A CRISPR-Cas9 system for multiple genome editing and pathway assembly in Candida tropicalis.
CRISPR-Cas9
Candida tropicalis
genome editing
pathway assembly
yeast promoters
Journal
Biotechnology and bioengineering
ISSN: 1097-0290
Titre abrégé: Biotechnol Bioeng
Pays: United States
ID NLM: 7502021
Informations de publication
Date de publication:
02 2020
02 2020
Historique:
received:
25
08
2019
revised:
09
10
2019
accepted:
22
10
2019
pubmed:
28
10
2019
medline:
7
2
2021
entrez:
27
10
2019
Statut:
ppublish
Résumé
Genetic manipulation is among the most important tools for synthetic biology; however, modifying multiple genes is extremely time-consuming and can sometimes be impossible when dealing with gene families. Here, we present a clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein 9 (Cas9) system for use in the diploid yeast Candida tropicalis that is vastly superior to traditional techniques. This system enables the rapid and reliable introduction of multiple genetic deletions or mutations, as well as a stable expression using an integrated CRISPR-Cas9 cassette or a transient CRISPR-Cas9 cassette, together with a short donor DNA. We further show that the system can be used to promote the in vivo assembly of multiple DNA fragments and their stable integration into a target locus (or loci) in C. tropicalis. Based on this system, we present a platform for the biosynthesis of β-carotene and its derivatives. These results enable the practical application of C. tropicalis and the application of the system to other organisms.
Substances chimiques
DNA, Fungal
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
531-542Subventions
Organisme : Natural Science Foundation of Jiangsu Province
ID : BK20171138
Pays : International
Organisme : 111 Project
ID : 111-2-06
Pays : International
Organisme : Top-notch Academic Programs Project of Jiangsu Higher Education Institutions
ID : none
Pays : International
Informations de copyright
© 2019 Wiley Periodicals, Inc.
Références
Ahmad, I., Shim, W. Y., & Kim, J. H. (2013). Enhancement of xylitol production in glycerol kinase disrupted Candida tropicalis by co-expression of three genes involved in glycerol metabolic pathway. Bioprocess and Biosystems Engineering, 36, 1279-1284. https://doi.org/10.1007/s00449-012-0872-4
Bahieldin, A., Gadalla, N. O., Al-Garni, S. M., Almehdar, H., Noor, S., Hassan, S. M., & Murata, N. (2014). Efficient production of lycopene in Saccharomyces cerevisiae by expression of synthetic crt genes from a plasmid harboring the ADH2 promoter. Plasmid, 72, 18-28. https://doi.org/10.1016/j.plasmid.2014.03.001
Cao, W., Li, H., Luo, J., Yin, J., & Wan, Y. (2017). High-level productivity of alpha,omega-dodecanedioic acid with a newly isolated Candida viswanathii strain. Journal of Industrial Microbiology and Biotechnology, 44(8), 1191-1202. https://doi.org/10.1007/s10295-017-1948-6
Casini, A., Olivieri, M., Petris, G., Montagna, C., Reginato, G., Maule, G., … Cereseto, A. (2018). A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nature Biotechnology, 36(3), 265-271. https://doi.org/10.1038/nbt.4066
Chen, W., Zhang, Y., Yeo, W. S., Bae, T., & Ji, Q. (2017). Rapid and efficient genome editing in Staphylococcus aureus by using an engineered CRISPR/Cas9 system. Journal of the American Chemical Society, 139(10), 3790-3795. https://doi.org/10.1021/jacs.6b13317
Davidson, R. C., Blankenship, J. R., Kraus, P. R., Berrios, M. D., Hull, C. M., D'Souza, C., … Heitman, J. (2002). A PCR-based strategy to generate integrative targeting alleles with large regions of homology. Microbiology, 148, 2607-2615. https://doi.org/10.1099/00221287-148-8-2607
Deaner, M., Mejia, J., & Alper, H. S. (2017). Enabling graded and large-scale multiplex of desired genes using a dual-mode dCas9 activator in Saccharomyces cerevisiae. ACS Synthetic Biology, 6(10), 1931-1943. https://doi.org/10.1021/acssynbio.7b00163
DiCarlo, J. E., Norville, J. E., Mali, P., Rios, X., Aach, J., & Church, G. M. (2013). Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Research, 41(7), 4336-4343. https://doi.org/10.1093/nar/gkt135
Engler, C., Kandzia, R., & Marillonnet, S. (2008). A one pot, one step, precision cloning method with high throughput capability. PLOS One, 3(11), 1-7. https://doi.org/10.1371/journal.pone.0003647. e3647.
Funk, I., Sieber, V., & Schmid, J. (2017). Effects of glucose concentration on 1,18-cis-octadec-9-enedioic acid biotransformation efficiency and lipid body formation in Candida tropicalis. Scientific Reports, 7(1), 13842. https://doi.org/10.1038/s41598-017-14173-7
Gao, S. L., Tong, Y. Y., Zhu, L., Ge, M., Zhang, Y. A., Chen, D. J., … Yang, S. (2017). Iterative integration of multiple-copy pathway genes in Yarrowia lipolytica for heterologous beta-carotene production. Metabolic Engineering, 41, 192-201. https://doi.org/10.1016/j.ymben.2017.04.004
Gao, Y., & Zhao, Y. (2014). Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. Journal of Integrative Plant Biology, 56(4), 343-349. https://doi.org/10.1111/jipb.12152
Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods, 6(5), 343-U341. https://doi.org/10.1038/Nmeth.1318
Halder, V., Porter, C. B. M., Chavez, A., & Shapiro, R. S. (2019). Design, execution, and analysis of CRISPR-Cas9-based deletions and genetic interaction networks in the fungal pathogen Candida albicans. Nature Protocols, 14(3), 955-975. https://doi.org/10.1038/s41596-018-0122-6
Holkenbrink, C., Dam, M. I., Kildegaard, K. R., Beder, J., Dahlin, J., Domenech Belda, D., & Borodina, I. (2018). EasyCloneYALI: CRISPR/Cas9-based synthetic toolbox for engineering of the yeast Yarrowia lipolytica. Biotechnology Journal, 13(9), 1-8. https://doi.org/10.1002/biot.201700543. e1700543.
Jakociunas, T., Rajkumar, A. S., Zhang, J., Arsovska, D., Rodriguez, A., Jendresen, C. B., …Keasling, J. D. (2015). CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae. ACS Synthetic Biology, 4(11), 1226-1234. https://doi.org/10.1021/acssynbio.5b00007
Juergens, H., Varela, J. A., de Vries, A. R. G., Perli, T., Gast, V. J. M., Gyurchev, N. Y., … Daran, J. M. G. (2018). Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid. FEMS Yeast Research, 18(3), 1-16. https://doi.org/10.1093/femsyr/foy012
Kuijpers, N. G., Chroumpi, S., Vos, T., Solis-Escalante, D., Bosman, L., Pronk, J. T., … Daran-Lapujade, P. (2013). One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae. FEMS Yeast Research, 13(8), 769-781. https://doi.org/10.1111/1567-1364.12087
Kumar, V., Krishania, M., Preet Sandhu, P., Ahluwalia, V., Gnansounou, E., & Sangwan, R. S. (2018). Efficient detoxification of corn cob hydrolysate with ion-exchange resins for enhanced xylitol production by Candida tropicalis MTCC 6192. Bioresource Technology, 251, 416-419. https://doi.org/10.1016/j.biortech.2017.11.039
Li, M. Z., & Elledge, S. J. (2007). Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nature Methods, 4(3), 251-256. https://doi.org/10.1038/Nmeth1010
Lian, J. Z., Bao, Z. H., Hu, S. M., & Zhao, H. M. (2018). Engineered CRISPR/Cas9 system for multiplex genome engineering of polyploid industrial yeast strains. Biotechnology and Bioengineering, 115(6), 1630-1635. https://doi.org/10.1002/bit.26569
Lombardi, L., Oliveira-Pacheco, J., & Butler, G. (2019). Plasmid-based CRISPR-Cas9 gene editing in multiple Candida species. mSphere, 4(2), 1-12. https://doi.org/10.1128/mSphere.00125-19
Lu, W. H., Ness, J. E., Xie, W. C., Zhang, X. Y., Minshull, J., & Gross, R. A. (2010). Biosynthesis of monomers for plastics from renewable oils. Journal of the American Chemical Society, 132(43), 15451-15455. https://doi.org/10.1021/ja107707v
Min, K., Ichikawa, Y., Woolford, C. A., & Mitchell, A. P. (2016). Candida albicans gene deletion with a transient CRISPR-Cas9 system. mSphere, 1(3), 1-9. https://doi.org/10.1128/mSphere.00130-16
Ng, H., & Dean, N. (2017). Dramatic improvement of CRISPR/Cas9 editing in Candida albicans by increased single guide RNA expression. mSphere, 2(2), 1-17. https://doi.org/10.1128/mSphere.00385-16
Picataggio, S., Rohrer, T., Deanda, K., Lanning, D., Reynolds, R., Mielenz, J., & Eirich, L. D. (1992). Metabolic engineering of Candida tropicalis for the production of long-chain dicarboxylic acids. Nature Biotechnology, 10(8), 894-898.
Ryan, O. W., Skerker, J. M., Maurer, M. J., Li, X., Tsai, J. C., Poddar, S., … Arkin, A. P. (2014). Selection of chromosomal DNA libraries using a multiplex CRISPR system. eLife, 3, 1-15. https://doi.org/10.7554/eLife.03703. e03703.
Schwartz, C. M., Hussain, M. S., Blenner, M., & Wheeldon, I. (2016). Synthetic RNA polymerase III promoters facilitate high-efficiency CRISPR-Cas9-mediated genome editing in Yarrowia lipolytica. ACS Synthetic Biology, 5(4), 356-359. https://doi.org/10.1021/acssynbio.5b00162
Shao, Y., Lu, N., Wu, Z., Cai, C., Wang, S., Zhang, L. L., … Qin, Z. (2018). Creating a functional single-chromosome yeast. Nature, 560(7718), 331-335. https://doi.org/10.1038/s41586-018-0382-x
Shapiro, R. S., Chavez, A., Porter, C. B. M., Hamblin, M., Kaas, C. S., DiCarlo, J. E., … Collins, J. J. (2018). A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nature Microbiology, 3(1), 73-82. https://doi.org/10.1038/s41564-017-0043-0
Shi, S. B., Liang, Y. Y., Zhang, M. Z. M., Ang, E. L., & Zhao, H. M. (2016). A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae. Metabolic Engineering, 33, 19-27. https://doi.org/10.1016/j.ymben.2015.10.011
Shifrut, E., Carnevale, J., Tobin, V., Roth, T. L., Woo, J. M., Bui, C. T., … Marson, A. (2018). Genome-wide CRISPR screens in primary human T cells reveal key regulators of immune function. Cell, 175(7), 1958-1971. https://doi.org/10.1016/j.cell.2018.10.024. e1915.
Vyas, V. K., Barrasa, M. I., & Fink, G. R. (2015). A Candida albicans CRISPR system permits genetic engineering of essential genes and gene families. Science Advances, 1(3), 1-6. https://doi.org/10.1126/sciadv.1500248. e1500248.
Wang, J., Peng, J., Fan, H., Xiu, X., Xue, L., Wang, L., … Wang, R. (2018). Development of mazF-based markerless genome editing system and metabolic pathway engineering in Candida tropicalis for producing long-chain dicarboxylic acids. Journal of Industrial Microbiology and Biotechnology, 971-981. https://doi.org/10.1007/s10295-018-2074-9
Xie, S., Shen, B., Zhang, C., Huang, X., & Zhang, Y. (2014). sgRNAcas9: A software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLOS One, 9(6), 1-9. https://doi.org/10.1371/journal.pone.0100448. e100448.
Zhang, L., Chen, X., Chen, Z., Wang, Z., Jiang, S., Li, L., … Fan, Y. (2016). Development of an efficient genetic manipulation strategy for sequential gene disruption and expression of different heterologous GFP genes in Candida tropicalis. Applied Microbiology and Biotechnology, 100(22), 9567-9580. https://doi.org/10.1007/s00253-016-7762-7
Zhang, Y. P., Wang, J., Wang, Z. B., Zhang, Y. M., Shi, S. B., Nielsen, J., … Liu, Z. H. (2019). A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae. Nature Communications, 10, 1053.
Zhou, J. T., Wu, R. H., Xue, X. L., & Qin, Z. J. (2016). CasHRA (Cas9-facilitated homologous recombination assembly) method of constructing megabase-sized DNA. Nucleic Acids Research, 44(14), e124.
Zhou, S. H., Ding, R. P., Chen, J., Du, G. C., Li, H. Z., & Zhou, J. W. (2017). Obtaining a panel of cascade promoter-5′-UTR complexes in Escherichia coli. ACS Synthetic Biology, 6(6), 1065-1075. https://doi.org/10.1021/acssynbio.7b00006