1
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Hussain MS, Anand V, Kumar M. Functional PAM sequence for DNA interference by CRISPR-Cas I-B system of Leptospira interrogans and the role of LinCas11b encoded within lincas8b. Int J Biol Macromol 2023; 237:124086. [PMID: 36940764 DOI: 10.1016/j.ijbiomac.2023.124086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/18/2023] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
Pathogenic species of Leptospira are recalcitrant for genetic manipulation using conventional tools, and therefore there is a need to explore techniques of higher efficiency. Application of endogenous CRISPR-Cas tool is emerging and efficient; nevertheless, it is limited by a poor understanding of interference machinery in the bacterial genome and its associated protospacer adjacent motif (PAM). In this study, interference machinery of CRISPR-Cas subtype I-B (Lin_I-B) from L. interrogans was experimentally validated in E. coli using the various identified PAM (TGA, ATG, ATA). The overexpression of the Lin_I-B interference machinery in E. coli demonstrated that LinCas5, LinCas6, LinCas7, and LinCas8b can self-assemble on cognate CRISPR RNA to form an interference complex (LinCascade). Moreover, a robust interference of target plasmids containing a protospacer with a PAM suggested a functional LinCascade. We also recognized a small open reading frame within lincas8b that independently co-translates LinCas11b. A mutant variant of LinCascade-Cas11b that lacks LinCas11b co-expression erred to mount target plasmid interference. At the same time, LinCas11b complementation in LinCascade-Cas11b rescued target plasmid interference. Thus, the present study establishes Leptospira subtype I-B interference machinery to be functional and, soon, may pave the way for scientists to harness it as a programmable endogenous genetic manipulation tool.
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Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Vineet Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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2
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Jarmoskaite I, AlSadhan I, Vaidyanathan PP, Herschlag D. How to measure and evaluate binding affinities. eLife 2020; 9:e57264. [PMID: 32758356 PMCID: PMC7452723 DOI: 10.7554/elife.57264] [Citation(s) in RCA: 237] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/05/2020] [Indexed: 12/23/2022] Open
Abstract
Quantitative measurements of biomolecule associations are central to biological understanding and are needed to build and test predictive and mechanistic models. Given the advances in high-throughput technologies and the projected increase in the availability of binding data, we found it especially timely to evaluate the current standards for performing and reporting binding measurements. A review of 100 studies revealed that in most cases essential controls for establishing the appropriate incubation time and concentration regime were not documented, making it impossible to determine measurement reliability. Moreover, several reported affinities could be concluded to be incorrect, thereby impacting biological interpretations. Given these challenges, we provide a framework for a broad range of researchers to evaluate, teach about, perform, and clearly document high-quality equilibrium binding measurements. We apply this framework and explain underlying fundamental concepts through experimental examples with the RNA-binding protein Puf4.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Ishraq AlSadhan
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Department of Chemical Engineering, Stanford UniversityStanfordUnited States
- Stanford ChEM-H, Stanford UniversityStanfordUnited States
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3
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Histone-like Nucleoid-Structuring Protein (H-NS) Paralogue StpA Activates the Type I-E CRISPR-Cas System against Natural Transformation in Escherichia coli. Appl Environ Microbiol 2020; 86:AEM.00731-20. [PMID: 32385085 DOI: 10.1128/aem.00731-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Working mechanisms of CRISPR-Cas systems have been intensively studied. However, far less is known about how they are regulated. The histone-like nucleoid-structuring protein H-NS binds the promoter of cas genes (P cas ) and suppresses the type I-E CRISPR-Cas system in Escherichia coli Although the H-NS paralogue StpA also binds P cas , its role in regulating the CRISPR-Cas system remains unidentified. Our previous work established that E. coli is able to take up double-stranded DNA during natural transformation. Here, we investigated the function of StpA in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli We first documented that although the activated type I-E CRISPR-Cas system, due to hns deletion, interfered with CRISPR-Cas-targeted plasmid transfer, stpA inactivation restored the level of natural transformation. Second, we showed that inactivating stpA reduced the transcriptional activity of P cas Third, by comparing transcriptional activities of the intact P cas and the P cas with a disrupted H-NS binding site in the hns and hns stpA null deletion mutants, we demonstrated that StpA activated transcription of cas genes by binding to the same site as H-NS in P cas Fourth, by expressing StpA with an arabinose-inducible promoter, we confirmed that StpA expressed at a low level stimulated the activity of P cas Finally, by quantifying the level of mature CRISPR RNA (crRNA), we demonstrated that StpA was able to promote the amount of crRNA. Taken together, our work establishes that StpA serves as a transcriptional activator in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli IMPORTANCE StpA is normally considered a molecular backup of the nucleoid-structuring protein H-NS, which was reported as a transcriptional repressor of the type I-E CRISPR-Cas system in Escherichia coli However, the role of StpA in regulating the type I-E CRISPR-Cas system remains elusive. Our previous work uncovered a new route for double-stranded DNA (dsDNA) entry during natural transformation of E. coli In this study, we show that StpA plays a role opposite to that of its paralogue H-NS in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli Our work not only expands our knowledge on CRISPR-Cas-mediated adaptive immunity against extracellular nucleic acids but also sheds new light on understanding the complex regulation mechanism of the CRISPR-Cas system. Moreover, the finding that paralogues StpA and H-NS share a DNA binding site but play opposite roles in transcriptional regulation indicates that higher-order compaction of bacterial chromatin by histone-like proteins could switch prokaryotic transcriptional modes.
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4
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Müller-Esparza H, Osorio-Valeriano M, Steube N, Thanbichler M, Randau L. Bio-Layer Interferometry Analysis of the Target Binding Activity of CRISPR-Cas Effector Complexes. Front Mol Biosci 2020; 7:98. [PMID: 32528975 PMCID: PMC7266957 DOI: 10.3389/fmolb.2020.00098] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/01/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems employ ribonucleoprotein complexes to identify nucleic acid targets with complementarity to bound CRISPR RNAs. Analyses of the high diversification of these effector complexes suggest that they can exhibit a wide spectrum of target requirements and binding affinities. Therefore, streamlined analysis techniques to study the interactions between nucleic acids and proteins are necessary to facilitate the characterization and comparison of CRISPR-Cas effector activities. Bio-layer Interferometry (BLI) is a technique that measures the interference pattern of white light that is reflected from a layer of biomolecules immobilized on the surface of a sensor tip (bio-layers) in real time and in solution. As streptavidin-coated sensors and biotinylated oligonucleotides are commercially available, this method enables straightforward measurements of the interaction of CRISPR-Cas complexes with different targets in a qualitative and quantitative fashion. Here, we present a general method to carry out binding assays with the Type I-Fv complex from Shewanella putrefaciens and the Type I-F complex from Shewanella baltica as model effectors. We report target specificities, dissociation constants and interactions with the Anti-CRISPR protein AcrF7 to highlight possible applications of this technique.
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Affiliation(s)
| | - Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, Marburg, Germany.,Max Planck Fellow Group "Bacterial Cell Biology", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Niklas Steube
- Department of Biology, University of Marburg, Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany.,Max Planck Fellow Group "Bacterial Cell Biology", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Lennart Randau
- Department of Biology, University of Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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5
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Vink JNA, Martens KJA, Vlot M, McKenzie RE, Almendros C, Estrada Bonilla B, Brocken DJW, Hohlbein J, Brouns SJJ. Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism. Mol Cell 2020; 77:39-50.e10. [PMID: 31735642 DOI: 10.1016/j.molcel.2019.10.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/31/2019] [Accepted: 10/11/2019] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here, we visualize individual Cascade complexes in a native type I CRISPR-Cas system. We uncover an exponential relation between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and affect CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.
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Affiliation(s)
- Jochem N A Vink
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Koen J A Martens
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands; Laboratory of Bionanotechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Rebecca E McKenzie
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Cristóbal Almendros
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Boris Estrada Bonilla
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daan J W Brocken
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, the Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands; Microspectroscopy Research Facility, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
| | - Stan J J Brouns
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
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6
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Pickar-Oliver A, Black JB, Lewis MM, Mutchnick KJ, Klann TS, Gilcrest KA, Sitton MJ, Nelson CE, Barrera A, Bartelt LC, Reddy TE, Beisel CL, Barrangou R, Gersbach CA. Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. Nat Biotechnol 2019; 37:1493-1501. [PMID: 31548729 PMCID: PMC6893126 DOI: 10.1038/s41587-019-0235-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/23/2019] [Indexed: 12/19/2022]
Abstract
Class 2 CRISPR-Cas systems, such as Cas9 and Cas12, have been widely used to target DNA sequences in eukaryotic genomes. However, class 1 CRISPR-Cas systems, which represent about 90% of all CRISPR systems in nature, remain largely unexplored for genome engineering applications. Here, we show that class 1 CRISPR-Cas systems can be expressed in mammalian cells and used for DNA targeting and transcriptional control. We repurpose type I variants of class 1 CRISPR-Cas systems from Escherichia coli and Listeria monocytogenes, which target DNA via a multi-component RNA-guided complex termed Cascade. We validate Cascade expression, complex formation and nuclear localization in human cells, and demonstrate programmable CRISPR RNA (crRNA)-mediated targeting of specific loci in the human genome. By tethering activation and repression domains to Cascade, we modulate the expression of targeted endogenous genes in human cells. This study demonstrates the use of Cascade as a CRISPR-based technology for targeted eukaryotic gene regulation, highlighting class 1 CRISPR-Cas systems for further exploration.
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Affiliation(s)
- Adrian Pickar-Oliver
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Mae M Lewis
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Kevin J Mutchnick
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Tyler S Klann
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Kylie A Gilcrest
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Madeleine J Sitton
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Christopher E Nelson
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Alejandro Barrera
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Luke C Bartelt
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Timothy E Reddy
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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7
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Krivoy A, Rutkauskas M, Kuznedelov K, Musharova O, Rouillon C, Severinov K, Seidel R. Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro. Nucleic Acids Res 2019; 46:4087-4098. [PMID: 29596641 PMCID: PMC5934681 DOI: 10.1093/nar/gky219] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/14/2018] [Indexed: 11/13/2022] Open
Abstract
In type I CRISPR-Cas systems, primed adaptation of new spacers into CRISPR arrays occurs when the effector Cascade-crRNA complex recognizes imperfectly matched targets that are not subject to efficient CRISPR interference. Thus, primed adaptation allows cells to acquire additional protection against mobile genetic elements that managed to escape interference. Biochemical and biophysical studies suggested that Cascade-crRNA complexes formed on fully matching targets (subject to efficient interference) and on partially mismatched targets that promote primed adaption are structurally different. Here, we probed Escherichia coli Cascade-crRNA complexes bound to matched and mismatched DNA targets using a magnetic tweezers assay. Significant differences in complex stabilities were observed consistent with the presence of at least two distinct conformations. Surprisingly, in vivo analysis demonstrated that all mismatched targets stimulated robust primed adaptation irrespective of conformational states observed in vitro. Our results suggest that primed adaptation is a direct consequence of a reduced interference efficiency and/or rate and is not a consequence of distinct effector complex conformations on target DNA.
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Affiliation(s)
- Andrey Krivoy
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Marius Rutkauskas
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Konstantin Kuznedelov
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Olga Musharova
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Christophe Rouillon
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Konstantin Severinov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
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8
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Gong L, Li M, Cheng F, Zhao D, Chen Y, Xiang H. Primed adaptation tolerates extensive structural and size variations of the CRISPR RNA guide in Haloarcula hispanica. Nucleic Acids Res 2019; 47:5880-5891. [PMID: 30957847 PMCID: PMC6582329 DOI: 10.1093/nar/gkz244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 12/13/2022] Open
Abstract
Recent studies on CRISPR adaptation revealed that priming is a major pathway of spacer acquisition, at least for the most prevalent type I systems. Priming is guided by a CRISPR RNA which fully/partially matches the invader DNA, but the plasticity of this RNA guide has not yet been characterized. In this study, we extensively modified the two conserved handles of a priming crRNA in Haloarcula hispanica, and altered the size of its central spacer part. Interestingly, priming is insusceptible to the full deletion of 3' handle, which seriously impaired crRNA stability and interference effects. With 3' handle deletion, further truncation of 5' handle revealed that its spacer-proximal 6 nucleotides could provide the least conserved sequence required for priming. Subsequent scanning mutation further identified critical nucleotides within 5' handle. Besides, priming was also shown to tolerate a wider size variation of the spacer part, compared to interference. These data collectively illustrate the high tolerance of priming to extensive structural/size variations of the crRNA guide, which highlights the structural flexibility of the crRNA-effector ribonucleoprotein complex. The observed high priming effectiveness suggests that primed adaptation promotes clearance of the fast-replicating and ever-evolving viral DNA, by rapidly and persistently multiplexing the interference pathway.
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Affiliation(s)
- Luyao Gong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feiyue Cheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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9
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Maier LK, Stachler AE, Brendel J, Stoll B, Fischer S, Haas KA, Schwarz TS, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Gophna U, Marchfelder A. The nuts and bolts of the Haloferax CRISPR-Cas system I-B. RNA Biol 2018; 16:469-480. [PMID: 29649958 PMCID: PMC6546412 DOI: 10.1080/15476286.2018.1460994] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Invading genetic elements pose a constant threat to prokaryotic survival, requiring an effective defence. Eleven years ago, the arsenal of known defence mechanisms was expanded by the discovery of the CRISPR-Cas system. Although CRISPR-Cas is present in the majority of archaea, research often focuses on bacterial models. Here, we provide a perspective based on insights gained studying CRISPR-Cas system I-B of the archaeon Haloferax volcanii. The system relies on more than 50 different crRNAs, whose stability and maintenance critically depend on the proteins Cas5 and Cas7, which bind the crRNA and form the Cascade complex. The interference machinery requires a seed sequence and can interact with multiple PAM sequences. H. volcanii stands out as the first example of an organism that can tolerate autoimmunity via the CRISPR-Cas system while maintaining a constitutively active system. In addition, the H. volcanii system was successfully developed into a tool for gene regulation.
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Affiliation(s)
| | | | | | | | | | - Karina A Haas
- a Biology II, Ulm University , Ulm , Germany.,b Microbiology and Biotechnology, Ulm University , Ulm , Germany
| | | | - Omer S Alkhnbashi
- c Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Georges-Köhler-Allee 106, Freiburg , Germany
| | - Kundan Sharma
- e Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, Göttingen , Germany.,f Ludwig Institute for Cancer Research, University of Oxford , Oxford , United Kingdom
| | - Henning Urlaub
- e Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, Göttingen , Germany.,g Institute for Clinical Chemistry, University Medical Center Göttingen , Robert Koch Straße 10, Göttingen , Germany
| | - Rolf Backofen
- c Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Georges-Köhler-Allee 106, Freiburg , Germany.,d Centre for Biological Signalling Studies (BIOSS), Cluster of Excellence, University of Freiburg , Germany
| | - Uri Gophna
- h School of Molecular Cell Biology & Biotechnology, George S. Wise, Faculty of Life Sciences, Tel Aviv University , Tel Aviv , Israel
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10
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Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proc Natl Acad Sci U S A 2018; 115:E5307-E5316. [PMID: 29784811 DOI: 10.1073/pnas.1803440115] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity consist of direct repeat arrays separated by unique spacers and multiple CRISPR-associated (cas) genes encoding proteins that mediate all stages of the CRISPR response. In addition to the relatively small set of core cas genes that are typically present in all CRISPR-Cas systems of a given (sub)type and are essential for the defense function, numerous genes occur in CRISPR-cas loci only sporadically. Some of these have been shown to perform various ancillary roles in CRISPR response, but the functional relevance of most remains unknown. We developed a computational strategy for systematically detecting genes that are likely to be functionally linked to CRISPR-Cas. The approach is based on a "CRISPRicity" metric that measures the strength of CRISPR association for all protein-coding genes from sequenced bacterial and archaeal genomes. Uncharacterized genes with CRISPRicity values comparable to those of cas genes are considered candidate CRISPR-linked genes. We describe additional criteria to predict functionally relevance for genes in the candidate set and identify 79 genes as strong candidates for functional association with CRISPR-Cas systems. A substantial majority of these CRISPR-linked genes reside in type III CRISPR-cas loci, which implies exceptional functional versatility of type III systems. Numerous candidate CRISPR-linked genes encode integral membrane proteins suggestive of tight membrane association of CRISPR-Cas systems, whereas many others encode proteins implicated in various signal transduction pathways. These predictions provide ample material for improving annotation of CRISPR-cas loci and experimental characterization of previously unsuspected aspects of CRISPR-Cas system functionality.
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11
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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.
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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
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12
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Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol 2017. [PMID: 28111461 DOI: 10.1038/nrmicro.2016.184.diversity] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas.
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Affiliation(s)
- Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Aaron Smargon
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - David Scott
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - David Cox
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Neena Pyzocha
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Winston Yan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Omar O Abudayyeh
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Jonathan S Gootenberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Kira S Makarova
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
- McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology Cambridge (MIT), Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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13
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Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol 2017; 15:169-182. [PMID: 28111461 DOI: 10.1038/nrmicro.2016.184] [Citation(s) in RCA: 637] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas.
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Affiliation(s)
- Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia.,National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Aaron Smargon
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - David Scott
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - David Cox
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Neena Pyzocha
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Winston Yan
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA
| | - Omar O Abudayyeh
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Jonathan S Gootenberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Kira S Makarova
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia.,Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.,McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology Cambridge (MIT), Massachusetts 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Kuznedelov K, Mekler V, Lemak S, Tokmina-Lukaszewska M, Datsenko KA, Jain I, Savitskaya E, Mallon J, Shmakov S, Bothner B, Bailey S, Yakunin AF, Severinov K, Semenova E. Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation. Nucleic Acids Res 2016; 44:10849-10861. [PMID: 27738137 PMCID: PMC5159557 DOI: 10.1093/nar/gkw914] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 09/29/2016] [Accepted: 10/03/2016] [Indexed: 12/26/2022] Open
Abstract
The Escherichia coli type I-E CRISPR-Cas system Cascade effector is a multisubunit complex that binds CRISPR RNA (crRNA). Through its 32-nucleotide spacer sequence, Cascade-bound crRNA recognizes protospacers in foreign DNA, causing its destruction during CRISPR interference or acquisition of additional spacers in CRISPR array during primed CRISPR adaptation. Within Cascade, the crRNA spacer interacts with a hexamer of Cas7 subunits. We show that crRNAs with a spacer length reduced to 14 nucleotides cause primed adaptation, while crRNAs with spacer lengths of more than 20 nucleotides cause both primed adaptation and target interference in vivo. Shortened crRNAs assemble into altered-stoichiometry Cascade effector complexes containing less than the normal amount of Cas7 subunits. The results show that Cascade assembly is driven by crRNA and suggest that multisubunit type I CRISPR effectors may have evolved from much simpler ancestral complexes.
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Affiliation(s)
- Konstantin Kuznedelov
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Vladimir Mekler
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | | | - Kirill A Datsenko
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Ishita Jain
- Waksman Institute of Microbiology, 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
| | - John Mallon
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,NCBI, NLM, NIH, Bethesda, MD 20894, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Scott Bailey
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA .,Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.,Peter the Great St Petersburg State Polytechnic University, St. Petersburg, 195251, Russia
| | - Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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15
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Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L. Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Nucleic Acids Res 2016; 44:5872-82. [PMID: 27216815 PMCID: PMC4937334 DOI: 10.1093/nar/gkw469] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/13/2016] [Indexed: 12/26/2022] Open
Abstract
Shewanella putrefaciens CN-32 contains a single Type I-Fv CRISPR-Cas system which confers adaptive immunity against bacteriophage infection. Three Cas proteins (Cas6f, Cas7fv, Cas5fv) and mature CRISPR RNAs were shown to be required for the assembly of an interference complex termed Cascade. The Cas protein-CRISPR RNA interaction sites within this complex were identified via mass spectrometry. Additional Cas proteins, commonly described as large and small subunits, that are present in all other investigated Cascade structures, were not detected. We introduced this minimal Type I system in Escherichia coli and show that it provides heterologous protection against lambda phage. The absence of a large subunit suggests that the length of the crRNA might not be fixed and recombinant Cascade complexes with drastically shortened and elongated crRNAs were engineered. Size-exclusion chromatography and small-angle X-ray scattering analyses revealed that the number of Cas7fv backbone subunits is adjusted in these shortened and extended Cascade variants. Larger Cascade complexes can still confer immunity against lambda phage infection in E. coli. Minimized Type I CRISPR-Cas systems expand our understanding of the evolution of Cascade assembly and diversity. Their adjustable crRNA length opens the possibility for customizing target DNA specificity.
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Affiliation(s)
- Daniel Gleditzsch
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Hanna Müller-Esparza
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Patrick Pausch
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany Department of Chemistry, Philipps University Marburg, D-35043 Marburg, Germany
| | - Kundan Sharma
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, D-37075 Göttingen, Germany
| | - Srivatsa Dwarakanath
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Henning Urlaub
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, D-37075 Göttingen, Germany Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany Department of Chemistry, Philipps University Marburg, D-35043 Marburg, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany
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16
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17
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Semenova E, Kuznedelov K, Datsenko KA, Boudry PM, Savitskaya EE, Medvedeva S, Beloglazova N, Logacheva M, Yakunin AF, Severinov K. The Cas6e ribonuclease is not required for interference and adaptation by the E. coli type I-E CRISPR-Cas system. Nucleic Acids Res 2015; 43:6049-61. [PMID: 26013814 PMCID: PMC4499155 DOI: 10.1093/nar/gkv546] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/12/2015] [Indexed: 11/30/2022] Open
Abstract
CRISPR-Cas are small RNA-based adaptive prokaryotic immunity systems protecting cells from foreign DNA or RNA. Type I CRISPR-Cas systems are composed of a multiprotein complex (Cascade) that, when bound to CRISPR RNA (crRNA), can recognize double-stranded DNA targets and recruit the Cas3 nuclease to destroy target-containing DNA. In the Escherichia coli type I-E CRISPR-Cas system, crRNAs are generated upon transcription of CRISPR arrays consisting of multiple palindromic repeats and intervening spacers through the function of Cas6e endoribonuclease, which cleaves at specific positions of repeat sequences of the CRISPR array transcript. Cas6e is also a component of Cascade. Here, we show that when mature unit-sized crRNAs are provided in a Cas6e-independent manner by transcription termination, the CRISPR-Cas system can function without Cas6e. The results should allow facile interrogation of various targets by type I-E CRISPR-Cas system in E. coli using unit-sized crRNAs generated by transcription.
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Affiliation(s)
- Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Kuznedelov
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kirill A Datsenko
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Pierre M Boudry
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Ekaterina E Savitskaya
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Sofia Medvedeva
- Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Maria Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA Skolkovo Institute of Science and Technology, Skolkovo 143025, Russia Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
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18
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Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie 2015; 117:119-28. [PMID: 25868999 DOI: 10.1016/j.biochi.2015.03.025] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/31/2015] [Indexed: 12/26/2022]
Abstract
Viruses are a common threat to cellular life, not the least to bacteria and archaea who constitute the majority of life on Earth. Consequently, a variety of mechanisms to resist virus infection has evolved. A recent discovery is the adaptive immune system in prokaryotes, a type of system previously thought to be present only in vertebrates. The system, called CRISPR-Cas, provide sequence-specific adaptive immunity and fundamentally affect our understanding of virus-host interaction. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize and clear infections. There has been rapid advancement in our understanding of this immune system and its applications, but there are many aspects that await elucidation making the field an exciting area of research. This review provides an overview of the field and highlights unresolved issues.
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Affiliation(s)
- Devashish Rath
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Lina Amlinger
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Archana Rath
- Department of Biotechnology, University of Mumbai, Mumbai 400098, India
| | - Magnus Lundgren
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden.
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