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Deng B, Xue J. HIV infection detection using CRISPR/Cas systems: Present and future prospects. Comput Struct Biotechnol J 2023; 21:4409-4423. [PMID: 37711183 PMCID: PMC10498128 DOI: 10.1016/j.csbj.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection poses substantial medical risks to global public health. An essential strategy to combat the HIV epidemic is timely and effective virus testing. CRISPR-based assays combine the highly compatible CRISPR system with different elements, yielding portability, digitization capabilities, low economic burden and low operational thresholds. The application of CRISPR-based assays has demonstrated rapid, accurate, and accessible means of pathogen testing, suggesting great potential as point-of-care (POC) assays. This review outlines the different types of CRISPR/Cas systems based on Cas proteins and their applications for the detection of HIV. Additionally, we also offer an overview of future perspectives on CRISPR-based methods for HIV detection, including advances in nucleic acid amplification-free testing, improved personal testing, and refined testing for HIV genotypes and drug-resistant strains.
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Affiliation(s)
- Bingpeng Deng
- Beijing Key Laboratory for Animal Models of Emerging and Re-Emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
| | - Jing Xue
- Beijing Key Laboratory for Animal Models of Emerging and Re-Emerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing 100021, China
- NHC Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
- Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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2
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Wiegand T, Wilkinson R, Santiago-Frangos A, Lynes M, Hatzenpichler R, Wiedenheft B. Functional and Phylogenetic Diversity of Cas10 Proteins. CRISPR J 2023; 6:152-162. [PMID: 36912817 PMCID: PMC10123807 DOI: 10.1089/crispr.2022.0085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/30/2023] [Indexed: 03/14/2023] Open
Abstract
Cas10 proteins are large subunits of type III CRISPR RNA (crRNA)-guided surveillance complexes, many of which have nuclease and cyclase activities. Here, we use computational and phylogenetic methods to identify and analyze 2014 Cas10 sequences from genomic and metagenomic databases. Cas10 proteins cluster into five distinct clades that mirror previously established CRISPR-Cas subtypes. Most Cas10 proteins (85.0%) have conserved polymerase active-site motifs, while HD-nuclease domains are less well conserved (36.0%). We identify Cas10 variants that are split over multiple genes or genetically fused to nucleases activated by cyclic nucleotides (i.e., NucC) or components of toxin-antitoxin systems (i.e., AbiEii). To clarify the functional diversification of Cas10 proteins, we cloned, expressed, and purified five representatives from three phylogenetically distinct clades. None of the Cas10s are functional cyclases in isolation, and activity assays performed with polymerase domain active site mutants indicate that previously reported Cas10 DNA-polymerase activity may be a result of contamination. Collectively, this work helps clarify the phylogenetic and functional diversity of Cas10 proteins in type III CRISPR systems.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Royce Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Andrew Santiago-Frangos
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Mackenzie Lynes
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Roland Hatzenpichler
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
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3
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Bhatia S, Pooja, Yadav SK. CRISPR-Cas for genome editing: Classification, mechanism, designing and applications. Int J Biol Macromol 2023; 238:124054. [PMID: 36933595 DOI: 10.1016/j.ijbiomac.2023.124054] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/24/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Clustered regularly interspersed short pallindromic repeats (CRISPR) and CRISPR associated proteins (Cas) system (CRISPR-Cas) came into light as prokaryotic defence mechanism for adaptive immune response. CRISPR-Cas works by integrating short sequences of the target genome (spacers) into the CRISPR locus. The locus containing spacers interspersed repeats is further expressed into small guide CRISPR RNA (crRNA) which is then deployed by the Cas proteins to evade the target genome. Based on the Cas proteins CRISPR-Cas is classified according to polythetic system of classification. The characteristic of the CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new arenas due to which today CRISPR-Cas has evolved as cutting end technique in the field of genome editing. Here, we discuss about the evolution of CRISPR, its classification and various Cas systems including the designing and molecular mechanism of CRISPR-Cas. Applications of CRISPR-Cas as a genome editing tools are also highlighted in the areas such as agriculture, and anticancer therapy. Briefly discuss the role of CRISPR and its Cas systems in the diagnosis of COVID-19 and its possible preventive measures. The challenges in existing CRISP-Cas technologies and their potential solutions are also discussed briefly.
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Affiliation(s)
- Simran Bhatia
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India; Regional Center for Biotechnology, Faridabad, India
| | - Pooja
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India
| | - Sudesh Kumar Yadav
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India; Regional Center for Biotechnology, Faridabad, India.
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4
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Abstract
CRISPR-Cas is a widespread adaptive immune system in bacteria and archaea that protects against viral infection by targeting specific invading nucleic acid sequences. Whereas some CRISPR-Cas systems sense and cleave viral DNA, type III and type VI CRISPR-Cas systems sense RNA that results from viral transcription and perhaps invasion by RNA viruses. The sequence-specific detection of viral RNA evokes a cell-wide response that typically involves global damage to halt the infection. How can one make sense of an immune strategy that encompasses broad, collateral effects rather than specific, targeted destruction? In this Review, we summarize the current understanding of RNA-targeting CRISPR-Cas systems. We detail the composition and properties of type III and type VI systems, outline the cellular defence processes that are instigated upon viral RNA sensing and describe the biological rationale behind the broad RNA-activated immune responses as an effective strategy to combat viral infection.
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5
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Grüschow S, Adamson CS, White MF. Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector. Nucleic Acids Res 2021; 49:13122-13134. [PMID: 34871408 PMCID: PMC8682760 DOI: 10.1093/nar/gkab1190] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Type III CRISPR systems detect invading RNA, resulting in the activation of the enzymatic Cas10 subunit. The Cas10 cyclase domain generates cyclic oligoadenylate (cOA) second messenger molecules, activating a variety of effector nucleases that degrade nucleic acids to provide immunity. The prophage-encoded Vibrio metoecus type III-B (VmeCmr) locus is uncharacterised, lacks the HD nuclease domain in Cas10 and encodes a NucC DNA nuclease effector that is also found associated with Cyclic-oligonucleotide-based anti-phage signalling systems (CBASS). Here we demonstrate that VmeCmr is activated by target RNA binding, generating cyclic-triadenylate (cA3) to stimulate a robust NucC-mediated DNase activity. The specificity of VmeCmr is probed, revealing the importance of specific nucleotide positions in segment 1 of the RNA duplex and the protospacer flanking sequence (PFS). We harness this programmable system to demonstrate the potential for a highly specific and sensitive assay for detection of the SARS-CoV-2 virus RNA with a limit of detection (LoD) of 2 fM using a commercial plate reader without any extrinsic amplification step. The sensitivity is highly dependent on the guide RNA used, suggesting that target RNA secondary structure plays an important role that may also be relevant in vivo.
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Affiliation(s)
- Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Catherine S Adamson
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
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Thompson MK, Sobol RW, Prakash A. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair. BIOLOGY 2021; 10:530. [PMID: 34198612 PMCID: PMC8232306 DOI: 10.3390/biology10060530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.
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Affiliation(s)
- Marlo K. Thompson
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
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7
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Molina R, Sofos N, Montoya G. Structural basis of CRISPR-Cas Type III prokaryotic defence systems. Curr Opin Struct Biol 2020; 65:119-129. [DOI: 10.1016/j.sbi.2020.06.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/06/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022]
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8
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Foster K, Grüschow S, Bailey S, White MF, Terns MP. Regulation of the RNA and DNA nuclease activities required for Pyrococcus furiosus Type III-B CRISPR-Cas immunity. Nucleic Acids Res 2020; 48:4418-4434. [PMID: 32198888 PMCID: PMC7192623 DOI: 10.1093/nar/gkaa176] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/28/2020] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
Type III CRISPR-Cas prokaryotic immune systems provide anti-viral and anti-plasmid immunity via a dual mechanism of RNA and DNA destruction. Upon target RNA interaction, Type III crRNP effector complexes become activated to cleave both target RNA (via Cas7) and target DNA (via Cas10). Moreover, trans-acting endoribonucleases, Csx1 or Csm6, can promote the Type III immune response by destroying both invader and host RNAs. Here, we characterize how the RNase and DNase activities associated with Type III-B immunity in Pyrococcus furiosus (Pfu) are regulated by target RNA features and second messenger signaling events. In vivo mutational analyses reveal that either the DNase activity of Cas10 or the RNase activity of Csx1 can effectively direct successful anti-plasmid immunity. Biochemical analyses confirmed that the Cas10 Palm domains convert ATP into cyclic oligoadenylate (cOA) compounds that activate the ribonuclease activity of Pfu Csx1. Furthermore, we show that the HEPN domain of the adenosine-specific endoribonuclease, Pfu Csx1, degrades cOA signaling molecules to provide an auto-inhibitory off-switch of Csx1 activation. Activation of both the DNase and cOA generation activities require target RNA binding and recognition of distinct target RNA 3' protospacer flanking sequences. Our results highlight the complex regulatory mechanisms controlling Type III CRISPR immunity.
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Affiliation(s)
- Kawanda Foster
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Scott Bailey
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Michael P Terns
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Chen H, Ino M, Shimono M, Wagh SG, Kobayashi K, Yaeno T, Yamaoka N, Bai G, Nishiguchi M. A Single Amino Acid Substitution in the Intervening Region of 129K Protein of Cucumber Green Mottle Mosaic Virus Resulted in Attenuated Symptoms. PHYTOPATHOLOGY 2020; 110:146-152. [PMID: 31559902 DOI: 10.1094/phyto-12-18-0478-fi] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cucumber green mottle mosaic virus (CGMMV), a member of the genus Tobamovirus, is a major threat to economically important cucurbit crops worldwide. An attenuated strain (SH33b) derived from a severe strain (SH) of CGMMV caused a reduction in the viral RNA accumulation and the attenuation of symptoms, and it has been successfully used to protect muskmelon plants against severe strains in Japan. In this study, we compared GFP-induced silencing suppression by the 129K protein and the methyltransferase domain plus intervening region (MTIR) of the 129K protein between the SH and SH33b strains, respectively. As a result, silencing suppression activity (SSA) in the GFP-silenced plants was inhibited efficiently by the MTIR and 129K protein of SH strain, and it coincided with drastically reduced accumulation of GFP-specific small interfering RNAs (siRNAs) but not by that of SH33b strain. Furthermore, analyses of siRNA binding capability (SBC) by the MTIR of 129K protein and 129K protein using electrophoretic mobility shift assay revealed that SBC was found with the MTIR and 129K protein of SH but not with that of SH33b, suggesting that a single amino acid mutation (E to G) in the MTIR is responsible for impaired SSA and SBC of SH33b. These data suggest that a single amino acid substitution in the intervening region of 129K protein of CGMMV resulted in attenuated symptoms by affecting RNA silencing suppression.
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Affiliation(s)
- H Chen
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
| | - M Ino
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - M Shimono
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - S G Wagh
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - K Kobayashi
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - T Yaeno
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - N Yamaoka
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - G Bai
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
- Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agriculture Research Service, Manhattan, KS 66506, U.S.A
| | - M Nishiguchi
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
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Han W, Stella S, Zhang Y, Guo T, Sulek K, Peng-Lundgren L, Montoya G, She Q. A Type III-B Cmr effector complex catalyzes the synthesis of cyclic oligoadenylate second messengers by cooperative substrate binding. Nucleic Acids Res 2019; 46:10319-10330. [PMID: 30239876 PMCID: PMC6212834 DOI: 10.1093/nar/gky844] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/10/2018] [Indexed: 12/18/2022] Open
Abstract
Recently, Type III-A CRISPR-Cas systems were found to catalyze the synthesis of cyclic oligoadenylates (cOAs), a second messenger that specifically activates Csm6, a Cas accessory RNase and confers antiviral defense in bacteria. To test if III-B CRISPR-Cas systems could mediate a similar CRISPR signaling pathway, the Sulfolobus islandicus Cmr-α ribonucleoprotein complex (Cmr-α-RNP) was purified from the native host and tested for cOA synthesis. We found that the system showed a robust production of cyclic tetra-adenylate (c-A4), and that c-A4 functions as a second messenger to activate the III-B-associated RNase Csx1 by binding to its CRISPR-associated Rossmann Fold domain. Investigation of the kinetics of cOA synthesis revealed that Cmr-α-RNP displayed positively cooperative binding to the adenosine triphosphate (ATP) substrate. Furthermore, mutagenesis of conserved domains in Cmr2α confirmed that, while Palm 2 hosts the active site of cOA synthesis, Palm 1 domain serves as the primary site in the enzyme-substrate interaction. Together, our data suggest that the two Palm domains cooperatively interact with ATP molecules to achieve a robust cOA synthesis by the III-B CRISPR-Cas system.
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Affiliation(s)
- Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N DK-2200, Denmark
| | - Stefano Stella
- Structural Molecular Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Yan Zhang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tong Guo
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N DK-2200, Denmark
| | - Karolina Sulek
- Clinical Proteomics, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Li Peng-Lundgren
- Protein Production and Characterization Platform, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N DK-2200, Denmark
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Wang F, Wang L, Zou X, Duan S, Li Z, Deng Z, Luo J, Lee SY, Chen S. Advances in CRISPR-Cas systems for RNA targeting, tracking and editing. Biotechnol Adv 2019; 37:708-729. [PMID: 30926472 DOI: 10.1016/j.biotechadv.2019.03.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only ~930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA-targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.
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Affiliation(s)
- Fei Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Xuan Zou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea
| | - Suling Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zhiqiang Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Jie Luo
- Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea.
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China.
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12
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Molecular mechanisms of III-B CRISPR–Cas systems in archaea. Emerg Top Life Sci 2018; 2:483-491. [DOI: 10.1042/etls20180023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/26/2018] [Accepted: 08/31/2018] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems provide the adaptive antiviral immunity against invasive genetic elements in archaea and bacteria. These immune systems are divided into at least six different types, among which Type III CRISPR–Cas systems show several distinct antiviral activities as demonstrated from the investigation of bacterial III-A and archaeal III-B systems in the past decade. First, although initial experiments suggested that III-A systems provided DNA interference activity, whereas III-B system was active only in RNA interference, these immune systems were subsequently found to mediate the transcription-dependent DNA interference and the dual DNA/RNA interference. Second, their ribonucleoprotein (RNP) complexes show target RNA (tgRNA) cleavage by a ruler mechanism and RNA-activated indiscriminate single-stranded DNA cleavage, the latter of which is subjected to spatiotemporal regulation such that the DNase activity occurs only at the right place in the right time. Third, RNPs of Type III systems catalyse the synthesis of cyclic oligoadenylates (cOAs) that function as second messengers to activate Csm6 and Csx1, both of which are potent Cas accessory RNases after activation. To date, Type III CRISPR systems are the only known antiviral immunity that utilizes multiple interference mechanisms for antiviral defence.
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13
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Gleditzsch D, Pausch P, Müller-Esparza H, Özcan A, Guo X, Bange G, Randau L. PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures. RNA Biol 2018; 16:504-517. [PMID: 30109815 PMCID: PMC6546366 DOI: 10.1080/15476286.2018.1504546] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Adaptive immunity of prokaryotes is mediated by CRISPR-Cas systems that employ a large variety of Cas protein effectors to identify and destroy foreign genetic material. The different targeting mechanisms of Cas proteins rely on the proper protection of the host genome sequence while allowing for efficient detection of target sequences, termed protospacers. A short DNA sequence, the protospacer-adjacent motif (PAM), is frequently used to mark proper target sites. Cas proteins have evolved a multitude of PAM-interacting domains, which enables them to cope with viral anti-CRISPR measures that alter the sequence or accessibility of PAM elements. In this review, we summarize known PAM recognition strategies for all CRISPR-Cas types. Available structures of target bound Cas protein effector complexes highlight the diversity of mechanisms and domain architectures that are employed to guarantee target specificity.
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Affiliation(s)
- Daniel Gleditzsch
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
| | - Patrick Pausch
- b Philipps-University-Marburg , LOEWE Center for synthetic Microbiology (Synmikro) & Faculty of Chemistry , Marburg , Germany
| | - Hanna Müller-Esparza
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
| | - Ahsen Özcan
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
| | - Xiaohan Guo
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
| | - Gert Bange
- b Philipps-University-Marburg , LOEWE Center for synthetic Microbiology (Synmikro) & Faculty of Chemistry , Marburg , Germany
| | - Lennart Randau
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
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14
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Burnight ER, Giacalone JC, Cooke JA, Thompson JR, Bohrer LR, Chirco KR, Drack AV, Fingert JH, Worthington KS, Wiley LA, Mullins RF, Stone EM, Tucker BA. CRISPR-Cas9 genome engineering: Treating inherited retinal degeneration. Prog Retin Eye Res 2018; 65:28-49. [PMID: 29578069 PMCID: PMC8210531 DOI: 10.1016/j.preteyeres.2018.03.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 12/18/2022]
Abstract
Gene correction is a valuable strategy for treating inherited retinal degenerative diseases, a major cause of irreversible blindness worldwide. Single gene defects cause the majority of these retinal dystrophies. Gene augmentation holds great promise if delivered early in the course of the disease, however, many patients carry mutations in genes too large to be packaged into adeno-associated viral vectors and some, when overexpressed via heterologous promoters, induce retinal toxicity. In addition to the aforementioned challenges, some patients have sustained significant photoreceptor cell loss at the time of diagnosis, rendering gene replacement therapy insufficient to treat the disease. These patients will require cell replacement to restore useful vision. Fortunately, the advent of induced pluripotent stem cell and CRISPR-Cas9 gene editing technologies affords researchers and clinicians a powerful means by which to develop strategies to treat patients with inherited retinal dystrophies. In this review we will discuss the current developments in CRISPR-Cas9 gene editing in vivo in animal models and in vitro in patient-derived cells to study and treat inherited retinal degenerative diseases.
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Affiliation(s)
- Erin R Burnight
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Joseph C Giacalone
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Jessica A Cooke
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Jessica R Thompson
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Laura R Bohrer
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Kathleen R Chirco
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Arlene V Drack
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - John H Fingert
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Kristan S Worthington
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States; Department of Biochemical Engineering, University of Iowa, Iowa City, IA, United States
| | - Luke A Wiley
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Robert F Mullins
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Edwin M Stone
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States
| | - Budd A Tucker
- Institute for Vision Research, Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States.
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15
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Han W, Li Y, Deng L, Feng M, Peng W, Hallstrøm S, Zhang J, Peng N, Liang YX, White MF, She Q. A type III-B CRISPR-Cas effector complex mediating massive target DNA destruction. Nucleic Acids Res 2017; 45:1983-1993. [PMID: 27986854 PMCID: PMC5389615 DOI: 10.1093/nar/gkw1274] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/07/2016] [Indexed: 12/26/2022] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) system protects archaea and bacteria by eliminating nucleic acid invaders in a crRNA-guided manner. The Sulfolobus islandicus type III-B Cmr–α system targets invading nucleic acid at both RNA and DNA levels and DNA targeting relies on the directional transcription of the protospacer in vivo. To gain further insight into the involved mechanism, we purified a native effector complex of III-B Cmr–α from S. islandicus and characterized it in vitro. Cmr–α cleaved RNAs complementary to crRNA present in the complex and its ssDNA destruction activity was activated by target RNA. The ssDNA cleavage required mismatches between the 5΄-tag of crRNA and the 3΄-flanking region of target RNA. An invader plasmid assay showed that mutation either in the histidine-aspartate acid (HD) domain (a quadruple mutation) or in the GGDD motif of the Cmr–2α protein resulted in attenuation of the DNA interference in vivo. However, double mutation of the HD motif only abolished the DNase activity in vitro. Furthermore, the activated Cmr–α binary complex functioned as a highly active DNase to destroy a large excess DNA substrate, which could provide a powerful means to rapidly degrade replicating viral DNA.
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Affiliation(s)
- Wenyuan Han
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ling Deng
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark
| | - Mingxia Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Wenfang Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark
| | - Søren Hallstrøm
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark
| | - Jing Zhang
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, DK-2200 Copenhagen N, Denmark.,State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
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16
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Kazlauskiene M, Kostiuk G, Venclovas Č, Tamulaitis G, Siksnys V. A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems. Science 2017; 357:605-609. [PMID: 28663439 DOI: 10.1126/science.aao0100] [Citation(s) in RCA: 307] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/22/2017] [Indexed: 12/26/2022]
Abstract
Type III CRISPR-Cas systems in prokaryotes provide immunity against invading nucleic acids through the coordinated degradation of transcriptionally active DNA and its transcripts by the Csm effector complex. The Cas10 subunit of the complex contains an HD nuclease domain that is responsible for DNA degradation and two Palm domains with elusive functions. In addition, Csm6, a ribonuclease that is not part of the complex, is also required to provide full immunity. We show here that target RNA binding by the Csm effector complex of Streptococcus thermophilus triggers Cas10 to synthesize cyclic oligoadenylates (cA n ; n = 2 to 6) by means of the Palm domains. Acting as signaling molecules, cyclic oligoadenylates bind Csm6 to activate its nonspecific RNA degradation. This cyclic oligoadenylate-based signaling pathway coordinates different components of CRISPR-Cas to prevent phage infection and propagation.
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Affiliation(s)
- Migle Kazlauskiene
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania
| | - Georgij Kostiuk
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania.
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Saulėtekio Avenue 7, 10257 Vilnius, Lithuania.
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17
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Type III CRISPR-Cas Immunity: Major Differences Brushed Aside. Trends Microbiol 2016; 25:49-61. [PMID: 27773522 DOI: 10.1016/j.tim.2016.09.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 09/21/2016] [Accepted: 09/27/2016] [Indexed: 12/26/2022]
Abstract
For a long time the mechanism of immunity provided by the Type III CRISPR-Cas systems appeared to be inconsistent: the Type III-A Csm complex of Staphylococcus epidermidis was first reported to target DNA while Type III-B Cmr complexes were shown to target RNA. This long-standing conundrum has now been resolved by finding that the Type III CRISPR-Cas systems are both RNases and target RNA-activated DNA nucleases. The immunity is achieved by coupling binding and cleavage of RNA transcripts to the degradation of invading DNA. The base-pairing potential between the target RNA and the CRISPR RNA (crRNA) 5'-handle seems to play an important role in discriminating self and non-self nucleic acids; however, the detailed mechanism remains to be uncovered.
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18
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Mönttinen HA, Ravantti JJ, Poranen MM. Common Structural Core of Three-Dozen Residues Reveals Intersuperfamily Relationships. Mol Biol Evol 2016; 33:1697-710. [DOI: 10.1093/molbev/msw047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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19
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Li Y, Pan S, Zhang Y, Ren M, Feng M, Peng N, Chen L, Liang YX, She Q. Harnessing Type I and Type III CRISPR-Cas systems for genome editing. Nucleic Acids Res 2016. [PMID: 26467477 DOI: 10.1093/nar/gkv1044.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are widespread in archaea and bacteria, and research on their molecular mechanisms has led to the development of genome-editing techniques based on a few Type II systems. However, there has not been any report on harnessing a Type I or Type III system for genome editing. Here, a method was developed to repurpose both CRISPR-Cas systems for genetic manipulation in Sulfolobus islandicus, a thermophilic archaeon. A novel type of genome-editing plasmid (pGE) was constructed, carrying an artificial mini-CRISPR array and a donor DNA containing a non-target sequence. Transformation of a pGE plasmid would yield two alternative fates to transformed cells: wild-type cells are to be targeted for chromosomal DNA degradation, leading to cell death, whereas those carrying the mutant gene would survive the cell killing and selectively retained as transformants. Using this strategy, different types of mutation were generated, including deletion, insertion and point mutations. We envision this method is readily applicable to different bacteria and archaea that carry an active CRISPR-Cas system of DNA interference provided the protospacer adjacent motif (PAM) of an uncharacterized PAM-dependent CRISPR-Cas system can be predicted by bioinformatic analysis.
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Affiliation(s)
- Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Saifu Pan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Min Ren
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingxia Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai 201306, China
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
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20
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Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods.
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21
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Estrella MA, Kuo FT, Bailey S. RNA-activated DNA cleavage by the Type III-B CRISPR-Cas effector complex. Genes Dev 2016; 30:460-70. [PMID: 26848046 PMCID: PMC4762430 DOI: 10.1101/gad.273722.115] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/11/2016] [Indexed: 02/06/2023]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat) system is an RNA-guided immune system that protects prokaryotes from invading genetic elements. This system represents an inheritable and adaptable immune system that is mediated by multisubunit effector complexes. In the Type III-B system, the Cmr effector complex has been found to cleave ssRNA in vitro. However, in vivo, it has been implicated in transcription-dependent DNA targeting. We show here that the Cmr complex from Thermotoga maritima can cleave an ssRNA target that is complementary to the CRISPR RNA. We also show that binding of a complementary ssRNA target activates an ssDNA-specific nuclease activity in the histidine-aspartate (HD) domain of the Cmr2 subunit of the complex. These data suggest a mechanism for transcription-coupled DNA targeting by the Cmr complex and provide a unifying mechanism for all Type III systems.
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Affiliation(s)
- Michael A Estrella
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Fang-Ting Kuo
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Scott Bailey
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
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22
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Elmore JR, Sheppard NF, Ramia N, Deighan T, Li H, Terns RM, Terns MP. Bipartite recognition of target RNAs activates DNA cleavage by the Type III-B CRISPR-Cas system. Genes Dev 2016; 30:447-59. [PMID: 26848045 PMCID: PMC4762429 DOI: 10.1101/gad.272153.115] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/03/2015] [Indexed: 12/18/2022]
Abstract
Here, Elmore et al. investigate how the Type III-B Cmr complex, which cleaves invader RNAs recognized by the CRISPR RNA (crRNA), functions. The findings demonstrate that the Cmr complex is a novel DNA nuclease activated by invader RNAs containing a crRNA target sequence and a protospacer-adjacent motif (rPAM). CRISPR–Cas systems eliminate nucleic acid invaders in bacteria and archaea. The effector complex of the Type III-B Cmr system cleaves invader RNAs recognized by the CRISPR RNA (crRNA ) of the complex. Here we show that invader RNAs also activate the Cmr complex to cleave DNA. As has been observed for other Type III systems, Cmr eliminates plasmid invaders in Pyrococcus furiosus by a mechanism that depends on transcription of the crRNA target sequence within the plasmid. Notably, we found that the target RNA per se induces DNA cleavage by the Cmr complex in vitro. DNA cleavage activity does not depend on cleavage of the target RNA but notably does require the presence of a short sequence adjacent to the target sequence within the activating target RNA (rPAM [RNA protospacer-adjacent motif]). The activated complex does not require a target sequence (or a PAM) in the DNA substrate. Plasmid elimination by the P. furiosus Cmr system also does not require the Csx1 (CRISPR-associated Rossman fold [CARF] superfamily) protein. Plasmid silencing depends on the HD nuclease and Palm domains of the Cmr2 (Cas10 superfamily) protein. The results establish the Cmr complex as a novel DNA nuclease activated by invader RNAs containing a crRNA target sequence and a rPAM.
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Affiliation(s)
- Joshua R Elmore
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Nolan F Sheppard
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Nancy Ramia
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32313, USA
| | - Trace Deighan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32313, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA; Department of Genetics, Florida State University, Tallahassee, Florida 32313, USA; Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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23
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Burroughs AM, Zhang D, Schäffer DE, Iyer LM, Aravind L. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Nucleic Acids Res 2015; 43:10633-54. [PMID: 26590262 PMCID: PMC4678834 DOI: 10.1093/nar/gkv1267] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/04/2015] [Indexed: 02/04/2023] Open
Abstract
Cyclic di- and linear oligo-nucleotide signals activate defenses against invasive nucleic acids in animal immunity; however, their evolutionary antecedents are poorly understood. Using comparative genomics, sequence and structure analysis, we uncovered a vast network of systems defined by conserved prokaryotic gene-neighborhoods, which encode enzymes generating such nucleotides or alternatively processing them to yield potential signaling molecules. The nucleotide-generating enzymes include several clades of the DNA-polymerase β-like superfamily (including Vibrio cholerae DncV), a minimal version of the CRISPR polymerase and DisA-like cyclic-di-AMP synthetases. Nucleotide-binding/processing domains include TIR domains and members of a superfamily prototyped by Smf/DprA proteins and base (cytokinin)-releasing LOG enzymes. They are combined in conserved gene-neighborhoods with genes for a plethora of protein superfamilies, which we predict to function as nucleotide-sensors and effectors targeting nucleic acids, proteins or membranes (pore-forming agents). These systems are sometimes combined with other biological conflict-systems such as restriction-modification and CRISPR/Cas. Interestingly, several are coupled in mutually exclusive neighborhoods with either a prokaryotic ubiquitin-system or a HORMA domain-PCH2-like AAA+ ATPase dyad. The latter are potential precursors of equivalent proteins in eukaryotic chromosome dynamics. Further, components from these nucleotide-centric systems have been utilized in several other systems including a novel diversity-generating system with a reverse transcriptase. We also found the Smf/DprA/LOG domain from these systems to be recruited as a predicted nucleotide-binding domain in eukaryotic TRPM channels. These findings point to evolutionary and mechanistic links, which bring together CRISPR/Cas, animal interferon-induced immunity, and several other systems that combine nucleic-acid-sensing and nucleotide-dependent signaling.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Daniel E Schäffer
- Montgomery Blair High School, Magnet Program, Silver Spring, MD 20901, USA
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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24
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Abstract
Bacterial adaptive immunity hinges on CRISPR-Cas systems that provide DNA-encoded, RNA-mediated targeting of exogenous nucleic acids. A plethora of CRISPR molecular machines occur broadly in prokaryotic genomes, with a diversity of Cas nucleases that can be repurposed for various applications.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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25
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Li Y, Pan S, Zhang Y, Ren M, Feng M, Peng N, Chen L, Liang YX, She Q. Harnessing Type I and Type III CRISPR-Cas systems for genome editing. Nucleic Acids Res 2015; 44:e34. [PMID: 26467477 PMCID: PMC4770200 DOI: 10.1093/nar/gkv1044] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/30/2015] [Indexed: 12/24/2022] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are widespread in archaea and bacteria, and research on their molecular mechanisms has led to the development of genome-editing techniques based on a few Type II systems. However, there has not been any report on harnessing a Type I or Type III system for genome editing. Here, a method was developed to repurpose both CRISPR-Cas systems for genetic manipulation in Sulfolobus islandicus, a thermophilic archaeon. A novel type of genome-editing plasmid (pGE) was constructed, carrying an artificial mini-CRISPR array and a donor DNA containing a non-target sequence. Transformation of a pGE plasmid would yield two alternative fates to transformed cells: wild-type cells are to be targeted for chromosomal DNA degradation, leading to cell death, whereas those carrying the mutant gene would survive the cell killing and selectively retained as transformants. Using this strategy, different types of mutation were generated, including deletion, insertion and point mutations. We envision this method is readily applicable to different bacteria and archaea that carry an active CRISPR-Cas system of DNA interference provided the protospacer adjacent motif (PAM) of an uncharacterized PAM-dependent CRISPR-Cas system can be predicted by bioinformatic analysis.
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Affiliation(s)
- Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Saifu Pan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Min Ren
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingxia Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai 201306, China
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
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26
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Gallo G, Augusto G, Rangel G, Zelanis A, Mori MA, Barbosa Campos C, Würtele M. Purification, crystallization, crystallographic analysis and phasing of the CRISPR-associated protein Csm2 from Thermotoga maritima. Acta Crystallogr F Struct Biol Commun 2015; 71:1223-7. [PMID: 26457510 PMCID: PMC4601583 DOI: 10.1107/s2053230x15014776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/06/2015] [Indexed: 12/26/2022] Open
Abstract
The clusters of regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) system consists of an intriguing machinery of proteins that confer bacteria and archaea with immunity against phages and plasmids via an RNA-guided interference mechanism. Here, the cloning, recombinant expression in Escherichia coli BL21 (DE3), purification, crystallization and preliminary X-ray diffraction analysis of Csm2 from Thermotoga maritima are reported. Csm2 is thought to be a component of an important protein complex of the type IIIA CRISPR-Cas system, which is involved in the CRISPR-Cas RNA-guided interference pathway. The structure of Csm2 was solved via cadmium single-wavelength anomalous diffraction (Cd-SAD) phasing. Owing to its involvement in the CRISPR-Cas system, the crystal structure of this protein could be of importance in elucidating the mechanism of type IIIA CRISPR-Cas systems in bacteria and archaea.
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Affiliation(s)
- Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo, Rua Talim 330, 12231-280 São José dos Campos-SP, Brazil
| | - Gilles Augusto
- Department of Science and Technology, Federal University of São Paulo, Rua Talim 330, 12231-280 São José dos Campos-SP, Brazil
| | - Giulliana Rangel
- Department of Science and Technology, Federal University of São Paulo, Rua Talim 330, 12231-280 São José dos Campos-SP, Brazil
| | - André Zelanis
- Department of Science and Technology, Federal University of São Paulo, Rua Talim 330, 12231-280 São José dos Campos-SP, Brazil
| | - Marcelo A. Mori
- Department of Biophysics, Federal University of São Paulo, Rua Botucatu 862, 04023-062 São Paulo-SP, Brazil
| | - Cláudia Barbosa Campos
- Department of Science and Technology, Federal University of São Paulo, Rua Talim 330, 12231-280 São José dos Campos-SP, Brazil
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo, Rua Talim 330, 12231-280 São José dos Campos-SP, Brazil
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Osawa T, Inanaga H, Numata T. Crystallization and preliminary X-ray diffraction analysis of the CRISPR-Cas RNA-silencing Cmr complex. Acta Crystallogr F Struct Biol Commun 2015; 71:735-40. [PMID: 26057804 PMCID: PMC4461339 DOI: 10.1107/s2053230x15007104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/09/2015] [Indexed: 11/10/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNA (crRNA) and CRISPR-associated (Cas) proteins constitute a prokaryotic adaptive immune system (CRISPR-Cas system) that targets and degrades invading genetic elements. The type III-B CRISPR-Cas Cmr complex, composed of the six Cas proteins (Cmr1-Cmr6) and a crRNA, captures and cleaves RNA complementary to the crRNA guide sequence. Here, a Cmr1-deficient functional Cmr (CmrΔ1) complex composed of Pyrococcus furiosus Cmr2-Cmr3, Archaeoglobus fulgidus Cmr4-Cmr5-Cmr6 and the 39-mer P. furiosus 7.01-crRNA was prepared. The CmrΔ1 complex was cocrystallized with single-stranded DNA (ssDNA) complementary to the crRNA guide by the vapour-diffusion method. The crystals diffracted to 2.1 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the triclinic space group P1, with unit-cell parameters a = 75.5, b = 76.2, c = 139.2 Å, α = 90.3, β = 104.8, γ = 118.6°. The asymmetric unit of the crystals is expected to contain one CmrΔ1-ssDNA complex, with a Matthews coefficient of 2.03 Å(3) Da(-1) and a solvent content of 39.5%.
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Affiliation(s)
- Takuo Osawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
| | - Hideko Inanaga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
| | - Tomoyuki Numata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
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Jackson RN, Wiedenheft B. A Conserved Structural Chassis for Mounting Versatile CRISPR RNA-Guided Immune Responses. Mol Cell 2015; 58:722-8. [PMID: 26028539 DOI: 10.1016/j.molcel.2015.05.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria and archaea rely on CRISPR (clustered regularly interspaced short palindromic repeats) RNA-guided adaptive immune systems for targeted elimination of foreign nucleic acids. These immune systems have been divided into three main types, and the first atomic-resolution structure of a type III RNA-guided immune complex provides new insights into the mechanisms of nucleic acid degradation. Here we compare the crystal structure of a type III complex to recently determined structures of DNA-targeting type I CRISPR complexes. Structural comparisons support previous assertions that type I and type III systems share a common ancestor and reveal how a conserved structural chassis is used to support RNA-, DNA-, or both RNA- and DNA-targeting mechanisms.
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Affiliation(s)
- Ryan N Jackson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
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Plagens A, Richter H, Charpentier E, Randau L. DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. FEMS Microbiol Rev 2015; 39:442-63. [PMID: 25934119 PMCID: PMC5965380 DOI: 10.1093/femsre/fuv019] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2015] [Indexed: 12/26/2022] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) adaptive immune systems use small guide RNAs, the CRISPR RNAs (crRNAs), to mark foreign genetic material, e.g. viral nucleic acids, for degradation. Archaea and bacteria encode a large variety of Cas proteins that bind crRNA molecules and build active ribonucleoprotein surveillance complexes. The evolution of CRISPR-Cas systems has resulted in a diversification of cas genes and a classification of the systems into three types and additional subtypes characterized by distinct surveillance and interfering complexes. Recent crystallographic and biochemical advances have revealed detailed insights into the assembly and DNA/RNA targeting mechanisms of the various complexes. Here, we review our knowledge on the molecular mechanism involved in the DNA and RNA interference stages of type I (Cascade: CRISPR-associated complex for antiviral defense), type II (Cas9) and type III (Csm, Cmr) CRISPR-Cas systems. We further highlight recently reported structural and mechanistic themes shared among these systems. This review details and compares the assembly and the DNA/RNA targeting mechanisms of the various surveillance complexes of prokaryotic CRISPR-Cas immune systems.
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Affiliation(s)
- André Plagens
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
| | - Hagen Richter
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
| | - Emmanuelle Charpentier
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden Hannover Medical School, Hannover 30625, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
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Osawa T, Inanaga H, Sato C, Numata T. Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog. Mol Cell 2015; 58:418-30. [PMID: 25921071 DOI: 10.1016/j.molcel.2015.03.018] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/18/2015] [Accepted: 03/11/2015] [Indexed: 10/23/2022]
Abstract
In prokaryotes, Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs), together with CRISPR-associated (Cas) proteins, capture and degrade invading genetic materials. In the type III-B CRISPR-Cas system, six Cas proteins (Cmr1-Cmr6) and a crRNA form an RNA silencing Cmr complex. Here we report the 2.1 Å crystal structure of the Cmr1-deficient, functional Cmr complex bound to single-stranded DNA, a substrate analog complementary to the crRNA guide. Cmr3 recognizes the crRNA 5' tag and defines the start position of the guide-target duplex, using its idiosyncratic loops. The β-hairpins of three Cmr4 subunits intercalate within the duplex, causing nucleotide displacements with 6 nt intervals, and thus periodically placing the scissile bonds near the crucial aspartate of Cmr4. The structure reveals the mechanism for specifying the periodic target cleavage sites from the crRNA 5' tag and provides insights into the assembly of the type III interference machineries and the evolution of the Cmr and Cascade complexes.
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Affiliation(s)
- Takuo Osawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
| | - Hideko Inanaga
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
| | - Chikara Sato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
| | - Tomoyuki Numata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.
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31
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Taylor DW, Zhu Y, Staals RHJ, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna JA. Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning. Science 2015; 348:581-5. [PMID: 25837515 PMCID: PMC4582657 DOI: 10.1126/science.aaa4535] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/11/2015] [Indexed: 12/16/2022]
Abstract
Adaptive immunity in bacteria involves RNA-guided surveillance complexes that use CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR RNAs (crRNAs) to target invasive nucleic acids for degradation. Whereas type I and type II CRISPR-Cas surveillance complexes target double-stranded DNA, type III complexes target single-stranded RNA. Near-atomic resolution cryo-electron microscopy reconstructions of native type III Cmr (CRISPR RAMP module) complexes in the absence and presence of target RNA reveal a helical protein arrangement that positions the crRNA for substrate binding. Thumblike β hairpins intercalate between segments of duplexed crRNA:target RNA to facilitate cleavage of the target at 6-nucleotide intervals. The Cmr complex is architecturally similar to the type I CRISPR-Cascade complex, suggesting divergent evolution of these immune systems from a common ancestor.
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Affiliation(s)
- David W Taylor
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA. California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Yifan Zhu
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands
| | - Jack E Kornfeld
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Akeo Shinkai
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan. RIKEN Structural Biology Laboratory, Kanagawa 230-0045, Japan
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands
| | - Eva Nogales
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA. California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA. Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Jennifer A Doudna
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA. California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA. Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. Department of Chemistry, University of California, Berkeley, CA 94720, USA. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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32
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Crystal structure of the Csm1 subunit of the Csm complex and its single-stranded DNA-specific nuclease activity. Structure 2015; 23:782-90. [PMID: 25773141 DOI: 10.1016/j.str.2015.01.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 01/02/2015] [Accepted: 01/29/2015] [Indexed: 11/20/2022]
Abstract
The CRISPR-Cas system is the RNA-guided immune defense mechanism in bacteria and archaea. Csm1 belongs to the Cas10 family, which is the common signature protein of the type III system. Csm1 is the largest subunit of the Csm interference complex in the type III-A subtype, which targets foreign DNA or RNA. Here, we report crystallographic and biochemical analyses of Thermococcus onnurineus Csm1, revealing a five-domain organization and single-stranded DNA (ssDNA)-specific nuclease activity associated with the N-terminal HD domain. This domain folds into permuted secondary structures in comparison with the HD domain of Cas3 and contains all the catalytically important residues. It exhibited both endo- and exonuclease activities in an Ni(2+) or Mn(2+)-dependent manner. The narrow width of the active-site cleft appears to restrict the substrate specificity to ssDNA and thus to prevent Csm1 from cleaving double-stranded chromosomal DNA. These data suggest that Csm1 may function in DNA interference by the Csm effector complex.
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33
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Hayes RP, Ke A. One more piece down to solve the III-A CRISPR puzzle. J Mol Biol 2015; 427:228-30. [PMID: 25451600 DOI: 10.1016/j.jmb.2014.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Robert P Hayes
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA.
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34
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Hale CR, Cocozaki A, Li H, Terns RM, Terns MP. Target RNA capture and cleavage by the Cmr type III-B CRISPR-Cas effector complex. Genes Dev 2014; 28:2432-43. [PMID: 25367038 PMCID: PMC4215187 DOI: 10.1101/gad.250712.114] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The effector complex of the Cmr/type III-B CRISPR–Cas system cleaves RNAs recognized by the crRNA of the complex and includes six protein subunits of unknown functions. Hale et al. used reconstituted Pyrococcus furiosus Cmr complexes and found that Cmr3 recognizes the signature crRNA tag sequence (and depends on protein–protein interactions with Cmr2, Cmr4, and Cmr5), each Cmr4 subunit mediates a target RNA cleavage, and Cmr1 and Cmr6 mediate an essential interaction between the 3′ region of the crRNA and the target RNA. The effector complex of the Cmr/type III-B CRISPR (clustered regularly interspaced short palindromic repeat)–Cas (CRISPR-associated) system cleaves RNAs recognized by the CRISPR RNA (crRNA) of the complex and includes six protein subunits of unknown functions. Using reconstituted Pyrococcus furiosus Cmr complexes, we found that each of the six Cmr proteins plays a critical role in either crRNA interaction or target RNA capture. Cmr2, Cmr3, Cmr4, and Cmr5 are all required for formation of a crRNA-containing complex detected by native gel electrophoresis, and the conserved 5′ repeat sequence tag and 5′-OH group of the crRNA are essential for the interaction. Interestingly, capture of the complementary target RNA additionally requires both Cmr1 and Cmr6. In detailed functional studies, we determined that P. furiosus Cmr complexes cleave target RNAs at 6-nucleotide (nt) intervals in the region of complementarity, beginning 5 nt downstream from the crRNA tag and continuing to within ∼14 nt of the 3′ end of the crRNA. Our findings indicate that Cmr3 recognizes the signature crRNA tag sequence (and depends on protein–protein interactions with Cmr2, Cmr4, and Cmr5), each Cmr4 subunit mediates a target RNA cleavage, and Cmr1 and Cmr6 mediate an essential interaction between the 3′ region of the crRNA and the target RNA.
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Affiliation(s)
- Caryn R Hale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Alexis Cocozaki
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA;
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA; Department of Genetics, Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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35
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Benda C, Ebert J, Scheltema RA, Schiller HB, Baumgärtner M, Bonneau F, Mann M, Conti E. Structural model of a CRISPR RNA-silencing complex reveals the RNA-target cleavage activity in Cmr4. Mol Cell 2014; 56:43-54. [PMID: 25280103 DOI: 10.1016/j.molcel.2014.09.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/29/2014] [Accepted: 08/29/2014] [Indexed: 12/26/2022]
Abstract
The Cmr complex is an RNA-guided endonuclease that cleaves foreign RNA targets as part of the CRISPR prokaryotic defense system. We investigated the molecular architecture of the P. furiosus Cmr complex using an integrative structural biology approach. We determined crystal structures of P. furiosus Cmr1, Cmr2, Cmr4, and Cmr6 and combined them with known structural information to interpret the cryo-EM map of the complex. To support structure determination, we obtained residue-specific interaction data using protein crosslinking and mass spectrometry. The resulting pseudoatomic model reveals how the superhelical backbone of the complex is defined by the polymerizing principles of Cmr4 and Cmr5 and how it is capped at the extremities by proteins of similar folds. The inner surface of the superhelix exposes conserved residues of Cmr4 that we show are required for target-cleavage activity. The structural and biochemical data thus identify Cmr4 as the conserved endoribonuclease of the Cmr complex.
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Affiliation(s)
- Christian Benda
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Judith Ebert
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard A Scheltema
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Herbert B Schiller
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marc Baumgärtner
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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36
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Tay M, Liu S, Yuan YA. Crystal structure of Thermobifida fusca Cse1 reveals target DNA binding site. Protein Sci 2014; 24:236-45. [PMID: 25420472 DOI: 10.1002/pro.2609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 11/21/2014] [Accepted: 11/21/2014] [Indexed: 11/06/2022]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) defense system is the only adaptive and inheritable immunity found in prokaryotes. The immunity is achieved through a multistep process of adaptation, expression, and interference. In the Type I-E system, interference is mediated by the CRISPR-associated complex for antiviral defense (Cascade), which recognizes invading double-stranded DNA (dsDNA) through the protospacer adjacent motif (PAM) by one of the Cascade components, Cse1. Here, we report the crystal structure of Thermobifida fusca Cse1 at 3.3 Å resolution. T. fusca Cse1 reveals the chair-like two-domain architecture with a well-defined flexible loop, L1, located at the larger N-terminal domain, which was not observed in previous structures of the single Cse1 protein. Structure-based mutagenesis analysis demonstrates that the well-defined flexible loop and a partially conserved structural motif ([FW]-X-[TH]) are involved in PAM binding and recognition, respectively. Moreover, structural docking of T. fusca Cse1 into Escherichia coli Cascade cryoelectron microscopy maps, coupled with structural comparison, reveals a conserved positive patch that is contiguous with Cse2 in the Cascade complex and adjacent to the Cas3 binding site, suggesting its role in R-loop formation/stabilization and the recruitment of Cas3 for target cleavage. Consistent with the structural observation, the introduction of alanine mutations at this positive patch abolished DNA binding activity by Cse1. Taken together, these results suggest that Cse1 is a critical Cascade component involved in Cascade assembly, dsDNA target recognition, R-loop formation, and Cas3 recruitment for target cleavage.
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Affiliation(s)
- Melanie Tay
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117543, Singapore
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37
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Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) loci and CRISPR-associated (Cas) proteins form an adaptive immune system that protects prokaryotes against plasmids and viruses. The Cmr complex, a type III-B effector complex, uses the CRISPR RNA (crRNA) as a guide to target RNA. Here, we show that the Cmr complex of Pyrococcus furiosus cleaves RNA at multiple sites that are 6 nt apart and are positioned relative to the 5′-end of the crRNA. We identified Cmr4 as the slicer and determined its crystal structure at 2.8 Å resolution. In the crystal, Cmr4 forms a helical filament that most likely reflects its structural organization in the Cmr complex. The putative active site is located at the inner surface of the filament where the guide and substrate RNA are thought to bind. The filament structure of Cmr4 accounts for multiple periodic cleavage sites on the substrate. Our study provides new insights into the structure and mechanism of the RNA-targeting Cmr complex.
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Affiliation(s)
- Xing Zhu
- National Institute of Biological Sciences at Beijing, Beijing 102206, China Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- National Institute of Biological Sciences at Beijing, Beijing 102206, China Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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38
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The RNA- and DNA-targeting CRISPR-Cas immune systems of Pyrococcus furiosus. Biochem Soc Trans 2014; 41:1416-21. [PMID: 24256230 DOI: 10.1042/bst20130056] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Using the hyperthermophile Pyrococcus furiosus, we have delineated several key steps in CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) invader defence pathways. P. furiosus has seven transcriptionally active CRISPR loci that together encode a total of 200 crRNAs (CRISPR RNAs). The 27 Cas proteins in this organism represent three distinct pathways and are primarily encoded in two large gene clusters. The Cas6 protein dices CRISPR locus transcripts to generate individual invader-targeting crRNAs. The mature crRNAs include a signature sequence element (the 5' tag) derived from the CRISPR locus repeat sequence that is important for function. crRNAs are tailored into distinct species and integrated into three distinct crRNA-Cas protein complexes that are all candidate effector complexes. The complex formed by the Cmr [Cas module RAMP (repeat-associated mysterious proteins)] (subtype III-B) proteins cleaves complementary target RNAs and can be programmed to cleave novel target RNAs in a prokaryotic RNAi-like manner. Evidence suggests that the other two CRISPR-Cas systems in P. furiosus, Csa (Cas subtype Apern) (subtype I-A) and Cst (Cas subtype Tneap) (subtype I-B), target invaders at the DNA level. Studies of the CRISPR-Cas systems from P. furiosus are yielding fundamental knowledge of mechanisms of crRNA biogenesis and silencing for three of the diverse CRISPR-Cas pathways, and reveal that organisms such as P. furiosus possess an arsenal of multiple RNA-guided mechanisms to resist diverse invaders. Our knowledge of the fascinating CRISPR-Cas pathways is leading in turn to our ability to co-opt these systems for exciting new biomedical and biotechnological applications.
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Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system protects prokaryotes from infection by viruses and other potential genome invaders. This system represents an inheritable and adaptable immune system that is mediated by large ribonucleoprotein complexes, the CRISPR-Cas effector complexes. The Cmr complex is unique among CRISPR-Cas effector complexes in that it destroys invading RNA and not DNA. To date, the Cmr complexes from two species have been characterized in vitro and, strikingly, they degrade RNA via distinct mechanisms. The possible in vivo targets, as well as our current knowledge of the Cmr complex, is reviewed in the present paper.
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40
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Electron microscopy studies of Type III CRISPR machines in Sulfolobus solfataricus. Biochem Soc Trans 2014; 41:1427-30. [PMID: 24256232 DOI: 10.1042/bst20130166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) system is an adaptive immune system that targets viruses and other mobile genetic elements in bacteria and archaea. Cells store information of past infections in their genome in repeat-spacer arrays. After transcription, these arrays are processed into unit-length crRNA (CRISPR RNA) that is loaded into effector complexes encoded by Cas (CRISPR-associated) genes. CRISPR-Cas complexes target invading nucleic acid for degradation. CRISPR effector complexes have been classified into three main types (I-III). Type III effector complexes share the Cas10 subunit. In the present paper, we discuss the structures of the two Type III effector complexes from Sulfolobus solfataricus, SsoCSM (subtype III-A) and SsoCMR (subtype III-B), obtained by electron microscopy and single particle analysis. We also compare these structures with Cascade (CRISPR-associated complex for antiviral defence) and with the RecA nucleoprotein.
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41
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van der Oost J, Westra ER, Jackson RN, Wiedenheft B. Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat Rev Microbiol 2014; 12:479-92. [PMID: 24909109 PMCID: PMC4225775 DOI: 10.1038/nrmicro3279] [Citation(s) in RCA: 507] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteria and archaea have evolved sophisticated adaptive immune systems, known as CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, which target and inactivate invading viruses and plasmids. Immunity is acquired by integrating short fragments of foreign DNA into CRISPR loci, and following transcription and processing of these loci, the CRISPR RNAs (crRNAs) guide the Cas proteins to complementary invading nucleic acid, which results in target interference. In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR-Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.
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Affiliation(s)
- John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Edze R Westra
- 1] Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands. [2] Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Ryan N Jackson
- Department of Microbiology and Immunology, Montana State University, PO Box 173520, Bozeman, Montana 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, PO Box 173520, Bozeman, Montana 59717, USA
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42
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Molecular mechanisms of CRISPR-mediated microbial immunity. Cell Mol Life Sci 2014; 71:449-65. [PMID: 23959171 PMCID: PMC3890593 DOI: 10.1007/s00018-013-1438-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/21/2013] [Accepted: 07/24/2013] [Indexed: 12/15/2022]
Abstract
Bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. Thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. Not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. Phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. The antagonistic interaction between bacteria and rapidly diversifying viruses promotes the evolution and dissemination of bacteriophage-resistance mechanisms in bacteria. Recently, an adaptive microbial immune system, named clustered regularly interspaced short palindromic repeats (CRISPR) and which provides acquired immunity against viruses and plasmids, has been identified. Unlike the restriction–modification anti-phage barrier that subjects to cleavage any foreign DNA lacking a protective methyl-tag in the target site, the CRISPR–Cas systems are invader-specific, adaptive, and heritable. In this review, we focus on the molecular mechanisms of interference/immunity provided by different CRISPR–Cas systems.
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Sun J, Jeon JH, Shin M, Shin HC, Oh BH, Kim JS. Crystal structure and CRISPR RNA-binding site of the Cmr1 subunit of the Cmr interference complex. ACTA ACUST UNITED AC 2014; 70:535-43. [DOI: 10.1107/s1399004713030290] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 11/05/2013] [Indexed: 12/26/2022]
Abstract
A multi-subunit ribonucleoprotein complex termed the Cmr RNA-silencing complex recognizes and destroys viral RNA in the CRISPR-mediated immune defence mechanism in many prokaryotes using an as yet unclear mechanism. InArchaeoglobus fulgidus, this complex consists of six subunits, Cmr1–Cmr6. Here, the crystal structure of Cmr1 fromA. fulgidusis reported, revealing that the protein is composed of two tightly associated ferredoxin-like domains. The domain located at the N-terminus is structurally most similar to the N-terminal ferredoxin-like domain of the CRISPR RNA-processing enzyme Cas6 fromPyrococcus furiosus. An ensuing mutational analysis identified a highly conserved basic surface patch that binds single-stranded nucleic acids specifically, including the mature CRISPR RNA, but in a sequence-independent manner. In addition, this subunit was found to cleave single-stranded RNA. Together, these studies elucidate the structure and the catalytic activity of the Cmr1 subunit.
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Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol Cell 2013; 52:135-145. [PMID: 24119403 DOI: 10.1016/j.molcel.2013.09.013] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/30/2013] [Accepted: 09/12/2013] [Indexed: 12/26/2022]
Abstract
The CRISPR-Cas system is a prokaryotic host defense system against genetic elements. The Type III-B CRISPR-Cas system of the bacterium Thermus thermophilus, the TtCmr complex, is composed of six different protein subunits (Cmr1-6) and one crRNA with a stoichiometry of Cmr112131445361:crRNA1. The TtCmr complex copurifies with crRNA species of 40 and 46 nt, originating from a distinct subset of CRISPR loci and spacers. The TtCmr complex cleaves the target RNA at multiple sites with 6 nt intervals via a 5' ruler mechanism. Electron microscopy revealed that the structure of TtCmr resembles a "sea worm" and is composed of a Cmr2-3 heterodimer "tail," a helical backbone of Cmr4 subunits capped by Cmr5 subunits, and a curled "head" containing Cmr1 and Cmr6. Despite having a backbone of only four Cmr4 subunits and being both longer and narrower, the overall architecture of TtCmr resembles that of Type I Cascade complexes.
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Spilman M, Cocozaki A, Hale C, Shao Y, Ramia N, Terns R, Terns M, Li H, Stagg S. Structure of an RNA silencing complex of the CRISPR-Cas immune system. Mol Cell 2013; 52:146-52. [PMID: 24119404 DOI: 10.1016/j.molcel.2013.09.008] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/08/2013] [Accepted: 08/20/2013] [Indexed: 12/11/2022]
Abstract
Bacterial and archaeal clustered regularly interspaced short palindromic repeat (CRISPR) loci capture virus and plasmid sequences and use them to recognize and eliminate these invaders. CRISPR RNAs (crRNAs) containing the acquired sequences are incorporated into effector complexes that destroy matching invader nucleic acids. The multicomponent Cmr effector complex cleaves RNA targets complementary to the crRNAs. Here, we report cryoelectron microscopy reconstruction of a functional Cmr complex bound with a target RNA at ~12 Å. Pairs of the Cmr4 and Cmr5 proteins form a helical core that is asymmetrically capped on each end by distinct pairs of the four remaining subunits: Cmr2 and Cmr3 at the conserved 5' crRNA tag sequence and Cmr1 and Cmr6 near the 3' end of the crRNA. The shape and organization of the RNA-targeting Cmr complex is strikingly similar to the DNA-targeting Cascade complex. Our results reveal a remarkably conserved architecture among very distantly related CRISPR-Cas complexes.
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Affiliation(s)
- Michael Spilman
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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Genetic characterization of antiplasmid immunity through a type III-A CRISPR-Cas system. J Bacteriol 2013; 196:310-7. [PMID: 24187086 DOI: 10.1128/jb.01130-13] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Many prokaryotes possess an adaptive immune system encoded by clustered regularly interspaced short palindromic repeats (CRISPRs). CRISPR loci produce small guide RNAs (crRNAs) that, in conjunction with flanking CRISPR-associated (cas) genes, combat viruses and block plasmid transfer by an antisense targeting mechanism. CRISPR-Cas systems have been classified into three types (I to III) that employ distinct mechanisms of crRNA biogenesis and targeting. The type III-A system in Staphylococcus epidermidis RP62a blocks the transfer of staphylococcal conjugative plasmids and harbors nine cas-csm genes. Previous biochemical analysis indicated that Cas10, Csm2, Csm3, Csm4, and Csm5 form a crRNA-containing ribonucleoprotein complex; however, the roles of these genes toward antiplasmid targeting remain unknown. Here, we determined the cas-csm genes that are required for antiplasmid immunity and used genetic and biochemical analyses to investigate the functions of predicted motifs and domains within these genes. We found that many mutations affected immunity by impacting the formation of the Cas10-Csm complex or crRNA biogenesis. Surprisingly, mutations in the predicted nuclease domains of the members of the Cas10-Csm complex had no detectable effect on antiplasmid immunity or crRNA biogenesis. In contrast, the deletion of csm6 and mutations in the cas10 Palm polymerase domain prevented CRISPR immunity without affecting either complex formation or crRNA production, suggesting their involvement in target destruction. By delineating the genetic requirements of this system, our findings further contribute to the mechanistic understanding of type III CRISPR-Cas systems.
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Ramia NF, Tang L, Cocozaki AI, Li H. Staphylococcus epidermidis Csm1 is a 3'-5' exonuclease. Nucleic Acids Res 2013; 42:1129-38. [PMID: 24121684 PMCID: PMC3902914 DOI: 10.1093/nar/gkt914] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) offer an adaptive immune system that protects bacteria and archaea from nucleic acid invaders through an RNA-mediated nucleic acid cleavage mechanism. Our knowledge of nucleic acid cleavage mechanisms is limited to three examples of widely different ribonucleoprotein particles that target either DNA or RNA. Staphylococcus epidermidis belongs to the Type III-A CRISPR system and has been shown to interfere with invading DNA in vivo. The Type III-A CRISPR system is characterized by the presence of Csm1, a member of Cas10 family of proteins, that has a permuted histidine–aspartate domain and a nucleotidyl cyclase-like domain, both of which contain sequence features characteristic of nucleases. In this work, we show in vitro that a recombinant S. epidermidis Csm1 cleaves single-stranded DNA and RNA exonucleolytically in the 3′–5′ direction. We further showed that both cleavage activities are divalent-metal-dependent and reside in the GGDD motif of the cyclase-like domain. Our data suggest that Csm1 may work in the context of an effector complex to degrade invading DNA and participate in CRISPR RNA maturation.
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Affiliation(s)
- Nancy F Ramia
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA and Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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Hrle A, Su AAH, Ebert J, Benda C, Randau L, Conti E. Structure and RNA-binding properties of the type III-A CRISPR-associated protein Csm3. RNA Biol 2013; 10:1670-8. [PMID: 24157656 DOI: 10.4161/rna.26500] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The prokaryotic adaptive immune system is based on the incorporation of genome fragments of invading viral genetic elements into clusters of regulatory interspaced short palindromic repeats (CRISPRs). The CRISPR loci are transcribed and processed into crRNAs, which are then used to target the invading nucleic acid for degradation. The large family of CRISPR-associated (Cas) proteins mediates this interference response. We have characterized Methanopyrus kandleri Csm3, a protein of the type III-A CRISPR-Cas complex. The 2.4 Å resolution crystal structure shows an elaborate four-domain fold organized around a core RRM-like domain. The overall architecture highlights the structural homology to Cas7, the Cas protein that forms the backbone of type I interference complexes. Csm3 binds unstructured RNAs in a sequence non-specific manner, suggesting that it interacts with the variable spacer sequence of the crRNA. The structural and biochemical data provide insights into the similarities and differences in this group of Cas proteins.
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Affiliation(s)
- Ajla Hrle
- Structural Cell Biology Department; Max Planck Institute of Biochemistry; Munich/Martinsried, Germany
| | - Andreas A H Su
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Straße 10, Marburg, Germany
| | - Judith Ebert
- Structural Cell Biology Department; Max Planck Institute of Biochemistry; Munich/Martinsried, Germany
| | - Christian Benda
- Structural Cell Biology Department; Max Planck Institute of Biochemistry; Munich/Martinsried, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Straße 10, Marburg, Germany
| | - Elena Conti
- Structural Cell Biology Department; Max Planck Institute of Biochemistry; Munich/Martinsried, Germany
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Abstract
CRISPR (cluster of regularly interspaced palindromic repeats) is a prokaryotic adaptive defence system, providing immunity against mobile genetic elements such as viruses. Genomically encoded crRNA (CRISPR RNA) is used by Cas (CRISPR-associated) proteins to target and subsequently degrade nucleic acids of invading entities in a sequence-dependent manner. The process is known as ‘interference’. In the present review we cover recent progress on the structural biology of the CRISPR/Cas system, focusing on the Cas proteins and complexes that catalyse crRNA biogenesis and interference. Structural studies have helped in the elucidation of key mechanisms, including the recognition and cleavage of crRNA by the Cas6 and Cas5 proteins, where remarkable diversity at the level of both substrate recognition and catalysis has become apparent. The RNA-binding RAMP (repeat-associated mysterious protein) domain is present in the Cas5, Cas6, Cas7 and Cmr3 protein families and RAMP-like domains are found in Cas2 and Cas10. Structural analysis has also revealed an evolutionary link between the small subunits of the type I and type III-B interference complexes. Future studies of the interference complexes and their constituent components will transform our understanding of the system.
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Osawa T, Inanaga H, Numata T. Crystallization and preliminary X-ray diffraction analysis of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA-silencing effector complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:585-7. [PMID: 23695584 DOI: 10.1107/s1744309113011202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/24/2013] [Indexed: 12/26/2022]
Abstract
Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci, found in prokaryotes, are transcribed to produce CRISPR RNAs (crRNAs). The Cmr proteins (Cmr1-6) and crRNA form a ribonucleoprotein complex that degrades target RNAs derived from invading genetic elements. Cmr2dHD, a Cmr2 variant lacking the N-terminal putative HD nuclease domain, and Cmr3 were co-expressed in Escherichia coli cells and co-purified as a complex. The Cmr2dHD-Cmr3 complex was co-crystallized with 3'-AMP by the vapour-diffusion method. The crystals diffracted to 2.6 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the orthorhombic space group I222, with unit-cell parameters a = 103.9, b = 136.7, c = 192.0 Å. The asymmetric unit of the crystals is expected to contain one Cmr2dHD-Cmr3 complex with a Matthews coefficient of 3.0 Å(3) Da(-1) and a solvent content of 59%.
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Affiliation(s)
- Takuo Osawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
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