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Dhingra Y, Sashital DG. Cas4/1 dual nuclease activities enable prespacer maturation and directional integration in a type I-G CRISPR-Cas system. bioRxiv 2023:2023.06.05.543779. [PMID: 37333257 PMCID: PMC10274657 DOI: 10.1101/2023.06.05.543779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
CRISPR-Cas adaptive immune systems uptake short 'spacer' sequences from foreign DNA and incorporate them into the host genome to serve as templates for crRNAs that guide interference against future infections. Adaptation in CRISPR systems is mediated by Cas1-Cas2 complexes that catalyze integration of prespacer substrates into the CRISPR array. Many DNA targeting systems also require Cas4 endonucleases for functional spacer acquisition. Cas4 selects prespacers containing a protospacer adjacent motif (PAM) and removes the PAM prior to integration, both of which are required to ensure host immunization. Cas1 has also been shown to function as a nuclease in some systems, but a role for this nuclease activity in adaptation has not been demonstrated. We identified a type I-G Cas4/1 fusion with a nucleolytically active Cas1 domain that can directly participate in prespacer processing. The Cas1 domain is both an integrase and a sequence-independent nuclease that cleaves the non-PAM end of a prespacer, generating optimal overhang lengths that enable integration at the leader side. The Cas4 domain sequence-specifically cleaves the PAM end of the prespacer, ensuring integration of the PAM end at the spacer side. The two domains have varying metal ion requirements. While Cas4 activity is Mn 2+ dependent, Cas1 preferentially uses Mg 2+ over Mn 2+ . The dual nuclease activity of Cas4/1 eliminates the need for additional factors in prespacer processing, making the adaptation module self-reliant for prespacer maturation and directional integration.
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Affiliation(s)
- Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, 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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Freidlin PJ, Nissan I, Luria A, Goldblatt D, Schaffer L, Kaidar-Shwartz H, Chemtob D, Dveyrin Z, Head SR, Rorman E. Structure and variation of CRISPR and CRISPR-flanking regions in deleted-direct repeat region Mycobacterium tuberculosis complex strains. BMC Genomics 2017; 18:168. [PMID: 28201993 PMCID: PMC5310062 DOI: 10.1186/s12864-017-3560-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/07/2017] [Indexed: 12/16/2022] Open
Abstract
Background CRISPR and CRISPR-flanking genomic regions are important for molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) strains, and potentially for adaptive immunity to phage and plasmid DNA, and endogenous roles in the bacterium. Genotyping in the Israel National Mycobacterium Reference Center Tel-Aviv of over 1500 MTBC strains from 2008–2013 showed three strains with validated negative 43-spacer spoligotypes, that is, with putatively deleted direct repeat regions (deleted-DR/CRISPR regions). Two isolates of each of three negative spoligotype MTBC (a total of 6 isolates) were subjected to Next Generation Sequencing (NGS). As positive controls, NGS was performed for three intact-DR isolates belonging to T3_Eth, the largest multiple-drug-resistant (MDR)-containing African-origin cluster in Israel. Other controls consisted of NGS reads and complete whole genome sequences from GenBank for 20 intact-DR MTBC and for 1 deleted-DR MTBC strain recognized as CAS by its defining RD deletion. Results NGS reads from negative spoligotype MTBC mapped to reference H37Rv NC_000962.3 suggested that the DR/CRISPR regions were completely deleted except for retention of the middle IS6110 mobile element. Clonally specific deletion of CRISPR-flanking genes also was observed, including deletion of at least cas2 and cas1 genes. Genomic RD deletions defined lineages corresponding to the major spoligotype families Beijing, EAI, and Haarlem, consistent with 24 loci MIRU-VNTR profiles. Analysis of NGS reads, and analysis of contigs obtained by manual PCR confirmed that all 43 gold standard DR/CRISPR spacers were missing in the deleted-DR genomes. Conclusions Although many negative spoligotype strains are recorded as spoligotype-international-type (SIT) 2669 in the SITVIT international database, this is the first time to our knowledge that it has been shown that negative spoligotype strains are found in at least 4 different 24 loci MIRU-VNTR and RD deletion families. We report for the first time negative spoligotype-associated total loss of CRISPR region spacers and repeats, with accompanying clonally specific loss of flanking genes, including at least CRISPR-associated genes cas2 and cas1. Since cas1 deleted E.coli shows increased sensitivity to DNA damage and impaired chromosomal segregation, we discussed the possibility of a similar phenotype in the deleted-DR strains and Beijing family strains as both lack the cas1 gene. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3560-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul Jeffrey Freidlin
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel.
| | - Israel Nissan
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | - Anna Luria
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel.,current address: Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Drora Goldblatt
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | | | - Hasia Kaidar-Shwartz
- National Mycobacterium Reference Center, National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | - Daniel Chemtob
- Department of Tuberculosis and AIDS, Ministry of Health, Jerusalem, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
| | | | - Efrat Rorman
- National Public Health Laboratory Tel Aviv, Ministry of Health, Tel Aviv, Israel
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Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol 2011; 79:484-502. [PMID: 21219465 PMCID: PMC3071548 DOI: 10.1111/j.1365-2958.2010.07465.x] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps. The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site. Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation. Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs. These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair.
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Affiliation(s)
- Mohan Babu
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Natalia Beloglazova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Robert Flick
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Chris Graham
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Tatiana Skarina
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Alla Gagarinova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Oxana Pogoutse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Greg Brown
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrew Binkowski
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Sadhna Phanse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Aled M. Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Alexander F. Yakunin
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
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