Application of CRISPR/Cas9 Gene Editing System in Obtaining Natural Products in Actinomycetes

doi:10.6023/cjoc202105035

Chinese Journal of Organic Chemistry ›› 2021, Vol. 41 ›› Issue (11): 4279-4288.DOI: 10.6023/cjoc202105035 Previous Articles Next Articles

REVIEWS

CRISPR/Cas9基因编辑系统在获取放线菌天然产物中的应用

乔怡^a, 张庆林^b^,^c, 陈单丹^b^,^c^,^*(), 刘美娜^a^,^*(), 刘文^b^,^c^,^*()

a 上海应用技术大学化学与环境工程学院上海 201418
b 中国科学院上海有机化学研究所生命有机化学国家重点实验室上海 200032
c 中国科学院上海有机化学研究所湖州生物制造创新中心浙江湖州 313000

收稿日期:2021-05-20 修回日期:2021-06-16 发布日期:2021-07-05
通讯作者: 陈单丹, 刘美娜, 刘文
基金资助:
国家自然科学基金(21977109); 国家自然科学基金(32030002); 国家自然科学基金(21750004); 国家重点研发计划(2019YFA0905400); 中国科学院战略性先导科技专项(XDB20020200); 中国科学院青年创新促进会(2017303)

Application of CRISPR/Cas9 Gene Editing System in Obtaining Natural Products in Actinomycetes

Yi Qiao^a, Qinglin Zhang^b^,^c, Dandan Chen^b^,^c(), Meina Liu^a(), Wen Liu^b^,^c()

a School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418
b State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032
c Huzhou Center of Bio-synthetic Innovation, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Huzhou, Zhejiang 313000

Received:2021-05-20 Revised:2021-06-16 Published:2021-07-05
Contact: Dandan Chen, Meina Liu, Wen Liu
Supported by:
National Natural Science Foundation of China(21977109); National Natural Science Foundation of China(32030002); National Natural Science Foundation of China(21750004); National Key R&D Program of China(2019YFA0905400); Strategic Priority Research Program of the Chinese Academy of Sciences(XDB20020200); Youth Innovation Promotion Association of the Chinese Academy of Sciences(2017303)

As important source of clinical drugs, the natural products in actinomycetes and their derivatives have been developed on a large scale and used in clinical practice. In order to achieve efficient synthesis of active natural products, structural derivation of new natural products, and targeted mining of unknown natural products, researches mainly focus on the biosynthetic gene clusters from actinomycetes, which should be rationally engineered by advanced biotechnology. CRISPR/ Cas, which represents the clustered regularly interspaced short palindromic repeats and the associated protein, is an adaptive immune system developed by some bacteria and archaea in the long-term natural evolution process to resist the invasion of foreign genetic materials. As a representative of gene editing system, the clustered regularly interspaced short palindromic repeats and the associated protein 9 (CRISPR/Cas9) has been widely used in the targeted editing of deoxyribonucleic acid (DNA) fragments, which provides unlimited possibilities for the development of biotechnology. This paper reviews the application of the CRISPR/Cas9 system in the genetic manipulation of actinomycetes, including the recent research progress in capture, editing and reconstruction of gene clusters, in situ homologous recombination and metabolic regulation, which involves the novel CRISPR/Cas9-mediated gene editing methods and the representative successful cases. This paper will provide valuable information for the efficient use of CRISPR/Cas9 to obtain natural products in actinomycetes.

Key words: actinomycetes, natural products, biosynthetic gene clusters, gene editing, the clustered regularly interspaced short palindromic repeats and the associated protein 9 (CRISPR/Cas9)

Cite this article

Yi Qiao, Qinglin Zhang, Dandan Chen, Meina Liu, Wen Liu. Application of CRISPR/Cas9 Gene Editing System in Obtaining Natural Products in Actinomycetes[J]. Chinese Journal of Organic Chemistry, 2021, 41(11): 4279-4288.

Export EndNote|Reference Manager|ProCite|BibTeX|RefWorks

share this article

Fig. & Tab. 8

References 49

[1]	Bérdy, J. J. Antibiot. (Tokyo) 2012, 65, 441. doi: 10.1038/ja.2012.54
[2]	Newman, D. J.; Cragg, G. M. J. Nat. Prod. 2020, 83, 770. doi: 10.1021/acs.jnatprod.9b01285 pmid: 32162523
[3]	Bode, H. B.; Müller, R. Angew. Chem., Int. Ed. 2005, 44, 6828. doi: 10.1002/(ISSN)1521-3773
[4]	Lin, Z.; Chen, D.; Liu, W. Sci. China Chem. 2016, 59, 1175. doi: 10.1007/s11426-016-0062-x
[5]	Chen, M.; Liu, J.; Duan, P. Natl. Sci. Rev. 2017, 4, 553. doi: 10.1093/nsr/nww045
[6]	Smanski, M. J.; Zhou, H.; Claesen, J. Nat. Rev. Microbiol. 2016, 14, 135. doi: 10.1038/nrmicro.2015.24
[7]	Baltz, R. H. J. Ind. Microbiol. Biotechnol. 2016, 43, 343. doi: 10.1007/s10295-015-1682-x
[8]	Medema, M. H.; Blin, K.; Cimermancic, P. Nucleic Acids Res. 2011, 39, W339. doi: 10.1093/nar/gkr466
[9]	Ziemert, N.; Alanjary, M.; Weber, T. Nat. Prod. Rep. 2016, 33, 988. doi: 10.1039/c6np00025h pmid: 27272205
[10]	Horvath, P.; Barrangou, R. Science 2010, 327, 167. doi: 10.1126/science.1179555
[11]	Smargon, A. A.; Shi, Y. J.; Yeo, G. W. Nat. Cell Biol. 2020, 22, 143. doi: 10.1038/s41556-019-0454-7 pmid: 32015437
[12]	Cong, L.; Ran, F. A.; Cox, D. Science 2013, 339, 819. doi: 10.1126/science.1231143 pmid: 23287718
[13]	Gasiunas, G.; Barrangou, R.; Horvath, P. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, E2579. doi: 10.1073/pnas.1208507109
[14]	Fonfara, I.; Le, R. A.; Chylinski, K. Nucleic Acids Res. 2014, 42, 2577. doi: 10.1093/nar/gkt1074 pmid: 24270795
[15]	Hsu, P. D.; Lander, E. S.; Zhang, F. Cell 2014, 157, 1262. doi: 10.1016/j.cell.2014.05.010
[16]	Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J. A.; Charpentier, E. Science 2012, 337, 816. doi: 10.1126/science.1225829
[17]	Blin, K.; Pedersen, L. E.; Weber, T. Synth. Syst. Biotechnol. 2016, 1, 118. doi: 10.1016/j.synbio.2016.01.003 pmid: 29062934
[18]	Burke, D. T.; Carle, G. F.; Olson, M. V. Biotechnol. 1992, 24, 172.
[19]	Fu, J.; Bian, X.; Hu, S. Nat. Biotechnol. 2012, 30, 440. doi: 10.1038/nbt.2183
[20]	Noskov, V.; Kouprina, N.; Leem, S. H. Nucleic Acids Res. 2002, 30, e8. doi: 10.1093/nar/30.2.e8
[21]	Hoang, T. T.; Karkhoff-Schweizer, R. R.; Kutchma, A. J. Gene 1998, 212, 77. pmid: 9661666
[22]	Li, L.; Jiang, W.; Lu, Y. Biotechnol. Adv. 2017, 35, 936. doi: 10.1016/j.biotechadv.2017.03.007
[23]	Yamanaka, K.; Reynolds, K. A.; Kersten, R. D. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 1957. doi: 10.1073/pnas.1319584111 pmid: 24449899
[24]	Lee, N. C.; Larionov, V.; Kouprina, N. Nucleic Acids Res. 2015, 43, e55. doi: 10.1093/nar/gkv112
[25]	Jiang, W.; Zhao, X.; Gabrieli, T.; Lou, C. B.; Ebenstein, Y.; Zhu, T. F. Nat. Commun. 2015, 6, 8101. doi: 10.1038/ncomms9101
[26]	Jiang, W.; Zhu, T. F. Nat. Protoc. 2016, 11, 960. doi: 10.1038/nprot.2016.055
[27]	Wang, H.; Li, Z.; Jia, R. Nucleic Acids Res. 2018, 46, 2697. doi: 10.1093/nar/gkx1296
[28]	Wang, J. W.; Wang, A.; Li, K. BioTechniques 2015, 58, 161. doi: 10.2144/000114261
[29]	Kang, H. S.; Charlop-Powers, Z.; Brady, S. F. ACS Synth. Biol. 2016, 5, 1002. doi: 10.1021/acssynbio.6b00080
[30]	Kim, H.; Ji, C.-H.; Je, H.-W. ACS Synth. Biol. 2020, 9, 175. doi: 10.1021/acssynbio.9b00382
[31]	Kim, S. H.; Lu, W.; Ahmadi, M. K. ACS Synth. Biol. 2019, 8, 109. doi: 10.1021/acssynbio.8b00361
[32]	Jiang, Y.; Chen, B.; Duan, C. Appl. Environ. Microbiol. 2015, 81, 2506. doi: 10.1128/AEM.04023-14
[33]	Li, Q.; Sun, B.; Chen, J. Acta Biochim. Biophys. Sin. 2021, 53, 620. doi: 10.1093/abbs/gmab036
[34]	Song, C.; Luan, J.; Cui, Q. ACS Synth. Biol. 2019, 8, 137. doi: 10.1021/acssynbio.8b00402
[35]	Alberti, F.; Corre, C. Nat. Prod. Rep. 2019, 36, 1237. doi: 10.1039/C8NP00081F
[36]	Cobb, R. E.; Wang, Y.; Zhao, H. ACS Synth. Biol. 2015, 4, 723. doi: 10.1021/sb500351f
[37]	Zhang, M. M.; Wong, F. T.; Wang, Y. Nat. Chem. Biol. 2017, 13, 607. doi: 10.1038/nchembio.2341
[38]	Huang, H.; Zheng, G.; Jiang, W. Acta Biochim. Biophys. Sin. 2015, 47, 231. doi: 10.1093/abbs/gmv007
[39]	Tong, Y.; Charusanti, P.; Zhang, L. ACS Synth. Biol. 2015, 4, 1020. doi: 10.1021/acssynbio.5b00038
[40]	Zeng, H.; Wen, S.; Xu, W. Appl. Microbiol. Biotechnol. 2015, 99, 10575. doi: 10.1007/s00253-015-6931-4 pmid: 26318449
[41]	Mo, J.; Wang, S.; Zhang, W. Synth. Syst. Biotechnol. 2019, 4, 86.
[42]	Liu, G.; Chater, K. F.; Chandra, G. Microbiol. Mol. Biol. Rev. 2013, 77, 112. doi: 10.1128/MMBR.00054-12
[43]	Bikard, D.; Jiang, W.; Samai, P. Nucleic Acids Res. 2013, 41, 7429. doi: 10.1093/nar/gkt520 pmid: 23761437
[44]	Qi, L. S.; Larson, M. H.; Gilbert, L. A. Cell 2013, 152, 1173. doi: 10.1016/j.cell.2013.02.022
[45]	Gilbert, L. A.; Larson, M. H.; Morsut, L. Cell 2013, 154, 442. doi: 10.1016/j.cell.2013.06.044 pmid: 23849981
[46]	Mali, P.; Aach, J.; Stranges, P. B. Nat. Biotechnol. 2013, 31, 833. doi: 10.1038/nbt.2675
[47]	Dong, C.; Fontana, J. Nat. Commun. 2018, 9, 2489. doi: 10.1038/s41467-018-04901-6
[48]	Zhang, X.; Tee, L.; Wang, X. Mol. Ther.-Nucleic Acids 2015, 4, e264. doi: 10.1038/mtna.2015.37
[49]	Su, Q.; Cheng, C.; Niu, J. Curr. Opin. Chem. Biol. 2021, 64, 10. doi: 10.1016/j.cbpa.2021.02.004

方法名称	核心技术	操作体系	技术参数	方法特点
CRISPR/Cas9介导的TAR克隆	CRISPR/Cas9 TAR	大肠杆菌酿酒酵母	抓取上限约60~70 kb	操作体系复杂、抓取片段较短
CATCH	CRISPR/Cas9 Gibson组装	体外大肠杆菌	抓取上限超过100 kb	技术要求较高、片段越长抓取越难
ExoCET	CRISPR/Cas9 RecET重组	大肠杆菌	抓取上限超过100 kb	操作体系相对简单、抓取片段较长
ICE	CRISPR/Cas9 T4聚合酶修复 Gibson组装	体外大肠杆菌	单位点编辑	大片段编辑的技术要求较高
mCRISTAR	CRISPR/Cas9 TAR	大肠杆菌酿酒酵母	2~4个位点同时编辑	操作较为简便
mpCRISTAR	CRISPR/Cas9 TAR	大肠杆菌酿酒酵母	4~8个位点同时编辑	操作较为灵活、步骤较多
miCASTAR	CRISPR/Cas9 TAR	体外酿酒酵母	2~4个位点同时编辑	操作体系相对简单、操作简便

方法名称	核心技术	操作体系	技术参数	方法特点
CRISPR/Cas9介导的TAR克隆	CRISPR/Cas9 TAR	大肠杆菌酿酒酵母	抓取上限约60~70 kb	操作体系复杂、抓取片段较短
CATCH	CRISPR/Cas9 Gibson组装	体外大肠杆菌	抓取上限超过100 kb	技术要求较高、片段越长抓取越难
ExoCET	CRISPR/Cas9 RecET重组	大肠杆菌	抓取上限超过100 kb	操作体系相对简单、抓取片段较长
ICE	CRISPR/Cas9 T4聚合酶修复 Gibson组装	体外大肠杆菌	单位点编辑	大片段编辑的技术要求较高
mCRISTAR	CRISPR/Cas9 TAR	大肠杆菌酿酒酵母	2~4个位点同时编辑	操作较为简便
mpCRISTAR	CRISPR/Cas9 TAR	大肠杆菌酿酒酵母	4~8个位点同时编辑	操作较为灵活、步骤较多
miCASTAR	CRISPR/Cas9 TAR	体外酿酒酵母	2~4个位点同时编辑	操作体系相对简单、操作简便

质粒名称	抗性标签	cas9基因启动子	sgRNA启动子	质粒特性
pCRISPomyces-1	阿伯拉霉素	组成型rpsLp	组成型gapdhp (crRNA) 组成型rpsLp (tracrRNA)	来源于pSG5的温敏型复制子
pCRISPomyces-2	阿伯拉霉素	组成型rpsLp	组成型gapdhp (sgRNA)	来源于pSG5的温敏型复制子
pKCcas9dO	阿伯拉霉素	诱导型tipAp	组成型j23199p (sgRNA)	来源于pSG5的温敏型复制子
pCRISPR-Cas9	阿伯拉霉素硫链丝菌素	诱导型tipAp	组成型ermEp* (sgRNA)	来源于pSG5的温敏型复制子
pCRISPR-dCas9	阿伯拉霉素硫链丝菌素	诱导型tipAp	组成型ermEp* (sgRNA)	来源于pSG5的温敏型复制子
pWHU2653	阿伯拉霉素	组成型aac(3) IVp	组成型ermEp* (sgRNA)	来源于pIJ101的复制子 CodA 反筛标签
pMWCas9	阿伯拉霉素硫链丝菌素	诱导型tipAp	组成型ermEp* (sgRNA)	来源于pIJ101的复制子 CodA反筛标签

质粒名称	抗性标签	cas9基因启动子	sgRNA启动子	质粒特性
pCRISPomyces-1	阿伯拉霉素	组成型rpsLp	组成型gapdhp (crRNA) 组成型rpsLp (tracrRNA)	来源于pSG5的温敏型复制子
pCRISPomyces-2	阿伯拉霉素	组成型rpsLp	组成型gapdhp (sgRNA)	来源于pSG5的温敏型复制子
pKCcas9dO	阿伯拉霉素	诱导型tipAp	组成型j23199p (sgRNA)	来源于pSG5的温敏型复制子
pCRISPR-Cas9	阿伯拉霉素硫链丝菌素	诱导型tipAp	组成型ermEp* (sgRNA)	来源于pSG5的温敏型复制子
pCRISPR-dCas9	阿伯拉霉素硫链丝菌素	诱导型tipAp	组成型ermEp* (sgRNA)	来源于pSG5的温敏型复制子
pWHU2653	阿伯拉霉素	组成型aac(3) IVp	组成型ermEp* (sgRNA)	来源于pIJ101的复制子 CodA 反筛标签
pMWCas9	阿伯拉霉素硫链丝菌素	诱导型tipAp	组成型ermEp* (sgRNA)	来源于pIJ101的复制子 CodA反筛标签

CRISPR/Cas9基因编辑系统在获取放线菌天然产物中的应用

Application of CRISPR/Cas9 Gene Editing System in Obtaining Natural Products in Actinomycetes

RichHTML

PDF

Knowledge

Abstract

Cite this article

share this article

Fig. & Tab. 8

References 49

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Xiurong Wu, Chaojiang Xiao, Yi Shen, Hongxia Tang, Junyi Zhu, Bei Jiang. Research Progress on Antimalarial Natural Sesquiterpenoids from Plants from 1972 to 2022 [J]. Chinese Journal of Organic Chemistry, 2023, 43(8): 2764-2789.
[2]	Ran Gao, Weisheng Tian. Synthesis of Azedarachol and 2α,3α,20R-Trihydroxypregnane-16β-methacrylate [J]. Chinese Journal of Organic Chemistry, 2022, 42(8): 2521-2526.
[3]	Fasheng Shi, Shengwen Wang, Huan Xu, Xingxing Lu, Xinling Yang, Tengda Sun, Changkai Wang, Xiaoming Zhang, Qing Yang, Yun Ling. Design, Synthesis and Fungicidal Actiνity of Noνel Thiosemicarbazide Compounds [J]. Chinese Journal of Organic Chemistry, 2022, 42(7): 2106-2116.
[4]	Yaqian Yan, Haoxin Wang, Yaoyao Li. Discovery of a New Polycyclic Tetramate Macrolactam 3-Hydroxycombamide I [J]. Chinese Journal of Organic Chemistry, 2022, 42(5): 1557-1561.
[5]	Mengmeng Xu, Quan Cai. Progress of Catalytic Asymmetric Diels-Alder Reactions of 2-Pyrones [J]. Chinese Journal of Organic Chemistry, 2022, 42(3): 698-713.
[6]	Haixia Shi, Yaoyao Li, Jing Zhu, Haoxin Wang, Yuemao Shen. Discovery of Germicidin Glucuronides from Streptomyces sp. LZ35 [J]. Chinese Journal of Organic Chemistry, 2021, 41(6): 2502-2506.
[7]	Ting Jiang, Hong Pu, Yanwen Duan, Xiaohui Yan, Yong Huang. New Natural Products of Streptomyces Sourced from Deep-Sea, Desert, Volcanic, and Polar Regions from 2009 to 2020 [J]. Chinese Journal of Organic Chemistry, 2021, 41(5): 1804-1820.
[8]	Jiao Yujie, Yan Yaqian, Liu Yan, Zhu Deyu, Shen Yuemao, Li Yaoyao. New Polycyclic Tetramate Macrolactam from Streptomyces sp. S001 [J]. Chinese Journal of Organic Chemistry, 2020, 40(6): 1779-1784.
[9]	Zhang Kun, Xie Xiangqian, Shi Haixia, Shen Yuemao, Wang Haoxin. ortho-Dialkyl-Substituted Aromatic Acids from Verrucosispora sp. NS0172 [J]. Chinese Journal of Organic Chemistry, 2020, 40(4): 1038-1042.
[10]	Shi Zhan, Nie Kerui, Liu Chang, Zhang Mingzhi, Zhang Weihua. Biological Activities of 3-(5-Oxazolyl)indole Natural Products and Advances on Synthesis of Its Derivatives [J]. Chinese Journal of Organic Chemistry, 2020, 40(2): 327-338.
[11]	Zhang Juchenga, Yang Xueqiong, Zhou Hao, Yang Yabin, Ding Zhongtao. New Natural Products of Rare Actinomycetes from 2006 to 2018 [J]. Chin. J. Org. Chem., 2019, 39(4): 982-1012.
[12]	Li Xiaojun, Zhang Wanbin, Gao Shuanhu. Total Synthesis of Complex Natural Products: Combination of Chemical Synthesis and Biosynthesis Strategies [J]. Chin. J. Org. Chem., 2018, 38(9): 2185-2198.
[13]	Jin Wenbing, Yuan Hua, Tang Gongli. Strategies for Construction of Cyclopropanes in Natural Products [J]. Chin. J. Org. Chem., 2018, 38(9): 2324-2334.
[14]	Chen Yang, Li Wei-Dong Z. Asymmetric Total Synthesis of (－)-Cephalotaxine [J]. Chin. J. Org. Chem., 2017, 37(8): 1885-1902.
[15]	Xiao Chunxia, Cao Lin, Wang Jia, Miao Yinlong, Fan Huafang. Advances in the Collective Synthesis of Lycopodium Alkaloids [J]. Chin. J. Org. Chem., 2017, 37(4): 810-823.