551
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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552
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Wei W, Zhang S, Fleming J, Chen Y, Li Z, Fan S, Liu Y, Wang W, Wang T, Liu Y, Ren B, Wang M, Jiao J, Chen Y, Zhou Y, Zhou Y, Gu S, Zhang X, Wan L, Chen T, Zhou L, Chen Y, Zhang XE, Li C, Zhang H, Bi L. Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features. FASEB J 2018; 33:1496-1509. [PMID: 29979631 DOI: 10.1096/fj.201800557rr] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems are prokaryotic adaptive immune systems against invading nucleic acids. CRISPR locus variability has been exploited in evolutionary and epidemiological studies of Mycobacterium tuberculosis, the causative agent of tuberculosis, for over 20 yr, yet the biological function of this type III-A system is largely unexplored. Here, using cell biology and biochemical, mutagenic, and RNA-seq approaches, we show it is active in invader defense and has features atypical of type III-A systems: mature CRISPR RNA (crRNA) in its crRNA-CRISPR/Cas protein complex are of uniform length (∼71 nt) and appear not to be subject to 3'-end processing after Cas6 cleavage of repeat RNA 8 nt from its 3' end. crRNAs generated resemble mature crRNA in type I systems, having both 5' (8 nt) and 3' (28 nt) repeat tags. Cas6 cleavage of repeat RNA is ion dependent, and accurate cleavage depends on the presence of a 3' hairpin in the repeat RNA and the sequence of its stem base nucleotides. This study unveils further diversity among CRISPR/Cas systems and provides insight into the crRNA recognition mechanism in M. tuberculosis, providing a foundation for investigating the potential of a type III-A-based genome editing system.-Wei, W., Zhang, S., Fleming, J., Chen, Y., Li, Z., Fan, S., Liu, Y., Wang, W., Wang, T., Liu, Y., Ren, B., Wang, M., Jiao, J., Chen, Y., Zhou, Y., Zhou, Y., Gu, S., Zhang, X., Wan, L., Chen, T., Zhou, L., Chen, Y., Zhang, X.-E., Li, C., Zhang, H., Bi, L. Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features.
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Affiliation(s)
- Wenjing Wei
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Ying Chen
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zihui Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Shanghua Fan
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yi Liu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Wei Wang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ting Wang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Baiguang Ren
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ming Wang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianjian Jiao
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Chen
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Yafeng Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Shoujin Gu
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
| | - Xiaoli Zhang
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Li Wan
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tao Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China; and
| | - Lin Zhou
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China; and
| | - Yong Chen
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Xian-En Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Chuanyou Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongtai Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lijun Bi
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China.,Guangdong Province Key Laboratory of Tuberculosis Systems Biology and Translational Medicine, Foshan, China
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553
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Zhu Y, Klompe SE, Vlot M, van der Oost J, Staals RHJ. Shooting the messenger: RNA-targetting CRISPR-Cas systems. Biosci Rep 2018; 38:BSR20170788. [PMID: 29748239 PMCID: PMC6013697 DOI: 10.1042/bsr20170788] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 12/26/2022] Open
Abstract
Since the discovery of CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associated genes) immune systems, astonishing progress has been made on revealing their mechanistic foundations. Due to the immense potential as genome engineering tools, research has mainly focussed on a subset of Cas nucleases that target DNA. In addition, however, distinct types of RNA-targetting CRISPR-Cas systems have been identified. The focus of this review will be on the interference mechanisms of the RNA targetting type III and type VI CRISPR-Cas systems, their biological relevance and their potential for applications.
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Affiliation(s)
- Yifan Zhu
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - Sanne E Klompe
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
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554
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He Y, Wang M, Liu M, Huang L, Liu C, Zhang X, Yi H, Cheng A, Zhu D, Yang Q, Wu Y, Zhao X, Chen S, Jia R, Zhang S, Liu Y, Yu Y, Zhang L. Cas1 and Cas2 From the Type II-C CRISPR-Cas System of Riemerella anatipestifer Are Required for Spacer Acquisition. Front Cell Infect Microbiol 2018; 8:195. [PMID: 29951376 PMCID: PMC6008519 DOI: 10.3389/fcimb.2018.00195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/24/2018] [Indexed: 12/22/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins provide acquired genetic immunity against the entry of mobile genetic elements (MGEs). The immune defense provided by various subtypes of the CRISPR-Cas system has been confirmed and is closely associated with the formation of immunological memory in CRISPR arrays, called CRISPR adaptation or spacer acquisition. However, whether type II-C CRISPR-Cas systems are also involved in spacer acquisition remains largely unknown. This study explores and provides some definitive evidence regarding spacer acquisition of the type II-C CRISPR-Cas system from Riemerella anatipestifer (RA) CH-2 (RA-CH-2). Firstly, introducing an exogenous plasmid into RA-CH-2 triggered spacer acquisition of RA CRISPR-Cas system, and the acquisition of new spacers led to plasmid instability in RA-CH-2. Furthermore, deletion of cas1 or cas2 of RA-CH-2 abrogated spacer acquisition and subsequently stabilized the exogenous plasmid, suggesting that both Cas1 and Cas2 are required for spacer acquisition of RA-CH-2 CRISPR-Cas system, consistent with the reported role of Cas1 and Cas2 in type I-E and II-A systems. Finally, assays for studying Cas1 nuclease activity and the interaction of Cas1 with Cas2 contributed to a better understanding of the adaptation mechanism of RA CRISPR-Cas system. This is the first experimental identification of the naïve adaptation of type II-C CRISPR-Cas system.
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Affiliation(s)
- Yang He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Chaoyue Liu
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Department of Microbiology and Immunology, North Sichuan Medical College, Nanchong, China
| | - Xin Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Haibo Yi
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Diseases and Human Health of Sichuan Province, Chengdu, China.,Avian Diseases Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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555
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Wolter F, Puchta H. The CRISPR/Cas revolution reaches the RNA world: Cas13, a new Swiss Army knife for plant biologists. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:767-775. [PMID: 29575326 DOI: 10.1111/tpj.13899] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/27/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
Application of the bacterial CRISPR/Cas systems to eukaryotes is revolutionizing biology. Cas9 and Cas12 (previously called Cpf1) are widely used as DNA nucleases for inducing site-specific DNA breaks for different kinds of genome engineering applications, and in their mutated forms as DNA-binding proteins to modify gene expression. Moreover, histone modifications, as well as cytosine methylation or base editing, were achieved with these systems in plants. Recently, with the discovery of the nuclease Cas13a (previously called C2c2), molecular biologists have obtained a system that enables sequence-specific cleavage of single-stranded RNA molecules. The latest experiments with this and also the alternative Cas13b system demonstrate that these proteins can be used in a similar manner in eukaryotes for RNA manipulation as Cas9 and Cas12 for DNA manipulations. The first application of Cas13a for post-transcriptional regulation of gene expression in plants has been reported. Recent results show that the system is also applicable for combating viral infection in plants. As single-stranded RNA viruses are by far the most abundant class of viruses in plants, the application of this system is of special promise for crops. More interesting applications are imminent for plant biologists, with nuclease dead versions of Cas13 enabling the ability to visualize RNA molecules in vivo, as well as to edit different kinds of RNA molecules at specific bases by deamination or to modify them by conjugation. Moreover, by combining DNA- and RNA-directed systems, the most complex of changes in plant metabolism might be achievable.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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556
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Chakraborty S. Inconclusive studies on possible CRISPR-Cas off-targets should moderate expectations about enzymes that have evolved to be non-specific. J Biosci 2018; 43:225-228. [PMID: 29872009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Sandeep Chakraborty
- R-44/1, Celia Engineers, T. T. C Industrial Area, Rabale, Navi Mumbai 400701, India,
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557
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Singh D, Mallon J, Poddar A, Wang Y, Tippana R, Yang O, Bailey S, Ha T. Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a). Proc Natl Acad Sci U S A 2018; 115:5444-5449. [PMID: 29735714 PMCID: PMC6003496 DOI: 10.1073/pnas.1718686115] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas9, which imparts adaptive immunity against foreign genomic invaders in certain prokaryotes, has been repurposed for genome-engineering applications. More recently, another RNA-guided CRISPR endonuclease called Cpf1 (also known as Cas12a) was identified and is also being repurposed. Little is known about the kinetics and mechanism of Cpf1 DNA interaction and how sequence mismatches between the DNA target and guide-RNA influence this interaction. We used single-molecule fluorescence analysis and biochemical assays to characterize DNA interrogation, cleavage, and product release by three Cpf1 orthologs. Our Cpf1 data are consistent with the DNA interrogation mechanism proposed for Cas9. They both bind any DNA in search of protospacer-adjacent motif (PAM) sequences, verify the target sequence directionally from the PAM-proximal end, and rapidly reject any targets that lack a PAM or that are poorly matched with the guide-RNA. Unlike Cas9, which requires 9 bp for stable binding and ∼16 bp for cleavage, Cpf1 requires an ∼17-bp sequence match for both stable binding and cleavage. Unlike Cas9, which does not release the DNA cleavage products, Cpf1 rapidly releases the PAM-distal cleavage product, but not the PAM-proximal product. Solution pH, reducing conditions, and 5' guanine in guide-RNA differentially affected different Cpf1 orthologs. Our findings have important implications on Cpf1-based genome engineering and manipulation applications.
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MESH Headings
- Acidaminococcus/enzymology
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- DNA Cleavage
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Endonucleases/chemistry
- Endonucleases/genetics
- Endonucleases/metabolism
- Genome, Bacterial
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
- Digvijay Singh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - John Mallon
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Anustup Poddar
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ramreddy Tippana
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Scott Bailey
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205
- Howard Hughes Medical Institute, Baltimore, MD 21205
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558
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Swarts DC, Jinek M. Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1481. [DOI: 10.1002/wrna.1481] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Daan C. Swarts
- Department of Biochemistry; University of Zurich; Zurich Switzerland
| | - Martin Jinek
- Department of Biochemistry; University of Zurich; Zurich Switzerland
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559
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Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proc Natl Acad Sci U S A 2018; 115:E5307-E5316. [PMID: 29784811 DOI: 10.1073/pnas.1803440115] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity consist of direct repeat arrays separated by unique spacers and multiple CRISPR-associated (cas) genes encoding proteins that mediate all stages of the CRISPR response. In addition to the relatively small set of core cas genes that are typically present in all CRISPR-Cas systems of a given (sub)type and are essential for the defense function, numerous genes occur in CRISPR-cas loci only sporadically. Some of these have been shown to perform various ancillary roles in CRISPR response, but the functional relevance of most remains unknown. We developed a computational strategy for systematically detecting genes that are likely to be functionally linked to CRISPR-Cas. The approach is based on a "CRISPRicity" metric that measures the strength of CRISPR association for all protein-coding genes from sequenced bacterial and archaeal genomes. Uncharacterized genes with CRISPRicity values comparable to those of cas genes are considered candidate CRISPR-linked genes. We describe additional criteria to predict functionally relevance for genes in the candidate set and identify 79 genes as strong candidates for functional association with CRISPR-Cas systems. A substantial majority of these CRISPR-linked genes reside in type III CRISPR-cas loci, which implies exceptional functional versatility of type III systems. Numerous candidate CRISPR-linked genes encode integral membrane proteins suggestive of tight membrane association of CRISPR-Cas systems, whereas many others encode proteins implicated in various signal transduction pathways. These predictions provide ample material for improving annotation of CRISPR-cas loci and experimental characterization of previously unsuspected aspects of CRISPR-Cas system functionality.
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560
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García-Martínez J, Maldonado RD, Guzmán NM, Mojica FJM. The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation. MICROBIAL CELL 2018; 5:262-268. [PMID: 29850463 PMCID: PMC5972030 DOI: 10.15698/mic2018.06.634] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
CRISPR-Cas represents a prokaryotic defense mechanism against invading genetic elements. Although there is a diversity of CRISPR-Cas systems, they all share similar, essential traits. In general, a CRISPR-Cas system consists of one or more groups of DNA repeats named CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), regularly separated by unique sequences referred to as spacers, and a set of functionally associated cas (CRISPR associated) genes typically located next to one of the repeat arrays. The origin of spacers is in many cases unknown but, when ascertained, they usually match foreign genetic molecules. The proteins encoded by some of the cas genes are in charge of the incorporation of new spacers upon entry of a genetic element. Other Cas proteins participate in generating CRISPR-spacer RNAs and perform the task of destroying nucleic acid molecules carrying sequences similar to the spacer. In this way, CRISPR-Cas provides protection against genetic intruders that could substantially affect the cell viability, thus acting as an adaptive immune system. However, this defensive action also hampers the acquisition of potentially beneficial, horizontally transferred genes, undermining evolution. Here we cover how the model bacterium Escherichia coli deals with CRISPR-Cas to tackle this major dilemma, evolution versus survival.
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Affiliation(s)
- Jesús García-Martínez
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain
| | - Rafael D Maldonado
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain
| | - Noemí M Guzmán
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain
| | - Francisco J M Mojica
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain.,I.M.E.M. Ramón Margalef. Universidad de Alicante, Campus de San Vicente, 03690 San Vicente del Raspeig (Alicante), Spain
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561
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Schindele P, Wolter F, Puchta H. Transforming plant biology and breeding with CRISPR/Cas9, Cas12 and Cas13. FEBS Lett 2018; 592:1954-1967. [PMID: 29710373 DOI: 10.1002/1873-3468.13073] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/09/2018] [Accepted: 04/23/2018] [Indexed: 12/26/2022]
Abstract
Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone nonhomologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change in plant genomes via homologous recombination have recently been developed. Cas9- and Cas12- mediated DNA binding is used to develop tools for many useful applications, such as transcriptional regulation or fluorescence-based imaging of specific chromosomal loci in plant genomes. Cas13 has recently been applied to degrade mRNAs and combat viral RNA replication. By the possibility to address multiple sequences with different guide RNAs and by the simultaneous use of different Cas proteins in a single cell, we should soon be able to achieve complex changes of plant metabolism in a controlled way.
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Affiliation(s)
| | - Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Germany
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562
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Mohanraju P, Van Der Oost J, Jinek M, Swarts DC. Heterologous Expression and Purification of CRISPR-Cas12a/Cpf1. Bio Protoc 2018; 8:e2842. [PMID: 34286046 DOI: 10.21769/bioprotoc.2842] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 04/17/2018] [Accepted: 04/25/2018] [Indexed: 12/27/2022] Open
Abstract
This protocol provides step by step instructions (Figure 1) for heterologous expression of Francisella novicida Cas12a (previously known as Cpf1) in Escherichia coli. It additionally includes a protocol for high-purity purification and briefly describes how activity assays can be performed. These protocols can also be used for purification of other Cas12a homologs and the purified proteins can be used for subsequent genome editing experiments. Figure 1. Timeline of activities for the heterologous expression and purification of Francisella novicida Cas12a (FnCas12a) from Escherichia coli.
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Affiliation(s)
- Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - John Van Der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daan C Swarts
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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563
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McMahon MA, Prakash TP, Cleveland DW, Bennett CF, Rahdar M. Chemically Modified Cpf1-CRISPR RNAs Mediate Efficient Genome Editing in Mammalian Cells. Mol Ther 2018; 26:1228-1240. [PMID: 29650467 PMCID: PMC5993945 DOI: 10.1016/j.ymthe.2018.02.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/27/2018] [Accepted: 02/27/2018] [Indexed: 11/17/2022] Open
Abstract
CRISPR-based gene editing is a powerful technology for engineering mammalian genomes. It holds the potential as a therapeutic, although much-needed in vivo delivery systems have yet to be established. Here, using the Cpf1-crRNA (CRISPR RNA) crystal structure as a guide, we synthesized a series of systematically truncated and chemically modified crRNAs, and identify positions that are amenable to modification while retaining gene-editing activity. Modified crRNAs were designed with the same modifications that provide protection against nucleases and enable wide distribution in vivo. We show crRNAs with chemically modified terminal nucleotides are exonuclease resistant while retaining gene-editing activity. Chemically modified or DNA-substituted nucleotides at select positions and up to 70% of the crRNA DNA specificity region are also well tolerated. In addition, gene-editing activity is maintained with phosphorothioate backbone substitutions in the crRNA DNA specificity region. Finally, we demonstrate that 42-mer synthetic crRNAs from the similar CRISPR-Cas9 system are taken up by cells, an attractive property for in vivo delivery. Our study is the first to show that chemically modified crRNAs of the CRISPR-Cpf1 system can functionally replace and mediate comparable gene editing to the natural crRNA, which holds the potential for enhancing both viral- and non-viral-mediated in vivo gene editing.
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Affiliation(s)
- Moira A McMahon
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | | | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
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564
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The best Cas scenario. Nat Med 2018; 24:528-530. [DOI: 10.1038/s41591-018-0038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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565
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Inconclusive studies on possible CRISPR-Cas off-targets should moderate expectations about enzymes that have evolved to be non-specific. J Biosci 2018. [DOI: 10.1007/s12038-018-9761-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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566
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Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA. Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein. Mol Cell 2018; 70:327-339.e5. [PMID: 29551514 PMCID: PMC5935466 DOI: 10.1016/j.molcel.2018.02.028] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/21/2022]
Abstract
Bacterial class 2 CRISPR-Cas systems utilize a single RNA-guided protein effector to mitigate viral infection. We aggregated genomic data from multiple sources and constructed an expanded database of predicted class 2 CRISPR-Cas systems. A search for novel RNA-targeting systems identified subtype VI-D, encoding dual HEPN domain-containing Cas13d effectors and putative WYL-domain-containing accessory proteins (WYL1 and WYL-b1 through WYL-b5). The median size of Cas13d proteins is 190 to 300 aa smaller than that of Cas13a-Cas13c. Despite their small size, Cas13d orthologs from Eubacterium siraeum (Es) and Ruminococcus sp. (Rsp) are active in both CRISPR RNA processing and targeting, as well as collateral RNA cleavage, with no target-flanking sequence requirements. The RspWYL1 protein stimulates RNA cleavage by both EsCas13d and RspCas13d, demonstrating a common regulatory mechanism for divergent Cas13d orthologs. The small size, minimal targeting constraints, and modular regulation of Cas13d effectors further expands the CRISPR toolkit for RNA manipulation and detection.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Proteins/chemistry
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Databases, Genetic
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Eubacterium/enzymology
- Eubacterium/genetics
- Gene Editing/methods
- Gene Expression Regulation, Bacterial
- Nucleic Acid Conformation
- Protein Domains
- Protein Structure, Secondary
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Ruminococcus/enzymology
- Ruminococcus/genetics
- Structure-Activity Relationship
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Affiliation(s)
| | | | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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567
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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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568
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Guo X, Chitale P, Sanjana NE. Target Discovery for Precision Medicine Using High-Throughput Genome Engineering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1016:123-145. [PMID: 29130157 DOI: 10.1007/978-3-319-63904-8_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past few years, programmable RNA-guided nucleases such as the CRISPR/Cas9 system have ushered in a new era of precision genome editing in diverse model systems and in human cells. Functional screens using large libraries of RNA guides can interrogate a large hypothesis space to pinpoint particular genes and genetic elements involved in fundamental biological processes and disease-relevant phenotypes. Here, we review recent high-throughput CRISPR screens (e.g. loss-of-function, gain-of-function, and targeting noncoding elements) and highlight their potential for uncovering novel therapeutic targets, such as those involved in cancer resistance to small molecular drugs and immunotherapies, tumor evolution, infectious disease, inborn genetic disorders, and other therapeutic challenges.
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Affiliation(s)
- Xinyi Guo
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Poonam Chitale
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Neville E Sanjana
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.
- Department of Biology, New York University, New York, NY, 10003, USA.
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569
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Crawley AB, Henriksen JR, Barrangou R. CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems. CRISPR J 2018; 1:171-181. [PMID: 31021201 PMCID: PMC6636876 DOI: 10.1089/crispr.2017.0022] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas adaptive immune systems of bacteria and archaea have catapulted into the scientific spotlight as genome editing tools. To aid researchers in the field, we have developed an automated pipeline, named CRISPRdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness. All six major types and 23 currently recognized subtypes and novel putative V-U types are detected. Here, we use the pipeline to identify and classify putative CRISPR-Cas systems in 2,777 complete genomes from the NCBI RefSeq database. This allows comparison to previous publications and investigation of the occurrence and size of CRISPR-Cas systems. Software available at http://github.com/crisprlab/CRISPRdisco provides reproducible, standardized, accessible, transparent, and high-throughput analysis methods available to all researchers in and beyond the CRISPR-Cas research community. This tool opens new avenues to enable classification within a complex nomenclature and provides analytical methods in a field that has evolved rapidly.
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Affiliation(s)
- Alexandra B Crawley
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
| | | | - Rodolphe Barrangou
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
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570
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Ishino Y, Krupovic M, Forterre P. History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology. J Bacteriol 2018; 200:e00580-17. [PMID: 29358495 PMCID: PMC5847661 DOI: 10.1128/jb.00580-17] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are well-known acquired immunity systems that are widespread in archaea and bacteria. The RNA-guided nucleases from CRISPR-Cas systems are currently regarded as the most reliable tools for genome editing and engineering. The first hint of their existence came in 1987, when an unusual repetitive DNA sequence, which subsequently was defined as a CRISPR, was discovered in the Escherichia coli genome during an analysis of genes involved in phosphate metabolism. Similar sequence patterns were then reported in a range of other bacteria as well as in halophilic archaea, suggesting an important role for such evolutionarily conserved clusters of repeated sequences. A critical step toward functional characterization of the CRISPR-Cas systems was the recognition of a link between CRISPRs and the associated Cas proteins, which were initially hypothesized to be involved in DNA repair in hyperthermophilic archaea. Comparative genomics, structural biology, and advanced biochemistry could then work hand in hand, not only culminating in the explosion of genome editing tools based on CRISPR-Cas9 and other class II CRISPR-Cas systems but also providing insights into the origin and evolution of this system from mobile genetic elements denoted casposons. To celebrate the 30th anniversary of the discovery of CRISPR, this minireview briefly discusses the fascinating history of CRISPR-Cas systems, from the original observation of an enigmatic sequence in E. coli to genome editing in humans.
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Affiliation(s)
- Yoshizumi Ishino
- Unité de Biologie Moléculaire du Gène Chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Mart Krupovic
- Unité de Biologie Moléculaire du Gène Chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Patrick Forterre
- Unité de Biologie Moléculaire du Gène Chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, Paris, France
- Institute of Integrative Cellular Biology, Université Paris Sud, Orsay, France
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571
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Klompe SE, Sternberg SH. Harnessing "A Billion Years of Experimentation": The Ongoing Exploration and Exploitation of CRISPR-Cas Immune Systems. CRISPR J 2018; 1:141-158. [PMID: 31021200 PMCID: PMC6636882 DOI: 10.1089/crispr.2018.0012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The famed physicist-turned-biologist, Max Delbrück, once remarked that, for physicists, "the field of bacterial viruses is a fine playground for serious children who ask ambitious questions." Early discoveries in that playground helped establish molecular genetics, and half a century later, biologists delving into the same field have ushered in the era of precision genome engineering. The focus has of course shifted-from bacterial viruses and their mechanisms of infection to the bacterial hosts and their mechanisms of immunity-but it is the very same evolutionary arms race that continues to awe and inspire researchers worldwide. In this review, we explore the remarkable diversity of CRISPR-Cas adaptive immune systems, describe the molecular components that mediate nucleic acid targeting, and outline the use of these RNA-guided machines for biotechnology applications. CRISPR-Cas research has yielded far more than just Cas9-based genome-editing tools, and the wide-reaching, innovative impacts of this fascinating biological playground are sure to be felt for years to come.
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Affiliation(s)
- Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
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572
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Zhu Y, Zhang F, Huang Z. Structural insights into the inactivation of CRISPR-Cas systems by diverse anti-CRISPR proteins. BMC Biol 2018; 16:32. [PMID: 29554913 PMCID: PMC5859409 DOI: 10.1186/s12915-018-0504-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A molecular arms race is progressively being unveiled between prokaryotes and viruses. Prokaryotes utilize CRISPR-mediated adaptive immune systems to kill the invading phages and mobile genetic elements, and in turn, the viruses evolve diverse anti-CRISPR proteins to fight back. The structures of several anti-CRISPR proteins have now been reported, and here we discuss their structural features, with a particular emphasis on topology, to discover their similarities and differences. We summarize the CRISPR-Cas inhibition mechanisms of these anti-CRISPR proteins in their structural context. Considering anti-CRISPRs in this way will provide important clues for studying their origin and evolution.
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Affiliation(s)
- Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
| | - Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
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573
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Hille F, Richter H, Wong SP, Bratovič M, Ressel S, Charpentier E. The Biology of CRISPR-Cas: Backward and Forward. Cell 2018. [DOI: 10.1016/j.cell.2017.11.032] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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574
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Casini A, Olivieri M, Petris G, Montagna C, Reginato G, Maule G, Lorenzin F, Prandi D, Romanel A, Demichelis F, Inga A, Cereseto A. A highly specific SpCas9 variant is identified by in vivo screening in yeast. Nat Biotechnol 2018; 36:265-271. [PMID: 29431739 PMCID: PMC6066108 DOI: 10.1038/nbt.4066] [Citation(s) in RCA: 312] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 12/22/2017] [Indexed: 01/01/2023]
Abstract
Despite the utility of CRISPR-Cas9 nucleases for genome editing, the potential for off-target activity limits their application, especially for therapeutic purposes. We developed a yeast-based assay to identify optimized Streptococcus pyogenes Cas9 (SpCas9) variants that enables simultaneous evaluation of on- and off-target activity. We screened a library of SpCas9 variants carrying random mutations in the REC3 domain and identified mutations that increased editing accuracy while maintaining editing efficiency. We combined four beneficial mutations to generate evoCas9, a variant that has fidelity exceeding both wild-type (79-fold improvement) and rationally designed Cas9 variants (fourfold average improvement), while maintaining near wild-type on-target editing efficiency (90% median residual activity). Evaluating evoCas9 on endogenous genomic loci, we demonstrated a substantially improved specificity and observed no off-target sites for four of the eight single guide RNAs (sgRNAs) tested. Finally, we showed that following long-term expression (40 d), evoCas9 strongly limited the nonspecific cleavage of a difficult-to-discriminate off-target site and fully abrogated the cleavage of two additional off-target sites.
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Affiliation(s)
- Antonio Casini
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Molecular Virology, Trento, Italy
| | - Michele Olivieri
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Molecular Virology, Trento, Italy
| | - Gianluca Petris
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Molecular Virology, Trento, Italy
| | - Claudia Montagna
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Molecular Virology, Trento, Italy
| | - Giordano Reginato
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Molecular Virology, Trento, Italy
| | - Giulia Maule
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Molecular Virology, Trento, Italy
| | - Francesca Lorenzin
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Computational Oncology, Trento, Italy
| | - Davide Prandi
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Computational Oncology, Trento, Italy
| | - Alessandro Romanel
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Computational Oncology, Trento, Italy
| | - Francesca Demichelis
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Computational Oncology, Trento, Italy
| | - Alberto Inga
- Centre for Integrative Biology (CIBIO), Laboratory of Transcriptional Networks, Trento, Italy
| | - Anna Cereseto
- Centre for Integrative Biology (CIBIO), University of Trento, Laboratory of Molecular Virology, Trento, Italy
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575
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Hong S, Ka D, Yoon SJ, Suh N, Jeong M, Suh JY, Bae E. CRISPR RNA and anti-CRISPR protein binding to the Xanthomonas albilineans Csy1-Csy2 heterodimer in the type I-F CRISPR-Cas system. J Biol Chem 2018; 293:2744-2754. [PMID: 29348170 PMCID: PMC5827448 DOI: 10.1074/jbc.ra117.001611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/12/2018] [Indexed: 01/07/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against bacteriophages. In type I-F CRISPR-Cas systems, multiple Cas proteins (Csy1-4) compose a surveillance complex (Csy complex) with CRISPR RNA (crRNA) for target recognition. Here, we report the biochemical characterization of the Csy1-Csy2 subcomplex from Xanthomonas albilineans, including the analysis of its interaction with crRNA and AcrF2, an anti-CRISPR (Acr) protein from a phage that infects Pseudomonas aeruginosa The X. albilineans Csy1 and Csy2 proteins (XaCsy1 and XaCsy2, respectively) formed a stable heterodimeric complex that specifically bound the 8-nucleotide (nt) 5'-handle of the crRNA. In contrast, the XaCsy1-XaCsy2 heterodimer exhibited reduced affinity for the 28-nt X. albilineans CRISPR repeat RNA containing the 5'-handle sequence. Chromatographic and calorimetric analyses revealed tight binding between the Acr protein from the P. aeruginosa phage and the heterodimeric subunit of the X. albilineans Csy complex, suggesting that AcrF2 recognizes conserved features of Csy1-Csy2 heterodimers. We found that neither XaCsy1 nor XaCsy2 alone forms a stable complex with AcrF2 and the 5'-handle RNA, indicating that XaCsy1-XaCsy2 heterodimerization is required for binding them. We also solved the crystal structure of AcrF2 to a resolution of 1.34 Å, enabling a more detailed structural analysis of the residues involved in the interactions with the Csy1-Csy2 heterodimer. Our results provide information about the order of events during the formation of the multisubunit crRNA-guided surveillance complex and suggest that the Acr protein inactivating type I-F CRISPR-Cas systems has broad specificity.
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Affiliation(s)
- Suji Hong
- From the Departments of Agricultural Biotechnology and
| | - Donghyun Ka
- From the Departments of Agricultural Biotechnology and
| | | | - Nayoung Suh
- Department of Pharmaceutical Engineering, Soon Chun Hyang University, Asan 31538, Korea, and
| | | | - Jeong-Yong Suh
- From the Departments of Agricultural Biotechnology and ,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea, ,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
| | - Euiyoung Bae
- From the Departments of Agricultural Biotechnology and ,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea, , To whom correspondence should be addressed:
Dept. of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea. Tel.:
82-2-880-4648; Fax:
82-2-873-3112; E-mail:
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576
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Abstract
Genome editing technologies have been revolutionized by the discovery of prokaryotic RNA-guided defense system called CRISPR-Cas. Cas9, a single effector protein found in type II CRISPR systems, has been at the heart of this genome editing revolution. Nearly half of the Cas9s discovered so far belong to the type II-C subtype but have not been explored extensively. Type II-C CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins. Cas9s are central players in type II-C systems since they function in multiple steps of the CRISPR pathway, including adaptation and interference. Type II-C CRISPR systems are found in bacteria and archaea from very diverse environments, resulting in Cas9s with unique and potentially useful properties. Certain type II-C Cas9s possess unusually long PAMs, function in unique conditions (e.g., elevated temperature), and tend to be smaller in size. Here, we review the biology, mechanism, and applications of the type II-C CRISPR systems with particular emphasis on their Cas9s.
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Affiliation(s)
- Aamir Mir
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
| | - Alireza Edraki
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
| | - Jooyoung Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
| | - Erik J. Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, U.S.A
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577
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Abstract
CRISPR-Cas genome editing technologies have revolutionized modern molecular biology by making targeted DNA edits simple and scalable. These technologies are developed by domesticating naturally occurring microbial adaptive immune systems that display wide diversity of functionality for targeted nucleic acid cleavage. Several CRISPR-Cas single effector enzymes have been characterized and engineered for use in mammalian cells. The unique properties of the single effector enzymes can make a critical difference in experimental use or targeting specificity. This review describes known single effector enzymes and discusses their use in genome engineering applications.
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Affiliation(s)
- Neena K. Pyzocha
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sidi Chen
- Department of Genetics, Yale University, 333 Cedar Street, New Haven, Connecticut 06510, United States
- System Biology Institute, 850 West Campus Drive, ISTC 361, West Haven, Connecticut 06516, United States
- MCGD Program, Yale University, 333 Cedar Street, New Haven, Connecticut 06510, United States
- Immunobiology Program, Yale University, 300 Cedar Street, New Haven, Connecticut 06520, United States
- Comprehensive Cancer Center, Yale University, New Haven, Connecticut 06510, United States
- Stem Cell Center, Yale University, New Haven, Connecticut 06510, United States
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578
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Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 2018; 360:439-444. [PMID: 29449508 DOI: 10.1126/science.aaq0179] [Citation(s) in RCA: 1369] [Impact Index Per Article: 228.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/07/2018] [Indexed: 12/11/2022]
Abstract
Rapid detection of nucleic acids is integral for clinical diagnostics and biotechnological applications. We recently developed a platform termed SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) that combines isothermal preamplification with Cas13 to detect single molecules of RNA or DNA. Through characterization of CRISPR enzymology and application development, we report here four advances integrated into SHERLOCK version 2 (SHERLOCKv2) (i) four-channel single-reaction multiplexing with orthogonal CRISPR enzymes; (ii) quantitative measurement of input as low as 2 attomolar; (iii) 3.5-fold increase in signal sensitivity by combining Cas13 with Csm6, an auxiliary CRISPR-associated enzyme; and (iv) lateral-flow readout. SHERLOCKv2 can detect Dengue or Zika virus single-stranded RNA as well as mutations in patient liquid biopsy samples via lateral flow, highlighting its potential as a multiplexable, portable, rapid, and quantitative detection platform of nucleic acids.
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Affiliation(s)
- Jonathan S Gootenberg
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.,McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA.,Department of Biological Engineering, MIT, Cambridge, MA 02139, USA.,Department of Systems Biology, Harvard University, Boston, MA 02115, USA
| | - Omar O Abudayyeh
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.,McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA.,Department of Biological Engineering, MIT, Cambridge, MA 02139, USA.,Department of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA
| | - Max J Kellner
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Julia Joung
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.,McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA.,Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - James J Collins
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.,Department of Biological Engineering, MIT, Cambridge, MA 02139, USA.,Department of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Feng Zhang
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA. .,McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA.,Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
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579
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Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 2018; 360:436-439. [PMID: 29449511 PMCID: PMC6628903 DOI: 10.1126/science.aar6245] [Citation(s) in RCA: 1952] [Impact Index Per Article: 325.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/22/2018] [Accepted: 02/05/2018] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing on the basis of its ability to generate targeted, double-stranded DNA breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. We find that target-activated, nonspecific single-stranded deoxyribonuclease (ssDNase) cleavage is also a property of other type V CRISPR-Cas12 enzymes. By combining Cas12a ssDNase activation with isothermal amplification, we create a method termed DNA endonuclease-targeted CRISPR trans reporter (DETECTR), which achieves attomolar sensitivity for DNA detection. DETECTR enables rapid and specific detection of human papillomavirus in patient samples, thereby providing a simple platform for molecular diagnostics.
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Affiliation(s)
- Janice S Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maria Da Costa
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xinran Tian
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joel M Palefsky
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94704, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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580
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Anderson EM, McClelland S, Maksimova E, Strezoska Ž, Basila M, Briner AE, Barrangou R, Smith AVB. Lactobacillus gasseri CRISPR-Cas9 characterization In Vitro reveals a flexible mode of protospacer-adjacent motif recognition. PLoS One 2018; 13:e0192181. [PMID: 29394276 PMCID: PMC5796720 DOI: 10.1371/journal.pone.0192181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/17/2018] [Indexed: 12/27/2022] Open
Abstract
While the CRISPR-Cas9 system from S. pyogenes is a powerful genome engineering tool, additional programmed nucleases would enable added flexibility in targeting space and multiplexing. Here, we characterized a CRISPR-Cas9 system from L. gasseri and found that it has modest activity in a cell-free lysate assay but no activity in mammalian cells even when altering promoter, position of tag sequences and NLS, and length of crRNA:tracrRNA. In the lysate assay we tested over 400 sequential crRNA target sequences and found that the Lga Cas9 PAM is NNGA/NDRA, different than NTAA predicted from the native bacterial host. In addition, we found multiple instances of consecutive crRNA target sites, indicating flexibility in either PAM sequence or distance from the crRNA target site. This work highlights the need for characterization of new CRISPR systems and highlights the non-triviality of porting them into eukaryotes as gene editing tools.
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Affiliation(s)
- Emily M. Anderson
- Dharmacon, a Horizon Discovery Group Company, Lafayette, CO, United States of America
| | - Shawn McClelland
- Dharmacon, a Horizon Discovery Group Company, Lafayette, CO, United States of America
| | - Elena Maksimova
- Dharmacon, a Horizon Discovery Group Company, Lafayette, CO, United States of America
| | - Žaklina Strezoska
- Dharmacon, a Horizon Discovery Group Company, Lafayette, CO, United States of America
| | - Megan Basila
- Dharmacon, a Horizon Discovery Group Company, Lafayette, CO, United States of America
| | - Alexandra E. Briner
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Anja van Brabant Smith
- Dharmacon, a Horizon Discovery Group Company, Lafayette, CO, United States of America
- * E-mail:
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581
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Donohoue PD, Barrangou R, May AP. Advances in Industrial Biotechnology Using CRISPR-Cas Systems. Trends Biotechnol 2018; 36:134-146. [PMID: 28778606 DOI: 10.1016/j.tibtech.2017.07.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 12/14/2022]
Abstract
The term 'clustered regularly interspaced short palindromic repeats' (CRISPR) has recently become synonymous with the genome-editing revolution. The RNA-guided endonuclease CRISPR-associated protein 9 (Cas9), in particular, has attracted attention for its promise in basic research and gene editing-based therapeutics. CRISPR-Cas systems are efficient and easily programmable nucleic acid-targeting tools, with uses reaching beyond research and therapeutic development into the precision breeding of plants and animals and the engineering of industrial microbes. CRISPR-Cas systems have potential for many microbial engineering applications, including bacterial strain typing, immunization of cultures, autoimmunity or self-targeted cell killing, and the engineering or control of metabolic pathways for improved biochemical synthesis. In this review, we explore the fundamental characteristics of CRISPR-Cas systems and highlight how these features can be used in industrial settings.
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Affiliation(s)
- Paul D Donohoue
- Caribou Biosciences, Inc., 2929 7th St., Suite 105, Berkeley, CA 94710, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Andrew P May
- Caribou Biosciences, Inc., 2929 7th St., Suite 105, Berkeley, CA 94710, USA; Current address: Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA.
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582
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Vlot M, Houkes J, Lochs SJ, Swarts DC, Zheng P, Kunne T, Mohanraju P, Anders C, Jinek M, van der Oost J, Dickman MJ, Brouns SJ. Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR-Cas effector complexes. Nucleic Acids Res 2018; 46:873-885. [PMID: 29253268 PMCID: PMC5778469 DOI: 10.1093/nar/gkx1264] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 01/06/2023] Open
Abstract
Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction-modification (R-M) and CRISPR-Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR-Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR-Cas systems by lowering the affinity of the Cascade and Cas9-crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR-Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems.
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Affiliation(s)
- Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Joep Houkes
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Silke J A Lochs
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Daan C Swarts
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Peiyuan Zheng
- ChELSI Institute Department of Chemical and Biological Engineering University of Sheffield, Sheffield, UK
| | - Tim Kunne
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Carolin Anders
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Mark J Dickman
- ChELSI Institute Department of Chemical and Biological Engineering University of Sheffield, Sheffield, UK
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Van der Maasweg 9, Delft University of Technology, 2629 HZ Delft, The Netherlands
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583
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Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 2018; 19:1. [PMID: 29301551 PMCID: PMC5755456 DOI: 10.1186/s13059-017-1381-1] [Citation(s) in RCA: 382] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/13/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. RESULTS CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs. CONCLUSIONS Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Fatimah Aljedaani
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Zuhaib Khan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shouwei Ding
- Center for Plant Cell Biology, Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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584
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Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts. Nat Commun 2018; 9:61. [PMID: 29302058 PMCID: PMC5754349 DOI: 10.1038/s41467-017-02557-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/11/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR–Cas systems offer an immune mechanism through which prokaryotic hosts can acquire heritable resistance to genetic parasites, including temperate phages. Co-transcriptional DNA and RNA targeting by type III-A CRISPR–Cas systems restricts temperate phage lytic infections while allowing lysogenic infections to be tolerated under conditions where the prophage targets are transcriptionally repressed. However, long-term consequences of this phenomenon have not been explored. Here we show that maintenance of conditionally tolerant type III-A systems can produce fitness costs within populations of Staphylococcus aureus lysogens. The fitness costs depend on the activity of prophage-internal promoters and type III-A Cas nucleases implicated in targeting, can be more severe in double lysogens, and are alleviated by spacer-target mismatches which do not abrogate immunity during the lytic cycle. These findings suggest that persistence of type III-A systems that target endogenous prophages could be enhanced by spacer-target mismatches, particularly among populations that are prone to polylysogenization. CRISPR-Cas systems, such as type III-A CRISPR-Cas, provide an immune mechanism for prokaryotic hosts to resist parasites, including phages. Here, the authors show that maintenance of conditionally tolerant type III-A systems can affect the fitness of Staphylococcus aureus lysogens.
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585
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Chew WL. Immunity to CRISPR Cas9 and Cas12a therapeutics. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10. [PMID: 29083112 DOI: 10.1002/wsbm.1408] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 12/27/2022]
Abstract
Genome-editing therapeutics are poised to treat human diseases. As we enter clinical trials with the most promising CRISPR-Cas9 and CRISPR-Cas12a (Cpf1) modalities, the risks associated with administering these foreign biomolecules into human patients become increasingly salient. Preclinical discovery with CRISPR-Cas9 and CRISPR-Cas12a systems and foundational gene therapy studies indicate that the host immune system can mount undesired responses against the administered proteins and nucleic acids, the gene-edited cells, and the host itself. These host defenses include inflammation via activation of innate immunity, antibody induction in humoral immunity, and cell death by T-cell-mediated cytotoxicity. If left unchecked, these immunological reactions can curtail therapeutic benefits and potentially lead to mortality. Ways to assay and reduce the immunogenicity of Cas9 and Cas12a proteins are therefore critical for ensuring patient safety and treatment efficacy, and for bringing us closer to realizing the vision of permanent genetic cures. WIREs Syst Biol Med 2018, 10:e1408. doi: 10.1002/wsbm.1408 This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Translational, Genomic, and Systems Medicine > Translational Medicine Translational, Genomic, and Systems Medicine > Therapeutic Methods.
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Affiliation(s)
- Wei Leong Chew
- Synthetic Biology, Genome Institute of Singapore, Singapore, Singapore
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586
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Mahas A, Neal Stewart C, Mahfouz MM. Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation. Biotechnol Adv 2018; 36:295-310. [DOI: 10.1016/j.biotechadv.2017.11.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/03/2017] [Accepted: 11/27/2017] [Indexed: 12/26/2022]
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587
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Metje-Sprink J, Menz J, Modrzejewski D, Sprink T. DNA-Free Genome Editing: Past, Present and Future. FRONTIERS IN PLANT SCIENCE 2018; 9:1957. [PMID: 30693009 PMCID: PMC6339908 DOI: 10.3389/fpls.2018.01957] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/17/2018] [Indexed: 05/18/2023]
Abstract
Genome Editing using engineered endonuclease (GEEN) systems rapidly took over the field of plant science and plant breeding. So far, Genome Editing techniques have been applied in more than fifty different plants; including model species like Arabidopsis; main crops like rice, maize or wheat as well as economically less important crops like strawberry, peanut and cucumber. These techniques have been used for basic research as proof-of-concept or to investigate gene functions in most of its applications. However, several market-oriented traits have been addressed including enhanced agronomic characteristics, improved food and feed quality, increased tolerance to abiotic and biotic stress and herbicide tolerance. These technologies are evolving at a tearing pace and especially the field of CRISPR based Genome Editing is advancing incredibly fast. CRISPR-Systems derived from a multitude of bacterial species are being used for targeted Gene Editing and many modifications have already been applied to the existing CRISPR-Systems such as (i) alter their protospacer adjacent motif (ii) increase their specificity (iii) alter their ability to cut DNA and (iv) fuse them with additional proteins. Besides, the classical transformation system using Agrobacteria tumefaciens or Rhizobium rhizogenes, other transformation technologies have become available and additional methods are on its way to the plant sector. Some of them are utilizing solely proteins or protein-RNA complexes for transformation, making it possible to alter the genome without the use of recombinant DNA. Due to this, it is impossible that foreign DNA is being incorporated into the host genome. In this review we will present the recent developments and techniques in the field of DNA-free Genome Editing, its advantages and pitfalls and give a perspective on technologies which might be available in the future for targeted Genome Editing in plants. Furthermore, we will discuss these techniques in the light of existing- and potential future regulations.
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588
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Perez Rojo F, Nyman RKM, Johnson AAT, Navarro MP, Ryan MH, Erskine W, Kaur P. CRISPR-Cas systems: ushering in the new genome editing era. Bioengineered 2018; 9:214-221. [PMID: 29968520 PMCID: PMC6067892 DOI: 10.1080/21655979.2018.1470720] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/25/2018] [Indexed: 12/26/2022] Open
Abstract
In recent years there has been great progress with the implementation and utilization of Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) systems in the world of genetic engineering. Many forms of CRISPR-Cas9 have been developed as genome editing tools and techniques and, most recently, several non-genome editing CRISPR-Cas systems have emerged. Most of the CRISPR-Cas systems have been classified as either Class I or Class II and are further divided among several subtypes within each class. Research teams and companies are currently in dispute over patents for these CRISPR-Cas systems as numerous powerful applications are concurrently under development. This mini review summarizes the appearance of CRISPR-Cas systems with a focus on the predominant CRISPR-Cas9 system as well as the classifications and subtypes for CRISPR-Cas. Non-genome editing uses of CRISPR-Cas are also highlighted and a brief overview of the commercialization of CRISPR is provided.
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Affiliation(s)
- Fernando Perez Rojo
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Rikard Karl Martin Nyman
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | | | - Maria Pazos Navarro
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Megan Helen Ryan
- Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - William Erskine
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Parwinder Kaur
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
- Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- Telethon Kids Institute, Subiaco, WA, Australia
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589
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Wolter F, Puchta H. Application of CRISPR/Cas to Understand Cis- and Trans-Regulatory Elements in Plants. Methods Mol Biol 2018; 1830:23-40. [PMID: 30043362 DOI: 10.1007/978-1-4939-8657-6_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The recent emergence of the CRISPR/Cas system as a genome editing tool enables simple, fast, and efficient induction of DNA double-strand breaks at precise positions in the genome. This has proven extremely useful for analysis and modification of protein-coding sequences. Regulatory sequences have received much less attention, but can now be quickly and easily disrupted as well. Editing of cis-regulatory elements (CRE) offers considerable potential for crop improvement via fine-tuning of gene expression that cannot be achieved by simple KO mutations, but its widespread application is still hampered by a lack of precise knowledge about functional motifs in CRE. As demonstrated for mammalian cells, CRISPR/Cas is also extremely useful for the identification and analysis of CRE in their native environment on a large scale using tiling screens. Transcriptional complexes are another promising target for crop genome editing, as demonstrated for pathogen resistance and regulation of flowering. The development of more diverse and sophisticated CRISPR/Cas tools for genome editing will allow even more efficient and powerful approaches for editing of regulatory sequences in the future.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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590
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Swiat MA, Dashko S, den Ridder M, Wijsman M, van der Oost J, Daran JM, Daran-Lapujade P. FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae. Nucleic Acids Res 2017; 45:12585-12598. [PMID: 29106617 PMCID: PMC5716609 DOI: 10.1093/nar/gkx1007] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/13/2017] [Indexed: 11/14/2022] Open
Abstract
Cpf1 is a new class II family of CRISPR-Cas RNA-programmable endonucleases with unique features that make it a very attractive alternative or complement to Cas9 for genome engineering. Using constitutively expressed Cpf1 from Francisella novicida, the present study demonstrates that FnCpf1 can mediate RNA-guided DNA cleavage at targeted genomic loci in the popular model and industrial yeast Saccharomyces cerevisiae. FnCpf1 very efficiently and precisely promoted repair DNA recombination with efficiencies up to 100%. Furthermore, FnCpf1 was shown to introduce point mutations with high fidelity. While editing multiple loci with Cas9 is hampered by the need for multiple or complex expression constructs, processing itself a customized CRISPR array FnCpf1 was able to edit four genes simultaneously in yeast with a 100% efficiency. A remarkable observation was the unexpected, strong preference of FnCpf1 to cleave DNA at target sites harbouring 5′-TTTV-3′ PAM sequences, a motif reported to be favoured by Cpf1 homologs of Acidaminococcus and Lachnospiraceae. The present study supplies several experimentally tested guidelines for crRNA design, as well as plasmids for FnCpf1 expression and easy construction of crRNA expression cassettes in S. cerevisiae. FnCpf1 proves to be a powerful addition to S. cerevisiae CRISPR toolbox.
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Affiliation(s)
- Michal A Swiat
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sofia Dashko
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Melanie Wijsman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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591
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Bernheim A, Calvo-Villamañán A, Basier C, Cui L, Rocha EPC, Touchon M, Bikard D. Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria. Nat Commun 2017; 8:2094. [PMID: 29234047 PMCID: PMC5727150 DOI: 10.1038/s41467-017-02350-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/22/2017] [Indexed: 12/26/2022] Open
Abstract
Type II CRISPR-Cas systems introduce double-strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation. These breaks can be the substrate of several DNA repair pathways, paving the way for interactions. We report that non-homologous end-joining (NHEJ) and type II-A CRISPR-Cas systems only co-occur once among 5563 fully sequenced prokaryotic genomes. We investigated experimentally the possible molecular interactions using the NHEJ pathway from Bacillus subtilis and the type II-A CRISPR-Cas systems from Streptococcus thermophilus and Streptococcus pyogenes. Our results suggest that the NHEJ system has no effect on CRISPR immunity. On the other hand, we provide evidence for the inhibition of NHEJ repair by the Csn2 protein. Our findings give insights on the complex interactions between CRISPR-Cas systems and repair mechanisms in bacteria, contributing to explain the scattered distribution of CRISPR-Cas systems in bacterial genome.
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Affiliation(s)
- Aude Bernheim
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr. Roux, 75015, Paris, France.,CNRS, UMR3525, 25-28 rue Dr. Roux, 75015, Paris, France.,Synthetic Biology Group, Institut Pasteur, 25-28 rue Dr. Roux, 75015, Paris, France.,AgroParisTech, 75005, Paris, France
| | | | - Clovis Basier
- Synthetic Biology Group, Institut Pasteur, 25-28 rue Dr. Roux, 75015, Paris, France
| | - Lun Cui
- Synthetic Biology Group, Institut Pasteur, 25-28 rue Dr. Roux, 75015, Paris, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr. Roux, 75015, Paris, France.,CNRS, UMR3525, 25-28 rue Dr. Roux, 75015, Paris, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr. Roux, 75015, Paris, France.,CNRS, UMR3525, 25-28 rue Dr. Roux, 75015, Paris, France
| | - David Bikard
- Synthetic Biology Group, Institut Pasteur, 25-28 rue Dr. Roux, 75015, Paris, France.
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592
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Gilbert RA, Kelly WJ, Altermann E, Leahy SC, Minchin C, Ouwerkerk D, Klieve AV. Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. Front Microbiol 2017; 8:2340. [PMID: 29259581 PMCID: PMC5723332 DOI: 10.3389/fmicb.2017.02340] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
The rumen is known to harbor dense populations of bacteriophages (phages) predicted to be capable of infecting a diverse range of rumen bacteria. While bacterial genome sequencing projects are revealing the presence of phages which can integrate their DNA into the genome of their host to form stable, lysogenic associations, little is known of the genetics of phages which utilize lytic replication. These phages infect and replicate within the host, culminating in host lysis, and the release of progeny phage particles. While lytic phages for rumen bacteria have been previously isolated, their genomes have remained largely uncharacterized. Here we report the first complete genome sequences of lytic phage isolates specifically infecting three genera of rumen bacteria: Bacteroides, Ruminococcus, and Streptococcus. All phages were classified within the viral order Caudovirales and include two phage morphotypes, representative of the Siphoviridae and Podoviridae families. The phage genomes displayed modular organization and conserved viral genes were identified which enabled further classification and determination of closest phage relatives. Co-examination of bacterial host genomes led to the identification of several genes responsible for modulating phage:host interactions, including CRISPR/Cas elements and restriction-modification phage defense systems. These findings provide new genetic information and insights into how lytic phages may interact with bacteria of the rumen microbiome.
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Affiliation(s)
- Rosalind A Gilbert
- Department of Agriculture and Fisheries, EcoSciences Precinct, Brisbane, QLD, Australia.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | | | - Eric Altermann
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Sinead C Leahy
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.,New Zealand Agricultural Greenhouse Gas Research Centre, Palmerston North, New Zealand
| | - Catherine Minchin
- Department of Agriculture and Fisheries, EcoSciences Precinct, Brisbane, QLD, Australia
| | - Diane Ouwerkerk
- Department of Agriculture and Fisheries, EcoSciences Precinct, Brisbane, QLD, Australia.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Athol V Klieve
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia.,School of Agriculture and Food Sciences, University of Queensland, Gatton Campus, Gatton, QLD, Australia
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593
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Koonin EV, Wolf YI, Katsnelson MI. Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states. Biol Direct 2017; 12:31. [PMID: 29202832 PMCID: PMC5715634 DOI: 10.1186/s13062-017-0202-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/22/2017] [Indexed: 01/02/2023] Open
Abstract
Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic diversity. Here we examine simple thought experiments to demonstrate that both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are evolutionarily unstable. REVIEWERS This article has been reviewed by Yitzhak Pilpel, Bojan Zagrovic, and Eric van Nimwegen.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Mikhail I Katsnelson
- Institute for Molecules and Materials, Radboud University, 6525AJ, Nijmegen, Netherlands
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594
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Fagen JR, Collias D, Singh AK, Beisel CL. Advancing the design and delivery of CRISPR antimicrobials. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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595
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Switchable Cas9. Curr Opin Biotechnol 2017; 48:119-126. [DOI: 10.1016/j.copbio.2017.03.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 03/26/2017] [Accepted: 03/30/2017] [Indexed: 02/07/2023]
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596
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Hunter FW, Tsai P, Kakadia PM, Bohlander SK, Print CG, Wilson WR. Development of capability for genome-scale CRISPR-Cas9 knockout screens in New Zealand. J R Soc N Z 2017. [DOI: 10.1080/03036758.2017.1400984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Francis W. Hunter
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Peter Tsai
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - Purvi M. Kakadia
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Stefan K. Bohlander
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Cristin G. Print
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Bioinformatics Institute, University of Auckland, Auckland, New Zealand
| | - William R. Wilson
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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597
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Jeon S, Lim JM, Lee HG, Shin SE, Kang NK, Park YI, Oh HM, Jeong WJ, Jeong BR, Chang YK. Current status and perspectives of genome editing technology for microalgae. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:267. [PMID: 29163669 PMCID: PMC5686953 DOI: 10.1186/s13068-017-0957-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/04/2017] [Indexed: 05/25/2023]
Abstract
Genome editing techniques are critical for manipulating genes not only to investigate their functions in biology but also to improve traits for genetic engineering in biotechnology. Genome editing has been greatly facilitated by engineered nucleases, dubbed molecular scissors, including zinc-finger nuclease (ZFN), TAL effector endonuclease (TALEN) and clustered regularly interspaced palindromic sequences (CRISPR)/Cas9. In particular, CRISPR/Cas9 has revolutionized genome editing fields with its simplicity, efficiency and accuracy compared to previous nucleases. CRISPR/Cas9-induced genome editing is being used in numerous organisms including microalgae. Microalgae have been subjected to extensive genetic and biological engineering due to their great potential as sustainable biofuel and chemical feedstocks. However, progress in microalgal engineering is slow mainly due to a lack of a proper transformation toolbox, and the same problem also applies to genome editing techniques. Given these problems, there are a few reports on successful genome editing in microalgae. It is, thus, time to consider the problems and solutions of genome editing in microalgae as well as further applications of this exciting technology for other scientific and engineering purposes.
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Affiliation(s)
- Seungjib Jeon
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Sung-Eun Shin
- LG Chem, 188 Munji-ro, Yuseong-gu, Daejeon, 34122 Republic of Korea
| | - Nam Kyu Kang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Byeong-ryool Jeong
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Yong Keun Chang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
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598
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A thermostable Cas9 with increased lifetime in human plasma. Nat Commun 2017; 8:1424. [PMID: 29127284 PMCID: PMC5681539 DOI: 10.1038/s41467-017-01408-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/14/2017] [Indexed: 12/22/2022] Open
Abstract
CRISPR-Cas9 is a powerful technology that has enabled genome editing in a wide range of species. However, the currently developed Cas9 homologs all originate from mesophilic bacteria, making them susceptible to degradation and unsuitable for applications requiring cleavage at elevated temperatures. Here, we show that the Cas9 protein from the thermophilic bacterium Geobacillus stearothermophilus (GeoCas9) catalyzes RNA-guided DNA cleavage at elevated temperatures. GeoCas9 is active at temperatures up to 70 °C, compared to 45 °C for Streptococcus pyogenes Cas9 (SpyCas9), which expands the temperature range for CRISPR-Cas9 applications. We also found that GeoCas9 is an effective tool for editing mammalian genomes when delivered as a ribonucleoprotein (RNP) complex. Together with an increased lifetime in human plasma, the thermostable GeoCas9 provides the foundation for improved RNP delivery in vivo and expands the temperature range of CRISPR-Cas9. While current CRISPR-Cas9 tools have revolutionized genome editing, they are not suitable for applications at elevated temperatures. Here, the authors characterize GeoCas9 from Geobacillus stearothermophilus, which is active up to 70°C and is stable in human plasma.
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599
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Scheben A, Wolter F, Batley J, Puchta H, Edwards D. Towards CRISPR/Cas crops - bringing together genomics and genome editing. THE NEW PHYTOLOGIST 2017; 216:682-698. [PMID: 28762506 DOI: 10.1111/nph.14702] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/31/2017] [Indexed: 05/19/2023]
Abstract
Contents 682 I. 682 II. 683 III. 684 IV. 685 V. 685 VI. 688 VII. 690 VIII. 694 694 References 694 SUMMARY: With the rapid increase in the global population and the impact of climate change on agriculture, there is a need for crops with higher yields and greater tolerance to abiotic stress. However, traditional crop improvement via genetic recombination or random mutagenesis is a laborious process and cannot keep pace with increasing crop demand. Genome editing technologies such as clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) allow targeted modification of almost any crop genome sequence to generate novel variation and accelerate breeding efforts. We expect a gradual shift in crop improvement away from traditional breeding towards cycles of targeted genome editing. Crop improvement using genome editing is not constrained by limited existing variation or the requirement to select alleles over multiple breeding generations. However, current applications of crop genome editing are limited by the lack of complete reference genomes, the sparse knowledge of potential modification targets, and the unclear legal status of edited crops. We argue that overcoming technical and social barriers to the application of genome editing will allow this technology to produce a new generation of high-yielding, climate ready crops.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Felix Wolter
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia
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600
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Cheng F, Gong L, Zhao D, Yang H, Zhou J, Li M, Xiang H. Harnessing the native type I-B CRISPR-Cas for genome editing in a polyploid archaeon. J Genet Genomics 2017; 44:541-548. [DOI: 10.1016/j.jgg.2017.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 12/26/2022]
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