合成生物学 ›› 2024, Vol. 5 ›› Issue (3): 658-671.DOI: 10.12211/2096-8280.2023-110
惠真1,2, 唐啸宇2
收稿日期:
2023-12-26
修回日期:
2024-03-17
出版日期:
2024-06-30
发布日期:
2024-07-12
通讯作者:
唐啸宇
作者简介:
基金资助:
Zhen HUI1,2, Xiaoyu TANG2
Received:
2023-12-26
Revised:
2024-03-17
Online:
2024-06-30
Published:
2024-07-12
Contact:
Xiaoyu TANG
摘要:
微生物作为天然产物的巨大宝库,一直以来都是研究人员挖掘和开发新的活性化合物的重要来源。目前,利用基因编辑工具发现、生物合成和代谢调控天然产物的研究方法受到该领域研究者的广泛关注。CRISPR/Cas9遗传编辑系统以其独特的灵活靶向优势克服了其他遗传编辑方法常见的对序列同源或位点限制,简化了实验步骤,提高了实验效率,促进了天然产物研究领域的发展。本文主要介绍CRISPR/Cas9系统在微生物天然产物发现、生物合成和工程改造方面的应用,分别从CRISPR/Cas9系统的发展、天然产物生物合成基因簇的克隆和遗传编辑、天然产物结构衍生化和代谢调节、沉默天然产物基因簇的激活这几个方面阐述CRISPR/Cas9系统在微生物天然产物研究领域的优势。最后,针对CRISPR/Cas9系统无法克服的重组效率和宿主适应性问题提供了可行的解决思路。相信随着合成生物学和信息技术的发展,越来越多的与CRISPR/Cas9系统相关的遗传操作工具和方法会被开发,将不断推动天然产物领域的发展进步。
中图分类号:
惠真, 唐啸宇. CRISPR/Cas9编辑系统在微生物天然产物研究中的应用[J]. 合成生物学, 2024, 5(3): 658-671.
Zhen HUI, Xiaoyu TANG. Applications of the CRISPR/Cas9 editing system in the study of microbial natural products[J]. Synthetic Biology Journal, 2024, 5(3): 658-671.
策略 | 生物合成基因簇 | 功能 | 生物合成基因簇来源/宿主 | 参考 文献 | |
---|---|---|---|---|---|
基因簇 克隆 | CATCH | Bacillaene | 基因簇线性化 | Bacillus subtilis str. 168 | [ |
Jadomycin | Streptomyces venezuelae ISP52030 | ||||
Chlortetracycline | S. aureofaciens ATCC 10762 | ||||
Pentaminomycins A-H | S. cacaoi CA-170360 | [ | |||
BH-18257 A-C | |||||
ICE & λ packaging system | Tu3010 | S. thiolactonus NRRL 15439 | [ | ||
Sisomicin | Micromonospora inyonensis DSM 46123 | ||||
CAPTURE | 43 uncharacterized BGCs | Streptomyces,Bacillus | [ | ||
CAT-FISHING | Marinolactam A | Micromonospora sp. 181 | [ | ||
基因簇 遗传编辑 | ICE | Tetronate RK-682 | 遗传突变 | Streptomyces sp. Strain 88-682 | [ |
Holomycin | S. clavuligerus TK24 | ||||
pCRISPomyces | Undecylprodigiosin, Actinorhodin | S. lividans 66 | [ | ||
Phosphinothricin tripeptide | S. viridochromogenes DSM 40736 | ||||
Macrolactam, Lanthipeptide | S. albus J1074 | ||||
CRISPR/Cas9 | Actinorhodin, Undecylprodigiosin | S. coelicolor M14 | [ | ||
CRISPR/Cas9-LigD | Actinorhodin | S. coelicolor A3(2) | [ | ||
CRISPRi | |||||
CRISPR/ Cas9-CodA(sm) | Actinorhodin | S. coelicolor M145 | [ | ||
CRISPR/Cas9 | Violacein | E. coli HME68 | [ | ||
Thalassospiramides | Pseudomonas putida EM383 | ||||
CBE/ABE | Undecylprodigiosin, Actinorhodin | S. coelicolor M145 | [ | ||
Avermectin | S. avermitilis MA4680 | ||||
产物 衍生化 | CRISPR/Cas9 & Gibson Assembly | Rapamycin | 组装模块编辑 | S. avermitilis SUKA | [ |
CRISPR/Cas9 | Enduracidin | Streptomyces fungicidicus ATCC 21013 | [ | ||
产物代谢调节 | CRISPR/Cas9 & TAR | Actinorhodin | 启动子工程 | S. albus J1074 | [ |
MSGE | Pristinamyicn Ⅱ, Chloramphenicol, YM-216391 | 多拷贝 | S. pristinaespiralis HCCB10218 S. coelicolor M145 | [ | |
CRISPR/Cas9 | Amorphadiene | 启动子工程,遗传突变, 多拷贝 | Bacillus subtilis | [ | |
CCTL | Actinorhodin | 启动子工程 | Streptomyces sp. 4F | [ | |
基因簇 激活 | CRISPR/Cas9 | Alteramide A, Macrolactam 2, FR-900098 | 启动子工程 | S. roseosporus NRRL15998 | [ |
mCRISTAR | Tetarimycin, Lazarimide, AB1210 | S. albus | [ | ||
mpCRISTAR | Acinorhodin | S. cerevisiae BY4727 | [ | ||
miCASTAR | Atolypene | Amycolatopsis tolypomycina NRRL B-24205 | [ | ||
CRISPR/Cas9-LigD | Amicetin | 遗传突变 | Streptomyces WAC6237 | [ | |
Thiolactomycin, 5-chloro-3-formylindole | Streptomyces WAC5374 | ||||
Phenanthroviridin aglycone | Streptomyces WAC8241 | ||||
CRISPRi/CRISPRa | Jadomycinb | 转录调控 | Streptomyces venezuelae | [ |
表1 CRISPR/Cas相关的生物合成基因簇编辑策略
Table 1 CRISPR/Cas-assisted biosynthetic gene cluster editing strategies
策略 | 生物合成基因簇 | 功能 | 生物合成基因簇来源/宿主 | 参考 文献 | |
---|---|---|---|---|---|
基因簇 克隆 | CATCH | Bacillaene | 基因簇线性化 | Bacillus subtilis str. 168 | [ |
Jadomycin | Streptomyces venezuelae ISP52030 | ||||
Chlortetracycline | S. aureofaciens ATCC 10762 | ||||
Pentaminomycins A-H | S. cacaoi CA-170360 | [ | |||
BH-18257 A-C | |||||
ICE & λ packaging system | Tu3010 | S. thiolactonus NRRL 15439 | [ | ||
Sisomicin | Micromonospora inyonensis DSM 46123 | ||||
CAPTURE | 43 uncharacterized BGCs | Streptomyces,Bacillus | [ | ||
CAT-FISHING | Marinolactam A | Micromonospora sp. 181 | [ | ||
基因簇 遗传编辑 | ICE | Tetronate RK-682 | 遗传突变 | Streptomyces sp. Strain 88-682 | [ |
Holomycin | S. clavuligerus TK24 | ||||
pCRISPomyces | Undecylprodigiosin, Actinorhodin | S. lividans 66 | [ | ||
Phosphinothricin tripeptide | S. viridochromogenes DSM 40736 | ||||
Macrolactam, Lanthipeptide | S. albus J1074 | ||||
CRISPR/Cas9 | Actinorhodin, Undecylprodigiosin | S. coelicolor M14 | [ | ||
CRISPR/Cas9-LigD | Actinorhodin | S. coelicolor A3(2) | [ | ||
CRISPRi | |||||
CRISPR/ Cas9-CodA(sm) | Actinorhodin | S. coelicolor M145 | [ | ||
CRISPR/Cas9 | Violacein | E. coli HME68 | [ | ||
Thalassospiramides | Pseudomonas putida EM383 | ||||
CBE/ABE | Undecylprodigiosin, Actinorhodin | S. coelicolor M145 | [ | ||
Avermectin | S. avermitilis MA4680 | ||||
产物 衍生化 | CRISPR/Cas9 & Gibson Assembly | Rapamycin | 组装模块编辑 | S. avermitilis SUKA | [ |
CRISPR/Cas9 | Enduracidin | Streptomyces fungicidicus ATCC 21013 | [ | ||
产物代谢调节 | CRISPR/Cas9 & TAR | Actinorhodin | 启动子工程 | S. albus J1074 | [ |
MSGE | Pristinamyicn Ⅱ, Chloramphenicol, YM-216391 | 多拷贝 | S. pristinaespiralis HCCB10218 S. coelicolor M145 | [ | |
CRISPR/Cas9 | Amorphadiene | 启动子工程,遗传突变, 多拷贝 | Bacillus subtilis | [ | |
CCTL | Actinorhodin | 启动子工程 | Streptomyces sp. 4F | [ | |
基因簇 激活 | CRISPR/Cas9 | Alteramide A, Macrolactam 2, FR-900098 | 启动子工程 | S. roseosporus NRRL15998 | [ |
mCRISTAR | Tetarimycin, Lazarimide, AB1210 | S. albus | [ | ||
mpCRISTAR | Acinorhodin | S. cerevisiae BY4727 | [ | ||
miCASTAR | Atolypene | Amycolatopsis tolypomycina NRRL B-24205 | [ | ||
CRISPR/Cas9-LigD | Amicetin | 遗传突变 | Streptomyces WAC6237 | [ | |
Thiolactomycin, 5-chloro-3-formylindole | Streptomyces WAC5374 | ||||
Phenanthroviridin aglycone | Streptomyces WAC8241 | ||||
CRISPRi/CRISPRa | Jadomycinb | 转录调控 | Streptomyces venezuelae | [ |
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