1
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Watts EA, Garrett SC, Catchpole RJ, Clark LM, Sanders TJ, Marshall CJ, Wenck BR, Vickerman RL, Santangelo TJ, Fuchs R, Robb B, Olson S, Graveley BR, Terns MP. Histones direct site-specific CRISPR spacer acquisition in model archaeon. Nat Microbiol 2023; 8:1682-1694. [PMID: 37550505 PMCID: PMC10823912 DOI: 10.1038/s41564-023-01446-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
CRISPR-Cas systems provide heritable immunity against viruses and other mobile genetic elements by incorporating fragments of invader DNA into the host CRISPR array as spacers. Integration of new spacers is localized to the 5' end of the array, and in certain Gram-negative Bacteria this polarized localization is accomplished by the integration host factor. For most other Bacteria and Archaea, the mechanism for 5' end localization is unknown. Here we show that archaeal histones play a key role in directing integration of CRISPR spacers. In Pyrococcus furiosus, deletion of either histone A or B impairs integration. In vitro, purified histones are sufficient to direct integration to the 5' end of the CRISPR array. Archaeal histone tetramers and bacterial integration host factor induce similar U-turn bends in bound DNA. These findings indicate a co-evolution of CRISPR arrays with chromosomal DNA binding proteins and a widespread role for binding and bending of DNA to facilitate accurate spacer integration.
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2
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DNA Motifs and an Accessory CRISPR Factor Determine Cas1 Binding and Integration Activity in Sulfolobus islandicus. Int J Mol Sci 2022; 23:ijms231710178. [PMID: 36077578 PMCID: PMC9456107 DOI: 10.3390/ijms231710178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
CRISPR-Cas systems empower prokaryotes with adaptive immunity against invasive mobile genetic elements. At the first step of CRISPR immunity adaptation, short DNA fragments from the invaders are integrated into CRISPR arrays at the leader-proximal end. To date, the mechanism of recognition of the leader-proximal end remains largely unknown. Here, in the Sulfolobus islandicus subtype I-A system, we show that mutations destroying the proximal region reduce CRISPR adaptation in vivo. We identify that a stem-loop structure is present on the leader-proximal end, and we demonstrate that Cas1 preferentially binds the stem-loop structure in vitro. Moreover, we demonstrate that the integrase activity of Cas1 is modulated by interacting with a CRISPR-associated factor Csa3a. When translocated to the CRISPR array, the Csa3a-Cas1 complex is separated by Csa3a binding to the leader-distal motif and Cas1 binding to the leader-proximal end. Mutation at the leader-distal motif reduces CRISPR adaptation efficiency, further confirming the in vivo function of leader-distal motif. Together, our results suggest a general model for binding of Cas1 protein to a leader motif and modulation of integrase activity by an accessory factor.
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3
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Prakash A, Kumar M. Transcriptional analysis of CRISPR I-B arrays of Leptospira interrogans serovar Lai and its processing by Cas6. Front Microbiol 2022; 13:960559. [PMID: 35966677 PMCID: PMC9372919 DOI: 10.3389/fmicb.2022.960559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
In the genome of various Leptospira interrogans serovars, the subtype I-B locus of CRISPR-Cas possesses either one or multiple CRISPR arrays. In silico database (CRISPRCasdb) for predicting CRISPR-Cas reveals seven CRISPR arrays in L. interrogans serovar Lai positioned between the two independent cas-operons. Here, we present the redefined repeat-spacer boundaries of the CRISPR subtype I-B locus of serovar Lai. Such refinement of boundaries of arrays in serovar Lai was done after comparison with the characterized array of another serovar Copenhageni and the manual analysis of CRISPR flanking sequences. Using the reverse transcription-PCR (RT-PCR), we account that the seven CRISPR are transcriptionally active in serovar Lai. Our RT-PCR and quantitative real-time PCR analysis of transcripts in serovar Lai indicated that seven CRISPR of subtype I-B transcribe together as a single precursor unit. Moreover, the cleavage of the two miniature pre-crRNA of the subtype I-B by Cas6 demonstrates the biogenesis of the expected size of mature crRNA essential for the guided interference of foreign DNA. This study features insight into transcription direction and the crRNA biogenesis in serovar Lai essential for RNA-mediated interference of invading nucleic acids.
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4
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Zhang X, An X. Adaptation by Type III CRISPR-Cas Systems: Breakthrough Findings and Open Questions. Front Microbiol 2022; 13:876174. [PMID: 35495695 PMCID: PMC9048733 DOI: 10.3389/fmicb.2022.876174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/03/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems acquire heritable defense memory against invading nucleic acids through adaptation. Type III CRISPR-Cas systems have unique and intriguing features of defense and are important in method development for Genetics research. We started to understand the common and unique properties of type III CRISPR-Cas adaptation in recent years. This review summarizes our knowledge regarding CRISPR-Cas adaptation with the emphasis on type III systems and discusses open questions for type III adaptation studies.
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Affiliation(s)
- Xinfu Zhang
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA, United States
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree breeding and Ecological Remediation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Xinfu Zhang,
| | - Xinmin An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Research Center of Tree breeding and Ecological Remediation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Xinmin An,
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5
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Zhang X, Garrett S, Graveley BR, Terns MP. Unique properties of spacer acquisition by the type III-A CRISPR-Cas system. Nucleic Acids Res 2021; 50:1562-1582. [PMID: 34893878 PMCID: PMC8860593 DOI: 10.1093/nar/gkab1193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Type III CRISPR-Cas systems have a unique mode of interference, involving crRNA-guided recognition of nascent RNA and leading to DNA and RNA degradation. How type III systems acquire new CRISPR spacers is currently not well understood. Here, we characterize CRISPR spacer uptake by a type III-A system within its native host, Streptococcus thermophilus. Adaptation by the type II-A system in the same host provided a basis for comparison. Cas1 and Cas2 proteins were critical for type III adaptation but deletion of genes responsible for crRNA biogenesis or interference did not detectably change spacer uptake patterns, except those related to host counter-selection. Unlike the type II-A system, type III spacers are acquired in a PAM- and orientation-independent manner. Interestingly, certain regions of plasmids and the host genome were particularly well-sampled during type III-A, but not type II-A, spacer uptake. These regions included the single-stranded origins of rolling-circle replicating plasmids, rRNA and tRNA encoding gene clusters, promoter regions of expressed genes and 5′ UTR regions involved in transcription attenuation. These features share the potential to form DNA secondary structures, suggesting a preferred substrate for type III adaptation. Lastly, the type III-A system adapted to and protected host cells from lytic phage infection.
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Affiliation(s)
- Xinfu Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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6
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Walker HE, Rizzo M, Fras Z, Jug B, Banach M, Penson PE. CRISPR Gene Editing in Lipid Disorders and Atherosclerosis: Mechanisms and Opportunities. Metabolites 2021; 11:857. [PMID: 34940615 PMCID: PMC8707018 DOI: 10.3390/metabo11120857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 12/04/2021] [Indexed: 12/24/2022] Open
Abstract
Elevated circulating concentrations of low-density lipoprotein cholesterol (LDL-C) have been conclusively demonstrated in epidemiological and intervention studies to be causally associated with the development of atherosclerotic cardiovascular disease. Enormous advances in LDL-C reduction have been achieved through the use of statins, and in recent years, through drugs targeting proprotein convertase subtilisin/kexin type 9 (PCSK9), a key regulator of the hepatic LDL-receptor. Existing approaches to PCSK9 targeting have used monoclonal antibodies or RNA interference. Although these approaches do not require daily dosing, as statins do, repeated subcutaneous injections are nevertheless necessary to maintain effectiveness over time. Recent experimental studies suggest that clustered regularly interspaced short palindromic repeats (CRISPR) gene-editing targeted at PCSK9 may represent a promising tool to achieve the elusive goal of a 'fire and forget' lifelong approach to LDL-C reduction. This paper will provide an overview of CRISPR technology, with a particular focus on recent studies with relevance to its potential use in atherosclerotic cardiovascular disease.
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Affiliation(s)
- Harry E. Walker
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton SO17 1BJ, UK;
| | - Manfredi Rizzo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (Promise), University of Palermo, 90133 Palermo, Italy;
| | - Zlatko Fras
- Centre for Preventive Cardiology, Division of Medicine, University Medical Centre Ljubljana, SI-1525 Ljubljana, Slovenia;
- Medical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Borut Jug
- Department of Vascular Diseases, University Medical Centre Ljubljana, SI-1525 Ljubljana, Slovenia;
| | - Maciej Banach
- Department of Preventive Cardiology and Lipidology, Medical University of Lodz, 93338 Lodz, Poland;
- Cardiovascular Research Centre, University of Zielona Gora, 65046 Zielona Gora, Poland
| | - Peter E. Penson
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK
- Liverpool Centre for Cardiovascular Science, Liverpool L7 8TX, UK
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7
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Lv W, Li T, Wang S, Wang H, Li X, Zhang S, Wang L, Xu Y, Wei W. The Application of the CRISPR/Cas9 System in the Treatment of Hepatitis B Liver Cancer. Technol Cancer Res Treat 2021; 20:15330338211045206. [PMID: 34605326 PMCID: PMC8493308 DOI: 10.1177/15330338211045206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system was originally discovered in prokaryotes and functions as part of the adaptive immune system. The experimental research of many scholars, as well as scientific and technological advancements, has allowed prokaryote-derived CRISPR/Cas genome-editing systems to transform our ability to manipulate, detect, image, and annotate specific DNA and RNA sequences in the living cells of diverse species. Through modern genetic engineering editing technology and high-throughput gene sequencing, we can edit and splice covalently closed circular DNA to silence it, and correct the mutation and deletion of liver cancer genes to achieve precise in situ repair of defective genes and prohibit viral infection or replication. Such manipulations do not destroy the structure of the entire genome and facilitate the cure of diseases. In this review, we discussed the possibility that CRISPR/Cas could be used as a treatment for patients with liver cancer caused by hepatitis B virus infection, and reviewed the challenges incurred by this effective gene-editing technology.
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Affiliation(s)
- Wei Lv
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tao Li
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shanshan Wang
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Huihui Wang
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xuemei Li
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shubing Zhang
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lianzi Wang
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei Wei
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
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8
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Wang X, Yuan Q, Zhang W, Ji S, Lv Y, Ren K, Lu M, Xiao Y. Sequence specific integration by the family 1 casposase from Candidatus Nitrosopumilus koreensis AR1. Nucleic Acids Res 2021; 49:9938-9952. [PMID: 34428286 PMCID: PMC8464041 DOI: 10.1093/nar/gkab725] [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: 06/10/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Casposase, a homolog of Cas1 integrase, is encoded by a superfamily of mobile genetic elements known as casposons. While family 2 casposase has been well documented in both function and structure, little is known about the other three casposase families. Here, we studied the family 1 casposase lacking the helix-turn-helix (HTH) domain from Candidatus Nitrosopumilus koreensis AR1 (Ca. N. koreensis). The determinants for integration by Ca. N. koreensis casposase were extensively investigated, and it was found that a 13-bp target site duplication (TSD) sequence, a minimal 3-bp leader and three different nucleotides of the TSD sequences are indispensable for target specific integration. Significantly, the casposase can site-specifically integrate a broad range of terminal inverted repeat (TIR)-derived oligonucleotides ranging from 7-nt to ∼4000-bp, and various oligonucleotides lacking the 5′-TTCTA-3′ motif at the 3′ end of TIR sequence can be integrated efficiently. Furthermore, similar to some Cas1 homologs, the casposase utilizes a 5′-ATAA-3′ motif in the TSD as a molecular ruler to dictate nucleophilic attack at 9-bp downstream of the end of the ruler during the spacer-side integration. By characterizing the family 1 Ca. N. koreensis casposase, we have extended our understanding on mechanistic similarities and evolutionary connections between casposons and the adaptation elements of CRISPR-Cas immunity.
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Affiliation(s)
- Xiaoke Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Qinling Yuan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Wenxuan Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Suyu Ji
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Yang Lv
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Kejing Ren
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Meiling Lu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing210009, China
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing210009, China.,Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
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9
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Tang D, Li H, Wu C, Jia T, He H, Yao S, Yu Y, Chen Q. A distinct structure of Cas1-Cas2 complex provides insights into the mechanism for the longer spacer acquisition in Pyrococcus furiosus. Int J Biol Macromol 2021; 183:379-386. [PMID: 33864868 DOI: 10.1016/j.ijbiomac.2021.04.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 02/08/2023]
Abstract
In the adaptation stage of CRISPR-Cas systems, the Cas1-Cas2 integrase captures and integrates new invader-derived spacers into the CRISPR locus, serving as a molecular memory of prior infection. As of yet, the structural information of Cas1-Cas2 complex is available only for two species. Here we present the crystal structure of Cas1-Cas2 complex of Pyrococcus furiosus, which showed a distinct architecture from the known Cas1-Cas2 complexes. The shorter C-terminal tail of Pfu Cas2 directs the Cas1 dimers go in the opposite direction, resulting in a different prespacer binding mode. Based on our structural and mutagenesis results, we modeled a prespacer with a shorter duplex and longer 3' overhangs to bind Pfu Cas1-Cas2 complex. The prespacer preference was confirmed by EMSA, fluorescence polarization, and in vitro integration assays. This model provides a potential explanation for the longer spacer acquisition observed in P. furiosus when deleting both cas4 genes. Our study highlights the diversity of the CRISPR adaptation module.
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Affiliation(s)
- Dongmei Tang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China
| | - Huijuan Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China
| | - Chengyong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China
| | - Tingting Jia
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China
| | - Haihuai He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China
| | - Shaohua Yao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China
| | - Yamei Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China.
| | - Qiang Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China.
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10
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Liu J, Cvirkaite-Krupovic V, Baquero DP, Yang Y, Zhang Q, Shen Y, Krupovic M. Virus-induced cell gigantism and asymmetric cell division in archaea. Proc Natl Acad Sci U S A 2021; 118:e2022578118. [PMID: 33782110 PMCID: PMC8054024 DOI: 10.1073/pnas.2022578118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Archaeal viruses represent one of the most mysterious parts of the global virosphere, with many virus groups sharing no evolutionary relationship to viruses of bacteria or eukaryotes. How these viruses interact with their hosts remains largely unexplored. Here we show that nonlytic lemon-shaped virus STSV2 interferes with the cell cycle control of its host, hyperthermophilic and acidophilic archaeon Sulfolobus islandicus, arresting the cell cycle in the S phase. STSV2 infection leads to transcriptional repression of the cell division machinery, which is homologous to the eukaryotic endosomal sorting complexes required for transport (ESCRT) system. The infected cells grow up to 20-fold larger in size, have 8,000-fold larger volume compared to noninfected cells, and accumulate massive amounts of viral and cellular DNA. Whereas noninfected Sulfolobus cells divide symmetrically by binary fission, the STSV2-infected cells undergo asymmetric division, whereby giant cells release normal-sized cells by budding, resembling the division of budding yeast. Reinfection of the normal-sized cells produces a new generation of giant cells. If the CRISPR-Cas system is present, the giant cells acquire virus-derived spacers and terminate the virus spread, whereas in its absence, the cycle continues, suggesting that CRISPR-Cas is the primary defense system in Sulfolobus against STSV2. Collectively, our results show how an archaeal virus manipulates the cell cycle, transforming the cell into a giant virion-producing factory.
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Affiliation(s)
- Junfeng Liu
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, 266237 Qingdao, China
| | | | - Diana P Baquero
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France
| | - Yunfeng Yang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, 266237 Qingdao, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 650500 Kunming, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, 266237 Qingdao, China;
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, 75015 Paris, France;
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11
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Garrett SC. Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array. Front Microbiol 2021; 12:664299. [PMID: 33868219 PMCID: PMC8047081 DOI: 10.3389/fmicb.2021.664299] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/12/2021] [Indexed: 01/22/2023] Open
Abstract
CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes) is a type of prokaryotic immune system that is unique in its ability to provide sequence-specific adaptive protection, which can be updated in response to new threats. CRISPR-Cas does this by storing fragments of DNA from invading genetic elements in an array interspersed with short repeats. The CRISPR array can be continuously updated through integration of new DNA fragments (termed spacers) at one end, but over time existing spacers become obsolete. To optimize immunity, spacer uptake, residency, and loss must be regulated. This mini-review summarizes what is known about how spacers are organized, maintained, and lost from CRISPR arrays.
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Affiliation(s)
- Sandra C Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, United States
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12
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Novel Strategy to Combat Antibiotic Resistance: A Sight into the Combination of CRISPR/Cas9 and Nanoparticles. Pharmaceutics 2021; 13:pharmaceutics13030352. [PMID: 33800235 PMCID: PMC7998274 DOI: 10.3390/pharmaceutics13030352] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
Antibiotic resistance is a significant crisis that threatens human health and safety worldwide. There is an urgent need for new strategies to control multidrug-resistant (MDR) bacterial infections. The latest breakthrough in gene-editing tools based on CRISPR/Cas9 has potential application in combating MDR bacterial infections because of their high targeting ability to specifically disrupt the drug resistance genes that microbes use for infection or to kill the pathogen directly. Despite the potential that CRISPR/Cas9 showed, its further utilization has been hampered by undesirable delivery efficiency in vivo. Nanotechnology offers an alternative way to overcome the shortcomings of traditional delivery methods of therapeutic agents. Advances in nanotechnology can improve the efficacy and safety of CRISPR/Cas9 components by using customized nanoparticle delivery systems. The combination of CRISPR/Cas9 and nanotechnology has the potential to open new avenues in the therapy of MDR bacterial infections. This review describes the recent advances related to CRISPR/Cas9 and nanoparticles for antimicrobial therapy and gene delivery, including the improvement in the packaging and localizing efficiency of the CRISPR/Cas9 components in the NP (nanoparticle)/CRISPR system. We pay particular attention to the strengths and limitations of the nanotechnology-based CRISPR/Cas9 delivery system to fight nosocomial pathogens.We highlight the need for more scientific research to explore the combinatorial efficacy of various nanoparticles and CRISPR technology to control and prevent antimicrobial resistance.
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13
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Zink IA, Wimmer E, Schleper C. Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales. Biomolecules 2020; 10:E1523. [PMID: 33172134 PMCID: PMC7694759 DOI: 10.3390/biom10111523] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.
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14
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Garrett S, Shiimori M, Watts EA, Clark L, Graveley BR, Terns MP. Primed CRISPR DNA uptake in Pyrococcus furiosus. Nucleic Acids Res 2020; 48:6120-6135. [PMID: 32421777 PMCID: PMC7293040 DOI: 10.1093/nar/gkaa381] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/15/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas adaptive immune systems are used by prokaryotes to defend against invaders like viruses and other mobile genetic elements. Immune memories are stored in the form of 'spacers' which are short DNA sequences that are captured from invaders and added to the CRISPR array during a process called 'adaptation'. Spacers are transcribed and the resulting CRISPR (cr)RNAs assemble with different Cas proteins to form effector complexes that recognize matching nucleic acid and destroy it ('interference'). Adaptation can be 'naïve', i.e. independent of any existing spacer matches, or it can be 'primed', i.e. spurred by the crRNA-mediated detection of a complete or partial match to an invader sequence. Here we show that primed adaptation occurs in Pyrococcus furiosus. Although P. furiosus has three distinct CRISPR-Cas interference systems (I-B, I-A and III-B), only the I-B system and Cas3 were necessary for priming. Cas4, which is important for selection and processing of new spacers in naïve adaptation, was also essential for priming. Loss of either the I-B effector proteins or Cas3 reduced naïve adaptation. However, when Cas3 and all crRNP genes were deleted, uptake of correctly processed spacers was observed, indicating that none of these interference proteins are necessary for naïve adaptation.
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Affiliation(s)
- Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Masami Shiimori
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Elizabeth A Watts
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Landon Clark
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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15
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Yu X, Wang L, Zou L, Li M, Li T, Hou L, Guo Y, Shen D, Sun G, Qu D, Cheng X, Chen L. Growth inhibition by bacterial Cas2Em proteins expressed in mammalian cells. Am J Transl Res 2020; 12:2499-2520. [PMID: 32655787 PMCID: PMC7344093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Clustered regularly interspaced short palindromic repeats (CRISPRs) and the CRISPR-associated (Cas) proteins are bacterial adaptive immune system for survival. In our previous study, we demonstrate that polyploid giant bacterial cells (PGBC) induced by Cas2 protein is a step required by new spacer acquisition reaction catalyzed by Cas1/Cas2 complex. We also demonstrated that a carboxyl terminal domain on Cas2Em (the protein Cas2 cloned from Elizabethkingia meningoseptica) is sufficient and enough for PGBC. Thus, the potential role of Cas2Em in microbial-host interaction was explored in this study. METHODS The impacts of Cas2Em on growth of both CHO-K1 and Hela cells were investigated. The subcellular localization and potential molecular target of Ca2Em were studied. RESULTS The growth of mammalian cells were inhibited by Cas2Em protein via G1 arresting and apoptosis. In addition, we also demonstrated that Cas2Em was tightly associated with nuclear outer membrane and could be immunoprecipitated with 14-3-3γ through a 30 amino acid domain (homology of CLK2). CONCLUSION Cas2Em significantly suppressed the growth of mammalian cells indicating Cas2 proteins play an important role in mammalian cells.
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Affiliation(s)
- Xin Yu
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
- Roche Innovation Center ShanghaiShanghai 201203, China
| | - Lei Wang
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Lin Zou
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Mengjie Li
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Tiansheng Li
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Linlin Hou
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Yameng Guo
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Danfeng Shen
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Guiqin Sun
- College of Medical Technology, Zhejiang Chinese Medical UniversityHangzhou 310053, Zhejiang, China
| | - Di Qu
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Xunjia Cheng
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
| | - Li Chen
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan UniversityShanghai 200032, China
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16
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Bernheim A, Bikard D, Touchon M, Rocha EPC. Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements. Nucleic Acids Res 2020; 48:748-760. [PMID: 31745554 PMCID: PMC7145637 DOI: 10.1093/nar/gkz1091] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 12/20/2022] Open
Abstract
Prokaryotes use CRISPR-Cas systems for adaptive immunity, but the reasons for the frequent existence of multiple CRISPRs and cas clusters remain poorly understood. Here, we analysed the joint distribution of CRISPR and cas genes in a large set of fully sequenced bacterial genomes and their mobile genetic elements. Our analysis suggests few negative and many positive epistatic interactions between Cas subtypes. The latter often result in complex genetic organizations, where a locus has a single adaptation module and diverse interference mechanisms that might provide more effective immunity. We typed CRISPRs that could not be unambiguously associated with a cas cluster and found that such complex loci tend to have unique type I repeats in multiple CRISPRs. Many chromosomal CRISPRs lack a neighboring Cas system and they often have repeats compatible with the Cas systems encoded in trans. Phages and 25 000 prophages were almost devoid of CRISPR-Cas systems, whereas 3% of plasmids had CRISPR-Cas systems or isolated CRISPRs. The latter were often compatible with the chromosomal cas clusters, suggesting that plasmids can co-opt the latter. These results highlight the importance of interactions between CRISPRs and cas present in multiple copies and in distinct genomic locations in the function and evolution of bacterial immunity.
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Affiliation(s)
- Aude Bernheim
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25–28 rue Dr. Roux, Paris 75015, France
- Synthetic Biology Group, Institut Pasteur, 25–28 rue Dr. Roux, Paris 75015, France
- AgroParisTech, F-75005 Paris, France
- Ecole doctorale Frontières du vivant, Université Paris Diderot, Université Sorbonne Paris Cité, 75013 Paris, France
| | - David Bikard
- Synthetic Biology Group, Institut Pasteur, 25–28 rue Dr. Roux, Paris 75015, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25–28 rue Dr. Roux, Paris 75015, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25–28 rue Dr. Roux, Paris 75015, France
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17
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Yoganand KN, Muralidharan M, Nimkar S, Anand B. Fidelity of prespacer capture and processing is governed by the PAM-mediated interactions of Cas1-2 adaptation complex in CRISPR-Cas type I-E system. J Biol Chem 2019; 294:20039-20053. [PMID: 31748409 PMCID: PMC6937570 DOI: 10.1074/jbc.ra119.009438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes deploy CRISPR-Cas-based RNA-guided adaptive immunity to fend off mobile genetic elements such as phages and plasmids. During CRISPR adaptation, which is the first stage of CRISPR immunity, the Cas1-2 integrase complex captures invader-derived prespacer DNA and specifically integrates it at the leader-repeat junction as spacers. For this integration, several variants of CRISPR-Cas systems use Cas4 as an indispensable nuclease for selectively processing the protospacer adjacent motif (PAM) containing prespacers to a defined length. Surprisingly, however, a few CRISPR-Cas systems, such as type I-E, are bereft of Cas4. Despite the absence of Cas4, how the prespacers show impeccable conservation for length and PAM selection in type I-E remains intriguing. Here, using in vivo and in vitro integration assays, deep sequencing, and exonuclease footprinting, we show that Cas1-2/I-E-via the type I-E-specific extended C-terminal tail of Cas1-displays intrinsic affinity for PAM containing prespacers of variable length in Escherichia coli Although Cas1-2/I-E does not prune the prespacers, its binding protects the prespacer boundaries from exonuclease action. This ensures the pruning of exposed ends by exonucleases to aptly sized substrates for integration into the CRISPR locus. In summary, our work reveals that in a few CRISPR-Cas variants, such as type I-E, the specificity of PAM selection resides with Cas1-2, whereas the prespacer processing is co-opted by cellular non-Cas exonucleases, thereby offsetting the need for Cas4.
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Affiliation(s)
- Kakimani Nagarajan Yoganand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Manasasri Muralidharan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Siddharth Nimkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Baskaran Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
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18
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Kim JG, Garrett S, Wei Y, Graveley BR, Terns MP. CRISPR DNA elements controlling site-specific spacer integration and proper repeat length by a Type II CRISPR-Cas system. Nucleic Acids Res 2019; 47:8632-8648. [PMID: 31392984 PMCID: PMC6895254 DOI: 10.1093/nar/gkz677] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR–Cas systems provide heritable immunity against viruses by capturing short invader DNA sequences, termed spacers, and incorporating them into the CRISPR loci of the prokaryotic host genome. Here, we investigate DNA elements that control accurate spacer uptake in the type II-A CRISPR locus of Streptococcus thermophilus. We determined that purified Cas1 and Cas2 proteins catalyze spacer integration with high specificity for CRISPR repeat junctions. We show that 10 bp of the CRISPR leader sequence is critical for stimulating polarized integration preferentially at the repeat proximal to the leader. Spacer integration proceeds through a two-step transesterification reaction where the 3′ hydroxyl groups of the spacer target both repeat borders on opposite strands. The leader-proximal end of the repeat is preferentially targeted for the first site of integration through recognition of sequences spanning the leader-repeat junction. Subsequently, second-site integration at the leader-distal end of the repeat is specified by multiple determinants including a length-defining mechanism relying on a repeat element proximal to the second site of integration. Our results highlight the intrinsic ability of type II Cas1/Cas2 proteins to coordinate directional and site-specific spacer integration into the CRISPR locus to ensure precise duplication of the repeat required for CRISPR immunity.
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Affiliation(s)
- Jenny G Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Yunzhou Wei
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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