1
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Bi M, Su W, Li J, Mo X. Insights into the inhibition of protospacer integration via direct interaction between Cas2 and AcrVA5. Nat Commun 2024; 15:3256. [PMID: 38627399 PMCID: PMC11021501 DOI: 10.1038/s41467-024-47713-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
Spacer acquisition step in CRISPR-Cas system involves the recognition and subsequent integration of protospacer by the Cas1-Cas2 complex in CRISPR-Cas systems. Here we report an anti-CRISPR protein, AcrVA5, and reveal the mechanisms by which it strongly inhibits protospacer integration. Our biochemical data shows that the integration by Cas1-Cas2 was abrogated in the presence of AcrVA5. AcrVA5 exhibits low binding affinity towards Cas2 and acetylates Cas2 at Lys55 on the binding interface of the Cas2 and AcrVA5 N-terminal peptide complex to inhibit the Cas2-mediated endonuclease activity. Moreover, a detailed structural comparison between our crystal structure and homolog structure shows that binding of AcrVA5 to Cas2 causes steric hindrance to the neighboring protospacer resulting in the partial disassembly of the Cas1-Cas2 and protospacer complex, as demonstrated by electrophoretic mobility shift assay. Our study focuses on this mechanism of spacer acquisition inhibition and provides insights into the biology of CRISPR-Cas systems.
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Affiliation(s)
- Mingfang Bi
- College of Veterinary Medicine, Jilin University, 130062, Changchun, Jilin, China
| | - Wenjing Su
- College of Veterinary Medicine, Jilin University, 130062, Changchun, Jilin, China
| | - Jiafu Li
- College of Veterinary Medicine, Jilin University, 130062, Changchun, Jilin, China
| | - Xiaobing Mo
- College of Veterinary Medicine, Jilin University, 130062, Changchun, Jilin, China.
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, Jilin University, 130062, Changchun, Jilin, China.
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2
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Shaibullah S, Shuhaimi N, Ker DS, Mohd-Sharif N, Ho KL, Teh AH, Waterman J, Tang TH, Wong RR, Nathan S, Mohamed R, Ng MJ, Fung SY, Jonet MA, Firdaus-Raih M, Ng CL. Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family. Commun Biol 2023; 6:920. [PMID: 37684342 PMCID: PMC10491678 DOI: 10.1038/s42003-023-05265-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Burkholderia pseudomallei is a highly versatile pathogen with ~25% of its genome annotated to encode hypothetical proteins. One such hypothetical protein, BPSL1038, is conserved across seven bacterial genera and 654 Burkholderia spp. Here, we present a 1.55 Å resolution crystal structure of BPSL1038. The overall structure folded into a modified βαββαβα ferredoxin fold similar to known Cas2 nucleases. The Cas2 equivalent catalytic aspartate (D11) pairs are conserved in BPSL1038 although B. pseudomallei has no known CRISPR associated system. Functional analysis revealed that BPSL1038 is a nuclease with endonuclease activity towards double-stranded DNA. The DNase activity is divalent ion independent and optimum at pH 6. The concentration of monovalent ions (Na+ and K+) is crucial for nuclease activity. An active site with a unique D11(X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D11(X20)SST motif and that the arginine residues R10 and R30 may interact with the nucleic acid backbone. The structural similarity of BPSL1038 to Cas2 proteins suggests that BPSL1038 may represent a sub-family of nucleases that share a common ancestor with Cas2.
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Affiliation(s)
- Sofiyah Shaibullah
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Nurshahirah Shuhaimi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - De-Sheng Ker
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Nurhikmah Mohd-Sharif
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, 43400, Selangor, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, 11900, Penang, Malaysia
| | - Jitka Waterman
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Thean-Hock Tang
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Rui-Rui Wong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
- Faculty of Health and Life Sciences, Inti International University, Persiaran Perdana, BBN, Nilai, 71800, Negeri Sembilan, Malaysia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Rahmah Mohamed
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Min Jia Ng
- Medicinal Mushroom Research Group (MMRG), Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Shin-Yee Fung
- Medicinal Mushroom Research Group (MMRG), Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Anuar Jonet
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia (NIBM), Jalan Bangi, Kajang, 43000, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia.
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3
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Kang YJ, Kim JH, Lee GH, Ha HJ, Park YH, Hong E, Park HH. The structure of AcrIC9 revealing the putative inhibitory mechanism of AcrIC9 against the type IC CRISPR-Cas system. IUCRJ 2023; 10:624-634. [PMID: 37668219 PMCID: PMC10478522 DOI: 10.1107/s2052252523007236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
CRISPR-Cas systems are known to be part of the bacterial adaptive immune system that provides resistance against intruders such as viruses, phages and other mobile genetic elements. To combat this bacterial defense mechanism, phages encode inhibitors called Acrs (anti-CRISPR proteins) that can suppress them. AcrIC9 is the most recently identified member of the AcrIC family that inhibits the type IC CRISPR-Cas system. Here, the crystal structure of AcrIC9 from Rhodobacter capsulatus is reported, which comprises a novel fold made of three central antiparallel β-strands surrounded by three α-helixes, a structure that has not been detected before. It is also shown that AcrIC9 can form a dimer via disulfide bonds generated by the Cys69 residue. Finally, it is revealed that AcrIC9 directly binds to the type IC cascade. Analysis and comparison of its structure with structural homologs indicate that AcrIC9 belongs to DNA-mimic Acrs that directly bind to the cascade complex and hinder the target DNA from binding to the cascade.
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Affiliation(s)
- Yong Jun Kang
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hyeong Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Gwan Hee Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Young-Hoon Park
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Eunmi Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
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4
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Smaruj P, Kieliszek M. Casposons - silent heroes of the CRISPR-Cas systems evolutionary history. EXCLI JOURNAL 2023; 22:70-83. [PMID: 36814855 PMCID: PMC9939771 DOI: 10.17179/excli2022-5581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/19/2022] [Indexed: 02/24/2023]
Abstract
Many archaeal and bacterial organisms possess an adaptive immunity system known as CRISPR-Cas. Its role is to recognize and degrade foreign DNA showing high similarity to repeats within the CRISPR array. In recent years computational techniques have been used to identify cas1 genes that are not associated with CRISPR systems, named cas1-solo. Often, cas1-solo genes are present in a conserved neighborhood of PolB-like polymerase genes, which is a characteristic feature of self-synthesizing, eukaryotic transposons of the Polinton class. Nearly all cas1-polB genomic islands are flanked by terminal inverted repeats and direct repeats which correspond to target site duplications. Considering the patchy taxonomic distribution of the identified islands in archaeal and bacterial genomes, they were characterized as a new superfamily of mobile genetic elements and called casposons. Here, we review recent experiments on casposons' mobility and discuss their discovery, classification, and evolutionary relationship with the CRISPR-Cas systems.
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Affiliation(s)
- Paulina Smaruj
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, United States of America,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-097 Warsaw, Poland,*To whom correspondence should be addressed: Paulina Smaruj, Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, United States of America, E-mail:
| | - Marek Kieliszek
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159 C, 02-776 Warsaw, Poland
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5
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Dhingra Y, Suresh SK, Juneja P, Sashital DG. PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation. Mol Cell 2022; 82:4353-4367.e6. [PMID: 36272411 PMCID: PMC9675710 DOI: 10.1016/j.molcel.2022.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/10/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Adaptation in CRISPR-Cas systems immunizes bacteria and archaea against mobile genetic elements. In many DNA-targeting systems, the Cas4-Cas1-Cas2 complex is required for selection and processing of DNA segments containing PAM sequences prior to integration of these "prespacer" substrates as spacers in the CRISPR array. We determined cryo-EM structures of the Cas4-Cas1-Cas2 adaptation complex from the type I-C system that encodes standalone Cas1 and Cas4 proteins. The structures reveal how Cas4 specifically reads out bases within the PAM sequence and how interactions with both Cas1 and Cas2 activate Cas4 endonuclease activity. The Cas4-PAM interaction ensures tight binding between the adaptation complex and the prespacer, significantly enhancing integration of the non-PAM end into the CRISPR array and ensuring correct spacer orientation. Corroborated with our biochemical results, Cas4-Cas1-Cas2 structures with substrates representing various stages of CRISPR adaptation reveal a temporally resolved mechanism for maturation and integration of functional spacers into the CRISPR array.
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Affiliation(s)
- Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Shravanti K Suresh
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Puneet Juneja
- Cryo-EM Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA.
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6
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Anand V, Prabhakaran HS, Gogoi P, Kanaujia SP, Kumar M. Structural and functional characterization of Cas2 of CRISPR-Cas subtype I-C lacking the CRISPR component. Front Mol Biosci 2022; 9:988569. [PMID: 36172044 PMCID: PMC9510766 DOI: 10.3389/fmolb.2022.988569] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022] Open
Abstract
The genome of pathogenic Leptospira interrogans serovars (Copenhageni and Lai) are predicted to have CRISPR-Cas of subtypes I-B and I-C. Cas2, one of the core Cas proteins, has a crucial role in adaptive defense against foreign nucleic acids. However, subtype I-C lacks the CRISPR element at its loci essential for RNA-mediated adaptive immunity against foreign nucleic acids. The reason for sustaining the expense of cas genes are unknown in the absence of a CRISPR array. Thus, Cas2C was chosen as a representative Cas protein from two well-studied serovars of Leptospira to address whether it is functional. In this study, the recombinant Cas2C of Leptospira serovars Copenhageni (rLinCas2C, 12 kDa) and Lai (rLinCas2C_Lai, 8.6 kDa) were overexpressed and purified. Due to natural frameshift mutation in the cas2c gene of serovar Lai, rLinCas2C_Lai was overexpressed and purified as a partially translated protein. Nevertheless, the recombinant Cas2C from each serovar exhibited metal-dependent DNase and metal-independent RNase activities. The crystal structure of rLinCas2C obtained at the resolution of 2.60 Å revealed the protein is in apostate conformation and contains N- (1–71 amino acids) and C-terminal (72–90 amino acids) regions, with the former possessing a ferredoxin fold. Substitution of the conserved residues (Tyr7, Asp8, Arg33, and Phe39) with alanine and deletion of Loop L2 resulted in compromised DNase activity. On the other hand, a moderate reduction in RNase activity was evident only in selective rLinCas2C mutants. Overall, in the absence of an array, the observed catalytic activity of Cas2C may be required for biological processes distinct from the CRISPR-Cas-associated function.
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Affiliation(s)
| | | | | | | | - Manish Kumar
- *Correspondence: Shankar Prasad Kanaujia, ; Manish Kumar,
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7
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Fapohunda FO, Qiao S, Pan Y, Wang H, Liu Y, Lü P. CRISPR Cas System: a Strategic Approach in Detection of Nucleic Acids. Microbiol Res 2022; 259:127000. [DOI: 10.1016/j.micres.2022.127000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/20/2022] [Accepted: 03/07/2022] [Indexed: 12/26/2022]
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Dixit B, Anand V, Hussain MS, Kumar M. The CRISPR-associated Cas4 protein from Leptospira interrogans demonstrate versatile nuclease activity. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100040. [PMID: 34841331 PMCID: PMC8610317 DOI: 10.1016/j.crmicr.2021.100040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022] Open
Abstract
The Cas4 protein is one of the core CRISPR-associated (Cas) proteins implicated in the adaptation module in many variants of the CRISPR-Cas system in prokaryotes against the invading genetic elements. Cas4 is recognized as a DNA exonuclease that contains a RecB nuclease domain and a Fe-S cluster-binding module. In Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130, the cas4 gene is functionally transcribed as an active component of the CRISPR-Cas I-B system. Investigation of nuclease activity of Cas4 (LinCas4) of the L. interrogans illustrated divalent-metal cofactor (Mn2+ or Mg2+) dependent endonuclease activity on the DNA substrate. In agreement, mutation of the selective metal interacting residues (Asp74 and Glu87) curtails the DNA cleavage activity in LinCas4. Computational modeling shows metal-ion interacting residues (Asp74 and Glu87) in the LinCas4 to be a part of the RecB motifs II and III, the same as other Cas4 orthologs. The mutation of a potential DNA interacting residue in the LinCas4 (LinCas4Y132A) or one of the four cysteine residues (LinCas4C18A) involved in coordinating the 4Fe-4S cluster did not perturb its DNase activity. Iron chelation assay of the purified LinCas4 demonstrated it in the apostate conformation. Reconstitution of the Fe-S cluster in the LinCas4 under in vitro condition displayed its coordination with four iron atoms per LinCas4 monomer and was confirmed by the UV and CD spectroscopy studies.
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Affiliation(s)
- Bhuvan Dixit
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Vineet Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Md. Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
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Guzmán NM, Esquerra-Ruvira B, Mojica FJM. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021; 24:473-498. [PMID: 34487299 PMCID: PMC8616872 DOI: 10.1007/s10123-021-00208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.
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Affiliation(s)
- Noemí M Guzmán
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Belén Esquerra-Ruvira
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain. .,Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain.
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10
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Isaev AB, Musharova OS, Severinov KV. Microbial Arsenal of Antiviral Defenses. Part II. BIOCHEMISTRY (MOSCOW) 2021; 86:449-470. [PMID: 33941066 DOI: 10.1134/s0006297921040064] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). The constant threat of phage infection is a major force that shapes evolution of microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering had been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection. In the first part defense associated with cell surface, roles of small molecules, and innate immunity systems relying on DNA modification were discussed. The second part focuses on adaptive immunity systems, abortive infection mechanisms, defenses associated with mobile genetic elements, and novel systems discovered in recent years through metagenomic mining.
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Affiliation(s)
- Artem B Isaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia.
| | - Olga S Musharova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia. .,Institute of Molecular Genetics, Moscow, 119334, Russia
| | - Konstantin V Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia. .,Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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11
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Butiuc-Keul A, Farkas A, Carpa R, Iordache D. CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes. Microb Physiol 2021; 32:2-17. [PMID: 34192695 DOI: 10.1159/000516643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/16/2021] [Indexed: 11/19/2022]
Abstract
Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (cas)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system's impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus - SARS-CoV-2; thus, the newest and promising applications are reviewed as well.
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Affiliation(s)
- Anca Butiuc-Keul
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Anca Farkas
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Rahela Carpa
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Dumitrana Iordache
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
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12
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Long C, Dai L, E C, Da LT, Yu J. Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2. Biophys J 2021; 120:3126-3137. [PMID: 34197800 PMCID: PMC8390960 DOI: 10.1016/j.bpj.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/10/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cas1 and Cas2 are highly conserved proteins across clustered-regularly-interspaced-short-palindromic-repeat-Cas systems and play a significant role in protospacer acquisition. Based on crystal structure of twofold symmetric Cas1-Cas2 in complex with dual-forked protospacer DNA (psDNA), we conducted all-atom molecular dynamics simulations to study the psDNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence, or PAMc, of Cas1-Cas2. In the simulation, we noticed that two active sites of Cas1 and Cas1’ bind asymmetrically to two identical PAMc on the psDNA captured from the crystal structure. For the modified psDNA containing only one PAMc, as that to be recognized by Cas1-Cas2 in general, our simulations show that the non-PAMc association site of Cas1-Cas2 remains destabilized until after the stably bound PAMc being cleaved at the corresponding association site. Thus, long-range correlation appears to exist upon the PAMc cleavage between the two active sites (∼10 nm apart) on Cas1-Cas2, which can be allosterically mediated by psDNA and Cas2 and Cas2’ in bridging. To substantiate such findings, we conducted repeated runs and further simulated Cas1-Cas2 in complex with synthesized psDNA sequences psL and psH, which have been measured with low and high frequency in acquisition, respectively. Notably, such intersite correlation becomes even more pronounced for the Cas1-Cas2 in complex with psH but remains low for the Cas1-Cas2 in complex with psL. Hence, our studies demonstrate that PAMc recognition and cleavage at one active site of Cas1-Cas2 may allosterically regulate non-PAMc association or even cleavage at the other site, and such regulation can be mediated by noncatalytic Cas2 and DNA protospacer to possibly support the ensued psDNA acquisition.
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Affiliation(s)
- Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Liqiang Dai
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China; Beijing Computational Science Research Center, Beijing, China
| | - Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai, China
| | - Jin Yu
- Departments of Physics and Astronomy and Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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14
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Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex. Nat Commun 2021; 12:2571. [PMID: 33958590 PMCID: PMC8102632 DOI: 10.1038/s41467-021-22900-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/26/2021] [Indexed: 02/03/2023] Open
Abstract
CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1-Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.
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15
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Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System. Structure 2020; 29:139-150.e3. [PMID: 33096014 DOI: 10.1016/j.str.2020.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/21/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
Bacterial type II toxin-antitoxin (TA) modules encode a toxic protein that downregulates metabolism and a specific antitoxin that binds and inhibits the toxin during normal growth. In non-typeable Haemophilus influenzae, a common cause of infections in humans, the vapXD locus was found to constitute a functional TA module and contribute to pathogenicity; however, the mode of action of VapD and the mechanism of inhibition by the VapX antitoxin remain unknown. Here, we report the structure of the intact H. influenzae VapXD complex, revealing an unusual 2:1 TA molecular stoichiometry where a Cas2-like homodimer of VapD binds a single VapX antitoxin. VapX consists of an oligonucleotide/oligosaccharide-binding domain that docks into an asymmetrical cavity on the toxin dimer. Structures of isolated VapD further reveal how a symmetrical toxin homodimer adapts to interacting with an asymmetrical antitoxin and suggest how a primordial TA system evolved to become part of CRISPR-Cas immunity systems.
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16
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Yu L, Marchisio MA. Types I and V Anti-CRISPR Proteins: From Phage Defense to Eukaryotic Synthetic Gene Circuits. Front Bioeng Biotechnol 2020; 8:575393. [PMID: 33102460 PMCID: PMC7556299 DOI: 10.3389/fbioe.2020.575393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins), a prokaryotic RNA-mediated adaptive immune system, has been repurposed for gene editing and synthetic gene circuit construction both in bacterial and eukaryotic cells. In the last years, the emergence of the anti-CRISPR proteins (Acrs), which are natural OFF-switches for CRISPR-Cas, has provided a new means to control CRISPR-Cas activity and promoted a further development of CRISPR-Cas-based biotechnological toolkits. In this review, we focus on type I and type V-A anti-CRISPR proteins. We first narrate Acrs discovery and analyze their inhibitory mechanisms from a structural perspective. Then, we describe their applications in gene editing and transcription regulation. Finally, we discuss the potential future usage-and corresponding possible challenges-of these two kinds of anti-CRISPR proteins in eukaryotic synthetic gene circuits.
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17
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Sasnauskas G, Siksnys V. CRISPR adaptation from a structural perspective. Curr Opin Struct Biol 2020; 65:17-25. [PMID: 32570107 DOI: 10.1016/j.sbi.2020.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
Abstract
Bacterial CRISPR-Cas systems provide adaptive immunity against viruses and other mobile genome elements. During the adaptation step cells become immunized by insertion of short fragments of foreign DNA, termed spacers, into the genomic region called a CRISPR array. Selection, processing and insertion of new spacers is an elaborate and precisely orchestrated reaction, which relies on the Cas1-Cas2 integrase complex and accessory proteins that vary among different types of CRISPR-Cas systems. This review focuses on CRISPR adaptation from the structural perspective, with the spotlight on adaptation proteins employed by type I and type II CRISPR-Cas systems.
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Affiliation(s)
- Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, Vilnius 10257, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, Vilnius 10257, Lithuania.
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18
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Abstract
CRISPR research began over 30 years ago with the incidental discovery of an unusual nucleotide arrangement in the Escherichia coli genome. It took 20 years to find the main function of CRISPR-Cas systems as an adaptive defence mechanism against invading nucleic acids, and our knowledge of their biology has steadily increased ever since. In parallel, the number of applications derived from CRISPR-Cas systems has risen spectacularly. The CRISPR-based genome editing tool is arguably the most exciting application in both basic and applied research. Lately, CRISPR-Cas research has partially shifted to the least understood aspect of its biology: the ability of CRISPR-Cas systems to acquire new immunities during the so-called adaptation step. To date, the most efficient natural system to readily acquire new spacers is the type II-A system of the gram-positive dairy bacterium Streptococcus thermophilus. The discovery of additional systems able to acquire new spacers will hopefully draw more attention to this step of CRISPR-Cas biology. This review focuses on the breakthroughs that have helped to unravel the adaptation phase and on questions that remain to be answered.
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Affiliation(s)
- Cas Mosterd
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
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19
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Shabbir MAB, Shabbir MZ, Wu Q, Mahmood S, Sajid A, Maan MK, Ahmed S, Naveed U, Hao H, Yuan Z. CRISPR-cas system: biological function in microbes and its use to treat antimicrobial resistant pathogens. Ann Clin Microbiol Antimicrob 2019; 18:21. [PMID: 31277669 PMCID: PMC6611046 DOI: 10.1186/s12941-019-0317-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022] Open
Abstract
The development of antibiotic resistance in bacteria is a major public health threat. Infection rates of resistant pathogens continue to rise against nearly all antimicrobials, which has led to development of different strategies to combat the antimicrobial resistance. In this review, we discuss how the newly popular CRISPR-cas system has been applied to combat antibiotic resistance in both extracellular and intracellular pathogens. We also review a recently developed method in which nano-size CRISPR complex was used without any phage to target the mecA gene. However, there is still challenge to practice these methods in field against emerging antimicrobial resistant pathogens.
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Affiliation(s)
- Muhammad Abu Bakr Shabbir
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Muhammad Zubair Shabbir
- Quality Operation Laboratory at University of Veterinary and Animal Sciences, Lahore, 54600, Pakistan
| | - Qin Wu
- National Reference Laboratory of Veterinary Drug Residues and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Sammina Mahmood
- Department of Botany, University of Education, Bank Road Campus, Lahore, Pakistan
| | - Abdul Sajid
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Muhammad Kashif Maan
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Saeed Ahmed
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Umer Naveed
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland, UK
| | - Haihong Hao
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Zonghui Yuan
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,National Reference Laboratory of Veterinary Drug Residues and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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20
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Ka D, Jang DM, Han BW, Bae E. Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. Nucleic Acids Res 2019; 46:9805-9815. [PMID: 30102386 PMCID: PMC6182153 DOI: 10.1093/nar/gky702] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR–Cas systems, the Cas1–Cas2 integrase complex and the subtype-specific Csn2 comprise the CRISPR adaptation module, which cooperates with the Cas9 nuclease effector for spacer selection. Here, we report the molecular organization of the Streptococcus pyogenes type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. We determined the crystal structure of S. pyogenes type II-A Cas2. Chromatographic and calorimetric analyses revealed the stoichiometry and topology of the type II-A adaptation module composed of Cas1, Cas2 and Csn2. We also demonstrated that Cas9 interacts with Csn2 in a direct and stoichiometric manner. Our results reveal a network of molecular interactions among type II-A Cas proteins and highlight the role of Csn2 in coordinating Cas components involved in the adaptation and interference stages of CRISPR-mediated immunity.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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21
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Lee H, Dhingra Y, Sashital DG. The Cas4-Cas1-Cas2 complex mediates precise prespacer processing during CRISPR adaptation. eLife 2019; 8:44248. [PMID: 31021314 PMCID: PMC6519985 DOI: 10.7554/elife.44248] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 04/19/2019] [Indexed: 12/15/2022] Open
Abstract
CRISPR adaptation immunizes bacteria and archaea against viruses. During adaptation, the Cas1-Cas2 complex integrates fragments of invader DNA as spacers in the CRISPR array. Recently, an additional protein Cas4 has been implicated in selection and processing of prespacer substrates for Cas1-Cas2, although this mechanism remains unclear. We show that Cas4 interacts directly with Cas1-Cas2 forming a Cas4-Cas1-Cas2 complex that captures and processes prespacers prior to integration. Structural analysis of the Cas4-Cas1-Cas2 complex reveals two copies of Cas4 that closely interact with the two integrase active sites of Cas1, suggesting a mechanism for substrate handoff following processing. We also find that the Cas4-Cas1-Cas2 complex processes single-stranded DNA provided in cis or in trans with a double-stranded DNA duplex. Cas4 cleaves precisely upstream of PAM sequences, ensuring the acquisition of functional spacers. Our results explain how Cas4 cleavage coordinates with Cas1-Cas2 integration and defines the exact cleavage sites and specificity of Cas4. Many people have now heard of CRISPR, or CRISPR-Cas9, as a gene editing technology. Yet CRISPR evolved in bacteria to protect them against viral infections. While parts of the CRISPR system are now being widely used, the research community still does not know everything about how the system operates in its natural setting. In bacteria, CRISPR protects against infection by making lasting records of viruses a cell has encountered. It cuts short sections from the viral DNA and keeps them as a way to fight the virus if it ever returns. The key proteins in collecting and storing the virus DNA are called Cas1, Cas2 and Cas4. Previous work suggests that Cas4 is important for cutting suitable lengths of DNA for storage. Yet, how Cas4, Cas1 and Cas2 work together to select, cut and store DNA is not well studied. Lee et al. have now used electron microscopy to examine how Cas1, Cas2 and Cas4 cooperate in the CRISPR system. The proteins studied came from bacteria called Bacillus halodurans. The structure revealed direct links between the Cas1 and Cas4 proteins that likely help to ensure these proteins are coordinated correctly to cut and store the DNA sections. Specifically, it showed that two Cas4 proteins interact with the two key active sites of Cas1. The findings also highlight that Cas4 cuts DNA at specific locations to make sure the resulting DNA sections are suitable for CRISPR protection. The close association between Cas1 and Cas4 could be a critical aspect of the reliability of the CRISPR system in protecting bacteria from viruses. There are more bacteria on Earth than any other living thing. Understanding their biology has wide ranging environmental, health and bioengineering applications. In addition, learning more about the CRISPR system could further expand its potential to drive revolutionary biotechnology tools derived from these bacterial immune systems.
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Affiliation(s)
- Hayun Lee
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, United States
| | - Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, United States
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, United States
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22
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Xiao G, Yi Y, Che R, Zhang Q, Imran M, Khan A, Yan J, Lin X. Characterization of CRISPR-Cas systems in Leptospira reveals potential application of CRISPR in genotyping of Leptospira interrogans. APMIS 2019; 127:202-216. [PMID: 30908774 DOI: 10.1111/apm.12935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
Leptospirosis is a zoonotic disease caused by pathogenic Leptospira. However, understanding of the pathogenic mechanism of Leptospira is still elusive due to the limited number of genetic tools available for this microorganism. Currently, the reason for the genetic inaccessibility of Leptospira is still unknown. It is well known that as an acquired immunity of bacteria, Clustered Regularly Interspaced Short Palindromic Repeat-CRISPR-associated gene (CRISPR-Cas) systems can help bacteria against invading mobile genetic elements. In this study, the occurrence and diversity of CRISPR-Cas systems in 41 genomes of Leptospira strains were investigated. Three subtypes (subtype I-B, subtype I-C and subtype I-E) of CRISPR-Cas systems were identified in both pathogenic and intermediate Leptospira species but not in saprophytic species. Noteworthy, the majority of pathogenic species harbor two different types of CRISPR-Cas systems (subtype I-B and subtype I-E). Furthermore, Cas2 protein of subtype I-C in L. interrogans exhibited a metal-dependent DNase activity in a nonspecific manner. CRISPR spacers in subtype I-B are highly conserved within the same serovars and hypervariable across different serovars of L. interrogans. Based on the subtype I-B CRISPR arrays, the serotypes of different L. interrogans strains were easily identified. Investigation of the origin of CRISPR spacers showed that 192 spacers (23.5%) matched to mobile genetic elements, indicating CRISPR-Cas systems may play an important role in the defense of foreign invading DNA.
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Affiliation(s)
- Guohui Xiao
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Yusi Yi
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Rongbo Che
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qinchao Zhang
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Muhammad Imran
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Abidullah Khan
- Department of Burns, School of Medicine, Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jie Yan
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Basic Medical Microbiology Division, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xu'ai Lin
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Basic Medical Microbiology Division, School of Medicine, Zhejiang University, Hangzhou, China
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23
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Karimian A, Azizian K, Parsian H, Rafieian S, Shafiei‐Irannejad V, Kheyrollah M, Yousefi M, Majidinia M, Yousefi B. CRISPR/Cas9 technology as a potent molecular tool for gene therapy. J Cell Physiol 2019; 234:12267-12277. [DOI: 10.1002/jcp.27972] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/19/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Ansar Karimian
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences Babol Iran
- Cancer & Immunology Research Center, Kurdistan University of Medical Sciences Sanandaj Iran
- Student Research Committee, Babol University of Medical Sciences Babol Iran
| | - Khalil Azizian
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Science Tabriz Iran
| | - Hadi Parsian
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences Babol Iran
| | - Sona Rafieian
- Department of Oral and Maxillofacial Pathology School of Dentistry, Zanjan University of Medical Sciences Zanjan Iran
| | | | - Maryam Kheyrollah
- Department of Molecular Medicine National Institue of Genetic Engeneering and Biotechnology Tehran Iran
| | - Mehdi Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences Tabriz Iran
- Immunology Research Center, Tabriz University of Medical Sciences Tabriz Iran
| | - Maryam Majidinia
- Tumor Research Center, Urmia University of Medical Sciences Urmia Iran
| | - Bahman Yousefi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences Tehran Iran
- Department of Biochemistry and Clinical Laboratories Faculty of Medicine, Tabriz University of Medical Science Tabriz Iran
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24
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Koonin EV. CRISPR: a new principle of genome engineering linked to conceptual shifts in evolutionary biology. BIOLOGY & PHILOSOPHY 2019; 34:9. [PMID: 30930513 PMCID: PMC6404382 DOI: 10.1007/s10539-018-9658-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and even the general public thanks to the unprecedented success of the new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids. CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems in general, are nevertheless costly because autoimmunity cannot be eliminated completely. In addition to the autoimmunity, the fitness cost of CRISPR-Cas systems appears to be determined by their inhibitory effect on horizontal gene transfer, curtailing evolutionary innovation. Hence the dynamic evolution of CRISPR-Cas loci that are frequently lost and (re)acquired by archaea and bacteria. Another fundamental biological feature of CRISPR-Cas is its intimate connection with programmed cell death and dormancy induction in microbes. In this and, possibly, other immune systems, active immune response appears to be coupled to a different form of defense, namely, "altruistic" shutdown of cellular functions resulting in protection of neighboring cells. Finally, analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements (MGE) to the origin of various components of CRISPR-Cas systems, furthermore, different biological systems that function by genome manipulation appear to have evolved convergently from unrelated MGE. The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894 USA
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25
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Wei W, Zhang S, Fleming J, Chen Y, Li Z, Fan S, Liu Y, Wang W, Wang T, Liu Y, Ren B, Wang M, Jiao J, Chen Y, Zhou Y, Zhou Y, Gu S, Zhang X, Wan L, Chen T, Zhou L, Chen Y, Zhang XE, Li C, Zhang H, Bi L. Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features. FASEB J 2018; 33:1496-1509. [PMID: 29979631 DOI: 10.1096/fj.201800557rr] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems are prokaryotic adaptive immune systems against invading nucleic acids. CRISPR locus variability has been exploited in evolutionary and epidemiological studies of Mycobacterium tuberculosis, the causative agent of tuberculosis, for over 20 yr, yet the biological function of this type III-A system is largely unexplored. Here, using cell biology and biochemical, mutagenic, and RNA-seq approaches, we show it is active in invader defense and has features atypical of type III-A systems: mature CRISPR RNA (crRNA) in its crRNA-CRISPR/Cas protein complex are of uniform length (∼71 nt) and appear not to be subject to 3'-end processing after Cas6 cleavage of repeat RNA 8 nt from its 3' end. crRNAs generated resemble mature crRNA in type I systems, having both 5' (8 nt) and 3' (28 nt) repeat tags. Cas6 cleavage of repeat RNA is ion dependent, and accurate cleavage depends on the presence of a 3' hairpin in the repeat RNA and the sequence of its stem base nucleotides. This study unveils further diversity among CRISPR/Cas systems and provides insight into the crRNA recognition mechanism in M. tuberculosis, providing a foundation for investigating the potential of a type III-A-based genome editing system.-Wei, W., Zhang, S., Fleming, J., Chen, Y., Li, Z., Fan, S., Liu, Y., Wang, W., Wang, T., Liu, Y., Ren, B., Wang, M., Jiao, J., Chen, Y., Zhou, Y., Zhou, Y., Gu, S., Zhang, X., Wan, L., Chen, T., Zhou, L., Chen, Y., Zhang, X.-E., Li, C., Zhang, H., Bi, L. Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features.
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Affiliation(s)
- Wenjing Wei
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Ying Chen
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zihui Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Shanghua Fan
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yi Liu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Wei Wang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ting Wang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Baiguang Ren
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ming Wang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianjian Jiao
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Chen
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Yafeng Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Shoujin Gu
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
| | - Xiaoli Zhang
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Li Wan
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tao Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China; and
| | - Lin Zhou
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China; and
| | - Yong Chen
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Xian-En Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Chuanyou Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongtai Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lijun Bi
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China.,Guangdong Province Key Laboratory of Tuberculosis Systems Biology and Translational Medicine, Foshan, China
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26
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Drabavicius G, Sinkunas T, Silanskas A, Gasiunas G, Venclovas Č, Siksnys V. DnaQ exonuclease-like domain of Cas2 promotes spacer integration in a type I-E CRISPR-Cas system. EMBO Rep 2018; 19:e45543. [PMID: 29891635 PMCID: PMC6030702 DOI: 10.15252/embr.201745543] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas systems constitute an adaptive immune system that provides acquired resistance against phages and plasmids in prokaryotes. Upon invasion of foreign nucleic acids, some cells integrate short fragments of foreign DNA as spacers into the CRISPR locus to memorize the invaders and acquire resistance in the subsequent round of infection. This immunization step called adaptation is the least understood part of the CRISPR-Cas immunity. We have focused here on the adaptation stage of Streptococcus thermophilus DGCC7710 type I-E CRISPR4-Cas (St4) system. Cas1 and Cas2 proteins conserved in nearly all CRISPR-Cas systems are required for spacer acquisition. The St4 CRISPR-Cas system is unique because the Cas2 protein is fused to an additional DnaQ exonuclease domain. Here, we demonstrate that St4 Cas1 and Cas2-DnaQ form a multimeric complex, which is capable of integrating DNA duplexes with 3'-overhangs (protospacers) in vitro We further show that the DnaQ domain of Cas2 functions as a 3'-5'-exonuclease that processes 3'-overhangs of the protospacer to promote integration.
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Affiliation(s)
| | - Tomas Sinkunas
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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27
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Cas4-Dependent Prespacer Processing Ensures High-Fidelity Programming of CRISPR Arrays. Mol Cell 2018; 70:48-59.e5. [PMID: 29602742 DOI: 10.1016/j.molcel.2018.03.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/13/2018] [Accepted: 02/28/2018] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas immune systems integrate short segments of foreign DNA as spacers into the host CRISPR locus to provide molecular memory of infection. Cas4 proteins are widespread in CRISPR-Cas systems and are thought to participate in spacer acquisition, although their exact function remains unknown. Here we show that Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4 interacts tightly with the Cas1 integrase, forming a heterohexameric complex containing two Cas1 dimers and two Cas4 subunits. In the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Our results reveal the critical role of Cas4 in maintaining fidelity during CRISPR adaptation, providing a structural and mechanistic model for prespacer processing and integration.
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28
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Jeong M, Kim I, Kim G, Ka D, Kim NK, Bae E, Ryu KS, Suh JY. Solution structure and dynamics of Xanthomonas albilineans
Cas2 provide mechanistic insight on nuclease activity. FEBS Lett 2018; 592:147-155. [DOI: 10.1002/1873-3468.12942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 09/30/2017] [Accepted: 12/10/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Migyeong Jeong
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Iktae Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Gowoon Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Donghyun Ka
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Nak-Kyun Kim
- Advanced Analysis Center; Korea Institute of Science and Technology; Seoul Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Team; Korea Basic Science Institute; Ochang Chungbuk Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences; Seoul National University; Seoul Korea
- Institute for Biomedical Sciences; Shinshu University; Nagano Japan
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29
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Leon LM, Mendoza SD, Bondy-Denomy J. How bacteria control the CRISPR-Cas arsenal. Curr Opin Microbiol 2017; 42:87-95. [PMID: 29169146 DOI: 10.1016/j.mib.2017.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/30/2017] [Accepted: 11/03/2017] [Indexed: 02/07/2023]
Abstract
CRISPR-Cas systems are adaptive immune systems that protect their hosts from predation by bacteriophages (phages) and parasitism by other mobile genetic elements (MGEs). Given the potent nuclease activity of CRISPR effectors, these enzymes must be carefully regulated to minimize toxicity and maximize anti-phage immunity. While attention has been given to the transcriptional regulation of these systems (reviewed in [1]), less consideration has been given to the crucial post-translational processes that govern enzyme activation and inactivation. Here, we review recent findings that describe how Cas nucleases are controlled in diverse systems to provide a robust anti-viral response while limiting auto-immunity. We also draw comparisons to a distinct bacterial immune system, restriction-modification.
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Affiliation(s)
- Lina M Leon
- Department of Microbiology & Immunology, University of California, San Francisco, United States
| | - Senén D Mendoza
- Department of Microbiology & Immunology, University of California, San Francisco, United States
| | - Joseph Bondy-Denomy
- Department of Microbiology & Immunology, University of California, San Francisco, United States; Quantitative Biosciences Institute, University of California, San Francisco, United States.
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30
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Ka D, Hong S, Jeong U, Jeong M, Suh N, Suh JY, Bae E. Structural and dynamic insights into the role of conformational switching in the nuclease activity of the Xanthomonas albilineans Cas2 in CRISPR-mediated adaptive immunity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:054701. [PMID: 28612041 PMCID: PMC5438308 DOI: 10.1063/1.4984052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/11/2017] [Indexed: 06/07/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins constitute a microbial, adaptive immune system countering invading nucleic acids. Cas2 is a universal Cas protein found in all types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition into CRISPR loci. In subtype I-C CRISPR-Cas systems, Cas2 proteins are metal-dependent double-stranded DNA (dsDNA) nucleases, and a pH-dependent conformational transition has been proposed as a prerequisite for catalytic action. Here, we report the crystal structure of Xanthomonas albilineans Cas2 (XaCas2) and provide experimental evidence of a pH-dependent conformational change during functional activation. XaCas2 crystallized at an acidic pH represented a catalytically inactive conformational state in which two Asp8 residues were too far apart to coordinate a single catalytic metal ion. Consistently, XaCas2 exhibited dsDNA nuclease activity only under neutral and basic conditions. Despite the overall structural similarity of the two protomers, significant conformational heterogeneity was evident in the putative hinge regions, suggesting that XaCas2 engages in hinge-bending conformational switching. The presence of a Trp residue in the hinge region enabled the investigation of hinge dynamics by fluorescence spectroscopy. The pH dependence of the fluorescence intensity overlapped precisely with that of nuclease activity. Mutational analyses further suggested that conformational activation proceeded via a rigid-body hinge-bending motion as both D8E and hinge mutations significantly reduced nuclease activity. Together, our results reveal strong correlations between the conformational states, catalytic activity, and hinge dynamics of XaCas2, and provide structural and dynamic insights into the conformational activation of the nuclease function of Cas2.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Suji Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Ugeene Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Migyeong Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Nayoung Suh
- Department of Pharmaceutical Engineering, Soon Chun Hyang University, Asan 31538, South Korea
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31
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Abstract
Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894;
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32
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Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex. Proc Natl Acad Sci U S A 2017; 114:E5122-E5128. [PMID: 28611213 DOI: 10.1073/pnas.1618421114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas14-Cas2-32 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA. Two Cas1 dimers assemble on a Cas2 domain dimeric core, which is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2. We developed a sensitive in vitro assay and demonstrated that Cas1-Cas2-3 catalyzed spacer integration into CRISPR arrays. The integrase domain of Cas1 was necessary, whereas integration was independent of the helicase or nuclease activities of Cas3. Integration required at least partially duplex protospacers with free 3'-OH groups, and leader-proximal integration was stimulated by integration host factor. In a coupled capture and integration assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity. These results provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexes and their integration mechanism.
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33
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Navas LE, Amadio AF, Ortiz EM, Sauka DH, Benintende GB, Berretta MF, Zandomeni RO. Complete Sequence and Organization of pFR260, the Bacillus thuringiensis INTA Fr7-4 Plasmid Harboring Insecticidal Genes. J Mol Microbiol Biotechnol 2017; 27:43-54. [DOI: 10.1159/000451056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/23/2016] [Indexed: 11/19/2022] Open
Abstract
We report the complete sequence and analysis of pFR260, a novel megaplasmid of 260,595 bp from the <i>Bacillus thuringiensis</i> strain INTA Fr7-4 isolated in Argentina. It carries 7 insecticidal genes: 3 <i>cry8</i> copies previously reported, 2 <i>vip1,</i> and 2 <i>vip2</i>. Also, it carries a gene encoding a putative atypical Cry protein. These genes are arranged in a region of approximately 105 kbp in size with characteristics of a pathogenicity island with a potential coleopteran-specific insecticide profile. DNA strand composition asymmetry, as determined by GC skew analysis, and the presence of a Rep protein involved in the initiation of replication suggest a bidirectional <i>theta</i> mechanism of replication. In addition, many genes involved in conjugation and a CRISPR-Cas system were detected. The pFR260 sequence was deposited in GenBank under accession number KX258624.
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34
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Koonin EV, Zhang F. Coupling immunity and programmed cell suicide in prokaryotes: Life-or-death choices. Bioessays 2016; 39:1-9. [DOI: 10.1002/bies.201600186] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information; National Library of Medicine; Bethesda MD USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard; Cambridge MA USA
- Department of Health Sciences and Technology; Massachusetts Institute of Technology; Cambridge MA USA
- McGovern Institute for Brain Research at MIT; Cambridge MA USA
- Departments of Brain and Cognitive Science and Biological Engineering; Cambridge MA USA
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35
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Jung TY, Park KH, An Y, Schulga A, Deyev S, Jung JH, Woo EJ. Structural features of Cas2 from Thermococcus onnurineus in CRISPR-cas system type IV. Protein Sci 2016; 25:1890-7. [PMID: 27400737 DOI: 10.1002/pro.2981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas is RNA-based prokaryotic immune systems that defend against exogenous genetic elements such as plasmids and viruses. Cas1 and Cas2 are highly conserved components that play an essential part in the adaptation stage of all CRISPR-Cas systems. Characterization of CRISPR-Cas genes in Thermococcus onnurineus reveals the association of the Cas2 gene with the putative type IV system that lacks Cas1 or its homologous genes. Here, we present a crystal structure of T. onnurineus Cas2 (Ton_Cas2) that exhibits a deep and wide cleft at an interface lined with positive residues (Arg16, Lys18, Lys19, Arg22, and Arg23). The obvious DNA recognizing loops in Cas2 from E. coli (Eco_Cas2) are absent in Ton_Cas2 and have significantly different shapes and electrostatic potential distributions around the putative nucleotide binding region. Furthermore, Ton_Cas2 lacks the hairpin motif at the C-terminus that is responsible for Cas1 binding in Eco_Cas2. These structural features could be a unique signature and indicate an altered functional mechanism in the adaptation stage of Cas2 in type IV CRISPR-Cas systems.
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Affiliation(s)
- Tae-Yang Jung
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, South Korea.,Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, South Korea
| | - Kwang-Hyun Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, South Korea
| | - Yan An
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, South Korea
| | - Alexy Schulga
- Molecular Immunology Laboratory, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sergey Deyev
- Molecular Immunology Laboratory, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Jong-Hyun Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, South Korea
| | - Eui-Jeon Woo
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, South Korea. .,Department of Analytical Bioscience, University of Science and Technology, Daejeon, 305-333, South Korea.
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36
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Savitskaya EE, Musharova OS, Severinov KV. Diversity of CRISPR-Cas-mediated mechanisms of adaptive immunity in prokaryotes and their application in biotechnology. BIOCHEMISTRY (MOSCOW) 2016; 81:653-61. [DOI: 10.1134/s0006297916070026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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37
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Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature 2016; 532:517-21. [PMID: 27096362 DOI: 10.1038/nature17945] [Citation(s) in RCA: 564] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/30/2016] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas systems that provide defence against mobile genetic elements in bacteria and archaea have evolved a variety of mechanisms to target and cleave RNA or DNA. The well-studied types I, II and III utilize a set of distinct CRISPR-associated (Cas) proteins for production of mature CRISPR RNAs (crRNAs) and interference with invading nucleic acids. In types I and III, Cas6 or Cas5d cleaves precursor crRNA (pre-crRNA) and the mature crRNAs then guide a complex of Cas proteins (Cascade-Cas3, type I; Csm or Cmr, type III) to target and cleave invading DNA or RNA. In type II systems, RNase III cleaves pre-crRNA base-paired with trans-activating crRNA (tracrRNA) in the presence of Cas9 (refs 13, 14). The mature tracrRNA-crRNA duplex then guides Cas9 to cleave target DNA. Here, we demonstrate a novel mechanism in CRISPR-Cas immunity. We show that type V-A Cpf1 from Francisella novicida is a dual-nuclease that is specific to crRNA biogenesis and target DNA interference. Cpf1 cleaves pre-crRNA upstream of a hairpin structure formed within the CRISPR repeats and thereby generates intermediate crRNAs that are processed further, leading to mature crRNAs. After recognition of a 5'-YTN-3' protospacer adjacent motif on the non-target DNA strand and subsequent probing for an eight-nucleotide seed sequence, Cpf1, guided by the single mature repeat-spacer crRNA, introduces double-stranded breaks in the target DNA to generate a 5' overhang. The RNase and DNase activities of Cpf1 require sequence- and structure-specific binding to the hairpin of crRNA repeats. Cpf1 uses distinct active domains for both nuclease reactions and cleaves nucleic acids in the presence of magnesium or calcium. This study uncovers a new family of enzymes with specific dual endoribonuclease and endonuclease activities, and demonstrates that type V-A constitutes the most minimalistic of the CRISPR-Cas systems so far described.
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MESH Headings
- Bacterial Proteins/metabolism
- Base Sequence
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Calcium/metabolism
- Calcium/pharmacology
- Catalytic Domain
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- DNA Cleavage/drug effects
- Francisella/enzymology
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/biosynthesis
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Substrate Specificity
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Affiliation(s)
- Ines Fonfara
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Hagen Richter
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Majda Bratovič
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
- Hannover Medical School, Hannover 30625, Germany
| | - Anaïs Le Rhun
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
| | - Emmanuelle Charpentier
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
- Max Planck Institute for Infection Biology, Department of Regulation in Infection Biology, Berlin 10117, Germany
- Hannover Medical School, Hannover 30625, Germany
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38
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Dixit B, Ghosh KK, Fernandes G, Kumar P, Gogoi P, Kumar M. Dual nuclease activity of a Cas2 protein in CRISPR-Cas subtype I-B ofLeptospira interrogans. FEBS Lett 2016; 590:1002-16. [DOI: 10.1002/1873-3468.12124] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/20/2016] [Accepted: 03/03/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Bhuvan Dixit
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Karukriti Kaushik Ghosh
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Gary Fernandes
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Pankaj Kumar
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
| | - Manish Kumar
- Department of Biosciences and Bioengineering; Indian Institute of Technology Guwahati; Assam India
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39
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Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system. Biochem J 2016; 473:1063-72. [PMID: 26929403 DOI: 10.1042/bcj20160078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/16/2016] [Indexed: 11/17/2022]
Abstract
CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in the interference stage to guide effector CRISPR associated (Cas) protein(s) to target complementary foreign invading DNA. Cas1 is the integrase enzyme that is central to the catalysis of spacer integration. There are many diverse types of CRISPR-Cas systems, including type I-F systems, which are typified by a unique Cas1-Cas2-3 adaptation complex. In the present study we characterize the Cas1 protein of the potato phytopathogen Pectobacterium atrosepticum, an important model organism for understanding spacer acquisition in type I-F CRISPR-Cas systems. We demonstrate by mutagenesis that Cas1 is essential for adaptation in vivo and requires a conserved aspartic acid residue. By X-ray crystallography, we show that although P. atrosepticum Cas1 adopts a fold conserved among other Cas1 proteins, it possesses remarkable asymmetry as a result of structural plasticity. In particular, we resolve for the first time a flexible, asymmetric loop that may be unique to type I-F Cas1 proteins, and we discuss the implications of these structural features for DNA binding and enzymatic activity.
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40
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I can see CRISPR now, even when phage are gone: a view on alternative CRISPR-Cas functions from the prokaryotic envelope. Curr Opin Infect Dis 2016; 28:267-74. [PMID: 25887612 DOI: 10.1097/qco.0000000000000154] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
PURPOSE OF REVIEW CRISPR-Cas systems are prokaryotic immune systems against invading nucleic acids that adapt as new environmental threats arise. There are emerging examples of CRISPR-Cas functions in bacterial physiology beyond their role in adaptive immunity. This highlights the poorly understood, but potentially common, moonlighting functions of these abundant systems. We propose that these noncanonical CRISPR-Cas activities have evolved to respond to stresses at the cell envelope. RECENT FINDINGS Here, we discuss recent literature describing the impact of the extracellular environment on the regulation of CRISPR-Cas systems, and the influence of CRISPR-Cas activity on bacterial physiology. These described noncanonical CRISPR-Cas functions allow the bacterial cell to respond to the extracellular environment, primarily through changes in envelope physiology. SUMMARY This review discusses the expanding noncanonical functions of CRISPR-Cas systems, including their roles in virulence, focusing mainly on their relationship to the cell envelope. We first examine the effects of the extracellular environment on regulation of CRISPR-Cas components, and then discuss the impact of CRISPR-Cas systems on bacterial physiology, concentrating on their roles in influencing interactions with the environment including host organisms.
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41
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Abstract
Since the first demonstration that CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against phages and plasmids, numerous studies have yielded key insights into the molecular mechanisms governing how these systems attack and degrade foreign DNA. However, the molecular mechanisms underlying the adaptation stage, in which new immunological memory is formed, have until recently represented a major unresolved question. In this Progress article, we discuss recent discoveries that have shown both how foreign DNA is identified by the CRISPR-Cas adaptation machinery and the molecular basis for its integration into the chromosome to form an immunological memory. Furthermore, we describe the roles of each of the specific CRISPR-Cas components that are involved in memory formation, and consider current models for their evolutionary origin.
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42
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Hickman AB, Dyda F. The casposon-encoded Cas1 protein from Aciduliprofundum boonei is a DNA integrase that generates target site duplications. Nucleic Acids Res 2015; 43:10576-87. [PMID: 26573596 PMCID: PMC4678821 DOI: 10.1093/nar/gkv1180] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 10/22/2015] [Indexed: 01/06/2023] Open
Abstract
Many archaea and bacteria have an adaptive immune system known as CRISPR which allows them to recognize and destroy foreign nucleic acid that they have previously encountered. Two CRISPR-associated proteins, Cas1 and Cas2, are required for the acquisition step of adaptation, in which fragments of foreign DNA are incorporated into the host CRISPR locus. Cas1 genes have also been found scattered in several archaeal and bacterial genomes, unassociated with CRISPR loci or other cas proteins. Rather, they are flanked by nearly identical inverted repeats and enclosed within direct repeats, suggesting that these genetic regions might be mobile elements (‘casposons’). To investigate this possibility, we have characterized the in vitro activities of the putative Cas1 transposase (‘casposase’) from Aciduliprofundum boonei. The purified Cas1 casposase can integrate both short oligonucleotides with inverted repeat sequences and a 2.8 kb excised mini-casposon into target DNA. Casposon integration occurs without target specificity and generates 14–15 basepair target site duplications, consistent with those found in casposon host genomes. Thus, Cas1 casposases carry out similar biochemical reactions as the CRISPR Cas1-Cas2 complex but with opposite substrate specificities: casposases integrate specific sequences into random target sites, whereas CRISPR Cas1-Cas2 integrates essentially random sequences into a specific site in the CRISPR locus.
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Affiliation(s)
- Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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43
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Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems. Cell 2015; 163:840-53. [PMID: 26478180 DOI: 10.1016/j.cell.2015.10.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/28/2015] [Accepted: 10/04/2015] [Indexed: 12/26/2022]
Abstract
Bacteria acquire memory of viral invaders by incorporating invasive DNA sequence elements into the host CRISPR locus, generating a new spacer within the CRISPR array. We report on the structures of Cas1-Cas2-dual-forked DNA complexes in an effort toward understanding how the protospacer is sampled prior to insertion into the CRISPR locus. Our study reveals a protospacer DNA comprising a 23-bp duplex bracketed by tyrosine residues, together with anchored flanking 3' overhang segments. The PAM-complementary sequence in the 3' overhang is recognized by the Cas1a catalytic subunits in a base-specific manner, and subsequent cleavage at positions 5 nt from the duplex boundary generates a 33-nt DNA intermediate that is incorporated into the CRISPR array via a cut-and-paste mechanism. Upon protospacer binding, Cas1-Cas2 undergoes a significant conformational change, generating a flat surface conducive to proper protospacer recognition. Here, our study provides important structure-based mechanistic insights into PAM-dependent spacer acquisition.
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44
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An updated evolutionary classification of CRISPR-Cas systems. NATURE REVIEWS. MICROBIOLOGY 2015. [PMID: 26411297 DOI: 10.1038/nrmicro3569.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
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45
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Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJM, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol 2015; 13:722-36. [PMID: 26411297 DOI: 10.1038/nrmicro3569] [Citation(s) in RCA: 1538] [Impact Index Per Article: 170.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Omer S Alkhnbashi
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Fabrizio Costa
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Shiraz A Shah
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Sita J Saunders
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27606, USA
| | - Stan J J Brouns
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703HB Wageningen, Netherlands
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Philippe Horvath
- DuPont Nutrition and Health, BP10, Dangé-Saint-Romain 86220, France
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Groupe de Recherche en Écologie Buccale, Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Francisco J M Mojica
- Departamento de Fisiología, Genética y Microbiología. Universidad de Alicante. 03080-Alicante, Spain
| | - Rebecca M Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, Georgia 30602, USA
| | - Michael P Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Davison Life Sciences Complex, Green Street, Athens, Georgia 30602, USA
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, M5S 3E5, Canada
| | - Roger A Garrett
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703HB Wageningen, Netherlands
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiberg, Georges-Kohler-Allee 106, 79110 Freiberg, Germany.,BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, Germany
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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46
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Rollie C, Schneider S, Brinkmann AS, Bolt EL, White MF. Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition. eLife 2015; 4. [PMID: 26284603 PMCID: PMC4574026 DOI: 10.7554/elife.08716] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
The adaptive prokaryotic immune system CRISPR-Cas provides RNA-mediated protection from invading genetic elements. The fundamental basis of the system is the ability to capture small pieces of foreign DNA for incorporation into the genome at the CRISPR locus, a process known as Adaptation, which is dependent on the Cas1 and Cas2 proteins. We demonstrate that Cas1 catalyses an efficient trans-esterification reaction on branched DNA substrates, which represents the reverse- or disintegration reaction. Cas1 from both Escherichia coli and Sulfolobus solfataricus display sequence specific activity, with a clear preference for the nucleotides flanking the integration site at the leader-repeat 1 boundary of the CRISPR locus. Cas2 is not required for this activity and does not influence the specificity. This suggests that the inherent sequence specificity of Cas1 is a major determinant of the adaptation process.
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Affiliation(s)
- Clare Rollie
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Stefanie Schneider
- Faculty of Medicine, Institute of Cell Biology, University of Duisburg-Essen, Essen, Germany
| | - Anna Sophie Brinkmann
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Edward L Bolt
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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47
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Liu S, Yuan Z, Yuan YA. Structural insights into specific crRNA G-rich sequence binding by Meiothermus ruber Cse2. J Struct Biol 2015; 190:122-34. [PMID: 25791617 DOI: 10.1016/j.jsb.2015.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats)-mediated defense against invading nucleic acids is a process recently discovered in prokaryotes, which includes recognition and incorporation of invading genetic elements, transcription and processing of CRISPR-RNA (crRNA) and targeting the invaders through base pair recognition. In the type I-E CRISPR-Cas system, Cse2 is proposed to provide a platform to facilitate the targeting of the invading dsDNA by crRNA. Here we report the crystal structure of Meiothermus ruber Cse2 at 2.8Å. M. ruber Cse2 adopts an α-helical bundle scaffold, harbors a positive surface for nucleic acid binding and a conserved dimer interface with strikingly low buried surface area. M. ruber Cse2 selectively binds to G-rich crRNA sequence, which is stripped off from the Cse2-crRNA and Cascade-crRNA complexes by ssDNA or dsDNA with complementary sequence. Stable M. ruber Cascade is readily formed by co-expression of M. ruber Cascade proteins together with G-rich crRNA in vitro. Docking of M. ruber Cse2 structures into the Escherichia coli Cascade Cryo-EM envelope reveals a curved elongated shallow groove for ssRNA binding, which adopts a similar dimer interface discovered by high-resolution crystal structure of Cse2 within E. Coli Cascade. Taken together, our data provides the structural insights into crRNA G-rich sequence recognition by M. ruber Cse2 and reveals the potential structural mechanism for M. ruber Cascade assembly and function.
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Affiliation(s)
- Su Liu
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Zuanning Yuan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Y Adam Yuan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; National University of Singapore (Suzhou) Research Institute, 377 Lin Quan Street, Suzhou Industrial Park, Jiangsu 215123, China.
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48
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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: 55] [Impact Index Per Article: 6.1] [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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49
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Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature 2015; 519:193-8. [PMID: 25707795 PMCID: PMC4359072 DOI: 10.1038/nature14237] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/15/2015] [Indexed: 12/20/2022]
Abstract
Bacteria and archaea insert spacer sequences acquired from foreign DNAs into CRISPR loci to generate immunological memory. The Escherichia coli Cas1–Cas2 complex mediates spacer acquisition in vivo, but the molecular mechanism of this process is unknown. Here we show that the purified Cas1–Cas2 complex integrates oligonucleotide DNA substrates into acceptor DNA to yield products similar to those generated by retroviral integrases and transposases. Cas1 is the catalytic subunit, whereas Cas2 substantially increases integration activity. Protospacer DNA with free 3'-OH ends and supercoiled target DNA are required, and integration occurs preferentially at the ends of CRISPR repeats and at sequences adjacent to cruciform structures abutting A-T rich regions, similar to the CRISPR leader sequence. Our results demonstrate the Cas1–Cas2 complex to be the minimal machinery that catalyzes spacer DNA acquisition and explain the significance of CRISPR repeats in providing sequence and structural specificity for Cas1–Cas2-mediated adaptive immunity.
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50
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Wei Y, Chesne MT, Terns RM, Terns MP. Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus. Nucleic Acids Res 2015; 43:1749-58. [PMID: 25589547 PMCID: PMC4330368 DOI: 10.1093/nar/gku1407] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are RNA-based immune systems that protect prokaryotes from invaders such as phages and plasmids. In adaptation, the initial phase of the immune response, short foreign DNA fragments are captured and integrated into host CRISPR loci to provide heritable defense against encountered foreign nucleic acids. Each CRISPR contains a ∼100-500 bp leader element that typically includes a transcription promoter, followed by an array of captured ∼35 bp sequences (spacers) sandwiched between copies of an identical ∼35 bp direct repeat sequence. New spacers are added immediately downstream of the leader. Here, we have analyzed adaptation to phage infection in Streptococcus thermophilus at the CRISPR1 locus to identify cis-acting elements essential for the process. We show that the leader and a single repeat of the CRISPR locus are sufficient for adaptation in this system. Moreover, we identified a leader sequence element capable of stimulating adaptation at a dormant repeat. We found that sequences within 10 bp of the site of integration, in both the leader and repeat of the CRISPR, are required for the process. Our results indicate that information at the CRISPR leader-repeat junction is critical for adaptation in this Type II-A system and likely other CRISPR-Cas systems.
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Affiliation(s)
- Yunzhou Wei
- Departments of Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia Athens, GA 30602, USA
| | - Megan T. Chesne
- Departments of Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia Athens, GA 30602, USA
| | - Rebecca M. Terns
- Departments of Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia Athens, GA 30602, USA
| | - Michael P. Terns
- Departments of Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia Athens, GA 30602, USA
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