Structural feature of type I CRISPR-Cas system and its application in gene editing

ZHANG Yuwen; YU Chenlin; DAI Xinchen; XIAO Yibei; LU Meiling

doi:10.11665/j.issn.1000-5048.20210604

Journal of China Pharmaceutical University > 2021 > 52(6): 675-683. > DOI: 10.11665/j.issn.1000-5048.20210604

ZHANG Yuwen, YU Chenlin, DAI Xinchen, XIAO Yibei, LU Meiling. Structural feature of type I CRISPR-Cas system and its application in gene editing[J]. Journal of China Pharmaceutical University, 2021, 52(6): 675-683. DOI: 10.11665/j.issn.1000-5048.20210604

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Structural feature of type I CRISPR-Cas system and its application in gene editing

1.
School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198
2.
School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China

Funds: This study was supported by the National Natural Science Foundation of China (No.31970547) and the Natural Science Foundation of Jiangsu Province (No.BK20190552)

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Received Date: March 31, 2021
Revised Date: April 20, 2021

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Abstract

Abstract

The CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated) system is an "adaptive immune system" found in the genomes of bacteria and archaea which is mediated by RNA and resists foreign nucleic acid invasion.Take advantage of specific recognition of target nucleic acid, CRISPR-Cas system can efficiently edit their target site or accurately regulate gene expression, and now have been developed into a powerful tool for gene editing.According to the different compositions of the effector complex, the system has been divided into two categories: class 1 (type I, type IV, and type III) and class 2 (type II, type V, and type VI).Class 2 system, like the CRISPR-Cas9, is widely used in basic research due to the earliest discovery and best research.However, class 1 has not been maturely developed and utilized though it makes up 90% of the entire CRISPR-Cas system.In this essay, the classification of subtype, the assembly of Cascade complex, the cleavage and degradation mechanism of Cas3, and the application in gene editing of class 1 type I CRISPR-Cas system will be discussed and summarized to provide new ideas and methods for further mechanism studying and application of this category.
- CRISPR-Cas system,
- Cascade complex,
- Cas3,
- gene editing,
- bacterial immunity

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References (42)

References

[1]	. J Bacteriol，1987，169（12）：5429-5433.
[2]	Jansen R，JDvEmbden，Gaastra W，et al. Identification of genes that are associated with DNA repeats in prokaryotes［J］. Mol Microbiol，2002，43（6）：1565-1575.
[3]	Kim S，Loeff L，Colombo S，et al. Selective loading and processing of prespacers for precise CRISPR adaptation［J］. Nature，2020，579（7797）：141-145.
[4]	Reimann V，Alkhnbashi OS，Saunders SJ，et al. Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs［J］. Nucleic Acids Res，2017，45（2）：915-925.
[5]	Musharova O，Sitnik V，Vlot M，et al. Systematic analysis of type I‐E Escherichia coli CRISPR‐Cas PAM sequences ability to promote interference and primed adaptation［J］. Mol Microbiol，2019，111（6）：1558-1570.
[6]	Makarova KS，Wolf YI，Iranzo J，et al. Evolutionary classification of CRISPR-Cas systems： a burst of class 2 and derived variants［J］. Nat Rev Microbiol，2020，18（2）：67-83.
[7]	Nu?ez JK，Kranzusch PJ，Noeske J，et al. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity［J］. Nat Struct Mol Biol，2014，21（6）：528-534.
[8]	Sinkunas T，Gasiunas G，Fremaux C，et al. Cas3 is a single-stranded DNA nuclease and ATP‐dependent helicase in the CRISPR/Cas immune system［J］. EMBO J，2011，30（7）：1335-1342.
[9]	Xiao Y，Luo M，Hayes RP，et al. Structure basis for directional R-loop formation and substrate handover mechanisms in type I CRISPR-Cas system［J］. Cell，2017，170（1）：48-60.
[10]	Jesser R，Behler J，Benda C，et al. Biochemical analysis of the Cas6-1 RNA endonuclease associated with the subtype I-D CRISPR-Cas system in Synechocystis sp. PCC 6803［J］. RNA Biol，2019，16（4）：481-491.
[11]	Makarova KS，Wolf YI，Alkhnbashi OS，et al. An updated evolutionary classification of CRISPR-Cas systems［J］. Nat Rev Microbiol，2015，13（11）：722-736.
[12]	Makarova KS，Koonin EV. Annotation and classification of CRISPR-Cas systems［J］. Methods Mol Biol，2015，1311：47-75.
[13]	Nam KH，Haitjema C，Liu X，et al. Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system［J］. Structure，2012，20（9）：1574-1584.
[14]	Fagerlund RD，Wilkinson ME，Klykov O，et al. Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex［J］. Proc Natl Acad Sci U S A，2017，114（26）：E5122-E5128.
[15]	McBride TM，Schwartz EA，Kumar A，et al. Diverse CRISPR-Cas complexes require independent translation of small and large subunits from a single gene［J］. Mol Cell，2020，80（6）：971-979.
[16]	Zhao H，Sheng G，Wang J，et al. Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli［J］. Nature，2014，515（7525）：147-150.
[17]	Dwarakanath S，Brenzinger S，Gleditzsch D，et al. Interference activity of a minimal type I CRISPR-Cas system from Shewanella putrefaciens［J］. Nucleic Acids Res，2015，43（18）：8913-8923.
[18]	Gu DH，Ha SC，Kim JS. A CRISPR RNA is closely related with the size of the Cascade nucleoprotein complex［J］. Front Microbiol，2019，10：2458.
[19]	Songailiene I，Rutkauskas M，Sinkunas T，et al. Decision-making in Cascade complexes harboring crRNAs of altered length［J］. Cell Rep，2019，28（12）：3157-3166.
[20]	Gleditzsch D，Müller-Esparza H，Pausch P，et al. Modulating the Cascade architecture of a minimal type I-F CRISPR-Cas system［J］. Nucleic Acids Res，2016，44（12）：5872-5882.
[21]	Pausch P，Müller-Esparza H，Gleditzsch D，et al. Structural variation of type I-F CRISPR RNA guided DNA surveillance［J］. Mol Cell，2017，67（4）：622-632.
[22]	O′Brien RE，Santos IC，Wrapp D，et al. Structural basis for assembly of non-canonical small subunits into type I-C Cascade［J］. Nat Commun，2020，11（1）：5931.
[23]	Lin J，Fuglsang A，Kjeldsen AL，et al. DNA targeting by subtype I-D CRISPR-Cas shows type I and type III features［J］. Nucleic Acids Res，2020，48（18）：10470-10478.
[24]	Ding Y，Li H，Chen L-L，et al. Recent advances in genome editing using CRISPR/Cas9［J］. Front Plant Sci，2016，7：703.
[25]	Jore MM，Lundgren M，van Duijn E，et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade［J］. Nat Struct Mol Biol，2011，18（5）：529-536.
[26]	Cooper LA，Stringer AM，Wade JT. Determining the specificity of cascade binding，interference，and primed adaptation in vivo in the Escherichia coli type I-E CRISPR-Cas system［J］. mBio，2018，9（2）：e02100-17.
[27]	Hochstrasser ML，Taylor DW，Kornfeld JE，et al. DNA targeting by a minimal CRISPR RNA-guided cascade［J］. Mol Cell，2016，63（5）：840-851.
[28]	Xiao Y，Luo M，Dolan AE，et al. Structure basis for RNA-guided DNA degradation by Cascade and Cas3［J］. Science，2018，361（6397）：eaat0839.
[29]	Li Y，Pan S，Zhang Y，et al. Harnessing type I and type III CRISPR-Cas systems for genome editing［J］. Nucleic Acids Res，2016，44（4）：e34.
[30]	Cheng F，Gong L，Zhao D，et al. Harnessing the native type I-B CRISPR-Cas for genome editing in a polyploid archaeon［J］. J Genet Genomics，2017，44（11）：541-548.
[31]	Cs?rg? B，León LM，Chau-Ly IJ，et al. A compact Cascade-Cas3 system for targeted genome engineering［J］. Nat Methods，2020，17（12）：1183-1190.
[32]	Minkenberg B，Wheatley M，Yang Y. CRISPR/Cas9-enabled multiplex genome editing and its application［J］. Prog Mol Biol Transl Sci，2017，149：111-132.
[33]	Pan X，Wu Z，Qi X. Research status and application progress of CRISPR/Cas9 delivery system［J］. J China Pharm Univ（中国药科大学学报），2020，51（1）：10-18.
[34]	Tuladhar R，Yeu Y，Piazza JT，et al. CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation［J］. Nat Commun，2019，10（1）：4056.
[35]	Smits AH，Ziebell F，Joberty G，et al. Biological plasticity rescues target activity in CRISPR knock outs［J］. Nat Methods，2019，16（11）：1087-1093.
[36]	Dolan AE，Hou Z，Xiao Y，et al. Introducing a spectrum of long-range genomic deletions in human embryonic stem cells using type I CRISPR-Cas［J］. Mol Cell，2019，74（5）：936-950.
[37]	Cameron P，Coons MM，Klompe SE，et al. Harnessing type I CRISPR-Cas systems for genome engineering in human cells［J］. Nat Biotechnol，2019，37（12）：1471-1477.
[38]	Chen Y，Liu J，Zhi S，et al. Repurposing type I-F CRISPR-Cas system as a transcriptional activation tool in human cells［J］. Nat Commun，2020，11（1）：3136.
[39]	Pickar-Oliver A，Black JB，Lewis MM，et al. Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells［J］. Nat Biotechnol，2019，37（12）：1493-1501.
[40]	Luo ML，Jackson RN，Denny SR，et al. The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers［J］. Nucleic Acids Res，2016，44（15）：7385-7394.
[41]	Künne T，Zhu Y，da Silva F，et al. Role of nucleotide identity in effective CRISPR target escape mutations［J］. Nucleic Acids Res，2018，46（19）：10395-10404.
[42]	Fu BXH，Wainberg M，Kundaje A，et al. High-throughput characterization of Cascade type I-E CRISPR guide efficacy reveals unexpected PAM diversity and target sequence preferences［J］. Genetics，2017，206（4）：1727-1738.

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