151
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Type I-F CRISPR-Cas Distribution and Array Dynamics in Legionella pneumophila. G3-GENES GENOMES GENETICS 2020; 10:1039-1050. [PMID: 31937548 PMCID: PMC7056967 DOI: 10.1534/g3.119.400813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In bacteria and archaea, several distinct types of CRISPR-Cas systems provide adaptive immunity through broadly similar mechanisms: short nucleic acid sequences derived from foreign DNA, known as spacers, engage in complementary base pairing with invasive genetic elements setting the stage for nucleases to degrade the target DNA. A hallmark of type I CRISPR-Cas systems is their ability to acquire spacers in response to both new and previously encountered invaders (naïve and primed acquisition, respectively). Our phylogenetic analyses of 43 L. pneumophila type I-F CRISPR-Cas systems and their resident genomes suggest that many of these systems have been horizontally acquired. These systems are frequently encoded on plasmids and can co-occur with nearly identical chromosomal loci. We show that two such co-occurring systems are highly protective and undergo efficient primed acquisition in the lab. Furthermore, we observe that targeting by one system’s array can prime spacer acquisition in the other. Lastly, we provide experimental and genomic evidence for a model in which primed acquisition can efficiently replenish a depleted type I CRISPR array following a mass spacer deletion event.
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152
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Swartjes T, Staals RH, van der Oost J. Editor's cut: DNA cleavage by CRISPR RNA-guided nucleases Cas9 and Cas12a. Biochem Soc Trans 2020; 48:207-219. [PMID: 31872209 PMCID: PMC7054755 DOI: 10.1042/bst20190563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022]
Abstract
Discovered as an adaptive immune system of prokaryotes, CRISPR-Cas provides many promising applications. DNA-cleaving Cas enzymes like Cas9 and Cas12a, are of great interest for genome editing. The specificity of these DNA nucleases is determined by RNA guides, providing great targeting adaptability. Besides this general method of programmable DNA cleavage, these nucleases have different biochemical characteristics, that can be exploited for different applications. Although Cas nucleases are highly promising, some room for improvement remains. New developments and discoveries like base editing, prime editing, and CRISPR-associated transposons might address some of these challenges.
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Affiliation(s)
- Thomas Swartjes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Raymond H.J. Staals
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
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153
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Béguin P, Chekli Y, Sezonov G, Forterre P, Krupovic M. Sequence motifs recognized by the casposon integrase of Aciduliprofundum boonei. Nucleic Acids Res 2020; 47:6386-6395. [PMID: 31114911 PMCID: PMC6614799 DOI: 10.1093/nar/gkz447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/17/2019] [Accepted: 05/20/2019] [Indexed: 01/01/2023] Open
Abstract
Casposons are a group of bacterial and archaeal DNA transposons encoding a specific integrase, termed casposase, which is homologous to the Cas1 enzyme responsible for the integration of new spacers into CRISPR loci. Here, we characterized the sequence motifs recognized by the casposase from a thermophilic archaeon Aciduliprofundum boonei. We identified a stretch of residues, located in the leader region upstream of the actual integration site, whose deletion or mutagenesis impaired the concerted integration reaction. However, deletions of two-thirds of the target site were fully functional. Various single-stranded 6-FAM-labelled oligonucleotides derived from casposon terminal inverted repeats were as efficiently incorporated as duplexes into the target site. This result suggests that, as in the case of spacer insertion by the CRISPR Cas1–Cas2 integrase, casposon integration involves splaying of the casposon termini, with single-stranded ends being the actual substrates. The sequence critical for incorporation was limited to the five terminal residues derived from the 3′ end of the casposon. Furthermore, we characterize the casposase from Nitrosopumilus koreensis, a marine member of the phylum Thaumarchaeota, and show that it shares similar properties with the A. boonei enzyme, despite belonging to a different family. These findings further reinforce the mechanistic similarities and evolutionary connection between the casposons and the adaptation module of the CRISPR–Cas systems.
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Affiliation(s)
- Pierre Béguin
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, 25-28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - Yankel Chekli
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, 25-28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - Guennadi Sezonov
- UMRS 1138 - Centre de Recherche des Cordeliers, Sorbonne Université, 15, rue de l'École de Médecine, 75006 Paris, France
| | - Patrick Forterre
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, 25-28 rue du Dr. Roux 75724 Paris cedex 15, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris- Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, Paris, France
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, 25-28 rue du Dr. Roux 75724 Paris cedex 15, France
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154
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Cas3 Protein-A Review of a Multi-Tasking Machine. Genes (Basel) 2020; 11:genes11020208. [PMID: 32085454 PMCID: PMC7074321 DOI: 10.3390/genes11020208] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 01/20/2023] Open
Abstract
Cas3 has essential functions in CRISPR immunity but its other activities and roles, in vitro and in cells, are less widely known. We offer a concise review of the latest understanding and questions arising from studies of Cas3 mechanism during CRISPR immunity, and highlight recent attempts at using Cas3 for genetic editing. We then spotlight involvement of Cas3 in other aspects of cell biology, for which understanding is lacking—these focus on CRISPR systems as regulators of cellular processes in addition to defense against mobile genetic elements.
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155
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Burmistrz M, Krakowski K, Krawczyk-Balska A. RNA-Targeting CRISPR-Cas Systems and Their Applications. Int J Mol Sci 2020; 21:ijms21031122. [PMID: 32046217 PMCID: PMC7036953 DOI: 10.3390/ijms21031122] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) systems have revolutionized modern molecular biology. Numerous types of these systems have been discovered to date. Many CRISPR-Cas systems have been used as a backbone for the development of potent research tools, with Cas9 being the most widespread. While most of the utilized systems are DNA-targeting, recently more and more attention is being gained by those that target RNA. Their ability to specifically recognize a given RNA sequence in an easily programmable way makes them ideal candidates for developing new research tools. In this review we summarize current knowledge on CRISPR-Cas systems which have been shown to target RNA molecules, that is type III (Csm/Cmr), type VI (Cas13), and type II (Cas9). We also present a list of available technologies based on these systems.
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156
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Wimmer F, Beisel CL. CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers. Front Microbiol 2020; 10:3078. [PMID: 32038537 PMCID: PMC6990116 DOI: 10.3389/fmicb.2019.03078] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas immune systems in bacteria and archaea record prior infections as spacers within each system’s CRISPR arrays. Spacers are normally derived from invasive genetic material and direct the immune system to complementary targets as part of future infections. However, not all spacers appear to be derived from foreign genetic material and instead can originate from the host genome. Their presence poses a paradox, as self-targeting spacers would be expected to induce an autoimmune response and cell death. In this review, we discuss the known frequency of self-targeting spacers in natural CRISPR-Cas systems, how these spacers can be incorporated into CRISPR arrays, and how the host can evade lethal attack. We also discuss how self-targeting spacers can become the basis for alternative functions performed by CRISPR-Cas systems that extend beyond adaptive immunity. Overall, the acquisition of genome-targeting spacers poses a substantial risk but can aid in the host’s evolution and potentially lead to or support new functionalities.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.,Medical Faculty, University of Würzburg, Würzburg, Germany
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157
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Tanna T, Schmidt F, Cherepkova MY, Okoniewski M, Platt RJ. Recording transcriptional histories using Record-seq. Nat Protoc 2020; 15:513-539. [DOI: 10.1038/s41596-019-0253-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/08/2019] [Indexed: 01/17/2023]
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158
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Hickman AB, Kailasan S, Genzor P, Haase AD, Dyda F. Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas. eLife 2020; 9:50004. [PMID: 31913120 PMCID: PMC6977970 DOI: 10.7554/elife.50004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/08/2020] [Indexed: 12/17/2022] Open
Abstract
Key to CRISPR-Cas adaptive immunity is maintaining an ongoing record of invading nucleic acids, a process carried out by the Cas1-Cas2 complex that integrates short segments of foreign genetic material (spacers) into the CRISPR locus. It is hypothesized that Cas1 evolved from casposases, a novel class of transposases. We show here that the Methanosarcina mazei casposase can integrate varied forms of the casposon end in vitro, and recapitulates several properties of CRISPR-Cas integrases including site-specificity. The X-ray structure of the casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. The differences between transposase and CRISPR-Cas integrase are largely architectural, and it appears that evolutionary change involved changes in protein-protein interactions to favor Cas2 binding over tetramerization; this in turn led to preferred integration of single spacers over two transposon ends.
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Affiliation(s)
- Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Shweta Kailasan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Pavol Genzor
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Astrid D Haase
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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159
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Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform. Nat Commun 2020; 11:95. [PMID: 31911609 PMCID: PMC6946703 DOI: 10.1038/s41467-019-14012-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
The flow of genetic material between bacteria is central to the adaptation and evolution of bacterial genomes. However, our knowledge about DNA transfer within complex microbiomes is lacking, with most studies of horizontal gene transfer (HGT) relying on bioinformatic analyses of genetic elements maintained on evolutionary timescales or experimental measurements of phenotypically trackable markers. Here, we utilize the CRISPR-Cas spacer acquisition process to detect DNA acquisition events from complex microbiota in real-time and at nucleotide resolution. In this system, an E. coli recording strain is exposed to a microbial sample and spacers are acquired from transferred plasmids and permanently stored in genomic CRISPR arrays. Sequencing and analysis of acquired spacers enables identification of the transferred plasmids. This approach allowed us to identify individual mobile elements without relying on phenotypic markers or post-transfer replication. We found that HGT into the recording strain in human clinical fecal samples can be extensive and is driven by different plasmid types, with the IncX type being the most actively transferred.
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160
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Abstract
Many bacteria and archaea have the unique ability to heritably alter their genomes by incorporating small fragments of foreign DNA, called spacers, into CRISPR loci. Once transcribed and processed into individual CRISPR RNAs, spacer sequences guide Cas effector nucleases to destroy complementary, invading nucleic acids. Collectively, these two processes are known as the CRISPR-Cas immune response. In this Progress article, we review recent studies that have advanced our understanding of the molecular mechanisms underlying spacer acquisition and that have revealed a fundamental link between the two phases of CRISPR immunity that ensures optimal immunity from newly acquired spacers. Finally, we highlight important open questions and discuss the potential basic and applied impact of spacer acquisition research.
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Affiliation(s)
- Jon McGinn
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
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161
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Calvo-Villamañán A, Bernheim A, Bikard D. Methods for the Analysis and Characterization of Defense Mechanisms Against Horizontal Gene Transfer: CRISPR Systems. Methods Mol Biol 2020; 2075:235-249. [PMID: 31584167 DOI: 10.1007/978-1-4939-9877-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CRISPR-Cas systems provide RNA-guided adaptive immunity to the majority of archaea and many bacteria. They are able to capture pieces of invading genetic elements in the form of novel spacers in an array of repeats. These elements can then be used as a memory to destroy incoming DNA through the action of RNA-guided nucleases. This chapter describes general procedures to determine the ability of CRISPR-Cas systems to capture novel sequences and to use them to block phages and horizontal gene transfer. All protocols are performed in Staphylococcus aureus using Type II-A CRISPR-Cas systems. Nonetheless, the protocols provided can be adapted to work with other bacteria and other types of CRISPR-Cas systems.
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Affiliation(s)
- Alicia Calvo-Villamañán
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- École Doctorale FIRE-Programme Bettencourt, Centre de Recherches Interdisciplinaires, Paris, France
| | - Aude Bernheim
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- École Doctorale FIRE-Programme Bettencourt, Centre de Recherches Interdisciplinaires, Paris, France
- Microbial Evolutionary Genomics, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- AgroParisTech, Paris, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France.
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162
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Ramachandran A, Summerville L, Learn BA, DeBell L, Bailey S. Processing and integration of functionally oriented prespacers in the Escherichia coli CRISPR system depends on bacterial host exonucleases. J Biol Chem 2019; 295:3403-3414. [PMID: 31914418 DOI: 10.1074/jbc.ra119.012196] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/20/2019] [Indexed: 12/22/2022] Open
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against viruses. During spacer adaptation, the Cas1-Cas2 complex selects fragments of foreign DNA, called prespacers, and integrates them into CRISPR arrays in an orientation that provides functional immunity. Cas4 is involved in both the trimming of prespacers and the cleavage of protospacer adjacent motif (PAM) in several type I CRISPR-Cas systems, but how the prespacers are processed in systems lacking Cas4, such as the type I-E and I-F systems, is not understood. In Escherichia coli, which has a type I-E system, Cas1-Cas2 preferentially selects prespacers with 3' overhangs via specific recognition of a PAM, but how these prespacers are integrated in a functional orientation in the absence of Cas4 is not known. Using a biochemical approach with purified proteins, as well as integration, prespacer protection, sequencing, and quantitative PCR assays, we show here that the bacterial 3'-5' exonucleases DnaQ and ExoT can trim long 3' overhangs of prespacers and promote integration in the correct orientation. We found that trimming by these exonucleases results in an asymmetric intermediate, because Cas1-Cas2 protects the PAM sequence, which helps to define spacer orientation. Our findings implicate the E. coli host 3'-5' exonucleases DnaQ and ExoT in spacer adaptation and reveal a mechanism by which spacer orientation is defined in E. coli.
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Affiliation(s)
- Anita Ramachandran
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Lesley Summerville
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Brian A Learn
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Lily DeBell
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Scott Bailey
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205.
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163
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Yoganand KN, Muralidharan M, Nimkar S, Anand B. Fidelity of prespacer capture and processing is governed by the PAM-mediated interactions of Cas1-2 adaptation complex in CRISPR-Cas type I-E system. J Biol Chem 2019; 294:20039-20053. [PMID: 31748409 PMCID: PMC6937570 DOI: 10.1074/jbc.ra119.009438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes deploy CRISPR-Cas-based RNA-guided adaptive immunity to fend off mobile genetic elements such as phages and plasmids. During CRISPR adaptation, which is the first stage of CRISPR immunity, the Cas1-2 integrase complex captures invader-derived prespacer DNA and specifically integrates it at the leader-repeat junction as spacers. For this integration, several variants of CRISPR-Cas systems use Cas4 as an indispensable nuclease for selectively processing the protospacer adjacent motif (PAM) containing prespacers to a defined length. Surprisingly, however, a few CRISPR-Cas systems, such as type I-E, are bereft of Cas4. Despite the absence of Cas4, how the prespacers show impeccable conservation for length and PAM selection in type I-E remains intriguing. Here, using in vivo and in vitro integration assays, deep sequencing, and exonuclease footprinting, we show that Cas1-2/I-E-via the type I-E-specific extended C-terminal tail of Cas1-displays intrinsic affinity for PAM containing prespacers of variable length in Escherichia coli Although Cas1-2/I-E does not prune the prespacers, its binding protects the prespacer boundaries from exonuclease action. This ensures the pruning of exposed ends by exonucleases to aptly sized substrates for integration into the CRISPR locus. In summary, our work reveals that in a few CRISPR-Cas variants, such as type I-E, the specificity of PAM selection resides with Cas1-2, whereas the prespacer processing is co-opted by cellular non-Cas exonucleases, thereby offsetting the need for Cas4.
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Affiliation(s)
- Kakimani Nagarajan Yoganand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Manasasri Muralidharan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Siddharth Nimkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Baskaran Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
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164
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González-Delgado A, Mestre MR, Martínez-Abarca F, Toro N. Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR-Cas system in Vibrio vulnificus. Nucleic Acids Res 2019; 47:10202-10211. [PMID: 31504832 PMCID: PMC6821258 DOI: 10.1093/nar/gkz746] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/26/2022] Open
Abstract
The association of reverse transcriptases (RTs) with CRISPR–Cas system has recently attracted interest because the RT activity appears to facilitate the RT-dependent acquisition of spacers from RNA molecules. However, our understanding of this spacer acquisition process remains limited. We characterized the in vivo acquisition of spacers mediated by an RT-Cas1 fusion protein linked to a type III-D system from Vibrio vulnificus strain YJ016, and showed that the adaptation module, consisting of the RT-Cas1 fusion, two different Cas2 proteins (A and B) and one of the two CRISPR arrays, was completely functional in a heterologous host. We found that mutations of the active site of the RT domain significantly decreased the acquisition of new spacers and showed that this RT-Cas1-associated adaptation module was able to incorporate spacers from RNA molecules into the CRISPR array. We demonstrated that the two Cas2 proteins of the adaptation module were required for spacer acquisition. Furthermore, we found that several sequence-specific features were required for the acquisition and integration of spacers derived from any region of the genome, with no bias along the 5′and 3′ends of coding sequences. This study provides new insight into the RT-Cas1 fusion protein-mediated acquisition of spacers from RNA molecules.
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Affiliation(s)
- Alejandro González-Delgado
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Mario Rodríguez Mestre
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Francisco Martínez-Abarca
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
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165
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Grainy J, Garrett S, Graveley BR, P Terns M. CRISPR repeat sequences and relative spacing specify DNA integration by Pyrococcus furiosus Cas1 and Cas2. Nucleic Acids Res 2019; 47:7518-7531. [PMID: 31219587 PMCID: PMC6698737 DOI: 10.1093/nar/gkz548] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/26/2022] Open
Abstract
Acquiring foreign spacer DNA into the CRISPR locus is an essential primary step of the CRISPR-Cas pathway in prokaryotes for developing host immunity to mobile genetic elements. Here, we investigate spacer integration in vitro using proteins from Pyrococcus furiosus and demonstrate that Cas1 and Cas2 are sufficient to accurately integrate spacers into a minimal CRISPR locus. Using high-throughput sequencing, we identified high frequency spacer integration occurring at the same CRISPR repeat border sites utilized in vivo, as well as at several non-CRISPR plasmid sequences which share features with repeats. Analysis of non-CRISPR integration sites revealed that Cas1 and Cas2 are directed to catalyze full-site spacer integration at specific DNA stretches where guanines and/or cytosines are 30 base pairs apart and the intervening sequence harbors several positionally conserved bases. Moreover, assaying a series of CRISPR repeat mutations, followed by sequencing of the integration products, revealed that the specificity of integration is primarily directed by sequences at the leader-repeat junction as well as an adenine-rich sequence block in the mid-repeat. Together, our results indicate that P. furiosus Cas1 and Cas2 recognize multiple sequence features distributed over a 30 base pair DNA region for accurate spacer integration at the CRISPR repeat.
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Affiliation(s)
- Julie Grainy
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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166
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Kim JG, Garrett S, Wei Y, Graveley BR, Terns MP. CRISPR DNA elements controlling site-specific spacer integration and proper repeat length by a Type II CRISPR-Cas system. Nucleic Acids Res 2019; 47:8632-8648. [PMID: 31392984 PMCID: PMC6895254 DOI: 10.1093/nar/gkz677] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 12/26/2022] Open
Abstract
CRISPR–Cas systems provide heritable immunity against viruses by capturing short invader DNA sequences, termed spacers, and incorporating them into the CRISPR loci of the prokaryotic host genome. Here, we investigate DNA elements that control accurate spacer uptake in the type II-A CRISPR locus of Streptococcus thermophilus. We determined that purified Cas1 and Cas2 proteins catalyze spacer integration with high specificity for CRISPR repeat junctions. We show that 10 bp of the CRISPR leader sequence is critical for stimulating polarized integration preferentially at the repeat proximal to the leader. Spacer integration proceeds through a two-step transesterification reaction where the 3′ hydroxyl groups of the spacer target both repeat borders on opposite strands. The leader-proximal end of the repeat is preferentially targeted for the first site of integration through recognition of sequences spanning the leader-repeat junction. Subsequently, second-site integration at the leader-distal end of the repeat is specified by multiple determinants including a length-defining mechanism relying on a repeat element proximal to the second site of integration. Our results highlight the intrinsic ability of type II Cas1/Cas2 proteins to coordinate directional and site-specific spacer integration into the CRISPR locus to ensure precise duplication of the repeat required for CRISPR immunity.
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Affiliation(s)
- Jenny G Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Yunzhou Wei
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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167
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Safari F, Sharifi M, Farajnia S, Akbari B, Karimi Baba Ahmadi M, Negahdaripour M, Ghasemi Y. The interaction of phages and bacteria: the co-evolutionary arms race. Crit Rev Biotechnol 2019; 40:119-137. [PMID: 31793351 DOI: 10.1080/07388551.2019.1674774] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the dawn of life, bacteria and phages are locked in a constant battle and both are perpetually changing their tactics to overcome each other. Bacteria use various strategies to overcome the invading phages, including adsorption inhibition, restriction-modification (R/E) systems, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, abortive infection (Abi), etc. To counteract, phages employ intelligent tactics for the nullification of bacterial defense systems, such as accessing host receptors, evading R/E systems, and anti-CRISPR proteins. Intense knowledge about the details of these defense pathways is the basis for their broad utilities in various fields of research from microbiology to biotechnology. Hence, in this review, we discuss some strategies used by bacteria to inhibit phage infections as well as phage tactics to circumvent bacterial defense systems. In addition, the application of these strategies will be described as a lesson learned from bacteria and phage combats. The ecological factors that affect the evolution of bacterial immune systems is the other issue represented in this review.
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Affiliation(s)
- Fatemeh Safari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehrdad Sharifi
- Department of Emergency Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, School of Medical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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168
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Almendros C, Nobrega FL, McKenzie RE, Brouns SJJ. Cas4-Cas1 fusions drive efficient PAM selection and control CRISPR adaptation. Nucleic Acids Res 2019; 47:5223-5230. [PMID: 30937444 PMCID: PMC6547450 DOI: 10.1093/nar/gkz217] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/15/2019] [Accepted: 03/28/2019] [Indexed: 12/24/2022] Open
Abstract
Microbes have the unique ability to acquire immunological memories from mobile genetic invaders to protect themselves from predation. To confer CRISPR resistance, new spacers need to be compatible with a targeting requirement in the invader's DNA called the protospacer adjacent motif (PAM). Many CRISPR systems encode Cas4 proteins to ensure new spacers are integrated that meet this targeting prerequisite. Here we report that a gene fusion between cas4 and cas1 from the Geobacter sulfurreducens I-U CRISPR-Cas system is capable of introducing functional spacers carrying interference proficient TTN PAM sequences at much higher frequencies than unfused Cas4 adaptation modules. Mutations of Cas4-domain catalytic residues resulted in dramatically decreased naïve and primed spacer acquisition, and a loss of PAM selectivity showing that the Cas4 domain controls Cas1 activity. We propose the fusion gene evolved to drive the acquisition of only PAM-compatible spacers to optimize CRISPR interference.
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Affiliation(s)
- Cristóbal Almendros
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
| | - Franklin L Nobrega
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
| | - Rebecca E McKenzie
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
| | - Stan J J Brouns
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands.,Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands
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169
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Nethery MA, Henriksen ED, Daughtry KV, Johanningsmeier SD, Barrangou R. Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage. BMC Genomics 2019; 20:902. [PMID: 31775607 PMCID: PMC6881996 DOI: 10.1186/s12864-019-6274-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract Background Lactobacillus buchneri is a lactic acid bacterium frequently associated with food bioprocessing and fermentation and has been found to be either beneficial or detrimental to industrial food processes depending on the application. The ability to metabolize lactic acid into acetic acid and 1,2-propandiol makes L. buchneri invaluable to the ensiling process, however, this metabolic activity leads to spoilage in other applications, and is especially damaging to the cucumber fermentation industry. This study aims to augment our genomic understanding of L. buchneri in order to make better use of the species in a wide range of applicable industrial settings. Results Whole-genome sequencing (WGS) was performed on seven phenotypically diverse strains isolated from spoiled, fermented cucumber and the ATCC type strain for L. buchneri, ATCC 4005. Here, we present our findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes, L. buchneri CD034 and NRRL B-30929. Overall, we see ~ 50% of all coding sequences are conserved across these ten strains. When these coding sequences are clustered by functional description, the strains appear to be enriched in mobile genetic elements, namely transposons. All isolates harbor at least one CRISPR-Cas system, and many contain putative prophage regions, some of which are targeted by the host’s own DNA-encoded spacer sequences. Conclusions Our findings provide new insights into the genomics of L. buchneri through whole genome sequencing and subsequent characterization of genomic features, building a platform for future studies and identifying elements for potential strain manipulation or engineering.
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Affiliation(s)
- Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA.,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | | | - Katheryne V Daughtry
- Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.,United States Department of Agriculture, Agricultural Research Service, Southeast Area, Food Science Research Unit, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC, 27695-7624, USA
| | - Suzanne D Johanningsmeier
- United States Department of Agriculture, Agricultural Research Service, Southeast Area, Food Science Research Unit, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC, 27695-7624, USA
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, USA. .,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
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170
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Barman A, Deb B, Chakraborty S. A glance at genome editing with CRISPR–Cas9 technology. Curr Genet 2019; 66:447-462. [DOI: 10.1007/s00294-019-01040-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/16/2022]
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171
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Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation. Cell Rep 2019; 22:3377-3384. [PMID: 29590607 PMCID: PMC5896167 DOI: 10.1016/j.celrep.2018.02.103] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/25/2018] [Accepted: 02/27/2018] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which the role is unknown. Here, we introduced the CRISPR adaptation genes cas1, cas2, and cas4 from the type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and observed that cas4 is strictly required for the selection of targets with protospacer adjacent motifs (PAMs) conferring I-D CRISPR interference in the native host Synechocystis. We propose a model in which Cas4 assists the CRISPR adaptation complex Cas1-2 by providing DNA substrates tailored for the correct PAM. Introducing functional spacers that target DNA sequences with the correct PAM is key to successful CRISPR interference, providing a better chance of surviving infection by mobile genetic elements. Cas4 facilitates the integration of PAM-compatible spacers Spacer length variation is dictated by Cas1-2 Cas4 shortens spacer length Cas4-selected PAMs license type I-D CRISPR interference
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172
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González-Delgado A, Mestre MR, Martínez-Abarca F, Toro N. Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR-Cas system in Vibrio vulnificus. Nucleic Acids Res 2019. [PMID: 31504832 DOI: 10.1093/nar/gkz746.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The association of reverse transcriptases (RTs) with CRISPR-Cas system has recently attracted interest because the RT activity appears to facilitate the RT-dependent acquisition of spacers from RNA molecules. However, our understanding of this spacer acquisition process remains limited. We characterized the in vivo acquisition of spacers mediated by an RT-Cas1 fusion protein linked to a type III-D system from Vibrio vulnificus strain YJ016, and showed that the adaptation module, consisting of the RT-Cas1 fusion, two different Cas2 proteins (A and B) and one of the two CRISPR arrays, was completely functional in a heterologous host. We found that mutations of the active site of the RT domain significantly decreased the acquisition of new spacers and showed that this RT-Cas1-associated adaptation module was able to incorporate spacers from RNA molecules into the CRISPR array. We demonstrated that the two Cas2 proteins of the adaptation module were required for spacer acquisition. Furthermore, we found that several sequence-specific features were required for the acquisition and integration of spacers derived from any region of the genome, with no bias along the 5'and 3'ends of coding sequences. This study provides new insight into the RT-Cas1 fusion protein-mediated acquisition of spacers from RNA molecules.
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Affiliation(s)
- Alejandro González-Delgado
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Mario Rodríguez Mestre
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Francisco Martínez-Abarca
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
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173
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Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas System. Genes (Basel) 2019; 10:genes10110872. [PMID: 31683605 PMCID: PMC6896009 DOI: 10.3390/genes10110872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Bacteria and archaea use CRISPR-Cas adaptive immunity systems to interfere with viruses, plasmids, and other mobile genetic elements. During the process of adaptation, CRISPR-Cas systems acquire immunity by incorporating short fragments of invaders’ genomes into CRISPR arrays. The acquisition of fragments of host genomes leads to autoimmunity and may drive chromosomal rearrangements, negative cell selection, and influence bacterial evolution. In this study, we investigated the role of proteins involved in genome stability maintenance in spacer acquisition by the Escherichia coli type I-E CRISPR-Cas system targeting its own genome. We show here, that the deletion of recJ decreases adaptation efficiency and affects accuracy of spacers incorporation into CRISPR array. Primed adaptation efficiency is also dramatically inhibited in double mutants lacking recB and sbcD but not in single mutants suggesting independent involvement and redundancy of RecBCD and SbcCD pathways in spacer acquisition. While the presence of at least one of two complexes is crucial for efficient primed adaptation, RecBCD and SbcCD affect the pattern of acquired spacers. Overall, our data suggest distinct roles of the RecBCD and SbcCD complexes and of RecJ in spacer precursor selection and insertion into CRISPR array and highlight the functional interplay between CRISPR-Cas systems and host genome maintenance mechanisms.
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174
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Li Y, Peng N. Endogenous CRISPR-Cas System-Based Genome Editing and Antimicrobials: Review and Prospects. Front Microbiol 2019; 10:2471. [PMID: 31708910 PMCID: PMC6824031 DOI: 10.3389/fmicb.2019.02471] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
CRISPR-Cas systems adapt “memories” via spacers from viruses and plasmids to develop adaptive immunity against mobile genetic elements. Mature CRISPR RNAs guide CRISPR-associated nucleases to site-specifically cleave target DNA or RNA, providing an efficient genome engineering tool for organisms of all three kingdoms. Cas9, Cas12, and Cas13 are single proteins with multiple domains that are the most widely used CRISPR nucleases of the Class 2 system. However, these CRISPR endonucleases are large in size, leading to difficulty for manipulation and toxicity for cells. Most archaeal genomes and half of the bacterial genomes encode different types of CRISPR-Cas systems. Therefore, developing endogenous CRISPR-Cas systems-based genome editing will simplify manipulations and increase editing efficiency in prokaryotic cells. Here, we review the current applications and discuss the prospects of using endogenous CRISPR nucleases for genome engineering and CRISPR-based antimicrobials.
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Affiliation(s)
- Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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175
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Detection of spacer precursors formed in vivo during primed CRISPR adaptation. Nat Commun 2019; 10:4603. [PMID: 31601800 PMCID: PMC6787059 DOI: 10.1038/s41467-019-12417-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/08/2019] [Indexed: 02/03/2023] Open
Abstract
Type I CRISPR-Cas loci provide prokaryotes with a nucleic-acid-based adaptive immunity against foreign DNA. Immunity involves adaptation, the integration of ~30-bp DNA fragments, termed prespacers, into the CRISPR array as spacers, and interference, the targeted degradation of DNA containing a protospacer. Interference-driven DNA degradation can be coupled with primed adaptation, in which spacers are acquired from DNA surrounding the targeted protospacer. Here we develop a method for strand-specific, high-throughput sequencing of DNA fragments, FragSeq, and apply this method to identify DNA fragments accumulated in Escherichia coli cells undergoing robust primed adaptation by a type I-E or type I-F CRISPR-Cas system. The detected fragments have sequences matching spacers acquired during primed adaptation and function as spacer precursors when introduced exogenously into cells by transformation. The identified prespacers contain a characteristic asymmetrical structure that we propose is a key determinant of integration into the CRISPR array in an orientation that confers immunity. Primed adaptation in the CRISPR-Cas system helps recognition of previously encountered sequence elements and promotes the formation of new memories. Here the authors characterized spacer precursors of type I-E and type I-F CRISPR-Cas system using in vivo models.
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176
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Filamentation initiated by Cas2 and its association with the acquisition process in cells. Int J Oral Sci 2019; 11:29. [PMID: 31578319 PMCID: PMC6802651 DOI: 10.1038/s41368-019-0063-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/18/2019] [Accepted: 07/07/2019] [Indexed: 12/15/2022] Open
Abstract
Cas1-and-Cas2-mediated new spacer acquisition is an essential process for bacterial adaptive immunity. The process is critical for the ecology of the oral microflora and oral health. Although molecular mechanisms for spacer acquisition are known, it has never been established if this process is associated with the morphological changes of bacteria. In this study, we demonstrated a novel Cas2-induced filamentation phenotype in E. coli that was regulated by co-expression of the Cas1 protein. A 30 amino acid motif at the carboxyl terminus of Cas2 is necessary for this function. By imaging analysis, we provided evidence to argue that Cas-induced filamentation is a step coupled with new spacer acquisition during which filaments are characterised by polyploidy with asymmetric cell division. This work may open new opportunities to investigate the adaptive immune response and microbial balance for oral health.
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177
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Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, Davidson AR. Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription. Cell 2019; 178:1452-1464.e13. [PMID: 31474367 PMCID: PMC6754177 DOI: 10.1016/j.cell.2019.07.046] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/06/2019] [Accepted: 07/25/2019] [Indexed: 12/26/2022]
Abstract
Phages express anti-CRISPR (Acr) proteins to inhibit CRISPR-Cas systems that would otherwise destroy their genomes. Most acr genes are located adjacent to anti-CRISPR-associated (aca) genes, which encode proteins with a helix-turn-helix DNA-binding motif. The conservation of aca genes has served as a signpost for the identification of acr genes, but the function of the proteins encoded by these genes has not been investigated. Here we reveal that an acr-associated promoter drives high levels of acr transcription immediately after phage DNA injection and that Aca proteins subsequently repress this transcription. Without Aca activity, this strong transcription is lethal to a phage. Our results demonstrate how sufficient levels of Acr proteins accumulate early in the infection process to inhibit existing CRISPR-Cas complexes in the host cell. They also imply that the conserved role of Aca proteins is to mitigate the deleterious effects of strong constitutive transcription from acr promoters.
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Affiliation(s)
- Sabrina Y Stanley
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Adair L Borges
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kuei-Ho Chen
- The J. David Gladstone Institutes, San Francisco, CA 94158 USA
| | - Danielle L Swaney
- The J. David Gladstone Institutes, San Francisco, CA 94158 USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- The J. David Gladstone Institutes, San Francisco, CA 94158 USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alan R Davidson
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.
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178
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Milicevic O, Repac J, Bozic B, Djordjevic M, Djordjevic M. A Simple Criterion for Inferring CRISPR Array Direction. Front Microbiol 2019; 10:2054. [PMID: 31551987 PMCID: PMC6737040 DOI: 10.3389/fmicb.2019.02054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022] Open
Abstract
Inferring transcriptional direction (orientation) of the CRISPR array is essential for many applications, including systematically investigating non-canonical CRISPR/Cas functions. The standard method, CRISPRDirection (embedded within CRISPRCasFinder), fails to predict the orientation (ND predictions) for ∼37% of the classified CRISPR arrays (>2200 loci); this goes up to >70% for the II-B subtype where non-canonical functions were first experimentally discovered. Alternatively, Potential Orientation (also embedded within CRISPRCasFinder), has a much smaller frequency of ND predictions but might have significantly lower accuracy. We propose a novel simple criterion, where the CRISPR array direction is assigned according to the direction of its associated cas genes (Cas Orientation). We systematically assess the performance of the three methods (Cas Orientation, CRISPRDirection, and Potential Orientation) across all CRISPR/Cas subtypes, by a mutual crosscheck of their predictions, and by comparing them to the experimental dataset. Interestingly, CRISPRDirection agrees much better with Cas Orientation than with Potential Orientation, despite CRISPRDirection and Potential Orientation being mutually related – Potential Orientation corresponding to one of six (heterogeneous) predictors employed by CRISPRDirection – and being unrelated to Cas Orientation. We find that Cas Orientation has much higher accuracy compared to Potential Orientation and comparable accuracy to CRISPRDirection – while accurately assigning an orientation to ∼95% of the CRISPR arrays that are non-determined by CRISPRDirection. Cas Orientation is, at the same time, simple to employ, requiring only (routine for prokaryotes) the prediction of the associated protein coding gene direction.
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Affiliation(s)
- Ognjen Milicevic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Multidisciplinary Ph.D. Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Jelena Repac
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
| | - Bojan Bozic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
| | | | - Marko Djordjevic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
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179
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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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180
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Abstract
The prokaryote-derived CRISPR-Cas genome editing systems have transformed our ability to manipulate, detect, image and annotate specific DNA and RNA sequences in living cells of diverse species. The ease of use and robustness of this technology have revolutionized genome editing for research ranging from fundamental science to translational medicine. Initial successes have inspired efforts to discover new systems for targeting and manipulating nucleic acids, including those from Cas9, Cas12, Cascade and Cas13 orthologues. Genome editing by CRISPR-Cas can utilize non-homologous end joining and homology-directed repair for DNA repair, as well as single-base editing enzymes. In addition to targeting DNA, CRISPR-Cas-based RNA-targeting tools are being developed for research, medicine and diagnostics. Nuclease-inactive and RNA-targeting Cas proteins have been fused to a plethora of effector proteins to regulate gene expression, epigenetic modifications and chromatin interactions. Collectively, the new advances are considerably improving our understanding of biological processes and are propelling CRISPR-Cas-based tools towards clinical use in gene and cell therapies.
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Affiliation(s)
- Adrian Pickar-Oliver
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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181
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Lam TJ, Ye Y. Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes. BMC Genomics 2019; 20:567. [PMID: 31288753 PMCID: PMC6617893 DOI: 10.1186/s12864-019-5922-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/21/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sequencing of microbiomes has accelerated the characterization of the diversity of CRISPR-Cas immune systems. However, the utilization of next generation short read sequences for the characterization of CRISPR-Cas dynamics remains limited due to the repetitive nature of CRISPR arrays. CRISPR arrays are comprised of short spacer segments (derived from invaders' genomes) interspaced between flanking repeat sequences. The repetitive structure of CRISPR arrays poses a computational challenge for the accurate assembly of CRISPR arrays from short reads. In this paper we evaluate the use of long read sequences for the analysis of CRISPR-Cas system dynamics in microbiomes. RESULTS We analyzed a dataset of Illumina's TruSeq Synthetic Long-Reads (SLR) derived from a gut microbiome. We showed that long reads captured CRISPR spacers at a high degree of redundancy, which highlights the spacer conservation of spacer sharing CRISPR variants, enabling the study of CRISPR array dynamics in ways difficult to achieve though short read sequences. We introduce compressed spacer graphs, a visual abstraction of spacer sharing CRISPR arrays, to provide a simplified view of complex organizational structures present within CRISPR array dynamics. Utilizing compressed spacer graphs, several key defining characteristics of CRISPR-Cas system dynamics were observed including spacer acquisition and loss events, conservation of the trailer end spacers, and CRISPR arrays' directionality (transcription orientation). Other result highlights include the observation of intense array contraction and expansion events, and reconstruction of a full-length genome for a potential invader (Faecalibacterium phage) based on identified spacers. CONCLUSION We demonstrate in an in silico system that long reads provide the necessary context for characterizing the organization of CRISPR arrays in a microbiome, and reveal dynamic and evolutionary features of CRISPR-Cas systems in a microbial population.
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Affiliation(s)
- Tony J Lam
- School of Informatics, Computing, and Engineering Indiana University, Bloomington, 47408, IN, USA
| | - Yuzhen Ye
- School of Informatics, Computing, and Engineering Indiana University, Bloomington, 47408, IN, USA.
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182
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Radovcic M, Killelea T, Savitskaya E, Wettstein L, Bolt EL, Ivancic-Bace I. CRISPR-Cas adaptation in Escherichia coli requires RecBCD helicase but not nuclease activity, is independent of homologous recombination, and is antagonized by 5' ssDNA exonucleases. Nucleic Acids Res 2019; 46:10173-10183. [PMID: 30189098 PMCID: PMC6212769 DOI: 10.1093/nar/gky799] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/25/2018] [Indexed: 12/29/2022] Open
Abstract
Prokaryotic adaptive immunity is established against mobile genetic elements (MGEs) by ‘naïve adaptation’ when DNA fragments from a newly encountered MGE are integrated into CRISPR–Cas systems. In Escherichia coli, DNA integration catalyzed by Cas1–Cas2 integrase is well understood in mechanistic and structural detail but much less is known about events prior to integration that generate DNA for capture by Cas1–Cas2. Naïve adaptation in E. coli is thought to depend on the DNA helicase-nuclease RecBCD for generating DNA fragments for capture by Cas1–Cas2. The genetics presented here show that naïve adaptation does not require RecBCD nuclease activity but that helicase activity may be important. RecA loading by RecBCD inhibits adaptation explaining previously observed adaptation phenotypes that implicated RecBCD nuclease activity. Genetic analysis of other E. coli nucleases and naïve adaptation revealed that 5′ ssDNA tailed DNA molecules promote new spacer acquisition. We show that purified E. coli Cas1–Cas2 complex binds to and nicks 5′ ssDNA tailed duplexes and propose that E. coli Cas1–Cas2 nuclease activity on such DNA structures supports naïve adaptation.
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Affiliation(s)
- Marin Radovcic
- Department of Biology, Faculty of Science, University of Zagreb, Croatia
| | - Tom Killelea
- School of Life Sciences, University of Nottingham, UK
| | - Ekaterina Savitskaya
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | | | - Edward L Bolt
- School of Life Sciences, University of Nottingham, UK
| | - Ivana Ivancic-Bace
- Department of Biology, Faculty of Science, University of Zagreb, Croatia
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183
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Adaptation processes that build CRISPR immunity: creative destruction, updated. Essays Biochem 2019; 63:227-235. [PMID: 31186288 DOI: 10.1042/ebc20180073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 01/01/2023]
Abstract
Prokaryotes can defend themselves against invading mobile genetic elements (MGEs) by acquiring immune memory against them. The memory is a DNA database located at specific chromosomal sites called CRISPRs (clustered regularly interspaced short palindromic repeats) that store fragments of MGE DNA. These are utilised to target and destroy returning MGEs, preventing re-infection. The effectiveness of CRISPR-based immune defence depends on 'adaptation' reactions that capture and integrate MGE DNA fragments into CRISPRs. This provides the means for immunity to be delivered against MGEs in 'interference' reactions. Adaptation and interference are catalysed by Cas (CRISPR-associated) proteins, aided by enzymes well known for other roles in cells. We survey the molecular biology of CRISPR adaptation, highlighting entirely new developments that may help us to understand how MGE DNA is captured. We focus on processes in Escherichia coli, punctuated with reference to other prokaryotes that illustrate how common requirements for adaptation, DNA capture and integration, can be achieved in different ways. We also comment on how CRISPR adaptation enzymes, and their antecedents, can be utilised for biotechnology.
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184
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Plateau P, Moch C, Blanquet S. Spermidine strongly increases the fidelity of Escherichia coli CRISPR Cas1-Cas2 integrase. J Biol Chem 2019; 294:11311-11322. [PMID: 31171718 DOI: 10.1074/jbc.ra119.007619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/03/2019] [Indexed: 12/20/2022] Open
Abstract
Site-selective CRISPR array expansion at the origin of bacterial adaptive immunity relies on recognition of sequence-dependent DNA structures by the conserved Cas1-Cas2 integrase. Off-target integration of a new spacer sequence outside canonical CRISPR arrays has been described in vitro However, this nonspecific integration activity is rare in vivo Here, we designed gel assays to monitor fluorescently labeled protospacer insertion in a supercoiled 3-kb plasmid harboring a minimal CRISPR locus derived from the Escherichia coli type I-E system. This assay enabled us to distinguish and quantify target and off-target insertion events catalyzed by E. coli Cas1-Cas2 integrase. We show that addition of the ubiquitous polyamine spermidine or of another polyamine, spermine, significantly alters the ratio between target and off-target insertions. Notably, addition of 2 mm spermidine quenched the off-target spacer insertion rate by a factor of 20-fold, and, in the presence of integration host factor, spermidine also increased insertion at the CRISPR locus 1.5-fold. The observation made in our in vitro system that spermidine strongly decreases nonspecific activity of Cas1-Cas2 integrase outside the leader-proximal region of a CRISPR array suggests that this polyamine plays a potential role in the fidelity of the spacer integration also in vivo.
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Affiliation(s)
- Pierre Plateau
- BIOC, CNRS, Ecole polytechnique, IP Paris, F-91128 Palaiseau, France
| | - Clara Moch
- BIOC, CNRS, Ecole polytechnique, IP Paris, F-91128 Palaiseau, France
| | - Sylvain Blanquet
- BIOC, CNRS, Ecole polytechnique, IP Paris, F-91128 Palaiseau, France
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185
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Abstract
Regulatory RNAs, present in many bacterial genomes and particularly in pathogenic bacteria such as Staphylococcus aureus, control the expression of genes encoding virulence factors or metabolic proteins. They are extremely diverse and include noncoding RNAs (sRNA), antisense RNAs, and some 5' or 3' untranslated regions of messenger RNAs that act as sensors for metabolites, tRNAs, or environmental conditions (e.g., temperature, pH). In this review we focus on specific examples of sRNAs of S. aureus that illustrate how numerous sRNAs and associated proteins are embedded in complex networks of regulation. In addition, we discuss the CRISPR-Cas systems defined as an RNA-interference-like mechanism, which also exist in staphylococcal strains.
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186
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Cas4 Nucleases Can Effect Specific Integration of CRISPR Spacers. J Bacteriol 2019; 201:JB.00747-18. [PMID: 30936372 DOI: 10.1128/jb.00747-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/26/2019] [Indexed: 01/19/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems incorporate short DNA fragments from invasive genetic elements into host CRISPR arrays in order to generate host immunity. Recently, we demonstrated that the Csa3a regulator protein triggers CCN protospacer-adjacent motif (PAM)-dependent CRISPR spacer acquisition in the subtype I-A CRISPR-Cas system of Sulfolobus islandicus However, the mechanisms underlying specific protospacer selection and spacer insertion remained unclear. Here, we demonstrate that two Cas4 family proteins (Cas4 and Csa1) have essential roles (i) in recognizing the 5' PAM and 3' nucleotide motif of protospacers and (ii) in determining both the spacer length and its orientation. Furthermore, we identify amino acid residues of the Cas4 proteins that facilitate these functions. Overexpression of the Cas4 and Csa1 proteins, and also that of an archaeal virus-encoded Cas4 protein, resulted in strongly reduced adaptation efficiency, and the former proteins yielded a high incidence of PAM-dependent atypical spacer integration or of PAM-independent spacer integration. We further demonstrated that in plasmid challenge experiments, overexpressed Cas4-mediated defective spacer acquisition in turn potentially enabled targeted DNA to escape subtype I-A CRISPR-Cas interference. In summary, these results define the specific involvement of diverse Cas4 proteins in in vivo CRISPR spacer acquisition. Furthermore, we provide support for an anti-CRISPR role for virus-encoded Cas4 proteins that involves compromising CRISPR-Cas interference activity by hindering spacer acquisition.IMPORTANCE The Cas4 family endonuclease is an essential component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. The Crenarchaeota Sulfolobus islandicus REY15A carries two cas4 genes (cas4 and csa1) linked to the CRISPR arrays. Here, we demonstrate that Cas4 and Csa1 are essential to CRISPR spacer acquisition in this organism. Both proteins specify the upstream and downstream conserved nucleotide motifs of the protospacers and define the spacer length and orientation in the acquisition process. Conserved amino acid residues, in addition to those recently reported, were identified to be important for these functions. More importantly, overexpression of the Sulfolobus viral Cas4 abolished spacer acquisition, providing support for an anti-CRISPR role for virus-encoded Cas4 proteins that inhibit spacer acquisition.
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187
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Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G, Siksnys V, Wigley DB. Structure of the DNA-Bound Spacer Capture Complex of a Type II CRISPR-Cas System. Mol Cell 2019; 75:90-101.e5. [PMID: 31080012 PMCID: PMC6620040 DOI: 10.1016/j.molcel.2019.04.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/08/2019] [Accepted: 04/11/2019] [Indexed: 12/26/2022]
Abstract
CRISPR and associated Cas proteins function as an adaptive immune system in prokaryotes to combat bacteriophage infection. During the immunization step, new spacers are acquired by the CRISPR machinery, but the molecular mechanism of spacer capture remains enigmatic. We show that the Cas9, Cas1, Cas2, and Csn2 proteins of a Streptococcus thermophilus type II-A CRISPR-Cas system form a complex and provide cryoelectron microscopy (cryo-EM) structures of three different assemblies. The predominant form, with the stoichiometry Cas18-Cas24-Csn28, referred to as monomer, contains ∼30 bp duplex DNA bound along a central channel. A minor species, termed a dimer, comprises two monomers that sandwich a further eight Cas1 and four Cas2 subunits and contains two DNA ∼30-bp duplexes within the channel. A filamentous form also comprises Cas18-Cas24-Csn28 units (typically 2-6) but with a different Cas1-Cas2 interface between them and a continuous DNA duplex running along a central channel.
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Affiliation(s)
- Martin Wilkinson
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | | | - Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | | | | | - Dale B Wigley
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
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188
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Fineran PC. Resistance is not futile: bacterial 'innate' and CRISPR-Cas 'adaptive' immune systems. MICROBIOLOGY-SGM 2019; 165:834-841. [PMID: 30958259 DOI: 10.1099/mic.0.000802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria are under a constant pressure from their viruses (phages) and other mobile genetic elements. They protect themselves through a range of defence strategies, which can be broadly classified as 'innate' and 'adaptive'. The bacterial innate immune systems include defences provided by restriction modification and abortive infection, among others. Bacterial adaptive immunity is elicited by a diverse range of CRISPR-Cas systems. Here, I discuss our research on both innate and adaptive phage resistance mechanisms and some of the evasion strategies employed by phages.
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Affiliation(s)
- Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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189
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Musharova O, Sitnik V, Vlot M, Savitskaya E, Datsenko KA, Krivoy A, Fedorov I, Semenova E, Brouns SJJ, Severinov K. Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation. Mol Microbiol 2019; 111:1558-1570. [PMID: 30875129 PMCID: PMC6568314 DOI: 10.1111/mmi.14237] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2019] [Indexed: 01/05/2023]
Abstract
CRISPR interference occurs when a protospacer recognized by the CRISPR RNA is destroyed by Cas effectors. In Type I CRISPR‐Cas systems, protospacer recognition can lead to «primed adaptation» – acquisition of new spacers from in cis located sequences. Type I CRISPR‐Cas systems require the presence of a trinucleotide protospacer adjacent motif (PAM) for efficient interference. Here, we investigated the ability of each of 64 possible trinucleotides located at the PAM position to induce CRISPR interference and primed adaptation by the Escherichia coli Type I‐E CRISPR‐Cas system. We observed clear separation of PAM variants into three groups: those unable to cause interference, those that support rapid interference and those that lead to reduced interference that occurs over extended periods of time. PAM variants unable to support interference also did not support primed adaptation; those that supported rapid interference led to no or low levels of adaptation, while those that caused attenuated levels of interference consistently led to highest levels of adaptation. The results suggest that primed adaptation is fueled by the products of CRISPR interference. Extended over time interference with targets containing «attenuated» PAM variants provides a continuous source of new spacers leading to high overall level of spacer acquisition.
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Affiliation(s)
- Olga Musharova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Vasily Sitnik
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Ekaterina Savitskaya
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, 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
| | - Andrey Krivoy
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Ivan Fedorov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Ekaterina Semenova
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, 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
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190
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Chou-Zheng L, Hatoum-Aslan A. A type III-A CRISPR-Cas system employs degradosome nucleases to ensure robust immunity. eLife 2019; 8:e45393. [PMID: 30942690 PMCID: PMC6447361 DOI: 10.7554/elife.45393] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/15/2019] [Indexed: 12/16/2022] Open
Abstract
CRISPR-Cas systems provide sequence-specific immunity against phages and mobile genetic elements using CRISPR-associated nucleases guided by short CRISPR RNAs (crRNAs). Type III systems exhibit a robust immune response that can lead to the extinction of a phage population, a feat coordinated by a multi-subunit effector complex that destroys invading DNA and RNA. Here, we demonstrate that a model type III system in Staphylococcus epidermidis relies upon the activities of two degradosome-associated nucleases, PNPase and RNase J2, to mount a successful defense. Genetic, molecular, and biochemical analyses reveal that PNPase promotes crRNA maturation, and both nucleases are required for efficient clearance of phage-derived nucleic acids. Furthermore, functional assays show that RNase J2 is essential for immunity against diverse mobile genetic elements originating from plasmid and phage. Altogether, our observations reveal the evolution of a critical collaboration between two nucleic acid degrading machines which ensures cell survival when faced with phage attack.
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Affiliation(s)
- Lucy Chou-Zheng
- Department of Biological SciencesThe University of AlabamaTuscaloosaUnited States
| | - Asma Hatoum-Aslan
- Department of Biological SciencesThe University of AlabamaTuscaloosaUnited States
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191
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The Mycobacterium tuberculosis CRISPR-Associated Cas1 Involves Persistence and Tolerance to Anti-Tubercular Drugs. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7861695. [PMID: 31061828 PMCID: PMC6466960 DOI: 10.1155/2019/7861695] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 11/29/2022]
Abstract
Tuberculosis remains one of the leading causes of death worldwide. Even if new antitubercular drugs are currently being developed, the rapid emergence and spread of drug-resistant strain remain a severe challenge. The CRISPR associated proteins 1 (Cas1), a most conserved endonuclease which is responsible for spacer integration into CRISPR arrays, was found deleted in many specific drug-resistant strains. The function of Cas1 is still unknown in Mycobacterium type III-A CRISPR family. In this study, the Cas1 (Rv2817c) defect was found in 57.14% of clinical isolates. To investigate the function of Cas1 in new spacer acquisition, we challenged Bacillus Calmette–Guérin (BCG) with a mycobacteriophage D29. Newly acquired spacer sequence matches D29 genome was not found by spacer deep-sequencing. We further expressed Cas1 in recombinant Mycobacterium smegmatis. We found that Cas1 increased the sensitivity to multiple anti-tuberculosis drugs by reducing the persistence during drug treatment. We also showed that Cas1 impaired the repair of DNA damage and changed the stress response of Mycobacterium smegmatis. This study provides a further understanding of Cas1 in Mycobacterium tuberculosis complex (MTBC) drug-resistance evolution and a new sight for the tuberculosis treatment.
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192
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Xiao G, Yi Y, Che R, Zhang Q, Imran M, Khan A, Yan J, Lin X. Characterization of CRISPR-Cas systems in Leptospira reveals potential application of CRISPR in genotyping of Leptospira interrogans. APMIS 2019; 127:202-216. [PMID: 30908774 DOI: 10.1111/apm.12935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
Leptospirosis is a zoonotic disease caused by pathogenic Leptospira. However, understanding of the pathogenic mechanism of Leptospira is still elusive due to the limited number of genetic tools available for this microorganism. Currently, the reason for the genetic inaccessibility of Leptospira is still unknown. It is well known that as an acquired immunity of bacteria, Clustered Regularly Interspaced Short Palindromic Repeat-CRISPR-associated gene (CRISPR-Cas) systems can help bacteria against invading mobile genetic elements. In this study, the occurrence and diversity of CRISPR-Cas systems in 41 genomes of Leptospira strains were investigated. Three subtypes (subtype I-B, subtype I-C and subtype I-E) of CRISPR-Cas systems were identified in both pathogenic and intermediate Leptospira species but not in saprophytic species. Noteworthy, the majority of pathogenic species harbor two different types of CRISPR-Cas systems (subtype I-B and subtype I-E). Furthermore, Cas2 protein of subtype I-C in L. interrogans exhibited a metal-dependent DNase activity in a nonspecific manner. CRISPR spacers in subtype I-B are highly conserved within the same serovars and hypervariable across different serovars of L. interrogans. Based on the subtype I-B CRISPR arrays, the serotypes of different L. interrogans strains were easily identified. Investigation of the origin of CRISPR spacers showed that 192 spacers (23.5%) matched to mobile genetic elements, indicating CRISPR-Cas systems may play an important role in the defense of foreign invading DNA.
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Affiliation(s)
- Guohui Xiao
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Yusi Yi
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Rongbo Che
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qinchao Zhang
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Muhammad Imran
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Abidullah Khan
- Department of Burns, School of Medicine, Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jie Yan
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Basic Medical Microbiology Division, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xu'ai Lin
- Department of Medical Microbiology and Parasitology, School of Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Basic Medical Microbiology Division, School of Medicine, Zhejiang University, Hangzhou, China
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193
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Abstract
The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.
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Affiliation(s)
- Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany
| | - Andrés Escalera-Maurer
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Majda Bratovič
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
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194
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McKenzie RE, Almendros C, Vink JNA, Brouns SJJ. Using CAPTURE to detect spacer acquisition in native CRISPR arrays. Nat Protoc 2019; 14:976-990. [PMID: 30742049 PMCID: PMC6831484 DOI: 10.1038/s41596-018-0123-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/20/2018] [Indexed: 11/09/2022]
Abstract
CRISPR-Cas systems are able to acquire immunological memories (spacers) from bacteriophages and plasmids in order to survive infection; however, this often occurs at low frequency within a population, which can make it difficult to detect. Here we describe CAPTURE (CRISPR adaptation PCR technique using reamplification and electrophoresis), a versatile and adaptable protocol to detect spacer-acquisition events by electrophoresis imaging with high-enough sensitivity to identify spacer acquisition in 1 in 105 cells. Our method harnesses two simple PCR steps, separated by automated electrophoresis and extraction of size-selected DNA amplicons, thus allowing the removal of unexpanded arrays from the sample pool and enabling 1,000-times more sensitive detection of new spacers than alternative PCR protocols. CAPTURE is a straightforward method that requires only 1 d to enable the detection of spacer acquisition in all native CRISPR systems and facilitate studies aimed both at unraveling the mechanism of spacer integration and more sensitive tracing of integration events in natural ecosystems.
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Affiliation(s)
- Rebecca E McKenzie
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Cristóbal Almendros
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Jochem N A Vink
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands.
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195
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van Sluijs L, van Houte S, van der Oost J, Brouns SJJ, Buckling A, Westra ER. Addiction systems antagonize bacterial adaptive immunity. FEMS Microbiol Lett 2019; 366:fnz047. [PMID: 30834930 PMCID: PMC6478593 DOI: 10.1093/femsle/fnz047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/04/2019] [Indexed: 02/06/2023] Open
Abstract
CRISPR-Cas systems provide adaptive immunity against mobile genetic elements, but employment of this resistance mechanism is often reported with a fitness cost for the host. Whether or not CRISPR-Cas systems are important barriers for the horizontal spread of conjugative plasmids, which play a crucial role in the spread of antibiotic resistance, will depend on the fitness costs of employing CRISPR-based defences and the benefits of resisting conjugative plasmids. To estimate these costs and benefits we measured bacterial fitness associated with plasmid immunity using Escherichia coli and the conjugative plasmid pOX38-Cm. We find that CRISPR-mediated immunity fails to confer a fitness benefit in the absence of antibiotics, despite the large fitness cost associated with carrying the plasmid in this context. Similar to many other conjugative plasmids, pOX38-Cm carries a CcdAB toxin-anti-toxin (TA) addiction system. These addiction systems encode long-lived toxins and short-lived anti-toxins, resulting in toxic effects following the loss of the TA genes from the bacterial host. Our data suggest that the lack of a fitness benefit associated with CRISPR-mediated defence is due to expression of the TA system before plasmid detection and degradation. As most antibiotic resistance plasmids encode TA systems this could have important consequences for the role of CRISPR-Cas systems in limiting the spread of antibiotic resistance.
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Affiliation(s)
- Lisa van Sluijs
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Stineke van Houte
- Environment and Sustainability Institute, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Stan JJ Brouns
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
| | - Edze R Westra
- Environment and Sustainability Institute, University of Exeter, Penryn campus, Penryn, TR10 9FE, UK
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196
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Wan H, Li J, Chang S, Lin S, Tian Y, Tian X, Wang M, Hu J. Probing the Behaviour of Cas1-Cas2 upon Protospacer Binding in CRISPR-Cas Systems using Molecular Dynamics Simulations. Sci Rep 2019; 9:3188. [PMID: 30816277 PMCID: PMC6395717 DOI: 10.1038/s41598-019-39616-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
Adaptation in CRISPR-Cas systems enables the generation of an immunological memory to defend against invading viruses. This process is driven by foreign DNA spacer (termed protospacer) selection and integration mediated by Cas1-Cas2 protein. Recently, different states of Cas1-Cas2, in its free form and in complex with protospacer DNAs, were solved by X-ray crystallography. In this paper, molecular dynamics (MD) simulations are employed to study crystal structures of one free and two protospacer-bound Cas1-Cas2 complexes. The simulated results indicate that the protospacer binding markedly increases the system stability, in particular when the protospacer containing the PAM-complementary sequence. The hydrogen bond and binding free energy calculations explain that PAM recognition introduces more specific interactions to increase the cleavage activity of Cas1. By using principal component analysis (PCA) and intramolecular angle calculation, this study observes two dominant slow motions associated with the binding of Ca1-Cas2 to the protospacer and potential target DNAs respectively. The comparison of DNA structural deformation further implies a cooperative conformational change of Cas1-Cas2 and protospacer for the target DNA capture. We propose that this cooperativity is the intrinsic requirement of the CRISPR integration complex formation. This study provides some new insights into the understanding of CRISPR-Cas adaptation.
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Affiliation(s)
- Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Jianming Li
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Shuoxin Lin
- Department of Electrical and Computer Engineering, James Clark School of Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Yuanxin Tian
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xuhong Tian
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Meihua Wang
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, 610106, China.
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197
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Loureiro A, da Silva GJ. CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool. Antibiotics (Basel) 2019; 8:E18. [PMID: 30823430 PMCID: PMC6466564 DOI: 10.3390/antibiotics8010018] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/14/2019] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Bacteriophages are pervasive viruses that infect bacteria, relying on their genetic machinery to replicate. In order to protect themselves from this kind of invader, bacteria developed an ingenious adaptive defence system, clustered regularly interspaced short palindromic repeats (CRISPR). Researchers soon realised that a specific type of CRISPR system, CRISPR-Cas9, could be modified into a simple and efficient genetic engineering technology, with several improvements over currently used systems. This discovery set in motion a revolution in genetics, with new and improved CRISPR systems being used in plenty of in vitro and in vivo experiments in recent years. This review illustrates the mechanisms behind CRISPR-Cas systems as a means of bacterial immunity against phage invasion and how these systems were engineered to originate new genetic manipulation tools. Newfound CRISPR-Cas technologies and the up-and-coming applications of these systems on healthcare and other fields of science are also discussed.
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Affiliation(s)
- Alexandre Loureiro
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Health Sciences Campus, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal.
| | - Gabriela Jorge da Silva
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Health Sciences Campus, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal.
- Center for Neurosciences Cell Biology, University of Coimbra, 3000-548 Coimbra, Portugal.
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198
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Endogenous Gene Regulation as a Predicted Main Function of Type I-E CRISPR/Cas System in E. coli. Molecules 2019; 24:molecules24040784. [PMID: 30795631 PMCID: PMC6413058 DOI: 10.3390/molecules24040784] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 11/16/2022] Open
Abstract
CRISPR/Cas is an adaptive bacterial immune system, whose CRISPR array can actively change in response to viral infections. However, Type I-E CRISPR/Cas in E. coli (an established model system), appears not to exhibit such active adaptation, which suggests that it might have functions other than immune response. Through computational analysis, we address the involvement of the system in non-canonical functions. To assess targets of CRISPR spacers, we align them against both E. coli genome and an exhaustive (~230) set of E. coli viruses. We systematically investigate the obtained alignments, such as hit distribution with respect to genome annotation, propensity to target mRNA, the target functional enrichment, conservation of CRISPR spacers and putative targets in related bacterial genomes. We find that CRISPR spacers have a statistically highly significant tendency to target i) host compared to phage genomes, ii) one of the two DNA strands, iii) genomic dsDNA rather than mRNA, iv) transcriptionally active regions, and v) sequences (cis-regulatory elements) with slower turn-over rate compared to CRISPR spacers (trans-factors). The results suggest that the Type I-E CRISPR/Cas system has a major role in transcription regulation of endogenous genes, with a potential to rapidly rewire these regulatory interactions, with targets being selected through naïve adaptation.
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199
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Wright AV, Wang JY, Burstein D, Harrington LB, Paez-Espino D, Kyrpides NC, Iavarone AT, Banfield JF, Doudna JA. A Functional Mini-Integrase in a Two-Protein-type V-C CRISPR System. Mol Cell 2019; 73:727-737.e3. [PMID: 30709710 PMCID: PMC6386590 DOI: 10.1016/j.molcel.2018.12.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/21/2018] [Accepted: 12/14/2018] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas immunity requires integration of short, foreign DNA fragments into the host genome at the CRISPR locus, a site consisting of alternating repeat sequences and foreign-derived spacers. In most CRISPR systems, the proteins Cas1 and Cas2 form the integration complex and are both essential for DNA acquisition. Most type V-C and V-D systems lack the cas2 gene and have unusually short CRISPR repeats and spacers. Here, we show that a mini-integrase comprising the type V-C Cas1 protein alone catalyzes DNA integration with a preference for short (17- to 19-base-pair) DNA fragments. The mini-integrase has weak specificity for the CRISPR array. We present evidence that the Cas1 proteins form a tetramer for integration. Our findings support a model of a minimal integrase with an internal ruler mechanism that favors shorter repeats and spacers. This minimal integrase may represent the function of the ancestral Cas1 prior to Cas2 adoption.
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Affiliation(s)
- Addison V Wright
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David Burstein
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Anthony T Iavarone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA.
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200
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McDonald ND, Regmi A, Morreale DP, Borowski JD, Boyd EF. CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species. BMC Genomics 2019; 20:105. [PMID: 30717668 PMCID: PMC6360697 DOI: 10.1186/s12864-019-5439-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
Background Bacteria are prey for many viruses that hijack the bacterial cell in order to propagate, which can result in bacterial cell lysis and death. Bacteria have developed diverse strategies to counteract virus predation, one of which is the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated (Cas) proteins immune defense system. Species within the bacterial family Vibrionaceae are marine organisms that encounter large numbers of phages. Our goal was to determine the significance of CRISPR-Cas systems as a mechanism of defense in this group by investigating their prevalence, phylogenetic distribution, and genome context. Results Herein, we describe all the CRISPR-Cas system types and their distribution within the family Vibrionaceae. In Vibrio cholerae genomes, we identified multiple variant type I-F systems, which were also present in 41 additional species. In a large number of Vibrio species, we identified a mini type I-F system comprised of tniQcas5cas7cas6f, which was always associated with Tn7-like transposons. The Tn7-like elements, in addition to the CRISPR-Cas system, also contained additional cargo genes such as restriction modification systems and type three secretion systems. A putative hybrid CRISPR-Cas system was identified containing type III-B genes followed by a type I-F cas6f and a type I-F CRISPR that was associated with a prophage in V. cholerae and V. metoecus strains. Our analysis identified CRISPR-Cas types I-C, I-E, I-F, II-B, III-A, III-B, III-D, and the rare type IV systems as well as cas loci architectural variants among 70 species. All systems described contained a CRISPR array that ranged in size from 3 to 179 spacers. The systems identified were present predominantly within mobile genetic elements (MGEs) such as genomic islands, plasmids, and transposon-like elements. Phylogenetic analysis of Cas proteins indicated that the CRISPR-Cas systems were acquired by horizontal gene transfer. Conclusions Our data show that CRISPR-Cas systems are phylogenetically widespread but sporadic in occurrence, actively evolving, and present on MGEs within Vibrionaceae. Electronic supplementary material The online version of this article (10.1186/s12864-019-5439-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathan D McDonald
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA
| | - Abish Regmi
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA
| | - Daniel P Morreale
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA
| | - Joseph D Borowski
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA
| | - E Fidelma Boyd
- Department of Biological Sciences, University of Delaware, 328 Wolf Hall, Newark, DE, 19716, USA.
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