1
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Hossain AA, Pigli YZ, Baca CF, Heissel S, Thomas A, Libis VK, Burian J, Chappie JS, Brady SF, Rice PA, Marraffini LA. DNA glycosylases provide antiviral defence in prokaryotes. Nature 2024; 629:410-416. [PMID: 38632404 PMCID: PMC11078745 DOI: 10.1038/s41586-024-07329-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Bacteria have adapted to phage predation by evolving a vast assortment of defence systems1. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data2. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library3 with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.
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Affiliation(s)
- Amer A Hossain
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Ying Z Pigli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Christian F Baca
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alexis Thomas
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Vincent K Libis
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Ján Burian
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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2
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Aviram N, Shilton AK, Lyn NG, Reis BS, Brivanlou A, Marraffini LA. The Cas10 nuclease activity relieves host dormancy to facilitate spacer acquisition and retention during type III-A CRISPR immunity. bioRxiv 2024:2024.02.11.579731. [PMID: 38405743 PMCID: PMC10888962 DOI: 10.1101/2024.02.11.579731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A hallmark of CRISPR immunity is the acquisition of short viral DNA sequences, known as spacers, that are transcribed into guide RNAs to recognize complementary sequences. The staphylococcal type III-A CRISPR-Cas system uses guide RNAs to locate viral transcripts and start a response that displays two mechanisms of immunity. When immunity is triggered by an early-expressed phage RNA, degradation of viral ssDNA can cure the host from infection. In contrast, when the RNA guide targets a late-expressed transcript, defense requires the activity of Csm6, a non-specific RNase. Here we show that Csm6 triggers a growth arrest of the host that provides immunity at the population level which hinders viral propagation to allow the replication of non-infected cells. We demonstrate that this mechanism leads to defense against not only the target phage but also other viruses present in the population that fail to replicate in the arrested cells. On the other hand, dormancy limits the acquisition and retention of spacers that trigger it. We found that the ssDNase activity of type III-A systems is required for the re-growth of a subset of the arrested cells, presumably through the degradation of the phage DNA, ending target transcription and inactivating the immune response. Altogether, our work reveals a built-in mechanism within type III-A CRISPR-Cas systems that allows the exit from dormancy needed for the subsistence of spacers that provide broad-spectrum immunity.
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Affiliation(s)
- Naama Aviram
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Amanda K Shilton
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Nia G Lyn
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Amir Brivanlou
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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3
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Banh DV, Roberts CG, Morales-Amador A, Berryhill BA, Chaudhry W, Levin BR, Brady SF, Marraffini LA. Author Correction: Bacterial cGAS senses a viral RNA to initiate immunity. Nature 2024; 625:E3. [PMID: 38052939 PMCID: PMC10764284 DOI: 10.1038/s41586-023-06929-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Affiliation(s)
- Dalton V Banh
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Adrian Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | | | - Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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4
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Baca CF, Yu Y, Rostøl JT, Majumder P, Patel DJ, Marraffini LA. The CRISPR effector Cam1 mediates membrane depolarization for phage defence. Nature 2024; 625:797-804. [PMID: 38200316 PMCID: PMC10808066 DOI: 10.1038/s41586-023-06902-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/27/2023] [Indexed: 01/12/2024]
Abstract
Prokaryotic type III CRISPR-Cas systems provide immunity against viruses and plasmids using CRISPR-associated Rossman fold (CARF) protein effectors1-5. Recognition of transcripts of these invaders with sequences that are complementary to CRISPR RNA guides leads to the production of cyclic oligoadenylate second messengers, which bind CARF domains and trigger the activity of an effector domain6,7. Whereas most effectors degrade host and invader nucleic acids, some are predicted to contain transmembrane helices without an enzymatic function. Whether and how these CARF-transmembrane helix fusion proteins facilitate the type III CRISPR-Cas immune response remains unknown. Here we investigate the role of cyclic oligoadenylate-activated membrane protein 1 (Cam1) during type III CRISPR immunity. Structural and biochemical analyses reveal that the CARF domains of a Cam1 dimer bind cyclic tetra-adenylate second messengers. In vivo, Cam1 localizes to the membrane, is predicted to form a tetrameric transmembrane pore, and provides defence against viral infection through the induction of membrane depolarization and growth arrest. These results reveal that CRISPR immunity does not always operate through the degradation of nucleic acids, but is instead mediated via a wider range of cellular responses.
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Affiliation(s)
- Christian F Baca
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University and Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - You Yu
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Puja Majumder
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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5
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Banh DV, Roberts CG, Morales-Amador A, Berryhill BA, Chaudhry W, Levin BR, Brady SF, Marraffini LA. Bacterial cGAS senses a viral RNA to initiate immunity. Nature 2023; 623:1001-1008. [PMID: 37968393 PMCID: PMC10686824 DOI: 10.1038/s41586-023-06743-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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] [Received: 03/08/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023]
Abstract
Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes from viral (phage) attack through the production of cyclic oligonucleotides, which activate effector proteins that trigger the death of the infected host1,2. How bacterial cyclases recognize phage infection is not known. Here we show that staphylococcal phages produce a structured RNA transcribed from the terminase subunit genes, termed CBASS-activating bacteriophage RNA (cabRNA), which binds to a positively charged surface of the CdnE03 cyclase and promotes the synthesis of the cyclic dinucleotide cGAMP to activate the CBASS immune response. Phages that escape the CBASS defence harbour mutations that lead to the generation of a longer form of the cabRNA that cannot activate CdnE03. As the mammalian cyclase OAS1 also binds viral double-stranded RNA during the interferon response, our results reveal a conserved mechanism for the activation of innate antiviral defence pathways.
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Affiliation(s)
- Dalton V Banh
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Cameron G Roberts
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Adrian Morales-Amador
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | | | - Waqas Chaudhry
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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6
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Kenney CT, Marraffini LA. Rarely acquired type II-A CRISPR-Cas spacers mediate anti-viral immunity through the targeting of a non-canonical PAM sequence. Nucleic Acids Res 2023; 51:7438-7450. [PMID: 37293964 PMCID: PMC10415147 DOI: 10.1093/nar/gkad501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023] Open
Abstract
The Streptococcus pyogenes type II-A CRISPR-Cas systems provides adaptive immunity through the acquisition of short DNA sequences from invading viral genomes, called spacers. Spacers are transcribed into short RNA guides that match regions of the viral genome followed by a conserved NGG DNA motif, known as the PAM. These RNA guides, in turn, are used by the Cas9 nuclease to find and destroy complementary DNA targets within the viral genome. While most of the spacers present in bacterial populations that survive phage infection target protospacers flanked by NGG sequences, there is a small fraction that target non-canonical PAMs. Whether these spacers originate through accidental acquisition of phage sequences and/or provide efficient defense is unknown. Here we found that many of them match phage target regions flanked by an NAGG PAM. Despite being scarcely present in bacterial populations, NAGG spacers provide substantial immunity in vivo and generate RNA guides that support robust DNA cleavage by Cas9 in vitro; with both activities comparable to spacers that target sequences followed by the canonical AGG PAM. In contrast, acquisition experiments showed that NAGG spacers are acquired at very low frequencies. We therefore conclude that discrimination against these sequences occurs during immunization of the host. Our results reveal unexpected differences in PAM recognition during the spacer acquisition and targeting stages of the type II-A CRISPR-Cas immune response.
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Affiliation(s)
- Claire T Kenney
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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7
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Hossain AA, Marraffini LA. CRISPR-assisted transposition: TnsC finds (and threads) the needle in the haystack. Mol Cell 2022; 82:3968-3969. [DOI: 10.1016/j.molcel.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
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8
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Maguin P, Varble A, Modell JW, Marraffini LA. Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response. Mol Cell 2022; 82:907-919.e7. [PMID: 35134339 PMCID: PMC8900293 DOI: 10.1016/j.molcel.2022.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/03/2021] [Accepted: 01/14/2022] [Indexed: 12/26/2022]
Abstract
Prokaryotic organisms have developed multiple defense systems against phages; however, little is known about whether and how these interact with each other. Here, we studied the connection between two of the most prominent prokaryotic immune systems: restriction-modification and CRISPR. While both systems employ enzymes that cleave a specific DNA sequence of the invader, CRISPR nucleases are programmed with phage-derived spacer sequences, which are integrated into the CRISPR locus upon infection. We found that restriction endonucleases provide a short-term defense, which is rapidly overcome through methylation of the phage genome. In a small fraction of the cells, however, restriction results in the acquisition of spacer sequences from the cleavage site, which mediates a robust type II-A CRISPR-Cas immune response against the methylated phage. This mechanism is reminiscent of eukaryotic immunity in which the innate response offers a first temporary line of defense and also activates a second and more robust adaptive response.
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Affiliation(s)
- Pascal Maguin
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Andrew Varble
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Joshua W. Modell
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Present address: Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe St., PCTB 803, Baltimore, MD 21205, USA
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Correspondence to:
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9
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Aviram N, Thornal AN, Zeevi D, Marraffini LA. Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system. Nucleic Acids Res 2022; 50:1661-1672. [PMID: 35048966 PMCID: PMC8860600 DOI: 10.1093/nar/gkab1299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas systems provide prokaryotic organisms with an adaptive defense mechanism that acquires immunological memories of infections. This is accomplished by integration of short fragments from the genome of invaders such as phages and plasmids, called ‘spacers’, into the CRISPR locus of the host. Depending on their genetic composition, CRISPR-Cas systems can be classified into six types, I-VI, however spacer acquisition has been extensively studied only in type I and II systems. Here, we used an inducible spacer acquisition assay to study this process in the type III-A CRISPR-Cas system of Staphylococcus epidermidis, in the absence of phage selection. Similarly to type I and II spacer acquisition, this type III system uses Cas1 and Cas2 to preferentially integrate spacers from the chromosomal terminus and free dsDNA ends produced after DNA breaks, in a manner that is enhanced by the AddAB DNA repair complex. Surprisingly, a different mode of spacer acquisition from rRNA and tRNA loci, which spans only the transcribed sequences of these genes and is not enhanced by AddAB, was also detected. Therefore, our findings reveal both common mechanistic principles that may be conserved in all CRISPR-Cas systems, as well as unique and intriguing features of type III spacer acquisition.
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Affiliation(s)
- Naama Aviram
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Ashley N Thornal
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - David Zeevi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Luciano A Marraffini
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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10
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Barrangou R, Marraffini LA. Turning CRISPR on with antibiotics. Cell Host Microbe 2022; 30:12-14. [PMID: 35026132 DOI: 10.1016/j.chom.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CRISPR-Cas systems have the ability to integrate invasive DNA sequences to build adaptive immunity in bacteria. In this issue Dimitriu et al. show bacteriostatic antibiotics prompt CRISPR acquisition events, illustrating how environmental conditions affect complex dynamics between host and virus and the corresponding biological and genetic arms race.
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Affiliation(s)
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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11
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Jakhanwal S, Cress BF, Maguin P, Lobba MJ, Marraffini LA, Doudna JA. A CRISPR-Cas9-integrase complex generates precise DNA fragments for genome integration. Nucleic Acids Res 2021; 49:3546-3556. [PMID: 33693715 PMCID: PMC8034620 DOI: 10.1093/nar/gkab123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 02/26/2021] [Indexed: 01/24/2023] Open
Abstract
CRISPR-Cas9 is an RNA-guided DNA endonuclease involved in bacterial adaptive immunity and widely repurposed for genome editing in human cells, animals and plants. In bacteria, RNA molecules that guide Cas9's activity derive from foreign DNA fragments that are captured and integrated into the host CRISPR genomic locus by the Cas1-Cas2 CRISPR integrase. How cells generate the specific lengths of DNA required for integrase capture is a central unanswered question of type II-A CRISPR-based adaptive immunity. Here, we show that an integrase supercomplex comprising guide RNA and the proteins Cas1, Cas2, Csn2 and Cas9 generates precisely trimmed 30-base pair DNA molecules required for genome integration. The HNH active site of Cas9 catalyzes exonucleolytic DNA trimming by a mechanism that is independent of the guide RNA sequence. These results show that Cas9 possesses a distinct catalytic capacity for generating immunological memory in prokaryotes.
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Affiliation(s)
- Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brady F Cress
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Pascal Maguin
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Marco J Lobba
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
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12
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Abstract
In 1944, the Journal of Experimental Medicine published the groundbreaking discovery that DNA is the molecule holding genetic information (1944. J. Exp. Med.https://doi.org/10.1084/jem.79.2.137). This seminal finding was the genesis of molecular biology and the beginning of an incredible journey to understand, read, and manipulate the genetic code.
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Affiliation(s)
- Pascal Maguin
- Laboratory of Bacteriology, The Rockefeller University, New York, NY
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY
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13
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Rostøl JT, Xie W, Kuryavyi V, Maguin P, Kao K, Froom R, Patel DJ, Marraffini LA. The Card1 nuclease provides defence during type III CRISPR immunity. Nature 2021; 590:624-629. [PMID: 33461211 PMCID: PMC7906951 DOI: 10.1038/s41586-021-03206-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
In the type III CRISPR-Cas immune response of prokaryotes, infection triggers the production of cyclic oligoadenylates that bind and activate proteins that contain a CARF domain1,2. Many type III loci are associated with proteins in which the CRISPR-associated Rossman fold (CARF) domain is fused to a restriction endonuclease-like domain3,4. However, with the exception of the well-characterized Csm6 and Csx1 ribonucleases5,6, whether and how these inducible effectors provide defence is not known. Here we investigated a type III CRISPR accessory protein, which we name cyclic-oligoadenylate-activated single-stranded ribonuclease and single-stranded deoxyribonuclease 1 (Card1). Card1 forms a symmetrical dimer that has a large central cavity between its CRISPR-associated Rossmann fold and restriction endonuclease domains that binds cyclic tetra-adenylate. The binding of ligand results in a conformational change comprising the rotation of individual monomers relative to each other to form a more compact dimeric scaffold, in which a manganese cation coordinates the catalytic residues and activates the cleavage of single-stranded-but not double-stranded-nucleic acids (both DNA and RNA). In vivo, activation of Card1 induces dormancy of the infected hosts to provide immunity against phage infection and plasmids. Our results highlight the diversity of strategies used in CRISPR systems to provide immunity.
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Affiliation(s)
- Jakob T. Rostøl
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Wei Xie
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vitaly Kuryavyi
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pascal Maguin
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Kevin Kao
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Ruby Froom
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Correspondence to ,
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA,Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA,Correspondence to ,
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14
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Abstract
Prokaryotes have developed numerous defense strategies to combat the constant threat posed by the diverse genetic parasites that endanger them. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas loci guard their hosts with an adaptive immune system against foreign nucleic acids. Protection starts with an immunization phase, in which short pieces of the invader's genome, known as spacers, are captured and integrated into the CRISPR locus after infection. Next, during the targeting phase, spacers are transcribed into CRISPR RNAs (crRNAs) that guide CRISPR-associated (Cas) nucleases to destroy the invader's DNA or RNA. Here we describe the many different molecular mechanisms of CRISPR targeting and how they are interconnected with the immunization phase through a third phase of the CRISPR-Cas immune response: primed spacer acquisition. In this phase, Cas proteins direct the crRNA-guided acquisition of additional spacers to achieve a more rapid and robust immunization of the population.
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Affiliation(s)
- Philip M. Nussenzweig
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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15
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Shilton AK, Marraffini LA. Shoot the Messenger! A New Phage Weapon to Neutralize the Type III CRISPR Immune Response. Mol Cell 2020; 78:568-569. [PMID: 32442502 DOI: 10.1016/j.molcel.2020.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Athukoralage et al. (2020) identify a new anti-CRISPR (Acr) that degrades cA4, a cyclic oligo-adenylate second messenger produced during the type III CRISPR immune response. This provides an effective way by which invaders can bypass downstream CRISPR effectors that rely on this signaling molecule.
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Affiliation(s)
- Amanda K Shilton
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY, USA.
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16
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Meeske AJ, Jia N, Cassel AK, Kozlova A, Liao J, Wiedmann M, Patel DJ, Marraffini LA. A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity. Science 2020; 369:54-59. [PMID: 32467331 PMCID: PMC7975689 DOI: 10.1126/science.abb6151] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/15/2020] [Indexed: 12/11/2022]
Abstract
The CRISPR RNA (crRNA)-guided nuclease Cas13 recognizes complementary viral transcripts to trigger the degradation of both host and viral RNA during the type VI CRISPR-Cas antiviral response. However, how viruses can counteract this immunity is not known. We describe a listeriaphage (ϕLS46) encoding an anti-CRISPR protein (AcrVIA1) that inactivates the type VI-A CRISPR system of Listeria seeligeri Using genetics, biochemistry, and structural biology, we found that AcrVIA1 interacts with the guide-exposed face of Cas13a, preventing access to the target RNA and the conformational changes required for nuclease activation. Unlike inhibitors of DNA-cleaving Cas nucleases, which cause limited immunosuppression and require multiple infections to bypass CRISPR defenses, a single dose of AcrVIA1 delivered by an individual virion completely dismantles type VI-A CRISPR-mediated immunity.
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Affiliation(s)
- Alexander J Meeske
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Ning Jia
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alice K Cassel
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Albina Kozlova
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Jingqiu Liao
- Department of Food Science, Cornell University, Ithaca, NY 14583, USA
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14583, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14583, USA
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14583, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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17
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Pyenson NC, Marraffini LA. Co-evolution within structured bacterial communities results in multiple expansion of CRISPR loci and enhanced immunity. eLife 2020; 9:e53078. [PMID: 32223887 PMCID: PMC7105378 DOI: 10.7554/elife.53078] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/12/2020] [Indexed: 12/26/2022] Open
Abstract
Type II CRISPR-Cas systems provide immunity against phages and plasmids that infect bacteria through the insertion of a short sequence from the invader's genome, known as the 'spacer', into the CRISPR locus. Spacers are transcribed into guide RNAs that direct the Cas9 nuclease to its target on the invader. In liquid cultures, most bacteria acquire a single spacer. Multiple spacer integration is a rare event which significance for immunity is poorly understood. Here, we found that when phage infections occur on solid media, a high proportion of the surviving colonies display complex morphologies that contain cells with multiple spacers. This is the result of the viral-host co-evolution, in which the immunity provided by the initial acquired spacer is easily overcome by escaper phages. Our results reveal the versatility of CRISPR-Cas immunity, which can respond with both single or multiple spacer acquisition schemes to solve challenges presented by different environments.
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Affiliation(s)
- Nora C Pyenson
- Laboratory of Bacteriology, The Rockefeller UniversityNew YorkUnited States
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
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18
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Garcia-Doval C, Schwede F, Berk C, Rostøl JT, Niewoehner O, Tejero O, Hall J, Marraffini LA, Jinek M. Activation and self-inactivation mechanisms of the cyclic oligoadenylate-dependent CRISPR ribonuclease Csm6. Nat Commun 2020; 11:1596. [PMID: 32221291 PMCID: PMC7101355 DOI: 10.1038/s41467-020-15334-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/28/2020] [Indexed: 12/26/2022] Open
Abstract
Bacterial and archaeal CRISPR-Cas systems provide RNA-guided immunity against genetic invaders such as bacteriophages and plasmids. Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic-oligoadenylate second messengers that activate downstream effectors, including Csm6 ribonucleases, via their CARF domains. Here, we show that Enteroccocus italicus Csm6 (EiCsm6) degrades its cognate cyclic hexa-AMP (cA6) activator, and report the crystal structure of EiCsm6 bound to a cA6 mimic. Our structural, biochemical, and in vivo functional assays reveal how cA6 recognition by the CARF domain activates the Csm6 HEPN domains for collateral RNA degradation, and how CARF domain-mediated cA6 cleavage provides an intrinsic off-switch to limit Csm6 activity in the absence of ring nucleases. These mechanisms facilitate rapid invader clearance and ensure termination of CRISPR interference to limit self-toxicity. Upon target RNA recognition, type III CRISPR-Cas systems produce cyclic oligoadenylates that activate effectors such as Csm6 ribonucleases. Here, Garcia-Doval et al. show that Enteroccocus italicus Csm6 degrades its cyclic hexa-AMP activator, and report the crystal structure of the protein bound to an activator mimic.
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Affiliation(s)
- Carmela Garcia-Doval
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Frank Schwede
- Biolog Life Science Institute GmbH & Co. KG, Flughafendamm 9a, D-28199, Bremen, Germany
| | - Christian Berk
- Department of Chemistry and Applied Biosciences, Institute for Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065-6399, USA
| | - Ole Niewoehner
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Oliver Tejero
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute for Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065-6399, USA.,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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19
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Abstract
Many bacteria and archaea have the unique ability to heritably alter their genomes by incorporating small fragments of foreign DNA, called spacers, into CRISPR loci. Once transcribed and processed into individual CRISPR RNAs, spacer sequences guide Cas effector nucleases to destroy complementary, invading nucleic acids. Collectively, these two processes are known as the CRISPR-Cas immune response. In this Progress article, we review recent studies that have advanced our understanding of the molecular mechanisms underlying spacer acquisition and that have revealed a fundamental link between the two phases of CRISPR immunity that ensures optimal immunity from newly acquired spacers. Finally, we highlight important open questions and discuss the potential basic and applied impact of spacer acquisition research.
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Affiliation(s)
- Jon McGinn
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
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20
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Nussenzweig PM, McGinn J, Marraffini LA. Cas9 Cleavage of Viral Genomes Primes the Acquisition of New Immunological Memories. Cell Host Microbe 2019; 26:515-526.e6. [PMID: 31585845 PMCID: PMC7558852 DOI: 10.1016/j.chom.2019.09.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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] [Received: 08/01/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023]
Abstract
Type II CRISPR-Cas systems defend prokaryotes from bacteriophage infection through the acquisition of short viral DNA sequences known as spacers, which are transcribed into short RNA guides to specify the targets of the Cas9 nuclease. To counter the potentially devastating propagation of escaper phages with mutations in the target sequences, the host population acquires many different spacers. Whether and how pre-existing spacers in type II systems affect the acquisition of new ones is unknown. Here, we demonstrate that previously acquired spacers promote additional spacer acquisition from the vicinity of the target DNA site cleaved by Cas9. Therefore, CRISPR immune cells acquire additional spacers at the same time as they destroy the infecting virus. This anticipates the rise of escapers or related viruses that could escape targeting by the first spacer acquired. Our results thus reveal Cas9's role in the generation of immunological memories.
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Affiliation(s)
- Philip M Nussenzweig
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
| | - Jon McGinn
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
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21
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Varble A, Marraffini LA. Three New Cs for CRISPR: Collateral, Communicate, Cooperate. Trends Genet 2019; 35:446-456. [PMID: 31036344 PMCID: PMC6525018 DOI: 10.1016/j.tig.2019.03.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 12/18/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) loci and their associated (cas) genes provide protection against invading phages and plasmids in prokaryotes. Typically, short sequences are captured from the genome of the invader, integrated into the CRISPR locus, and transcribed into short RNAs that direct RNA-guided Cas nucleases to the nucleic acids of the invader for their degradation. Recent work in the field has revealed unexpected features of the CRISPR-Cas mechanism: (i) collateral, nonspecific, cleavage of host nucleic acids; (ii) secondary messengers that amplify the immune response; and (iii) immunosuppression of CRISPR targeting by phage-encoded inhibitors. Here, we review these new and exciting findings.
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Affiliation(s)
- Andrew Varble
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
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22
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Meeske AJ, Nakandakari-Higa S, Marraffini LA. Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature 2019; 570:241-245. [PMID: 31142834 PMCID: PMC6570424 DOI: 10.1038/s41586-019-1257-5] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022]
Abstract
Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci of prokaryotes are composed of 30-40 bp repeats separated by equally short sequences of plasmid and bacteriophage origin known as spacers1–3. Spacers are transcribed and processed into short CRISPR RNAs (crRNAs) that are used as guides by CRISPR-associated (Cas) nucleases to recognize and destroy complementary sequences (known as protospacers) within invaders4,5. In contrast to most Cas nucleases which destroy the invader’s DNA4–7, the type VI effector nuclease Cas13 employs RNA guides to locate complementary transcripts and catalyze both sequence-specific cis-, and non-specific trans-RNA cleavage8. While it has been hypothesized that Cas13 naturally defends against RNA phages8, type VI spacer sequences have exclusively been found to match the genomes of double-stranded DNA (dsDNA) phages9,10, suggesting that Cas13 can provide immunity against these invaders. However, whether and how Cas13 utilizes the cis- and/or trans-RNA cleavage activities in defending against dsDNA phages is not understood. Here we show that trans-cleavage of transcripts halts the growth of the host cell and results in the abortion of the infectious cycle. This depletes the phage population and provides herd immunity to uninfected bacteria. Phages harboring target mutations, which easily evade DNA-targeting CRISPR systems11–13, are also depleted due to the activation of Cas13 by co-infecting wild type phages. Thus, by acting on the host rather than directly targeting the virus, type VI CRISPR systems not only provide robust defense against DNA phages but also prevent outbreaks of CRISPR-resistant phage.
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Affiliation(s)
- Alexander J Meeske
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
| | | | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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23
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Maji B, Gangopadhyay SA, Lee M, Shi M, Wu P, Heler R, Mok B, Lim D, Siriwardena SU, Paul B, Dančík V, Vetere A, Mesleh MF, Marraffini LA, Liu DR, Clemons PA, Wagner BK, Choudhary A. A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9. Cell 2019; 177:1067-1079.e19. [PMID: 31051099 PMCID: PMC7182439 DOI: 10.1016/j.cell.2019.04.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [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] [Received: 12/14/2017] [Revised: 09/17/2018] [Accepted: 04/03/2019] [Indexed: 12/26/2022]
Abstract
The precise control of CRISPR-Cas9 activity is required for a number of genome engineering technologies. Here, we report a generalizable platform that provided the first synthetic small-molecule inhibitors of Streptococcus pyogenes Cas9 (SpCas9) that weigh <500 Da and are cell permeable, reversible, and stable under physiological conditions. We developed a suite of high-throughput assays for SpCas9 functions, including a primary screening assay for SpCas9 binding to the protospacer adjacent motif, and used these assays to screen a structurally diverse collection of natural-product-like small molecules to ultimately identify compounds that disrupt the SpCas9-DNA interaction. Using these synthetic anti-CRISPR small molecules, we demonstrated dose and temporal control of SpCas9 and catalytically impaired SpCas9 technologies, including transcription activation, and identified a pharmacophore for SpCas9 inhibition using structure-activity relationships. These studies establish a platform for rapidly identifying synthetic, miniature, cell-permeable, and reversible inhibitors against both SpCas9 and next-generation CRISPR-associated nucleases.
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Affiliation(s)
- Basudeb Maji
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Soumyashree A Gangopadhyay
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Miseon Lee
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mengchao Shi
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Peng Wu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Beverly Mok
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sachini U Siriwardena
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bishwajit Paul
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Vlado Dančík
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amedeo Vetere
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 11231, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA.
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24
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Abstract
Athukoralage et al. (2018) identify a new class of nuclease that degrades cyclic oligoadenylate (cOA), a second messenger that activates non-specific RNA degradation by the type III CRISPR-Cas accessory RNase Csm6/Csx1. This discovery provides a mechanism for regulating the degradation of foreign transcripts during the type III CRISPR immune response.
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Affiliation(s)
- Charlie Y Mo
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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25
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Varble A, Meaden S, Barrangou R, Westra ER, Marraffini LA. Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci. Nat Microbiol 2019; 4:956-963. [PMID: 30886355 PMCID: PMC6533911 DOI: 10.1038/s41564-019-0400-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/31/2019] [Indexed: 11/09/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) loci and their associated (cas) genes encode an adaptive immune system that protects prokaryotes from viral1 and plasmid2 invaders. Following viral (phage) infection, a small fraction of the prokaryotic cells are able to integrate a small sequence of the invader's genome into the CRISPR array1. These sequences, known as spacers, are transcribed and processed into small CRISPR RNA guides3-5 that associate with Cas nucleases to specify a viral target for destruction6-9. Although CRISPR-cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizontal gene transfer10-12, the drivers of CRISPR dissemination remain unclear. Here, we show that spacers can recombine with phage target sequences to mediate a form of specialized transduction of CRISPR elements. Phage targets in phage 85, ΦNM1, ΦNM4 and Φ12 can recombine with spacers in either chromosomal or plasmid-borne CRISPR loci in Staphylococcus, leading to either the transfer of CRISPR-adjacent genes or the propagation of acquired immunity to other bacteria in the population, respectively. Our data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer.
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Affiliation(s)
- Andrew Varble
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Sean Meaden
- Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, UK
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Edze R Westra
- Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, UK
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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26
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Clarke R, Heler R, MacDougall MS, Yeo NC, Chavez A, Regan M, Hanakahi L, Church GM, Marraffini LA, Merrill BJ. Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks. Mol Cell 2019; 71:42-55.e8. [PMID: 29979968 DOI: 10.1016/j.molcel.2018.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/06/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022]
Abstract
The ability to target the Cas9 nuclease to DNA sequences via Watson-Crick base pairing with a single guide RNA (sgRNA) has provided a dynamic tool for genome editing and an essential component of adaptive immune systems in bacteria. After generating a double-stranded break (DSB), Cas9 remains stably bound to DNA. Here, we show persistent Cas9 binding blocks access to the DSB by repair enzymes, reducing genome editing efficiency. Cas9 can be dislodged by translocating RNA polymerases, but only if the polymerase approaches from one direction toward the Cas9-DSB complex. By exploiting these RNA-polymerase/Cas9 interactions, Cas9 can be conditionally converted into a multi-turnover nuclease, mediating increased mutagenesis frequencies in mammalian cells and enhancing bacterial immunity to bacteriophages. These consequences of a stable Cas9-DSB complex provide insights into the evolution of protospacer adjacent motif (PAM) sequences and a simple method of improving selection of highly active sgRNAs for genome editing.
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Affiliation(s)
- Ryan Clarke
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Matthew S MacDougall
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nan Cher Yeo
- Department of Genetics, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alejandro Chavez
- Department of Genetics, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Maureen Regan
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA; Genome Editing Core, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Leslyn Hanakahi
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Rockford Health Science Campus, Rockford, IL 61107, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | | | - Bradley J Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA; Genome Editing Core, University of Illinois at Chicago, Chicago, IL 60607, USA.
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27
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Heler R, Wright AV, Vucelja M, Doudna JA, Marraffini LA. Spacer Acquisition Rates Determine the Immunological Diversity of the Type II CRISPR-Cas Immune Response. Cell Host Microbe 2019; 25:242-249.e3. [PMID: 30709780 DOI: 10.1016/j.chom.2018.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 10/02/2018] [Accepted: 12/14/2018] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems provide acquired immunity in prokaryotes. Upon infection, short sequences from the phage genome, known as spacers, are inserted between the CRISPR repeats. Spacers are transcribed into small RNA molecules that guide nucleases to their targets. The forces that shape the distribution of newly acquired spacers, which is observed to be uneven, are poorly understood. We studied the spacer patterns that arise after phage infection of Staphylococcus aureus harboring the Streptococcus pyogenes type II-A CRISPR-Cas system. We observed that spacer patterns are established early during the CRISPR-Cas immune response and correlate with spacer acquisition rates, but not with spacer targeting efficiency. The rate of spacer acquisition depended on sequence elements within the spacer, which in turn determined the abundance of different spacers within the adapted population. Our results reveal how the two main forces of the CRISPR-Cas immune response, acquisition and targeting, affect the generation of immunological diversity.
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Affiliation(s)
- Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Addison V Wright
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marija Vucelja
- Department of Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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28
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Rostøl JT, Marraffini LA. Non-specific degradation of transcripts promotes plasmid clearance during type III-A CRISPR-Cas immunity. Nat Microbiol 2019; 4:656-662. [PMID: 30692669 PMCID: PMC6430669 DOI: 10.1038/s41564-018-0353-x] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022]
Abstract
Type III-A CRISPR-Cas systems employ the Cas10-Csm complex to destroy bacteriophages and plasmids, using a guide RNA to locate complementary RNA molecules from the invader and trigger an immune response that eliminates the infecting DNA. In addition, these systems possess the non-specific RNase Csm6 which provides further protection for the host. While the role of Csm6 in immunity during phage infection was previously determined, how this RNase is used against plasmids is unclear. Here we show that S. epidermidis Csm6 is required for immunity when transcription across the plasmid target is infrequent, leading to impaired target recognition and inefficient DNA degradation by the Cas10-Csm complex. In these conditions Csm6 causes a growth arrest in the host and prevents further plasmid replication through the indiscriminate degradation of host and plasmid transcripts. In contrast, when plasmid target sequences are efficiently transcribed, Csm6 is dispensable and DNA degradation by Cas10 is sufficient for anti-plasmid immunity. Csm6 therefore provides robustness to the type III-A CRISPR-Cas immune response against difficult targets for the Cas10-Csm complex.
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Affiliation(s)
- Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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29
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Wang L, Mo CY, Wasserman MR, Rostøl JT, Marraffini LA, Liu S. Dynamics of Cas10 Govern Discrimination between Self and Non-self in Type III CRISPR-Cas Immunity. Mol Cell 2018; 73:278-290.e4. [PMID: 30503774 DOI: 10.1016/j.molcel.2018.11.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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] [Received: 06/28/2018] [Revised: 10/11/2018] [Accepted: 11/05/2018] [Indexed: 12/26/2022]
Abstract
Adaptive immune systems must accurately distinguish between self and non-self in order to defend against invading pathogens while avoiding autoimmunity. Type III CRISPR-Cas systems employ guide RNA to recognize complementary RNA targets, which triggers the degradation of both the invader's transcripts and their template DNA. These systems can broadly eliminate foreign targets with multiple mutations but circumvent damage to the host genome. To explore the molecular basis for these features, we use single-molecule fluorescence microscopy to study the interaction between a type III-A ribonucleoprotein complex and various RNA substrates. We find that Cas10-the DNase effector of the complex-displays rapid conformational fluctuations on foreign RNA targets, but is locked in a static configuration on self RNA. Target mutations differentially modulate Cas10 dynamics and tune the CRISPR interference activity in vivo. These findings highlight the central role of the internal dynamics of CRISPR-Cas complexes in self versus non-self discrimination and target specificity.
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Affiliation(s)
- Ling Wang
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Charlie Y Mo
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Michael R Wasserman
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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30
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Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ. Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity. Mol Cell 2018; 73:264-277.e5. [PMID: 30503773 DOI: 10.1016/j.molcel.2018.11.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/10/2018] [Accepted: 11/05/2018] [Indexed: 12/20/2022]
Abstract
Type ΙΙΙ CRISPR-Cas systems provide robust immunity against foreign RNA and DNA by sequence-specific RNase and target RNA-activated sequence-nonspecific DNase and RNase activities. We report on cryo-EM structures of Thermococcus onnurineus CsmcrRNA binary, CsmcrRNA-target RNA and CsmcrRNA-target RNAanti-tag ternary complexes in the 3.1 Å range. The topological features of the crRNA 5'-repeat tag explains the 5'-ruler mechanism for defining target cleavage sites, with accessibility of positions -2 to -5 within the 5'-repeat serving as sensors for avoidance of autoimmunity. The Csm3 thumb elements introduce periodic kinks in the crRNA-target RNA duplex, facilitating cleavage of the target RNA with 6-nt periodicity. Key Glu residues within a Csm1 loop segment of CsmcrRNA adopt a proposed autoinhibitory conformation suggestive of DNase activity regulation. These structural findings, complemented by mutational studies of key intermolecular contacts, provide insights into CsmcrRNA complex assembly, mechanisms underlying RNA targeting and site-specific periodic cleavage, regulation of DNase cleavage activity, and autoimmunity suppression.
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Affiliation(s)
- Ning Jia
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Charlie Y Mo
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Chongyuan Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | | | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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31
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Meeske AJ, Marraffini LA. RNA Guide Complementarity Prevents Self-Targeting in Type VI CRISPR Systems. Mol Cell 2018; 71:791-801.e3. [PMID: 30122537 PMCID: PMC7955661 DOI: 10.1016/j.molcel.2018.07.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [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] [Received: 06/04/2018] [Revised: 07/06/2018] [Accepted: 07/12/2018] [Indexed: 12/26/2022]
Abstract
All immune systems use precise target recognition to interrogate foreign invaders. During CRISPR-Cas immunity, prokaryotes capture short spacer sequences from infecting viruses and insert them into the CRISPR array. Transcription and processing of the CRISPR locus generate small RNAs containing the spacer and repeat sequences that guide Cas nucleases to cleave a complementary protospacer in the invading nucleic acids. In most CRISPR systems, sequences flanking the protospacer drastically affect cleavage. Here, we investigated the target requirements of the recently discovered RNA-targeting type VI-A CRISPR-Cas system in its natural host, Listeria seeligeri. We discovered that target RNAs with extended complementarity between the protospacer flanking sequence and the repeat sequence of the guide RNA are not cleaved by the type VI-A nuclease Cas13, neither in vivo nor in vitro. These findings establish fundamental rules for the design of Cas13-based technologies and provide a mechanism for preventing self-targeting in type VI-A systems.
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Affiliation(s)
- Alexander J Meeske
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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32
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Pyenson NC, Marraffini LA. Type III CRISPR-Cas systems: when DNA cleavage just isn't enough. Curr Opin Microbiol 2017; 37:150-154. [PMID: 28865392 DOI: 10.1016/j.mib.2017.08.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/12/2017] [Accepted: 08/15/2017] [Indexed: 12/26/2022]
Abstract
Type III CRISPR-Cas systems have a unique targeting mechanism that requires the transcription of the DNA target and results in the degradation of not only the genome of the invader but also its transcripts. Here we discuss the most recent studies describing dual DNA and RNA targeting by these systems, as well as the implications of this complex molecular mechanism for immunity in vivo.
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Affiliation(s)
- Nora C Pyenson
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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33
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Niewoehner O, Garcia-Doval C, Rostøl JT, Berk C, Schwede F, Bigler L, Hall J, Marraffini LA, Jinek M. Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers. Nature 2017; 548:543-548. [PMID: 28722012 DOI: 10.1038/nature23467] [Citation(s) in RCA: 286] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/10/2017] [Indexed: 12/26/2022]
Abstract
In many prokaryotes, type III clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated (Cas) systems detect and degrade invasive genetic elements by an RNA-guided, RNA-targeting multisubunit interference complex. The CRISPR-associated protein Csm6 additionally contributes to interference by functioning as a standalone RNase that degrades invader RNA transcripts, but the mechanism linking invader sensing to Csm6 activity is not understood. Here we show that Csm6 proteins are activated through a second messenger generated by the type III interference complex. Upon target RNA binding by the interference complex, its Cas10 subunit converts ATP into a cyclic oligoadenylate product, which allosterically activates Csm6 by binding to its CRISPR-associated Rossmann fold (CARF) domain. CARF domain mutations that abolish allosteric activation inhibit Csm6 activity in vivo, and mutations in the Cas10 Palm domain phenocopy loss of Csm6. Together, these results point to an unprecedented mechanism for regulation of CRISPR interference that bears striking conceptual similarity to oligoadenylate signalling in mammalian innate immunity.
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Affiliation(s)
- Ole Niewoehner
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Carmela Garcia-Doval
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065-6399, USA
| | - Christian Berk
- Department of Chemistry and Applied Biosciences, Institute for Pharmaceutical Sciences, Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH, Flughafendamm 9a, D-28199 Bremen, Germany
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute for Pharmaceutical Sciences, Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065-6399, USA
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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34
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Heler R, Wright AV, Vucelja M, Bikard D, Doudna JA, Marraffini LA. Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response. Mol Cell 2016; 65:168-175. [PMID: 28017588 DOI: 10.1016/j.molcel.2016.11.031] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/23/2016] [Accepted: 11/18/2016] [Indexed: 12/26/2022]
Abstract
CRISPR loci and their associated (Cas) proteins encode a prokaryotic immune system that protects against viruses and plasmids. Upon infection, a low fraction of cells acquire short DNA sequences from the invader. These sequences (spacers) are integrated in between the repeats of the CRISPR locus and immunize the host against the matching invader. Spacers specify the targets of the CRISPR immune response through transcription into short RNA guides that direct Cas nucleases to the invading DNA molecules. Here we performed random mutagenesis of the RNA-guided Cas9 nuclease to look for variants that provide enhanced immunity against viral infection. We identified a mutation, I473F, that increases the rate of spacer acquisition by more than two orders of magnitude. Our results highlight the role of Cas9 during CRISPR immunization and provide a useful tool to study this rare process and develop it as a biotechnological application.
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Affiliation(s)
- Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Addison V Wright
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marija Vucelja
- Department of Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - David Bikard
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA.
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35
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McGinn J, Marraffini LA. CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration. Mol Cell 2016; 64:616-623. [PMID: 27618488 DOI: 10.1016/j.molcel.2016.08.038] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems defend prokaryotes against viruses and plasmids. Short DNA segments of the invader, known as spacers, are stored in the CRISPR array as immunological memories. New spacers are added invariably to the 5' end of the array; therefore, the first spacer matches the latest foreign threat. Whether this highly polarized order of spacer insertion influences CRISPR-Cas immunity has not been explored. Here we show that a conserved sequence located immediately upstream of the CRISPR array specifies the site of new spacer integration. Mutation of this sequence results in erroneous incorporation of new spacers into the middle of the array. We show that spacers added through polarized acquisition give rise to more robust CRISPR-Cas immunity than spacers added to the middle of the array. This study demonstrates that the CRISPR-Cas system specifies the site of spacer integration to optimize the immune response against the most immediate threat to the host.
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Affiliation(s)
- Jon McGinn
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA.
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36
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Sontheimer EJ, Marraffini LA. CRISPR goes retro. Science 2016; 351:920-1. [DOI: 10.1126/science.aaf2851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
RNA contributes directly to the immunological memory recorded in CRISPR sequences
[Also see Research Article by
Silas
et al.
]
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Affiliation(s)
- Erik J. Sontheimer
- RNA Therapeutics Institute, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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37
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Abstract
To engage in adaptive symbioses or genetic exchange, organisms must interact with foreign, non-self elements despite the risks of predation and parasitism. By surveying the interface between self and non-self, immune systems can help ensure the benevolence of these interactions without isolating their hosts altogether. In this Essay, we examine prokaryotic restriction-modification and CRISPR-Cas (clustered, regularly interspaced palindromic repeat-CRISPR-associated proteins) activities and discuss their analogy to mammalian immune pathways. We further explain how their capacities for resistance and tolerance are optimized to reduce parasitism and immunopathology during encounters with non-self.
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Affiliation(s)
- Gregory W Goldberg
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, USA
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38
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Jiang W, Samai P, Marraffini LA. Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity. Cell 2016; 164:710-21. [PMID: 26853474 DOI: 10.1016/j.cell.2015.12.053] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/30/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022]
Abstract
Type III-A CRISPR-Cas systems defend prokaryotes against viral infection using CRISPR RNA (crRNA)-guided nucleases that perform co-transcriptional cleavage of the viral target DNA and its transcripts. Whereas DNA cleavage is essential for immunity, the function of RNA targeting is unknown. Here, we show that transcription-dependent targeting results in a sharp increase of viral genomes in the host cell when the target is located in a late-expressed phage gene. In this targeting condition, mutations in the active sites of the type III-A RNases Csm3 and Csm6 lead to the accumulation of the target phage mRNA and abrogate immunity. Csm6 is also required to provide defense in the presence of mutated phage targets, when DNA cleavage efficiency is reduced. Our results show that the degradation of phage transcripts by CRISPR-associated RNases ensures robust immunity in situations that lead to a slow clearance of the target DNA.
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Affiliation(s)
- Wenyan Jiang
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Poulami Samai
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Abstract
Prokaryotic organisms are threatened by a large array of viruses and have developed numerous defence strategies. Among these, only clustered, regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity against foreign elements. Upon viral injection, a small sequence of the viral genome, known as a spacer, is integrated into the CRISPR locus to immunize the host cell. Spacers are transcribed into small RNA guides that direct the cleavage of the viral DNA by Cas nucleases. Immunization through spacer acquisition enables a unique form of evolution whereby a population not only rapidly acquires resistance to its predators but also passes this resistance mechanism vertically to its progeny.
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Affiliation(s)
- Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
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40
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Abstract
Prokaryotic CRISPR-Cas loci encode proteins that function as an adaptive immune system against infectious viruses and plasmids. Immunity is mediated by Cas nucleases and small RNA guides, which specify a cleavage site within the genome of the invader. In type II CRISPR-Cas systems, the RNA-guided Cas9 nuclease cleaves the DNA. Cas9 can be reprogrammed to create double-strand DNA breaks in the genomes of a variety of organisms, from bacteria to human cells. Repair of Cas9 lesions by homologous recombination or nonhomologous end joining mechanisms can lead to the introduction of specific nucleotide substitutions or indel mutations, respectively. Furthermore, a nuclease-null Cas9 has been developed to regulate endogenous gene expression and to label genomic loci in living cells. Targeted genome editing and gene regulation mediated by Cas9 are easy to program, scale, and multiplex, allowing researchers to decipher the causal link between genetic and phenotypic variation. In this review, we describe the most notable applications of Cas9 in basic biology, translational medicine, synthetic biology, biotechnology, and other fields.
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Affiliation(s)
- Wenyan Jiang
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065;
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41
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Samai P, Pyenson N, Jiang W, Goldberg GW, Hatoum-Aslan A, Marraffini LA. Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity. Cell 2015; 161:1164-1174. [PMID: 25959775 DOI: 10.1016/j.cell.2015.04.027] [Citation(s) in RCA: 289] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/31/2015] [Accepted: 04/07/2015] [Indexed: 12/26/2022]
Abstract
Immune systems must recognize and destroy different pathogens that threaten the host. CRISPR-Cas immune systems protect prokaryotes from viral and plasmid infection utilizing small CRISPR RNAs that are complementary to the invader's genome and specify the targets of RNA-guided Cas nucleases. Type III CRISPR-Cas immunity requires target transcription, and whereas genetic studies demonstrated DNA targeting, in vitro data have shown crRNA-guided RNA cleavage. The molecular mechanism behind these disparate activities is not known. Here, we show that transcription across the targets of the Staphylococcus epidermidis type III-A CRISPR-Cas system results in the cleavage of the target DNA and its transcripts, mediated by independent active sites within the Cas10-Csm ribonucleoprotein effector complex. Immunity against plasmids and DNA viruses requires DNA, but not RNA, cleavage activity. Our studies reveal a highly versatile mechanism of CRISPR immunity that can defend microorganisms against diverse DNA and RNA invaders.
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Affiliation(s)
- Poulami Samai
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Nora Pyenson
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Wenyan Jiang
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Gregory W Goldberg
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Asma Hatoum-Aslan
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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42
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Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA. Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 2015; 519:199-202. [PMID: 25707807 PMCID: PMC4385744 DOI: 10.1038/nature14245] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/20/2015] [Indexed: 12/22/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their associated (Cas) proteins provide adaptive immunity against viral infection in prokaryotes. Upon infection, short phage sequences known as spacers integrate between CRISPR repeats and are transcribed into small RNA molecules that guide the Cas9 nuclease to the viral targets (protospacers). Streptococcus pyogenes Cas9 cleavage of the viral genome requires the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) sequence immediately downstream of the viral target. It is not known whether and how viral sequences flanked by the correct PAM are chosen as new spacers. Here we show that Cas9 selects functional spacers by recognizing their PAM during spacer acquisition. The replacement of cas9 with alleles that lack the PAM recognition motif or recognize an NGGNG PAM eliminated or changed PAM specificity during spacer acquisition, respectively. Cas9 associates with other proteins of the acquisition machinery (Cas1, Cas2 and Csn2), presumably to provide PAM-specificity to this process. These results establish a new function for Cas9 in the genesis of prokaryotic immunological memory.
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Affiliation(s)
- Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Poulami Samai
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Joshua W Modell
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Catherine Weiner
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Gregory W Goldberg
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - David Bikard
- 1] Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA [2] Synthetic Biology Group, Institut Pasteur, 28 Rue du Dr. Roux, 75015 Paris, France
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
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43
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Bikard D, Euler CW, Jiang W, Nussenzweig PM, Goldberg GW, Duportet X, Fischetti VA, Marraffini LA. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol 2014; 32:1146-50. [PMID: 25282355 PMCID: PMC4317352 DOI: 10.1038/nbt.3043] [Citation(s) in RCA: 544] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 09/09/2014] [Indexed: 01/14/2023]
Abstract
Antibiotics target conserved bacterial cellular pathways or growth functions and therefore cannot selectively kill specific members of a complex microbial population. Here, we develop programmable, sequence-specific antimicrobials using the RNA-guided nuclease Cas9 (refs.1,2) delivered by a bacteriophage. We show that Cas9, reprogrammed to target virulence genes, kills virulent, but not avirulent, Staphylococcus aureus. Reprogramming the nuclease to target antibiotic resistance genes destroys staphylococcal plasmids that harbor antibiotic resistance genes and immunizes avirulent staphylococci to prevent the spread of plasmid-borne resistance genes. We also show that CRISPR-Cas9 antimicrobials function in vivo to kill S. aureus in a mouse skin colonization model. This technology creates opportunities to manipulate complex bacterial populations in a sequence-specific manner.
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Affiliation(s)
- David Bikard
- 1] Laboratory of Bacteriology, The Rockefeller University, New York, New York, USA. [2] Present address: Synthetic Biology Group, Institut Pasteur, Paris, France
| | - Chad W Euler
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
| | - Wenyan Jiang
- Laboratory of Bacteriology, The Rockefeller University, New York, New York, USA
| | | | - Gregory W Goldberg
- Laboratory of Bacteriology, The Rockefeller University, New York, New York, USA
| | - Xavier Duportet
- 1] INRIA Paris-Rocquencourt, Rocquencourt, France. [2] Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
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Goldberg GW, Jiang W, Bikard D, Marraffini LA. Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting. Nature 2014; 514:633-7. [PMID: 25174707 PMCID: PMC4214910 DOI: 10.1038/nature13637] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/02/2014] [Indexed: 12/12/2022]
Abstract
A fundamental feature of immune systems is the ability to distinguish pathogenic from self and commensal elements, and to attack the former but tolerate the latter1. Prokaryotic CRISPR-Cas immune systems defend against phage infection using Cas nucleases and small RNA guides that specify one or more target sites for cleavage of the viral genome2,3. Temperate phages are viruses that can integrate into the bacterial chromosome, and they can carry genes that provide a fitness advantage to the lysogenic host4,5. However, CRISPR-Cas targeting that relies strictly on DNA sequence recognition provides indiscriminate immunity to both lytic and lysogenic infection by temperate phages6—compromising the genetic stability of these potentially beneficial elements altogether. Here we show that the Staphylococcus epidermidis CRISPR-Cas system can prevent lytic infection but tolerate lysogenization by temperate phages. Conditional tolerance is achieved through transcription-dependent DNA targeting, and ensures that targeting is resumed upon induction of the prophage lytic cycle. Our results provide evidence for the functional divergence of CRISPR-Cas systems and highlight the importance of targeting mechanism diversity. In addition, they extend the concept of ‘tolerance to non-self’ to the prokaryotic branch of adaptive immunity.
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Affiliation(s)
- Gregory W Goldberg
- Laboratory of Bacteriology, The Rockefeller University, New York, New York 10065, USA
| | - Wenyan Jiang
- Laboratory of Bacteriology, The Rockefeller University, New York, New York 10065, USA
| | - David Bikard
- 1] Laboratory of Bacteriology, The Rockefeller University, New York, New York 10065, USA [2] Synthetic Biology Group, Institut Pasteur, 28 Rue du Dr. Roux, 75015 Paris, France
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, New York 10065, USA
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Charpentier E, Marraffini LA. Editorial overview: Novel technologies in microbiology: Recent advances in techniques in microbiology. Curr Opin Microbiol 2014; 19:viii-x. [PMID: 25017933 DOI: 10.1016/j.mib.2014.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuelle Charpentier
- Helmholtz Centre for Infection Research and Hannover Medical School, 38124 Braunschweig, Germany; The Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden.
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR), and associated proteins (Cas) comprise the CRISPR-Cas system, which confers adaptive immunity against exogenic elements in many bacteria and most archaea. CRISPR-mediated immunization occurs through the uptake of DNA from invasive genetic elements such as plasmids and viruses, followed by its integration into CRISPR loci. These loci are subsequently transcribed and processed into small interfering RNAs that guide nucleases for specific cleavage of complementary sequences. Conceptually, CRISPR-Cas shares functional features with the mammalian adaptive immune system, while also exhibiting characteristics of Lamarckian evolution. Because immune markers spliced from exogenous agents are integrated iteratively in CRISPR loci, they constitute a genetic record of vaccination events and reflect environmental conditions and changes over time. Cas endonucleases, which can be reprogrammed by small guide RNAs have shown unprecedented potential and flexibility for genome editing and can be repurposed for numerous DNA targeting applications including transcriptional control.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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Heler R, Marraffini LA, Bikard D. Adapting to new threats: the generation of memory by CRISPR-Cas immune systems. Mol Microbiol 2014; 93:1-9. [PMID: 24806524 DOI: 10.1111/mmi.12640] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2014] [Indexed: 12/11/2022]
Abstract
Clustered, regularly interspaced, short palindromic repeats (CRISPR) loci and their associated genes (cas) confer bacteria and archaea with adaptive immunity against phages and other invading genetic elements. A fundamental requirement of any immune system is the ability to build a memory of past infections in order to deal more efficiently with recurrent infections. The adaptive feature of CRISPR-Cas immune systems relies on their ability to memorize DNA sequences of invading molecules and integrate them in between the repetitive sequences of the CRISPR array in the form of 'spacers'. The transcription of a spacer generates a small antisense RNA that is used by RNA-guided Cas nucleases to cleave the invading nucleic acid in order to protect the cell from infection. The acquisition of new spacers allows the CRISPR-Cas immune system to rapidly adapt against new threats and is therefore termed 'adaptation'. Recent studies have begun to elucidate the genetic requirements for adaptation and have demonstrated that rather than being a stochastic process, the selection of new spacers is influenced by several factors. We review here our current knowledge of the CRISPR adaptation mechanism.
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Affiliation(s)
- Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, 10065, USA
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Abstract
CRISPR-Cas encodes an adaptive immune system that defends prokaryotes against infectious viruses and plasmids. Immunity is mediated by Cas nucleases, which use small RNA guides (the crRNAs) to specify a cleavage site within the genome of invading nucleic acids. In type II CRISPR-Cas systems, the DNA-cleaving activity is performed by a single enzyme Cas9 guided by an RNA duplex. Using synthetic single RNA guides, Cas9 can be reprogrammed to create specific double-stranded DNA breaks in the genomes of a variety of organisms, ranging from human cells to bacteria, and thus constitutes a powerful tool for genetic engineering. Here we describe recent advancements in our understanding of type II CRISPR-Cas immunity and how these studies led to revolutionary genome editing applications.
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Affiliation(s)
- Emmanuelle Charpentier
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany; The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden; Hannover Medical School, Hannover 30625, Germany.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA.
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Hatoum-Aslan A, Marraffini LA. Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens. Curr Opin Microbiol 2014; 17:82-90. [PMID: 24581697 PMCID: PMC3942673 DOI: 10.1016/j.mib.2013.12.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/29/2013] [Accepted: 12/02/2013] [Indexed: 02/08/2023]
Abstract
CRISPR-Cas systems protect prokaryotes from viruses and plasmids and function primarily as an adaptive immune system in these organisms. Recent discoveries, however, revealed unexpected roles for CRISPR loci as barriers to horizontal gene transfer and as modulators of gene expression. We review how both of these functions of CRISPR-Cas systems can affect the emergence and virulence of human bacterial pathogens.
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Affiliation(s)
- Asma Hatoum-Aslan
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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50
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) loci and their associated cas (CRISPR-associated) genes provide adaptive immunity against viruses (phages) and other mobile genetic elements in bacteria and archaea. While most of the early work has largely been dominated by examples of CRISPR-Cas systems directing the cleavage of phage or plasmid DNA, recent studies have revealed a more complex landscape where CRISPR-Cas loci might be involved in gene regulation. In this review, we summarize the role of these loci in the regulation of gene expression as well as the recent development of synthetic gene regulation using engineered CRISPR-Cas systems.
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