1
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Bigelyte G, Duchovska B, Zedaveinyte R, Sasnauskas G, Sinkunas T, Dalgediene I, Tamulaitiene G, Silanskas A, Kazlauskas D, Valančauskas L, Madariaga-Marcos J, Seidel R, Siksnys V, Karvelis T. Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing. Nucleic Acids Res 2024; 52:3234-3248. [PMID: 38261981 PMCID: PMC11013384 DOI: 10.1093/nar/gkae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/20/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024] Open
Abstract
Cas9 and Cas12 nucleases of class 2 CRISPR-Cas systems provide immunity in prokaryotes through RNA-guided cleavage of foreign DNA. Here we characterize a set of compact CRISPR-Cas12m (subtype V-M) effector proteins and show that they provide protection against bacteriophages and plasmids through the targeted DNA binding rather than DNA cleavage. Biochemical assays suggest that Cas12m effectors can act as roadblocks inhibiting DNA transcription and/or replication, thereby triggering interference against invaders. Cryo-EM structure of Gordonia otitidis (Go) Cas12m ternary complex provided here reveals the structural mechanism of DNA binding ensuring interference. Harnessing GoCas12m innate ability to bind DNA target we fused it with adenine deaminase TadA-8e and showed an efficient A-to-G editing in Escherichia coli and human cells. Overall, this study expands our understanding of the functionally diverse Cas12 protein family, revealing DNA-binding dependent interference mechanism of Cas12m effectors that could be harnessed for engineering of compact base-editing tools.
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Affiliation(s)
- Greta Bigelyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Brigita Duchovska
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Rimante Zedaveinyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Indre Dalgediene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Lukas Valančauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Julene Madariaga-Marcos
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
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2
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Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O. An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis. Cell 2023; 186:4920-4935.e23. [PMID: 37776859 DOI: 10.1016/j.cell.2023.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/27/2023] [Accepted: 08/23/2023] [Indexed: 10/02/2023]
Abstract
SpCas9 and AsCas12a are widely utilized as genome-editing tools in human cells. However, their relatively large size poses a limitation for delivery by cargo-size-limited adeno-associated virus (AAV) vectors. The type V-F Cas12f from Acidibacillus sulfuroxidans is exceptionally compact (422 amino acids) and has been harnessed as a compact genome-editing tool. Here, we developed an approach, combining deep mutational scanning and structure-informed design, to successfully generate two AsCas12f activity-enhanced (enAsCas12f) variants. Remarkably, the enAsCas12f variants exhibited genome-editing activities in human cells comparable with those of SpCas9 and AsCas12a. The cryoelectron microscopy (cryo-EM) structures revealed that the mutations stabilize the dimer formation and reinforce interactions with nucleic acids to enhance their DNA cleavage activities. Moreover, enAsCas12f packaged with partner genes in an all-in-one AAV vector exhibited efficient knock-in/knock-out activities and transcriptional activation in mice. Taken together, enAsCas12f variants could offer a minimal genome-editing platform for in vivo gene therapy.
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Affiliation(s)
- Tomohiro Hino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Satoshi N Omura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryoya Nakagawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Tomoki Togashi
- Department of Biochemistry, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan; Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, Ishikawa 920-0942, Japan
| | - Satoru N Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takafumi Hiramoto
- Department of Biochemistry, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan
| | - Satoshi Tasaka
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hisato Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takeshi Tokuyama
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Hideki Uosaki
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Tochigi 329-0498, Japan
| | - Soh Ishiguro
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC V6S 0L4, Canada
| | - Madina Kagieva
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC V6S 0L4, Canada
| | - Hiroyuki Yamano
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yuki Ozaki
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideto Mori
- Institute for Advanced Biosciences, Keio University, Yamagata 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; Curreio, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuzuru Itoh
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Nozomu Yachie
- School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC V6S 0L4, Canada; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, 565-0871, Japan; Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tsukasa Ohmori
- Department of Biochemistry, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan; Center for Gene Therapy Research, Jichi Medical University, Tochigi 329-0498, Japan.
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
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3
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Karvelis T, Siksnys V. Fanzors: Mysterious TnpB-Like Bacterial Transposon-Related RNA-Guided DNA Nucleases of Eukaryotes. CRISPR J 2023; 6:310-312. [PMID: 37594268 DOI: 10.1089/crispr.2023.29164.tka] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Affiliation(s)
- Tautvydas Karvelis
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Department of Protein - DNA Interactions, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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4
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Sasnauskas G, Tamulaitiene G, Druteika G, Carabias A, Silanskas A, Kazlauskas D, Venclovas Č, Montoya G, Karvelis T, Siksnys V. TnpB structure reveals minimal functional core of Cas12 nuclease family. Nature 2023; 616:384-389. [PMID: 37020015 DOI: 10.1038/s41586-023-05826-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/10/2023] [Indexed: 04/07/2023]
Abstract
The widespread TnpB proteins of IS200/IS605 transposon family have recently emerged as the smallest RNA-guided nucleases capable of targeted genome editing in eukaryotic cells1,2. Bioinformatic analysis identified TnpB proteins as the likely predecessors of Cas12 nucleases3-5, which along with Cas9 are widely used for targeted genome manipulation. Whereas Cas12 family nucleases are well characterized both biochemically and structurally6, the molecular mechanism of TnpB remains unknown. Here we present the cryogenic-electron microscopy structures of the Deinococcus radiodurans TnpB-reRNA (right-end transposon element-derived RNA) complex in DNA-bound and -free forms. The structures reveal the basic architecture of TnpB nuclease and the molecular mechanism for DNA target recognition and cleavage that is supported by biochemical experiments. Collectively, these results demonstrate that TnpB represents the minimal structural and functional core of the Cas12 protein family and provide a framework for developing TnpB-based genome editing tools.
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Affiliation(s)
- Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gytis Druteika
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Arturo Carabias
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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5
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Henkel-Heinecke S, Bigelyte G, Karvelis T, Siksnys V, Seidel R. Dynamics of R-loop formation by CRISPR-Cas12f1 effector complexes. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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6
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Karvelis T, Druteika G, Bigelyte G, Budre K, Zedaveinyte R, Silanskas A, Kazlauskas D, Venclovas Č, Siksnys V. Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease. Nature 2021; 599:692-696. [PMID: 34619744 PMCID: PMC8612924 DOI: 10.1038/s41586-021-04058-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023]
Abstract
Transposition has a key role in reshaping genomes of all living organisms1. Insertion sequences of IS200/IS605 and IS607 families2 are among the simplest mobile genetic elements and contain only the genes that are required for their transposition and its regulation. These elements encode tnpA transposase, which is essential for mobilization, and often carry an accessory tnpB gene, which is dispensable for transposition. Although the role of TnpA in transposon mobilization of IS200/IS605 is well documented, the function of TnpB has remained largely unknown. It had been suggested that TnpB has a role in the regulation of transposition, although no mechanism for this has been established3-5. A bioinformatic analysis indicated that TnpB might be a predecessor of the CRISPR-Cas9/Cas12 nucleases6-8. However, no biochemical activities have been ascribed to TnpB. Here we show that TnpB of Deinococcus radiodurans ISDra2 is an RNA-directed nuclease that is guided by an RNA, derived from the right-end element of a transposon, to cleave DNA next to the 5'-TTGAT transposon-associated motif. We also show that TnpB could be reprogrammed to cleave DNA target sites in human cells. Together, this study expands our understanding of transposition mechanisms by highlighting the role of TnpB in transposition, experimentally confirms that TnpB is a functional progenitor of CRISPR-Cas nucleases and establishes TnpB as a prototype of a new system for genome editing.
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Affiliation(s)
- Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Gytis Druteika
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Greta Bigelyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Karolina Budre
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rimante Zedaveinyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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7
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Bigelyte G, Young JK, Karvelis T, Budre K, Zedaveinyte R, Djukanovic V, Van Ginkel E, Paulraj S, Gasior S, Jones S, Feigenbutz L, Clair GS, Barone P, Bohn J, Acharya A, Zastrow-Hayes G, Henkel-Heinecke S, Silanskas A, Seidel R, Siksnys V. Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells. Nat Commun 2021; 12:6191. [PMID: 34702830 PMCID: PMC8548392 DOI: 10.1038/s41467-021-26469-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Class 2 CRISPR systems are exceptionally diverse, nevertheless, all share a single effector protein that contains a conserved RuvC-like nuclease domain. Interestingly, the size of these CRISPR-associated (Cas) nucleases ranges from >1000 amino acids (aa) for Cas9/Cas12a to as small as 400-600 aa for Cas12f. For in vivo genome editing applications, compact RNA-guided nucleases are desirable and would streamline cellular delivery approaches. Although miniature Cas12f effectors have been shown to cleave double-stranded DNA, targeted DNA modification in eukaryotic cells has yet to be demonstrated. Here, we biochemically characterize two miniature type V-F Cas nucleases, SpCas12f1 (497 aa) and AsCas12f1 (422 aa), and show that SpCas12f1 functions in both plant and human cells to produce targeted modifications with outcomes in plants being enhanced with short heat pulses. Our findings pave the way for the development of miniature Cas12f1-based genome editing tools.
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Affiliation(s)
- Greta Bigelyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Joshua K Young
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA.
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Karolina Budre
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rimante Zedaveinyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | | | | | - Stephen Gasior
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | - Spencer Jones
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | | | - Grace St Clair
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | | | - Jennifer Bohn
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | - Ananta Acharya
- Molecular Engineering, Corteva Agriscience™, Johnston, IA, USA
| | | | | | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ralf Seidel
- Institute of Experimental Physics, Leipzig University, Leipzig, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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8
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Kopu̅stas A, Ivanovaitė Š, Rakickas T, Pocevičiu̅tė E, Paksaitė J, Karvelis T, Zaremba M, Manakova E, Tutkus M. Oriented Soft DNA Curtains for Single-Molecule Imaging. Langmuir 2021; 37:3428-3437. [PMID: 33689355 PMCID: PMC8280724 DOI: 10.1021/acs.langmuir.1c00066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Over the past 20 years, single-molecule methods have become extremely important for biophysical studies. These methods, in combination with new nanotechnological platforms, can significantly facilitate experimental design and enable faster data acquisition. A nanotechnological platform, which utilizes a flow-stretch of immobilized DNA molecules, called DNA Curtains, is one of the best examples of such combinations. Here, we employed new strategies to fabricate a flow-stretch assay of stably immobilized and oriented DNA molecules using a protein template-directed assembly. In our assay, a protein template patterned on a glass coverslip served for directional assembly of biotinylated DNA molecules. In these arrays, DNA molecules were oriented to one another and maintained extended by either single- or both-end immobilization to the protein templates. For oriented both-end DNA immobilization, we employed heterologous DNA labeling and protein template coverage with the antidigoxigenin antibody. In contrast to single-end immobilization, both-end immobilization does not require constant buffer flow for keeping DNAs in an extended configuration, allowing us to study protein-DNA interactions at more controllable reaction conditions. Additionally, we increased the immobilization stability of the biotinylated DNA molecules using protein templates fabricated from traptavidin. Finally, we demonstrated that double-tethered Soft DNA Curtains can be used in nucleic acid-interacting protein (e.g., CRISPR-Cas9) binding assay that monitors the binding location and position of individual fluorescently labeled proteins on DNA.
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Affiliation(s)
- Aurimas Kopu̅stas
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Šaru̅nė Ivanovaitė
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
| | - Tomas Rakickas
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
| | - Ernesta Pocevičiu̅tė
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Justė Paksaitė
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Tautvydas Karvelis
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Marijonas Tutkus
- Departments
of Molecular Compound Physics, Nanoengineering, and Functional Materials and Electronics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius LT-02300, Lithuania
- Life
Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
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9
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Gasiunas G, Young JK, Karvelis T, Kazlauskas D, Urbaitis T, Jasnauskaite M, Grusyte MM, Paulraj S, Wang PH, Hou Z, Dooley SK, Cigan M, Alarcon C, Chilcoat ND, Bigelyte G, Curcuru JL, Mabuchi M, Sun Z, Fuchs RT, Schildkraut E, Weigele PR, Jack WE, Robb GB, Venclovas Č, Siksnys V. A catalogue of biochemically diverse CRISPR-Cas9 orthologs. Nat Commun 2020; 11:5512. [PMID: 33139742 PMCID: PMC7606464 DOI: 10.1038/s41467-020-19344-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/02/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial Cas9 nucleases from type II CRISPR-Cas antiviral defence systems have been repurposed as genome editing tools. Although these proteins are found in many microbes, only a handful of variants are used for these applications. Here, we use bioinformatic and biochemical analyses to explore this largely uncharacterized diversity. We apply cell-free biochemical screens to assess the protospacer adjacent motif (PAM) and guide RNA (gRNA) requirements of 79 Cas9 proteins, thus identifying at least 7 distinct gRNA classes and 50 different PAM sequence requirements. PAM recognition spans the entire spectrum of T-, A-, C-, and G-rich nucleotides, from single nucleotide recognition to sequence strings longer than 4 nucleotides. Characterization of a subset of Cas9 orthologs using purified components reveals additional biochemical diversity, including both narrow and broad ranges of temperature dependence, staggered-end DNA target cleavage, and a requirement for long stretches of homology between gRNA and DNA target. Our results expand the available toolset of RNA-programmable CRISPR-associated nucleases.
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Affiliation(s)
| | - Joshua K Young
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA.
| | - Tautvydas Karvelis
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | - Darius Kazlauskas
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | - Tomas Urbaitis
- CasZyme, Vilnius, LT-10257, Lithuania
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | | | | | - Sushmitha Paulraj
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Po-Hao Wang
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
- Inari Agriculture, West Lafayette, IN, 47906, USA
| | - Zhenglin Hou
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Shane K Dooley
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Mark Cigan
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
- Genus plc, Deforest, WI, 53532, USA
| | - Clara Alarcon
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - N Doane Chilcoat
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Greta Bigelyte
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | | | | | - Zhiyi Sun
- New England Biolabs, Ipswich, MA, 01938, USA
| | | | | | | | | | | | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania
| | - Virginijus Siksnys
- CasZyme, Vilnius, LT-10257, Lithuania.
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10257, Lithuania.
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10
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Karvelis T, Bigelyte G, Young JK, Hou Z, Zedaveinyte R, Budre K, Paulraj S, Djukanovic V, Gasior S, Silanskas A, Venclovas Č, Siksnys V. PAM recognition by miniature CRISPR-Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Res 2020; 48:5016-5023. [PMID: 32246713 PMCID: PMC7229846 DOI: 10.1093/nar/gkaa208] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, CRISPR-associated (Cas) nucleases have revolutionized the genome editing field. Being guided by an RNA to cleave double-stranded (ds) DNA targets near a short sequence termed a protospacer adjacent motif (PAM), Cas9 and Cas12 offer unprecedented flexibility, however, more compact versions would simplify delivery and extend application. Here, we present a collection of 10 exceptionally compact (422–603 amino acids) CRISPR–Cas12f nucleases that recognize and cleave dsDNA in a PAM dependent manner. Categorized as class 2 type V-F, they originate from the previously identified Cas14 family and distantly related type V-U3 Cas proteins found in bacteria. Using biochemical methods, we demonstrate that a 5′ T- or C-rich PAM sequence triggers dsDNA target cleavage. Based on this discovery, we evaluated whether they can protect against invading dsDNA in Escherichia coli and find that some but not all can. Altogether, our findings show that miniature Cas12f nucleases can protect against invading dsDNA like much larger class 2 CRISPR effectors and have the potential to be harnessed as programmable nucleases for genome editing.
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Affiliation(s)
- Tautvydas Karvelis
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Greta Bigelyte
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | | | | | | | - Karolina Budre
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | | | | | | | - Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
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11
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Mullally G, van Aelst K, Naqvi MM, Diffin FM, Karvelis T, Gasiunas G, Siksnys V, Szczelkun MD. 5' modifications to CRISPR-Cas9 gRNA can change the dynamics and size of R-loops and inhibit DNA cleavage. Nucleic Acids Res 2020; 48:6811-6823. [PMID: 32496535 PMCID: PMC7337959 DOI: 10.1093/nar/gkaa477] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022] Open
Abstract
A key aim in exploiting CRISPR-Cas is gRNA engineering to introduce additional functionalities, ranging from individual nucleotide changes that increase efficiency of on-target binding to the inclusion of larger functional RNA aptamers or ribonucleoproteins (RNPs). Cas9-gRNA interactions are crucial for complex assembly, but several distinct regions of the gRNA are amenable to modification. We used in vitro ensemble and single-molecule assays to assess the impact of gRNA structural alterations on RNP complex formation, R-loop dynamics, and endonuclease activity. Our results indicate that RNP formation was unaffected by any of our modifications. R-loop formation and DNA cleavage activity were also essentially unaffected by modification of the Upper Stem, first Hairpin and 3' end. In contrast, we found that 5' additions of only two or three nucleotides could reduce R-loop formation and cleavage activity of the RuvC domain relative to a single nucleotide addition. Such modifications are a common by-product of in vitro transcribed gRNA. We also observed that addition of a 20 nt RNA hairpin to the 5' end of a gRNA still supported RNP formation but produced a stable ∼9 bp R-loop that could not activate DNA cleavage. Consideration of these observations will assist in successful gRNA design.
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Affiliation(s)
- Grace Mullally
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Kara van Aelst
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Mohsin M Naqvi
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Fiona M Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Giedrius Gasiunas
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
- CasZyme, Vilnius, Lithuania
| | | | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
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12
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Abstract
In recent years, Cas9 has revolutionized the genome-editing field and enabled a broad range of applications from basic biology to biotechnology and medicine. Cas9 specificity is dictated by base pairing of the guide RNA to the complementary DNA strand, however to initiate hybridization, a short protospacer adjacent motif (PAM) sequence is required in the vicinity of the target sequence. The PAM is recognized by the Cas9 protein and varies between Cas9s. There are thousands of type II CRISPR-Cas9 sequences available in sequence databases. To characterize the PAM recognition diversity provided by Cas9 orthologs, we developed a phylogeny-guided bioinformatics approach and streamlined our experimental procedures for Cas9 expression and RNP complex assembly using cell lysates and in vitro translation mixtures. This approach could be easily adapted for the characterization of other CRISPR-Cas nucleases that require PAM sequences and generate double-strand breaks following target recognition.
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Affiliation(s)
| | - Joshua K Young
- Department of Molecular Engineering, Corteva Agriscience™ Agriculture Division of DowDuPont™, Johnston, IA, United States
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13
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Abstract
In the past few years, the Cas9 endonuclease from the type II CRISPR-Cas bacterial antiviral defense system has revolutionized the genome editing field. Guided by an RNA molecule, Cas9 can be reprogrammed to target almost any DNA sequence: the only limitation being the short nucleotide sequence in the vicinity of the target, termed the PAM, which is characteristic for each Cas9 protein. Streptococcus pyogenes Cas9 which recognizes the NGG PAM is currently most widely used for genome manipulation. However, Cas9 orthologues and engineered Cas9 variants offer expanded genome targeting capabilities, improved specificity and biochemical properties.
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Affiliation(s)
- Tautvydas Karvelis
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedrius Gasiunas
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
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14
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Karvelis T, Gasiunas G, Siksnys V. Methods for decoding Cas9 protospacer adjacent motif (PAM) sequences: A brief overview. Methods 2017; 121-122:3-8. [PMID: 28344037 DOI: 10.1016/j.ymeth.2017.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/09/2017] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Recently the Cas9, an RNA guided DNA endonuclease, emerged as a powerful tool for targeted genome manipulations. Cas9 protein can be reprogrammed to cleave, bind or nick any DNA target by simply changing crRNA sequence, however a short nucleotide sequence, termed PAM, is required to initiate crRNA hybridization to the DNA target. PAM sequence is recognized by Cas9 protein and must be determined experimentally for each Cas9 variant. Exploration of Cas9 orthologs could offer a diversity of PAM sequences and novel biochemical properties that may be beneficial for genome editing applications. Here we briefly review and compare Cas9 PAM identification assays that can be adopted for other PAM-dependent CRISPR-Cas systems.
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Affiliation(s)
- Tautvydas Karvelis
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedrius Gasiunas
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania.
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15
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Karvelis T, Gasiunas G, Young J, Bigelyte G, Silanskas A, Cigan M, Siksnys V. Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements. Genome Biol 2015; 16:253. [PMID: 26585795 PMCID: PMC4653880 DOI: 10.1186/s13059-015-0818-7] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/28/2015] [Indexed: 12/26/2022] Open
Abstract
To expand the repertoire of Cas9s available for genome targeting, we present a new in vitro method for the simultaneous examination of guide RNA and protospacer adjacent motif (PAM) requirements. The method relies on the in vitro cleavage of plasmid libraries containing a randomized PAM as a function of Cas9-guide RNA complex concentration. Using this method, we accurately reproduce the canonical PAM preferences for Streptococcus pyogenes, Streptococcus thermophilus CRISPR3 (Sth3), and CRISPR1 (Sth1). Additionally, PAM and sgRNA solutions for a novel Cas9 protein from Brevibacillus laterosporus are provided by the assay and are demonstrated to support functional activity in vitro and in plants.
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Affiliation(s)
- Tautvydas Karvelis
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania
| | - Giedrius Gasiunas
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania
| | - Joshua Young
- DuPont Pioneer, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA
| | - Greta Bigelyte
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania
| | - Mark Cigan
- DuPont Pioneer, 7300 NW 62nd Avenue, Johnston, IA, 50131, USA.
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241, Vilnius, Lithuania.
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16
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Glemzaite M, Balciunaite E, Karvelis T, Gasiunas G, Grusyte MM, Alzbutas G, Jurcyte A, Anderson EM, Maksimova E, Smith AJ, Lubys A, Zaliauskiene L, Siksnys V. Targeted gene editing by transfection of in vitro reconstituted Streptococcus thermophilus Cas9 nuclease complex. RNA Biol 2015; 12:1-4. [PMID: 25826410 PMCID: PMC4615908 DOI: 10.1080/15476286.2015.1017209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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17
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Szczelkun MD, Tikhomirova MS, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, Siksnys V, Seidel R. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc Natl Acad Sci U S A 2014; 111:9798-803. [PMID: 24912165 PMCID: PMC4103346 DOI: 10.1073/pnas.1402597111] [Citation(s) in RCA: 299] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems protect bacteria and archaea from infection by viruses and plasmids. Central to this defense is a ribonucleoprotein complex that produces RNA-guided cleavage of foreign nucleic acids. In DNA-targeting CRISPR-Cas systems, the RNA component of the complex encodes target recognition by forming a site-specific hybrid (R-loop) with its complement (protospacer) on an invading DNA while displacing the noncomplementary strand. Subsequently, the R-loop structure triggers DNA degradation. Although these reactions have been reconstituted, the exact mechanism of R-loop formation has not been fully resolved. Here, we use single-molecule DNA supercoiling to directly observe and quantify the dynamics of torque-dependent R-loop formation and dissociation for both Cascade- and Cas9-based CRISPR-Cas systems. We find that the protospacer adjacent motif (PAM) affects primarily the R-loop association rates, whereas protospacer elements distal to the PAM affect primarily R-loop stability. Furthermore, Cascade has higher torque stability than Cas9 by using a conformational locking step. Our data provide direct evidence for directional R-loop formation, starting from PAM recognition and expanding toward the distal protospacer end. Moreover, we introduce DNA supercoiling as a quantitative tool to explore the sequence requirements and promiscuities of orthogonal CRISPR-Cas systems in rapidly emerging gene-targeting applications.
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Affiliation(s)
- Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom;
| | - Maria S Tikhomirova
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany;Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany; and
| | - Tomas Sinkunas
- Department of Protein-Nucleic Acid Interactions, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Giedrius Gasiunas
- Department of Protein-Nucleic Acid Interactions, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Tautvydas Karvelis
- Department of Protein-Nucleic Acid Interactions, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Patrizia Pschera
- Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany; and
| | - Virginijus Siksnys
- Department of Protein-Nucleic Acid Interactions, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Ralf Seidel
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany;Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany; and
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18
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Karvelis T, Gasiunas G, Miksys A, Barrangou R, Horvath P, Siksnys V. crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus. RNA Biol 2013; 10:841-51. [PMID: 23535272 PMCID: PMC3737341 DOI: 10.4161/rna.24203] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Cas9-crRNA complex of the Streptococcus thermophilus DGCC7710 CRISPR3-Cas system functions as an RNA-guided endonuclease with crRNA-directed target sequence recognition and protein-mediated DNA cleavage. We show here that an additional RNA molecule, tracrRNA (trans-activating CRISPR RNA), co-purifies with the Cas9 protein isolated from the heterologous E. coli strain carrying the S. thermophilus DGCC7710 CRISPR3-Cas system. We provide experimental evidence that tracrRNA is required for Cas9-mediated DNA interference both in vitro and in vivo. We show that Cas9 specifically promotes duplex formation between the precursor crRNA (pre-crRNA) transcript and tracrRNA, in vitro. Furthermore, the housekeeping RNase III contributes to primary pre-crRNA-tracrRNA duplex cleavage for mature crRNA biogenesis. RNase III, however, is not required in the processing of a short pre-crRNA transcribed from a minimal CRISPR array containing a single spacer. Finally, we show that an in vitro-assembled ternary Cas9-crRNA-tracrRNA complex cleaves DNA. This study further specifies the molecular basis for crRNA-based re-programming of Cas9 to specifically cleave any target DNA sequence for precise genome surgery. The processes for crRNA maturation and effector complex assembly established here will contribute to the further development of the Cas9 re-programmable system for genome editing applications.
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