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Pandey H, Yadav B, Shah K, Kaur R, Choudhary D, Sharma N, Rishi V. A new method for the robust expression and single-step purification of dCas9 for CRISPR interference/activation (CRISPRi/a) applications. Protein Expr Purif 2024; 220:106500. [PMID: 38718989 DOI: 10.1016/j.pep.2024.106500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated enzyme 9) is known for its simplicity, versatility, and scalability in genome editing applications. In vitro Cas9, when complexed with sgRNA, binds and cleaves the complementary target sequences with almost perfect precision. The enzyme is exploited for various applications in understanding and changing gene function. dCas9 (deactivated or dead Cas9) is a double mutated version of Cas9 that bears mutations in the nuclease domains of the enzyme and thus cannot cleave the target DNA. dCas9 is equally advantageous since it can alter gene expression using various transcriptional activators CRISPRa and repressors CRISPRi. Additionally, dCas9 can bind to the desired target gene without cleaving it, making it a unique reagent to study the kinetics and stability of RNA-protein-DNA interactions required to design more efficient and specific gene-editing nucleases. An appreciable quantity of pure and homogeneous protein is needed to characterise dCas9 for its structural and functional understanding. This study used an N-terminal acidic tag to express the dCas9 in an E. coli-bacterial host. A simple single-step protocol for robust and efficient production of dCas9 has been described. The study and methods are distinctive as the purification is performed in a single step using inexpensive multi-modal hydroxyapatite chromatography. The purified protein can be used in different in vitro and in vivo studies.
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Affiliation(s)
- Harshita Pandey
- National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, Mohali, Punjab, 140306, India; Regional Center for Biotechnology, Faridabad, Haryana, 160014, India
| | - Binduma Yadav
- National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, Mohali, Punjab, 140306, India; Regional Center for Biotechnology, Faridabad, Haryana, 160014, India
| | - Koushik Shah
- National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, Mohali, Punjab, 140306, India
| | - Raminder Kaur
- National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, Mohali, Punjab, 140306, India
| | - Diksha Choudhary
- National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, Mohali, Punjab, 140306, India; Regional Center for Biotechnology, Faridabad, Haryana, 160014, India
| | - Nishtha Sharma
- National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, Mohali, Punjab, 140306, India
| | - Vikas Rishi
- National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, Mohali, Punjab, 140306, India.
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2
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Schmitz M, Querques I, Oberli S, Chanez C, Jinek M. Structural basis for the assembly of the type V CRISPR-associated transposon complex. Cell 2022; 185:4999-5010.e17. [PMID: 36435179 PMCID: PMC9798831 DOI: 10.1016/j.cell.2022.11.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/26/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022]
Abstract
CRISPR-Cas systems have been co-opted by Tn7-like transposable elements to direct RNA-guided transposition. Type V-K CRISPR-associated transposons rely on the concerted activities of the pseudonuclease Cas12k, the AAA+ ATPase TnsC, the Zn-finger protein TniQ, and the transposase TnsB. Here we present a cryo-electron microscopic structure of a target DNA-bound Cas12k-transposon recruitment complex comprised of RNA-guided Cas12k, TniQ, a polymeric TnsC filament and, unexpectedly, the ribosomal protein S15. Complex assembly, mediated by a network of interactions involving the guide RNA, TniQ, and S15, results in R-loop completion. TniQ contacts two TnsC protomers at the Cas12k-proximal filament end, likely nucleating its polymerization. Transposition activity assays corroborate our structural findings, implying that S15 is a bona fide component of the type V crRNA-guided transposon machinery. Altogether, our work uncovers key mechanistic aspects underpinning RNA-mediated assembly of CRISPR-associated transposons to guide their development as programmable tools for site-specific insertion of large DNA payloads.
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Affiliation(s)
- Michael Schmitz
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Irma Querques
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Seraina Oberli
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland.
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3
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D’Agostino Y, Frigato E, Noviello TM, Toni M, Frabetti F, Cigliano L, Ceccarelli M, Sordino P, Cerulo L, Bertolucci C, D’Aniello S. Loss of circadian rhythmicity in bdnf knockout zebrafish larvae. iScience 2022; 25:104054. [PMID: 35345456 PMCID: PMC8957028 DOI: 10.1016/j.isci.2022.104054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 01/14/2022] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) plays a pivotal role in neuronal growth and differentiation, neuronal plasticity, learning, and memory. Using CRISPR/Cas9 technology, we generated a vital Bdnf null mutant line in zebrafish and carried out its molecular and behavioral characterization. Although no defects are evident on a morphological inspection, 66% of coding genes and 37% of microRNAs turned out to be differentially expressed in bdnf−/− compared with wild type sibling embryos. We deeply investigated the circadian clock pathway and confirmed changes in the rhythmic expression of clock (arntl1a, clock1a and clock2) and clock-controlled (aanat2) genes. The modulatory role of Bdnf on the zebrafish circadian clock was then validated by behavioral tests highlighting the absence of circadian activity rhythms in bdnf−/− larvae. The circadian behavior was partially rescued by pharmacological treatment. The bdnf−/− zebrafish line presented here is the first valuable and stable vertebrate model for the study of BDNF-related neurodevelopmental diseases Generation of a viable bdnf KO line in zebrafish Bdnf deficiency affects locomotor activity and thigmotaxis in larvae Differential RNA-seq analysis shows changes in expression of circadian clock genes Bdnf mutant fails in the generation of the behavioral circadian rhythmicity
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Trogu S, Ermert AL, Stahl F, Nogué F, Gans T, Hughes J. Multiplex CRISPR-Cas9 mutagenesis of the phytochrome gene family in Physcomitrium (Physcomitrella) patens. PLANT MOLECULAR BIOLOGY 2021; 107:327-336. [PMID: 33346897 PMCID: PMC8648701 DOI: 10.1007/s11103-020-01103-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
We mutated all seven Physcomitrium (Physcomitrella) patens phytochrome genes using highly-efficient CRISPR-Cas9 procedures. We thereby identified phy5a as the phytochrome primarily responsible for inhibiting gravitropism, proving the utility of the mutant library. The CRISPR-Cas9 system is a powerful tool for genome editing. Here we report highly-efficient multiplex CRISPR-Cas9 editing of the seven-member phytochrome gene family in the model bryophyte Physcomitrium (Physcomitrella) patens. Based on the co-delivery of an improved Cas9 plasmid with multiple sgRNA plasmids and an efficient screening procedure to identify high-order multiple mutants prior to sequencing, we demonstrate successful targeting of all seven PHY genes in a single transfection. We investigated further aspects of the CRISPR methodology in Physcomitrella, including the significance of spacing between paired sgRNA targets and the efficacy of NHEJ and HDR in repairing the chromosome when excising a complete locus. As proof-of-principle, we show that the septuple phy- mutant remains gravitropic in light, in line with expectations, and on the basis of data from lower order multiplex knockouts conclude that phy5a is the principal phytochrome responsible for inhibiting gravitropism in light. We expect, therefore, that this mutant collection will be valuable for further studies of phytochrome function and that the methods we describe will allow similar approaches to revealing specific functions in other gene families.
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Affiliation(s)
- Silvia Trogu
- Institute for Plant Physiology, Justus Liebig University, Senckenbergstrasse 3, 35390, Giessen, Germany
| | - Anna Lena Ermert
- Institute for Plant Physiology, Justus Liebig University, Senckenbergstrasse 3, 35390, Giessen, Germany
| | - Fabian Stahl
- Institute for Plant Physiology, Justus Liebig University, Senckenbergstrasse 3, 35390, Giessen, Germany
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Tanja Gans
- Institute for Plant Physiology, Justus Liebig University, Senckenbergstrasse 3, 35390, Giessen, Germany
| | - Jon Hughes
- Institute for Plant Physiology, Justus Liebig University, Senckenbergstrasse 3, 35390, Giessen, Germany.
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Querques I, Schmitz M, Oberli S, Chanez C, Jinek M. Target site selection and remodelling by type V CRISPR-transposon systems. Nature 2021; 599:497-502. [PMID: 34759315 PMCID: PMC7613401 DOI: 10.1038/s41586-021-04030-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/16/2021] [Indexed: 11/09/2022]
Abstract
Canonical CRISPR-Cas systems provide adaptive immunity against mobile genetic elements1. However, type I-F, I-B and V-K systems have been adopted by Tn7-like transposons to direct RNA-guided transposon insertion2-7. Type V-K CRISPR-associated transposons rely on the pseudonuclease Cas12k, the transposase TnsB, the AAA+ ATPase TnsC and the zinc-finger protein TniQ7, but the molecular mechanism of RNA-directed DNA transposition has remained elusive. Here we report cryo-electron microscopic structures of a Cas12k-guide RNA-target DNA complex and a DNA-bound, polymeric TnsC filament from the CRISPR-associated transposon system of the photosynthetic cyanobacterium Scytonema hofmanni. The Cas12k complex structure reveals an intricate guide RNA architecture and critical interactions mediating RNA-guided target DNA recognition. TnsC helical filament assembly is ATP-dependent and accompanied by structural remodelling of the bound DNA duplex. In vivo transposition assays corroborate key features of the structures, and biochemical experiments show that TniQ restricts TnsC polymerization, while TnsB interacts directly with TnsC filaments to trigger their disassembly upon ATP hydrolysis. Together, these results suggest that RNA-directed target selection by Cas12k primes TnsC polymerization and DNA remodelling, generating a recruitment platform for TnsB to catalyse site-specific transposon insertion. Insights from this work will inform the development of CRISPR-associated transposons as programmable site-specific gene insertion tools.
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Affiliation(s)
- Irma Querques
- Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Michael Schmitz
- Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Seraina Oberli
- Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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6
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Ghaemi A, Bagheri E, Abnous K, Taghdisi SM, Ramezani M, Alibolandi M. CRISPR-cas9 genome editing delivery systems for targeted cancer therapy. Life Sci 2020; 267:118969. [PMID: 33385410 DOI: 10.1016/j.lfs.2020.118969] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
The prokaryotic CRISPR-Cas systems could be applied as revolutionized genome editing tool in live cells of various species to modify, visualize and identify definite sequences of DNA and RNA. CRISPR-Cas could edit the genome by homology-directed repair and non-homologous end joining mechanisms. Furthermore, DNA-targeting modification by CRISPR-Cas methodology provides opportunity for diagnosis, therapy and the genetic disorders investigation. Here, we summarized delivery systems employed for CRISPR-Cas9 for genome editing. Then preclinical studies of the CRISPR-Cas9-based therapeutics will be discussed considering the associated challenges and developments in its translation to clinic for cancer therapy.
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Affiliation(s)
- Asma Ghaemi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Bagheri
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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7
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Bhatt S, Chalmers R. Targeted DNA transposition in vitro using a dCas9-transposase fusion protein. Nucleic Acids Res 2019; 47:8126-8135. [PMID: 31429873 PMCID: PMC6735945 DOI: 10.1093/nar/gkz552] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/21/2022] Open
Abstract
Homology-directed genome engineering is limited by transgene size. Although DNA transposons are more efficient with large transgenes, random integrations are potentially mutagenic. Here we present an in vitro mechanistic study that demonstrates efficient Cas9 targeting of the mariner transposon Hsmar1. Integrations were unidirectional and tightly constrained to one side of the sgRNA binding site. Further analysis of the nucleoprotein intermediates demonstrated that the transposase and Cas9 moieties can bind their respective substrates independently or in concert. Kinetic analysis of the reaction in the presence of the Cas9 target-DNA revealed a delay between first and second strand cleavage at the transposon end. This step involves a significant conformational change that may be hindered by the properties of the interdomainal linker. Otherwise, the transposase moiety behaved normally and was proficient for integration in vitro and in Escherichia coli. Specific integration into the lacZ gene in E. coli was obscured by a high background of random integrations. Nevertheless, Cas9 is an attractive candidate for transposon-targeting because it has a high affinity and long dwell-time at its target site. This will facilitate a future optogenetic strategy for the temporal control of integration, which will increase the ratio of targeted to untargeted events.
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Affiliation(s)
- Shivam Bhatt
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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8
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Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing. Proc Natl Acad Sci U S A 2019; 116:20959-20968. [PMID: 31570623 DOI: 10.1073/pnas.1818461116] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off-targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target single-guide RNA (sgRNA) are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher homology-directed repair rates, and very low nonspecific genome editing compared to SpCas9. We demonstrate FnCas9-mediated correction of the sickle cell mutation in patient-derived induced pluripotent stem cells and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.
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9
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Clarke R, Heler R, MacDougall MS, Yeo NC, Chavez A, Regan M, Hanakahi L, Church GM, Marraffini LA, Merrill BJ. Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks. Mol Cell 2019; 71:42-55.e8. [PMID: 29979968 DOI: 10.1016/j.molcel.2018.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/06/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022]
Abstract
The ability to target the Cas9 nuclease to DNA sequences via Watson-Crick base pairing with a single guide RNA (sgRNA) has provided a dynamic tool for genome editing and an essential component of adaptive immune systems in bacteria. After generating a double-stranded break (DSB), Cas9 remains stably bound to DNA. Here, we show persistent Cas9 binding blocks access to the DSB by repair enzymes, reducing genome editing efficiency. Cas9 can be dislodged by translocating RNA polymerases, but only if the polymerase approaches from one direction toward the Cas9-DSB complex. By exploiting these RNA-polymerase/Cas9 interactions, Cas9 can be conditionally converted into a multi-turnover nuclease, mediating increased mutagenesis frequencies in mammalian cells and enhancing bacterial immunity to bacteriophages. These consequences of a stable Cas9-DSB complex provide insights into the evolution of protospacer adjacent motif (PAM) sequences and a simple method of improving selection of highly active sgRNAs for genome editing.
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Affiliation(s)
- Ryan Clarke
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Robert Heler
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
| | - Matthew S MacDougall
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nan Cher Yeo
- Department of Genetics, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alejandro Chavez
- Department of Genetics, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Maureen Regan
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA; Genome Editing Core, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Leslyn Hanakahi
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Rockford Health Science Campus, Rockford, IL 61107, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | | | - Bradley J Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA; Genome Editing Core, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Uribe RV, van der Helm E, Misiakou MA, Lee SW, Kol S, Sommer MOA. Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla. Cell Host Microbe 2019; 25:233-241.e5. [PMID: 30737174 DOI: 10.1016/j.chom.2019.01.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/24/2018] [Accepted: 01/02/2019] [Indexed: 01/07/2023]
Abstract
CRISPR-Cas systems in bacteria and archaea provide immunity against bacteriophages and plasmids. To overcome CRISPR immunity, phages have acquired anti-CRISPR genes that reduce CRISPR-Cas activity. Using a synthetic genetic circuit, we developed a high-throughput approach to discover anti-CRISPR genes from metagenomic libraries based on their functional activity rather than sequence homology or genetic context. We identified 11 DNA fragments from soil, animal, and human metagenomes that circumvent Streptococcus pyogenes Cas9 activity in our selection strain. Further in vivo and in vitro characterization of a subset of these hits validated the activity of four anti-CRISPRs. Notably, homologs of some of these anti-CRISPRs were detected in seven different phyla, namely Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, and Balneolaeota, and have high sequence identity suggesting recent horizontal gene transfer. Thus, anti-CRISPRs against type II-A CRISPR-Cas systems are widely distributed across bacterial phyla, suggesting a more complex ecological role than previously appreciated.
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Affiliation(s)
- Ruben V Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Eric van der Helm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Maria-Anna Misiakou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Sang-Woo Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark.
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11
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Pan F, Hou K, Li DD, Su TJ, Wu W. Exopolysaccharides from the fungal endophytic Fusarium sp. A14 isolated from Fritillaria unibracteata Hsiao et KC Hsia and their antioxidant and antiproliferation effects. J Biosci Bioeng 2018; 127:231-240. [PMID: 30177486 DOI: 10.1016/j.jbiosc.2018.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 07/08/2018] [Accepted: 07/26/2018] [Indexed: 12/19/2022]
Abstract
Exopolysaccharides (EPSs) are high-molecular-weight carbohydrates with a wide range of biophysiological activities, such as antioxidant activity, immunostimulatory activity, antitumor activity, hepatoprotective activity, and antifatigue effects. In the present work, two water-soluble EPSs, namely, A14EPS-1 and A14EPS-2, were isolated and purified from the fungal endophytic strain A14 using ethanol precipitation, DEAE-cellulose ion exchange chromatography and Sepharose G-150 gel filtration chromatography. A14EPS-1 (∼2.4 × 104 Da, the major fraction) was mainly composed of mannose, rhamnose, glucose, galactose, xylose and arabinose with a molar ratio of 0.31:0.55:10.00:0.34:0.03:0.06. The major monosaccharide of A14EPS-1 was pyranose, which was connected by α-glycosidic linkages. And the side chains of A14EPS-1 may be composed of rhamnose, arabinose, glucose and galactose; moreover, the backbone of A14EPS-1 may be composed of rhamnose, xylose, arabinose and glucose. A14EPS-2 (∼0.5 × 104 Da) was mainly composed of mannose, rhamnose, glucose, galactose, xylose and arabinose in a ratio of 0.16:0.88:10.00:0.39:0.06:0.06. Pyranose was observed in both the α- and β-configurations in A14EPS-2, and the α configuration was dominant. In addition, the results of the bioactivity assays indicated that both A14EPS-1 and A14EPS-2 had moderate antioxidant activity in vitro, and A14EPS-2 showed a moderate antiproliferation effect on human hepatocellular carcinoma HepG2 cells.
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Affiliation(s)
- Feng Pan
- Department of Production of Special Utilizated Plant, Agronomy College, Sichuan Agricultural University, No. 211, Huimin Rd, Wenjiang Region, Chengdu, 611130 Sichuan, PR China
| | - Kai Hou
- Department of Production of Special Utilizated Plant, Agronomy College, Sichuan Agricultural University, No. 211, Huimin Rd, Wenjiang Region, Chengdu, 611130 Sichuan, PR China
| | - Dan-Dan Li
- Department of Production of Special Utilizated Plant, Agronomy College, Sichuan Agricultural University, No. 211, Huimin Rd, Wenjiang Region, Chengdu, 611130 Sichuan, PR China
| | - Tian-Jiao Su
- Department of Production of Special Utilizated Plant, Agronomy College, Sichuan Agricultural University, No. 211, Huimin Rd, Wenjiang Region, Chengdu, 611130 Sichuan, PR China
| | - Wei Wu
- Department of Production of Special Utilizated Plant, Agronomy College, Sichuan Agricultural University, No. 211, Huimin Rd, Wenjiang Region, Chengdu, 611130 Sichuan, PR China.
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12
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Moore CT, Christie KA, Marshall J, Nesbit MA. Personalised genome editing – The future for corneal dystrophies. Prog Retin Eye Res 2018; 65:147-165. [DOI: 10.1016/j.preteyeres.2018.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/21/2022]
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13
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Cromwell CR, Sung K, Park J, Krysler AR, Jovel J, Kim SK, Hubbard BP. Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity. Nat Commun 2018; 9:1448. [PMID: 29654299 PMCID: PMC5899152 DOI: 10.1038/s41467-018-03927-0] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/22/2018] [Indexed: 12/26/2022] Open
Abstract
Off-target DNA cleavage is a paramount concern when applying CRISPR-Cas9 gene-editing technology to functional genetics and human therapeutic applications. Here, we show that incorporation of next-generation bridged nucleic acids (2',4'-BNANC[N-Me]) as well as locked nucleic acids (LNA) at specific locations in CRISPR-RNAs (crRNAs) broadly reduces off-target DNA cleavage by Cas9 in vitro and in cells by several orders of magnitude. Using single-molecule FRET experiments we show that BNANC incorporation slows Cas9 kinetics and improves specificity by inducing a highly dynamic crRNA-DNA duplex for off-target sequences, which shortens dwell time in the cleavage-competent, "zipped" conformation. In addition to describing a robust technique for improving the precision of CRISPR/Cas9-based gene editing, this study illuminates an application of synthetic nucleic acids.
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Affiliation(s)
| | - Keewon Sung
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinho Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Amanda R Krysler
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2R7, Canada
| | - Juan Jovel
- The Applied Genomics Core, Office of Research, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Basil P Hubbard
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2R7, Canada.
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14
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Vlot M, Houkes J, Lochs SJ, Swarts DC, Zheng P, Kunne T, Mohanraju P, Anders C, Jinek M, van der Oost J, Dickman MJ, Brouns SJ. Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR-Cas effector complexes. Nucleic Acids Res 2018; 46:873-885. [PMID: 29253268 PMCID: PMC5778469 DOI: 10.1093/nar/gkx1264] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 01/06/2023] Open
Abstract
Prokaryotes encode various host defense systems that provide protection against mobile genetic elements. Restriction-modification (R-M) and CRISPR-Cas systems mediate host defense by sequence specific targeting of invasive DNA. T-even bacteriophages employ covalent modifications of nucleobases to avoid binding and therefore cleavage of their DNA by restriction endonucleases. Here, we describe that DNA glucosylation of bacteriophage genomes affects interference of some but not all CRISPR-Cas systems. We show that glucosyl modification of 5-hydroxymethylated cytosines in the DNA of bacteriophage T4 interferes with type I-E and type II-A CRISPR-Cas systems by lowering the affinity of the Cascade and Cas9-crRNA complexes for their target DNA. On the contrary, the type V-A nuclease Cas12a (also known as Cpf1) is not impaired in binding and cleavage of glucosylated target DNA, likely due to a more open structural architecture of the protein. Our results suggest that CRISPR-Cas systems have contributed to the selective pressure on phages to develop more generic solutions to escape sequence specific host defense systems.
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Affiliation(s)
- Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Joep Houkes
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Silke J A Lochs
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Daan C Swarts
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Peiyuan Zheng
- ChELSI Institute Department of Chemical and Biological Engineering University of Sheffield, Sheffield, UK
| | - Tim Kunne
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Carolin Anders
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Mark J Dickman
- ChELSI Institute Department of Chemical and Biological Engineering University of Sheffield, Sheffield, UK
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Van der Maasweg 9, Delft University of Technology, 2629 HZ Delft, The Netherlands
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15
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Lovendahl KN, Hayward AN, Gordon WR. Sequence-Directed Covalent Protein-DNA Linkages in a Single Step Using HUH-Tags. J Am Chem Soc 2017; 139:7030-7035. [PMID: 28481515 DOI: 10.1021/jacs.7b02572] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a robust strategy to covalently link proteins and DNA using HUH-endonuclease domains as fusion partners (HUH-tags). We show that HUH-tags react robustly with specific sequences of unmodified single-stranded DNA, and we have identified five tags that react orthogonally with distinct DNA sequences. We demonstrate the versatility of HUH-tags as fusion partners in Cas9-mediated gene editing and the construction of doubly DNA-tethered proteins for single-molecule studies. Finally we demonstrate application to cellular imaging in live and fixed cells.
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Affiliation(s)
- Klaus N Lovendahl
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Amanda N Hayward
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Wendy R Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States
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16
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Cellular Reprogramming, Genome Editing, and Alternative CRISPR Cas9 Technologies for Precise Gene Therapy of Duchenne Muscular Dystrophy. Stem Cells Int 2017; 2017:8765154. [PMID: 28607562 PMCID: PMC5451761 DOI: 10.1155/2017/8765154] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/23/2017] [Accepted: 03/28/2017] [Indexed: 01/02/2023] Open
Abstract
In the past decade, the development of two innovative technologies, namely, induced pluripotent stem cells (iPSCs) and the CRISPR Cas9 system, has enabled researchers to model diseases derived from patient cells and precisely edit DNA sequences of interest, respectively. In particular, Duchenne muscular dystrophy (DMD) has been an exemplary monogenic disease model for combining these technologies to demonstrate that genome editing can correct genetic mutations in DMD patient-derived iPSCs. DMD is an X-linked genetic disorder caused by mutations that disrupt the open reading frame of the dystrophin gene, which plays a critical role in stabilizing muscle cells during contraction and relaxation. The CRISPR Cas9 system has been shown to be capable of targeting the dystrophin gene and rescuing its expression in in vitro patient-derived iPSCs and in vivo DMD mouse models. In this review, we highlight recent advances made using the CRISPR Cas9 system to correct genetic mutations and discuss how emerging CRISPR technologies and iPSCs in a combined platform can play a role in bringing a therapy for DMD closer to the clinic.
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17
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Barrangou R, Doudna JA. Applications of CRISPR technologies in research and beyond. Nat Biotechnol 2016; 34:933-941. [DOI: 10.1038/nbt.3659] [Citation(s) in RCA: 577] [Impact Index Per Article: 72.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 07/31/2016] [Indexed: 02/06/2023]
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18
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Shao M, Xu TR, Chen CS. The big bang of genome editing technology: development and application of the CRISPR/Cas9 system in disease animal models. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2016; 37:191-204. [PMID: 27469250 PMCID: PMC4980067 DOI: 10.13918/j.issn.2095-8137.2016.4.191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/20/2016] [Indexed: 12/17/2022]
Abstract
Targeted genome editing technology has been widely used in biomedical studies. The CRISPR-associated RNA-guided endonuclease Cas9 has become a versatile genome editing tool. The CRISPR/Cas9 system is useful for studying gene function through efficient knock-out, knock-in or chromatin modification of the targeted gene loci in various cell types and organisms. It can be applied in a number of fields, such as genetic breeding, disease treatment and gene functional investigation. In this review, we introduce the most recent developments and applications, the challenges, and future directions of Cas9 in generating disease animal model. Derived from the CRISPR adaptive immune system of bacteria, the development trend of Cas9 will inevitably fuel the vital applications from basic research to biotechnology and bio-medicine.
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Affiliation(s)
- Ming Shao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming Yunnan 650500, China;Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Tian-Rui Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming Yunnan 650500, China.
| | - Ce-Shi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
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19
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Anders C, Bargsten K, Jinek M. Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Mol Cell 2016; 61:895-902. [PMID: 26990992 PMCID: PMC5065715 DOI: 10.1016/j.molcel.2016.02.020] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 01/19/2023]
Abstract
The RNA-guided endonuclease Cas9 from Streptococcus pyogenes (SpCas9) forms the core of a powerful genome editing technology. DNA cleavage by SpCas9 is dependent on the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) in the target DNA, restricting the choice of targetable sequences. To address this limitation, artificial SpCas9 variants with altered PAM specificities have recently been developed. Here we report crystal structures of the VQR, EQR, and VRER SpCas9 variants bound to target DNAs containing their preferred PAM sequences. The structures reveal that the non-canonical PAMs are recognized by an induced fit mechanism. Besides mediating sequence-specific base recognition, the amino acid substitutions introduced in the SpCas9 variants facilitate conformational remodeling of the PAM region of the bound DNA. Guided by the structural data, we engineered a SpCas9 variant that specifically recognizes NAAG PAMs. Taken together, these studies inform further development of Cas9-based genome editing tools.
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Affiliation(s)
- Carolin Anders
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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