1
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Mishra G, Srivastava K, Rais J, Dixit M, Kumari Singh V, Chandra Mishra L. CRISPR-Cas9: A Potent Gene-editing Tool for the Treatment of Cancer. Curr Mol Med 2024; 24:191-204. [PMID: 36788695 DOI: 10.2174/1566524023666230213094308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 02/16/2023]
Abstract
The prokaryotic adaptive immune system has clustered regularly interspaced short palindromic repeat. CRISPR-associated protein (CRISPR-Cas) genome editing systems have been harnessed. A robust programmed technique for efficient and accurate genome editing and gene targeting has been developed. Engineered cell therapy, in vivo gene therapy, animal modeling, and cancer diagnosis and treatment are all possible applications of this ground-breaking approach. Multiple genetic and epigenetic changes in cancer cells induce malignant cell growth and provide chemoresistance. The capacity to repair or ablate such mutations has enormous potential in the fight against cancer. The CRISPR-Cas9 genome editing method has recently become popular in cancer treatment research due to its excellent efficiency and accuracy. The preceding study has shown therapeutic potential in expanding our anticancer treatments by using CRISPR-Cas9 to directly target cancer cell genomic DNA in cellular and animal cancer models. In addition, CRISPR-Cas9 can combat oncogenic infections and test anticancer medicines. It may design immune cells and oncolytic viruses for cancer immunotherapeutic applications. In this review, these preclinical CRISPRCas9- based cancer therapeutic techniques are summarised, along with the hurdles and advancements in converting therapeutic CRISPR-Cas9 into clinical use. It will increase their applicability in cancer research.
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Affiliation(s)
- Gauri Mishra
- Department of Zoology, Swami Shraddhanand College, University of Delhi-110036, Delhi, India
- Division Radiopharmaceuticals and Radiation Biology, Institute of Nuclear Medicine and Allied Sciences, Brig SK Mazumdar Road, Delhi-110054, India
| | - Kamakshi Srivastava
- Department of Zoology, Swami Shraddhanand College, University of Delhi-110036, Delhi, India
| | - Juhi Rais
- Department of Nuclear Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow-226014, India
| | - Manish Dixit
- Department of Nuclear Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow-226014, India
| | - Vandana Kumari Singh
- Department of Zoology, Hansraj College, University of Delhi- 110007, Dehli, India
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2
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Oh GS, An S, Kim S. Harnessing CRISPR-Cas adaptation for RNA recording and beyond. BMB Rep 2024; 57:40-49. [PMID: 38053290 PMCID: PMC10828431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 12/07/2023] Open
Abstract
Prokaryotes encode clustered regularly interspaced short palindromic repeat (CRISPR) arrays and CRISPR-associated (Cas) genes as an adaptive immune machinery. CRISPR-Cas systems effectively protect hosts from the invasion of foreign enemies, such as bacteriophages and plasmids. During a process called 'adaptation', non-self-nucleic acid fragments are acquired as spacers between repeats in the host CRISPR array, to establish immunological memory. The highly conserved Cas1-Cas2 complexes function as molecular recorders to integrate spacers in a time course manner, which can subsequently be expressed as crRNAs complexed with Cas effector proteins for the RNAguided interference pathways. In some of the RNA-targeting type III systems, Cas1 proteins are fused with reverse transcriptase (RT), indicating that RT-Cas1-Cas2 complexes can acquire RNA transcripts for spacer acquisition. In this review, we summarize current studies that focus on the molecular structure and function of the RT-fused Cas1-Cas2 integrase, and its potential applications as a directional RNA-recording tool in cells. Furthermore, we highlight outstanding questions for RT-Cas1-Cas2 studies and future directions for RNA-recording CRISPR technologies. [BMB Reports 2024; 57(1): 40-49].
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Affiliation(s)
- Gyeong-Seok Oh
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Seongjin An
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Sungchul Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
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3
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Santiago-Frangos A, Henriques WS, Wiegand T, Gauvin CC, Buyukyoruk M, Graham AB, Wilkinson RA, Triem L, Neselu K, Eng ET, Lander GC, Wiedenheft B. Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays. Nat Struct Mol Biol 2023; 30:1675-1685. [PMID: 37710013 PMCID: PMC10872659 DOI: 10.1038/s41594-023-01097-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023]
Abstract
Bacteria and archaea acquire resistance to viruses and plasmids by integrating fragments of foreign DNA into the first repeat of a CRISPR array. However, the mechanism of site-specific integration remains poorly understood. Here, we determine a 560-kDa integration complex structure that explains how Pseudomonas aeruginosa Cas (Cas1-Cas2/3) and non-Cas proteins (for example, integration host factor) fold 150 base pairs of host DNA into a U-shaped bend and a loop that protrude from Cas1-2/3 at right angles. The U-shaped bend traps foreign DNA on one face of the Cas1-2/3 integrase, while the loop places the first CRISPR repeat in the Cas1 active site. Both Cas3 proteins rotate 100 degrees to expose DNA-binding sites on either side of the Cas2 homodimer, which each bind an inverted repeat motif in the leader. Leader sequence motifs direct Cas1-2/3-mediated integration to diverse repeat sequences that have a 5'-GT. Collectively, this work reveals new DNA-binding surfaces on Cas2 that are critical for DNA folding and site-specific delivery of foreign DNA.
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Affiliation(s)
| | - William S Henriques
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Colin C Gauvin
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Murat Buyukyoruk
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Ava B Graham
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Royce A Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Lenny Triem
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Kasahun Neselu
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY, USA
| | - Edward T Eng
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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4
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Tang D, Jia T, Luo Y, Mou B, Cheng J, Qi S, Yao S, Su Z, Yu Y, Chen Q. DnaQ mediates directional spacer acquisition in the CRISPR-Cas system by a time-dependent mechanism. Innovation (N Y) 2023; 4:100495. [PMID: 37663930 PMCID: PMC10470216 DOI: 10.1016/j.xinn.2023.100495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/06/2023] [Indexed: 09/05/2023] Open
Abstract
In the spacer acquisition stage of CRISPR-Cas immunity, spacer orientation and protospacer adjacent motif (PAM) removal are two prerequisites for functional spacer integration. Cas4 has been implicated in both processing the prespacer and determining the spacer orientation. In Cas4-lacking systems, host 3'-5' DnaQ family exonucleases were recently reported to play a Cas4-like role. However, the molecular details of DnaQ functions remain elusive. Here, we characterized the spacer acquisition of the adaptation module of the Streptococcus thermophilus type I-E system, in which a DnaQ domain naturally fuses with Cas2. We presented X-ray crystal structures and cryo-electron microscopy structures of this adaptation module. Our biochemical data showed that DnaQ trimmed PAM-containing and PAM-deficient overhangs with different efficiencies. Based on these results, we proposed a time-dependent model for DnaQ-mediated spacer acquisition to elucidate PAM removal and spacer orientation determination in Cas4-lacking CRISPR-Cas systems.
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Affiliation(s)
- Dongmei Tang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tingting Jia
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yongbo Luo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Biqin Mou
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Cheng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shaohua Yao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhaoming Su
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yamei Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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5
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Dhingra Y, Sashital DG. Cas4/1 dual nuclease activities enable prespacer maturation and directional integration in a type I-G CRISPR-Cas system. J Biol Chem 2023; 299:105178. [PMID: 37607619 PMCID: PMC10504553 DOI: 10.1016/j.jbc.2023.105178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023] Open
Abstract
CRISPR-Cas adaptive immune systems uptake short "spacer" sequences from foreign DNA and incorporate them into the host genome to serve as templates for CRISPR RNAs that guide interference against future infections. Adaptation in CRISPR systems is mediated by Cas1-Cas2 complexes that catalyze integration of prespacer substrates into the CRISPR array. Many DNA targeting systems also require Cas4 endonucleases for functional spacer acquisition. Cas4 selects prespacers containing a protospacer adjacent motif (PAM) and removes the PAM prior to integration, both of which are required to ensure host immunization. Cas1 has also been shown to function as a nuclease in some systems, but a role for this nuclease activity in adaptation has not been demonstrated. We identified a type I-G Cas4/1 fusion with a nucleolytically active Cas1 domain that can directly participate in prespacer processing. The Cas1 domain is both an integrase and a sequence-independent nuclease that cleaves the non-PAM end of a prespacer, generating optimal overhang lengths that enable integration at the leader side. The Cas4 domain sequence specifically cleaves the PAM end of the prespacer, ensuring integration of the PAM end at the spacer side. The two domains have varying metal ion requirements. While Cas4 activity is Mn2+ dependent, Cas1 preferentially uses Mg2+ over Mn2+. The dual nuclease activity of Cas4/1 eliminates the need for additional factors in prespacer processing making the adaptation module self-reliant for prespacer maturation and directional integration.
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Affiliation(s)
- Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, Iowa, USA.
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6
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Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA. Genome expansion by a CRISPR trimmer-integrase. Nature 2023:10.1038/s41586-023-06178-2. [PMID: 37316664 DOI: 10.1038/s41586-023-06178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/08/2023] [Indexed: 06/16/2023]
Abstract
CRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity1. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1-Cas2 integrase is necessary but not sufficient2-5. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation6,7, but many CRISPR-Cas systems lack Cas48. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1-Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited9,10 exonucleases for faithful acquisition of new CRISPR immune sequences.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Owen T Tuck
- Department of Chemistry, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Gary Li
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Basem Al-Shayeb
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Julia Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, CA, USA.
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7
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Dhingra Y, Sashital DG. Cas4/1 dual nuclease activities enable prespacer maturation and directional integration in a type I-G CRISPR-Cas system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543779. [PMID: 37333257 PMCID: PMC10274657 DOI: 10.1101/2023.06.05.543779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
CRISPR-Cas adaptive immune systems uptake short 'spacer' sequences from foreign DNA and incorporate them into the host genome to serve as templates for crRNAs that guide interference against future infections. Adaptation in CRISPR systems is mediated by Cas1-Cas2 complexes that catalyze integration of prespacer substrates into the CRISPR array. Many DNA targeting systems also require Cas4 endonucleases for functional spacer acquisition. Cas4 selects prespacers containing a protospacer adjacent motif (PAM) and removes the PAM prior to integration, both of which are required to ensure host immunization. Cas1 has also been shown to function as a nuclease in some systems, but a role for this nuclease activity in adaptation has not been demonstrated. We identified a type I-G Cas4/1 fusion with a nucleolytically active Cas1 domain that can directly participate in prespacer processing. The Cas1 domain is both an integrase and a sequence-independent nuclease that cleaves the non-PAM end of a prespacer, generating optimal overhang lengths that enable integration at the leader side. The Cas4 domain sequence-specifically cleaves the PAM end of the prespacer, ensuring integration of the PAM end at the spacer side. The two domains have varying metal ion requirements. While Cas4 activity is Mn 2+ dependent, Cas1 preferentially uses Mg 2+ over Mn 2+ . The dual nuclease activity of Cas4/1 eliminates the need for additional factors in prespacer processing, making the adaptation module self-reliant for prespacer maturation and directional integration.
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Affiliation(s)
- Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Dipali G. Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA
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8
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McBride TM, Cameron SC, Fineran PC, Fagerlund RD. The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems. Biochem J 2023; 480:471-488. [PMID: 37052300 DOI: 10.1042/bcj20220073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 04/14/2023]
Abstract
Prokaryotes have adaptive defence mechanisms that protect them from mobile genetic elements and viral infection. One defence mechanism is called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins). There are six different types of CRISPR-Cas systems and multiple subtypes that vary in composition and mode of action. Type I and III CRISPR-Cas systems utilise multi-protein complexes, which differ in structure, nucleic acid binding and cleaving preference. The type I-D system is a chimera of type I and III systems. Recently, there has been a burst of research on the type I-D CRISPR-Cas system. Here, we review the mechanism, evolution and biotechnological applications of the type I-D CRISPR-Cas system.
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Affiliation(s)
- Tess M McBride
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Shaharn C Cameron
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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9
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CRISPR-Cas adaptation in Escherichia coli. Biosci Rep 2023; 43:232582. [PMID: 36809461 PMCID: PMC10011333 DOI: 10.1042/bsr20221198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/23/2023] Open
Abstract
Prokaryotes use the adaptive immunity mediated via the Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated (CRISPR-Cas) system for protection against invading elements such as phages and plasmids. The immunity is achieved by capturing small DNA fragments or spacers from foreign nucleic acids (protospacers) and integrating them into the host CRISPR locus. This step of CRISPR-Cas immunity called 'naïve CRISPR adaptation' requires the conserved Cas1-Cas2 complex and is often supported by variable host proteins that assist in spacer processing and integration. Bacteria that have acquired new spacers become immune to the same invading elements when reinfected. CRISPR-Cas immunity can also be updated by integrating new spacers from the same invading elements, a process called 'primed adaptation'. Only properly selected and integrated spacers are functional in the next steps of CRISPR immunity when their processed transcripts are used for RNA-guided target recognition and interference (target degradation). Capturing, trimming, and integrating new spacers in the correct orientation are universal steps of adaptation to all CRISPR-Cas systems, but some details are CRISPR-Cas type-specific and species-specific. In this review, we provide an overview of the mechanisms of CRISPR-Cas class 1 type I-E adaptation in Escherichia coli as a general model for adaptation processes (DNA capture and integration) that have been studied in detail. We focus on the role of host non-Cas proteins involved in adaptation, particularly on the role of homologous recombination.
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10
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Shiriaeva AA, Kuznedelov K, Fedorov I, Musharova O, Khvostikov T, Tsoy Y, Kurilovich E, Smith GR, Semenova E, Severinov K. Host nucleases generate prespacers for primed adaptation in the E. coli type I-E CRISPR-Cas system. SCIENCE ADVANCES 2022; 8:eabn8650. [PMID: 36427302 PMCID: PMC9699676 DOI: 10.1126/sciadv.abn8650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acids. In Escherichia coli, immunity is acquired upon integration of 33-bp spacers into CRISPR arrays. DNA targets complementary to spacers get degraded and serve as a source of new spacers during a process called primed adaptation. Precursors of such spacers, prespacers, are ~33-bp double-stranded DNA fragments with a ~4-nt 3' overhang. The mechanism of prespacer generation is not clear. Here, we use FragSeq and biochemical approaches to determine enzymes involved in generation of defined prespacer ends. We demonstrate that RecJ is the main exonuclease trimming 5' ends of prespacer precursors, although its activity can be partially substituted by ExoVII. The RecBCD complex allows single strand-specific RecJ to process double-stranded regions flanking prespacers. Our results reveal intricate functional interactions of genome maintenance proteins with CRISPR interference and adaptation machineries during generation of prespacers capable of integration into CRISPR arrays.
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Affiliation(s)
- Anna A. Shiriaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Saint Petersburg State University, Saint Petersburg 199034, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Kuznedelov
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ivan Fedorov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Institute of Gene Biology, Russian Academy of Science, Moscow 119334, Russia
| | - Olga Musharova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow 123182, Russia
| | - Timofey Khvostikov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Yuliya Tsoy
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Elena Kurilovich
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Gerald R. Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ekaterina Semenova
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Severinov
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
- Institute of Molecular Genetics, National Research Center Kurchatov Institute, Moscow 123182, Russia
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11
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Dhingra Y, Suresh SK, Juneja P, Sashital DG. PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation. Mol Cell 2022; 82:4353-4367.e6. [PMID: 36272411 PMCID: PMC9675710 DOI: 10.1016/j.molcel.2022.09.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/10/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Adaptation in CRISPR-Cas systems immunizes bacteria and archaea against mobile genetic elements. In many DNA-targeting systems, the Cas4-Cas1-Cas2 complex is required for selection and processing of DNA segments containing PAM sequences prior to integration of these "prespacer" substrates as spacers in the CRISPR array. We determined cryo-EM structures of the Cas4-Cas1-Cas2 adaptation complex from the type I-C system that encodes standalone Cas1 and Cas4 proteins. The structures reveal how Cas4 specifically reads out bases within the PAM sequence and how interactions with both Cas1 and Cas2 activate Cas4 endonuclease activity. The Cas4-PAM interaction ensures tight binding between the adaptation complex and the prespacer, significantly enhancing integration of the non-PAM end into the CRISPR array and ensuring correct spacer orientation. Corroborated with our biochemical results, Cas4-Cas1-Cas2 structures with substrates representing various stages of CRISPR adaptation reveal a temporally resolved mechanism for maturation and integration of functional spacers into the CRISPR array.
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Affiliation(s)
- Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Shravanti K Suresh
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA
| | - Puneet Juneja
- Cryo-EM Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, & Molecular Biology, Iowa State University, Ames, IA, USA.
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12
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Wang JY, Pausch P, Doudna JA. Structural biology of CRISPR-Cas immunity and genome editing enzymes. Nat Rev Microbiol 2022; 20:641-656. [PMID: 35562427 DOI: 10.1038/s41579-022-00739-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2022] [Indexed: 12/20/2022]
Abstract
CRISPR-Cas systems provide resistance against foreign mobile genetic elements and have a wide range of genome editing and biotechnological applications. In this Review, we examine recent advances in understanding the molecular structures and mechanisms of enzymes comprising bacterial RNA-guided CRISPR-Cas immune systems and deployed for wide-ranging genome editing applications. We explore the adaptive and interference aspects of CRISPR-Cas function as well as open questions about the molecular mechanisms responsible for genome targeting. These structural insights reflect close evolutionary links between CRISPR-Cas systems and mobile genetic elements, including the origins and evolution of CRISPR-Cas systems from DNA transposons, retrotransposons and toxin-antitoxin modules. We discuss how the evolution and structural diversity of CRISPR-Cas systems explain their functional complexity and utility as genome editing tools.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick Pausch
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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13
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Cui N, Faure G, Singh A, Macrae R, Zhang F. Microfluidic Enrichment and Computational Analysis of Rare Sequences from Mixed Genomic Samples for Metagenomic Mining. CRISPR J 2022; 5:677-684. [PMID: 36206017 PMCID: PMC9595627 DOI: 10.1089/crispr.2022.0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Many powerful molecular biology tools have their origins in natural systems, including restriction modification enzymes and the CRISPR effectors, Cas9, Cas12, and Cas13. Heightened interest in these systems has led to mining of genomic and metagenomic data to identify new orthologs of these proteins, new types of CRISPR systems, and uncharacterized natural systems with novel mechanisms. To accelerate metagenomic mining, we developed a high-throughput, low-cost droplet microfluidic-based method for enrichment of rare sequences in a mixed starting population. Using a computational pipeline, we then searched in the enriched data for the presence of CRISPR-Cas systems, identifying a previously unknown CRISPR-Cas system. Our approach enables researchers to efficiently mine metagenomic samples for sequences of interest, greatly accelerating the search for nature's treasures.
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Affiliation(s)
- Naiwen Cui
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guihem Faure
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ankita Singh
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rhiannon Macrae
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Address correspondence to: Feng Zhang, PhD, Broad Institute of MIT and Harvard, 75 Ames St. Cambridge, MA 02142, USA,
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14
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Recording gene expression order in DNA by CRISPR addition of retron barcodes. Nature 2022; 608:217-225. [PMID: 35896746 PMCID: PMC9357182 DOI: 10.1038/s41586-022-04994-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 06/17/2022] [Indexed: 02/03/2023]
Abstract
Biological processes depend on the differential expression of genes over time, but methods to make physical recordings of these processes are limited. Here we report a molecular system for making time-ordered recordings of transcriptional events into living genomes. We do this through engineered RNA barcodes, based on prokaryotic retrons1, that are reverse transcribed into DNA and integrated into the genome using the CRISPR-Cas system2. The unidirectional integration of barcodes by CRISPR integrases enables reconstruction of transcriptional event timing based on a physical record through simple, logical rules rather than relying on pretrained classifiers or post hoc inferential methods. For disambiguation in the field, we will refer to this system as a Retro-Cascorder.
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15
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A truncated anti-CRISPR protein prevents spacer acquisition but not interference. Nat Commun 2022; 13:2802. [PMID: 35589712 PMCID: PMC9120153 DOI: 10.1038/s41467-022-30310-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/26/2022] [Indexed: 11/15/2022] Open
Abstract
CRISPR-Cas systems in prokaryotic cells provide an adaptive immunity against invading nucleic acids. For example, phage infection leads to addition of new immunity (spacer acquisition) and DNA cleavage (interference) in the bacterial model species Streptococcus thermophilus, which primarily relies on Cas9-containing CRISPR-Cas systems. Phages can counteract this defense system through mutations in the targeted protospacers or by encoding anti-CRISPR proteins (ACRs) that block Cas9 interference activity. Here, we show that S. thermophilus can block ACR-containing phages when the CRISPR immunity specifically targets the acr gene. This in turn selects for phage mutants carrying a deletion within the acr gene. Remarkably, a truncated acrIIA allele, found in a wild-type virulent streptococcal phage, does not block the interference activity of Cas9 but still prevents the acquisition of new immunities, thereby providing an example of an ACR specifically inhibiting spacer acquisition. Phages can use ACR proteins that inhibit the adaptive immunity activities of bacterial CRISPR-Cas systems. Here, Philippe et al. show that these systems can block ACR-containing phages by targeting the acr gene, and this can select for phage mutants carrying a deletion within acr that does not block DNA cleavage (interference) but prevents the addition of new immunity (spacer acquisition).
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16
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McKenzie RE, Keizer EM, Vink JNA, van Lopik J, Büke F, Kalkman V, Fleck C, Tans SJ, Brouns SJJ. Single cell variability of CRISPR-Cas interference and adaptation. Mol Syst Biol 2022; 18:e10680. [PMID: 35467080 PMCID: PMC10561596 DOI: 10.15252/msb.202110680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/26/2022] Open
Abstract
While CRISPR-Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time-lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we found large cell-to-cell variability, which originates from primed CRISPR adaptation. Faster growth and cell division and higher levels of Cascade increase the chance of clearance by interference, while slower growth is associated with increased chances of clearance by priming. Our findings suggest that Cascade binding to the mutated invader DNA, rather than spacer integration, is the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond quickly to invading threats. We conjecture that CRISPR-Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.
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Affiliation(s)
- Rebecca E McKenzie
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Emma M Keizer
- Biometris, Department of Mathematical and Statistical MethodsWageningen UniversityWageningenThe Netherlands
| | - Jochem N A Vink
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Jasper van Lopik
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Ferhat Büke
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Vera Kalkman
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Christian Fleck
- Freiburg Center for Data Analysis and Modeling (FDM)Spatial Systems Biology GroupUniversity of FreiburgFreiburgGermany
| | - Sander J Tans
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Stan J J Brouns
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
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17
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Lee H, Sashital DG. Creating memories: molecular mechanisms of CRISPR adaptation. Trends Biochem Sci 2022; 47:464-476. [DOI: 10.1016/j.tibs.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/22/2022]
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18
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Aviram N, Thornal AN, Zeevi D, Marraffini LA. Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system. Nucleic Acids Res 2022; 50:1661-1672. [PMID: 35048966 PMCID: PMC8860600 DOI: 10.1093/nar/gkab1299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas systems provide prokaryotic organisms with an adaptive defense mechanism that acquires immunological memories of infections. This is accomplished by integration of short fragments from the genome of invaders such as phages and plasmids, called ‘spacers’, into the CRISPR locus of the host. Depending on their genetic composition, CRISPR-Cas systems can be classified into six types, I-VI, however spacer acquisition has been extensively studied only in type I and II systems. Here, we used an inducible spacer acquisition assay to study this process in the type III-A CRISPR-Cas system of Staphylococcus epidermidis, in the absence of phage selection. Similarly to type I and II spacer acquisition, this type III system uses Cas1 and Cas2 to preferentially integrate spacers from the chromosomal terminus and free dsDNA ends produced after DNA breaks, in a manner that is enhanced by the AddAB DNA repair complex. Surprisingly, a different mode of spacer acquisition from rRNA and tRNA loci, which spans only the transcribed sequences of these genes and is not enhanced by AddAB, was also detected. Therefore, our findings reveal both common mechanistic principles that may be conserved in all CRISPR-Cas systems, as well as unique and intriguing features of type III spacer acquisition.
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Affiliation(s)
- Naama Aviram
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Ashley N Thornal
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - David Zeevi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Luciano A Marraffini
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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19
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Mechanism for Cas4-assisted directional spacer acquisition in CRISPR-Cas. Nature 2021; 598:515-520. [PMID: 34588691 PMCID: PMC9164213 DOI: 10.1038/s41586-021-03951-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/25/2021] [Indexed: 02/08/2023]
Abstract
Prokaryotes adapt to challenges from mobile genetic elements by integrating spacers derived from foreign DNA in the CRISPR array1. Spacer insertion is carried out by the Cas1-Cas2 integrase complex2-4. A substantial fraction of CRISPR-Cas systems use a Fe-S cluster containing Cas4 nuclease to ensure that spacers are acquired from DNA flanked by a protospacer adjacent motif (PAM)5,6 and inserted into the CRISPR array unidirectionally, so that the transcribed CRISPR RNA can guide target searching in a PAM-dependent manner. Here we provide a high-resolution mechanistic explanation for the Cas4-assisted PAM selection, spacer biogenesis and directional integration by type I-G CRISPR in Geobacter sulfurreducens, in which Cas4 is naturally fused with Cas1, forming Cas4/Cas1. During biogenesis, only DNA duplexes possessing a PAM-embedded 3'-overhang trigger Cas4/Cas1-Cas2 assembly. During this process, the PAM overhang is specifically recognized and sequestered, but is not cleaved by Cas4. This 'molecular constipation' prevents the PAM-side prespacer from participating in integration. Lacking such sequestration, the non-PAM overhang is trimmed by host nucleases and integrated to the leader-side CRISPR repeat. Half-integration subsequently triggers PAM cleavage and Cas4 dissociation, allowing spacer-side integration. Overall, the intricate molecular interaction between Cas4 and Cas1-Cas2 selects PAM-containing prespacers for integration and couples the timing of PAM processing with the stepwise integration to establish directionality.
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20
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Guzmán NM, Esquerra-Ruvira B, Mojica FJM. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021; 24:473-498. [PMID: 34487299 PMCID: PMC8616872 DOI: 10.1007/s10123-021-00208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.
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Affiliation(s)
- Noemí M Guzmán
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Belén Esquerra-Ruvira
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain. .,Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain.
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21
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Ma CH, Javanmardi K, Finkelstein IJ, Jayaram M. Disintegration promotes protospacer integration by the Cas1-Cas2 complex. eLife 2021; 10:65763. [PMID: 34435949 PMCID: PMC8390005 DOI: 10.7554/elife.65763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/11/2021] [Indexed: 12/16/2022] Open
Abstract
‘Disintegration’—the reversal of transposon DNA integration at a target site—is regarded as an abortive off-pathway reaction. Here, we challenge this view with a biochemical investigation of the mechanism of protospacer insertion, which is mechanistically analogous to DNA transposition, by the Streptococcus pyogenes Cas1-Cas2 complex. In supercoiled target sites, the predominant outcome is the disintegration of one-ended insertions that fail to complete the second integration event. In linear target sites, one-ended insertions far outnumber complete protospacer insertions. The second insertion event is most often accompanied by the disintegration of the first, mediated either by the 3′-hydroxyl exposed during integration or by water. One-ended integration intermediates may mature into complete spacer insertions via DNA repair pathways that are also involved in transposon mobility. We propose that disintegration-promoted integration is functionally important in the adaptive phase of CRISPR-mediated bacterial immunity, and perhaps in other analogous transposition reactions.
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Affiliation(s)
- Chien-Hui Ma
- Department of Molecular Biosciences and Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, United States
| | - Kamyab Javanmardi
- Department of Molecular Biosciences and Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, United States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, United States.,Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, United States
| | - Makkuni Jayaram
- Department of Molecular Biosciences and Institute of Cell and Molecular Biology, University of Texas at Austin, Austin, United States
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22
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Santiago-Frangos A, Buyukyoruk M, Wiegand T, Krishna P, Wiedenheft B. Distribution and phasing of sequence motifs that facilitate CRISPR adaptation. Curr Biol 2021; 31:3515-3524.e6. [PMID: 34174210 PMCID: PMC8552246 DOI: 10.1016/j.cub.2021.05.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/30/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022]
Abstract
CRISPR-associated proteins (Cas1 and Cas2) integrate foreign DNA at the "leader" end of CRISPR loci. Several CRISPR leader sequences are reported to contain a binding site for a DNA-bending protein called integration host factor (IHF). IHF-induced DNA bending kinks the leader of type I-E CRISPRs, recruiting an upstream sequence motif that helps dock Cas1-2 onto the first repeat of the CRISPR locus. To determine the prevalence of IHF-directed CRISPR adaptation, we analyzed 15,274 bacterial and archaeal CRISPR leaders. These experiments reveal multiple IHF binding sites and diverse upstream sequence motifs in a subset of the I-C, I-E, I-F, and II-C CRISPR leaders. We identify subtype-specific motifs and show that the phase of these motifs is critical for CRISPR adaptation. Collectively, this work clarifies the prevalence and mechanism(s) of IHF-dependent CRISPR adaptation and suggests that leader sequences and adaptation proteins may coevolve under the selective pressures of foreign genetic elements like plasmids or phages.
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Affiliation(s)
| | - Murat Buyukyoruk
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Pushya Krishna
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
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23
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Kieper SN, Almendros C, Haagsma AC, Barendregt A, Heck AJR, Brouns SJJ. Cas4-Cas1 Is a Protospacer Adjacent Motif-Processing Factor Mediating Half-Site Spacer Integration During CRISPR Adaptation. CRISPR J 2021; 4:536-548. [PMID: 34406043 DOI: 10.1089/crispr.2021.0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The immunization of bacteria and archaea against invading viruses via CRISPR adaptation is critically reliant on the efficient capture, accurate processing, and integration of CRISPR spacers into the host genome. The adaptation proteins Cas1 and Cas2 are sufficient for successful spacer acquisition in some CRISPR-Cas systems. However, many CRISPR-Cas systems additionally require the Cas4 protein for efficient adaptation. Cas4 has been implied in the selection and processing of spacer precursors, but the detailed mechanistic understanding of how Cas4 contributes to CRISPR adaptation is lacking. Here, we biochemically reconstitute the CRISPR-Cas type I-D adaptation system and show two functionally distinct adaptation complexes: Cas4-Cas1 and Cas1-Cas2. The Cas4-Cas1 complex recognizes and cleaves protospacer adjacent motif (PAM) sequences in 3' overhangs in a sequence-specific manner, while the Cas1-Cas2 complex defines the cleavage of non-PAM sites via host-factor nucleases. Both sub-complexes are capable of mediating half-site integration, facilitating the integration of processed spacers in the correct interference-proficient orientation. We provide a model in which an asymmetric adaptation complex differentially acts on PAM- and non-PAM-containing overhangs, providing cues for the correct orientation of spacer integration.
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Affiliation(s)
- Sebastian N Kieper
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands; Utrecht, Netherlands.,Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands; Utrecht, Netherlands
| | - Cristóbal Almendros
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands; Utrecht, Netherlands.,Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands; Utrecht, Netherlands
| | - Anna C Haagsma
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands; Utrecht, Netherlands.,Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands; Utrecht, Netherlands
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; and Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; and Utrecht, Netherlands.,Netherlands Proteomics Center, Utrecht, Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands; Utrecht, Netherlands.,Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands; Utrecht, Netherlands
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24
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Long C, Dai L, E C, Da LT, Yu J. Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2. Biophys J 2021; 120:3126-3137. [PMID: 34197800 PMCID: PMC8390960 DOI: 10.1016/j.bpj.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/10/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cas1 and Cas2 are highly conserved proteins across clustered-regularly-interspaced-short-palindromic-repeat-Cas systems and play a significant role in protospacer acquisition. Based on crystal structure of twofold symmetric Cas1-Cas2 in complex with dual-forked protospacer DNA (psDNA), we conducted all-atom molecular dynamics simulations to study the psDNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence, or PAMc, of Cas1-Cas2. In the simulation, we noticed that two active sites of Cas1 and Cas1’ bind asymmetrically to two identical PAMc on the psDNA captured from the crystal structure. For the modified psDNA containing only one PAMc, as that to be recognized by Cas1-Cas2 in general, our simulations show that the non-PAMc association site of Cas1-Cas2 remains destabilized until after the stably bound PAMc being cleaved at the corresponding association site. Thus, long-range correlation appears to exist upon the PAMc cleavage between the two active sites (∼10 nm apart) on Cas1-Cas2, which can be allosterically mediated by psDNA and Cas2 and Cas2’ in bridging. To substantiate such findings, we conducted repeated runs and further simulated Cas1-Cas2 in complex with synthesized psDNA sequences psL and psH, which have been measured with low and high frequency in acquisition, respectively. Notably, such intersite correlation becomes even more pronounced for the Cas1-Cas2 in complex with psH but remains low for the Cas1-Cas2 in complex with psL. Hence, our studies demonstrate that PAMc recognition and cleavage at one active site of Cas1-Cas2 may allosterically regulate non-PAMc association or even cleavage at the other site, and such regulation can be mediated by noncatalytic Cas2 and DNA protospacer to possibly support the ensued psDNA acquisition.
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Affiliation(s)
- Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Liqiang Dai
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China; Beijing Computational Science Research Center, Beijing, China
| | - Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai, China
| | - Jin Yu
- Departments of Physics and Astronomy and Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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25
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Zabrady K, Zabrady M, Kolesar P, Li AWH, Doherty AJ. CRISPR-Associated Primase-Polymerases are implicated in prokaryotic CRISPR-Cas adaptation. Nat Commun 2021; 12:3690. [PMID: 34140468 PMCID: PMC8211822 DOI: 10.1038/s41467-021-23535-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/04/2021] [Indexed: 12/24/2022] Open
Abstract
CRISPR-Cas pathways provide prokaryotes with acquired “immunity” against foreign genetic elements, including phages and plasmids. Although many of the proteins associated with CRISPR-Cas mechanisms are characterized, some requisite enzymes remain elusive. Genetic studies have implicated host DNA polymerases in some CRISPR-Cas systems but CRISPR-specific replicases have not yet been discovered. We have identified and characterised a family of CRISPR-Associated Primase-Polymerases (CAPPs) in a range of prokaryotes that are operonically associated with Cas1 and Cas2. CAPPs belong to the Primase-Polymerase (Prim-Pol) superfamily of replicases that operate in various DNA repair and replication pathways that maintain genome stability. Here, we characterise the DNA synthesis activities of bacterial CAPP homologues from Type IIIA and IIIB CRISPR-Cas systems and establish that they possess a range of replicase activities including DNA priming, polymerisation and strand-displacement. We demonstrate that CAPPs operonically-associated partners, Cas1 and Cas2, form a complex that possesses spacer integration activity. We show that CAPPs physically associate with the Cas proteins to form bespoke CRISPR-Cas complexes. Finally, we propose how CAPPs activities, in conjunction with their partners, may function to undertake key roles in CRISPR-Cas adaptation. CAPPs are putative Primase-Polymerases associated with CRISPR-Cas operons. Here, the authors show CAPPs genetic and physical association with Cas1 and Cas2, their capacity to function as DNA-dependent DNA primases and DNA polymerases, and that Cas1-Cas2 complex adjacent to CAPP has bona fide spacer integration activity.
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Affiliation(s)
- Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Matej Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Peter Kolesar
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Arthur W H Li
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
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26
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Prespacers formed during primed adaptation associate with the Cas1-Cas2 adaptation complex and the Cas3 interference nuclease-helicase. Proc Natl Acad Sci U S A 2021; 118:2021291118. [PMID: 34035168 PMCID: PMC8179228 DOI: 10.1073/pnas.2021291118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Primed adaptation allows rapid acquisition of protective spacers derived from foreign mobile genetic elements into CRISPR arrays of the host. Primed adaptation requires ongoing CRISPR interference that destroys foreign genetic elements, but the nature of this requirement is unknown. Using the Escherichia coli I-E CRISPR-Cas as a model, we show that prespacers, short fragments of foreign DNA on their way to become incorporated into CRISPR arrays as spacers, are associated with both the adaptation integrase Cas1 and the interference nuclease Cas3, implying physical association of the interference and adaptation machineries during priming. For Type I CRISPR-Cas systems, a mode of CRISPR adaptation named priming has been described. Priming allows specific and highly efficient acquisition of new spacers from DNA recognized (primed) by the Cascade-crRNA (CRISPR RNA) effector complex. Recognition of the priming protospacer by Cascade-crRNA serves as a signal for engaging the Cas3 nuclease–helicase required for both interference and primed adaptation, suggesting the existence of a primed adaptation complex (PAC) containing the Cas1–Cas2 adaptation integrase and Cas3. To detect this complex in vivo, we here performed chromatin immunoprecipitation with Cas3-specific and Cas1-specific antibodies using cells undergoing primed adaptation. We found that prespacers are bound by both Cas1 (presumably, as part of the Cas1–Cas2 integrase) and Cas3, implying direct physical association of the interference and adaptation machineries as part of PAC.
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27
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Jakhanwal S, Cress BF, Maguin P, Lobba MJ, Marraffini LA, Doudna JA. A CRISPR-Cas9-integrase complex generates precise DNA fragments for genome integration. Nucleic Acids Res 2021; 49:3546-3556. [PMID: 33693715 PMCID: PMC8034620 DOI: 10.1093/nar/gkab123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2021] [Accepted: 02/26/2021] [Indexed: 01/24/2023] Open
Abstract
CRISPR-Cas9 is an RNA-guided DNA endonuclease involved in bacterial adaptive immunity and widely repurposed for genome editing in human cells, animals and plants. In bacteria, RNA molecules that guide Cas9's activity derive from foreign DNA fragments that are captured and integrated into the host CRISPR genomic locus by the Cas1-Cas2 CRISPR integrase. How cells generate the specific lengths of DNA required for integrase capture is a central unanswered question of type II-A CRISPR-based adaptive immunity. Here, we show that an integrase supercomplex comprising guide RNA and the proteins Cas1, Cas2, Csn2 and Cas9 generates precisely trimmed 30-base pair DNA molecules required for genome integration. The HNH active site of Cas9 catalyzes exonucleolytic DNA trimming by a mechanism that is independent of the guide RNA sequence. These results show that Cas9 possesses a distinct catalytic capacity for generating immunological memory in prokaryotes.
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Affiliation(s)
- Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brady F Cress
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Pascal Maguin
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Marco J Lobba
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
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28
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Philippe C, Moineau S. The endless battle between phages and CRISPR-Cas systems in Streptococcus thermophilus. Biochem Cell Biol 2021; 99:397-402. [PMID: 33534660 DOI: 10.1139/bcb-2020-0593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This review describes the contribution of basic research on phage-bacteria interactions to the understanding of CRISPR-Cas systems and their various applications. It focuses on the natural function of CRISPR-Cas systems as adaptive defense mechanisms against mobile genetic elements such as bacteriophage genomes and plasmids. Some of the advances in the characterization of the type II-A CRISPR-Cas system of Streptococcus thermophilus and Streptococcus pyogenes led to the development of the CRISPR-Cas9 genome-editing technology. We mostly discuss the 3 stages of the CRISPR-Cas system in S. thermophilus, namely the adaptation stage, which is unique to this resistance mechanism; the CRISPR RNA biogenesis; and the DNA-cutting activity in the interference stage to protect bacteria against phages. Finally, we look into applications of CRISPR-Cas in microbiology, including overcoming limitations in genome editing.
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Affiliation(s)
- Cécile Philippe
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, QC G1V 0A6, Canada
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29
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Abstract
Prokaryotes have developed numerous defense strategies to combat the constant threat posed by the diverse genetic parasites that endanger them. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas loci guard their hosts with an adaptive immune system against foreign nucleic acids. Protection starts with an immunization phase, in which short pieces of the invader's genome, known as spacers, are captured and integrated into the CRISPR locus after infection. Next, during the targeting phase, spacers are transcribed into CRISPR RNAs (crRNAs) that guide CRISPR-associated (Cas) nucleases to destroy the invader's DNA or RNA. Here we describe the many different molecular mechanisms of CRISPR targeting and how they are interconnected with the immunization phase through a third phase of the CRISPR-Cas immune response: primed spacer acquisition. In this phase, Cas proteins direct the crRNA-guided acquisition of additional spacers to achieve a more rapid and robust immunization of the population.
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Affiliation(s)
- Philip M. Nussenzweig
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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30
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Li H, Cui X, Sun L, Deng X, Liu S, Zou X, Li B, Wang C, Wang Y, Liu Y, Lu B, Cao B. High concentration of Cas12a effector tolerates more mismatches on ssDNA. FASEB J 2020; 35:e21153. [PMID: 33159392 DOI: 10.1096/fj.202001475r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/26/2022]
Abstract
Rapid pathogen detection is critical for prompt treatment, interrupting transmission routes, and decreasing morbidity and mortality. The V-type CRISPR system had been used for rapid pathogen detection. However, whether single-stranded DNA in CRISPR system can cause false positives remains undetermined. Herein, we show that high molar concentration of Cas12a effector tolerated more mismatches on ssDNA and activated its trans-cleavage activity at six base matches. Reducing Cas12a and crRNA molar concentration increased the minimal base-match number required for Cas12a ssDNA activation to 11, which reducing nonspecific activation. We then established a Cas12a-based M tuberculosis detection system with a primer having an 8 bp overlap with crRNA. This system did not exhibit primer-induced false positives, and minimum detection copy reached 1 copy/uL (inputting 1-μL sample) in standard strains. The Cas12a-based M tuberculosis detection system showed 80.0% sensitivity and 100.0% specificity in verification using clinical specimens, compared with Xpert MTB/RIF, which showed 72.0% sensitivity and 90.9% specificity. All these results prove that appropriate concentration of cas12a effector can effectively perform nucleic acid detection.
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Affiliation(s)
- Haibo Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Xiaojing Cui
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Lingxiao Sun
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Xiaoyan Deng
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Clinical Center for Pulmonary Infections, Capital Medical University, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, P. R. China
| | - Shuai Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China.,Clinical Center for Pulmonary Infections, Capital Medical University, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, P. R. China
| | - Xiaohui Zou
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Binbin Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Chunlei Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Yeming Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China.,Clinical Center for Pulmonary Infections, Capital Medical University, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, P. R. China
| | - Yinmei Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Binghuai Lu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China
| | - Bin Cao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Centre for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, P. R. China.,Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, P. R. China.,National Clinical Research Center for Respiratory Diseases, Capital Medical University, Beijing, P. R. China.,Clinical Center for Pulmonary Infections, Capital Medical University, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, P. R. China
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31
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Wiegand T, Semenova E, Shiriaeva A, Fedorov I, Datsenko K, Severinov K, Wiedenheft B. Reproducible Antigen Recognition by the Type I-F CRISPR-Cas System. CRISPR J 2020; 3:378-387. [PMID: 33095052 PMCID: PMC7580607 DOI: 10.1089/crispr.2020.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CRISPR-associated proteins 1 and 2 (Cas1-2) are necessary and sufficient for new spacer acquisition in some CRISPR-Cas systems (e.g., type I-E), but adaptation in other systems (e.g., type II-A) involves the crRNA-guided surveillance complex. Here we show that the type I-F Cas1-2/3 proteins are necessary and sufficient to produce low levels of spacer acquisition, but the presence of the type I-F crRNA-guided surveillance complex (Csy) improves the efficiency of adaptation and significantly increases the fidelity of protospacer adjacent motif selection. Sequences selected for integration are preferentially derived from specific regions of extrachromosomal DNA, and patterns of spacer selection are highly reproducible between independent biological replicates. This work helps define the role of the Csy complex in I-F adaptation and reveals that actively replicating mobile genetic elements have antigenic signatures that facilitate their integration during CRISPR adaptation.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA; Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
| | - Anna Shiriaeva
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Microbiology, Peter the Great St. Petersburg Polytechnic University, Saint-Petersburg, Russia; Russian Academy of Sciences, Moscow, Russia
| | - Ivan Fedorov
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
| | - Kirill Datsenko
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia; and Russian Academy of Sciences, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA; Russian Academy of Sciences, Moscow, Russia
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32
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Histone-like Nucleoid-Structuring Protein (H-NS) Paralogue StpA Activates the Type I-E CRISPR-Cas System against Natural Transformation in Escherichia coli. Appl Environ Microbiol 2020; 86:AEM.00731-20. [PMID: 32385085 DOI: 10.1128/aem.00731-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Working mechanisms of CRISPR-Cas systems have been intensively studied. However, far less is known about how they are regulated. The histone-like nucleoid-structuring protein H-NS binds the promoter of cas genes (P cas ) and suppresses the type I-E CRISPR-Cas system in Escherichia coli Although the H-NS paralogue StpA also binds P cas , its role in regulating the CRISPR-Cas system remains unidentified. Our previous work established that E. coli is able to take up double-stranded DNA during natural transformation. Here, we investigated the function of StpA in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli We first documented that although the activated type I-E CRISPR-Cas system, due to hns deletion, interfered with CRISPR-Cas-targeted plasmid transfer, stpA inactivation restored the level of natural transformation. Second, we showed that inactivating stpA reduced the transcriptional activity of P cas Third, by comparing transcriptional activities of the intact P cas and the P cas with a disrupted H-NS binding site in the hns and hns stpA null deletion mutants, we demonstrated that StpA activated transcription of cas genes by binding to the same site as H-NS in P cas Fourth, by expressing StpA with an arabinose-inducible promoter, we confirmed that StpA expressed at a low level stimulated the activity of P cas Finally, by quantifying the level of mature CRISPR RNA (crRNA), we demonstrated that StpA was able to promote the amount of crRNA. Taken together, our work establishes that StpA serves as a transcriptional activator in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli IMPORTANCE StpA is normally considered a molecular backup of the nucleoid-structuring protein H-NS, which was reported as a transcriptional repressor of the type I-E CRISPR-Cas system in Escherichia coli However, the role of StpA in regulating the type I-E CRISPR-Cas system remains elusive. Our previous work uncovered a new route for double-stranded DNA (dsDNA) entry during natural transformation of E. coli In this study, we show that StpA plays a role opposite to that of its paralogue H-NS in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli Our work not only expands our knowledge on CRISPR-Cas-mediated adaptive immunity against extracellular nucleic acids but also sheds new light on understanding the complex regulation mechanism of the CRISPR-Cas system. Moreover, the finding that paralogues StpA and H-NS share a DNA binding site but play opposite roles in transcriptional regulation indicates that higher-order compaction of bacterial chromatin by histone-like proteins could switch prokaryotic transcriptional modes.
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33
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Abstract
CRISPR research began over 30 years ago with the incidental discovery of an unusual nucleotide arrangement in the Escherichia coli genome. It took 20 years to find the main function of CRISPR-Cas systems as an adaptive defence mechanism against invading nucleic acids, and our knowledge of their biology has steadily increased ever since. In parallel, the number of applications derived from CRISPR-Cas systems has risen spectacularly. The CRISPR-based genome editing tool is arguably the most exciting application in both basic and applied research. Lately, CRISPR-Cas research has partially shifted to the least understood aspect of its biology: the ability of CRISPR-Cas systems to acquire new immunities during the so-called adaptation step. To date, the most efficient natural system to readily acquire new spacers is the type II-A system of the gram-positive dairy bacterium Streptococcus thermophilus. The discovery of additional systems able to acquire new spacers will hopefully draw more attention to this step of CRISPR-Cas biology. This review focuses on the breakthroughs that have helped to unravel the adaptation phase and on questions that remain to be answered.
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Affiliation(s)
- Cas Mosterd
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, QC G1V 0A6, Canada
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34
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Real-time observation of CRISPR spacer acquisition by Cas1-Cas2 integrase. Nat Struct Mol Biol 2020; 27:489-499. [PMID: 32367067 PMCID: PMC7241818 DOI: 10.1038/s41594-020-0415-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/16/2020] [Indexed: 01/13/2023]
Abstract
Cas1 integrase associates with Cas2 to insert short DNA fragments into a CRISPR array, establishing nucleic acid memory in prokaryotes. Here we applied single-molecule FRET methods to the Enterococcus faecalis (Efa) Cas1–Cas2 system to establish a kinetic framework describing target-searching, integration, and post-synapsis events. EfaCas1–Cas2 on its own is not able to find the CRISPR repeat in the CRISPR array; it only does so after prespacer loading. The leader sequence adjacent to the repeat further stabilizes EfaCas1–Cas2 contacts, enabling leader-side integration and subsequent spacer-side integration. The resulting post-synaptic complex has a surprisingly short mean lifetime. Remarkably, transcription efficiently resolves the postsynaptic complex and we predict that this is a conserved mechanism that ensures efficient and directional spacer integration in many CRISPR systems. Overall, our study provides a complete model of spacer acquisition, which can be harnessed for DNA-based information storage and cell lineage tracing technologies.
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35
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Dhingra Y, Sashital DG. Updating the CRISPR Catalogue. CRISPR J 2020; 3:78-80. [PMID: 32315221 DOI: 10.1089/crispr.2020.29088.ydh] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yukti Dhingra
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, USA
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