François, J. M., and Parrou, J.-L. (2009) Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol. Biol. 10, 99, 10.1186/1471-2199-10-99