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Structure and mechanism of the RNA dependent RNase Cas13a from Rhodobacter capsulatus. Commun Biol 2022; 5:71. [PMID: 35058543 PMCID: PMC8776769 DOI: 10.1038/s42003-022-03025-4] [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: 06/28/2021] [Accepted: 12/27/2021] [Indexed: 11/09/2022] Open
Abstract
Cas13a are single-molecule effectors of the Class II, Type VI family of CRISPR-Cas systems that are part of the bacterial and archaeal defense systems. These RNA-guided and RNA-activated RNA endonucleases are characterized by their ability to cleave target RNAs complementary to the crRNA-spacer sequence, as well as bystander RNAs in a sequence-unspecific manner. Due to cleavage of cellular transcripts they induce dormancy in the host cell and thus protect the bacterial population by aborting the infectious cycle of RNA-phages. Here we report the structural and functional characterization of a Cas13a enzyme from the photo-auxotrophic purple bacteria Rhodobacter capsulatus. The X-ray crystal structure of the RcCas13a-crRNA complex reveals its distinct crRNA recognition mode as well as the enzyme in its contracted, pre-activation conformation. Using site-directed mutagenesis in combination with mass spectrometry, we identified key residues responsible for pre-crRNA processing by RcCas13a in its distinct catalytic site, and elucidated the acid-base mediated cleavage reaction mechanism. In addition, RcCas13a cleaves target-RNA as well as bystander-RNAs in Escherichia coli which requires its catalytic active HEPN (higher eukaryotes and prokaryotes nucleotide binding) domain nuclease activity. Our data provide further insights into the molecular mechanisms and function of this intriguing family of RNA-dependent RNA endonucleases that are already employed as efficient tools for RNA detection and regulation of gene expression. The structure of the Cas13a RNase from the purple bacterium R. capsulatus in complex with its crRNA is reported here. The study reveals that the enzyme combines shape and sequence-specific readout to recognize its crRNA.
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Sohail M, Xie S, Zhang X, Li B. Methodologies in visualizing the activation of CRISPR/Cas: The last mile in developing CRISPR-Based diagnostics and biosensing – A review. Anal Chim Acta 2022; 1205:339541. [DOI: 10.1016/j.aca.2022.339541] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
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Deogharia M, Gurha P. The "guiding" principles of noncoding RNA function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 13:e1704. [PMID: 34856642 DOI: 10.1002/wrna.1704] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/09/2021] [Accepted: 11/11/2021] [Indexed: 12/25/2022]
Abstract
The human genome is pervasively transcribed and yet only a small fraction of these RNAs (less than 2%) are known to code for proteins. The vast majority of the RNAs are classified as noncoding RNAs (ncRNAs) and are further subgrouped as small (shorter than 200 bases) and long noncoding RNAs. The ncRNAs have been identified in all three domains of life and regulate diverse cellular processes through transcriptional and posttranscriptional gene regulation. Most of these RNAs work in conjunction with proteins forming a wide array of base pairing interactions. The determinants of these base pairing interactions are now becoming more evident and show striking similarities among the diverse group of ncRNAs. Here we present a mechanistic overview of pairing between RNA-RNA or RNA-DNA that dictates the function of ncRNAs; we provide examples to illustrate that ncRNAs work through shared evolutionary mechanisms that encompasses a guide-target interaction, involving not only classical Watson-Crick but also noncanonical Wobble and Hoogsteen base pairing. We also highlight the similarities in target selection, proofreading, and the ruler mechanism of ncRNA-protein complexes that confers target specificity and target site selection. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA-Based Catalysis > RNA-Mediated Cleavage RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Manisha Deogharia
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.,University of Texas Health Sciences Center at Houston, Houston, Texas, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.,University of Texas Health Sciences Center at Houston, Houston, Texas, USA
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Wang SY, Du YC, Wang DX, Ma JY, Tang AN, Kong DM. Signal amplification and output of CRISPR/Cas-based biosensing systems: A review. Anal Chim Acta 2021; 1185:338882. [PMID: 34711321 DOI: 10.1016/j.aca.2021.338882] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/30/2021] [Accepted: 07/23/2021] [Indexed: 12/14/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) proteins are powerful gene-editing tools because of their ability to accurately recognize and manipulate nucleic acids. Besides gene-editing function, they also show great promise in biosensing applications due to the superiority of easy design and precise targeting. To improve the performance of CRISPR/Cas-based biosensing systems, various nucleic acid-based signal amplification techniques are elaborately incorporated. The incorporation of these amplification techniques not only greatly increases the detection sensitivity and specificity, but also extends the detectable target range, as well as makes the use of various signal output modes possible. Therefore, summarizing the use of signal amplification techniques in sensing systems and elucidating their roles in improving sensing performance are very necessary for the development of more superior CRISPR/Cas-based biosensors for various applications. In this review, CRISPR/Cas-based biosensors are summarized from two aspects: the incorporation of signal amplification techniques in three kinds of CRISPR/Cas-based biosensing systems (Cas9, Cas12 and Cas13-based ones) and the signal output modes used by these biosensors. The challenges and prospects for the future development of CRISPR/Cas-based biosensors are also discussed.
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Affiliation(s)
- Si-Yuan Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China.
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An B, Zhang H, Su X, Guo Y, Wu T, Ge Y, Zhu F, Cui L. Rapid and Sensitive Detection of Salmonella spp. Using CRISPR-Cas13a Combined With Recombinase Polymerase Amplification. Front Microbiol 2021; 12:732426. [PMID: 34733250 PMCID: PMC8558462 DOI: 10.3389/fmicb.2021.732426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
Salmonella spp. is one of the most common foodborne disease-causing pathogens that can cause severe diseases in very low infectious doses. Rapid and sensitive detecting Salmonella spp. is advantageous to the control of its spread. In this study, a conserved short fragment of the Salmonella invA gene was selected and used to design primers and specific crRNA (CRISPR RNA) for establishing a one-tube and two-step reaction system for Salmonella spp. detection, by combining recombinase polymerase amplification (RPA) with CRISPR-Cas13a (Clustered Regularly Interspaced Short Palindromic Repeats associated protein 13a) cleavage. The established one-tube RPA-Cas13a method can complete the detection within 20 min and the two-step RPA-Cas13a method detection time within 45 min. The designed primers were highly specific to Salmonella spp. and had no cross-reaction with the other nine diarrheal bacteria. The one-tube RPA-Cas13a could detect the Salmonella genome with the limit of 102 copies, which was the same as real-time polymerase chain reaction (PCR), but less sensitive than two-step RPA-Cas13a (100 copies). The detection results of one-tube or two-step RPA-Cas13a and real-time PCR were highly consistent in clinical samples. One-tube RPA-Cas13a developed in this study provides a simple, rapid, and specific detection method for Salmonella spp. While two-step assay was more sensitive and suitable for samples at low abundance.
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Affiliation(s)
- Bailin An
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,College of Pharmacy, Nankai University, Tianjin, China
| | - Hongbin Zhang
- Jiangyin City Center for Disease Control and Prevention, Wuxi, China
| | - Xuan Su
- College of Pharmacy, Nankai University, Tianjin, China
| | - Yue Guo
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tao Wu
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yiyue Ge
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Fengcai Zhu
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Lunbiao Cui
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
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Wu Y, Jin W, Wang Q, Zhou J, Wang Y, Tan Y, Cui X, Tong F, Yang E, Wang J, Kang C. Precise editing of FGFR3-TACC3 fusion genes with CRISPR-Cas13a in glioblastoma. Mol Ther 2021; 29:3305-3318. [PMID: 34274537 PMCID: PMC8571169 DOI: 10.1016/j.ymthe.2021.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/10/2021] [Accepted: 07/07/2021] [Indexed: 11/28/2022] Open
Abstract
FGFR3-TACC3 (F3-T3) gene fusions are regarded as a "low-hanging fruit" paradigm for precision therapy in human glioblastoma (GBM). Small molecules designed to target the kinase in FGFR currently serve as one form of potential treatment but cause off-target effects and toxicity. Here, CRISPR-Cas13a, which is known to directly suppress gene expression at the transcriptional level and induce a collateral effect in eukaryotes, was leveraged as a possible precision therapy in cancer cells harboring F3-T3 fusion genes. A library consisting of crRNAs targeting the junction site of F3-T3 was designed, and an in silico simulation scheme was created to select the optimal crRNA candidates. An optimal crRNA, crRNA1, showed efficiency and specificity in inducing the collateral effect in only U87 cells expressing F3-T3 (U87-F3-T3). Expression profiles obtained with microarray analysis were consistent with induction of the collateral effect by the CRISPR-Cas13a system. Tumor cell proliferation and colony formation were decreased in U87-F3-T3 cells expressing the Cas13a-based tool, and tumor growth was suppressed in an orthotopic tumor model in mice. These findings demonstrate that the CRISPR-Cas13a system induces the collateral damage effect in cancer cells and provides a viable strategy for precision tumor therapy based on the customized design of a CRISPR-Cas13a-based tool against F3-T3 fusion genes.
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MESH Headings
- Animals
- Biomarkers, Tumor
- CRISPR-Cas Systems
- Cell Line, Tumor
- Disease Models, Animal
- Disease Progression
- Gene Editing
- Gene Expression
- Gene Expression Profiling
- Glioblastoma/genetics
- Glioblastoma/pathology
- Heterografts
- Humans
- Hydrogen Bonding
- Mice
- Microtubule-Associated Proteins/chemistry
- Microtubule-Associated Proteins/genetics
- Models, Molecular
- Nucleic Acid Conformation
- Oncogene Proteins, Fusion/chemistry
- Oncogene Proteins, Fusion/genetics
- Protein Binding
- Protein Conformation
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Receptor, Fibroblast Growth Factor, Type 3/chemistry
- Receptor, Fibroblast Growth Factor, Type 3/genetics
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Affiliation(s)
- Ye Wu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China
| | - Weili Jin
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China
| | - Qixue Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China
| | - Junhu Zhou
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China
| | - Yunfei Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China
| | - Yanli Tan
- Department of Pathology, Hebei University School of Basic Medical Sciences, Hebei 071000, China; Department of Pathology, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, China
| | - Xiaoteng Cui
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China
| | - Fei Tong
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China
| | - Eryan Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China
| | - Jian Wang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Shandong University, 107 Wenhua Xi Road, Jinan 250012, China; Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, 5009 Bergen, Norway.
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin City, Tianjin 300052, China.
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57
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Kordyś M, Sen R, Warkocki Z. Applications of the versatile CRISPR-Cas13 RNA targeting system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1694. [PMID: 34553495 DOI: 10.1002/wrna.1694] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas are adaptable natural prokaryotic defense systems that act against invading viruses and plasmids. Among the six currently known major CRISPR-Cas types, the type VI CRISPR-Cas13 is the only one known to exclusively bind and cleave foreign RNA. Within the last couple of years, this system has been adapted to serve numerous, and sometimes not obvious, applications, including some that might be developed as effective molecular therapies. Indeed, Cas13 has been adapted to kill antibiotic-resistant bacteria. In a cell-free environment, Cas13 has been used in the development of highly specific, sensitive, multiplexing-capable, and field-adaptable detection tools. Importantly, Cas13 can be reprogrammed and applied to eukaryotes to either combat pathogenic RNA viruses or in the regulation of gene expression, facilitating the knockdown of mRNA, circular RNA, and noncoding RNA. Furthermore, Cas13 has been harnessed for in vivo RNA modifications including programmable regulation of alternative splicing, A-to-I and C to U editing, and m6A modifications. Finally, approaches allowing for the detection and characterization of RNA-interacting proteins have also been demonstrated. Here, we provide a comprehensive overview of the applications utilizing CRISPR-Cas13 that illustrate its versatility. We also discuss the most important limitations of the CRISPR-Cas13-based technologies, and controversies regarding them. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Martyna Kordyś
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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58
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Gong S, Zhang S, Lu F, Pan W, Li N, Tang B. CRISPR/Cas-Based In Vitro Diagnostic Platforms for Cancer Biomarker Detection. Anal Chem 2021; 93:11899-11909. [PMID: 34427091 DOI: 10.1021/acs.analchem.1c02533] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Timely diagnosis is of great benefit to improve the survival rate of cancer patients. Body fluid cancer biomarker detection is a critical kind of noninvasive method for cancer diagnosis. Nevertheless, traditional methods for cancer biomarker detection always rely on a large-scale instrument and involve sophisticated operation. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based in vitro diagnosis can simplify the detection procedures and improve sensitivity and specificity, holding great promise as the next-generation molecular diagnostic technology. In this Feature, we introduce the working mechanisms of different kinds of CRISPR/Cas systems for biosensing and CRISPR/Cas-mediated detection strategies for different kinds of cancer biomarkers including nucleic acids, proteins, and extracellular vesicles. In addition, the perspective and challenges of CRISPR/Cas-based strategies for cancer biomarkers are discussed.
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Affiliation(s)
- Shaohua Gong
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Shiqi Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Fei Lu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
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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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60
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Recent advances in CRISPR technologies for genome editing. Arch Pharm Res 2021; 44:537-552. [PMID: 34164771 DOI: 10.1007/s12272-021-01336-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/01/2021] [Indexed: 02/06/2023]
Abstract
The discovery of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system, and its development into a set of powerful tools for manipulating the genome, has revolutionized genome editing. Precise, targeted CRISPR/Cas-based genome editing has become the most widely used platform in organisms ranging from plants to animals. The CRISPR/Cas system has been extensively modified to increase its efficiency and fidelity. In addition, the fusion of various protein motifs to Cas effector proteins has facilitated diverse set of genetic manipulations, such as base editing, transposition, recombination, and epigenetic regulation. The CRISPR/Cas system is undergoing continuous development to overcome current limitations, including off-target effects, narrow targeting scope, and issues associated with the delivery of CRISPR components for genome engineering and therapeutic approaches. Here, we review recent progress in a diverse array of CRISPR/Cas-based tools. We also describe limitations and concerns related to the use of CRISPR/Cas technologies.
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61
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Palaz F, Kalkan AK, Can Ö, Demir AN, Tozluyurt A, Özcan A, Ozsoz M. CRISPR-Cas13 System as a Promising and Versatile Tool for Cancer Diagnosis, Therapy, and Research. ACS Synth Biol 2021; 10:1245-1267. [PMID: 34037380 DOI: 10.1021/acssynbio.1c00107] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Over the past decades, significant progress has been made in targeted cancer therapy. In precision oncology, molecular profiling of cancer patients enables the use of targeted cancer therapeutics. However, current diagnostic methods for molecular analysis of cancer are costly and require sophisticated equipment. Moreover, targeted cancer therapeutics such as monoclonal antibodies and small-molecule drugs may cause off-target effects and they are available for only a minority of cancer driver proteins. Therefore, there is still a need for versatile, efficient, and precise tools for cancer diagnostics and targeted cancer treatment. In recent years, the CRISPR-based genome and transcriptome engineering toolbox has expanded rapidly. Particularly, the RNA-targeting CRISPR-Cas13 system has unique biochemical properties, making Cas13 a promising tool for cancer diagnosis, therapy, and research. Cas13-based diagnostic methods allow early detection and monitoring of cancer markers from liquid biopsy samples without the need for complex instrumentation. In addition, Cas13 can be used for targeted cancer therapy through degrading and manipulating cancer-associated transcripts with high efficiency and specificity. Moreover, Cas13-mediated programmable RNA manipulation tools offer invaluable opportunities for cancer research, identification of drug-resistance mechanisms, and discovery of novel therapeutic targets. Here, we review and discuss the current use and potential applications of the CRISPR-Cas13 system in cancer diagnosis, therapy, and research. Thus, researchers will gain a deep understanding of CRISPR-Cas13 technologies, which have the potential to be used as next-generation cancer diagnostics and therapeutics.
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Affiliation(s)
- Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | | | - Özgür Can
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Ayça Nur Demir
- Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar 03100, Turkey
| | - Abdullah Tozluyurt
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Ahsen Özcan
- Institute of Genetic Engineering and Biotechnology, TUBITAK Marmara Research Center, Kocaeli 41470, Turkey
| | - Mehmet Ozsoz
- Department of Biomedical Engineering, Near East University, 10 Mersin, Nicosia, Turkey
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Yao R, Xu Y, Wang L, Wang D, Ren L, Ren C, Li C, Li X, Ni W, He Y, Hu R, Guo T, Li Y, Li L, Wang X, Hu S. CRISPR-Cas13a-Based Detection for Bovine Viral Diarrhea Virus. Front Vet Sci 2021; 8:603919. [PMID: 34179152 PMCID: PMC8219879 DOI: 10.3389/fvets.2021.603919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/21/2021] [Indexed: 12/26/2022] Open
Abstract
Bovine Viral Diarrhea Virus (BVDV) is the main pathogen of bovine viral diarrhea disease (BVD), which leads to enormous economic losses in the cattle industry. A sensitive and specific detection for BVDV is advantageous to the control of BVDV. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have been used for detecting virus RNA. In this study, the expression and purification of LwCas13a protein was optimized and the RNase activity of LwCas13a in vitro was verified. CRISPR-LwCas13a system could detect BVDV virus and BVDV RNA with high specificity and simplicity. The detection limit of the LwCas13a system was 103 pM, and there were no cross-reactions with HEK293T and MDBK. In summary, a sensitive, specific, and simple nucleic acid detection method based on CRISPR-Cas13a was developed for BVDV. This method provides a new detection strategy for early diagnosis of BVDV.
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Affiliation(s)
- Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Lang Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Linchang Ren
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Changling Ren
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Cunyuan Li
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yanhua He
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Tao Guo
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yaxin Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Lei Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Xiaokui Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, China
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63
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Wang B, Zhang T, Yin J, Yu Y, Xu W, Ding J, Patel DJ, Yang H. Structural basis for self-cleavage prevention by tag:anti-tag pairing complementarity in type VI Cas13 CRISPR systems. Mol Cell 2021; 81:1100-1115.e5. [PMID: 33472057 PMCID: PMC8274241 DOI: 10.1016/j.molcel.2020.12.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/26/2020] [Accepted: 12/18/2020] [Indexed: 12/21/2022]
Abstract
Bacteria and archaea apply CRISPR-Cas surveillance complexes to defend against foreign invaders. These invading genetic elements are captured and integrated into the CRISPR array as spacer elements, guiding sequence-specific DNA/RNA targeting and cleavage. Recently, in vivo studies have shown that target RNAs with extended complementarity with repeat sequences flanking the target element (tag:anti-tag pairing) can dramatically reduce RNA cleavage by the type VI-A Cas13a system. Here, we report the cryo-EM structure of Leptotrichia shahii LshCas13acrRNA in complex with target RNA harboring tag:anti-tag pairing complementarity, with the observed conformational changes providing a molecular explanation for inactivation of the composite HEPN domain cleavage activity. These structural insights, together with in vitro biochemical and in vivo cell-based assays on key mutants, define the molecular principles underlying Cas13a's capacity to target and discriminate between self and non-self RNA targets. Our studies illuminate approaches to regulate Cas13a's cleavage activity, thereby influencing Cas13a-mediated biotechnological applications.
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Affiliation(s)
- Beibei Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Tianlong Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Yin
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - You Yu
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wenhao Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Hui Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
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64
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Ke Y, Huang S, Ghalandari B, Li S, Warden AR, Dang J, Kang L, Zhang Y, Wang Y, Sun Y, Wang J, Cui D, Zhi X, Ding X. Hairpin-Spacer crRNA-Enhanced CRISPR/Cas13a System Promotes the Specificity of Single Nucleotide Polymorphism (SNP) Identification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003611. [PMID: 33747742 PMCID: PMC7967054 DOI: 10.1002/advs.202003611] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/05/2020] [Indexed: 06/12/2023]
Abstract
The Cas13a system has great potential in RNA interference and molecular diagnostic fields. However, lacking guidelines for crRNA design hinders practical applications of the Cas13a system in RNA editing and single nucleotide polymorphism identification. This study posits that crRNAs with hairpin spacers improve the specificity of CRISPR/Cas13a system (termed hs-CRISPR). Gibbs free energy analysis suggests that the hairpin-spacer crRNAs (hs-crRNAs) suppress Cas13a's affinity to off-target RNA. A hepatitis B virus DNA genotyping platform is established to further validate the high-specificity of hs-CRISPR/Cas13a system. Compared to ordinary crRNA, hs-crRNAs increase the specificity by threefold without sacrificing the sensitivity of the CRISPR/Cas13a system. Furthermore, the mechanism of the Cas13a/hs-crRNA/target RNA composition is elucidated with theoretical simulations. This work builds on the fundamental understanding of Cas13a activation and offers significant improvements for the rational design of crRNA for the CRISPR/Cas13a system.
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Affiliation(s)
- Yuqing Ke
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Shiyi Huang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Behafarid Ghalandari
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Sijie Li
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Antony R. Warden
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Jingqi Dang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Lin Kang
- State Key Laboratory of Pathogen and BiosecurityInstitute of Microbiology and EpidemiologyBeijing100071China
| | - Yu Zhang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Yunqing Wang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Yiqing Sun
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Jinglin Wang
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Daxiang Cui
- Shanghai Engineering Centre for Intelligent Diagnosis and Treatment InstrumentSchool of Electronic Information and Electrical EngineeringShanghai Jiao Tong UniversityShanghai200240China
| | - Xiao Zhi
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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65
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Safari F, Afarid M, Rastegari B, Borhani-Haghighi A, Barekati-Mowahed M, Behzad-Behbahani A. CRISPR systems: Novel approaches for detection and combating COVID-19. Virus Res 2021; 294:198282. [PMID: 33428981 PMCID: PMC7832022 DOI: 10.1016/j.virusres.2020.198282] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/13/2020] [Accepted: 12/27/2020] [Indexed: 02/06/2023]
Abstract
Type V and VI CRISPR enzymes are RNA-guided, DNA and RNA-targeting effectors that allow specific gene knockdown. Cas12 and Cas13 are CRISPR proteins that are efficient agents for diagnosis and combating single-stranded RNA (ssRNA) viruses. The programmability of these proteins paves the way for the detection and degradation of RNA viruses by targeting RNAs complementary to its CRISPR RNA (crRNA). Approximately two-thirds of viruses causing diseases contain ssRNA genomes. The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has caused the outbreak of the coronavirus disease 2019 (COVID-19), which has infected more than 88 million people worldwide with near 2 million deaths since December 2019. Thus, accurate and rapid diagnostic and therapeutic tools are essential for early detection and treatment of this widespread infectious disease. For us, the CRISPR based platforms seem to be a plausible new approach for an accurate detection and treatment of SARS-CoV-2. In this review, we talk about Cas12 and Cas13 CRISPR systems and their applications in diagnosis and treatment of RNA virus mediated diseases. In continue, the SARS-CoV-2 pathogenicity, and its conventional diagnostics and antivirals will be discussed. Moreover, we highlight novel CRISPR based diagnostic platforms and therapies for COVID-19. We also discuss the challenges of diagnostic CRISPR based platforms as well as clarifying the proposed solution for high efficient selective in vivo delivery of CRISPR components into SARS-CoV-2-infected cells.
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Affiliation(s)
- Fatemeh Safari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Afarid
- Shooshtari Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Banafsheh Rastegari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mazyar Barekati-Mowahed
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, OH, USA
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
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66
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Pillon MC, Gordon J, Frazier MN, Stanley RE. HEPN RNases - an emerging class of functionally distinct RNA processing and degradation enzymes. Crit Rev Biochem Mol Biol 2021; 56:88-108. [PMID: 33349060 PMCID: PMC7856873 DOI: 10.1080/10409238.2020.1856769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding) RNases are an emerging class of functionally diverse RNA processing and degradation enzymes. Members are defined by a small α-helical bundle encompassing a short consensus RNase motif. HEPN dimerization is a universal requirement for RNase activation as the conserved RNase motifs are precisely positioned at the dimer interface to form a composite catalytic center. While the core HEPN fold is conserved, the organization surrounding the HEPN dimer can support large structural deviations that contribute to their specialized functions. HEPN RNases are conserved throughout evolution and include bacterial HEPN RNases such as CRISPR-Cas and toxin-antitoxin associated nucleases, as well as eukaryotic HEPN RNases that adopt large multi-component machines. Here we summarize the canonical elements of the growing HEPN RNase family and identify molecular features that influence RNase function and regulation. We explore similarities and differences between members of the HEPN RNase family and describe the current mechanisms for HEPN RNase activation and inhibition.
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Affiliation(s)
- Monica C. Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Meredith N. Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E. Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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67
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Panoutsopoulos AA. Known drugs and small molecules in the battle for COVID-19 treatment. Genes Dis 2020; 7:528-534. [PMID: 32837982 PMCID: PMC7305491 DOI: 10.1016/j.gendis.2020.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/04/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
COVID-19 has been declared a pandemic by the World Health Organization on March 11th and since then more than 3 million cases and a quarter million deaths have occurred due to it. The urge to find a resultful treatment or cure is now pressing more than any other time since the outbreak of the pandemic. Researchers all over the world from different fields of expertise are trying to find the most suitable drugs, that are already known to treat other diseases, and could tackle the process of SARS-CoV2 through which it invades and replicates in human cells. Here, we discuss five of the most promising drugs that can potentially play a major role in the treatment of COVID-19. While nicotine and ivermectin may be blocking transport abilities of the virus or its components, famotidine, remdesivir and chloroquine in combination with zinc ions can deactivate important enzymes needed for the replication of the virus. While clinical trials for some of these drugs have already started, it is common knowledge that lack of organization between countries, institutes and hospitals might slow down the whole process for an official treatment based in wide, randomized, placebo controlled trials.
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Affiliation(s)
- Alexios A. Panoutsopoulos
- Department of Pathology and Laboratory Medicine, University of California, Davis, CA, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Northern California, 2425 Stockton Boulevard, Sacramento, CA, 95817, USA
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68
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.
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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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69
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Mechanisms for target recognition and cleavage by the Cas12i RNA-guided endonuclease. Nat Struct Mol Biol 2020; 27:1069-1076. [PMID: 32895556 DOI: 10.1038/s41594-020-0499-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/06/2020] [Indexed: 12/27/2022]
Abstract
Cas12i is a recently identified type V CRISPR-Cas endonuclease that predominantly cleaves the non-target strand of a double-stranded DNA substrate. This nicking activity of Cas12i could potentially be used for genome editing with high specificity. To elucidate its mechanisms for target recognition and cleavage, we determined cryo-EM structures of Cas12i in multiple functional states. Cas12i pre-orders a seven-nucleotide seed sequence of the crRNA for target recognition and undergoes a two-step activation through crRNA-DNA hybridization. Formation of 14 base pairs activates the nickase activity, and 28-bp hybridization promotes cleavage of the target strand. The atomic structures and mechanistic insights gained should facilitate the manipulation of Cas12i for genome editing applications.
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70
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Panoutsopoulos AA. Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms. ACTA ACUST UNITED AC 2020; 2:859-864. [PMID: 32838145 PMCID: PMC7303432 DOI: 10.1007/s42399-020-00360-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2020] [Indexed: 12/15/2022]
Abstract
COVID-19 has been declared a pandemic by the World Health Organization on March 11, and since then, more than 3 million cases and a quarter million deaths have occurred due to it. Lately, there is a growing evidence for an ophthalmologic symptom (conjunctivitis) to be connected with the disease. This seems to happen in early stages of the infection by SARS-CoV-2, and thus, it is of major importance to understand the mechanism through which the virus can facilitate such a symptom. Here, we are proposing a molecular mechanism through which the novel coronavirus could act in order to affect the eye and use it as another, secondary but alternative, point of entry to the host organism.
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Affiliation(s)
- Alexios A Panoutsopoulos
- Department of Pathology and Laboratory Medicine, University of California, Davis, CA USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Northern California, 2425 Stockton Boulevard, Sacramento, CA 95817 USA
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71
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Zhang N, Jing X, Liu Y, Chen M, Zhu X, Jiang J, Wang H, Li X, Hao P. Interfering with retrotransposition by two types of CRISPR effectors: Cas12a and Cas13a. Cell Discov 2020; 6:30. [PMID: 32435507 PMCID: PMC7235257 DOI: 10.1038/s41421-020-0164-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
CRISPRs are a promising tool being explored in combating exogenous retroviral pathogens and in disabling endogenous retroviruses for organ transplantation. The Cas12a and Cas13a systems offer novel mechanisms of CRISPR actions that have not been evaluated for retrovirus interference. Particularly, a latest study revealed that the activated Cas13a provided bacterial hosts with a "passive protection" mechanism to defend against DNA phage infection by inducing cell growth arrest in infected cells, which is especially significant as it endows Cas13a, a RNA-targeting CRISPR effector, with mount defense against both RNA and DNA invaders. Here, by refitting long terminal repeat retrotransposon Tf1 as a model system, which shares common features with retrovirus regarding their replication mechanism and life cycle, we repurposed CRISPR-Cas12a and -Cas13a to interfere with Tf1 retrotransposition, and evaluated their different mechanisms of action. Cas12a exhibited strong inhibition on retrotransposition, allowing marginal Tf1 transposition that was likely the result of a lasting pool of Tf1 RNA/cDNA intermediates protected within virus-like particles. The residual activities, however, were completely eliminated with new constructs for persistent crRNA targeting. On the other hand, targeting Cas13a to Tf1 RNA intermediates significantly inhibited Tf1 retrotransposition. However, unlike in bacterial hosts, the sustained activation of Cas13a by Tf1 transcripts did not cause cell growth arrest in S. pombe, indicating that virus-activated Cas13a likely acted differently in eukaryotic cells. The study gained insight into the actions of novel CRISPR mechanisms in combating retroviral pathogens, and established system parameters for developing new strategies in treatment of retrovirus-related diseases.
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Affiliation(s)
- Niubing Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
- School of Life Sciences, Henan University, 475000 Kaifeng, Henan China
| | - Xinyun Jing
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Yuanhua Liu
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Minjie Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
- School of Life Sciences, Henan University, 475000 Kaifeng, Henan China
| | - Xianfeng Zhu
- School of Life Sciences, Henan University, 475000 Kaifeng, Henan China
| | - Jing Jiang
- School of Life Sciences, Henan University, 475000 Kaifeng, Henan China
| | - Hongbing Wang
- Department of Physiology, Michigan State University, East Lansing, MI USA
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031 China
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72
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High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage. Cell Rep 2020; 26:3741-3751.e5. [PMID: 30917325 DOI: 10.1016/j.celrep.2019.02.094] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/07/2019] [Accepted: 02/22/2019] [Indexed: 12/14/2022] Open
Abstract
Type VI CRISPR-Cas systems contain programmable single-effector RNA-guided RNases, including Cas13b, one of the four known family members. Cas13b, which has been used for both RNA editing and nucleic acid detection, is unique among type VI CRISPR effectors in its linear domain architecture and CRISPR RNA (crRNA) structure. Here, we report the crystal structure of Prevotella buccae Cas13b (PbuCas13b) bound to crRNA at 1.65 Å resolution. This structure, combined with biochemical experiments assaying the stability, kinetics, and function of Cas13b, provides a mechanistic model for Cas13b target RNA recognition and identifies features responsible for target and cleavage specificity. Based on these observations, we generated Cas13b variants with altered cleavage preferences, which may expand the utility of nuclease-based RNA detection assays and other applications of Cas13b in mammalian cells.
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73
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He Q, Yu D, Bao M, Korensky G, Chen J, Shin M, Kim J, Park M, Qin P, Du K. High-throughput and all-solution phase African Swine Fever Virus (ASFV) detection using CRISPR-Cas12a and fluorescence based point-of-care system. Biosens Bioelectron 2020; 154:112068. [DOI: 10.1016/j.bios.2020.112068] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/21/2019] [Accepted: 02/01/2020] [Indexed: 12/27/2022]
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74
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Pillon MC, Goslen KH, Gordon J, Wells ML, Williams JG, Stanley RE. It takes two (Las1 HEPN endoribonuclease domains) to cut RNA correctly. J Biol Chem 2020; 295:5857-5870. [PMID: 32220933 DOI: 10.1074/jbc.ra119.011193] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 03/23/2020] [Indexed: 12/26/2022] Open
Abstract
The ribosome biogenesis factor Las1 is an essential endoribonuclease that is well-conserved across eukaryotes and a newly established member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain-containing nuclease family. HEPN nucleases participate in diverse RNA cleavage pathways and share a short HEPN nuclease motif (RφXXXH) important for RNA cleavage. Most HEPN nucleases participate in stress-activated RNA cleavage pathways; Las1 plays a fundamental role in processing pre-rRNA. Underscoring the significance of Las1 function in the cell, mutations in the human LAS1L (LAS1-like) gene have been associated with neurological dysfunction. Two juxtaposed HEPN nuclease motifs create Las1's composite nuclease active site, but the roles of the individual HEPN motif residues are poorly defined. Here using a combination of in vivo experiments in Saccharomyces cerevisiae and in vitro assays, we show that both HEPN nuclease motifs are required for Las1 nuclease activity and fidelity. Through in-depth sequence analysis and systematic mutagenesis, we determined the consensus HEPN motif in the Las1 subfamily and uncovered its canonical and specialized elements. Using reconstituted Las1 HEPN-HEPN' chimeras, we defined the molecular requirements for RNA cleavage. Intriguingly, both copies of the Las1 HEPN motif were important for nuclease function, revealing that both HEPN motifs participate in coordinating the RNA within the Las1 active site. We also established that conformational flexibility of the two HEPN domains is important for proper nuclease function. The results of our work reveal critical information about how dual HEPN domains come together to drive Las1-mediated RNA cleavage.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Kevin H Goslen
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Jacob Gordon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Melissa L Wells
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709.
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75
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Behler J, Hess WR. Approaches to study CRISPR RNA biogenesis and the key players involved. Methods 2020; 172:12-26. [PMID: 31325492 DOI: 10.1016/j.ymeth.2019.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/29/2019] [Accepted: 07/15/2019] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins provide an inheritable and adaptive immune system against phages and foreign genetic elements in many bacteria and archaea. The three stages of CRISPR-Cas immunity comprise adaptation, CRISPR RNA (crRNA) biogenesis and interference. The maturation of the pre-crRNA into mature crRNAs, short guide RNAs that target invading nucleic acids, is crucial for the functionality of CRISPR-Cas defense systems. Mature crRNAs assemble with Cas proteins into the ribonucleoprotein (RNP) effector complex and guide the Cas nucleases to the cognate foreign DNA or RNA target. Experimental approaches to characterize these crRNAs, the specific steps toward their maturation and the involved factors, include RNA-seq analyses, enzyme assays, methods such as cryo-electron microscopy, the crystallization of proteins, or UV-induced protein-RNA crosslinking coupled to mass spectrometry analysis. Complex and multiple interactions exist between CRISPR-cas-encoded specific riboendonucleases such as Cas6, Cas5d and Csf5, endonucleases with dual functions in maturation and interference such as the enzymes of the Cas12 and Cas13 families, and nucleases belonging to the cell's degradosome such as RNase E, PNPase and RNase J, both in the maturation as well as in interference. The results of these studies have yielded a picture of unprecedented diversity of sequences, enzymes and biochemical mechanisms.
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Affiliation(s)
- Juliane Behler
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany; University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany.
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76
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Chen Q, Tian T, Xiong E, Wang P, Zhou X. CRISPR/Cas13a Signal Amplification Linked Immunosorbent Assay for Femtomolar Protein Detection. Anal Chem 2019; 92:573-577. [PMID: 31849223 DOI: 10.1021/acs.analchem.9b04403] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The enzyme-linked immunosorbent assay (ELISA) is a basic technique used in analytical and clinical investigations. However, conventional ELISA is still not sensitive enough to detect ultralow concentrations of biomarkers for the early diagnosis of cancer, cardiovascular risk, neurological disorders, and infectious diseases. Herein we show a mechanism utilizing the CRISPR/Cas13a-based signal export amplification strategy, which double-amplifies the output signal by T7 RNA polymerase transcription and CRISPR/Cas13a collateral cleavage activity. This process is termed the CRISPR/Cas13a signal amplification linked immunosorbent assay (CLISA). The proposed method was validated by detecting an inflammatory factor, human interleukin-6 (human IL-6), and a tumor marker, human vascular endothelial growth factor (human VEGF), which achieved limit of detection (LOD) values of 45.81 fg/mL (2.29 fM) and 32.27 fg/mL (0.81 fM), respectively, demonstrating that CLISA is at least 102-fold more sensitive than conventional ELISA.
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Affiliation(s)
- Qian Chen
- School of Chemistry and Materials Science , Jiangsu Normal University , Xuzhou 221116 , China
| | - Tian Tian
- School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Erhu Xiong
- School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Po Wang
- School of Chemistry and Materials Science , Jiangsu Normal University , Xuzhou 221116 , China
| | - Xiaoming Zhou
- School of Life Sciences , South China Normal University , Guangzhou 510631 , China
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77
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78
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Zhang Z, Wang Q, Liu Q, Zheng Y, Zheng C, Yi K, Zhao Y, Gu Y, Wang Y, Wang C, Zhao X, Shi L, Kang C, Liu Y. Dual-Locking Nanoparticles Disrupt the PD-1/PD-L1 Pathway for Efficient Cancer Immunotherapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1905751. [PMID: 31709671 DOI: 10.1002/adma.201905751] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/15/2019] [Indexed: 06/10/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) enzyme, Cas13a, holds great promise in cancer treatment due to its potential for selective destruction of tumor cells via collateral effects after target recognition. However, these collateral effects do not specifically target tumor cells and may cause safety issues when administered systemically. Herein, a dual-locking nanoparticle (DLNP) that can restrict CRISPR/Cas13a activation to tumor tissues is described. DLNP has a core-shell structure, in which the CRISPR/Cas13a system (plasmid DNA, pDNA) is encapsulated inside the core with a dual-responsive polymer layer. This polymer layer endows the DLNP with enhanced stability during blood circulation or in normal tissues and facilitates cellular internalization of the CRISPR/Cas13a system and activation of gene editing upon entry into tumor tissue. After carefully screening and optimizing the CRISPR RNA (crRNA) sequence that targets programmed death-ligand 1 (PD-L1), DLNP demonstrates the effective activation of T-cell-mediated antitumor immunity and the reshaping of immunosuppressive tumor microenvironment (TME) in B16F10-bearing mice, resulting in significantly enhanced antitumor effect and improved survival rate. Further development by replacing the specific crRNA of target genes can potentially make DLNP a universal platform for the rapid development of safe and efficient cancer immunotherapies.
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Affiliation(s)
- Zhanzhan Zhang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Qixue Wang
- Tianjin Neurological Institute, Key Laboratory of Post-Neurotrauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Qi Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yadan Zheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chunxiong Zheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Kaikai Yi
- Tianjin Neurological Institute, Key Laboratory of Post-Neurotrauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yu Zhao
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yu Gu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Ying Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chun Wang
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xinzhi Zhao
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Linqi Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Chunsheng Kang
- Tianjin Neurological Institute, Key Laboratory of Post-Neurotrauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin, 300071, China
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Pei Y, Lu M. Programmable RNA manipulation in living cells. Cell Mol Life Sci 2019; 76:4861-4867. [PMID: 31367845 PMCID: PMC11105762 DOI: 10.1007/s00018-019-03252-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/23/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
RNAs are responsible for mediating genetic information flow within the cell. RNA splicing, modification, trafficking, translation, and stability are all controlled at the transcript level. However, biological tools to study and manipulate them in a programmable fashion are currently limited. In this review, we summarize recent advances regarding available RNA-targeting systems discovered so far, including CRISPR-based technologies-Cas9 and Cas13, and programmable RNA-binding proteins-PUF and PPR. These tools allow transcript-specific manipulation in gene expression.
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Affiliation(s)
- Yu Pei
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Mingxing Lu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong.
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80
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Ghogare R, Williamson-Benavides B, Ramírez-Torres F, Dhingra A. CRISPR-associated nucleases: the Dawn of a new age of efficient crop improvement. Transgenic Res 2019; 29:1-35. [PMID: 31677059 DOI: 10.1007/s11248-019-00181-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/23/2019] [Indexed: 12/26/2022]
Abstract
The world stands at a new threshold today. As a planet, we face various challenges, and the key one is how to continue to produce enough food, feed, fiber, and fuel to support the burgeoning population. In the past, plant breeding and the ability to genetically engineer crops contributed to increasing food production. However, both approaches rely on random mixing or integration of genes, and the process can be unpredictable and time-consuming. Given the challenge of limited availability of natural resources and changing environmental conditions, the need to rapidly and precisely improve crops has become urgent. The discovery of CRISPR-associated endonucleases offers a precise yet versatile platform for rapid crop improvement. This review summarizes a brief history of the discovery of CRISPR-associated nucleases and their application in genome editing of various plant species. Also provided is an overview of several new endonucleases reported recently, which can be utilized for editing of specific genes in plants through various forms of DNA sequence alteration. Genome editing, with its ever-expanding toolset, increased efficiency, and its potential integration with the emerging synthetic biology approaches hold promise for efficient crop improvement to meet the challenge of supporting the needs of future generations.
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81
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Dedow LK, Bailey-Serres J. Searching for a Match: Structure, Function and Application of Sequence-Specific RNA-Binding Proteins. PLANT & CELL PHYSIOLOGY 2019; 60:1927-1938. [PMID: 31329953 DOI: 10.1093/pcp/pcz072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/11/2019] [Indexed: 05/21/2023]
Abstract
Plants encode over 1800 RNA-binding proteins (RBPs) that modulate a myriad of steps in gene regulation from chromatin organization to translation, yet only a small number of these proteins and their target transcripts have been functionally characterized. Two classes of eukaryotic RBPs, pentatricopeptide repeat (PPR) and pumilio/fem-3 binding factors (PUF), recognize and bind to specific sequential RNA sequences through protein-RNA interactions. These modular proteins possess helical structural units containing key residues with high affinity for specific nucleotides, whose sequential order determines binding to a specific target RNA sequence. PPR proteins are nucleus-encoded, but largely regulate post-transcriptional gene regulation within plastids and mitochondria, including splicing, translation and RNA editing. Plant PUFs are involved in gene regulatory processes within the cell nucleus and cytoplasm. The modular structures of PPRs and PUFs that determine sequence specificity has facilitated identification of their RNA targets and biological functions. The protein-based RNA-targeting of PPRs and PUFs contrasts to the prokaryotic cluster regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas) that target RNAs in prokaryotes. Together the PPR, PUF and CRISPR-Cas systems provide varied opportunities for RNA-targeted engineering applications.
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82
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Pillon MC, Hsu AL, Krahn JM, Williams JG, Goslen KH, Sobhany M, Borgnia MJ, Stanley RE. Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex. Nat Struct Mol Biol 2019; 26:830-839. [PMID: 31488907 PMCID: PMC6733591 DOI: 10.1038/s41594-019-0289-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022]
Abstract
Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The endoribonuclease (RNase) Las1 and the polynucleotide kinase (PNK) Grc3 assemble into a multienzyme complex, herein designated RNase PNK, to orchestrate processing of precursor ribosomal RNA (rRNA). RNase PNK belongs to the functionally diverse HEPN nuclease superfamily, whose members rely on distinct cues for nuclease activation. To establish how RNase PNK coordinates its dual enzymatic activities, we solved a series of cryo-EM structures of Chaetomium thermophilum RNase PNK in multiple conformational states. The structures reveal that RNase PNK adopts a butterfly-like architecture, harboring a composite HEPN nuclease active site flanked by discrete RNA kinase sites. We identify two molecular switches that coordinate nuclease and kinase function. Together, our structures and corresponding functional studies establish a new mechanism of HEPN nuclease activation essential for ribosome production.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, USA
| | - Kevin H Goslen
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, USA
| | - Mack Sobhany
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC, USA.
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83
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Jing X, Xie B, Chen L, Zhang N, Jiang Y, Qin H, Wang H, Hao P, Yang S, Li X. Implementation of the CRISPR-Cas13a system in fission yeast and its repurposing for precise RNA editing. Nucleic Acids Res 2019; 46:e90. [PMID: 29860393 PMCID: PMC6125684 DOI: 10.1093/nar/gky433] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/08/2018] [Indexed: 12/13/2022] Open
Abstract
In contrast to genome editing, which introduces genetic changes at the DNA level, disrupting or editing gene transcripts provides a distinct approach to perturbing a genetic system, offering benefits complementary to classic genetic approaches. To develop a new toolset for manipulating RNA, we first implemented a member of the type VI CRISPR systems, Cas13a from Leptotrichia shahii (LshCas13a), in Schizosaccharomyces pombe, an important model organism employed by biologists to study key cellular mechanisms conserved from yeast to humans. This approach was shown to knock down targeted endogenous gene transcripts with different efficiencies. Second, we engineered an RNA editing system by tethering an inactive form of LshCas13a (dCas13) to the catalytic domain of human adenosine deaminase acting on RNA type 2 (hADAR2d), which was shown to be programmable with crRNA to target messenger RNAs and precisely edit specific nucleotide residues. We optimized system parameters using a dual-fluorescence reporter and demonstrated the utility of the system in editing randomly selected endogenous gene transcripts. We further used it to restore the transposition of retrotransposon Tf1 mutants in fission yeast, providing a potential novel toolset for retrovirus manipulation and interference.
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Affiliation(s)
- Xinyun Jing
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Bingran Xie
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Longxian Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Niubing Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.,School of Life Sciences, Henan University, Kaifeng 475000, China
| | - Yiyi Jiang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hang Qin
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hongbing Wang
- Department of Physiology, Michigan State University, East Lansing, Michigan, United States of America
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Abstract
Abstract
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.
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85
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Zhang B, Ye Y, Ye W, Perčulija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S. Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d. Nat Commun 2019; 10:2544. [PMID: 31186424 PMCID: PMC6559982 DOI: 10.1038/s41467-019-10507-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/16/2019] [Indexed: 12/18/2022] Open
Abstract
Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg2+ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3'-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.
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Affiliation(s)
- Bo Zhang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266237, Qingdao, China
| | - Yangmiao Ye
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Weiwei Ye
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Han Jiang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yiyang Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yu Li
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Jing Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Jinying Lin
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Siqi Wang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Qi Chen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Rd., 10617, Taipei, Taiwan
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China.
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266237, Qingdao, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
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86
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Geraldi A, Giri-Rachman EA. Synthetic biology-based portable in vitro diagnostic platforms. ALEXANDRIA JOURNAL OF MEDICINE 2019. [DOI: 10.1016/j.ajme.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Almando Geraldi
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Mulyorejo, Surabaya, 60115, Indonesia
| | - Ernawati Arifin Giri-Rachman
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha No. 10, Bandung, 40132, Indonesia
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87
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Qin P, Park M, Alfson KJ, Tamhankar M, Carrion R, Patterson JL, Griffiths A, He Q, Yildiz A, Mathies R, Du K. Rapid and Fully Microfluidic Ebola Virus Detection with CRISPR-Cas13a. ACS Sens 2019; 4:1048-1054. [PMID: 30860365 DOI: 10.1021/acssensors.9b00239] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Highly infectious illness caused by pathogens is endemic especially in developing nations where there is limited laboratory infrastructure and trained personnel. Rapid point-of-care (POC) serological assays with minimal sample manipulation and low cost are desired in clinical practice. In this study, we report an automated POC system for Ebola RNA detection with RNA-guided RNA endonuclease Cas13a, utilizing its collateral RNA degradation after its activation. After automated microfluidic mixing and hybridization, nonspecific cleavage products of Cas13a are immediately measured by a custom integrated fluorometer which is small in size and convenient for in-field diagnosis. Within 5 min, a detection limit of 20 pfu/mL (5.45 × 107 copies/mL) of purified Ebola RNA is achieved. This isothermal and fully solution-based diagnostic method is rapid, amplification-free, simple, and sensitive, thus establishing a key technology toward a useful POC diagnostic platform.
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Affiliation(s)
- Peiwu Qin
- Department of Physics, University of California, Berkeley, Berkeley, California 94720, United States
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Myeongkee Park
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Dong-A University, Busan 49315, Republic of Korea
| | - Kendra J. Alfson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Manasi Tamhankar
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Jean L. Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts 02118, United States
| | - Qian He
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Ahmet Yildiz
- Department of Physics, University of California, Berkeley, Berkeley, California 94720, United States
| | - Richard Mathies
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ke Du
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
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88
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O'Connell MR. Molecular Mechanisms of RNA Targeting by Cas13-containing Type VI CRISPR-Cas Systems. J Mol Biol 2019; 431:66-87. [PMID: 29940185 DOI: 10.1016/j.jmb.2018.06.029] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 12/11/2022]
Abstract
Prokaryotic adaptive immune systems use Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR-associated (Cas) proteins for RNA-guided cleavage of foreign genetic elements. The focus of this review, Type VI CRISPR-Cas systems, contain a single protein, Cas13 (formerly C2c2) that when assembled with a CRISPR RNA (crRNA) forms a crRNA-guided RNA-targeting effector complex. Type VI CRISPR-Cas systems can be divided into four subtypes (A-D) based on Cas13 phylogeny. All Cas13 proteins studied to date possess two enzymatically distinct ribonuclease activities that are required for optimal interference. One RNase is responsible for pre-crRNA processing to form mature Type VI interference complexes, while the other RNase activity provided by the two Higher Eukaryotes and Prokaryotes Nucleotide-binding (HEPN) domains, is required for degradation of target-RNA during viral interference. In this review, I will compare and contrast what is known about the molecular architecture and behavior of Type VI (A-D) CRISPR-Cas13 interference complexes, how this allows them to carry out their RNA-targeting function, how Type VI accessory proteins are able to modulate Cas13 activity, and how together all of these features have led to the rapid development of a range of RNA-targeting applications. Throughout I will also discuss some of the outstanding questions regarding Cas13's molecular behavior, and its role in bacterial adaptive immunity and RNA-targeting applications.
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Affiliation(s)
- Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
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89
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Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 2018; 362:839-842. [PMID: 30337455 PMCID: PMC6659742 DOI: 10.1126/science.aav4294] [Citation(s) in RCA: 583] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/06/2018] [Indexed: 12/18/2022]
Abstract
CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 to 1400 amino acids) has been considered essential to their specific DNA- or RNA-targeting activities. Here we present a set of CRISPR-Cas systems from uncultivated archaea that contain Cas14, a family of exceptionally compact RNA-guided nucleases (400 to 700 amino acids). Despite their small size, Cas14 proteins are capable of targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements. Moreover, target recognition by Cas14 triggers nonspecific cutting of ssDNA molecules, an activity that enables high-fidelity single-nucleotide polymorphism genotyping (Cas14-DETECTR). Metagenomic data show that multiple CRISPR-Cas14 systems evolved independently and suggest a potential evolutionary origin of single-effector CRISPR-based adaptive immunity.
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Affiliation(s)
- Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David Burstein
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
| | - Janice S Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Isaac P Witte
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
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90
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Terns MP. CRISPR-Based Technologies: Impact of RNA-Targeting Systems. Mol Cell 2018; 72:404-412. [PMID: 30388409 PMCID: PMC6239212 DOI: 10.1016/j.molcel.2018.09.018] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/06/2018] [Accepted: 09/13/2018] [Indexed: 12/26/2022]
Abstract
DNA-targeting CRISPR-Cas systems, such as those employing the RNA-guided Cas9 or Cas12 endonucleases, have revolutionized our ability to predictably edit genomes and control gene expression. Here, I summarize information on RNA-targeting CRISPR-Cas systems and describe recent advances in converting them into powerful and programmable RNA-binding and cleavage tools with a wide range of novel and important biotechnological and biomedical applications.
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Affiliation(s)
- Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA; Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
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91
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Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D. Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d. Cell 2018; 175:212-223.e17. [PMID: 30241607 PMCID: PMC6179368 DOI: 10.1016/j.cell.2018.09.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/01/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas endonucleases directed against foreign nucleic acids mediate prokaryotic adaptive immunity and have been tailored for broad genetic engineering applications. Type VI-D CRISPR systems contain the smallest known family of single effector Cas enzymes, and their signature Cas13d ribonuclease employs guide RNAs to cleave matching target RNAs. To understand the molecular basis for Cas13d function and explain its compact molecular architecture, we resolved cryoelectron microscopy structures of Cas13d-guide RNA binary complex and Cas13d-guide-target RNA ternary complex to 3.4 and 3.3 Å resolution, respectively. Furthermore, a 6.5 Å reconstruction of apo Cas13d combined with hydrogen-deuterium exchange revealed conformational dynamics that have implications for RNA scanning. These structures, together with biochemical and cellular characterization, provide insights into its RNA-guided, RNA-targeting mechanism and delineate a blueprint for the rational design of improved transcriptome engineering technologies.
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Affiliation(s)
- Cheng Zhang
- Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Silvana Konermann
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Nicholas J Brideau
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter Lotfy
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Xuebing Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Timothy Strutzenberg
- Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Patrick D Hsu
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Dmitry Lyumkis
- Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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92
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Tambe A, East-Seletsky A, Knott GJ, Doudna JA, O'Connell MR. RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a. Cell Rep 2018; 24:1025-1036. [PMID: 30044970 PMCID: PMC6085867 DOI: 10.1016/j.celrep.2018.06.105] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/24/2018] [Accepted: 06/27/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas13a enzymes are RNA-guided, RNA-activated RNases. Their properties have been exploited as powerful tools for RNA detection, RNA imaging, and RNA regulation. However, the relationship between target RNA binding and HEPN (higher eukaryotes and prokaryotes nucleotide binding) domain nuclease activation is poorly understood. Using sequencing experiments coupled with in vitro biochemistry, we find that Cas13a target RNA binding affinity and HEPN-nuclease activity are differentially affected by the number and the position of mismatches between the guide and the target. We identify a central binding seed for which perfect base pairing is required for target binding and a separate nuclease switch for which imperfect base pairing results in tight binding, but not HEPN-nuclease activation. These results demonstrate that the binding and cleavage activities of Cas13a are decoupled, highlighting a complex specificity landscape. Our findings underscore a need to consider the range of effects off-target recognition has on Cas13a RNA binding and cleavage behavior for RNA-targeting tool development.
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Affiliation(s)
- Akshay Tambe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexandra East-Seletsky
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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93
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Zhu Y, Klompe SE, Vlot M, van der Oost J, Staals RHJ. Shooting the messenger: RNA-targetting CRISPR-Cas systems. Biosci Rep 2018; 38:BSR20170788. [PMID: 29748239 PMCID: PMC6013697 DOI: 10.1042/bsr20170788] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 12/26/2022] Open
Abstract
Since the discovery of CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associated genes) immune systems, astonishing progress has been made on revealing their mechanistic foundations. Due to the immense potential as genome engineering tools, research has mainly focussed on a subset of Cas nucleases that target DNA. In addition, however, distinct types of RNA-targetting CRISPR-Cas systems have been identified. The focus of this review will be on the interference mechanisms of the RNA targetting type III and type VI CRISPR-Cas systems, their biological relevance and their potential for applications.
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Affiliation(s)
- Yifan Zhu
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - Sanne E Klompe
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen 6708 WE, The Netherlands
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94
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Huang CH, Lee KC, Doudna JA. Applications of CRISPR-Cas Enzymes in Cancer Therapeutics and Detection. Trends Cancer 2018; 4:499-512. [PMID: 29937048 PMCID: PMC6299457 DOI: 10.1016/j.trecan.2018.05.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022]
Abstract
Cancer is a complex disease caused by combinations of cellular genetic alterations and heterogeneous microenvironments. The use of the robust and programmable CRISPR-Cas systems has greatly improved genome editing for precision cancer modeling and enabled multiplexed genetic manipulation for cancer treatment and mutation detection. In this review, we outline the current CRISPR-Cas toolkit, and discuss the promises and hurdles in translating this revolutionary technology into effective and safe clinical applications for cancer treatment and diagnosis.
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Affiliation(s)
- Chun-Hao Huang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ko-Chuan Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
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95
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Khan MZ, Amin I, Hameed A, Mansoor S. CRISPR-Cas13a: Prospects for Plant Virus Resistance. Trends Biotechnol 2018; 36:1207-1210. [PMID: 29903474 DOI: 10.1016/j.tibtech.2018.05.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas13a is an efficient RNA targeting and editing tool characterized recently in prokaryotes. This system can be recruited to engineer resistance against plant RNA viruses and regulate gene expression. We discuss some important achievements in using the CRISPR-Cas13a system to confer resistance against plant RNA viruses.
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Affiliation(s)
- Muhammad Zuhaib Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
| | - Amir Hameed
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan.
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
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96
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Yan WX, Chong S, Zhang H, Makarova KS, Koonin EV, Cheng DR, Scott DA. Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein. Mol Cell 2018; 70:327-339.e5. [PMID: 29551514 PMCID: PMC5935466 DOI: 10.1016/j.molcel.2018.02.028] [Citation(s) in RCA: 278] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/21/2022]
Abstract
Bacterial class 2 CRISPR-Cas systems utilize a single RNA-guided protein effector to mitigate viral infection. We aggregated genomic data from multiple sources and constructed an expanded database of predicted class 2 CRISPR-Cas systems. A search for novel RNA-targeting systems identified subtype VI-D, encoding dual HEPN domain-containing Cas13d effectors and putative WYL-domain-containing accessory proteins (WYL1 and WYL-b1 through WYL-b5). The median size of Cas13d proteins is 190 to 300 aa smaller than that of Cas13a-Cas13c. Despite their small size, Cas13d orthologs from Eubacterium siraeum (Es) and Ruminococcus sp. (Rsp) are active in both CRISPR RNA processing and targeting, as well as collateral RNA cleavage, with no target-flanking sequence requirements. The RspWYL1 protein stimulates RNA cleavage by both EsCas13d and RspCas13d, demonstrating a common regulatory mechanism for divergent Cas13d orthologs. The small size, minimal targeting constraints, and modular regulation of Cas13d effectors further expands the CRISPR toolkit for RNA manipulation and detection.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Proteins/chemistry
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Databases, Genetic
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Eubacterium/enzymology
- Eubacterium/genetics
- Gene Editing/methods
- Gene Expression Regulation, Bacterial
- Nucleic Acid Conformation
- Protein Domains
- Protein Structure, Secondary
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Ruminococcus/enzymology
- Ruminococcus/genetics
- Structure-Activity Relationship
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Affiliation(s)
| | | | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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97
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Klompe SE, Sternberg SH. Harnessing "A Billion Years of Experimentation": The Ongoing Exploration and Exploitation of CRISPR-Cas Immune Systems. CRISPR J 2018; 1:141-158. [PMID: 31021200 PMCID: PMC6636882 DOI: 10.1089/crispr.2018.0012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The famed physicist-turned-biologist, Max Delbrück, once remarked that, for physicists, "the field of bacterial viruses is a fine playground for serious children who ask ambitious questions." Early discoveries in that playground helped establish molecular genetics, and half a century later, biologists delving into the same field have ushered in the era of precision genome engineering. The focus has of course shifted-from bacterial viruses and their mechanisms of infection to the bacterial hosts and their mechanisms of immunity-but it is the very same evolutionary arms race that continues to awe and inspire researchers worldwide. In this review, we explore the remarkable diversity of CRISPR-Cas adaptive immune systems, describe the molecular components that mediate nucleic acid targeting, and outline the use of these RNA-guided machines for biotechnology applications. CRISPR-Cas research has yielded far more than just Cas9-based genome-editing tools, and the wide-reaching, innovative impacts of this fascinating biological playground are sure to be felt for years to come.
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Affiliation(s)
- Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
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98
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Marshall JM, Akbari OS. Can CRISPR-Based Gene Drive Be Confined in the Wild? A Question for Molecular and Population Biology. ACS Chem Biol 2018; 13:424-430. [PMID: 29370514 DOI: 10.1021/acschembio.7b00923] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The recent discovery of CRISPR and its application as a gene editing tool has enabled a range of gene drive systems to be engineered with greater ease. In order for the benefits of this technology to be realized, in some circumstances drive systems should be developed that are capable of both spreading into populations to achieve their desired impact and being recalled in the event of unwanted consequences or public disfavor. We review the performance of three broad categories of drive systems at achieving these goals: threshold-dependent drives, homing-based drive and remediation systems, and temporally self-limiting systems such as daisy-chain drives.
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Affiliation(s)
- John M Marshall
- Divisions of Biostatistics and Epidemiology, School of Public Health, University of California , Berkeley, California 94720, United States
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San Diego , La Jolla, California 92093, United States of America
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99
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100
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Stella S, Alcón P, Montoya G. Class 2 CRISPR-Cas RNA-guided endonucleases: Swiss Army knives of genome editing. Nat Struct Mol Biol 2017; 24:882-892. [PMID: 29035385 DOI: 10.1038/nsmb.3486] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/18/2017] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas is a bacterial defense system against phage infection and nucleic acid invasion. Class 2 type II CRISPR-Cas9 has also been widely used for genome engineering. Here, we review novel insights into the CRISPR class 2 type V enzymes, specifically Cpf1 and C2c1, which display different DNA-recognition and cleavage characteristics than those of Cas9, the best-characterized member of class 2. Recent structures of these ribonucleoprotein complexes that capture several stages of the endonuclease reaction have provided molecular details of recognition, unzipping and cleavage of the target DNA, allowing their comparison with Cas9. A detailed understanding of these mechanisms is crucial for improving these genome engineering tools and expanding the genomic space that can be targeted.
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Affiliation(s)
- Stefano Stella
- Protein Structure & Function Programme, Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pablo Alcón
- Protein Structure & Function Programme, Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Guillermo Montoya
- Protein Structure & Function Programme, Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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