51
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Shmakov SA, Wolf YI, Savitskaya E, Severinov KV, Koonin EV. Mapping CRISPR spaceromes reveals vast host-specific viromes of prokaryotes. Commun Biol 2020; 3:321. [PMID: 32572116 PMCID: PMC7308287 DOI: 10.1038/s42003-020-1014-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/15/2020] [Indexed: 12/04/2022] Open
Abstract
CRISPR arrays contain spacers, some of which are homologous to genome segments of viruses and other parasitic genetic elements and are employed as portion of guide RNAs to recognize and specifically inactivate the target genomes. However, the fraction of the spacers in sequenced CRISPR arrays that reliably match protospacer sequences in genomic databases is small, leaving the question of the origin(s) open for the great majority of the spacers. Here, we extend the spacer analysis by examining the distribution of partial matches (matching k-mers) between spacers and genomes of viruses infecting the given host as well as the host genomes themselves. The results indicate that most of the spacers originate from the host-specific viromes, whereas self-targeting is strongly selected against. However, we present evidence that the vast majority of the viruses comprising the viromes currently remain unknown although they are likely to be related to identified viruses.
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Affiliation(s)
- Sergey A Shmakov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | | | - Konstantin V Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, New Jersey, 08854, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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52
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Kiga K, Tan XE, Ibarra-Chávez R, Watanabe S, Aiba Y, Sato'o Y, Li FY, Sasahara T, Cui B, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Azam AH, Suzuki M, Penadés JR, Cui L. Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria. Nat Commun 2020; 11:2934. [PMID: 32523110 PMCID: PMC7287087 DOI: 10.1038/s41467-020-16731-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/13/2020] [Indexed: 02/08/2023] Open
Abstract
The emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. Here we report the development of a series of CRISPR-Cas13a-based antibacterial nucleocapsids, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus by recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs are generated by packaging programmed CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibit strong bacterial killing activities upon recognizing target genes regardless of their location. Moreover, we also demonstrate that the CapsidCas13a(s) can be applied to detect bacterial genes through gene-specific depletion of bacteria without employing nucleic acid manipulation and optical visualization devices. Our data underscore the potential of CapsidCas13a(s) as both therapeutic agents against antimicrobial-resistant bacteria and nonchemical agents for detection of bacterial genes. CRISPR technology is emerging as a potential antimicrobial against antimicrobial-resistant bacteria. Here the authors develop a bacteriophage delivered Cas13a system for killing target bacteria and detecting bacterial genes.
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Affiliation(s)
- Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Rodrigo Ibarra-Chávez
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Sato'o
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Feng-Yu Li
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Bintao Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Moriyuki Kawauchi
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Tanit Boonsiri
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Taki
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Aa Haeruman Azam
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - José R Penadés
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Tochigi, Japan.
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53
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Peng X, Mayo-Muñoz D, Bhoobalan-Chitty Y, Martínez-Álvarez L. Anti-CRISPR Proteins in Archaea. Trends Microbiol 2020; 28:913-921. [PMID: 32499102 DOI: 10.1016/j.tim.2020.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/26/2022]
Abstract
Anti-CRISPR (Acr) proteins are natural inhibitors of CRISPR-Cas immune systems. To date, Acrs inhibiting types I, II, III, V, and VI CRISPR-Cas systems have been characterized. While most known Acrs are derived from bacterial phages and prophages, very few have been characterized in the domain Archaea, despite the nearly ubiquitous presence of CRISPR-Cas in archaeal cells. Here we summarize the discovery and characterization of the archaeal Acrs with the representatives encoded by a model archaeal virus, Sulfolobus islandicus rod-shaped virus 2 (SIRV2). AcrID1 inhibits subtype I-D CRISPR-Cas immunity through direct interaction with the large subunit Cas10d of the effector complex, and AcrIIIB1 inhibits subtype III-B CRISPR-Cas immunity through a mechanism interfering with middle/late gene targeting. Future development of efficient screening methods will be key to uncovering the diversity of archaeal Acrs.
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Affiliation(s)
- Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
| | - David Mayo-Muñoz
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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54
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Foster K, Grüschow S, Bailey S, White MF, Terns MP. Regulation of the RNA and DNA nuclease activities required for Pyrococcus furiosus Type III-B CRISPR-Cas immunity. Nucleic Acids Res 2020; 48:4418-4434. [PMID: 32198888 PMCID: PMC7192623 DOI: 10.1093/nar/gkaa176] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/28/2020] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
Type III CRISPR-Cas prokaryotic immune systems provide anti-viral and anti-plasmid immunity via a dual mechanism of RNA and DNA destruction. Upon target RNA interaction, Type III crRNP effector complexes become activated to cleave both target RNA (via Cas7) and target DNA (via Cas10). Moreover, trans-acting endoribonucleases, Csx1 or Csm6, can promote the Type III immune response by destroying both invader and host RNAs. Here, we characterize how the RNase and DNase activities associated with Type III-B immunity in Pyrococcus furiosus (Pfu) are regulated by target RNA features and second messenger signaling events. In vivo mutational analyses reveal that either the DNase activity of Cas10 or the RNase activity of Csx1 can effectively direct successful anti-plasmid immunity. Biochemical analyses confirmed that the Cas10 Palm domains convert ATP into cyclic oligoadenylate (cOA) compounds that activate the ribonuclease activity of Pfu Csx1. Furthermore, we show that the HEPN domain of the adenosine-specific endoribonuclease, Pfu Csx1, degrades cOA signaling molecules to provide an auto-inhibitory off-switch of Csx1 activation. Activation of both the DNase and cOA generation activities require target RNA binding and recognition of distinct target RNA 3' protospacer flanking sequences. Our results highlight the complex regulatory mechanisms controlling Type III CRISPR immunity.
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Affiliation(s)
- Kawanda Foster
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Scott Bailey
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Michael P Terns
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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55
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Weissman JL, Stoltzfus A, Westra ER, Johnson PLF. Avoidance of Self during CRISPR Immunization. Trends Microbiol 2020; 28:543-553. [PMID: 32544441 DOI: 10.1016/j.tim.2020.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023]
Abstract
The battle between microbes and their viruses is ancient and ongoing. Clustered regularly interspaced short palindromic repeat (CRISPR) immunity, the first and, to date, only form of adaptive immunity found in prokaryotes, represents a flexible mechanism to recall past infections while also adapting to a changing pathogenic environment. Critical to the role of CRISPR as an adaptive immune mechanism is its capacity for self versus non-self recognition when acquiring novel immune memories. Yet, CRISPR systems vary widely in both how and to what degree they can distinguish foreign from self-derived genetic material. We document known and hypothesized mechanisms that bias the acquisition of immune memory towards non-self targets. We demonstrate that diversity is the rule, with many widespread but no universal mechanisms for self versus non-self recognition.
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Affiliation(s)
- Jake L Weissman
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, NIST, Gaithersburg, MD 20899, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Edze R Westra
- Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, UK
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56
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The arms race between bacteria and their phage foes. Nature 2020; 577:327-336. [PMID: 31942051 DOI: 10.1038/s41586-019-1894-8] [Citation(s) in RCA: 409] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/13/2019] [Indexed: 12/26/2022]
Abstract
Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.
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57
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An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature 2020; 577:572-575. [PMID: 31942067 PMCID: PMC6986909 DOI: 10.1038/s41586-019-1909-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023]
Abstract
The CRISPR system in bacteria and archaea provides adaptive immunity against mobile genetic elements. Type III CRISPR systems detect viral RNA, resulting in the activation of two regions of the Cas10 protein: an HD nuclease domain (which degrades viral DNA)1,2 and a cyclase domain (which synthesizes cyclic oligoadenylates from ATP)3-5. Cyclic oligoadenylates in turn activate defence enzymes with a CRISPR-associated Rossmann fold domain6, sculpting a powerful antiviral response7-10 that can drive viruses to extinction7,8. Cyclic nucleotides are increasingly implicated in host-pathogen interactions11-13. Here we identify a new family of viral anti-CRISPR (Acr) enzymes that rapidly degrade cyclic tetra-adenylate (cA4). The viral ring nuclease AcrIII-1 is widely distributed in archaeal and bacterial viruses and in proviruses. The enzyme uses a previously unknown fold to bind cA4 specifically, and a conserved active site to rapidly cleave this signalling molecule, allowing viruses to neutralize the type III CRISPR defence system. The AcrIII-1 family has a broad host range, as it targets cA4 signalling molecules rather than specific CRISPR effector proteins. Our findings highlight the crucial role of cyclic nucleotide signalling in the conflict between viruses and their hosts.
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58
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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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59
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Padayachee J, Singh M. Therapeutic applications of CRISPR/Cas9 in breast cancer and delivery potential of gold nanomaterials. Nanobiomedicine (Rij) 2020; 7:1849543520983196. [PMID: 33488814 PMCID: PMC7768851 DOI: 10.1177/1849543520983196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Globally, approximately 1 in 4 cancers in women are diagnosed as breast cancer (BC). Despite significant advances in the diagnosis and therapy BCs, many patients develop metastases or relapses. Hence, novel therapeutic strategies are required, that can selectively and efficiently kill malignant cells. Direct targeting of the genetic and epigenetic aberrations that occur in BC development is a promising strategy to overcome the limitations of current therapies, which target the tumour phenotype. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, composed of only an easily modifiable single guide RNA (sgRNA) sequence bound to a Cas9 nuclease, has revolutionised genome editing due to its simplicity and efficiency compared to earlier systems. CRISPR/Cas9 and its associated catalytically inactivated dCas9 variants facilitate the knockout of overexpressed genes, correction of mutations in inactivated genes, and reprogramming of the epigenetic landscape to impair BC growth. To achieve efficient genome editing in vivo, a vector is required to deliver the components to target cells. Gold nanomaterials, including gold nanoparticles and nanoclusters, display many advantageous characteristics that have facilitated their widespread use in theranostics, as delivery vehicles, and imaging and photothermal agents. This review highlights the therapeutic applications of CRISPR/Cas9 in treating BCs, and briefly describes gold nanomaterials and their potential in CRISPR/Cas9 delivery.
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Affiliation(s)
| | - Moganavelli Singh
- Nano-Gene and Drug Delivery Laboratory, Discipline of Biochemistry, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Durban, South Africa
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60
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61
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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] [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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62
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Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog. Cell Host Microbe 2019; 26:325-335.e5. [PMID: 31492655 DOI: 10.1016/j.chom.2019.08.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/20/2019] [Accepted: 08/13/2019] [Indexed: 12/26/2022]
Abstract
Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered "hyper-targeted" phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.
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Affiliation(s)
- Paola Soto-Perez
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jordan E Bisanz
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joel D Berry
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kathy N Lam
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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63
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Nasef M, Muffly MC, Beckman AB, Rowe SJ, Walker FC, Hatoum-Aslan A, Dunkle JA. Regulation of cyclic oligoadenylate synthesis by the Staphylococcus epidermidis Cas10-Csm complex. RNA (NEW YORK, N.Y.) 2019; 25:948-962. [PMID: 31076459 PMCID: PMC6633199 DOI: 10.1261/rna.070417.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
CRISPR-Cas systems are a class of adaptive immune systems in prokaryotes that use small CRISPR RNAs (crRNAs) in conjunction with CRISPR-associated (Cas) nucleases to recognize and degrade foreign nucleic acids. Recent studies have revealed that Type III CRISPR-Cas systems synthesize second messenger molecules previously unknown to exist in prokaryotes, cyclic oligoadenylates (cOA). These molecules activate the Csm6 nuclease to promote RNA degradation and may also coordinate additional cellular responses to foreign nucleic acids. Although cOA production has been reconstituted and characterized for a few bacterial and archaeal Type III systems, cOA generation and its regulation have not been explored for the Staphylococcus epidermidis Type III-A CRISPR-Cas system, a longstanding model for CRISPR-Cas function. Here, we demonstrate that this system performs Mg2+-dependent synthesis of 3-6 nt cOA. We show that activation of cOA synthesis is perturbed by single nucleotide mismatches between the crRNA and target RNA at discrete positions, and that synthesis is antagonized by Csm3-mediated target RNA cleavage. Altogether, our results establish the requirements for cOA production in a model Type III CRISPR-Cas system and suggest a natural mechanism to dampen immunity once the foreign RNA is destroyed.
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Affiliation(s)
- Mohamed Nasef
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Mary C Muffly
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Andrew B Beckman
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Sebastian J Rowe
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Forrest C Walker
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Asma Hatoum-Aslan
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Jack A Dunkle
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
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64
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Guo T, Zheng F, Zeng Z, Yang Y, Li Q, She Q, Han W. Cmr3 regulates the suppression on cyclic oligoadenylate synthesis by tag complementarity in a Type III-B CRISPR-Cas system. RNA Biol 2019; 16:1513-1520. [PMID: 31298604 DOI: 10.1080/15476286.2019.1642725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Type III CRISPR-Cas systems code for a multi-subunit ribonucleoprotein (RNP) complex that mediates DNA cleavage and synthesizes cyclic oligoadenylate (cOA) second messenger to confer anti-viral immunity. Both immune activities are to be activated upon binding to target RNA transcripts by their complementarity to crRNA, and autoimmunity avoidance is determined by extended complementarity between the 5'-repeat tag of crRNA and 3'-flanking sequences of target transcripts (anti-tag). However, as to how the strategy could achieve stringent autoimmunity avoidance remained elusive. In this study, we systematically investigated how the complementarity of the crRNA 5'-tag and anti-tag (i.e., tag complementarity) could affect the interference activities (DNA cleavage activity and cOA synthesis activity) of Cmr-α, a type III-B system in Sulfolobus islandicus Rey15A. The results revealed an increasing suppression on both activities by increasing degrees of tag complementarity and a critical function of the 7th nucleotide of crRNA in avoiding autoimmunity. More importantly, mutagenesis of Cmr3α exerts either positive or negative effects on the cOA synthesis activity depending on the degrees of tag complementarity, suggesting that the subunit, coupling with the interaction between crRNA tag and anti-tag, function in facilitating immunity and avoiding autoimmunity in Type III-B systems.
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Affiliation(s)
- Tong Guo
- Danish Archaea Center, Department of Biology, University of Copenhagen , Copenhagen N , Denmark
| | - Fan Zheng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Yang Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Qi Li
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Qunxin She
- Danish Archaea Center, Department of Biology, University of Copenhagen , Copenhagen N , Denmark.,State Key Laboratory of Microbial Technology, Shandong University , Qingdao , China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
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65
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Abstract
How RNA-targeting CRISPR-Cas13 functions as a phage defense system has been mysterious. Recently in Nature, Meeske et al. (2019) demonstrate that Cas13 provides potent immunity to dsDNA phages without cutting their genome. By sensing phage transcripts and destroying RNA nonspecifically to arrest the cell into dormancy, Cas13 provides herd immunity.
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Affiliation(s)
- Senén D Mendoza
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, 94143
| | - Joseph Bondy-Denomy
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, 94143.
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66
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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] [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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67
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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: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [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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68
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Pan S, Li Q, Deng L, Jiang S, Jin X, Peng N, Liang Y, She Q, Li Y. A seed motif for target RNA capture enables efficient immune defence by a type III-B CRISPR-Cas system. RNA Biol 2019; 16:1166-1178. [PMID: 31096876 DOI: 10.1080/15476286.2019.1618693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems provide an adaptive defence against foreign nucleic acids guided by small RNAs (crRNAs) in archaea and bacteria. The Type III CRISPR systems are reported to carry RNase, RNA-activated DNase and cyclic oligoadenylate (cOA) synthetase activity, and are significantly different from other CRISPR systems. However, detailed features of target recognition, which are essential for enhancing target specificity remain unknown in Type III CRISPR systems. Here, we show that the Type III-B Cmr-α system in S. islandicus generates two constant lengths of crRNA independent of the length of the spacer. Either mutation at the 3'-end of crRNA or target truncation greatly influences the target capture and cleavage by the Cmr-α effector complex. Furthermore, we found that cleavage at the tag-proximal site on the target RNA by the Cmr-α RNP complex is delayed relative to the other sites, which probably provides Cas10 more time to function as a guard against invaders. Using a mutagenesis assay in vivo, we discovered that a seed motif located at the tag-distal region of the crRNA is required by Cmr1α for target RNA capture by the Cmr-α system thereby enhancing target specificity and efficiency. These findings further refine the model for immune defence of Type III-B CRISPR-Cas system, commencing on capture, cleavage and regulation.
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Affiliation(s)
- Saifu Pan
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Qi Li
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Ling Deng
- b Archaea Centre, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Suping Jiang
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Xuexia Jin
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Nan Peng
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Yunxiang Liang
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Qunxin She
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China.,b Archaea Centre, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Yingjun Li
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
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69
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Verma R, Sahu R, Singh DD, Egbo TE. A CRISPR/Cas9 based polymeric nanoparticles to treat/inhibit microbial infections. Semin Cell Dev Biol 2019; 96:44-52. [PMID: 30986568 DOI: 10.1016/j.semcdb.2019.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/11/2019] [Indexed: 12/17/2022]
Abstract
The latest breakthrough towards the adequate and decisive methods of gene editing tools provided by CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR Associated System), has been repurposed into a tool for genetically engineering eukaryotic cells and now considered as the major innovation in gene-related disorders. Nanotechnology has provided an alternate way to overcome the conventional problems where methods to deliver therapeutic agents have failed. The use of nanotechnology has the potential to safe-side the CRISPR/Cas9 components delivery by using customized polymeric nanoparticles for safety and efficacy. The pairing of two (CRISPR/Cas9 and nanotechnology) has the potential for opening new avenues in therapeutic use. In this review, we will discuss the most recent advances in developing nanoparticle-based CRISPR/Cas9 gene editing cargo delivery with a focus on several polymeric nanoparticles including fabrication proposals to combat microbial infections.
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Affiliation(s)
- Richa Verma
- Center for Nanobiotechnology Research, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Rajnish Sahu
- Center for Nanobiotechnology Research, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University, Jaipur, Rajasthan, 303002, India
| | - Timothy E Egbo
- Department of Biological Sciences, College of Science Technology Engineering and Mathematics, Alabama State University, Montgomery, AL, 36104, USA.
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70
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Johnson K, Learn BA, Estrella MA, Bailey S. Target sequence requirements of a type III-B CRISPR-Cas immune system. J Biol Chem 2019; 294:10290-10299. [PMID: 31110048 DOI: 10.1074/jbc.ra119.008728] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/07/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are RNA-based immune systems that protect many prokaryotes from invasion by viruses and plasmids. Type III CRISPR systems are unique, as their targeting mechanism requires target transcription. Upon transcript binding, DNA cleavage by type III effector complexes is activated. Type III systems must differentiate between invader and native transcripts to prevent autoimmunity. Transcript origin is dictated by the sequence that flanks the 3' end of the RNA target site (called the PFS). However, how the PFS is recognized may vary among different type III systems. Here, using purified proteins and in vitro assays, we define how the type III-B effector from the hyperthermophilic bacterium Thermotoga maritima discriminates between native and invader transcripts. We show that native transcripts are recognized by base pairing at positions -2 to -5 of the PFS and by a guanine at position -1, which is not recognized by base pairing. We also show that mismatches with the RNA target are highly tolerated in this system, except for those nucleotides adjacent to the PFS. These findings define the target requirement for the type III-B system from T. maritima and provide a framework for understanding the target requirements of type III systems as a whole.
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Affiliation(s)
- Kaitlin Johnson
- From the Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health and
| | - Brian A Learn
- From the Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health and
| | - Michael A Estrella
- From the Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health and
| | - Scott Bailey
- From the Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health and .,Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
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71
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Chou-Zheng L, Hatoum-Aslan A. A type III-A CRISPR-Cas system employs degradosome nucleases to ensure robust immunity. eLife 2019; 8:e45393. [PMID: 30942690 PMCID: PMC6447361 DOI: 10.7554/elife.45393] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/15/2019] [Indexed: 12/16/2022] Open
Abstract
CRISPR-Cas systems provide sequence-specific immunity against phages and mobile genetic elements using CRISPR-associated nucleases guided by short CRISPR RNAs (crRNAs). Type III systems exhibit a robust immune response that can lead to the extinction of a phage population, a feat coordinated by a multi-subunit effector complex that destroys invading DNA and RNA. Here, we demonstrate that a model type III system in Staphylococcus epidermidis relies upon the activities of two degradosome-associated nucleases, PNPase and RNase J2, to mount a successful defense. Genetic, molecular, and biochemical analyses reveal that PNPase promotes crRNA maturation, and both nucleases are required for efficient clearance of phage-derived nucleic acids. Furthermore, functional assays show that RNase J2 is essential for immunity against diverse mobile genetic elements originating from plasmid and phage. Altogether, our observations reveal the evolution of a critical collaboration between two nucleic acid degrading machines which ensures cell survival when faced with phage attack.
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Affiliation(s)
- Lucy Chou-Zheng
- Department of Biological SciencesThe University of AlabamaTuscaloosaUnited States
| | - Asma Hatoum-Aslan
- Department of Biological SciencesThe University of AlabamaTuscaloosaUnited States
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72
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Wang F, Wang L, Zou X, Duan S, Li Z, Deng Z, Luo J, Lee SY, Chen S. Advances in CRISPR-Cas systems for RNA targeting, tracking and editing. Biotechnol Adv 2019; 37:708-729. [PMID: 30926472 DOI: 10.1016/j.biotechadv.2019.03.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only ~930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA-targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.
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Affiliation(s)
- Fei Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Xuan Zou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea
| | - Suling Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zhiqiang Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Jie Luo
- Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea.
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China.
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73
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Abstract
Bacteria are under constant attack from bacteriophages (phages), bacterial parasites that are the most abundant biological entity on earth. To resist phage infection, bacteria have evolved an impressive arsenal of anti-phage systems. Recent advances have significantly broadened and deepened our understanding of how bacteria battle phages, spearheaded by new systems like CRISPR-Cas. This review aims to summarize bacterial anti-phage mechanisms, with an emphasis on the most recent developments in the field.
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Affiliation(s)
- Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Luciano Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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74
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Nayeemul Bari SM, Hatoum-Aslan A. CRISPR-Cas10 assisted editing of virulent staphylococcal phages. Methods Enzymol 2018; 616:385-409. [PMID: 30691652 DOI: 10.1016/bs.mie.2018.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phages are the most abundant entities in the biosphere and profoundly impact the bacterial populations within and around us. They attach to a specific host, inject their DNA, hijack the host's cellular processes, and replicate exponentially while destroying the host. Historically, phages have been exploited as powerful antimicrobials, and phage-derived proteins have constituted the basis for numerous biotechnological applications. Only in recent years have metagenomic studies revealed that phage genomes harbor a rich reservoir of genetic diversity, which might afford further therapeutic and/or biotechnological value. Nevertheless, functions for the majority of phage genes remain unknown, and due to their swift and destructive replication cycle, many phages are intractable by current genetic engineering techniques. Whether to advance the basic understanding of phage biology or to tap into their potential applications, efficient methods for phage genetic engineering are needed. Recent reports have shown that CRISPR-Cas systems, a class of prokaryotic immune systems that protect against phage infection, can be harnessed to engineer diverse phages. In this chapter, we describe methods to genetically manipulate virulent phages using CRISPR-Cas10, a Type III-A CRISPR-Cas system native to Staphylococcus epidermidis. A method for engineering phages that infect a CRISPR-less Staphylococcus aureus host is also described. Both approaches have proved successful in isolating desired phage mutants with 100% efficiency, demonstrating that CRISPR-Cas10 constitutes a powerful tool for phage genetic engineering. The relatively widespread presence of Type III CRISPR-Cas systems in bacteria and archaea imply that similar strategies may be used to manipulate the genomes of diverse prokaryotic viruses.
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Affiliation(s)
- S M Nayeemul Bari
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Asma Hatoum-Aslan
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States.
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75
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Weissman JL, Fagan WF, Johnson PLF. Selective Maintenance of Multiple CRISPR Arrays Across Prokaryotes. CRISPR J 2018; 1:405-413. [PMID: 31021246 DOI: 10.1089/crispr.2018.0034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Prokaryotes are under nearly constant attack by viral pathogens. To protect against this threat of infection, bacteria and archaea have evolved a wide array of defense mechanisms, singly and in combination. While immune diversity in a single organism likely reduces the chance of pathogen evolutionary escape, it remains puzzling why many prokaryotes also have multiple, seemingly redundant, copies of the same type of immune system. Here, we focus on the highly flexible CRISPR adaptive immune system, which is present in multiple copies in a surprising 28% of the prokaryotic genomes in RefSeq. We use a comparative genomics approach looking across all prokaryotes to demonstrate that on average, organisms are under selection to maintain more than one CRISPR array. Given this surprising conclusion, we consider several hypotheses concerning the source of selection and include a theoretical analysis of the possibility that a trade-off between memory span and learning speed could select for both "long-term memory" and "short-term memory" CRISPR arrays.
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Affiliation(s)
- Jake L Weissman
- Department of Biology, University of Maryland College Park , College Park, Maryland
| | - William F Fagan
- Department of Biology, University of Maryland College Park , College Park, Maryland
| | - Philip L F Johnson
- Department of Biology, University of Maryland College Park , College Park, Maryland
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76
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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: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [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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77
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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: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [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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78
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Künne T, Zhu Y, da Silva F, Konstantinides N, McKenzie RE, Jackson RN, Brouns S. Role of nucleotide identity in effective CRISPR target escape mutations. Nucleic Acids Res 2018; 46:10395-10404. [PMID: 30107450 PMCID: PMC6212716 DOI: 10.1093/nar/gky687] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/16/2018] [Accepted: 08/10/2018] [Indexed: 12/26/2022] Open
Abstract
Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets only minimally affect target DNA binding. Structural modeling of Cascade-bound targets with mismatches shows that steric clashes of mismatched guanines lead to unfavorable conformations of the RNA-DNA duplex. This effect has strong implications for the natural selection of target site mutations that lead to effective escape from type I CRISPR-Cas systems.
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MESH Headings
- Base Pairing
- Base Sequence
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Cytosine/chemistry
- Cytosine/metabolism
- DNA Helicases/genetics
- DNA Helicases/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Guanine/chemistry
- Guanine/metabolism
- Mutation
- Plasmids/chemistry
- Plasmids/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
- Tim Künne
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Laboratory of Food Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Yifan Zhu
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Fausia da Silva
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Nico Konstantinides
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Rebecca E McKenzie
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Ryan N Jackson
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT, USA
| | - Stan JJ Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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79
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Terns MP. CRISPR-Based Technologies: Impact of RNA-Targeting Systems. Mol Cell 2018; 72:404-412. [PMID: 30388409 PMCID: PMC6239212 DOI: 10.1016/j.molcel.2018.09.018] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/06/2018] [Accepted: 09/13/2018] [Indexed: 12/26/2022]
Abstract
DNA-targeting CRISPR-Cas systems, such as those employing the RNA-guided Cas9 or Cas12 endonucleases, have revolutionized our ability to predictably edit genomes and control gene expression. Here, I summarize information on RNA-targeting CRISPR-Cas systems and describe recent advances in converting them into powerful and programmable RNA-binding and cleavage tools with a wide range of novel and important biotechnological and biomedical applications.
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Affiliation(s)
- Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA; Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
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80
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Schmidt F, Cherepkova MY, Platt RJ. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 2018; 562:380-385. [DOI: 10.1038/s41586-018-0569-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/21/2018] [Indexed: 12/11/2022]
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81
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Millen AM, Samson JE, Tremblay DM, Magadán AH, Rousseau GM, Moineau S, Romero DA. Lactococcus lactis type III-A CRISPR-Cas system cleaves bacteriophage RNA. RNA Biol 2018; 16:461-468. [PMID: 30081743 DOI: 10.1080/15476286.2018.1502589] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas defends microbial cells against invading nucleic acids including viral genomes. Recent studies have shown that type III-A CRISPR-Cas systems target both RNA and DNA in a transcription-dependent manner. We previously found a type III-A system on a conjugative plasmid in Lactococcus lactis which provided resistance against virulent phages of the Siphoviridae family. Its naturally occurring spacers are oriented to generate crRNAs complementary to target phage mRNA, suggesting transcription-dependent targeting. Here, we show that only constructs whose spacers produce crRNAs complementary to the phage mRNA confer phage resistance in L. lactis. In vivo nucleic acid cleavage assays showed that cleavage of phage dsDNA genome was not detected within phage-infected L. lactis cells. On the other hand, Northern blots indicated that the lactococcal CRISPR-Cas cleaves phage mRNA in vivo. These results cannot exclude that single-stranded phage DNA is not being targeted, but phage DNA replication has been shown to be impaired.
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Affiliation(s)
- Anne M Millen
- a Technology & Innovation , DuPont Nutrition and Health , Madison , WI , USA
| | - Julie E Samson
- b Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire , Université Laval , Québec City , QC , Canada
| | - Denise M Tremblay
- b Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire , Université Laval , Québec City , QC , Canada.,c Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire , Université Laval , Québec City , QC , Canada
| | - Alfonso H Magadán
- b Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire , Université Laval , Québec City , QC , Canada
| | - Geneviève M Rousseau
- b Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire , Université Laval , Québec City , QC , Canada
| | - Sylvain Moineau
- b Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire , Université Laval , Québec City , QC , Canada.,c Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire , Université Laval , Québec City , QC , Canada
| | - Dennis A Romero
- a Technology & Innovation , DuPont Nutrition and Health , Madison , WI , USA
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82
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Makarova KS, Wolf YI, Koonin EV. Classification and Nomenclature of CRISPR-Cas Systems: Where from Here? CRISPR J 2018; 1:325-336. [PMID: 31021272 DOI: 10.1089/crispr.2018.0033] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As befits an immune mechanism, CRISPR-Cas systems are highly variable with respect to Cas protein sequences, gene composition, and organization of the genomic loci. Optimal classification of CRISPR-Cas systems and rational nomenclature for CRISPR-associated genes are essential for further progress of CRISPR research. These are highly challenging tasks because of the complexity of CRISPR-Cas and their fast evolution, including frequent module shuffling, as well as the lack of universal markers for a consistent evolutionary classification. The complexity and variability of CRISPR-Cas systems necessitate a multipronged approach to classification and nomenclature. We present a brief summary of the current state of the art and discuss further directions in this area.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information , National Library of Medicine, Bethesda, Maryland
| | - Yuri I Wolf
- National Center for Biotechnology Information , National Library of Medicine, Bethesda, Maryland
| | - Eugene V Koonin
- National Center for Biotechnology Information , National Library of Medicine, Bethesda, Maryland
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83
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Gleditzsch D, Pausch P, Müller-Esparza H, Özcan A, Guo X, Bange G, Randau L. PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures. RNA Biol 2018; 16:504-517. [PMID: 30109815 PMCID: PMC6546366 DOI: 10.1080/15476286.2018.1504546] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Adaptive immunity of prokaryotes is mediated by CRISPR-Cas systems that employ a large variety of Cas protein effectors to identify and destroy foreign genetic material. The different targeting mechanisms of Cas proteins rely on the proper protection of the host genome sequence while allowing for efficient detection of target sequences, termed protospacers. A short DNA sequence, the protospacer-adjacent motif (PAM), is frequently used to mark proper target sites. Cas proteins have evolved a multitude of PAM-interacting domains, which enables them to cope with viral anti-CRISPR measures that alter the sequence or accessibility of PAM elements. In this review, we summarize known PAM recognition strategies for all CRISPR-Cas types. Available structures of target bound Cas protein effector complexes highlight the diversity of mechanisms and domain architectures that are employed to guarantee target specificity.
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Affiliation(s)
- Daniel Gleditzsch
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
| | - Patrick Pausch
- b Philipps-University-Marburg , LOEWE Center for synthetic Microbiology (Synmikro) & Faculty of Chemistry , Marburg , Germany
| | - Hanna Müller-Esparza
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
| | - Ahsen Özcan
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
| | - Xiaohan Guo
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
| | - Gert Bange
- b Philipps-University-Marburg , LOEWE Center for synthetic Microbiology (Synmikro) & Faculty of Chemistry , Marburg , Germany
| | - Lennart Randau
- a Prokaryotic Small RNA Biology Group, Max-Planck-Institute for terrestrial Microbiology & LOEWE Center for synthetic Microbiology (Synmikro) , Marburg , Germany
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84
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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: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [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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85
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Tambe A, East-Seletsky A, Knott GJ, Doudna JA, O'Connell MR. RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a. Cell Rep 2018; 24:1025-1036. [PMID: 30044970 PMCID: PMC6085867 DOI: 10.1016/j.celrep.2018.06.105] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/24/2018] [Accepted: 06/27/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas13a enzymes are RNA-guided, RNA-activated RNases. Their properties have been exploited as powerful tools for RNA detection, RNA imaging, and RNA regulation. However, the relationship between target RNA binding and HEPN (higher eukaryotes and prokaryotes nucleotide binding) domain nuclease activation is poorly understood. Using sequencing experiments coupled with in vitro biochemistry, we find that Cas13a target RNA binding affinity and HEPN-nuclease activity are differentially affected by the number and the position of mismatches between the guide and the target. We identify a central binding seed for which perfect base pairing is required for target binding and a separate nuclease switch for which imperfect base pairing results in tight binding, but not HEPN-nuclease activation. These results demonstrate that the binding and cleavage activities of Cas13a are decoupled, highlighting a complex specificity landscape. Our findings underscore a need to consider the range of effects off-target recognition has on Cas13a RNA binding and cleavage behavior for RNA-targeting tool development.
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Affiliation(s)
- Akshay Tambe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexandra East-Seletsky
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, 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; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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86
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Guo T, Han W, She Q. Tolerance of Sulfolobus SMV1 virus to the immunity of I-A and III-B CRISPR-Cas systems in Sulfolobus islandicus. RNA Biol 2018; 16:549-556. [PMID: 29629622 DOI: 10.1080/15476286.2018.1460993] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Sulfolobus islandicus Rey15A encodes one Type I-A and two Type III-B systems, all of which are active in mediating nucleic acids interference. However, the effectiveness of each CRISPR system against virus infection was not tested in this archaeon. Here we constructed S. islandicus strains that constitutively express the antiviral immunity from either I-A, or III-B, or I-A plus III-B systems against SMV1 and tested the response of each host to SMV1 infection. We found that, although both CRISPR immunities showed a strong inhibition to viral DNA replication at an early stage of incubation, the host I-A CRISPR immunity gradually lost the control on virus proliferation, allowing accumulation of cellular viral DNA and release of a large number of viral particles. In contrast, the III-B CRISPR immunity showed a tight control on both viral DNA replication and virus particle formation. Furthermore, the SMV1 tolerance to the I-A CRISPR immunity did not result from the occurrence of escape mutations, suggesting the virus probably encodes an anti-CRISPR protein (Acr) to compromise the host I-A CRISPR immunity. Together, this suggests that the interplay between viral Acrs and CRISPR-Cas systems in thermophilic archaea could have shaped the stable virus-host relationship that is observed for many archaeal viruses.
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Affiliation(s)
- Tong Guo
- a Archaea Center, Department of Biology , University of Copenhagen, Copenhagen Biocenter , Copenhagen N , Denmark
| | - Wenyuan Han
- a Archaea Center, Department of Biology , University of Copenhagen, Copenhagen Biocenter , Copenhagen N , Denmark
| | - Qunxin She
- a Archaea Center, Department of Biology , University of Copenhagen, Copenhagen Biocenter , Copenhagen N , Denmark.,b State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology , Huazhong Agricultural University , Wuhan , China
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87
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Rouillon C, Athukoralage JS, Graham S, Grüschow S, White MF. Control of cyclic oligoadenylate synthesis in a type III CRISPR system. eLife 2018; 7:36734. [PMID: 29963983 PMCID: PMC6053304 DOI: 10.7554/elife.36734] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/01/2018] [Indexed: 12/15/2022] Open
Abstract
The CRISPR system for prokaryotic adaptive immunity provides RNA-mediated protection from viruses and mobile genetic elements. When viral RNA transcripts are detected, type III systems adopt an activated state that licenses DNA interference and synthesis of cyclic oligoadenylate (cOA). cOA activates nucleases and transcription factors that orchestrate the antiviral response. We demonstrate that cOA synthesis is subject to tight temporal control, commencing on target RNA binding, and is deactivated rapidly as target RNA is cleaved and dissociates. Mismatches in the target RNA are well tolerated and still activate the cyclase domain, except when located close to the 3' end of the target. Phosphorothioate modification reduces target RNA cleavage and stimulates cOA production. The 'RNA shredding' activity originally ascribed to type III systems may thus be a reflection of an exquisite mechanism for control of the Cas10 subunit, rather than a direct antiviral defence.
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Affiliation(s)
- Christophe Rouillon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Januka S Athukoralage
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
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88
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Hatoum-Aslan A. Phage Genetic Engineering Using CRISPR⁻Cas Systems. Viruses 2018; 10:E335. [PMID: 29921752 PMCID: PMC6024849 DOI: 10.3390/v10060335] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/17/2018] [Accepted: 06/17/2018] [Indexed: 12/26/2022] Open
Abstract
Since their discovery over a decade ago, the class of prokaryotic immune systems known as CRISPR⁻Cas have afforded a suite of genetic tools that have revolutionized research in model organisms spanning all domains of life. CRISPR-mediated tools have also emerged for the natural targets of CRISPR⁻Cas immunity, the viruses that specifically infect bacteria, or phages. Despite their status as the most abundant biological entities on the planet, the majority of phage genes have unassigned functions. This reality underscores the need for robust genetic tools to study them. Recent reports have demonstrated that CRISPR⁻Cas systems, specifically the three major types (I, II, and III), can be harnessed to genetically engineer phages that infect diverse hosts. Here, the mechanisms of each of these systems, specific strategies used, and phage editing efficacies will be reviewed. Due to the relatively wide distribution of CRISPR⁻Cas systems across bacteria and archaea, it is anticipated that these immune systems will provide generally applicable tools that will advance the mechanistic understanding of prokaryotic viruses and accelerate the development of novel technologies based on these ubiquitous organisms.
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Affiliation(s)
- Asma Hatoum-Aslan
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA.
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89
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Huber I, Potapova K, Kuhn A, Schmidt H, Hinrichs J, Rohde C, Beyer W. 1st German Phage Symposium-Conference Report. Viruses 2018; 10:v10040158. [PMID: 29596346 PMCID: PMC5923452 DOI: 10.3390/v10040158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 03/23/2018] [Accepted: 03/25/2018] [Indexed: 12/12/2022] Open
Abstract
In Germany, phage research and application can be traced back to the beginning of the 20th century. However, with the triumphal march of antibiotics around the world, the significance of bacteriophages faded in most countries, and respective research mainly focused on fundamental questions and niche applications. After a century, we pay tribute to the overuse of antibiotics that led to multidrug resistance and calls for new strategies to combat pathogenic microbes. Against this background, bacteriophages came into the spotlight of researchers and practitioners again resulting in a fast growing “phage community”. In October 2017, part of this community met at the 1st German Phage Symposium to share their knowledge and experiences. The participants discussed open questions and challenges related to phage therapy and the application of phages in general. This report summarizes the presentations given, highlights the main points of the round table discussion and concludes with an outlook for the different aspects of phage application.
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Affiliation(s)
- Irene Huber
- Hohenheim Research Center for Health Sciences, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Katerina Potapova
- Hohenheim Research Center for Health Sciences, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Andreas Kuhn
- Hohenheim Research Center for Health Sciences, University of Hohenheim, 70599 Stuttgart, Germany.
- Institute of Microbiology, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Herbert Schmidt
- Hohenheim Research Center for Health Sciences, University of Hohenheim, 70599 Stuttgart, Germany.
- Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Jörg Hinrichs
- Hohenheim Research Center for Health Sciences, University of Hohenheim, 70599 Stuttgart, Germany.
- Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Christine Rohde
- Leibniz-Institute DSMZ—German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany.
| | - Wolfgang Beyer
- Hohenheim Research Center for Health Sciences, University of Hohenheim, 70599 Stuttgart, Germany.
- Institute of Animal Sciences, University of Hohenheim, 70599 Stuttgart, Germany.
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90
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Hille F, Richter H, Wong SP, Bratovič M, Ressel S, Charpentier E. The Biology of CRISPR-Cas: Backward and Forward. Cell 2018. [DOI: 10.1016/j.cell.2017.11.032] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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91
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Niewoehner O, Jinek M. Specialized Weaponry: How a Type III-A CRISPR-Cas System Excels at Combating Phages. Cell Host Microbe 2018; 22:258-259. [PMID: 28910631 DOI: 10.1016/j.chom.2017.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas-mediated defense against phage invaders usually requires recognition of short sequences, termed protospacer-adjacent motifs (PAMs), in phage DNA. In this issue of Cell Host & Microbe, Pyenson et al. (2017) show that the lack of a PAM requirement in some CRISPR-Cas systems prevents interference evasion and facilitates phage extinction.
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Affiliation(s)
- Ole Niewoehner
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland.
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92
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Vlot M, Houkes J, Lochs SJ, Swarts DC, Zheng P, Kunne T, Mohanraju P, Anders C, Jinek M, van der Oost J, Dickman MJ, Brouns SJ. Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR-Cas effector complexes. Nucleic Acids Res 2018; 46:873-885. [PMID: 29253268 PMCID: PMC5778469 DOI: 10.1093/nar/gkx1264] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 01/06/2023] Open
Abstract
Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction-modification (R-M) and CRISPR-Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR-Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR-Cas systems by lowering the affinity of the Cascade and Cas9-crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR-Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems.
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Affiliation(s)
- Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Joep Houkes
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Silke J A Lochs
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Daan C Swarts
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Peiyuan Zheng
- ChELSI Institute Department of Chemical and Biological Engineering University of Sheffield, Sheffield, UK
| | - Tim Kunne
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Carolin Anders
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Mark J Dickman
- ChELSI Institute Department of Chemical and Biological Engineering University of Sheffield, Sheffield, UK
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Van der Maasweg 9, Delft University of Technology, 2629 HZ Delft, The Netherlands
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93
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Incomplete prophage tolerance by type III-A CRISPR-Cas systems reduces the fitness of lysogenic hosts. Nat Commun 2018; 9:61. [PMID: 29302058 PMCID: PMC5754349 DOI: 10.1038/s41467-017-02557-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/11/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR–Cas systems offer an immune mechanism through which prokaryotic hosts can acquire heritable resistance to genetic parasites, including temperate phages. Co-transcriptional DNA and RNA targeting by type III-A CRISPR–Cas systems restricts temperate phage lytic infections while allowing lysogenic infections to be tolerated under conditions where the prophage targets are transcriptionally repressed. However, long-term consequences of this phenomenon have not been explored. Here we show that maintenance of conditionally tolerant type III-A systems can produce fitness costs within populations of Staphylococcus aureus lysogens. The fitness costs depend on the activity of prophage-internal promoters and type III-A Cas nucleases implicated in targeting, can be more severe in double lysogens, and are alleviated by spacer-target mismatches which do not abrogate immunity during the lytic cycle. These findings suggest that persistence of type III-A systems that target endogenous prophages could be enhanced by spacer-target mismatches, particularly among populations that are prone to polylysogenization. CRISPR-Cas systems, such as type III-A CRISPR-Cas, provide an immune mechanism for prokaryotic hosts to resist parasites, including phages. Here, the authors show that maintenance of conditionally tolerant type III-A systems can affect the fitness of Staphylococcus aureus lysogens.
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