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Cheng A, Harikrishna JA, Redwood CS, Lit LC, Nath SK, Chua KH. Genetics Matters: Voyaging from the Past into the Future of Humanity and Sustainability. Int J Mol Sci 2022; 23:ijms23073976. [PMID: 35409335 PMCID: PMC8999725 DOI: 10.3390/ijms23073976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
The understanding of how genetic information may be inherited through generations was established by Gregor Mendel in the 1860s when he developed the fundamental principles of inheritance. The science of genetics, however, began to flourish only during the mid-1940s when DNA was identified as the carrier of genetic information. The world has since then witnessed rapid development of genetic technologies, with the latest being genome-editing tools, which have revolutionized fields from medicine to agriculture. This review walks through the historical timeline of genetics research and deliberates how this discipline might furnish a sustainable future for humanity.
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Affiliation(s)
- Acga Cheng
- Institute of Biological Science, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (J.A.H.)
| | - Jennifer Ann Harikrishna
- Institute of Biological Science, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Charles S. Redwood
- Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK;
| | - Lei Cheng Lit
- Department of Physiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Swapan K. Nath
- Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Correspondence: (S.K.N.); (K.H.C.)
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (S.K.N.); (K.H.C.)
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102
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Poudel R, Rodriguez LT, Reisch CR, Rivers AR. GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes. Gigascience 2022; 11:giac007. [PMID: 35365834 PMCID: PMC8975720 DOI: 10.1093/gigascience/giac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/01/2021] [Accepted: 01/13/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR-Cas systems have expanded the possibilities for gene editing in bacteria and eukaryotes. There are many excellent tools for designing CRISPR-Cas guide RNAs (gRNAs) for model organisms with standard Cas enzymes. GuideMaker is intended as a fast and easy-to-use design tool for challenging projects with (i) non-standard Cas enzymes, (ii) non-model organisms, or (iii) projects that need to design a panel of gRNA for genome-wide screens. FINDINGS GuideMaker can rapidly design gRNAs for gene targets across the genome using a degenerate protospacer-adjacent motif (PAM) and a genome. The tool applies hierarchical navigable small world graphs to speed up the comparison of guide RNAs and optionally provides on-target and off-target scoring. This allows the user to design effective gRNAs targeting all genes in a typical bacterial genome in ∼1-2 minutes. CONCLUSIONS GuideMaker enables the rapid design of genome-wide gRNA for any CRISPR-Cas enzyme in non-model organisms. While GuideMaker is designed with prokaryotic genomes in mind, it can efficiently process eukaryotic genomes as well. GuideMaker is available as command-line software, a stand-alone web application, and a tool in the CyCverse Discovery Environment. All versions are available under a Creative Commons CC0 1.0 Universal Public Domain Dedication.
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Affiliation(s)
- Ravin Poudel
- Genomics and Bioinformatics Research Unit, USDA Agricultural Research Service, Gainesville, FL 32608, USA
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32601, USA
| | - Lidimarie Trujillo Rodriguez
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32601, USA
| | - Christopher R Reisch
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32601, USA
| | - Adam R Rivers
- Genomics and Bioinformatics Research Unit, USDA Agricultural Research Service, Gainesville, FL 32608, USA
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103
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Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex. Commun Biol 2022; 5:279. [PMID: 35351985 PMCID: PMC8964682 DOI: 10.1038/s42003-022-03187-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
The small RNA-mediated immunity in bacteria depends on foreign RNA-activated and self RNA-inhibited enzymatic activities. The multi-subunit Type III-A CRISPR-Cas effector complex (Csm) exemplifies this principle and is in addition regulated by cellular metabolites such as divalent metals and ATP. Recognition of the foreign or cognate target RNA (CTR) triggers its single-stranded deoxyribonuclease (DNase) and cyclic oligoadenylate (cOA) synthesis activities. The same activities remain dormant in the presence of the self or non-cognate target RNA (NTR) that differs from CTR only in its 3′-protospacer flanking sequence (3′-PFS). Here we employ electron cryomicroscopy (cryoEM), functional assays, and comparative cross-linking to study in vivo assembled mesophilic Lactococcus lactis Csm (LlCsm) at the three functional states: apo, the CTR- and the NTR-bound. Unlike previously studied Csm complexes, we observed binding of 3′-PFS to Csm in absence of bound ATP and analyzed the structures of the four RNA cleavage sites. Interestingly, comparative crosslinking results indicate a tightening of the Csm3-Csm4 interface as a result of CTR but not NTR binding, reflecting a possible role of protein dynamics change during activation. This study presents Cryo-EM structures of the Lactococcus lactis Type III-A CRISPR-Cas effector complex in three functional states, including bound forms with cognate and non-cognate target RNA. The results suggest changing protein dynamics during effector complex activation.
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Maguin P, Varble A, Modell JW, Marraffini LA. Cleavage of viral DNA by restriction endonucleases stimulates the type II CRISPR-Cas immune response. Mol Cell 2022; 82:907-919.e7. [PMID: 35134339 PMCID: PMC8900293 DOI: 10.1016/j.molcel.2022.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/03/2021] [Accepted: 01/14/2022] [Indexed: 12/26/2022]
Abstract
Prokaryotic organisms have developed multiple defense systems against phages; however, little is known about whether and how these interact with each other. Here, we studied the connection between two of the most prominent prokaryotic immune systems: restriction-modification and CRISPR. While both systems employ enzymes that cleave a specific DNA sequence of the invader, CRISPR nucleases are programmed with phage-derived spacer sequences, which are integrated into the CRISPR locus upon infection. We found that restriction endonucleases provide a short-term defense, which is rapidly overcome through methylation of the phage genome. In a small fraction of the cells, however, restriction results in the acquisition of spacer sequences from the cleavage site, which mediates a robust type II-A CRISPR-Cas immune response against the methylated phage. This mechanism is reminiscent of eukaryotic immunity in which the innate response offers a first temporary line of defense and also activates a second and more robust adaptive response.
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Affiliation(s)
- Pascal Maguin
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Andrew Varble
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Joshua W. Modell
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Present address: Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe St., PCTB 803, Baltimore, MD 21205, USA
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Correspondence to:
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105
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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106
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107
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Puig-Serra P, Casado-Rosas MC, Martinez-Lage M, Olalla-Sastre B, Alonso-Yanez A, Torres-Ruiz R, Rodriguez-Perales S. CRISPR Approaches for the Diagnosis of Human Diseases. Int J Mol Sci 2022; 23:ijms23031757. [PMID: 35163678 PMCID: PMC8836363 DOI: 10.3390/ijms23031757] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas is a prokaryotic self-defense system, widely known for its use as a gene-editing tool. Because of their high specificity to detect DNA and RNA sequences, different CRISPR systems have been adapted for nucleic acid detection. CRISPR detection technologies differ highly among them, since they are based on four of the six major subtypes of CRISPR systems. In just 5 years, the CRISPR diagnostic field has rapidly expanded, growing from a set of specific molecular biology discoveries to multiple FDA-authorized COVID-19 tests and the establishment of several companies. CRISPR-based detection methods are coupled with pre-existing preamplification and readout technologies, achieving sensitivity and reproducibility comparable to the current gold standard nucleic acid detection methods. Moreover, they are very versatile, can be easily implemented to detect emerging pathogens and new clinically relevant mutations, and offer multiplexing capability. The advantages of the CRISPR-based diagnostic approaches are a short sample-to-answer time and no requirement of laboratory settings; they are also much more affordable than current nucleic acid detection procedures. In this review, we summarize the applications and development trends of the CRISPR/Cas13 system in the identification of particular pathogens and mutations and discuss the challenges and future prospects of CRISPR-based diagnostic platforms in biomedicine.
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Affiliation(s)
- Pilar Puig-Serra
- Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas (CNIO), Molecular Cytogenetics & Genome Editing Unit, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; (P.P.-S.); (M.C.C.-R.); (M.M.-L.); (B.O.-S.); (A.A.-Y.)
| | - Maria Cruz Casado-Rosas
- Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas (CNIO), Molecular Cytogenetics & Genome Editing Unit, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; (P.P.-S.); (M.C.C.-R.); (M.M.-L.); (B.O.-S.); (A.A.-Y.)
| | - Marta Martinez-Lage
- Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas (CNIO), Molecular Cytogenetics & Genome Editing Unit, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; (P.P.-S.); (M.C.C.-R.); (M.M.-L.); (B.O.-S.); (A.A.-Y.)
| | - Beatriz Olalla-Sastre
- Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas (CNIO), Molecular Cytogenetics & Genome Editing Unit, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; (P.P.-S.); (M.C.C.-R.); (M.M.-L.); (B.O.-S.); (A.A.-Y.)
| | - Alejandro Alonso-Yanez
- Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas (CNIO), Molecular Cytogenetics & Genome Editing Unit, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; (P.P.-S.); (M.C.C.-R.); (M.M.-L.); (B.O.-S.); (A.A.-Y.)
| | - Raul Torres-Ruiz
- Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas (CNIO), Molecular Cytogenetics & Genome Editing Unit, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; (P.P.-S.); (M.C.C.-R.); (M.M.-L.); (B.O.-S.); (A.A.-Y.)
- Centro de Investigacion Energeticas Medioambientales y Tecnologicas (CIEMAT), Advanced Therapies Unit, Hematopoietic Innovative Therapies Division, Instituto de Investigacion Sanitaria Fundacion Jimenez Diaz (IIS-FJD, UAM), 28040 Madrid, Spain
- Correspondence: (R.T.-R.); (S.R.-P.)
| | - Sandra Rodriguez-Perales
- Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncologicas (CNIO), Molecular Cytogenetics & Genome Editing Unit, Melchor Fernandez Almagro, 3, 28029 Madrid, Spain; (P.P.-S.); (M.C.C.-R.); (M.M.-L.); (B.O.-S.); (A.A.-Y.)
- Correspondence: (R.T.-R.); (S.R.-P.)
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108
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Lee H, Sashital DG. Creating memories: molecular mechanisms of CRISPR adaptation. Trends Biochem Sci 2022; 47:464-476. [DOI: 10.1016/j.tibs.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/22/2022]
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109
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Xia P, Dutta A, Gupta K, Batish M, Parashar V. Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems. J Biol Chem 2022; 298:101591. [PMID: 35038453 PMCID: PMC8844856 DOI: 10.1016/j.jbc.2022.101591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/28/2023] Open
Abstract
RNA interference by type III CRISPR systems results in the synthesis of cyclic oligoadenylate (cOA) second messengers, which are known to bind and regulate various CARF domain-containing nuclease receptors. The CARF domain-containing Csa3 family of transcriptional factors associated with the DNA-targeting type I CRISPR systems regulate expression of various CRISPR and DNA repair genes in many prokaryotes. In this study, we extend the known receptor repertoire of cOA messengers to include transcriptional factors by demonstrating specific binding of cyclic tetra-adenylate (cA4) to Saccharolobus solfataricus Csa3 (Csa3Sso). Our 2.0-Å resolution X-ray crystal structure of cA4-bound full-length Csa3Sso reveals the binding of its CARF domain to an elongated conformation of cA4. Using cA4 binding affinity analyses of Csa3Sso mutants targeting the observed Csa3Sso•cA4 structural interface, we identified a Csa3-specific cA4 binding motif distinct from a more widely conserved cOA-binding CARF motif. Using a rational surface engineering approach, we increased the cA4 binding affinity of Csa3Sso up to ∼145-fold over the wildtype, which has potential applications for future second messenger-driven CRISPR gene expression and editing systems. Our in-solution Csa3Sso structural analysis identified cA4-induced allosteric and asymmetric conformational rearrangement of its C-terminal winged helix-turn-helix effector domains, which could potentially be incompatible to DNA binding. However, specific in vitro binding of the purified Csa3Sso to its putative promoter (PCas4a) was found to be cA4 independent, suggesting a complex mode of Csa3Sso regulation. Overall, our results support cA4-and Csa3-mediated cross talk between type III and type I CRISPR systems.
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Affiliation(s)
- Pengjun Xia
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Anirudha Dutta
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Kushol Gupta
- The Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Vijay Parashar
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA.
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110
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Aviram N, Thornal AN, Zeevi D, Marraffini LA. Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system. Nucleic Acids Res 2022; 50:1661-1672. [PMID: 35048966 PMCID: PMC8860600 DOI: 10.1093/nar/gkab1299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas systems provide prokaryotic organisms with an adaptive defense mechanism that acquires immunological memories of infections. This is accomplished by integration of short fragments from the genome of invaders such as phages and plasmids, called ‘spacers’, into the CRISPR locus of the host. Depending on their genetic composition, CRISPR-Cas systems can be classified into six types, I-VI, however spacer acquisition has been extensively studied only in type I and II systems. Here, we used an inducible spacer acquisition assay to study this process in the type III-A CRISPR-Cas system of Staphylococcus epidermidis, in the absence of phage selection. Similarly to type I and II spacer acquisition, this type III system uses Cas1 and Cas2 to preferentially integrate spacers from the chromosomal terminus and free dsDNA ends produced after DNA breaks, in a manner that is enhanced by the AddAB DNA repair complex. Surprisingly, a different mode of spacer acquisition from rRNA and tRNA loci, which spans only the transcribed sequences of these genes and is not enhanced by AddAB, was also detected. Therefore, our findings reveal both common mechanistic principles that may be conserved in all CRISPR-Cas systems, as well as unique and intriguing features of type III spacer acquisition.
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Affiliation(s)
- Naama Aviram
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Ashley N Thornal
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - David Zeevi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Luciano A Marraffini
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
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111
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Díaz-Galicia E, Grünberg R, Arold ST. How to Find the Right RNA-Sensing CRISPR-Cas System for an In Vitro Application. BIOSENSORS 2022; 12:53. [PMID: 35200314 PMCID: PMC8869480 DOI: 10.3390/bios12020053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems have a great and still largely untapped potential for in vitro applications, in particular, for RNA biosensing. However, there is currently no systematic guide on selecting the most appropriate RNA-targeting CRISPR-Cas system for a given application among thousands of potential candidates. We provide an overview of the currently described Cas effector systems and review existing Cas-based RNA detection methods. We then propose a set of systematic selection criteria for selecting CRISPR-Cas candidates for new applications. Using this approach, we identify four candidates for in vitro RNA.
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Affiliation(s)
- Escarlet Díaz-Galicia
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Raik Grünberg
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, F-34090 Montpellier, France
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112
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Wimmer E, Zink IA, Schleper C. Reprogramming CRISPR-Mediated RNA Interference for Silencing of Essential Genes in Sulfolobales. Methods Mol Biol 2022; 2522:177-201. [PMID: 36125750 DOI: 10.1007/978-1-0716-2445-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The manipulation of gene expression levels in vivo is often key to elucidating gene function and regulatory network interactions, especially when it comes to the investigation of essential genes that cannot be deleted from the model organism's genome. Several techniques have been developed for prokaryotes that allow to interfere with transcription initiation of specific genes by blocking or modifying promoter regions. However, a tool functionally similar to RNAi used in eukaryotes to efficiently degrade mRNA posttranscriptionally did not exist until recently. Type III CRISPR-Cas systems use small RNAs (crRNAs) that guide effector complexes (encoded by cas genes) which act as site-specific RNA endonuclease and can thus be harnessed for targeted posttranscriptional gene silencing. Guide RNAs complementary to the desired target mRNA that, in addition, exhibit complementarity to repeat sequences found in the CRISPR arrays, effectively suppress unspecific DNA and RNA activities of the CRISPR-Cas complexes. Here we describe the use of endogenous type III CRISPR-Cas systems in two model organisms of Crenarchaeota, Saccharolobus solfataricus and Sulfolobus acidocaldarius.
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Affiliation(s)
- Erika Wimmer
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria
| | - Isabelle Anna Zink
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Vienna, Austria.
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113
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Zaib S, Saleem MA, Khan I. CRISPR-Cas9 Genome Engineering: Trends in Medicine and Health. Mini Rev Med Chem 2022; 22:410-421. [PMID: 34517795 DOI: 10.2174/1389557521666210913112030] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/13/2020] [Accepted: 01/14/2021] [Indexed: 11/22/2022]
Abstract
The ability to engineer biological systems and organisms holds enormous potential for applications across basic science, medicine, and biotechnology. Over the past few decades, the development of CRISPR (clustered regularly interspaced short palindromic repeat) has revolutionized the whole genetic engineering process utilizing the principles of Watson-Crick base pairing. CRISPRCas9 technology offers the simplest, fastest, most versatile, reliable, and precise method of genetic manipulation, thus enabling geneticists and medical researchers to edit parts of the genome by removing, adding, or altering sections of the DNA sequence. The current review focuses on the applications of CRISPR-Cas9 in the field of medical research. Compared with other gene-editing technologies, CRISPR/Cas9 demonstrates numerous advantages for the treatment of various medical conditions, including cancer, hepatitis B, cardiovascular diseases, or even high cholesterol. Given its promising performance, CRISPR/Cas9 gene-editing technology will surely help in the therapy of several disorders while addressing the issues pertaining to the minimization of the off-target effects of gene editing and incomplete matches between sgRNA and genomic DNA by Cas9.
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Affiliation(s)
- Sumera Zaib
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore-54590, Pakistan
| | - Mushtaq A Saleem
- Ghazi National Institute of Engineering & Sciences -GNIES, Dera Ghazi Khan-32200, Pakistan
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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The application of genome-wide CRISPR-Cas9 screens to dissect the molecular mechanisms of toxins. Comput Struct Biotechnol J 2022; 20:5076-5084. [PMID: 36187925 PMCID: PMC9489804 DOI: 10.1016/j.csbj.2022.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Many toxins are life-threatening to both animals and humans. However, specific antidotes are not available for most of those toxins. The molecular mechanisms underlying the toxicology of well-known toxins are not yet fully characterized. Recently, the advance in CRISPR-Cas9 technologies has greatly accelerated the process of revealing the toxic mechanisms of some common toxins on hosts from a genome-wide perspective. The high-throughput CRISPR screen has made it feasible to untangle complicated interactions between a particular toxin and its corresponding targeting tissue(s). In this review, we present an overview of recent advances in molecular dissection of toxins’ cytotoxicity by using genome-wide CRISPR screens, summarize the components essential for toxin-specific CRISPR screens, and propose new strategies for future research.
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115
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Chou-Zheng L, Hatoum-Aslan A. Critical roles for 'housekeeping' nucleases in type III CRISPR-Cas immunity. eLife 2022; 11:81897. [PMID: 36479971 PMCID: PMC9762709 DOI: 10.7554/elife.81897] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
CRISPR-Cas systems are a family of adaptive immune systems that use small CRISPR RNAs (crRNAs) and CRISPR-associated (Cas) nucleases to protect prokaryotes from invading plasmids and viruses (i.e., phages). Type III systems launch a multilayered immune response that relies upon both Cas and non-Cas cellular nucleases, and although the functions of Cas components have been well described, the identities and roles of non-Cas participants remain poorly understood. Previously, we showed that the type III-A CRISPR-Cas system in Staphylococcus epidermidis employs two degradosome-associated nucleases, PNPase and RNase J2, to promote crRNA maturation and eliminate invading nucleic acids (Chou-Zheng and Hatoum-Aslan, 2019). Here, we identify RNase R as a third 'housekeeping' nuclease critical for immunity. We show that RNase R works in concert with PNPase to complete crRNA maturation and identify specific interactions with Csm5, a member of the type III effector complex, which facilitate nuclease recruitment/stimulation. Furthermore, we demonstrate that RNase R and PNPase are required to maintain robust anti-plasmid immunity, particularly when targeted transcripts are sparse. Altogether, our findings expand the known repertoire of accessory nucleases required for type III immunity and highlight the remarkable capacity of these systems to interface with diverse cellular pathways to ensure successful defense.
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Affiliation(s)
- Lucy Chou-Zheng
- Microbiology Department, University of Illinois Urbana-ChampaignUrbanaUnited States
| | - Asma Hatoum-Aslan
- Microbiology Department, University of Illinois Urbana-ChampaignUrbanaUnited States
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116
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Abstract
:
Clustered regularly interspaced short palindromic repeats along with CRISPR-associated protein
mechanisms preserve the memory of previous experiences with DNA invaders, in particular spacers
that are embedded in CRISPR arrays between coordinate repeats. There has been a fast progression in
the comprehension of this immune system and its implementations; however, there are numerous points
of view that anticipate explanations to make the field an energetic research zone. The efficiency of
CRISPR-Cas depends upon well-considered single guide RNA; for this purpose, many bioinformatics
methods and tools are created to support the design of greatly active and precise single guide RNA. Insilico
single guide RNA architecture is a crucial point for effective gene editing by means of the
CRISPR technique. Persistent attempts have been made to improve in-silico single guide RNA formulation
having great on-target effectiveness and decreased off-target effects. This review offers a summary
of the CRISPR computational tools to help different researchers pick a specific tool for their work according
to pros and cons, along with new thoughts to make new computational tools to overcome all existing
limitations.
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Affiliation(s)
- Mohsin Ali Nasir
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
| | - Samia Nawaz
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
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117
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Grüschow S, Adamson CS, White MF. Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector. Nucleic Acids Res 2021; 49:13122-13134. [PMID: 34871408 PMCID: PMC8682760 DOI: 10.1093/nar/gkab1190] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Type III CRISPR systems detect invading RNA, resulting in the activation of the enzymatic Cas10 subunit. The Cas10 cyclase domain generates cyclic oligoadenylate (cOA) second messenger molecules, activating a variety of effector nucleases that degrade nucleic acids to provide immunity. The prophage-encoded Vibrio metoecus type III-B (VmeCmr) locus is uncharacterised, lacks the HD nuclease domain in Cas10 and encodes a NucC DNA nuclease effector that is also found associated with Cyclic-oligonucleotide-based anti-phage signalling systems (CBASS). Here we demonstrate that VmeCmr is activated by target RNA binding, generating cyclic-triadenylate (cA3) to stimulate a robust NucC-mediated DNase activity. The specificity of VmeCmr is probed, revealing the importance of specific nucleotide positions in segment 1 of the RNA duplex and the protospacer flanking sequence (PFS). We harness this programmable system to demonstrate the potential for a highly specific and sensitive assay for detection of the SARS-CoV-2 virus RNA with a limit of detection (LoD) of 2 fM using a commercial plate reader without any extrinsic amplification step. The sensitivity is highly dependent on the guide RNA used, suggesting that target RNA secondary structure plays an important role that may also be relevant in vivo.
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Affiliation(s)
- Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Catherine S Adamson
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
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118
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Devi V, Harjai K, Chhibber S. Self-targeting spacers in CRISPR-array: Accidental occurrence or evolutionarily conserved phenomenon. J Basic Microbiol 2021; 62:4-12. [PMID: 34904260 DOI: 10.1002/jobm.202100514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/18/2021] [Accepted: 11/27/2021] [Indexed: 11/12/2022]
Abstract
In recent years, a tremendous amount of inquisitiveness among scientists in the clustered regularly interspaced short palindrome repeats (CRISPR)-CRISPR-associated proteins (Cas) has led to many studies to delineate their exact role in prokaryotes. CRISPR-Cas is an adaptive immune system that protects prokaryotes from phages and mobile genetic elements. It incorporates small DNA fragment of the invader in the CRISPR-array and protects the host from future invasion by them. In a few instances, the CRISPR-array also incorporates self-targeting spacers, most likely by accident or leaky incorporation. A significant number of spacers are found to match with the host genes across the species; however, self-targeting spacers have not been investigated in detail in most of the organisms. The presence of self-targeting spacers in the CRISPR-array led to speculation that the CRISPR-Cas system has a lot more to offer than just being the conventional adaptive immune system. It has been implicated in gene regulation and autoimmunity more or less equally. In this review, an attempt has been made to understand self-targeting spacers in the context of gene regulation, autoimmunity, and its avoidance strategies.
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Affiliation(s)
- Veena Devi
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh, India
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119
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Zhang X, Garrett S, Graveley BR, Terns MP. Unique properties of spacer acquisition by the type III-A CRISPR-Cas system. Nucleic Acids Res 2021; 50:1562-1582. [PMID: 34893878 PMCID: PMC8860593 DOI: 10.1093/nar/gkab1193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Type III CRISPR-Cas systems have a unique mode of interference, involving crRNA-guided recognition of nascent RNA and leading to DNA and RNA degradation. How type III systems acquire new CRISPR spacers is currently not well understood. Here, we characterize CRISPR spacer uptake by a type III-A system within its native host, Streptococcus thermophilus. Adaptation by the type II-A system in the same host provided a basis for comparison. Cas1 and Cas2 proteins were critical for type III adaptation but deletion of genes responsible for crRNA biogenesis or interference did not detectably change spacer uptake patterns, except those related to host counter-selection. Unlike the type II-A system, type III spacers are acquired in a PAM- and orientation-independent manner. Interestingly, certain regions of plasmids and the host genome were particularly well-sampled during type III-A, but not type II-A, spacer uptake. These regions included the single-stranded origins of rolling-circle replicating plasmids, rRNA and tRNA encoding gene clusters, promoter regions of expressed genes and 5′ UTR regions involved in transcription attenuation. These features share the potential to form DNA secondary structures, suggesting a preferred substrate for type III adaptation. Lastly, the type III-A system adapted to and protected host cells from lytic phage infection.
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Affiliation(s)
- Xinfu Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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120
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Liu Y, Zhang L, Guo M, Chen L, Wu B, Huang H. Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2. J Biol Chem 2021; 297:101357. [PMID: 34756887 PMCID: PMC8633003 DOI: 10.1016/j.jbc.2021.101357] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/26/2022] Open
Abstract
It has been shown that phages have evolved anti-CRISPR (Acr) proteins to inhibit host CRISPR-Cas systems. Most acr genes are located upstream of anti-CRISPR-associated (aca) genes, which is instrumental for identifying these acr genes. Thus far, eight Aca families (Aca1-Aca8) have been identified, all proteins of which share low sequence homology and bind to different target DNA sequences. Recently, Aca1 and Aca2 proteins were discovered to function as repressors by binding to acr-aca promoters, thus implying a potential anti-anti-CRISPR mechanism. However, the structural basis for the repression roles of Aca proteins is still unknown. Here, we elucidated apo-structures of Aca1 and Aca2 proteins and their complex structures with their cognate operator DNA in two model systems, the Pseudomonas phage JBD30 and the Pectobacterium carotovorum template phage ZF40. In combination with biochemical and cellular assays, our study unveils dimerization and DNA-recognition mechanisms of Aca1 and Aca2 family proteins, thus revealing the molecular basis for Aca1-and Aca2-mediated anti-CRISPR repression. Our results also shed light on understanding the repression roles of other Aca family proteins and autoregulation roles of acr-aca operons.
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Affiliation(s)
- Yanhong Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China; Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Linsheng Zhang
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Maochao Guo
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Liu Chen
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
| | - Hongda Huang
- Department of Biology, School of Life Sciences, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China.
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121
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Del Piano A, Kecman T, Schmid M, Barbieri R, Brocchieri L, Tornaletti S, Firrito C, Minati L, Bernabo P, Signoria I, Lauria F, Gillingwater TH, Viero G, Clamer M. Phospho-RNA sequencing with circAID-p-seq. Nucleic Acids Res 2021; 50:e23. [PMID: 34850942 PMCID: PMC8887461 DOI: 10.1093/nar/gkab1158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/27/2021] [Accepted: 11/09/2021] [Indexed: 11/14/2022] Open
Abstract
Most RNA footprinting approaches that require ribonuclease cleavage generate RNA fragments bearing a phosphate or cyclic phosphate group at their 3′ end. Unfortunately, current library preparation protocols rely only on a 3′ hydroxyl group for adaptor ligation or poly-A tailing. Here, we developed circAID-p-seq, a PCR-free library preparation for selective 3′ phospho-RNA sequencing. As a proof of concept, we applied circAID-p-seq to ribosome profiling, which is based on sequencing of RNA fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast and highly efficient sequencing of phospho-RNA fragments from eukaryotic cells and tissues. We used circAID-p-seq to portray ribosome occupancy in transcripts, providing a versatile and PCR-free strategy to possibly unravel any endogenous 3′-phospho RNA molecules.
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Affiliation(s)
- Alessia Del Piano
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Tea Kecman
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | | | | | - Luciano Brocchieri
- TB-Seq, Inc., 458 Carlton Court, Ste H, South San Francisco, CA 94080, USA
| | - Silvia Tornaletti
- TB-Seq, Inc., 458 Carlton Court, Ste H, South San Francisco, CA 94080, USA
| | | | - Luca Minati
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | - Paola Bernabo
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | - Ilaria Signoria
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
| | - Fabio Lauria
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
| | - Thomas H Gillingwater
- Edinburgh Medical School: Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
| | - Gabriella Viero
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
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122
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Javaid N, Choi S. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency. Front Cell Dev Biol 2021; 9:761709. [PMID: 34901007 PMCID: PMC8652214 DOI: 10.3389/fcell.2021.761709] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The diverse applications of genetically modified cells and organisms require more precise and efficient genome-editing tool such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas). The CRISPR/Cas system was originally discovered in bacteria as a part of adaptive-immune system with multiple types. Its engineered versions involve multiple host DNA-repair pathways in order to perform genome editing in host cells. However, it is still challenging to get maximum genome-editing efficiency with fewer or no off-targets. Here, we focused on factors affecting the genome-editing efficiency and precision of CRISPR/Cas system along with its defense-mechanism, orthologues, and applications.
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Affiliation(s)
- Nasir Javaid
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, South Korea
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123
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Chao CC, Shen PW, Tzeng TY, Kung HJ, Tsai TF, Wong YH. Human iPSC-Derived Neurons as A Platform for Deciphering the Mechanisms behind Brain Aging. Biomedicines 2021; 9:1635. [PMID: 34829864 PMCID: PMC8615703 DOI: 10.3390/biomedicines9111635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
With an increased life expectancy among humans, aging has recently emerged as a major focus in biomedical research. The lack of in vitro aging models-especially for neurological disorders, where access to human brain tissues is limited-has hampered the progress in studies on human brain aging and various age-associated neurodegenerative diseases at the cellular and molecular level. In this review, we provide an overview of age-related changes in the transcriptome, in signaling pathways, and in relation to epigenetic factors that occur in senescent neurons. Moreover, we explore the current cell models used to study neuronal aging in vitro, including immortalized cell lines, primary neuronal culture, neurons directly converted from fibroblasts (Fib-iNs), and iPSC-derived neurons (iPSC-iNs); we also discuss the advantages and limitations of these models. In addition, the key phenotypes associated with cellular senescence that have been observed by these models are compared. Finally, we focus on the potential of combining human iPSC-iNs with genome editing technology in order to further our understanding of brain aging and neurodegenerative diseases, and discuss the future directions and challenges in the field.
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Affiliation(s)
- Chuan-Chuan Chao
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Department of Neurology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Po-Wen Shen
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan;
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Tsai-Yu Tzeng
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Biochemistry and Molecular Medicine, Comprehensive Cancer Center, University of California at Davis, Sacramento, CA 95817, USA
| | - Ting-Fen Tsai
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Hui Wong
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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124
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Guzmán NM, Esquerra-Ruvira B, Mojica FJM. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021; 24:473-498. [PMID: 34487299 PMCID: PMC8616872 DOI: 10.1007/s10123-021-00208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.
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Affiliation(s)
- Noemí M Guzmán
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Belén Esquerra-Ruvira
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain.
- Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain.
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125
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Viral recombination systems limit CRISPR-Cas targeting through the generation of escape mutations. Cell Host Microbe 2021; 29:1482-1495.e12. [PMID: 34582782 DOI: 10.1016/j.chom.2021.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 06/24/2021] [Accepted: 09/02/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems provide immunity to bacteria by programing Cas nucleases with RNA guides that recognize and cleave infecting viral genomes. Bacteria and their viruses each encode recombination systems that could repair the cleaved viral DNA. However, it is unknown whether and how these systems can affect CRISPR immunity. Bacteriophage λ uses the Red system (gam-exo-bet) to promote recombination between related phages. Here, we show that λ Red also mediates evasion of CRISPR-Cas targeting. Gam inhibits the host E. coli RecBCD recombination system, allowing recombination and repair of the cleaved DNA by phage Exo-Beta, which promotes the generation of mutations within the CRISPR target sequence. Red recombination is strikingly more efficient than the host's RecBCD-RecA in the production of large numbers of phages that escape CRISPR targeting. These results reveal a role for Red-like systems in the protection of bacteriophages against sequence-specific nucleases, which may facilitate their spread across viral genomes.
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126
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Kolesnik MV, Fedorova I, Karneyeva KA, Artamonova DN, Severinov KV. Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1301-1314. [PMID: 34903162 PMCID: PMC8527444 DOI: 10.1134/s0006297921100114] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022]
Abstract
The emergence and persistence of selfish genetic elements is an intrinsic feature of all living systems. Cellular organisms have evolved a plethora of elaborate defense systems that limit the spread of such genetic parasites. CRISPR-Cas are RNA-guided defense systems used by prokaryotes to recognize and destroy foreign nucleic acids. These systems acquire and store fragments of foreign nucleic acids and utilize the stored sequences as guides to recognize and destroy genetic invaders. CRISPR-Cas systems have been extensively studied, as some of them are used in various genome editing technologies. Although Type III CRISPR-Cas systems are among the most common CRISPR-Cas systems, they are also some of the least investigated ones, mostly due to the complexity of their action compared to other CRISPR-Cas system types. Type III effector complexes specifically recognize and cleave RNA molecules. The recognition of the target RNA activates the effector large subunit - the so-called CRISPR polymerase - which cleaves DNA and produces small cyclic oligonucleotides that act as signaling molecules to activate auxiliary effectors, notably non-specific RNases. In this review, we provide a historical overview of the sometimes meandering pathway of the Type III CRISPR research. We also review the current data on the structures and activities of Type III CRISPR-Cas systems components, their biological roles, and evolutionary history. Finally, using structural modeling with AlphaFold2, we show that the archaeal HRAMP signature protein, which heretofore has had no assigned function, is a degenerate relative of Type III CRISPR-Cas signature protein Cas10, suggesting that HRAMP systems have descended from Type III CRISPR-Cas systems or their ancestors.
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Affiliation(s)
- Matvey V Kolesnik
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Iana Fedorova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Karyna A Karneyeva
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Daria N Artamonova
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Konstantin V Severinov
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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127
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Vink JNA, Baijens JHL, Brouns SJJ. PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. Genome Biol 2021; 22:281. [PMID: 34593010 PMCID: PMC8482600 DOI: 10.1186/s13059-021-02495-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR-Cas biology, including target requirements such as the protospacer adjacent motif (PAM). However, studies have so far been limited by a low number of mapped spacers in the database. RESULTS By using vast metagenomic sequence databases, we map approximately one-third of more than 200,000 unique CRISPR spacers from a variety of microbes and derive a catalog of more than two hundred unique PAM sequences associated with specific CRISPR-Cas subtypes. These PAMs are further used to correctly assign the orientation of CRISPR arrays, revealing conserved patterns between the last nucleotides of the CRISPR repeat and PAM. We could also deduce CRISPR-Cas subtype-specific preferences for targeting either template or coding strand of open reading frames. While some DNA-targeting systems (type I-E and type II systems) prefer the template strand and avoid mRNA, other DNA- and RNA-targeting systems (types I-A and I-B and type III systems) prefer the coding strand and mRNA. In addition, we find large-scale evidence that both CRISPR-Cas adaptation machinery and CRISPR arrays are shared between different CRISPR-Cas systems. This could lead to simultaneous DNA and RNA targeting of invaders, which may be effective at combating mobile genetic invaders. CONCLUSIONS This study has broad implications for our understanding of how CRISPR-Cas systems work in a wide range of organisms for which only the genome sequence is known.
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Affiliation(s)
- Jochem N A Vink
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Jan H L Baijens
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.
- Kavli Institute of Nanoscience, Delft, The Netherlands.
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128
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Lemak S, Serbanescu MA, Khusnutdinova AN, Ruszkowski M, Beloglazova N, Xu X, Brown G, Cui H, Tan K, Joachimiak A, Cvitkovitch DG, Savchenko A, Yakunin AF. Structural and biochemical insights into CRISPR RNA processing by the Cas5c ribonuclease SMU1763 from Streptococcus mutans. J Biol Chem 2021; 297:101251. [PMID: 34592310 PMCID: PMC8524198 DOI: 10.1016/j.jbc.2021.101251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 12/01/2022] Open
Abstract
The cariogenic pathogen Streptococcus mutans contains two CRISPR systems (type I-C and type II-A) with the Cas5c protein (SmuCas5c) involved in processing of long CRISPR RNA transcripts (pre-crRNA) containing repeats and spacers to mature crRNA guides. In this study, we determined the crystal structure of SmuCas5c at a resolution of 1.72 Å, which revealed the presence of an N-terminal modified RNA recognition motif and a C-terminal twisted β-sheet domain with four bound sulphate molecules. Analysis of surface charge and residue conservation of the SmuCas5c structure suggested the location of an RNA-binding site in a shallow groove formed by the RNA recognition motif domain with several conserved positively charged residues (Arg39, Lys52, Arg109, Arg127, and Arg134). Purified SmuCas5c exhibited metal-independent ribonuclease activity against single-stranded pre-CRISPR RNAs containing a stem-loop structure with a seven-nucleotide stem and a pentaloop. We found SmuCas5c cleaves substrate RNA within the repeat sequence at a single cleavage site located at the 3'-base of the stem but shows significant tolerance to substrate sequence variations downstream of the cleavage site. Structure-based mutational analysis revealed that the conserved residues Tyr50, Lys120, and His121 comprise the SmuCas5c catalytic residues. In addition, site-directed mutagenesis of positively charged residues Lys52, Arg109, and Arg134 located near the catalytic triad had strong negative effects on the RNase activity of this protein, suggesting that these residues are involved in RNA binding. Taken together, our results reveal functional diversity of Cas5c ribonucleases and provide further insight into the molecular mechanisms of substrate selectivity and activity of these enzymes.
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Affiliation(s)
- Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - M Anca Serbanescu
- Faculty of Dentistry, Dental Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, Illinois, USA
| | - Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kemin Tan
- X-Ray Science Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Andrzej Joachimiak
- X-Ray Science Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dennis G Cvitkovitch
- Faculty of Dentistry, Dental Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, UK.
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129
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van Beljouw SPB, Haagsma AC, Rodríguez-Molina A, van den Berg DF, Vink JNA, Brouns SJJ. The gRAMP CRISPR-Cas effector is an RNA endonuclease complexed with a caspase-like peptidase. Science 2021; 373:1349-1353. [PMID: 34446442 DOI: 10.1126/science.abk2718] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Sam P B van Beljouw
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Anna C Haagsma
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Alicia Rodríguez-Molina
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Daan F van den Berg
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Jochem N A Vink
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
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130
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Rajput M, Choudhary K, Kumar M, Vivekanand V, Chawade A, Ortiz R, Pareek N. RNA Interference and CRISPR/Cas Gene Editing for Crop Improvement: Paradigm Shift towards Sustainable Agriculture. PLANTS 2021; 10:plants10091914. [PMID: 34579446 PMCID: PMC8467553 DOI: 10.3390/plants10091914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 01/09/2023]
Abstract
With the rapid population growth, there is an urgent need for innovative crop improvement approaches to meet the increasing demand for food. Classical crop improvement approaches involve, however, a backbreaking process that cannot equipoise with increasing crop demand. RNA-based approaches i.e., RNAi-mediated gene regulation and the site-specific nuclease-based CRISPR/Cas9 system for gene editing has made advances in the efficient targeted modification in many crops for the higher yield and resistance to diseases and different stresses. In functional genomics, RNA interference (RNAi) is a propitious gene regulatory approach that plays a significant role in crop improvement by permitting the downregulation of gene expression by small molecules of interfering RNA without affecting the expression of other genes. Gene editing technologies viz. the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) have appeared prominently as a powerful tool for precise targeted modification of nearly all crops' genome sequences to generate variation and accelerate breeding efforts. In this regard, the review highlights the diverse roles and applications of RNAi and CRISPR/Cas9 system as powerful technologies to improve agronomically important plants to enhance crop yields and increase tolerance to environmental stress (biotic or abiotic). Ultimately, these technologies can prove to be important in view of global food security and sustainable agriculture.
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Affiliation(s)
- Meenakshi Rajput
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer 305801, Rajasthan, India; (M.R.); (K.C.); (M.K.)
| | - Khushboo Choudhary
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer 305801, Rajasthan, India; (M.R.); (K.C.); (M.K.)
| | - Manish Kumar
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer 305801, Rajasthan, India; (M.R.); (K.C.); (M.K.)
| | - V. Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology, Jaipur 302017, Rajasthan, India;
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden;
- Correspondence: (A.C.); (N.P.)
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden;
| | - Nidhi Pareek
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer 305801, Rajasthan, India; (M.R.); (K.C.); (M.K.)
- Correspondence: (A.C.); (N.P.)
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131
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Programmable RNA targeting with the single-protein CRISPR effector Cas7-11. Nature 2021; 597:720-725. [PMID: 34489594 DOI: 10.1038/s41586-021-03886-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 08/09/2021] [Indexed: 12/13/2022]
Abstract
CRISPR-Cas interference is mediated by Cas effector nucleases that are either components of multisubunit complexes-in class 1 CRISPR-Cas systems-or domains of a single protein-in class 2 systems1-3. Here we show that the subtype III-E effector Cas7-11 is a single-protein effector in the class 1 CRISPR-Cas systems originating from the fusion of a putative Cas11 domain and multiple Cas7 subunits that are derived from subtype III-D. Cas7-11 from Desulfonema ishimotonii (DiCas7-11), when expressed in Escherichia coli, has substantial RNA interference effectivity against mRNAs and bacteriophages. Similar to many class 2 effectors-and unique among class 1 systems-DiCas7-11 processes pre-CRISPR RNA into mature CRISPR RNA (crRNA) and cleaves RNA at positions defined by the target:spacer duplex, without detectable non-specific activity. We engineered Cas7-11 for RNA knockdown and editing in mammalian cells. We show that Cas7-11 has no effects on cell viability, whereas other RNA-targeting tools (such as short hairpin RNAs and Cas13) show substantial cell toxicity4,5. This study illustrates the evolution of a single-protein effector from multisubunit class 1 effector complexes, expanding our understanding of the diversity of CRISPR systems. Cas7-11 provides the basis for new programmable RNA-targeting tools that are free of collateral activity and cell toxicity.
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132
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Huang M, Liu M, Huang L, Wang M, Jia R, Zhu D, Chen S, Zhao X, Zhang S, Gao Q, Zhang L, Cheng A. The activation and limitation of the bacterial natural transformation system: The function in genome evolution and stability. Microbiol Res 2021; 252:126856. [PMID: 34454311 DOI: 10.1016/j.micres.2021.126856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 12/26/2022]
Abstract
Bacteria can take up exogenous naked DNA and integrate it into their genomes, which has been regarded as a main contributor to bacterial evolution. The competent status of bacteria is influenced by environmental cues and by the immune systems of bacteria. Here, we review recent advances in understanding the working mechanisms underlying activation of the natural transformation system and limitations thereof. Environmental stresses including the presence of antimicrobials can activate the natural transformation system. However, bacterial enzymes (nucleases), non-coding RNAs, specific DNA sequences, the restriction-modification (R-M) systems, CRISPR-Cas systems and prokaryotic Argonaute proteins (Agos) are have been found to be involved in the limitation of the natural transformation system. Together, this review represents an opportunity to gain insight into bacterial genome stability and evolution.
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Affiliation(s)
- Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Li Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, PR China.
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133
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Steens JA, Zhu Y, Taylor DW, Bravo JPK, Prinsen SHP, Schoen CD, Keijser BJF, Ossendrijver M, Hofstra LM, Brouns SJJ, Shinkai A, van der Oost J, Staals RHJ. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. Nat Commun 2021; 12:5033. [PMID: 34413302 PMCID: PMC8376896 DOI: 10.1038/s41467-021-25337-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Characteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3' end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5' end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range.
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Affiliation(s)
- Jurre A Steens
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- Scope Biosciences, Wageningen, The Netherlands
| | - Yifan Zhu
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | - Cor D Schoen
- BioInteractions and Plant Health, Wageningen Plant Research, Wageningen, The Netherlands
| | | | | | - L Marije Hofstra
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
| | - Akeo Shinkai
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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134
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Lin J, Shen Y, Ni J, She Q. A type III-A CRISPR-Cas system mediates co-transcriptional DNA cleavage at the transcriptional bubbles in close proximity to active effectors. Nucleic Acids Res 2021; 49:7628-7643. [PMID: 34197611 PMCID: PMC8287949 DOI: 10.1093/nar/gkab590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 12/26/2022] Open
Abstract
Many type III CRISPR–Cas systems rely on the cyclic oligoadenylate (cOA) signaling pathway to exert immunization. However, LdCsm, a type III-A lactobacilli immune system mediates efficient plasmid clearance in spite of lacking cOA signaling. Thus, the system provides a good model for detailed characterization of the RNA-activated DNase in vitro and in vivo. We found ATP functions as a ligand to enhance the LdCsm ssDNase, and the ATP enhancement is essential for in vivo plasmid clearance. In vitro assays demonstrated LdCsm cleaved transcriptional bubbles at any positions in non-template strand, suggesting that DNA cleavage may occur for transcribing DNA. Destiny of target plasmid versus nontarget plasmid in Escherichia coli cells was investigated, and this revealed that the LdCsm effectors mediated co-transcriptional DNA cleavage to both target and nontarget plasmids, suggesting LdCsm effectors can mediate DNA cleavage to any transcriptional bubbles in close proximity upon activation. Subcellular locations of active LdCsm effectors were then manipulated by differential expression of LdCsm and CTR, and the data supported the hypothesis. Strikingly, stepwise induction experiments indicated allowing diffusion of LdCsm effector led to massive chromosomal DNA degradation, suggesting this unique IIIA system can facilitate infection abortion to eliminate virus-infected cells.
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Affiliation(s)
- Jinzhong Lin
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Jimo, Qingdao, Shandong 266237, P.R. China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Jimo, Qingdao, Shandong 266237, P.R. China
| | - Jinfeng Ni
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Jimo, Qingdao, Shandong 266237, P.R. China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Jimo, Qingdao, Shandong 266237, P.R. China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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135
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Jia N, Patel DJ. Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins. Nat Rev Mol Cell Biol 2021; 22:563-579. [PMID: 34089013 DOI: 10.1038/s41580-021-00371-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
CRISPR loci and Cas proteins provide adaptive immunity in prokaryotes against invading bacteriophages and plasmids. In response, bacteriophages have evolved a broad spectrum of anti-CRISPR proteins (anti-CRISPRs) to counteract and overcome this immunity pathway. Numerous anti-CRISPRs have been identified to date, which suppress single-subunit Cas effectors (in CRISPR class 2, type II, V and VI systems) and multisubunit Cascade effectors (in CRISPR class 1, type I and III systems). Crystallography and cryo-electron microscopy structural studies of anti-CRISPRs bound to effector complexes, complemented by functional experiments in vitro and in vivo, have identified four major CRISPR-Cas suppression mechanisms: inhibition of CRISPR-Cas complex assembly, blocking of target binding, prevention of target cleavage, and degradation of cyclic oligonucleotide signalling molecules. In this Review, we discuss novel mechanistic insights into anti-CRISPR function that have emerged from X-ray crystallography and cryo-electron microscopy studies, and how these structures in combination with function studies provide valuable tools for the ever-growing CRISPR-Cas biotechnology toolbox, to be used for precise and robust genome editing and other applications.
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Affiliation(s)
- Ning Jia
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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136
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Lu J, Fang W, Huang J, Li S. The application of genome editing technology in fish. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:326-346. [PMID: 37073287 PMCID: PMC10077250 DOI: 10.1007/s42995-021-00091-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Abstract
The advent and development of genome editing technology has opened up the possibility of directly targeting and modifying genomic sequences in the field of life sciences with rapid developments occurring in the last decade. As a powerful tool to decipher genome data at the molecular biology level, genome editing technology has made important contributions to elucidating many biological problems. Currently, the three most widely used genome editing technologies include: zinc finger nucleases (ZFN), transcription activator like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR). Researchers are still striving to create simpler, more efficient, and accurate techniques, such as engineered base editors and new CRISPR/Cas systems, to improve editing efficiency and reduce off-target rate, as well as a near-PAMless SpCas9 variants to expand the scope of genome editing. As one of the important animal protein sources, fish has significant economic value in aquaculture. In addition, fish is indispensable for research as it serves as the evolutionary link between invertebrates and higher vertebrates. Consequently, genome editing technologies were applied extensively in various fish species for basic functional studies as well as applied research in aquaculture. In this review, we focus on the application of genome editing technologies in fish species detailing growth, gender, and pigmentation traits. In addition, we have focused on the construction of a zebrafish (Danio rerio) disease model and high-throughput screening of functional genes. Finally, we provide some of the future perspectives of this technology.
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Affiliation(s)
- Jianguo Lu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080 China
| | - Wenyu Fang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
| | - Shizhu Li
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082 China
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137
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Zhao J, Tan Z, Wang L, Lei C, Nie Z. A ligation-driven CRISPR-Cas biosensing platform for non-nucleic acid target detections. Chem Commun (Camb) 2021; 57:7051-7054. [PMID: 34179901 DOI: 10.1039/d1cc02578c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Herein, we describe a CRISPR-Cas12a sensing platform activated by a DNA ligation reaction for the sensitive detection of non-nucleic acid targets, including NAD+, ATP and polynucleotide kinase (PNK). In this design, the DNA ligation reaction triggered by these biomolecules generates DNA duplexes, which can activate the nuclease activity of Cas12a to produce amplified fluorescence signals. As a result, this work provides an alternative strategy to expand the applicability of the CRISPR-Cas system into the detection of non-nucleic acid biomolecules.
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Affiliation(s)
- Jiali Zhao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China.
| | - Zhen Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China.
| | - Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China.
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China.
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138
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Isaev AB, Musharova OS, Severinov KV. Microbial Arsenal of Antiviral Defenses. Part II. BIOCHEMISTRY (MOSCOW) 2021; 86:449-470. [PMID: 33941066 DOI: 10.1134/s0006297921040064] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). The constant threat of phage infection is a major force that shapes evolution of microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering had been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection. In the first part defense associated with cell surface, roles of small molecules, and innate immunity systems relying on DNA modification were discussed. The second part focuses on adaptive immunity systems, abortive infection mechanisms, defenses associated with mobile genetic elements, and novel systems discovered in recent years through metagenomic mining.
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Affiliation(s)
- Artem B Isaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia.
| | - Olga S Musharova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia. .,Institute of Molecular Genetics, Moscow, 119334, Russia
| | - Konstantin V Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia. .,Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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139
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Perčulija V, Lin J, Zhang B, Ouyang S. Functional Features and Current Applications of the RNA-Targeting Type VI CRISPR-Cas Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004685. [PMID: 34254038 PMCID: PMC8209922 DOI: 10.1002/advs.202004685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/26/2021] [Indexed: 05/14/2023]
Abstract
CRISPR-Cas systems are a form of prokaryotic adaptive immunity that employs RNA-guided endonucleases (Cas effectors) to cleave foreign genetic elements. Due to their simplicity, targeting programmability, and efficiency, single-effector CRISPR-Cas systems have great potential for application in research, biotechnology, and therapeutics. While DNA-targeting Cas effectors such as Cas9 and Cas12a have become indispensable tools for genome editing in the past decade, the more recent discovery of RNA-targeting CRISPR-Cas systems has opened the door for implementation of CRISPR-Cas technology in RNA manipulation. With an increasing number of studies reporting their application in transcriptome engineering, viral interference, nucleic acid detection, and RNA imaging, type VI CRISPR-Cas systems and the associated Cas13 effectors particularly hold promise as RNA-targeting or RNA-binding tools. However, even though previous structural and biochemical characterization provided a firm basis for leveraging type VI CRISPR-Cas systems into such tools, the lack of comprehension of certain mechanisms underlying their functions hinders more sophisticated and conventional use. This review will summarize current knowledge on structural and mechanistic properties of type VI CRISPR-Cas systems, give an overview on the reported applications, and discuss functional features that need further investigation in order to improve performance of Cas13-based tools.
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Affiliation(s)
- Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
- International College of Chinese StudiesFujian Normal UniversityFuzhou350117China
| | - Jinying Lin
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
| | - Bo Zhang
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and Technology (Qingdao)Qingdao266237China
- National Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
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140
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Xue C, Greene EC. DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing. Trends Genet 2021; 37:639-656. [PMID: 33896583 PMCID: PMC8187289 DOI: 10.1016/j.tig.2021.02.008] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/14/2022]
Abstract
Many clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based genome editing technologies take advantage of Cas nucleases to induce DNA double-strand breaks (DSBs) at desired locations within a genome. Further processing of the DSBs by the cellular DSB repair machinery is then necessary to introduce desired mutations, sequence insertions, or gene deletions. Thus, the accuracy and efficiency of genome editing are influenced by the cellular DSB repair pathways. DSBs are themselves highly genotoxic lesions and as such cells have evolved multiple mechanisms for their repair. These repair pathways include homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single-strand annealing (SSA). In this review, we briefly highlight CRISPR-Cas9 and then describe the mechanisms of DSB repair. Finally, we summarize recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced DSBs.
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Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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141
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Padilha VA, Alkhnbashi OS, Tran VD, Shah SA, Carvalho ACPLF, Backofen R. Casboundary: automated definition of integral Cas cassettes. Bioinformatics 2021; 37:1352-1359. [PMID: 33226067 PMCID: PMC8208735 DOI: 10.1093/bioinformatics/btaa984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION CRISPR-Cas are important systems found in most archaeal and many bacterial genomes, providing adaptive immunity against mobile genetic elements in prokaryotes. The CRISPR-Cas systems are encoded by a set of consecutive cas genes, here termed cassette. The identification of cassette boundaries is key for finding cassettes in CRISPR research field. This is often carried out by using Hidden Markov Models and manual annotation. In this article, we propose the first method able to automatically define the cassette boundaries. In addition, we present a Cas-type predictive model used by the method to assign each gene located in the region defined by a cassette's boundaries a Cas label from a set of pre-defined Cas types. Furthermore, the proposed method can detect potentially new cas genes and decompose a cassette into its modules. RESULTS We evaluate the predictive performance of our proposed method on data collected from the two most recent CRISPR classification studies. In our experiments, we obtain an average similarity of 0.86 between the predicted and expected cassettes. Besides, we achieve F-scores above 0.9 for the classification of cas genes of known types and 0.73 for the unknown ones. Finally, we conduct two additional study cases, where we investigate the occurrence of potentially new cas genes and the occurrence of module exchange between different genomes. AVAILABILITY AND IMPLEMENTATION https://github.com/BackofenLab/Casboundary. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Victor A Padilha
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, SP 13566-590, Brazil
| | - Omer S Alkhnbashi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Van Dinh Tran
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Shiraz A Shah
- COPSAC, Copenhagen University Hospitals Herlev and Gentofte, DK-2820 Gentofte, Denmark
| | - André C P L F Carvalho
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, SP 13566-590, Brazil
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
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142
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Long C, Dai L, E C, Da LT, Yu J. Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2. Biophys J 2021; 120:3126-3137. [PMID: 34197800 PMCID: PMC8390960 DOI: 10.1016/j.bpj.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/10/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cas1 and Cas2 are highly conserved proteins across clustered-regularly-interspaced-short-palindromic-repeat-Cas systems and play a significant role in protospacer acquisition. Based on crystal structure of twofold symmetric Cas1-Cas2 in complex with dual-forked protospacer DNA (psDNA), we conducted all-atom molecular dynamics simulations to study the psDNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence, or PAMc, of Cas1-Cas2. In the simulation, we noticed that two active sites of Cas1 and Cas1’ bind asymmetrically to two identical PAMc on the psDNA captured from the crystal structure. For the modified psDNA containing only one PAMc, as that to be recognized by Cas1-Cas2 in general, our simulations show that the non-PAMc association site of Cas1-Cas2 remains destabilized until after the stably bound PAMc being cleaved at the corresponding association site. Thus, long-range correlation appears to exist upon the PAMc cleavage between the two active sites (∼10 nm apart) on Cas1-Cas2, which can be allosterically mediated by psDNA and Cas2 and Cas2’ in bridging. To substantiate such findings, we conducted repeated runs and further simulated Cas1-Cas2 in complex with synthesized psDNA sequences psL and psH, which have been measured with low and high frequency in acquisition, respectively. Notably, such intersite correlation becomes even more pronounced for the Cas1-Cas2 in complex with psH but remains low for the Cas1-Cas2 in complex with psL. Hence, our studies demonstrate that PAMc recognition and cleavage at one active site of Cas1-Cas2 may allosterically regulate non-PAMc association or even cleavage at the other site, and such regulation can be mediated by noncatalytic Cas2 and DNA protospacer to possibly support the ensued psDNA acquisition.
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Affiliation(s)
- Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Liqiang Dai
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China; Beijing Computational Science Research Center, Beijing, China
| | - Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai, China
| | - Jin Yu
- Departments of Physics and Astronomy and Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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143
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Santiago-Frangos A, Hall LN, Nemudraia A, Nemudryi A, Krishna P, Wiegand T, Wilkinson RA, Snyder DT, Hedges JF, Cicha C, Lee HH, Graham A, Jutila MA, Taylor MP, Wiedenheft B. Intrinsic signal amplification by type III CRISPR-Cas systems provides a sequence-specific SARS-CoV-2 diagnostic. Cell Rep Med 2021; 2:100319. [PMID: 34075364 PMCID: PMC8157118 DOI: 10.1016/j.xcrm.2021.100319] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/04/2021] [Accepted: 05/20/2021] [Indexed: 12/23/2022]
Abstract
There is an urgent need for inexpensive new technologies that enable fast, reliable, and scalable detection of viruses. Here, we repurpose the type III CRISPR-Cas system for sensitive and sequence-specific detection of SARS-CoV-2. RNA recognition by the type III CRISPR complex triggers Cas10-mediated polymerase activity, which simultaneously generates pyrophosphates, protons, and cyclic oligonucleotides. We show that all three Cas10-polymerase products are detectable using colorimetric or fluorometric readouts. We design ten guide RNAs that target conserved regions of SARS-CoV-2 genomes. Multiplexing improves the sensitivity of amplification-free RNA detection from 107 copies/μL for a single guide RNA to 106 copies/μL for ten guides. To decrease the limit of detection to levels that are clinically relevant, we developed a two-pot reaction consisting of RT-LAMP followed by T7-transcription and type III CRISPR-based detection. The two-pot reaction has a sensitivity of 200 copies/μL and is completed using patient samples in less than 30 min.
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Affiliation(s)
| | - Laina N. Hall
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Anna Nemudraia
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Artem Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Pushya Krishna
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Royce A. Wilkinson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Deann T. Snyder
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Jodi F. Hedges
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Calvin Cicha
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Helen H. Lee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Ava Graham
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Mark A. Jutila
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Matthew P. Taylor
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
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144
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Seok H, Deng R, Cowan DB, Wang DZ. Application of CRISPR-Cas9 gene editing for congenital heart disease. Clin Exp Pediatr 2021; 64:269-279. [PMID: 33677855 PMCID: PMC8181018 DOI: 10.3345/cep.2020.02096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/15/2021] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR-Cas9) is an ancient prokaryotic defense system that precisely cuts foreign genomic DNA under the control of a small number of guide RNAs. The CRISPR-Cas9 system facilitates efficient double-stranded DNA cleavage that has been recently adopted for genome editing to create or correct inherited genetic mutations causing disease. Congenital heart disease (CHD) is generally caused by genetic mutations such as base substitutions, deletions, and insertions, which result in diverse developmental defects and remains a leading cause of birth defects. Pediatric CHD patients exhibit a spectrum of cardiac abnormalities such as septal defects, valvular defects, and abnormal chamber development. CHD onset occurs during the prenatal period and often results in early lethality during childhood. Because CRISPR-Cas9-based genome editing technology has gained considerable attention for its potential to prevent and treat diseases, we will review the CRISPR-Cas9 system as a genome editing tool and focus on its therapeutic application for CHD.
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Affiliation(s)
- Heeyoung Seok
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Rui Deng
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Douglas B Cowan
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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145
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Taylor HN, Laderman E, Armbrust M, Hallmark T, Keiser D, Bondy-Denomy J, Jackson RN. Positioning Diverse Type IV Structures and Functions Within Class 1 CRISPR-Cas Systems. Front Microbiol 2021; 12:671522. [PMID: 34093491 PMCID: PMC8175902 DOI: 10.3389/fmicb.2021.671522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/26/2021] [Indexed: 12/26/2022] Open
Abstract
Type IV CRISPR systems encode CRISPR associated (Cas)-like proteins that combine with small RNAs to form multi-subunit ribonucleoprotein complexes. However, the lack of Cas nucleases, integrases, and other genetic features commonly observed in most CRISPR systems has made it difficult to predict type IV mechanisms of action and biological function. Here we summarize recent bioinformatic and experimental advancements that collectively provide the first glimpses into the function of specific type IV subtypes. We also provide a bioinformatic and structural analysis of type IV-specific proteins within the context of multi-subunit (class 1) CRISPR systems, informing future studies aimed at elucidating the function of these cryptic systems.
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Affiliation(s)
- Hannah N. Taylor
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Eric Laderman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | - Matt Armbrust
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Thomson Hallmark
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Dylan Keiser
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | - Ryan N. Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
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146
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Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex. Nat Commun 2021; 12:2571. [PMID: 33958590 PMCID: PMC8102632 DOI: 10.1038/s41467-021-22900-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/26/2021] [Indexed: 02/03/2023] Open
Abstract
CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1-Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.
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147
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Zhao R, Yang Y, Zheng F, Zeng Z, Feng W, Jin X, Wang J, Yang K, Liang YX, She Q, Han W. A Membrane-Associated DHH-DHHA1 Nuclease Degrades Type III CRISPR Second Messenger. Cell Rep 2021; 32:108133. [PMID: 32937129 DOI: 10.1016/j.celrep.2020.108133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/21/2020] [Accepted: 08/20/2020] [Indexed: 12/26/2022] Open
Abstract
Type III CRISPR-Cas systems initiate an intracellular signaling pathway to confer immunity. The signaling pathway includes synthesis of cyclic oligo-adenylate (cOA) and activation of the RNase activity of type III accessory ribonuclease Csm6/Csx1 by cOA. After the immune response, cOA should be cleared on time to avoid constant cellular RNA degradation. In this study, we find a metal-dependent cOA degradation activity in Sulfolobus islandicus. The activity is associated with the cell membrane and able to accelerate cOA clearance at a high cOA level. Further, we show that a metal-dependent and membrane-associated DHH-DHHA1 family nuclease (MAD) rapidly cleaves cOA and deactivates Csx1 ribonuclease. The cOA degradation efficiency of MAD is much higher than the cellular ring nuclease. However, the subcellular organization may prevent it from degrading nascent cOA. Together, the data suggest that MAD acts as the second cOA degrader after the ring nuclease to remove diffused redundant cOA.
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Affiliation(s)
- Ruiliang Zhao
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yang Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Fan Zheng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Wenqian Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xuexia Jin
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Jiayi Wang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ke Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, 266237 Qingdao, China; Danish Archaea Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, 2200 Copenhagen N, Denmark
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China.
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148
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Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive, heritable immunity against their viruses (bacteriophages and phages) and other parasitic genetic elements. CRISPR-Cas systems are highly diverse, and we are only beginning to understand their relative importance in phage defense. In this review, we will discuss when and why CRISPR-Cas immunity against phages evolves, and how this, in turn, selects for the evolution of immune evasion by phages. Finally, we will discuss our current understanding of if, and when, we observe coevolution between CRISPR-Cas systems and phages, and how this may be influenced by the mechanism of CRISPR-Cas immunity.
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149
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Prakash A, Kumar M. Characterizing the transcripts of Leptospira CRISPR I-B array and its processing with endoribonuclease LinCas6. Int J Biol Macromol 2021; 182:785-795. [PMID: 33862076 DOI: 10.1016/j.ijbiomac.2021.04.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/08/2021] [Accepted: 04/10/2021] [Indexed: 12/26/2022]
Abstract
In Leptospira interrogans serovar Copenhageni, the CRISPR-Cas I-B locus possesses a CRISPR array between the two independent cas-operons. Using the reverse transcription-PCR and the in vitro endoribonuclease assay with Cas6 of Leptospira (LinCas6), we account that the CRISPR is transcriptionally active and is conventionally processed. The LinCas6 specifically excises at one site within the synthetic cognate repeat RNA or the repeats of precursor-CRISPR RNA (pre-crRNA) in the sense direction. In contrast, the antisense repeat RNA is cleaved at multiple sites. LinCas6 functions as a single turnover endoribonuclease on its repeat RNA substrate, where substitution of one of predicted active site residues (His38) resulted in reduced activity. This study highlights the comprehensive understanding of the Leptospira CRISPR array transcription and its processing by LinCas6 that is central to RNA-mediated CRISPR-Cas I-B adaptive immunity.
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Affiliation(s)
- Aman Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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150
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Riediger M, Spät P, Bilger R, Voigt K, Maček B, Hess WR. Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). THE PLANT CELL 2021; 33:248-269. [PMID: 33793824 PMCID: PMC8136920 DOI: 10.1093/plcell/koaa017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/12/2020] [Indexed: 05/23/2023]
Abstract
Although regulatory small RNAs have been reported in photosynthetic cyanobacteria, the lack of clear RNA chaperones involved in their regulation poses a conundrum. Here, we analyzed the full complement of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in Synechocystis 6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished, supporting the high quality of this approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include an YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. The Synechocystis Grad-seq resource is available online at https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/ providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism.
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Affiliation(s)
- Matthias Riediger
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Philipp Spät
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Raphael Bilger
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Karsten Voigt
- IT Administration, Institute of Biology 3, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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