51
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Wiegand T, Karambelkar S, Bondy-Denomy J, Wiedenheft B. Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression. Annu Rev Microbiol 2020; 74:21-37. [PMID: 32503371 DOI: 10.1146/annurev-micro-020518-120107] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
More than 50 protein families have been identified that inhibit CRISPR (clustered regularly interspaced short palindromic repeats)-Cas-mediated adaptive immune systems. Here, we analyze the available anti-CRISPR (Acr) structures and describe common themes and unique mechanisms of stoichiometric and enzymatic suppressors of CRISPR-Cas. Stoichiometric inhibitors often function as molecular decoys of protein-binding partners or nucleic acid targets, while enzymatic suppressors covalently modify Cas ribonucleoprotein complexes or degrade immune signaling molecules. We review mechanistic insights that have been revealed by structures of Acrs, discuss some of the trade-offs associated with each of these strategies, and highlight how Acrs are regulated and deployed in the race to overcome adaptive immunity.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA;
| | - Shweta Karambelkar
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, California 94143, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, Berkeley, California 94720, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA;
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52
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Zuo Z, Liu J. Allosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage. Curr Opin Struct Biol 2020; 62:166-174. [PMID: 32070859 PMCID: PMC7308215 DOI: 10.1016/j.sbi.2020.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 12/29/2022]
Abstract
The CRISPR-Cas9 system from Streptococcus pyogenes has been exploited as a programmable RNA-guided DNA-targeting and DNA-editing platform. This evolutionary tool enables diverse genetic manipulations with unprecedented precision and ease. Cas9 is an allosteric enzyme, which is allosterically regulated in conformational activation, target recognition, and DNA cleavage. Here, we outline the underlying allosteric control over the Cas9 complex assembly and targeting specificity. We further review the strategies for mitigating intrinsic Cas9 off-target effects through allosteric modulations and the advances in engineering controllable Cas9 systems that are responsive to external allosteric signals. Future development of highly specific, tunable CRISPR-Cas9 systems through allosteric modulations would greatly benefit applications that require both conditional control and high precision.
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Affiliation(s)
- Zhicheng Zuo
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
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53
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Hirakawa M, Krishnakumar R, Timlin J, Carney J, Butler K. Gene editing and CRISPR in the clinic: current and future perspectives. Biosci Rep 2020; 40:BSR20200127. [PMID: 32207531 PMCID: PMC7146048 DOI: 10.1042/bsr20200127] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.
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Affiliation(s)
| | - Raga Krishnakumar
- Systems Biology, Sandia National Laboratories, Livermore, CA 94551, U.S.A
| | - Jerilyn A. Timlin
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - James P. Carney
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - Kimberly S. Butler
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
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54
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Mitchell BP, Hsu RV, Medrano MA, Zewde NT, Narkhede YB, Palermo G. Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9. Front Mol Biosci 2020; 7:39. [PMID: 32258048 PMCID: PMC7093078 DOI: 10.3389/fmolb.2020.00039] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas9 is the forefront technology for editing the genome. In this system, the Cas9 protein is programmed with guide RNAs to process DNA sequences that match the guide RNA forming an RNA:DNA hybrid structure. However, the binding of DNA sequences that do not fully match the guide RNA can limit the applicability of CRISPR-Cas9 for genome editing, resulting in the so-called off-target effects. Here, molecular dynamics is used to probe the effect of DNA base pair mismatches within the RNA:DNA hybrid in CRISPR-Cas9. Molecular simulations revealed that the presence of mismatched pairs in the DNA at distal sites with respect to the Protospacer Adjacent Motif (PAM) recognition sequence induces an extended opening of the RNA:DNA hybrid, leading to novel interactions established by the unwound nucleic acids and the protein counterpart. On the contrary, mismatched pairs upstream of the RNA:DNA hybrid are rapidly incorporated within the heteroduplex, with minor effect on the protein-nucleic acid interactions. As a result, mismatched pairs at PAM distal ends interfere with the activation of the catalytic HNH domain, while mismatches fully embedded in the RNA:DNA do not affect the HNH dynamics and enable its activation to cleave the DNA. These findings provide a mechanistic understanding to the intriguing experimental evidence that PAM distal mismatches hamper a proper function of HNH, explaining also why mismatches within the heteroduplex are much more tolerated. This constitutes a step forward in understanding off-target effects in CRISPR-Cas9, which encourages novel structure-based engineering efforts aimed at preventing the onset of off-target effects.
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Affiliation(s)
- Brandon P. Mitchell
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Rohaine V. Hsu
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Marco A. Medrano
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Nehemiah T. Zewde
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Yogesh B. Narkhede
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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55
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Swartjes T, Staals RH, van der Oost J. Editor's cut: DNA cleavage by CRISPR RNA-guided nucleases Cas9 and Cas12a. Biochem Soc Trans 2020; 48:207-219. [PMID: 31872209 PMCID: PMC7054755 DOI: 10.1042/bst20190563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022]
Abstract
Discovered as an adaptive immune system of prokaryotes, CRISPR-Cas provides many promising applications. DNA-cleaving Cas enzymes like Cas9 and Cas12a, are of great interest for genome editing. The specificity of these DNA nucleases is determined by RNA guides, providing great targeting adaptability. Besides this general method of programmable DNA cleavage, these nucleases have different biochemical characteristics, that can be exploited for different applications. Although Cas nucleases are highly promising, some room for improvement remains. New developments and discoveries like base editing, prime editing, and CRISPR-associated transposons might address some of these challenges.
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Affiliation(s)
- Thomas Swartjes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Raymond H.J. Staals
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
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56
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López Del Amo V, Bishop AL, Sánchez C HM, Bennett JB, Feng X, Marshall JM, Bier E, Gantz VM. A transcomplementing gene drive provides a flexible platform for laboratory investigation and potential field deployment. Nat Commun 2020; 11:352. [PMID: 31953404 PMCID: PMC6969112 DOI: 10.1038/s41467-019-13977-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
CRISPR-based gene drives can spread through wild populations by biasing their own transmission above the 50% value predicted by Mendelian inheritance. These technologies offer population-engineering solutions for combating vector-borne diseases, managing crop pests, and supporting ecosystem conservation efforts. Current technologies raise safety concerns for unintended gene propagation. Herein, we address such concerns by splitting the drive components, Cas9 and gRNAs, into separate alleles to form a trans-complementing split-gene-drive (tGD) and demonstrate its ability to promote super-Mendelian inheritance of the separate transgenes. This dual-component configuration allows for combinatorial transgene optimization and increases safety by restricting escape concerns to experimentation windows. We employ the tGD and a small-molecule-controlled version to investigate the biology of component inheritance and resistant allele formation, and to study the effects of maternal inheritance and impaired homology on efficiency. Lastly, mathematical modeling of tGD spread within populations reveals potential advantages for improving current gene-drive technologies for field population modification.
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Affiliation(s)
- Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Héctor M Sánchez C
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720, USA
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0349, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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57
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Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y. Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States. Mol Cell 2019; 76:938-952.e5. [PMID: 31668930 PMCID: PMC6934045 DOI: 10.1016/j.molcel.2019.09.025] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 08/13/2019] [Accepted: 09/20/2019] [Indexed: 12/21/2022]
Abstract
High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of meningococcal Cas9 homologs in complex with sgRNA, dsDNA, or the AcrIIC3 anti-CRISPR protein. DNA-bound structures represent an early step of target recognition, a later HNH pre-catalytic state, the HNH catalytic state, and a cleaved-target-DNA-bound state. In the HNH catalytic state of Nme1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, providing a high-resolution view of the active conformation. The HNH active conformation activates the RuvC domain. Our structures explain how Nme1Cas9 and Nme2Cas9 read distinct PAM sequences and how AcrIIC3 inhibits Nme1Cas9 activity. These structures provide insights into Cas9 domain rearrangements, guide-target engagement, cleavage mechanism, and anti-CRISPR inhibition, facilitating the optimization of these genome-editing platforms.
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Affiliation(s)
- Wei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Zhi Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Chao Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kangkang Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Raed Ibraheim
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Xue Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Min Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiuyu Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Sheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Yang
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China.
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58
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Whinn KS, van Oijen AM, Ghodke H. Spy-ing on Cas9: Single-molecule tools reveal the enzymology of Cas9. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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59
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Zhang Q, Wen F, Zhang S, Jin J, Bi L, Lu Y, Li M, Xi XG, Huang X, Shen B, Sun B. The post-PAM interaction of RNA-guided spCas9 with DNA dictates its target binding and dissociation. SCIENCE ADVANCES 2019; 5:eaaw9807. [PMID: 31763447 PMCID: PMC6853773 DOI: 10.1126/sciadv.aaw9807] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/17/2019] [Indexed: 05/19/2023]
Abstract
Cas9 is an RNA-guided endonuclease that targets complementary DNA for cleavage and has been repurposed for many biological usages. Cas9 activities are governed by its direct interactions with DNA. However, information about this interplay and the mechanism involved in its direction of Cas9 activity remain obscure. Using a single-molecule approach, we probed Cas9/sgRNA/DNA interactions along the DNA sequence and found two stable interactions flanking the protospacer adjacent motif (PAM). Unexpectedly, one of them is located approximately 14 base pairs downstream of the PAM (post-PAM interaction), which is beyond the apparent footprint of Cas9 on DNA. Loss or occupation of this interaction site on DNA impairs Cas9 binding and cleavage. Consistently, a downstream helicase could readily displace DNA-bound Cas9 by disrupting this relatively weak post-PAM interaction. Our work identifies a critical interaction of Cas9 with DNA that dictates its binding and dissociation, which may suggest distinct strategies to modulate Cas9 activity.
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Affiliation(s)
- Qian Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fengcai Wen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiachuan Jin
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ying Lu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ming Li
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xu-Guang Xi
- LBPA, IDA, ENS de Cachan, CNRS, Université Paris-Saclay, Cachan F-94235, France
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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60
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Cas9 Allosteric Inhibition by the Anti-CRISPR Protein AcrIIA6. Mol Cell 2019; 76:922-937.e7. [PMID: 31604602 DOI: 10.1016/j.molcel.2019.09.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/02/2019] [Accepted: 09/06/2019] [Indexed: 12/26/2022]
Abstract
In the arms race against bacteria, bacteriophages have evolved diverse anti-CRISPR proteins (Acrs) that block CRISPR-Cas immunity. Acrs play key roles in the molecular coevolution of bacteria with their predators, use a variety of mechanisms of action, and provide tools to regulate Cas-based genome manipulation. Here, we present structural and functional analyses of AcrIIA6, an Acr from virulent phages, exploring its unique anti-CRISPR action. Our cryo-EM structures and functional data of AcrIIA6 binding to Streptococcus thermophilus Cas9 (St1Cas9) show that AcrIIA6 acts as an allosteric inhibitor and induces St1Cas9 dimerization. AcrIIA6 reduces St1Cas9 binding affinity for DNA and prevents DNA binding within cells. The PAM and AcrIIA6 recognition sites are structurally close and allosterically linked. Mechanistically, AcrIIA6 affects the St1Cas9 conformational dynamics associated with PAM binding. Finally, we identify a natural St1Cas9 variant resistant to AcrIIA6 illustrating Acr-driven mutational escape and molecular diversification of Cas9 proteins.
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61
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Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing. Proc Natl Acad Sci U S A 2019; 116:20959-20968. [PMID: 31570623 DOI: 10.1073/pnas.1818461116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off-targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target single-guide RNA (sgRNA) are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher homology-directed repair rates, and very low nonspecific genome editing compared to SpCas9. We demonstrate FnCas9-mediated correction of the sickle cell mutation in patient-derived induced pluripotent stem cells and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.
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62
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Dasgupta B, Miyashita O, Tama F. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images. Biochim Biophys Acta Gen Subj 2019; 1864:129420. [PMID: 31472175 DOI: 10.1016/j.bbagen.2019.129420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Atomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial. METHOD We aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image. RESULTS The algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations. CONCLUSIONS The proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail. GENERAL SIGNIFICANCE High-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.
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Affiliation(s)
- Bhaskar Dasgupta
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Osamu Miyashita
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Florence Tama
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan; Department of Physics, Graduate School of Science, Nagoya University, Aichi, 464-8602, Japan; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, 464-8601, Japan.
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63
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Zuo Z, Zolekar A, Babu K, Lin VJT, Hayatshahi HS, Rajan R, Wang YC, Liu J. Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain. eLife 2019; 8:e46500. [PMID: 31361218 PMCID: PMC6706240 DOI: 10.7554/elife.46500] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/21/2019] [Indexed: 12/21/2022] Open
Abstract
The CRISPR-associated endonuclease Cas9 from Streptococcus pyogenes (SpyCas9), along with a programmable single-guide RNA (sgRNA), has been exploited as a significant genome-editing tool. Despite the recent advances in determining the SpyCas9 structures and DNA cleavage mechanism, the cleavage-competent conformation of the catalytic HNH nuclease domain of SpyCas9 remains largely elusive and debatable. By integrating computational and experimental approaches, we unveiled and validated the activated Cas9-sgRNA-DNA ternary complex in which the HNH domain is neatly poised for cleaving the target DNA strand. In this catalysis model, the HNH employs the catalytic triad of D839-H840-N863 for cleavage catalysis, rather than previously implicated D839-H840-D861, D837-D839-H840, or D839-H840-D861-N863. Our study contributes critical information to defining the catalytic conformation of the HNH domain and advances the knowledge about the conformational activation underlying Cas9-mediated DNA cleavage.
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Affiliation(s)
- Zhicheng Zuo
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
- College of Chemistry and Chemical EngineeringShanghai University of Engineering ScienceShanghaiChina
| | - Ashwini Zolekar
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research CenterUniversity of OklahomaNormanUnited States
| | - Victor JT Lin
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Hamed S Hayatshahi
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research CenterUniversity of OklahomaNormanUnited States
| | - Yu-Chieh Wang
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
| | - Jin Liu
- Department of Pharmaceutical SciencesUNT System College of Pharmacy, University of North Texas Health Science CenterFort WorthUnited States
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Kim D, Luk K, Wolfe SA, Kim JS. Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases. Annu Rev Biochem 2019; 88:191-220. [PMID: 30883196 DOI: 10.1146/annurev-biochem-013118-111730] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Programmable nucleases and deaminases, which include zinc-finger nucleases, transcription activator-like effector nucleases, CRISPR RNA-guided nucleases, and RNA-guided base editors, are now widely employed for the targeted modification of genomes in cells and organisms. These gene-editing tools hold tremendous promise for therapeutic applications. Importantly, these nucleases and deaminases may display off-target activity through the recognition of near-cognate DNA sequences to their target sites, resulting in collateral damage to the genome in the form of local mutagenesis or genomic rearrangements. For therapeutic genome-editing applications with these classes of programmable enzymes, it is essential to measure and limit genome-wide off-target activity. Herein, we discuss the key determinants of off-target activity for these systems. We describe various cell-based and cell-free methods for identifying genome-wide off-target sites and diverse strategies that have been developed for reducing the off-target activity of programmable gene-editing enzymes.
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Affiliation(s)
- Daesik Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea;
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Republic of Korea;
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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65
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Huston NC, Tycko J, Tillotson EL, Wilson CJ, Myer VE, Jayaram H, Steinberg BE. Identification of Guide-Intrinsic Determinants of Cas9 Specificity. CRISPR J 2019; 2:172-185. [PMID: 31225747 PMCID: PMC6694761 DOI: 10.1089/crispr.2019.0009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Considerable effort has been devoted to developing a comprehensive understanding of CRISPR nuclease specificity. In silico predictions and multiple genome-wide cellular and biochemical approaches have revealed a basic understanding of the Cas9 specificity profile. However, none of these approaches has delivered a model that allows accurate prediction of a CRISPR nuclease's ability to cleave a site based entirely on the sequence of the guide RNA (gRNA) and the target. We describe a library-based biochemical assay that directly reports the cleavage efficiency of a particular Cas9-guide complex by measuring both uncleaved and cleaved target molecules over a wide range of mismatched library members. We applied our assay using libraries of targets to evaluate the specificity of Staphylococcus aureus Cas9 under a variety of experimental conditions. Surprisingly, our data show an unexpectedly high variation in the random gRNA:target DNA mismatch tolerance when cleaving with different gRNAs, indicating guide-intrinsic mismatch permissiveness and challenging the assumption of universal specificity models. We use data generated by our assay to create the first off-target, guide-specific cleavage models. The barcoded libraries of targets approach is rapid, highly modular, and capable of generating protein- and guide-specific models, as well as illuminating the biophysics of Cas9 binding versus cutting. These models may be useful in identifying potential off-targets, and the gRNA-intrinsic nature of mismatch tolerance argues for coupling these specificity models with orthogonal methods for a more complete assessment of gRNA specificity.
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Affiliation(s)
| | - Josh Tycko
- Editas Medicine, Cambridge, Massaschusetts
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66
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Ricci C, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS CENTRAL SCIENCE 2019; 5:651-662. [PMID: 31041385 PMCID: PMC6487449 DOI: 10.1021/acscentsci.9b00020] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Indexed: 05/02/2023]
Abstract
CRISPR-Cas9 is the state-of-the-art technology for editing and manipulating nucleic acids. However, the occurrence of off-target mutations can limit its applicability. Here, all-atom enhanced molecular dynamics (MD) simulations-using Gaussian accelerated MD (GaMD)-are used to decipher the mechanism of off-target binding at the molecular level. GaMD reveals that base pair mismatches in the target DNA at distal sites with respect to the protospacer adjacent motif (PAM) can induce an extended opening of the RNA:DNA heteroduplex, which leads to newly formed interactions between the unwound DNA and the L2 loop of the catalytic HNH domain. These conserved interactions constitute a "lock" effectively decreasing the conformational freedom of the HNH domain and hampering its activation for cleavage. Remarkably, depending on their positions at PAM distal sites, DNA mismatches responsible for off-target cleavages are unable to "lock" the HNH domain, thereby leading to the unselective cleavage of DNA sequences. In consistency with the available experimental data, the ability to "lock" the catalytic HNH domain in an inactive "conformational checkpoint" is shown to be a key determinant in the onset of off-target effects. This mechanistic rationale contributes in clarifying a long lasting open issue in the CRISPR-Cas9 function and poses the foundation for designing novel and more specific Cas9 variants, which could be obtained by magnifying the "locking" interactions between HNH and the target DNA in the presence of any incorrect off-target sequence, thus preventing undesired cleavages.
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Affiliation(s)
- Clarisse
G. Ricci
- Department
of Pharmacology, Department of Chemistry and Biochemistry, and National Biomedical
Computation Resource, University of California
San Diego, La Jolla, California 92093, United States
| | - Janice S. Chen
- Department of Molecular
and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, Innovative Genomics
Institute, and Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, University
of California Berkeley, Berkeley, California 94720, United States
| | - Yinglong Miao
- Center
for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Martin Jinek
- Department
of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jennifer A. Doudna
- Department of Molecular
and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, Innovative Genomics
Institute, and Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, University
of California Berkeley, Berkeley, California 94720, United States
| | - J. Andrew McCammon
- Department
of Pharmacology, Department of Chemistry and Biochemistry, and National Biomedical
Computation Resource, University of California
San Diego, La Jolla, California 92093, United States
| | - Giulia Palermo
- Department
of Bioengineering, Bourns College of Engineering, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
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67
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Babu K, Amrani N, Jiang W, Yogesha S, Nguyen R, Qin PZ, Rajan R. Bridge Helix of Cas9 Modulates Target DNA Cleavage and Mismatch Tolerance. Biochemistry 2019; 58:1905-1917. [PMID: 30916546 PMCID: PMC6496953 DOI: 10.1021/acs.biochem.8b01241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems are RNA-guided nucleases that provide adaptive immune protection for bacteria and archaea against intruding genomic materials. The programmable nature of CRISPR-targeting mechanisms has enabled their adaptation as powerful genome engineering tools. Cas9, a type II CRISPR effector protein, has been widely used for gene-editing applications owing to the fact that a single-guide RNA can direct Cas9 to cleave desired genomic targets. An understanding of the role of different domains of the protein and guide RNA-induced conformational changes of Cas9 in selecting target DNA has been and continues to enable development of Cas9 variants with reduced off-targeting effects. It has been previously established that an arginine-rich bridge helix (BH) present in Cas9 is critical for its activity. In the present study, we show that two proline substitutions within a loop region of the BH of Streptococcus pyogenes Cas9 impair the DNA cleavage activity by accumulating nicked products and reducing target DNA linearization. This in turn imparts a higher selectivity in DNA targeting. We discuss the probable mechanisms by which the BH-loop contributes to target DNA recognition.
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Affiliation(s)
- Kesavan Babu
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Sherman Center, AS5.2007, Worcester MA 01605, USA
| | - Wei Jiang
- Department of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, CA, 90089, USA
| | - S.D. Yogesha
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
- Current Address: Krystal Biotech, Inc. 2100 Wharton Street, Suite 701 Pittsburgh, PA, 15203, USA
| | - Richard Nguyen
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
- Current Address: College of Medicine, University of Oklahoma, Stanton L Young Blvd, Oklahoma City, OK 73117
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, 3430 S. Vermont Ave., Los Angeles, CA, 90089, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
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68
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Croop B, Zhang C, Lim Y, Gelfand RM, Han KY. Recent advancement of light-based single-molecule approaches for studying biomolecules. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1445. [PMID: 30724484 DOI: 10.1002/wsbm.1445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/01/2018] [Accepted: 01/08/2019] [Indexed: 12/27/2022]
Abstract
Recent advances in single-molecule techniques have led to new discoveries in analytical chemistry, biophysics, and medicine. Understanding the structure and behavior of single biomolecules provides a wealth of information compared to studying large ensembles. However, developing single-molecule techniques is challenging and requires advances in optics, engineering, biology, and chemistry. In this paper, we will review the state of the art in single-molecule applications with a focus over the last few years of development. The advancements covered will mainly include light-based in vitro methods, and we will discuss the fundamentals of each with a focus on the platforms themselves. We will also summarize their limitations and current and future applications to the wider biological and chemical fields. This article is categorized under: Laboratory Methods and Technologies > Imaging Laboratory Methods and Technologies > Macromolecular Interactions, Methods Analytical and Computational Methods > Analytical Methods.
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Affiliation(s)
- Benjamin Croop
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Chenyi Zhang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Youngbin Lim
- Department of Bioengineering, Stanford University, Stanford, California
| | - Ryan M Gelfand
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
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69
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Yoon H, Zhao LN, Warshel A. Exploring the Catalytic Mechanism of Cas9 Using Information Inferred from Endonuclease VII. ACS Catal 2019; 9:1329-1336. [PMID: 34046245 PMCID: PMC8153514 DOI: 10.1021/acscatal.8b04324] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidating the nature of the gene editing mechanism of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is an important task in view of the role of this breakthrough to the advancement of human medicine. In particular, it is crucial to understand the catalytic mechanism of Cas9 (one of the CRISPR associated proteins) and its role in confirming accurate editing. Thus, we focus in this work on an attempt to analyze the catalytic mechanism of Cas9. Considering the absence of detailed structural information on the active form of Cas9, we use an empirical valence bond (EVB) which is calibrated on the closely related mechanism of T4 endonuclease VII. The calibrated EVB is then used in studying the reaction of Cas9, while trying several structural models. It is found that the catalytic activation requires a large conformational change, where K848 or other positively charged group moves from a relatively large distance toward the scissile phosphate. This conformational change leads to the change in position of the Mg2+ ion and to a major reduction in the activation barrier for the catalytic reaction. Our finding provides an important clue on the nature of the catalytic activation of CAS9 and thus should help in elucidating a key aspect of the gene editing process. For example, the approach used here should be effective in exploring the nature of off target activation and its relationship to the energetics of the unwinding process. This strategy may offer ways to improve the selectivity of Cas9.
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Affiliation(s)
- Hanwool Yoon
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| | - Li Na Zhao
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Ave, Los Angeles, California 90089-1062, United States
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70
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Wilkinson RA, Martin C, Nemudryi AA, Wiedenheft B. CRISPR RNA-guided autonomous delivery of Cas9. Nat Struct Mol Biol 2019; 26:14-24. [PMID: 30598555 PMCID: PMC7703833 DOI: 10.1038/s41594-018-0173-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/13/2018] [Indexed: 02/06/2023]
Abstract
Cas9 is an endonuclease that can be programed to autonomously deliver diverse effectors to specified genetic addresses. High-resolution structures of this protein and its associated CRISPR RNA guide explain the molecular mechanisms of CRISPR-RNA-guided DNA recognition and provide a molecular blueprint that has facilitated structure-guided functional remodeling. Here we retrace events that led from early efforts to understand the central role of Cas9 in CRISPR-mediated adaptive immunity to contemporary efforts aimed at developing and deploying this enzyme for programmable genetic editing.
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Affiliation(s)
- Royce A Wilkinson
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Coleman Martin
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Artem A Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA.
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71
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Abstract
Though making up nearly half of the known CRISPR-Cas9 family of enzymes, the Type II-C CRISPR-Cas9 has been underexplored for their molecular mechanisms and potential in safe gene editing applications. In comparison with the more popular Type II-A CRISPR-Cas9, the Type II-C enzymes are generally smaller in size and utilize longer base pairing in identification of their DNA substrates. These characteristics suggest easier portability and potentially less off-targets for Type II-C in gene editing applications. We describe identification and biochemical characterization of a thermophilic Type II-C CRISPR-Cas from Acidothermus cellulolyticus (AceCas9). We describe several library-based methods that enabled us to identify the PAM sequence and elements critical to protospacer mismatch surveillance of AceCas9.
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72
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Abstract
Fluorescent labeling of proteins is a critical requirement for single-molecule imaging studies. Many protein labeling strategies require harsh conditions or large epitopes that can inactivate the target protein, either by decreasing the protein's enzymatic activity or by blocking protein-protein interactions. Here, we provide a detailed protocol to efficiently label CRISPR-Cas complexes with a small fluorescent peptide via sortase-mediated transpeptidation. The sortase tag consists of just a few amino acids that are specifically recognized at either the N- or the C-terminus, making this strategy advantageous when the protein is part of a larger complex. Sortase is active at high ionic strength, 4°C, and with a broad range of organic fluorophores. We discuss the design, optimization, and single-molecule fluorescent imaging of CRISPR-Cas complexes on DNA curtains. Sortase-mediated transpeptidation is a versatile addition to the protein labeling toolkit.
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73
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Stella S, Mesa P, Thomsen J, Paul B, Alcón P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G. Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity. Cell 2018; 175:1856-1871.e21. [PMID: 30503205 DOI: 10.1016/j.cell.2018.10.045] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/27/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
Cas12a, also known as Cpf1, is a type V-A CRISPR-Cas RNA-guided endonuclease that is used for genome editing based on its ability to generate specific dsDNA breaks. Here, we show cryo-EM structures of intermediates of the cleavage reaction, thus visualizing three protein regions that sense the crRNA-DNA hybrid assembly triggering the catalytic activation of Cas12a. Single-molecule FRET provides the thermodynamics and kinetics of the conformational activation leading to phosphodiester bond hydrolysis. These findings illustrate why Cas12a cuts its target DNA and unleashes unspecific cleavage activity, degrading ssDNA molecules after activation. In addition, we show that other crRNAs are able to displace the R-loop inside the protein after target DNA cleavage, terminating indiscriminate ssDNA degradation. We propose a model whereby the conformational activation of the enzyme results in indiscriminate ssDNA cleavage. The displacement of the R-loop by a new crRNA molecule will reset Cas12a specificity, targeting new DNAs.
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Affiliation(s)
- Stefano Stella
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pablo Mesa
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pablo Alcón
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Simon B Jensen
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Bhargav Saligram
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Matias E Moses
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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74
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Wang L, Mo CY, Wasserman MR, Rostøl JT, Marraffini LA, Liu S. Dynamics of Cas10 Govern Discrimination between Self and Non-self in Type III CRISPR-Cas Immunity. Mol Cell 2018; 73:278-290.e4. [PMID: 30503774 DOI: 10.1016/j.molcel.2018.11.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/11/2018] [Accepted: 11/05/2018] [Indexed: 12/26/2022]
Abstract
Adaptive immune systems must accurately distinguish between self and non-self in order to defend against invading pathogens while avoiding autoimmunity. Type III CRISPR-Cas systems employ guide RNA to recognize complementary RNA targets, which triggers the degradation of both the invader's transcripts and their template DNA. These systems can broadly eliminate foreign targets with multiple mutations but circumvent damage to the host genome. To explore the molecular basis for these features, we use single-molecule fluorescence microscopy to study the interaction between a type III-A ribonucleoprotein complex and various RNA substrates. We find that Cas10-the DNase effector of the complex-displays rapid conformational fluctuations on foreign RNA targets, but is locked in a static configuration on self RNA. Target mutations differentially modulate Cas10 dynamics and tune the CRISPR interference activity in vivo. These findings highlight the central role of the internal dynamics of CRISPR-Cas complexes in self versus non-self discrimination and target specificity.
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Affiliation(s)
- Ling Wang
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Charlie Y Mo
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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75
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Raper AT, Stephenson AA, Suo Z. Sharpening the Scissors: Mechanistic Details of CRISPR/Cas9 Improve Functional Understanding and Inspire Future Research. J Am Chem Soc 2018; 140:11142-11152. [PMID: 30160947 DOI: 10.1021/jacs.8b05469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interest in CRISPR/Cas9 remains high level as new applications of the revolutionary gene-editing tool continue to emerge. While key structural and biochemical findings have illuminated major steps in the enzymatic mechanism of Cas9, several important details remain unidentified or poorly characterized that may contribute to known functional limitations. Here we describe the foundation of research that has led to a fundamental understanding of Cas9 and address mechanistic uncertainties that restrict continued development of this gene-editing platform, including specificity for the protospacer adjacent motif, propensity for off-target binding and cleavage, as well as interactions with cellular components during gene editing. Discussion of these topics and considerations should inspire future research to hone this remarkable technology and advance CRISPR/Cas9 to new heights.
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Affiliation(s)
- Austin T Raper
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Anthony A Stephenson
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Zucai Suo
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States.,The James Comprehensive Cancer Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Department of Biomedical Sciences , College of Medicine, Florida State University , Tallahassee , Florida 32306 , United States
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76
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SUN LL, SU YY, GAO YJ, Li W, LYU H, LI B, LI D. Progresses of Single Molecular Fluorescence Resonance Energy Transfer in Studying Biomacromolecule Dynamic Process. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61088-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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77
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Osuka S, Isomura K, Kajimoto S, Komori T, Nishimasu H, Shima T, Nureki O, Uemura S. Real-time observation of flexible domain movements in CRISPR-Cas9. EMBO J 2018; 37:embj.201796941. [PMID: 29650679 PMCID: PMC5978321 DOI: 10.15252/embj.201796941] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 02/07/2018] [Accepted: 02/14/2018] [Indexed: 12/24/2022] Open
Abstract
The CRISPR‐associated protein Cas9 is widely used for genome editing because it cleaves target DNA through the assistance of a single‐guide RNA (sgRNA). Structural studies have revealed the multi‐domain architecture of Cas9 and suggested sequential domain movements of Cas9 upon binding to the sgRNA and the target DNA. These studies also hinted at the flexibility between domains; however, it remains unclear whether these flexible movements occur in solution. Here, we directly observed dynamic fluctuations of multiple Cas9 domains, using single‐molecule FRET. We found that the flexible domain movements allow Cas9 to adopt transient conformations beyond those captured in the crystal structures. Importantly, the HNH nuclease domain only accessed the DNA cleavage position during such flexible movements, suggesting the importance of this flexibility in the DNA cleavage process. Our FRET data also revealed the conformational flexibility of apo‐Cas9, which may play a role in the assembly with the sgRNA. Collectively, our results highlight the potential role of domain fluctuations in driving Cas9‐catalyzed DNA cleavage.
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Affiliation(s)
- Saki Osuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazushi Isomura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shohei Kajimoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomotaka Komori
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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78
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Abstract
The bacterial CRISPR-Cas9 immune system has been harnessed as a powerful and versatile genome-editing tool and holds immense promise for future therapeutic applications. Despite recent advances in understanding Cas9 structures and its functional mechanism, little is known about the catalytic state of the Cas9 HNH nuclease domain, and identifying how the divalent metal ions affect the HNH domain conformational transition remains elusive. A deeper understanding of Cas9 activation and its cleavage mechanism can enable further optimization of Cas9-based genome-editing specificity and efficiency. Using two distinct molecular dynamics simulation techniques, we have obtained a cross-validated catalytically active state of Cas9 HNH domain primed for cutting the target DNA strand. Moreover, herein we demonstrate the essential roles of the catalytic Mg2+ for the active state formation and stability. Importantly, we suggest that the derived catalytic conformation of the HNH domain can be exploited for rational engineering of Cas9 variants with enhanced specificity.
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