201
|
Goren MG, Doron S, Globus R, Amitai G, Sorek R, Qimron U. Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array. Cell Rep 2017; 16:2811-2818. [PMID: 27626652 PMCID: PMC5039180 DOI: 10.1016/j.celrep.2016.08.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/01/2016] [Accepted: 08/12/2016] [Indexed: 12/24/2022] Open
Abstract
Prokaryotic adaptive immune systems are composed of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins. These systems adapt to new threats by integrating short nucleic acids, termed spacers, into the CRISPR array. The functional motifs in the repeat and the mechanism by which a constant repeat size is maintained are still elusive. Here, through a series of mutations within the repeat of the CRISPR-Cas type I-E, we identify motifs that are crucial for adaptation and show that they serve as anchor sites for two molecular rulers determining the size of the new repeat. Adaptation products from various repeat mutants support a model in which two motifs in the repeat bind to two different sites in the adaptation complex that are 8 and 16 bp away from the active site. This model significantly extends our understanding of the adaptation process and broadens the scope of its applications. Inverted repeats in the type I-E CRISPR-Cas system are essential for adaptation Each inverted repeat encodes a motif serving as an anchor site for a molecular ruler These molecular rulers determine the spacer insertion site regardless of the sequence The findings support a model considering all known steps in spacer adaptation
Collapse
Affiliation(s)
- Moran G Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Shany Doron
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rea Globus
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel.
| |
Collapse
|
202
|
Wei Y, Terns MP. CRISPR Outsourcing: Commissioning IHF for Site-Specific Integration of Foreign DNA at the CRISPR Array. Mol Cell 2017; 62:803-804. [PMID: 27315553 DOI: 10.1016/j.molcel.2016.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this issue of Molecular Cell, Nuñez et al. (2016) report that site-specific integration of foreign DNA into CRISPR loci by the Cas1-Cas2 integrase complex is promoted by a host factor, IHF (integration host factor), that binds and bends CRISPR leader DNA.
Collapse
Affiliation(s)
- Yunzhou Wei
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - 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.
| |
Collapse
|
203
|
Liu T, Liu Z, Ye Q, Pan S, Wang X, Li Y, Peng W, Liang Y, She Q, Peng N. Coupling transcriptional activation of CRISPR-Cas system and DNA repair genes by Csa3a in Sulfolobus islandicus. Nucleic Acids Res 2017; 45:8978-8992. [PMID: 28911114 PMCID: PMC5587795 DOI: 10.1093/nar/gkx612] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 07/05/2017] [Indexed: 12/16/2022] Open
Abstract
CRISPR-Cas system provides the adaptive immunity against invading genetic elements in prokaryotes. Recently, we demonstrated that Csa3a regulator mediates spacer acquisition in Sulfolobus islandicus by activating the expression of Type I-A adaptation cas genes. However, links between the activation of spacer adaptation and CRISPR transcription/processing, and the requirement for DNA repair genes during spacer acquisition remained poorly understood. Here, we demonstrated that de novo spacer acquisition required Csa1, Cas1, Cas2 and Cas4 proteins of the Sulfolobus Type I-A system. Disruption of genes implicated in crRNA maturation or DNA interference led to a significant accumulation of acquired spacers, mainly derived from host genomic DNA. Transcriptome and proteome analyses showed that Csa3a activated expression of adaptation cas genes, CRISPR RNAs, and DNA repair genes, including herA helicase, nurA nuclease and DNA polymerase II genes. Importantly, Csa3a specifically bound the promoters of the above DNA repair genes, suggesting that they were directly activated by Csa3a for adaptation. The Csa3a regulator also specifically bound to the leader sequence to activate CRISPR transcription in vivo. Our data indicated that the Csa3a regulator couples transcriptional activation of the CRISPR-Cas system and DNA repair genes for spacer adaptation and efficient interference of invading genetic elements.
Collapse
Affiliation(s)
- Tao Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Zhenzhen Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qing Ye
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Saifu Pan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaodi Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China.,Archaeal Centre, Department of Biology, University of Copenhagen, Ole Maal⊘es Vej 5, DK-2200 Copenhagen N, Denmark
| | - Wenfang Peng
- Archaeal Centre, Department of Biology, University of Copenhagen, Ole Maal?es Vej 5, DK-2200 Copenhagen N, Denmark
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qunxin She
- Archaeal Centre, Department of Biology, University of Copenhagen, Ole Maal?es Vej 5, DK-2200 Copenhagen N, Denmark
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| |
Collapse
|
204
|
Rao C, Chin D, Ensminger AW. Priming in a permissive type I-C CRISPR-Cas system reveals distinct dynamics of spacer acquisition and loss. RNA (NEW YORK, N.Y.) 2017; 23:1525-1538. [PMID: 28724535 PMCID: PMC5602111 DOI: 10.1261/rna.062083.117] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/08/2017] [Indexed: 06/07/2023]
Abstract
CRISPR-Cas is a bacterial and archaeal adaptive immune system that uses short, invader-derived sequences termed spacers to target invasive nucleic acids. Upon recognition of previously encountered invaders, the system can stimulate secondary spacer acquisitions, a process known as primed adaptation. Previous studies of primed adaptation have been complicated by intrinsically high interference efficiency of most systems against bona fide targets. As such, most primed adaptation to date has been studied within the context of imperfect sequence complementarity between spacers and targets. Here, we take advantage of a native type I-C CRISPR-Cas system in Legionella pneumophila that displays robust primed adaptation even within the context of a perfectly matched target. Using next-generation sequencing to survey acquired spacers, we observe strand bias and positional preference that are consistent with a 3'-5' translocation of the adaptation machinery. We show that spacer acquisition happens in a wide range of frequencies across the plasmid, including a remarkable hotspot that predominates irrespective of the priming strand. We systematically characterize protospacer sequence constraints in both adaptation and interference and reveal extensive flexibilities regarding the protospacer adjacent motif in both processes. Lastly, in a strain with a genetically truncated CRISPR array, we observe increased interference efficiency, which, when coupled with forced maintenance of a targeted plasmid, provides a useful experimental system to study spacer loss. Based on these observations, we propose that the Legionella pneumophila type I-C system represents a powerful model to study primed adaptation and the interplay between CRISPR interference and adaptation.
Collapse
Affiliation(s)
- Chitong Rao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Denny Chin
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Alexander W Ensminger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Public Health Ontario, Toronto, Ontario M5G 1M1, Canada
| |
Collapse
|
205
|
Abstract
Bacteria and archaea use CRISPR-Cas adaptive immune systems to defend themselves from infection by bacteriophages (phages). These RNA-guided nucleases are powerful weapons in the fight against foreign DNA, such as phages and plasmids, as well as a revolutionary gene editing tool. Phages are not passive bystanders in their interactions with CRISPR-Cas systems, however; recent discoveries have described phage genes that inhibit CRISPR-Cas function. More than 20 protein families, previously of unknown function, have been ascribed anti-CRISPR function. Here, we discuss how these CRISPR-Cas inhibitors were discovered and their modes of action were elucidated. We also consider the potential impact of anti-CRISPRs on bacterial and phage evolution. Finally, we speculate about the future of this field.
Collapse
Affiliation(s)
- Adair L Borges
- Department of Microbiology and Immunology, University of California, San Francisco, California 94158;
| | - Alan R Davidson
- Department of Molecular Genetics and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, California 94158;
| |
Collapse
|
206
|
Abstract
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR “dark matter.” We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. The principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers match any sequences in the current databases, and of these, only a minority correspond to known parasitic elements. We show that nearly all spacers with matches originate from viral or plasmid genomes that are either free or have been integrated into the host genome. We further demonstrate that spacers with no matches have the same properties as those of identifiable origins, strongly suggesting that all spacers originate from mobile elements.
Collapse
|
207
|
Bikard D, Barrangou R. Using CRISPR-Cas systems as antimicrobials. Curr Opin Microbiol 2017; 37:155-160. [PMID: 28888103 DOI: 10.1016/j.mib.2017.08.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/05/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022]
Abstract
Although CRISPR-Cas systems naturally evolved to provide adaptive immunity in bacteria and archaea, Cas nucleases can be co-opted to target chromosomal sequences rather than invasive genetic elements. Although genome editing is the primary outcome of self-targeting using CRISPR-based technologies in eukaryotes, self-targeting by CRISPR is typically lethal in bacteria. Here, we discuss how DNA damage introduced by Cas nucleases in bacteria can efficiently and specifically lead to plasmid curing or drive cell death. Specifically, we discuss how various CRISPR-Cas systems can be engineered and delivered using phages or phagemids as vectors. These principles establish CRISPR-Cas systems as potent and programmable antimicrobials, and open new avenues for the development of CRISPR-based tools for selective removal of bacterial pathogens and precise microbiome composition alteration.
Collapse
Affiliation(s)
- David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris 75015, France.
| | - Rodolphe Barrangou
- Department of Food, Processing and Nutritional Sciences, North Carolina State University, NC, USA.
| |
Collapse
|
208
|
Li M, Gong L, Zhao D, Zhou J, Xiang H. The spacer size of I-B CRISPR is modulated by the terminal sequence of the protospacer. Nucleic Acids Res 2017; 45:4642-4654. [PMID: 28379481 PMCID: PMC5416893 DOI: 10.1093/nar/gkx229] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/25/2017] [Indexed: 12/29/2022] Open
Abstract
Prokaryotes memorize invader information by incorporating alien DNA as spacers into CRISPR arrays. Although the spacer size has been suggested to be predefined by the architecture of the acquisition complex, there is usually an unexpected heterogeneity. Here, we explored the causes of this heterogeneity in Haloarcula hispanica I-B CRISPR. High-throughput sequencing following adaptation assays demonstrated significant size variation among 37 957 new spacers, which appeared to be sequence-dependent. Consistently, the third nucleotide at the spacer 3΄-end (PAM-distal end) showed an evident bias for cytosine and mutating this cytosine in the protospacer sequence could change the final spacer size. In addition, slippage of the 5΄-end (PAM-end), which contributed to most of the observed PAM (protospacer adjacent motif) inaccuracy, also tended to change the spacer size. We propose that both ends of the PAM-protospacer sequence should exhibit nucleotide selectivity (with different stringencies), which fine-tunes the structural ruler, to a certain extent, to specify the spacer size.
Collapse
Affiliation(s)
- Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Luyao Gong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
209
|
Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M. Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition. Sci Rep 2017; 7:10392. [PMID: 28871175 PMCID: PMC5583386 DOI: 10.1038/s41598-017-10876-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I. The f-CAR conveniently analyzes and compares many samples, allowing new insights into adaptation. For instance, we show that in an E. coli culture the majority of acquisition events occur in late exponential phase.
Collapse
Affiliation(s)
- Lina Amlinger
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Mirthe Hoekzema
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Magnus Lundgren
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
210
|
Toms A, Barrangou R. On the global CRISPR array behavior in class I systems. Biol Direct 2017; 12:20. [PMID: 28851439 PMCID: PMC5575924 DOI: 10.1186/s13062-017-0193-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/17/2017] [Indexed: 12/26/2022] Open
Abstract
Background Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes. CRISPR diversity, nomenclature, occurrence, and biological functions have generated a plethora of data that created a need to understand the size and distribution of these various systems to appreciate their features and complexity. Results By utilizing a statistical framework and visual analytic techniques, we have been able to test several hypotheses about CRISPR loci in bacterial class I systems. Quantitatively, though CRISPR loci can expand to hundreds of spacers, the mean and median sizes are 40 and 25, respectively, reflecting rather modest acquisition and/or retention overall. Histograms uncovered that CRISPR array size displayed a parametric distribution, which was confirmed by a goodness-of fit test. Mapping the frequency of CRISPR loci on a standardized chromosome plot revealed that CRISPRs have a higher probability of occurring at clustered locations along the positive or negative strand. Lastly, when multiple arrays occur in a particular system, the size of a particular CRISPR array varies with its distance from the cas operon, reflecting acquisition and expansion biases. Conclusions This study establishes that bacterial Class I CRISPR array size tends to follow a geometric distribution; these CRISPRs are not randomly distributed along the chromosome; and the CRISPR array closest to the cas genes is typically larger than loci in trans. Overall, we provide an analytical framework to understand the features and behavior of CRISPR-Cas systems through a quantitative lens. Reviewers This article was reviewed by Eugene Koonin (NIH-NCBI) and Uri Gophna (Tel Aviv University). Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0193-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alice Toms
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA. .,Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Schaub Hall, Campus box 7624, Raleigh, NC, 27695-7624, USA.
| |
Collapse
|
211
|
Peters JE, Makarova KS, Shmakov S, Koonin EV. Recruitment of CRISPR-Cas systems by Tn7-like transposons. Proc Natl Acad Sci U S A 2017; 114:E7358-E7366. [PMID: 28811374 PMCID: PMC5584455 DOI: 10.1073/pnas.1709035114] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference. Phylogenetic analysis demonstrates that evolution of the CRISPR-Cas-containing transposons included a single, ancestral capture of a type I-F locus and two independent instances of type I-B loci capture. We show that the transposon-associated CRISPR arrays contain spacers homologous to plasmid and temperate phage sequences and, in some cases, chromosomal sequences adjacent to the transposon. We hypothesize that the transposon-encoded CRISPR-Cas systems generate displacement (R-loops) in the cognate DNA sites, targeting the transposon to these sites and thus facilitating their spread via plasmids and phages. These findings suggest the existence of RNA-guided transposition and fit the guns-for-hire concept whereby mobile genetic elements capture host defense systems and repurpose them for different stages in the life cycle of the element.
Collapse
Affiliation(s)
- Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853;
| | - Kira S Makarova
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894
| | - Sergey Shmakov
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894;
| |
Collapse
|
212
|
Musharova O, Klimuk E, Datsenko KA, Metlitskaya A, Logacheva M, Semenova E, Severinov K, Savitskaya E. Spacer-length DNA intermediates are associated with Cas1 in cells undergoing primed CRISPR adaptation. Nucleic Acids Res 2017; 45:3297-3307. [PMID: 28204574 PMCID: PMC5389516 DOI: 10.1093/nar/gkx097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/06/2017] [Indexed: 01/16/2023] Open
Abstract
During primed CRISPR adaptation spacers are preferentially selected from DNA recognized by CRISPR interference machinery, which in the case of Type I CRISPR-Cas systems consists of CRISPR RNA (crRNA) bound effector Cascade complex that locates complementary targets, and Cas3 executor nuclease/helicase. A complex of Cas1 and Cas2 proteins is capable of inserting new spacers in the CRISPR array. Here, we show that in Escherichia coli cells undergoing primed adaptation, spacer-sized fragments of foreign DNA are associated with Cas1. Based on sensitivity to digestion with nucleases, the associated DNA is not in a standard double-stranded state. Spacer-sized fragments are cut from one strand of foreign DNA in Cas1- and Cas3-dependent manner. These fragments are generated from much longer S1-nuclease sensitive fragments of foreign DNA that require Cas3 for their production. We propose that in the course of CRISPR interference Cas3 generates fragments of foreign DNA that are recognized by the Cas1-Cas2 adaptation complex, which excises spacer-sized fragments and channels them for insertion into CRISPR array.
Collapse
Affiliation(s)
- Olga Musharova
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Evgeny Klimuk
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Kirill A Datsenko
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Maria Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ekaterina Semenova
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ekaterina Savitskaya
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| |
Collapse
|
213
|
Moch C, Fromant M, Blanquet S, Plateau P. DNA binding specificities of Escherichia coli Cas1-Cas2 integrase drive its recruitment at the CRISPR locus. Nucleic Acids Res 2017; 45:2714-2723. [PMID: 28034956 PMCID: PMC5389526 DOI: 10.1093/nar/gkw1309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/15/2016] [Indexed: 11/22/2022] Open
Abstract
Prokaryotic adaptive immunity relies on the capture of fragments of invader DNA (protospacers) followed by their recombination at a dedicated acceptor DNA locus. This integrative mechanism, called adaptation, needs both Cas1 and Cas2 proteins. Here, we studied in vitro the binding of an Escherichia coli Cas1–Cas2 complex to various protospacer and acceptor DNA molecules. We show that, to form a long-lived ternary complex containing Cas1–Cas2, the acceptor DNA must carry a CRISPR locus, and the protospacer must not contain 3΄-single-stranded overhangs longer than 5 bases. In addition, the acceptor DNA must be supercoiled. Formation of the ternary complex is synergistic, in such that the binding of Cas1–Cas2 to acceptor DNA is reinforced in the presence of a protospacer. Mutagenesis analysis at the CRISPR locus indicates that the presence in the acceptor plasmid of the palindromic motif found in CRISPR repeats drives stable ternary complex formation. Most of the mutations in this motif are deleterious even if they do not prevent cruciform structure formation. The leader sequence of the CRISPR locus is fully dispensable. These DNA binding specificities of the Cas1–Cas2 integrase are likely to play a major role in the recruitment of this enzyme at the CRISPR locus.
Collapse
Affiliation(s)
- Clara Moch
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Michel Fromant
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Sylvain Blanquet
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Pierre Plateau
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| |
Collapse
|
214
|
Fu BXH, Wainberg M, Kundaje A, Fire AZ. High-Throughput Characterization of Cascade type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences. Genetics 2017; 206:1727-1738. [PMID: 28634160 PMCID: PMC5560783 DOI: 10.1534/genetics.117.202580] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/29/2017] [Indexed: 12/18/2022] Open
Abstract
Interactions between Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs and CRISPR-associated (Cas) proteins form an RNA-guided adaptive immune system in prokaryotes. The adaptive immune system utilizes segments of the genetic material of invasive foreign elements in the CRISPR locus. The loci are transcribed and processed to produce small CRISPR RNAs (crRNAs), with degradation of invading genetic material directed by a combination of complementarity between RNA and DNA and in some cases recognition of adjacent motifs called PAMs (Protospacer Adjacent Motifs). Here we describe a general, high-throughput procedure to test the efficacy of thousands of targets, applying this to the Escherichia coli type I-E Cascade (CRISPR-associated complex for antiviral defense) system. These studies were followed with reciprocal experiments in which the consequence of CRISPR activity was survival in the presence of a lytic phage. From the combined analysis of the Cascade system, we found that (i) type I-E Cascade PAM recognition is more expansive than previously reported, with at least 22 distinct PAMs, with many of the noncanonical PAMs having CRISPR-interference abilities similar to the canonical PAMs; (ii) PAM positioning appears precise, with no evidence for tolerance to PAM slippage in interference; and (iii) while increased guanine-cytosine (GC) content in the spacer is associated with higher CRISPR-interference efficiency, high GC content (>62.5%) decreases CRISPR-interference efficiency. Our findings provide a comprehensive functional profile of Cascade type I-E interference requirements and a method to assay spacer efficacy that can be applied to other CRISPR-Cas systems.
Collapse
Affiliation(s)
- Becky Xu Hua Fu
- Department of Genetics, Stanford University School of Medicine, California 94305
| | - Michael Wainberg
- Department of Computer Science, Stanford University, California 94305
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, California 94305
- Department of Computer Science, Stanford University, California 94305
| | - Andrew Z Fire
- Department of Genetics, Stanford University School of Medicine, California 94305
- Department of Pathology, Stanford University School of Medicine, California 94305
| |
Collapse
|
215
|
Sequential eviction of crowded nucleoprotein complexes by the exonuclease RecBCD molecular motor. Proc Natl Acad Sci U S A 2017; 114:E6322-E6331. [PMID: 28716908 DOI: 10.1073/pnas.1701368114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In physiological settings, all nucleic acids motor proteins must travel along substrates that are crowded with other proteins. However, the physical basis for how motor proteins behave in these highly crowded environments remains unknown. Here, we use real-time single-molecule imaging to determine how the ATP-dependent translocase RecBCD travels along DNA occupied by tandem arrays of high-affinity DNA binding proteins. We show that RecBCD forces each protein into its nearest adjacent neighbor, causing rapid disruption of the protein-nucleic acid interaction. This mechanism is not the same way that RecBCD disrupts isolated nucleoprotein complexes on otherwise naked DNA. Instead, molecular crowding itself completely alters the mechanism by which RecBCD removes tightly bound protein obstacles from DNA.
Collapse
|
216
|
CRISPR-Cas adaptive immunity and the three Rs. Biosci Rep 2017; 37:BSR20160297. [PMID: 28674106 PMCID: PMC5518543 DOI: 10.1042/bsr20160297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/26/2017] [Accepted: 07/03/2017] [Indexed: 12/11/2022] Open
Abstract
In this summary, we focus on fundamental biology of Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)-Cas (CRISPR-associated proteins) adaptive immunity in bacteria. Emphasis is placed on emerging information about functional interplay between Cas proteins and proteins that remodel DNA during homologous recombination (HR), DNA replication or DNA repair. We highlight how replication forks may act as ‘trigger points’ for CRISPR adaptation events, and the potential for cascade-interference complexes to act as precise roadblocks in DNA replication by an invader MGE (mobile genetic element), without the need for DNA double-strand breaks.
Collapse
|
217
|
Spacer capture and integration by a type I-F Cas1-Cas2-3 CRISPR adaptation complex. Proc Natl Acad Sci U S A 2017; 114:E5122-E5128. [PMID: 28611213 DOI: 10.1073/pnas.1618421114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas adaptive immune systems capture DNA fragments from invading bacteriophages and plasmids and integrate them as spacers into bacterial CRISPR arrays. In type I-E and II-A CRISPR-Cas systems, this adaptation process is driven by Cas1-Cas2 complexes. Type I-F systems, however, contain a unique fusion of Cas2, with the type I effector helicase and nuclease for invader destruction, Cas3. By using biochemical, structural, and biophysical methods, we present a structural model of the 400-kDa Cas14-Cas2-32 complex from Pectobacterium atrosepticum with bound protospacer substrate DNA. Two Cas1 dimers assemble on a Cas2 domain dimeric core, which is flanked by two Cas3 domains forming a groove where the protospacer binds to Cas1-Cas2. We developed a sensitive in vitro assay and demonstrated that Cas1-Cas2-3 catalyzed spacer integration into CRISPR arrays. The integrase domain of Cas1 was necessary, whereas integration was independent of the helicase or nuclease activities of Cas3. Integration required at least partially duplex protospacers with free 3'-OH groups, and leader-proximal integration was stimulated by integration host factor. In a coupled capture and integration assay, Cas1-Cas2-3 processed and integrated protospacers independent of Cas3 activity. These results provide insight into the structure of protospacer-bound type I Cas1-Cas2-3 adaptation complexes and their integration mechanism.
Collapse
|
218
|
A decade of discovery: CRISPR functions and applications. Nat Microbiol 2017; 2:17092. [PMID: 28581505 DOI: 10.1038/nmicrobiol.2017.92] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/05/2017] [Indexed: 12/26/2022]
Abstract
This year marks the tenth anniversary of the identification of the biological function of CRISPR-Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR-Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology. Lastly, we provide a perspective on the impacts the field has had on science and beyond.
Collapse
|
219
|
Bradde S, Vucelja M, Teşileanu T, Balasubramanian V. Dynamics of adaptive immunity against phage in bacterial populations. PLoS Comput Biol 2017; 13:e1005486. [PMID: 28414716 PMCID: PMC5411097 DOI: 10.1371/journal.pcbi.1005486] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 05/01/2017] [Accepted: 03/29/2017] [Indexed: 01/21/2023] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We propose a population dynamical model where immunity can be both acquired and lost. The model predicts regimes where bacterial and phage populations can co-exist, others where the populations exhibit damped oscillations, and still others where one population is driven to extinction. Our model considers two key parameters: (1) ease of acquisition and (2) spacer effectiveness in conferring immunity. Analytical calculations and numerical simulations show that if spacers differ mainly in ease of acquisition, or if the probability of acquiring them is sufficiently high, bacteria develop a diverse population of spacers. On the other hand, if spacers differ mainly in their effectiveness, their final distribution will be highly peaked, akin to a “winner-take-all” scenario, leading to a specialized spacer distribution. Bacteria can interpolate between these limiting behaviors by actively tuning their overall acquisition probability. The CRISPR system in bacteria and archaea provides adaptive immunity by incorporating foreign DNA (spacers) into the genome, and later targeting DNA sequences that match these spacers. The way in which bacteria choose spacer sequences from a clonal phage population is not understood. Our model considers competing effects of ease of acquisition and effectiveness against infections in shaping the spacer distribution. The model suggests that a diverse spacer population results when the acquisition rate is high, or when spacers are similarly effective. At moderate acquisition rates, the spacer distribution becomes highly sensitive to spacer effectiveness. There is a rich landscape of behaviors including bacteria-phage coexistence and oscillations in the populations.
Collapse
Affiliation(s)
- Serena Bradde
- Initiative for the Theoretical Sciences, The Graduate Center, CUNY, New York, New York, United States of America
- David Rittenhouse Laboratories, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marija Vucelja
- Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America
- Department of Physics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Tiberiu Teşileanu
- Initiative for the Theoretical Sciences, The Graduate Center, CUNY, New York, New York, United States of America
- David Rittenhouse Laboratories, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Vijay Balasubramanian
- Initiative for the Theoretical Sciences, The Graduate Center, CUNY, New York, New York, United States of America
- David Rittenhouse Laboratories, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
220
|
Claverie JM, Abergel C. CRISPR-Cas-like system in giant viruses: why MIMIVIRE is not likely to be an adaptive immune system. Virol Sin 2017; 31:193-6. [PMID: 27315813 DOI: 10.1007/s12250-016-3801-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Jean-Michel Claverie
- Structural and Genomic Information Laboratory (UMR7256), CNRS Aix Marseille University, Mediterranean Institute of Microbiology (FR 3479), Marseille, France.
| | - Chantal Abergel
- Structural and Genomic Information Laboratory (UMR7256), CNRS Aix Marseille University, Mediterranean Institute of Microbiology (FR 3479), Marseille, France.
| |
Collapse
|
221
|
Jackson SA, McKenzie RE, Fagerlund RD, Kieper SN, Fineran PC, Brouns SJJ. CRISPR-Cas: Adapting to change. Science 2017; 356:356/6333/eaal5056. [PMID: 28385959 DOI: 10.1126/science.aal5056] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bacteria and archaea are engaged in a constant arms race to defend against the ever-present threats of viruses and invasion by mobile genetic elements. The most flexible weapons in the prokaryotic defense arsenal are the CRISPR-Cas adaptive immune systems. These systems are capable of selective identification and neutralization of foreign DNA and/or RNA. CRISPR-Cas systems rely on stored genetic memories to facilitate target recognition. Thus, to keep pace with a changing pool of hostile invaders, the CRISPR memory banks must be regularly updated with new information through a process termed CRISPR adaptation. In this Review, we outline the recent advances in our understanding of the molecular mechanisms governing CRISPR adaptation. Specifically, the conserved protein machinery Cas1-Cas2 is the cornerstone of adaptive immunity in a range of diverse CRISPR-Cas systems.
Collapse
Affiliation(s)
- Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Post Office Box 56, Dunedin 9054, New Zealand
| | - Rebecca E McKenzie
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Post Office Box 56, Dunedin 9054, New Zealand
| | - Sebastian N Kieper
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Post Office Box 56, Dunedin 9054, New Zealand. .,Bio-Protection Research Centre, University of Otago, Post Office Box 56, Dunedin 9054, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands. .,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| |
Collapse
|
222
|
CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity. Nature 2017; 544:101-104. [PMID: 28355179 PMCID: PMC5540373 DOI: 10.1038/nature21719] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/22/2017] [Indexed: 12/19/2022]
Abstract
CRISPR-Cas systems provide protection against viral1 and plasmid2 infection by capturing short DNA sequences from these invaders and integrating them into the CRISPR locus of the prokaryotic host1. These sequences, known as spacers, are transcribed into short RNA guides3–5 that specify the cleavage site of Cas nucleases in the genome of the invader6–8. When spacer sequences are acquired during viral infection is not known. To investigate this, we followed spacer acquisition in Staphylococcus aureus cells harboring a type II CRISPR-Cas9 system after infection with the staphylococcal bacteriophage ϕ12. We found that new spacers are acquired immediately following infection preferentially from the cos site, the viral free DNA end that is first injected into the cell. Analysis of spacer acquisition after infection with mutant phages demonstrated that most spacers are acquired during DNA injection, but not during other stages of the viral cycle that produce free DNA ends, such as DNA replication or packaging. Finally, we showed that spacers acquired from early-injected genomic regions, which direct Cas9 cleavage of the viral DNA immediately after infection, provide better immunity than spacers acquired from late-injected regions. Our results reveal that CRISPR-Cas systems exploit the phage life cycle to generate a pattern of spacer acquisition that ensures the success of the CRISPR immune response.
Collapse
|
223
|
Hynes AP, Lemay ML, Trudel L, Deveau H, Frenette M, Tremblay DM, Moineau S. Detecting natural adaptation of the Streptococcus thermophilus CRISPR-Cas systems in research and classroom settings. Nat Protoc 2017; 12:547-565. [PMID: 28207002 DOI: 10.1038/nprot.2016.186] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems have been adapted into a powerful genome-editing tool. The basis for the flexibility of the tool lies in the adaptive nature of CRISPR-Cas as a bacterial immune system. Here, we describe a protocol to experimentally demonstrate the adaptive nature of this bacterial immune system by challenging the model organism for the study of CRISPR adaptation, Streptococcus thermophilus, with phages in order to detect natural CRISPR immunization. A bacterial culture is challenged with lytic phages, the surviving cells are screened by PCR for expansion of their CRISPR array and the newly acquired specificities are mapped to the genome of the phage. Furthermore, we offer three variants of the assay to (i) promote adaptation by challenging the system using defective viruses, (ii) challenge the system using plasmids to generate plasmid-resistant strains and (iii) bias the system to obtain natural immunity against a specifically targeted DNA sequence. The core protocol and its variants serve as a means to explore CRISPR adaptation, discover new CRISPR-Cas systems and generate bacterial strains that are resistant to phages or refractory to undesired genes or plasmids. In addition, the core protocol has served in teaching laboratories at the undergraduate level, demonstrating both its robust nature and educational value. Carrying out the core protocol takes 4 h of hands-on time over 7 d. Unlike sequence-based methods for detecting natural CRISPR adaptation, this phage-challenge-based approach results in the isolation of CRISPR-immune bacteria for downstream characterization and use.
Collapse
Affiliation(s)
- Alexander P Hynes
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada
| | - Marie-Laurence Lemay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada
| | - Luc Trudel
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
| | - Hélène Deveau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada
| | - Denise M Tremblay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada
| |
Collapse
|
224
|
Koonin EV. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol Direct 2017; 12:5. [PMID: 28187792 PMCID: PMC5303251 DOI: 10.1186/s13062-017-0177-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
Abstract Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes. The archaeal pAgo machinery is the direct ancestor of eukaryotic RNAi that, however, acquired additional components, such as Dicer, and enormously diversified through multiple duplications. In contrast, eukaryotes lack any heritage of the CRISPR-Cas systems, conceivably, due to the cellular toxicity of some Cas proteins that would get activated as a result of operon disruption in eukaryotes. The adaptive immunity function in eukaryotes is taken over partly by the PIWI RNA branch of RNAi and partly by protein-based immunity. In this review, I briefly discuss the interplay between homology and analogy in the evolution of RNA- and DNA-guided immunity, and attempt to formulate some general evolutionary principles for this ancient class of defense systems. Reviewers This article was reviewed by Mikhail Gelfand and Bojan Zagrovic.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| |
Collapse
|
225
|
Abstract
Prokaryotes and eukaryotes evolved relatively similar RNA-based molecular mechanisms to fight potentially deleterious nucleic acids coming from phages, transposons, or viruses. Short RNAs guide effector complexes toward their targets to be silenced or eliminated. These short immunity RNAs are transcribed from clustered loci. Unexpectedly and strikingly, bacterial and eukaryotic immunity RNA clusters share substantial functional and mechanistic resemblances in fighting nucleic acid intruders.
Collapse
Affiliation(s)
- Brice Felden
- Inserm U835 Biochimie Pharmaceutique, Rennes University, F-35043 Rennes, France
- Biosit, Rennes University/Université Européenne de Bretagne, F-35043 Rennes, France
| | - Luc Paillard
- Biosit, Rennes University/Université Européenne de Bretagne, F-35043 Rennes, France
- Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, F-35043 Rennes, France
| |
Collapse
|
226
|
Leenay RT, Beisel CL. Deciphering, Communicating, and Engineering the CRISPR PAM. J Mol Biol 2017; 429:177-191. [PMID: 27916599 PMCID: PMC5235977 DOI: 10.1016/j.jmb.2016.11.024] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/15/2016] [Accepted: 11/25/2016] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) loci and their flanking CRISPR-associated (cas) genes make up RNA-guided, adaptive immune systems in prokaryotes whose effector proteins have become powerful tools for basic research and biotechnology. While the Cas effector proteins are remarkably diverse, they commonly rely on protospacer-adjacent motifs (PAMs) as the first step in target recognition. PAM sequences are known to vary considerably between systems and have proven to be difficult to predict, spurring the need for new tools to rapidly identify and communicate these sequences. Recent advances have also shown that Cas proteins can be engineered to alter PAM recognition, opening new opportunities to develop CRISPR-based tools with enhanced targeting capabilities. In this review, we discuss the properties of the CRISPR PAM and the emerging tools for determining, visualizing, and engineering PAM recognition. We also propose a standard means of orienting the PAM to simplify how its location and sequence are communicated.
Collapse
Affiliation(s)
- Ryan T Leenay
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States.
| |
Collapse
|
227
|
Bernheim A. [Why so rare if so essentiel: the determinants of the sparse distribution of CRISPR-Cas systems in bacterial genomes]. Biol Aujourdhui 2017; 211:255-264. [PMID: 29956652 DOI: 10.1051/jbio/2018005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 11/14/2022]
Abstract
CRISPR-Cas (Cluster of Regularly Interspaced Short Palindromic Repeats) systems confer bacteria and archaea an adaptative immunity against phages and other invading genetic elements playing an important role in bacterial evolution. However, despite the protection they generate and high rate of horizontal transfer, less than 50% of bacterial genomes harbor a CRISPR-Cas system. As a comparison, 90% of archaea encode a CRISPR-Cas system and a bacterial genome codes for two restriction modification systems on average. This review describes CRISPR-Cas systems distribution in bacterial genomes and then details the different hypotheses put forward to explain the relative scarcity of CRISPR-Cas systems. More specifically, phage escape mechanisms, ecological factors such as phage diversity and abundance and intrinsic costs, such as maintenance or autoimmunity, are discussed. Overall, a better understanding of the downsides of encoding CRISPR-Cas systems is essential to explain their evolutionary dynamics and their relative success in different environments and clades.
Collapse
Affiliation(s)
- Aude Bernheim
- Synthetic Biology Group, Institut Pasteur, 25-28 rue Dr. Roux, 75015 Paris, France - Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, 75015 Paris, France - AgroParisTech, 75005 Paris, France
| |
Collapse
|
228
|
Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. New CRISPR-Cas systems from uncultivated microbes. Nature 2016; 542:237-241. [PMID: 28005056 PMCID: PMC5300952 DOI: 10.1038/nature21059] [Citation(s) in RCA: 368] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 12/22/2022]
Abstract
CRISPR-Cas systems provide microbes with adaptive immunity by employing short sequences, termed spacers, that guide Cas proteins to cleave foreign DNA1,2. Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences3,4. The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research5. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured. Metagenomics, the sequencing of DNA extracted from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms6,7. Here, using genome-resolved metagenomics, we identified novel CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet identified. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in E. coli. Interrogation of environmental microbial communities combined with in vivo experiments allows access to an unprecedented diversity of genomes whose content will expand the repertoire of microbe-based biotechnologies.
Collapse
Affiliation(s)
- David Burstein
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Steven C Strutt
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Karthik Anantharaman
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.,Department of Chemistry, University of California, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Innovative Genomics Initiative, University of California, Berkeley, California 94720, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California 94720, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA
| |
Collapse
|
229
|
Heler R, Wright AV, Vucelja M, Bikard D, Doudna JA, Marraffini LA. Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response. Mol Cell 2016; 65:168-175. [PMID: 28017588 DOI: 10.1016/j.molcel.2016.11.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/23/2016] [Accepted: 11/18/2016] [Indexed: 12/26/2022]
Abstract
CRISPR loci and their associated (Cas) proteins encode a prokaryotic immune system that protects against viruses and plasmids. Upon infection, a low fraction of cells acquire short DNA sequences from the invader. These sequences (spacers) are integrated in between the repeats of the CRISPR locus and immunize the host against the matching invader. Spacers specify the targets of the CRISPR immune response through transcription into short RNA guides that direct Cas nucleases to the invading DNA molecules. Here we performed random mutagenesis of the RNA-guided Cas9 nuclease to look for variants that provide enhanced immunity against viral infection. We identified a mutation, I473F, that increases the rate of spacer acquisition by more than two orders of magnitude. Our results highlight the role of Cas9 during CRISPR immunization and provide a useful tool to study this rare process and develop it as a biotechnological application.
Collapse
Affiliation(s)
- Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Addison V Wright
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marija Vucelja
- Department of Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - David Bikard
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
230
|
|
231
|
Koonin EV, Zhang F. Coupling immunity and programmed cell suicide in prokaryotes: Life-or-death choices. Bioessays 2016; 39:1-9. [DOI: 10.1002/bies.201600186] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information; National Library of Medicine; Bethesda MD USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard; Cambridge MA USA
- Department of Health Sciences and Technology; Massachusetts Institute of Technology; Cambridge MA USA
- McGovern Institute for Brain Research at MIT; Cambridge MA USA
- Departments of Brain and Cognitive Science and Biological Engineering; Cambridge MA USA
| |
Collapse
|
232
|
Yoganand KNR, Sivathanu R, Nimkar S, Anand B. Asymmetric positioning of Cas1-2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system. Nucleic Acids Res 2016; 45:367-381. [PMID: 27899566 PMCID: PMC5224486 DOI: 10.1093/nar/gkw1151] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 01/21/2023] Open
Abstract
CRISPR-Cas system epitomizes prokaryote-specific quintessential adaptive defense machinery that limits the genome invasion of mobile genetic elements. It confers adaptive immunity to bacteria by capturing a protospacer fragment from invading foreign DNA, which is later inserted into the leader proximal end of CRIPSR array and serves as immunological memory to recognize recurrent invasions. The universally conserved Cas1 and Cas2 form an integration complex that is known to mediate the protospacer invasion into the CRISPR array. However, the mechanism by which this protospacer fragment gets integrated in a directional fashion into the leader proximal end is elusive. Here, we employ CRISPR/dCas9 mediated immunoprecipitation and genetic analysis to identify Integration Host Factor (IHF) as an indispensable accessory factor for spacer acquisition in Escherichia coli Further, we show that the leader region abutting the first CRISPR repeat localizes IHF and Cas1-2 complex. IHF binding to the leader region induces bending by about 120° that in turn engenders the regeneration of the cognate binding site for protospacer bound Cas1-2 complex and brings it in proximity with the first CRISPR repeat. This appears to guide Cas1-2 complex to orient the protospacer invasion towards the leader-repeat junction thus driving the integration in a polarized fashion.
Collapse
Affiliation(s)
- K N R Yoganand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - R Sivathanu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Siddharth Nimkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - B Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| |
Collapse
|
233
|
Heussler GE, Miller JL, Price CE, Collins AJ, O'Toole GA. Requirements for Pseudomonas aeruginosa Type I-F CRISPR-Cas Adaptation Determined Using a Biofilm Enrichment Assay. J Bacteriol 2016; 198:3080-3090. [PMID: 27573013 PMCID: PMC5075037 DOI: 10.1128/jb.00458-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated protein) systems are diverse and found in many archaea and bacteria. These systems have mainly been characterized as adaptive immune systems able to protect against invading mobile genetic elements, including viruses. The first step in this protection is acquisition of spacer sequences from the invader DNA and incorporation of those sequences into the CRISPR array, termed CRISPR adaptation. Progress in understanding the mechanisms and requirements of CRISPR adaptation has largely been accomplished using overexpression of cas genes or plasmid loss assays; little work has focused on endogenous CRISPR-acquired immunity from viral predation. Here, we developed a new biofilm-based assay system to enrich for Pseudomonas aeruginosa strains with new spacer acquisition. We used this assay to demonstrate that P. aeruginosa rapidly acquires spacers protective against DMS3vir, an engineered lytic variant of the Mu-like bacteriophage DMS3, through primed CRISPR adaptation from spacers present in the native CRISPR2 array. We found that for the P. aeruginosa type I-F system, the cas1 gene is required for CRISPR adaptation, recG contributes to (but is not required for) primed CRISPR adaptation, recD is dispensable for primed CRISPR adaptation, and finally, the ability of a putative priming spacer to prime can vary considerably depending on the specific sequences of the spacer. IMPORTANCE Our understanding of CRISPR adaptation has expanded largely through experiments in type I CRISPR systems using plasmid loss assays, mutants of Escherichia coli, or cas1-cas2 overexpression systems, but there has been little focus on studying the adaptation of endogenous systems protecting against a lytic bacteriophage. Here we describe a biofilm system that allows P. aeruginosa to rapidly gain spacers protective against a lytic bacteriophage. This approach has allowed us to probe the requirements for CRISPR adaptation in the endogenous type I-F system of P. aeruginosa Our data suggest that CRISPR-acquired immunity in a biofilm may be one reason that many P. aeruginosa strains maintain a CRISPR-Cas system.
Collapse
Affiliation(s)
- Gary E Heussler
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jon L Miller
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Courtney E Price
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Alan J Collins
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| |
Collapse
|
234
|
Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system. Proc Natl Acad Sci U S A 2016; 114:131-135. [PMID: 27849583 DOI: 10.1073/pnas.1617415113] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas are prokaryotic adaptive immune systems that provide protection against bacteriophage (phage) and other parasites. Little is known about how CRISPR-Cas systems are regulated, preventing prediction of phage dynamics in nature and manipulation of phage resistance in clinical settings. Here, we show that the bacterium Pseudomonas aeruginosa PA14 uses the cell-cell communication process, called quorum sensing, to activate cas gene expression, to increase CRISPR-Cas targeting of foreign DNA, and to promote CRISPR adaptation, all at high cell density. This regulatory mechanism ensures maximum CRISPR-Cas function when bacterial populations are at highest risk for phage infection. We demonstrate that CRISPR-Cas activity and acquisition of resistance can be modulated by administration of pro- and antiquorum-sensing compounds. We propose that quorum-sensing inhibitors could be used to suppress the CRISPR-Cas adaptive immune system to enhance medical applications, including phage therapies.
Collapse
|
235
|
Efficient CRISPR-Mediated Post-Transcriptional Gene Silencing in a Hyperthermophilic Archaeon Using Multiplexed crRNA Expression. G3-GENES GENOMES GENETICS 2016; 6:3161-3168. [PMID: 27507792 PMCID: PMC5068938 DOI: 10.1534/g3.116.032482] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-mediated RNA degradation is catalyzed by a type III system in the hyperthermophilic archaeon Sulfolobus solfataricus. Earlier work demonstrated that the system can be engineered to target specifically mRNA of an endogenous host reporter gene, namely the β-galactosidase in S. solfataricus. Here, we investigated the effect of single and multiple spacers targeting the mRNA of a second reporter gene, α-amylase, at the same, and at different, locations respectively, using a minimal CRISPR (miniCR) locus supplied on a viral shuttle vector. The use of increasing numbers of spacers reduced mRNA levels at progressively higher levels, with three crRNAs (CRISPR RNAs) leading to ∼ 70–80% reduction, and five spacers resulting in an α-amylase gene knockdown of > 90% measured on both mRNA and protein activity levels. Our results indicate that this technology can be used to increase or modulate gene knockdown for efficient post-transcriptional gene silencing in hyperthermophilic archaea, and potentially also in other organisms.
Collapse
|
236
|
Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Nat Commun 2016; 7:12853. [PMID: 27694798 PMCID: PMC5059440 DOI: 10.1038/ncomms12853] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 08/08/2016] [Indexed: 12/20/2022] Open
Abstract
CRISPR–Cas systems provide bacteria with adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, we use high-throughput sequencing to analyse millions of spacer acquisition events in wild-type populations of Pectobacterium atrosepticum. Plasmids not previously encountered, or plasmids that had escaped CRISPR–Cas targeting via point mutation, are used to provoke naive or primed spacer acquisition, respectively. The origin, location and order of spacer acquisition show that spacer selection through priming initiates near the site of CRISPR–Cas recognition (the protospacer), but on the displaced strand, and is consistent with 3′–5′ translocation of the Cas1:Cas2-3 acquisition machinery. Newly acquired spacers determine the location and strand specificity of subsequent spacers and demonstrate that interference-driven spacer acquisition (‘targeted acquisition') is a major contributor to adaptation in type I-F CRISPR–Cas systems. Finally, we show that acquisition of self-targeting spacers is occurring at a constant rate in wild-type cells and can be triggered by foreign DNA with similarity to the bacterial chromosome. Prokaryotic CRISPR-Cas systems provide adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, Staals et al. analyse millions of such events in a native CRISPR-Cas system, showing that newly acquired spacers provoke additional rounds of spacer acquisition.
Collapse
|
237
|
Elf J. Hypothesis: Homologous Recombination Depends on Parallel Search. Cell Syst 2016; 3:325-327. [DOI: 10.1016/j.cels.2016.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Indexed: 10/20/2022]
|
238
|
Wilkinson M, Chaban Y, Wigley DB. Mechanism for nuclease regulation in RecBCD. eLife 2016; 5. [PMID: 27644322 PMCID: PMC5030088 DOI: 10.7554/elife.18227] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/29/2016] [Indexed: 11/30/2022] Open
Abstract
In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is catalysed by AddAB, AdnAB or RecBCD-type helicase-nucleases. These enzyme complexes are highly processive, duplex unwinding and degrading machines that require tight regulation. Here, we report the structure of E.coli RecBCD, determined by cryoEM at 3.8 Å resolution, with a DNA substrate that reveals how the nuclease activity of the complex is activated once unwinding progresses. Extension of the 5’-tail of the unwound duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves a SH3 domain that binds to a region of the RecB subunit in a binding mode that is distinct from others observed previously in SH3 domains and, to our knowledge, this is the first example of peptide-binding of an SH3 domain in a bacterial system. DOI:http://dx.doi.org/10.7554/eLife.18227.001
Collapse
Affiliation(s)
- Martin Wilkinson
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Yuriy Chaban
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Dale B Wigley
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
239
|
Severinov K, Ispolatov I, Semenova E. The Influence of Copy-Number of Targeted Extrachromosomal Genetic Elements on the Outcome of CRISPR-Cas Defense. Front Mol Biosci 2016; 3:45. [PMID: 27630990 PMCID: PMC5005344 DOI: 10.3389/fmolb.2016.00045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/16/2016] [Indexed: 12/26/2022] Open
Abstract
Prokaryotic type I CRISPR-Cas systems respond to the presence of mobile genetic elements such as plasmids and phages in two different ways. CRISPR interference efficiently destroys foreign DNA harboring protospacers fully matching CRISPR RNA spacers. In contrast, even a single mismatch between a spacer and a protospacer can render CRISPR interference ineffective but causes primed adaptation-efficient and specific acquisition of additional spacers from foreign DNA into the CRISPR array of the host. It has been proposed that the interference and primed adaptation pathways are mediated by structurally different complexes formed by the effector Cascade complex on matching and mismatched protospacers. Here, we present experimental evidence and present a simple mathematical model that shows that when plasmid copy number maintenance/phage genome replication is taken into account, the two apparently different outcomes of the CRISPR-Cas response can be accounted for by just one kind of effector complex on both targets. The results underscore the importance of consideration of targeted genome biology when considering consequences of CRISPR-Cas systems action.
Collapse
Affiliation(s)
- Konstantin Severinov
- Skolkovo Institute of Science and TechnologySkolkovo, Russia
- Waksman Institute of Microbiology, Rutgers, The State University of New JerseyPiscataway, NJ, USA
- Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia
| | - Iaroslav Ispolatov
- Skolkovo Institute of Science and TechnologySkolkovo, Russia
- Department of Physics, University of Santiago de ChileSantiago, Chile
| | - Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, The State University of New JerseyPiscataway, NJ, USA
| |
Collapse
|
240
|
Künne T, Kieper SN, Bannenberg JW, Vogel AIM, Miellet WR, Klein M, Depken M, Suarez-Diez M, Brouns SJJ. Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation. Mol Cell 2016; 63:852-64. [PMID: 27546790 DOI: 10.1016/j.molcel.2016.07.011] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/01/2016] [Accepted: 07/15/2016] [Indexed: 11/16/2022]
Abstract
Prokaryotes use a mechanism called priming to update their CRISPR immunological memory to rapidly counter revisiting, mutated viruses, and plasmids. Here we have determined how new spacers are produced and selected for integration into the CRISPR array during priming. We show that Cas3 couples CRISPR interference to adaptation by producing DNA breakdown products that fuel the spacer integration process in a two-step, PAM-associated manner. The helicase-nuclease Cas3 pre-processes target DNA into fragments of about 30-100 nt enriched for thymine-stretches in their 3' ends. The Cas1-2 complex further processes these fragments and integrates them sequence-specifically into CRISPR repeats by coupling of a 3' cytosine of the fragment. Our results highlight that the selection of PAM-compliant spacers during priming is enhanced by the combined sequence specificities of Cas3 and the Cas1-2 complex, leading to an increased propensity of integrating functional CTT-containing spacers.
Collapse
Affiliation(s)
- Tim Künne
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Sebastian N Kieper
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Jasper W Bannenberg
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Anne I M Vogel
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Willem R Miellet
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Misha Klein
- Kavli Institute of Nanoscience and Department of BioNanoscience, Delft University of Technology, 2629 HZ, Delft, the Netherlands
| | - Martin Depken
- Kavli Institute of Nanoscience and Department of BioNanoscience, Delft University of Technology, 2629 HZ, Delft, the Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Stan J J Brouns
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands; Kavli Institute of Nanoscience and Department of BioNanoscience, Delft University of Technology, 2629 HZ, Delft, the Netherlands.
| |
Collapse
|
241
|
Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 2016; 353:aad5147. [PMID: 27493190 DOI: 10.1126/science.aad5147] [Citation(s) in RCA: 407] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adaptive immunity had been long thought of as an exclusive feature of animals. However, the discovery of the CRISPR-Cas defense system, present in almost half of prokaryotic genomes, proves otherwise. Because of the everlasting parasite-host arms race, CRISPR-Cas has rapidly evolved through horizontal transfer of complete loci or individual modules, resulting in extreme structural and functional diversity. CRISPR-Cas systems are divided into two distinct classes that each consist of three types and multiple subtypes. We discuss recent advances in CRISPR-Cas research that reveal elaborate molecular mechanisms and provide for a plausible scenario of CRISPR-Cas evolution. We also briefly describe the latest developments of a wide range of CRISPR-based applications.
Collapse
Affiliation(s)
- Prarthana Mohanraju
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Bernd Zetsche
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands.
| |
Collapse
|
242
|
Casane D, Laurenti P. [The CRISPR case, « ready-made » mutations and Lamarckian evolution of an adaptive immunity system]. Med Sci (Paris) 2016; 32:640-5. [PMID: 27406776 DOI: 10.1051/medsci/20163206029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Since genetics has shown that mutation predates selection, biology has developed within the Darwinian paradigm framework. However, a mechanism that produces favorable mutations preferentially in response to adaptive constraints has been recently identified. This mechanism, the CRISPR-Cas adaptive immunity system, is considered as a bona fide example of Lamarckian evolution, even if it only reflects loosely Lamarck's ideas. This unusual evolutionary process is made possible by two prokaryotic properties: i) somatic and germinal cells are not distinct sets of cells; ii) Archae and Bacteria very frequently integrate DNA fragments from the environment, and they therefore have access to a source of "ready-made" useful genetic information. The CRISPR-Cas is a defense system against viruses and plasmids that is based on the integration of genomic fragments of these infectious agents into the host genome, and that protects the host against subsequent infections. Therefore, this mechanism does produce advantageous mutations by integrating DNA from the environment and allowing its transmission to descendants. In conclusion, most of the time evolution relies on purely Darwinian processes, i.e. mutations occurring at random, but in a small minority of cases the occurrence of mutations is more or less biased, and is therefore more or less Lamarckian. Although they are rare, such processes are nevertheless important to our understanding of the plurality of modes of evolution.
Collapse
Affiliation(s)
- Didier Casane
- Laboratoire évolution, génomes, comportement, écologie, CNRS université Paris-Sud, UMR9191, IRD UMR 247, avenue de la Terrasse, 91198 Gif-sur-Yvette, France - Université Paris-Diderot, Sorbonne Paris-Cité, Paris, France
| | - Patrick Laurenti
- Laboratoire évolution, génomes, comportement, écologie, CNRS université Paris-Sud, UMR9191, IRD UMR 247, avenue de la Terrasse, 91198 Gif-sur-Yvette, France - Université Paris-Diderot, Sorbonne Paris-Cité, Paris, France
| |
Collapse
|
243
|
Savitskaya EE, Musharova OS, Severinov KV. Diversity of CRISPR-Cas-mediated mechanisms of adaptive immunity in prokaryotes and their application in biotechnology. BIOCHEMISTRY (MOSCOW) 2016; 81:653-61. [DOI: 10.1134/s0006297916070026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
244
|
Taylor AF, Amundsen SK, Smith GR. Unexpected DNA context-dependence identifies a new determinant of Chi recombination hotspots. Nucleic Acids Res 2016; 44:8216-28. [PMID: 27330137 PMCID: PMC5041463 DOI: 10.1093/nar/gkw541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/03/2016] [Indexed: 11/23/2022] Open
Abstract
Homologous recombination occurs especially frequently near special chromosomal sites called hotspots. In Escherichia coli, Chi hotspots control RecBCD enzyme, a protein machine essential for the major pathway of DNA break-repair and recombination. RecBCD generates recombinogenic single-stranded DNA ends by unwinding DNA and cutting it a few nucleotides to the 3′ side of 5′ GCTGGTGG 3′, the sequence historically equated with Chi. To test if sequence context affects Chi activity, we deep-sequenced the products of a DNA library containing 10 random base-pairs on each side of the Chi sequence and cut by purified RecBCD. We found strongly enhanced cutting at Chi with certain preferred sequences, such as A or G at nucleotides 4–7, on the 3′ flank of the Chi octamer. These sequences also strongly increased Chi hotspot activity in E. coli cells. Our combined enzymatic and genetic results redefine the Chi hotspot sequence, implicate the nuclease domain in Chi recognition, indicate that nicking of one strand at Chi is RecBCD's biologically important reaction in living cells, and enable more precise analysis of Chi's role in recombination and genome evolution.
Collapse
Affiliation(s)
- Andrew F Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| |
Collapse
|
245
|
Highly efficient primed spacer acquisition from targets destroyed by the Escherichia coli type I-E CRISPR-Cas interfering complex. Proc Natl Acad Sci U S A 2016; 113:7626-31. [PMID: 27325762 DOI: 10.1073/pnas.1602639113] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated (Cas) immunity relies on adaptive acquisition of spacers-short fragments of foreign DNA. For the type I-E CRISPR-Cas system from Escherichia coli, efficient "primed" adaptation requires Cas effector proteins and a CRISPR RNA (crRNA) whose spacer partially matches a segment (protospacer) in target DNA. Primed adaptation leads to selective acquisition of additional spacers from DNA molecules recognized by the effector-crRNA complex. When the crRNA spacer fully matches a protospacer, CRISPR interference-that is, target destruction without acquisition of additional spacers-is observed. We show here that when the rate of degradation of DNA with fully and partially matching crRNA targets is made equal, fully matching protospacers stimulate primed adaptation much more efficiently than partially matching ones. The result indicates that different functional outcomes of CRISPR-Cas response to two kinds of protospacers are not caused by different structures formed by the effector-crRNA complex but are due to the more rapid destruction of targets with fully matching protospacers.
Collapse
|
246
|
Shipman SL, Nivala J, Macklis JD, Church GM. Molecular recordings by directed CRISPR spacer acquisition. Science 2016; 353:aaf1175. [PMID: 27284167 DOI: 10.1126/science.aaf1175] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/22/2016] [Indexed: 01/15/2023]
Abstract
The ability to write a stable record of identified molecular events into a specific genomic locus would enable the examination of long cellular histories and have many applications, ranging from developmental biology to synthetic devices. We show that the type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas system of Escherichia coli can mediate acquisition of defined pieces of synthetic DNA. We harnessed this feature to generate records of specific DNA sequences into a population of bacterial genomes. We then applied directed evolution so as to alter the recognition of a protospacer adjacent motif by the Cas1-Cas2 complex, which enabled recording in two modes simultaneously. We used this system to reveal aspects of spacer acquisition, fundamental to the CRISPR-Cas adaptation process. These results lay the foundations of a multimodal intracellular recording device.
Collapse
Affiliation(s)
- Seth L Shipman
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Department of Stem Cell and Regenerative Biology, Center for Brain Science, and Harvard Stem Cell Institute, Harvard University, Bauer Laboratory 103, Cambridge, MA 02138, USA. Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Jeff Nivala
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology, Center for Brain Science, and Harvard Stem Cell Institute, Harvard University, Bauer Laboratory 103, Cambridge, MA 02138, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
247
|
Anti-cas spacers in orphan CRISPR4 arrays prevent uptake of active CRISPR-Cas I-F systems. Nat Microbiol 2016; 1:16081. [PMID: 27573106 DOI: 10.1038/nmicrobiol.2016.81] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/28/2016] [Indexed: 11/09/2022]
Abstract
Archaea and bacteria harbour clustered regularly interspaced short palindromic repeats (CRISPR) loci. These arrays encode RNA molecules (crRNA), each containing a sequence of a single repeat-intervening spacer. The crRNAs guide CRISPR-associated (Cas) proteins to cleave nucleic acids complementary to the crRNA spacer, thus interfering with targeted foreign elements. Notably, pre-existing spacers may trigger the acquisition of new spacers from the target molecule by means of a primed adaptation mechanism. Here, we show that naturally occurring orphan CRISPR arrays that contain spacers matching sequences of the cognate (absent) cas genes are able to elicit both primed adaptation and direct interference against genetic elements carrying those genes. Our findings show the existence of an anti-cas mechanism that prevents the transfer of a fully equipped CRISPR-Cas system. Hence, they suggest that CRISPR immunity may be undesired by particular prokaryotes, potentially because they could limit possibilities for gaining favourable sequences by lateral transfer.
Collapse
|
248
|
Abstract
The repair of DNA by homologous recombination is an essential, efficient, and high-fidelity process that mends DNA lesions formed during cellular metabolism; these lesions include double-stranded DNA breaks, daughter-strand gaps, and DNA cross-links. Genetic defects in the homologous recombination pathway undermine genomic integrity and cause the accumulation of gross chromosomal abnormalities-including rearrangements, deletions, and aneuploidy-that contribute to cancer formation. Recombination proceeds through the formation of joint DNA molecules-homologously paired but metastable DNA intermediates that are processed by several alternative subpathways-making recombination a versatile and robust mechanism to repair damaged chromosomes. Modern biophysical methods make it possible to visualize, probe, and manipulate the individual molecules participating in the intermediate steps of recombination, revealing new details about the mechanics of genetic recombination. We review and discuss the individual stages of homologous recombination, focusing on common pathways in bacteria, yeast, and humans, and place particular emphasis on the molecular mechanisms illuminated by single-molecule methods.
Collapse
Affiliation(s)
- Jason C Bell
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, California 95616;
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, California 95616;
| |
Collapse
|
249
|
Bell JC, Kowalczykowski SC. RecA: Regulation and Mechanism of a Molecular Search Engine. Trends Biochem Sci 2016; 41:491-507. [PMID: 27156117 PMCID: PMC4892382 DOI: 10.1016/j.tibs.2016.04.002] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/19/2022]
Abstract
Homologous recombination maintains genomic integrity by repairing broken chromosomes. The broken chromosome is partially resected to produce single-stranded DNA (ssDNA) that is used to search for homologous double-stranded DNA (dsDNA). This homology driven 'search and rescue' is catalyzed by a class of DNA strand exchange proteins that are defined in relation to Escherichia coli RecA, which forms a filament on ssDNA. Here, we review the regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous sequence among a vast excess of heterologous DNA. Given that RecA is the prototypic DNA strand exchange protein, its behavior affords insight into the actions of eukaryotic RAD51 orthologs and their regulators, BRCA2 and other tumor suppressors.
Collapse
Affiliation(s)
- Jason C Bell
- Department of Microbiology and Molecular Genetics and Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics and Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.
| |
Collapse
|
250
|
Nuñez J, Bai L, Harrington L, Hinder T, Doudna J. CRISPR Immunological Memory Requires a Host Factor for Specificity. Mol Cell 2016; 62:824-833. [DOI: 10.1016/j.molcel.2016.04.027] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/05/2016] [Accepted: 04/22/2016] [Indexed: 10/21/2022]
|