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Severi AA, Akbari B. CRISPR-Cas9 delivery strategies and applications: Review and update. Genesis 2024; 62:e23598. [PMID: 38727638 DOI: 10.1002/dvg.23598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 06/28/2024]
Abstract
Nowadays, a significant part of the investigations carried out in the medical field belong to cancer treatment. Generally, conventional cancer treatments, including chemotherapy, radiotherapy, and surgery, which have been used for a long time, are not sufficient, especially in malignant cancers. Because genetic mutations cause cancers, researchers are trying to treat these diseases using genetic engineering tools. One of them is clustered regularly interspaced short palindromic repeats (CRISPR), a powerful tool in genetic engineering in the last decade. CRISPR, which forms the CRISPR-Cas structure with its endonuclease protein, Cas, is known as a part of the immune system (adaptive immunity) in bacteria and archaea. Among the types of Cas proteins, Cas9 endonuclease has been used in many scientific studies due to its high accuracy and efficiency. This review reviews the CRISPR system, focusing on the history, classification, delivery methods, applications, new generations, and challenges of CRISPR-Cas9 technology.
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Affiliation(s)
- Ali Alizadeh Severi
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Science, Kermanshah, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Science, Kermanshah, Iran
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2
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Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024; 300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA-cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
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Affiliation(s)
- Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Kole Long
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Swarmistha Devi Aribam
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.
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3
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Valdivia-Francia F, Sendoel A. No country for old methods: New tools for studying microproteins. iScience 2024; 27:108972. [PMID: 38333695 PMCID: PMC10850755 DOI: 10.1016/j.isci.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their small size, recent technological advancements such as ribosome profiling, mass spectrometry-based strategies and advanced computational approaches have led to the annotation of more than 7000 sORFs in the human genome. Despite the vast progress, only a tiny portion of these microproteins have been characterized and an important challenge in the field lies in identifying functionally relevant microproteins and understanding their role in different cellular contexts. In this review, we explore the recent advancements in sORF research, focusing on the new methodologies and computational approaches that have facilitated their identification and functional characterization. Leveraging these new tools hold great promise for dissecting the diverse cellular roles of microproteins and will ultimately pave the way for understanding their role in the pathogenesis of diseases and identifying new therapeutic targets.
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Affiliation(s)
- Fabiola Valdivia-Francia
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
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4
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McLaurin KA, Li H, Khalili K, Mactutus CF, Booze RM. HIV-1 mRNA knockdown with CRISPR/CAS9 enhances neurocognitive function. J Neurovirol 2024; 30:71-85. [PMID: 38355914 PMCID: PMC11035469 DOI: 10.1007/s13365-024-01193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
Mixed glia are infiltrated with HIV-1 virus early in the course of infection leading to the development of a persistent viral reservoir in the central nervous system. Modification of the HIV-1 genome using gene editing techniques, including CRISPR/Cas9, has shown great promise towards eliminating HIV-1 viral reservoirs; whether these techniques are capable of removing HIV-1 viral proteins from mixed glia, however, has not been systematically evaluated. Herein, the efficacy of adeno-associated virus 9 (AAV9)-CRISPR/Cas9 gene editing for eliminating HIV-1 messenger RNA (mRNA) from cortical mixed glia was evaluated in vitro and in vivo. In vitro, a within-subjects experimental design was utilized to treat mixed glia isolated from neonatal HIV-1 transgenic (Tg) rats with varying doses (0, 0.9, 1.8, 2.7, 3.6, 4.5, or 5.4 µL corresponding to a physical titer of 0, 4.23 × 109, 8.46 × 109, 1.269 × 1010, 1.692 × 1010, 2.115 × 1010, and 2.538 × 1010 gc/µL) of CRISPR/Cas9 for 72 h. Dose-dependent decreases in the number of HIV-1 mRNA, quantified using an innovative in situ hybridization technique, were observed in a subset (i.e., n = 5 out of 8) of primary mixed glia. In vivo, HIV-1 Tg rats were retro-orbitally inoculated with CRISPR/Cas9 for two weeks, whereby treatment resulted in profound excision (i.e., approximately 53.2%) of HIV-1 mRNA from the medial prefrontal cortex. Given incomplete excision of the HIV-1 viral genome, the clinical relevance of HIV-1 mRNA knockdown for eliminating neurocognitive impairments was evaluated via examination of temporal processing, a putative neurobehavioral mechanism underlying HIV-1-associated neurocognitive disorders (HAND). Indeed, treatment with CRISPR/Cas9 protractedly, albeit not permanently, restored the developmental trajectory of temporal processing. Proof-of-concept studies, therefore, support the susceptibility of mixed glia to gene editing and the potential of CRISPR/Cas9 to serve as a novel therapeutic strategy for HAND, even in the absence of full viral eradication.
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Affiliation(s)
- Kristen A McLaurin
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S Limestone Street, Lexington, KY, 40508, USA
| | - Hailong Li
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
| | - Kamel Khalili
- Center for Neurovirology and Gene Editing, Department of Microbiology, Immunology, and Inflammation, Lewis Katz School of Medicine, Temple University, 3500 N. Broad Street, 7th Floor, Philadelphia, PA, 19140, USA
| | - Charles F Mactutus
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA
| | - Rosemarie M Booze
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA.
- Department of Psychology, Carolina Trustees Professor and Bicentennial Endowed Chair of Behavioral Neuroscience, University of South Carolina, 1512 Pendleton Street, Columbia, SC, 29208, USA.
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5
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Koonin EV, Gootenberg JS, Abudayyeh OO. Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox. Biochemistry 2023; 62:3465-3487. [PMID: 37192099 PMCID: PMC10734277 DOI: 10.1021/acs.biochem.3c00159] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Indexed: 05/18/2023]
Abstract
CRISPR systems mediate adaptive immunity in bacteria and archaea through diverse effector mechanisms and have been repurposed for versatile applications in therapeutics and diagnostics thanks to their facile reprogramming with RNA guides. RNA-guided CRISPR-Cas targeting and interference are mediated by effectors that are either components of multisubunit complexes in class 1 systems or multidomain single-effector proteins in class 2. The compact class 2 CRISPR systems have been broadly adopted for multiple applications, especially genome editing, leading to a transformation of the molecular biology and biotechnology toolkit. The diversity of class 2 effector enzymes, initially limited to the Cas9 nuclease, was substantially expanded via computational genome and metagenome mining to include numerous variants of Cas12 and Cas13, providing substrates for the development of versatile, orthogonal molecular tools. Characterization of these diverse CRISPR effectors uncovered many new features, including distinct protospacer adjacent motifs (PAMs) that expand the targeting space, improved editing specificity, RNA rather than DNA targeting, smaller crRNAs, staggered and blunt end cuts, miniature enzymes, promiscuous RNA and DNA cleavage, etc. These unique properties enabled multiple applications, such as harnessing the promiscuous RNase activity of the type VI effector, Cas13, for supersensitive nucleic acid detection. class 1 CRISPR systems have been adopted for genome editing, as well, despite the challenge of expressing and delivering the multiprotein class 1 effectors. The rich diversity of CRISPR enzymes led to rapid maturation of the genome editing toolbox, with capabilities such as gene knockout, base editing, prime editing, gene insertion, DNA imaging, epigenetic modulation, transcriptional modulation, and RNA editing. Combined with rational design and engineering of the effector proteins and associated RNAs, the natural diversity of CRISPR and related bacterial RNA-guided systems provides a vast resource for expanding the repertoire of tools for molecular biology and biotechnology.
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Affiliation(s)
- Eugene V. Koonin
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Jonathan S. Gootenberg
- McGovern
Institute for Brain Research at MIT, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Omar O. Abudayyeh
- McGovern
Institute for Brain Research at MIT, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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6
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Hu Y, Liu L, Jiang Q, Fang W, Chen Y, Hong Y, Zhai X. CRISPR/Cas9: a powerful tool in colorectal cancer research. J Exp Clin Cancer Res 2023; 42:308. [PMID: 37993945 PMCID: PMC10664500 DOI: 10.1186/s13046-023-02901-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant cancers worldwide and seriously threatens human health. The clustered regulatory interspaced short palindromic repeat/CRISPR-associate nuclease 9 (CRISPR/Cas9) system is an adaptive immune system of bacteria or archaea. Since its introduction, research into various aspects of treatment approaches for CRC has been accelerated, including investigation of the oncogenes, tumor suppressor genes (TSGs), drug resistance genes, target genes, mouse model construction, and especially in genome-wide library screening. Furthermore, the CRISPR/Cas9 system can be utilized for gene therapy for CRC, specifically involving in the molecular targeted drug delivery or targeted knockout in vivo. In this review, we elucidate the mechanism of the CRISPR/Cas9 system and its comprehensive applications in CRC. Additionally, we discussed the issue of off-target effects associated with CRISPR/Cas9, which serves to restrict its practical application. Future research on CRC should in-depth and systematically utilize the CRISPR/Cas9 system thereby achieving clinical practice.
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Affiliation(s)
- Yang Hu
- Department of Gastroenterology, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Liang Liu
- Department of Orthopedic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Qi Jiang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Weiping Fang
- Department of Gastroenterology, The First People's Hospital of Jiande, Hangzhou, 311600, China
| | - Yazhu Chen
- West China Hospital of Sichuan University, Chengdu, 610044, China.
| | - Yuntian Hong
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Xiang Zhai
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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Zhang S, Wang Y, Mao D, Wang Y, Zhang H, Pan Y, Wang Y, Teng S, Huang P. Current trends of clinical trials involving CRISPR/Cas systems. Front Med (Lausanne) 2023; 10:1292452. [PMID: 38020120 PMCID: PMC10666174 DOI: 10.3389/fmed.2023.1292452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
The CRISPR/Cas9 system is a powerful genome editing tool that has made enormous impacts on next-generation molecular diagnostics and therapeutics, especially for genetic disorders that traditional therapies cannot cure. Currently, CRISPR-based gene editing is widely applied in basic, preclinical, and clinical studies. In this review, we attempt to identify trends in clinical studies involving CRISPR techniques to gain insights into the improvement and contribution of CRISPR/Cas technologies compared to traditional modified modalities. The review of clinical trials is focused on the applications of the CRISPR/Cas systems in the treatment of cancer, hematological, endocrine, and immune system diseases, as well as in diagnostics. The scientific basis underlined is analyzed. In addition, the challenges of CRISPR application in disease therapies and recent advances that expand and improve CRISPR applications in precision medicine are discussed.
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Affiliation(s)
- Songyang Zhang
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Yidi Wang
- The Third Affiliated Hospital of Jilin University, Changchun, China
| | - Dezhi Mao
- The Third Affiliated Hospital of Jilin University, Changchun, China
| | - Yue Wang
- The Second Affiliated Hospital of Jilin University, Changchun, China
| | - Hong Zhang
- The Third Affiliated Hospital of Jilin University, Changchun, China
| | - Yihan Pan
- The Second Affiliated Hospital of Jilin University, Changchun, China
| | - Yuezeng Wang
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Shuzhi Teng
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
| | - Ping Huang
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, China
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Grünberger F, Schmid G, El Ahmad Z, Fenk M, Vogl K, Reichelt R, Hausner W, Urlaub H, Lenz C, Grohmann D. Uncovering the temporal dynamics and regulatory networks of thermal stress response in a hyperthermophile using transcriptomics and proteomics. mBio 2023; 14:e0217423. [PMID: 37843364 PMCID: PMC10746257 DOI: 10.1128/mbio.02174-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
Facing rapid fluctuations in their natural environment, extremophiles, like the hyperthermophilic archaeon Pyrococcus furiosus, exhibit remarkable adaptability to extreme conditions. However, our understanding of their dynamic cellular responses remains limited. This study integrates RNA-sequencing and mass spectrometry data, thereby elucidating transcriptomic and proteomic responses to heat and cold shock stress in P. furiosus. Our results reveal rapid and dynamic changes in gene and protein expression following these stress responses. Heat shock triggers extensive transcriptome reprogramming, orchestrated by the transcriptional regulator Phr, targeting a broader gene repertoire than previously demonstrated. For heat shock signature genes, RNA levels swiftly return to baseline upon recovery, while protein levels remain persistently upregulated, reflecting a rapid but sustained response. Intriguingly, cold shock at 4°C elicits distinct short- and long-term responses at both RNA and protein levels. Cluster analysis identified gene sets with either congruent or contrasting trends in RNA and protein changes, representing well-separated arCOG groups tailored to their individual cellular responses. Particularly, upregulation of ribosomal proteins and significant enrichment of 5'-leadered sequences in cold-shock responsive genes suggest that translation regulation is important during cold shock adaption. Further investigating transcriptomic features, we reveal that thermal stress genes are equipped with basal sequence elements, such as strong promoter and poly(U)-terminators, facilitating a regulated response of the respective transcription units. Our study provides a comprehensive overview of the cellular response to temperature stress, advancing our understanding of stress response mechanisms in hyperthermophilic archaea and providing valuable insights into the molecular adaptations that facilitate life in extreme environments.IMPORTANCEExtreme environments provide unique challenges for life, and the study of extremophiles can shed light on the mechanisms of adaptation to such conditions. Pyrococcus furiosus, a hyperthermophilic archaeon, is a model organism for studying thermal stress response mechanisms. In this study, we used an integrated analysis of RNA-sequencing and mass spectrometry data to investigate the transcriptomic and proteomic responses of P. furiosus to heat and cold shock stress and recovery. Our results reveal the rapid and dynamic changes in gene and protein expression patterns associated with these stress responses, as well as the coordinated regulation of different gene sets in response to different stressors. These findings provide valuable insights into the molecular adaptations that facilitate life in extreme environments and advance our understanding of stress response mechanisms in hyperthermophilic archaea.
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Affiliation(s)
- Felix Grünberger
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Georg Schmid
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Zubeir El Ahmad
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Martin Fenk
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Katharina Vogl
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Robert Reichelt
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Winfried Hausner
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Dina Grohmann
- Institute of Biochemistry, Genetics and Microbiology, Institute of Microbiology and Archaea Centre, Single-Molecule Biochemistry Lab and Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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9
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McLaurin KA, Li H, Khalili K, Mactutus CF, Booze RM. HIV-1 mRNA Knockdown with CRISPR/Cas9 Enhances Neurocognitive Function. RESEARCH SQUARE 2023:rs.3.rs-3266933. [PMID: 37886577 PMCID: PMC10602171 DOI: 10.21203/rs.3.rs-3266933/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Mixed glia are infiltrated with HIV-1 virus early in the course of infection leading to the development of a persistent viral reservoir in the central nervous system. Modification of the HIV-1 genome using gene editing techniques, including CRISPR/Cas9, has shown great promise towards eliminating HIV-1 viral reservoirs; whether these techniques are capable of removing HIV-1 viral proteins from mixed glia, however, has not been systematically evaluated. Herein, the efficacy of adeno-associated virus 9 (AAV9)-CRISPR/Cas9 gene editing for eliminating HIV-1 mRNA from cortical mixed glia was evaluated in vitro and in vivo. In vitro, a within-subjects experimental design was utilized to treat mixed glia isolated from neonatal HIV-1 transgenic (Tg) rats with varying doses (0, 0.9, 1.8, 2.7, 3.6, 4.5, or 5.4 μL) of CRISPR/Cas9 for 72 hours. Dose-dependent decreases in the number of HIV-1 mRNA, quantified using an innovative in situ hybridization technique, were observed in a subset (i.e., n=5 out of 8) of primary mixed glia. In vivo, HIV-1 Tg rats were retro-orbitally inoculated with CRISPR/Cas9 for two weeks, whereby treatment resulted in profound excision (i.e., approximately 53.2%) of HIV-1 mRNA from the mPFC. Given incomplete excision of the HIV-1 viral genome, the clinical relevance of HIV-1 mRNA knockdown for eliminating neurocognitive impairments was evaluated via examination of temporal processing, a putative neurobehavioral mechanism underlying HIV-1 associated neurocognitive disorders (HAND). Indeed, treatment with CRISPR/Cas9 partially restored the developmental trajectory of temporal processing. Proof-of-concept studies, therefore, support the susceptibility of mixed glia to gene editing and the potential of CRISPR/Cas9 to serve as a novel therapeutic strategy for HAND, even in the absence of full viral eradication.
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10
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Ronai I. How molecular techniques are developed from natural systems. Genetics 2023; 224:iyad067. [PMID: 37184565 PMCID: PMC10324945 DOI: 10.1093/genetics/iyad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
A striking characteristic of the molecular techniques of genetics is that they are derived from natural occurring systems. RNA interference, for example, utilizes a mechanism that evolved in eukaryotes to destroy foreign nucleic acid. Other case studies I highlight are restriction enzymes, DNA sequencing, polymerase chain reaction, gene targeting, fluorescent proteins (such as, green fluorescent protein), induced pluripotent stem cells, and clustered regularly interspaced short palindromic repeats-CRISPR associated 9. The natural systems' strategy for technique development means that biologists utilize the activity of a mechanism's effector (protein or RNA) and exploit biological specificity (protein or nucleic acid can cause precise reactions). I also argue that the developmental trajectory of novel molecular techniques, such as RNA interference, has 4 characteristic phases. The first phase is discovery of a biological phenomenon. The second phase is identification of the biological mechanism's trigger(s): the effector and biological specificity. The third phase is the application of the trigger(s) as a technique. The final phase is the maturation and refinement of the technique. Developing new molecular techniques from nature is crucial for future genetic research.
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Affiliation(s)
- Isobel Ronai
- Charles Perkins Centre and School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, Australia
- Department of Organismic and Evolutionary Biology, Harvard University
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11
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Zein-Eddine R, Refrégier G, Cervantes J, Yokobori NK. The future of CRISPR in Mycobacterium tuberculosis infection. J Biomed Sci 2023; 30:34. [PMID: 37245014 DOI: 10.1186/s12929-023-00932-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic repeats (CRISPR)-Cas systems rapidly raised from a bacterial genetic curiosity to the most popular tool for genetic modifications which revolutionized the study of microbial physiology. Due to the highly conserved nature of the CRISPR locus in Mycobacterium tuberculosis, the etiological agent of one of the deadliest infectious diseases globally, initially, little attention was paid to its CRISPR locus, other than as a phylogenetic marker. Recent research shows that M. tuberculosis has a partially functional Type III CRISPR, which provides a defense mechanism against foreign genetic elements mediated by the ancillary RNAse Csm6. With the advent of CRISPR-Cas based gene edition technologies, our possibilities to explore the biology of M. tuberculosis and its interaction with the host immune system are boosted. CRISPR-based diagnostic methods can lower the detection threshold to femtomolar levels, which could contribute to the diagnosis of the still elusive paucibacillary and extrapulmonary tuberculosis cases. In addition, one-pot and point-of-care tests are under development, and future challenges are discussed. We present in this literature review the potential and actual impact of CRISPR-Cas research on human tuberculosis understanding and management. Altogether, the CRISPR-revolution will revitalize the fight against tuberculosis with more research and technological developments.
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Affiliation(s)
- Rima Zein-Eddine
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, Route de Saclay 91120, Palaiseau, France
| | - Guislaine Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-Sur-Yvette, France
| | - Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, 79905, USA
| | - Noemí Kaoru Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS and CONICET, C1282AFF, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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12
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Kushwaha SK, Kumar AA, Gupta H, Marathe SA. The Phylogenetic Study of the CRISPR-Cas System in Enterobacteriaceae. Curr Microbiol 2023; 80:196. [PMID: 37118221 DOI: 10.1007/s00284-023-03298-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/07/2023] [Indexed: 04/30/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) system is a bacterial and archaeal adaptive immune system undergoing rapid multifaceted evolution. This evolution plausibly occurs due to the genetic exchanges of complete loci or individual entities. Here, we systematically investigate the evolutionary framework of the CRISPR-Cas system in six Enterobacteriaceae species and its evolutionary association with housekeeping genes as determined by the gyrB phenogram. The strains show high variability in the cas3 gene and the CRISPR1 locus among the closely related Enterobacteriaceae species, hinting at a series of genetic exchanges. The CRISPR leader is conserved, especially toward the distal end, and could be a core region of the leader. The spacers are conserved within the strains of most species, while some strains show unique sets of spacers. However, inter-species spacer conservation was rarely observed. For a considerable proportion of these spacers, protospacer sources were not detected. These results advance our understanding of the dynamics of the CRISPR-Cas system; however, the biological functions are yet to be characterised.
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Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Aryahi A Kumar
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Hardik Gupta
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India.
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13
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Farzanehpour M, Miri A, Ghorbani Alvanegh A, Esmaeili Gouvarchinghaleh H. Viral Vectors, Exosomes, and Vexosomes: Potential Armamentarium for Delivering CRISPR/Cas to Cancer Cells. Biochem Pharmacol 2023; 212:115555. [PMID: 37075815 DOI: 10.1016/j.bcp.2023.115555] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023]
Abstract
The underlying cause of cancer is genetic disruption, so gene editing technologies, particularly CRISPR/Cas systems can be used to go against cancer. The field of gene therapy has undergone many transitions over its 40-year history. Despite its many successes, it has also suffered many failures in the battle against malignancies, causing really adverse effects instead of therapeutic outcomes. At the tip of this double-edged sword are viral and non-viral-based vectors, which have profoundly transformed the way scientists and clinicians develop therapeutic platforms. Viruses such as lentivirus, adenovirus, and adeno-associated viruses are the most common viral vectors used for delivering the CRISPR/Cas system into human cells. In addition, among non-viral vectors, exosomes, especially tumor-derived exosomes (TDEs), have proven to be quite effective at delivering this gene editing tool. The combined use of viral vectors and exosomes, called vexosomes, seems to be a solution to overcoming the obstacles of both delivery systems.
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Affiliation(s)
- Mahdieh Farzanehpour
- Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Miri
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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14
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Wiegand T, Wilkinson R, Santiago-Frangos A, Lynes M, Hatzenpichler R, Wiedenheft B. Functional and Phylogenetic Diversity of Cas10 Proteins. CRISPR J 2023; 6:152-162. [PMID: 36912817 PMCID: PMC10123807 DOI: 10.1089/crispr.2022.0085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/30/2023] [Indexed: 03/14/2023] Open
Abstract
Cas10 proteins are large subunits of type III CRISPR RNA (crRNA)-guided surveillance complexes, many of which have nuclease and cyclase activities. Here, we use computational and phylogenetic methods to identify and analyze 2014 Cas10 sequences from genomic and metagenomic databases. Cas10 proteins cluster into five distinct clades that mirror previously established CRISPR-Cas subtypes. Most Cas10 proteins (85.0%) have conserved polymerase active-site motifs, while HD-nuclease domains are less well conserved (36.0%). We identify Cas10 variants that are split over multiple genes or genetically fused to nucleases activated by cyclic nucleotides (i.e., NucC) or components of toxin-antitoxin systems (i.e., AbiEii). To clarify the functional diversification of Cas10 proteins, we cloned, expressed, and purified five representatives from three phylogenetically distinct clades. None of the Cas10s are functional cyclases in isolation, and activity assays performed with polymerase domain active site mutants indicate that previously reported Cas10 DNA-polymerase activity may be a result of contamination. Collectively, this work helps clarify the phylogenetic and functional diversity of Cas10 proteins in type III CRISPR systems.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Royce Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Andrew Santiago-Frangos
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Mackenzie Lynes
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Roland Hatzenpichler
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
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15
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Bhatia S, Pooja, Yadav SK. CRISPR-Cas for genome editing: Classification, mechanism, designing and applications. Int J Biol Macromol 2023; 238:124054. [PMID: 36933595 DOI: 10.1016/j.ijbiomac.2023.124054] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/24/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Clustered regularly interspersed short pallindromic repeats (CRISPR) and CRISPR associated proteins (Cas) system (CRISPR-Cas) came into light as prokaryotic defence mechanism for adaptive immune response. CRISPR-Cas works by integrating short sequences of the target genome (spacers) into the CRISPR locus. The locus containing spacers interspersed repeats is further expressed into small guide CRISPR RNA (crRNA) which is then deployed by the Cas proteins to evade the target genome. Based on the Cas proteins CRISPR-Cas is classified according to polythetic system of classification. The characteristic of the CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new arenas due to which today CRISPR-Cas has evolved as cutting end technique in the field of genome editing. Here, we discuss about the evolution of CRISPR, its classification and various Cas systems including the designing and molecular mechanism of CRISPR-Cas. Applications of CRISPR-Cas as a genome editing tools are also highlighted in the areas such as agriculture, and anticancer therapy. Briefly discuss the role of CRISPR and its Cas systems in the diagnosis of COVID-19 and its possible preventive measures. The challenges in existing CRISP-Cas technologies and their potential solutions are also discussed briefly.
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Affiliation(s)
- Simran Bhatia
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India; Regional Center for Biotechnology, Faridabad, India
| | - Pooja
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India
| | - Sudesh Kumar Yadav
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India; Regional Center for Biotechnology, Faridabad, India.
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16
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The genome editing revolution. Trends Biotechnol 2023; 41:396-409. [PMID: 36709094 DOI: 10.1016/j.tibtech.2022.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/28/2023]
Abstract
A series of spectacular scientific discoveries and technological advances in the second half of the 20th century have provided the basis for the ongoing genome editing revolution. The elucidation of structural and functional features of DNA and RNA was followed by pioneering studies on genome editing: Molecular biotechnology was born. Since then, four decades followed during which progress of scientific insights and technological methods continued at an overwhelming pace. Fundamental insights into microbial host-virus interactions led to the development of tools for genome editing using restriction enzymes or the revolutionary CRISPR-Cas technology. In this review, we provide a historical overview of milestones that led to the genome editing revolution and speculate about future trends in biotechnology.
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17
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Ahmadi SE, Soleymani M, Shahriyary F, Amirzargar MR, Ofoghi M, Fattahi MD, Safa M. Viral vectors and extracellular vesicles: innate delivery systems utilized in CRISPR/Cas-mediated cancer therapy. Cancer Gene Ther 2023:10.1038/s41417-023-00597-z. [PMID: 36854897 PMCID: PMC9971689 DOI: 10.1038/s41417-023-00597-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/13/2023] [Accepted: 02/01/2023] [Indexed: 03/02/2023]
Abstract
Gene editing-based therapeutic strategies grant the power to override cell machinery and alter faulty genes contributing to disease development like cancer. Nowadays, the principal tool for gene editing is the clustered regularly interspaced short palindromic repeats-associated nuclease 9 (CRISPR/Cas9) system. In order to bring this gene-editing system from the bench to the bedside, a significant hurdle remains, and that is the delivery of CRISPR/Cas to various target cells in vivo and in vitro. The CRISPR-Cas system can be delivered into mammalian cells using various strategies; among all, we have reviewed recent research around two natural gene delivery systems that have been proven to be compatible with human cells. Herein, we have discussed the advantages and limitations of viral vectors, and extracellular vesicles (EVs) in delivering the CRISPR/Cas system for cancer therapy purposes.
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Affiliation(s)
- Seyed Esmaeil Ahmadi
- grid.411746.10000 0004 4911 7066Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maral Soleymani
- grid.411230.50000 0000 9296 6873School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fahimeh Shahriyary
- grid.411746.10000 0004 4911 7066Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Amirzargar
- grid.411746.10000 0004 4911 7066Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahya Ofoghi
- Division of Clinical Laboratory, Tehran Hospital of Petroleum Industry, Tehran, Iran ,grid.411600.2Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Davood Fattahi
- grid.411600.2Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
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18
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Isola G. Prospective Advances in Genome Editing Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:301-313. [DOI: 10.1007/978-981-19-5642-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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19
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Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. Visualizing the Nucleome Using the CRISPR–Cas9 System: From in vitro to in vivo. BIOCHEMISTRY (MOSCOW) 2023; 88:S123-S149. [PMID: 37069118 PMCID: PMC9940691 DOI: 10.1134/s0006297923140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
One of the latest methods in modern molecular biology is labeling genomic loci in living cells using fluorescently labeled Cas protein. The NIH Foundation has made the mapping of the 4D nucleome (the three-dimensional nucleome on a timescale) a priority in the studies aimed to improve our understanding of chromatin organization. Fluorescent methods based on CRISPR-Cas are a significant step forward in visualization of genomic loci in living cells. This approach can be used for studying epigenetics, cell cycle, cellular response to external stimuli, rearrangements during malignant cell transformation, such as chromosomal translocations or damage, as well as for genome editing. In this review, we focused on the application of CRISPR-Cas fluorescence technologies as components of multimodal imaging methods for in vivo mapping of chromosomal loci, in particular, attribution of fluorescence signal to morphological and anatomical structures in a living organism. The review discusses the approaches to the highly sensitive, high-precision labeling of CRISPR-Cas components, delivery of genetically engineered constructs into cells and tissues, and promising methods for molecular imaging.
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Affiliation(s)
- Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Gerel A Abushinova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
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20
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Flusche T, Rajan R. Molecular Details of DNA Integration by CRISPR-Associated Proteins During Adaptation in Bacteria and Archaea. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1414:27-43. [PMID: 35852729 DOI: 10.1007/5584_2022_730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in bacteria and archaea, where immunological memory is retained in the CRISPR locus as short pieces of the intruding nucleic acid, termed spacers. The adaptation to new infections occurs through the integration of a new spacer into the CRISPR array. For immune protection, spacers are transcribed into CRISPR RNAs (crRNA) that are used to guide the effector nuclease of the system in sequence-dependent target cleavage. Spacers originate as a prespacer from either DNA or RNA depending on the CRISPR-Cas system being observed, and the nearly universal Cas proteins, Cas1 and Cas2, insert the prespacer into the CRISPR locus during adaptation in all systems that contain them. The mechanism of site-specific prespacer integration varies across CRISPR classes and types, and distinct differences can even be found within the same subtype. In this review, the current knowledge on the mechanisms of prespacer integration in type II-A CRISPR-Cas systems will be described. Comparisons of the currently characterized type II-A systems show that distinct mechanisms exist within different members of this subtype and are correlated to sequence-specific interactions of Cas proteins and the DNA elements present in the CRISPR array. These observations indicate that nature has fine-tuned the mechanistic details while performing the basic step of DNA integration by Cas proteins, which offers unique advantages to develop Cas1-Cas2-based biotechnology.
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Affiliation(s)
- Tamara Flusche
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, USA.
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21
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CRISPR-Cas9 Technology for the Creation of Biological Avatars Capable of Modeling and Treating Pathologies: From Discovery to the Latest Improvements. Cells 2022; 11:cells11223615. [PMID: 36429042 PMCID: PMC9688409 DOI: 10.3390/cells11223615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
This is a spectacular moment for genetics to evolve in genome editing, which encompasses the precise alteration of the cellular DNA sequences within various species. One of the most fascinating genome-editing technologies currently available is Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its associated protein 9 (CRISPR-Cas9), which have integrated deeply into the research field within a short period due to its effectiveness. It became a standard tool utilized in a broad spectrum of biological and therapeutic applications. Furthermore, reliable disease models are required to improve the quality of healthcare. CRISPR-Cas9 has the potential to diversify our knowledge in genetics by generating cellular models, which can mimic various human diseases to better understand the disease consequences and develop new treatments. Precision in genome editing offered by CRISPR-Cas9 is now paving the way for gene therapy to expand in clinical trials to treat several genetic diseases in a wide range of species. This review article will discuss genome-editing tools: CRISPR-Cas9, Zinc Finger Nucleases (ZFNs), and Transcription Activator-Like Effector Nucleases (TALENs). It will also encompass the importance of CRISPR-Cas9 technology in generating cellular disease models for novel therapeutics, its applications in gene therapy, and challenges with novel strategies to enhance its specificity.
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22
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Abstract
Advances in our understanding of prokaryotic antiphage defense mechanisms in the past few years have revealed a multitude of new cyclic nucleotide signaling molecules that play a crucial role in switching infected cells into an antiviral state. Defense pathways including type III CRISPR (clustered regularly interspaced palindromic repeats), CBASS (cyclic nucleotide-based antiphage signaling system), PYCSAR (pyrimidine cyclase system for antiphage resistance), and Thoeris all use cyclic nucleotides as second messengers to activate a diverse range of effector proteins. These effectors typically degrade or disrupt key cellular components such as nucleic acids, membranes, or metabolites, slowing down viral replication kinetics at great cost to the infected cell. Mechanisms to manipulate the levels of cyclic nucleotides are employed by cells to regulate defense pathways and by viruses to subvert them. Here we review the discovery and mechanism of the key pathways, signaling molecules and effectors, parallels and differences between the systems, open questions, and prospects for future research in this area.
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Affiliation(s)
- Januka S Athukoralage
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews, United Kingdom;
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23
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Shang S, Cai XS, Qi LS. Computation empowers CRISPR discovery and technology. NATURE COMPUTATIONAL SCIENCE 2022; 2:533-535. [PMID: 38177471 DOI: 10.1038/s43588-022-00321-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Affiliation(s)
- Stephen Shang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xiangmeng S Cai
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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24
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Ilyina TS. Adaptive Immunity Systems of Bacteria: Association with Self-Synthesizing Transposons, Polyfunctionality. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2022. [DOI: 10.3103/s0891416822030065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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25
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Ille AM, Lamont H, Mathews MB. The Central Dogma revisited: Insights from protein synthesis, CRISPR, and beyond. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1718. [PMID: 35199457 DOI: 10.1002/wrna.1718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/28/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Francis Crick advanced two distinct but interrelated fundamental principles of molecular biology: (1) the Sequence Hypothesis and (2) the Central Dogma. The Sequence Hypothesis defines biological information transfer as the residue-by-residue transfer of sequence information between nucleic acids and to proteins. This is commonly summarized as DNA ➔ RNA ➔ protein and is colloquially referred to as the Central Dogma. More specifically, however, the Central Dogma expounded by Crick included a critical restriction, stipulating that "once sequential information has passed into protein it cannot get out again." Under this definition, the Central Dogma has stood the test of time despite challenges. In principle, a violation of the Central Dogma could transpire through synthetic biology or by natural occurrence. To address these possibilities, we draw insights from existing modes of information transfer in protein synthesis and from synthetic Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR) gene-editing. We introduce a three-part evaluation scheme, which we apply to the CRISPR/Cas9 system and the more recent CRISPR prime editing system. Potential mechanisms by which engineered sequence editing systems might violate the Central Dogma are considered. We conclude that although information transfer in protein synthesis and CRISPR gene-editing remain within the bounds of the Central Dogma, the underlying mechanisms point toward an avenue of synthetic biology that could directly violate the Central Dogma. Finally, we speculate on some of the theoretical and practical implications of a protein-derived information transfer system. This article is categorized under: RNA Evolution and Genomics > Ribonomics RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Mechanisms.
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Affiliation(s)
- Alexander M Ille
- School of Graduate Studies, Rutgers University, Newark, New Jersey, USA
| | - Hannah Lamont
- School of Graduate Studies, Rutgers University, Newark, New Jersey, USA
| | - Michael B Mathews
- School of Graduate Studies, Rutgers University, Newark, New Jersey, USA
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
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26
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Gostimskaya I. CRISPR-Cas9: A History of Its Discovery and Ethical Considerations of Its Use in Genome Editing. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:777-788. [PMID: 36171658 PMCID: PMC9377665 DOI: 10.1134/s0006297922080090] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
The development of a method for genome editing based on CRISPR-Cas9 technology was awarded The Nobel Prize in Chemistry in 2020, less than a decade after the discovery of all principal molecular components of the system. For the first time in history a Nobel prize was awarded to two women, Emmanuelle Charpentier and Jennifer Doudna, who made key discoveries in the field of DNA manipulation with the CRISPR-Cas9 system, so-called "genetic scissors". It is difficult to overestimate the importance of the technique as it enables one not only to manipulate genomes of model organisms in scientific experiments, and modify characteristics of important crops and animals, but also has the potential of introducing revolutionary changes in medicine, especially in treatment of genetic diseases. The original biological function of CRISPR-Cas9 system is the protection of prokaryotes from mobile genetic elements, in particular viruses. Currently, CRISPR-Cas9 and related technologies have been successfully used to cure life-threatening diseases, make coronavirus detection tests, and even to modify human embryo cells with the consequent birth of babies carrying the introduced modifications. This intervention with human germplasm cells resulted in wide disapproval in the scientific community due to ethical concerns, and calls for a moratorium on inheritable genomic manipulations. This review focuses on the history of the discovery of the CRISPR-Cas9 system with some aspects of its current applications, including ethical concerns about its use in humans.
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27
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Devi V, Harjai K, Chhibber S. CRISPR-Cas systems: role in cellular processes beyond adaptive immunity. Folia Microbiol (Praha) 2022; 67:837-850. [PMID: 35854181 PMCID: PMC9296112 DOI: 10.1007/s12223-022-00993-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/10/2022] [Indexed: 11/28/2022]
Abstract
Clustered regularly interspaced short palindromic repeats and associated Cas proteins (CRISPR-Cas) are the only known adaptive immune system in prokaryotes. CRISPR-Cas system provides sequence-specific immunity against invasion by foreign genetic elements. It carries out its functions by incorporating a small part of the invading DNA sequence, termed as spacer into the CRISPR array. Although the CRISPR-Cas systems are mainly responsible for adaptive immune functions, their alternative role in the gene regulation, bacterial pathophysiology, virulence, and evolution has started to unravel. In several species, these systems are revealed to regulate the processes beyond adaptive immunity by employing various components of CRISPR-Cas machinery, independently or in combination. The molecular mechanisms entailing the regulatory processes are not clear in most of the instances. In this review, we have discussed some well-known and some recently established noncanonical functions of CRISPR-Cas system and its fast-extending applications in other biological processes.
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Affiliation(s)
- Veena Devi
- Department of Microbiology, Panjab University, Chandigarh, India
- , Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh, India.
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28
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Wörtz J, Smith V, Fallmann J, König S, Thuraisingam T, Walther P, Urlaub H, Stadler PF, Allers T, Hille F, Marchfelder A. Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair. Front Microbiol 2022; 13:822304. [PMID: 35495653 PMCID: PMC9051519 DOI: 10.3389/fmicb.2022.822304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas constitutes an adaptive prokaryotic defence system against invasive nucleic acids like viruses and plasmids. Beyond their role in immunity, CRISPR-Cas systems have been shown to closely interact with components of cellular DNA repair pathways, either by regulating their expression or via direct protein-protein contact and enzymatic activity. The integrase Cas1 is usually involved in the adaptation phase of CRISPR-Cas immunity but an additional role in cellular DNA repair pathways has been proposed previously. Here, we analysed the capacity of an archaeal Cas1 from Haloferax volcanii to act upon DNA damage induced by oxidative stress and found that a deletion of the cas1 gene led to reduced survival rates following stress induction. In addition, our results indicate that Cas1 is directly involved in DNA repair as the enzymatically active site of the protein is crucial for growth under oxidative conditions. Based on biochemical assays, we propose a mechanism by which Cas1 plays a similar function to DNA repair protein Fen1 by cleaving branched intermediate structures. The present study broadens our understanding of the functional link between CRISPR-Cas immunity and DNA repair by demonstrating that Cas1 and Fen1 display equivalent roles during archaeal DNA damage repair.
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Affiliation(s)
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jörg Fallmann
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Sabine König
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Peter F. Stadler
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Competence Center for Scalable Data Services and Solutions, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Center for RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
- Santa Fe Institute, Santa Fe, NM, United States
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Anita Marchfelder
- Biology II, Ulm University, Ulm, Germany
- *Correspondence: Anita Marchfelder,
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Gupta R, Ghosh A, Chakravarti R, Singh R, Ravichandiran V, Swarnakar S, Ghosh D. Cas13d: A New Molecular Scissor for Transcriptome Engineering. Front Cell Dev Biol 2022; 10:866800. [PMID: 35433685 PMCID: PMC9008242 DOI: 10.3389/fcell.2022.866800] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
The discovery of Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its associated Cas endonucleases in bacterial and archaeal species allowed scientists to modify, utilized, and revolutionize this tool for genetic alterations in any species. Especially the type II CRISPR-Cas9 system has been extensively studied and utilized for precise and efficient DNA manipulation in plant and mammalian systems over the past few decades. Further, the discovery of the type V CRISPR-Cas12 (Cpf1) system provides more flexibility and precision in DNA manipulation in prokaryotes, plants, and animals. However, much effort has been made to employ and utilize the above CRISPR tools for RNA manipulation but the ability of Cas9 and Cas12 to cut DNA involves the nuisance of off-target effects on genes and thus may not be employed in all RNA-targeting applications. Therefore, the search for new and diverse Cas effectors which can precisely detect and manipulate the targeted RNA begins and this led to the discovery of a novel RNA targeting class 2, type VI CRISPR-Cas13 system. The CRISPR-Cas13 system consists of single RNA-guided Cas13 effector nucleases that solely target single-stranded RNA (ssRNA) in a programmable way without altering the DNA. The Cas13 effectors family comprises four subtypes (a-d) and each subtype has distinctive primary sequence divergence except the two consensuses Higher eukaryotes and prokaryotes nucleotide-binding domain (HEPN) that includes RNase motifs i.e. R-X4-6-H. These two HEPN domains are solely responsible for executing targetable RNA cleavage activity with high efficiency. Further, recent studies have shown that Cas13d exhibits higher efficiency and specificity in cleaving targeted RNA in the mammalian system compared to other Cas13 endonucleases of the Cas13 enzyme family. In addition to that, Cas13d has shown additional advantages over other Cas13 variants, structurally as well as functionally which makes it a prominent and superlative tool for RNA engineering and editing. Therefore considering the advantages of Cas13d over previously characterized Cas13 subtypes, in this review, we encompass the structural and mechanistic properties of type VI CRISPR-Cas13d systems, an overview of the current reported various applications of Cas13d, and the prospects to improve Cas13d based tools for diagnostic and therapeutic purposes.
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Affiliation(s)
- Rahul Gupta
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Arijit Ghosh
- National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Rudra Chakravarti
- National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Rajveer Singh
- National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, India
- *Correspondence: Dipanjan Ghosh, ; Snehasikta Swarnakar, ; Velayutham Ravichandiran,
| | - Snehasikta Swarnakar
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- *Correspondence: Dipanjan Ghosh, ; Snehasikta Swarnakar, ; Velayutham Ravichandiran,
| | - Dipanjan Ghosh
- National Institute of Pharmaceutical Education and Research, Kolkata, India
- *Correspondence: Dipanjan Ghosh, ; Snehasikta Swarnakar, ; Velayutham Ravichandiran,
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Jie Q, Lei S, Qu C, Wu H, Liu Y, Huang P, Teng S. 利用CRISPR/Cas9基因编辑技术治疗β-地中海贫血的最新进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Lan XR, Liu ZL, Niu DK. Precipitous Increase of Bacterial CRISPR-Cas Abundance at Around 45°C. Front Microbiol 2022; 13:773114. [PMID: 35300480 DOI: 10.3389/fmicb.2022.773114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Although performing adaptive immunity, CRISPR-Cas systems are present in only 40% of bacterial genomes. We observed an abrupt increase of bacterial CRISPR-Cas abundance at around 45°C. Phylogenetic comparative analyses confirmed that the abundance correlates with growth temperature only at the temperature range around 45°C. From the literature, we noticed that the diversities of cellular predators (like protozoa, nematodes, and myxobacteria) have a steep decline at this temperature range. The grazing risk faced by bacteria reduces substantially at around 45°C and almost disappears above 60°C. We propose that viral lysis would become the dominating factor of bacterial mortality, and antivirus immunity has a higher priority at higher temperatures. In temperature ranges where the abundance of cellular predators does not change with temperature, the growth temperatures of bacteria would not significantly affect their CRISPR-Cas contents. The hypothesis predicts that bacteria should also be rich in CRISPR-Cas systems if they live in other extreme conditions inaccessible to grazing predators.
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Affiliation(s)
- Xin-Ran Lan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Zhi-Ling Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
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Abstract
The principal biological function of bacterial and archaeal CRISPR systems is RNA-guided adaptive immunity against viruses and other mobile genetic elements (MGEs). These systems show remarkable evolutionary plasticity and functional versatility at multiple levels, including both the defense mechanisms that lead to direct, specific elimination of the target DNA or RNA and those that cause programmed cell death (PCD) or induction of dormancy. This flexibility is also evident in the recruitment of CRISPR systems for nondefense functions. Defective CRISPR systems or individual CRISPR components have been recruited by transposons for RNA-guided transposition, by plasmids for interplasmid competition, and by viruses for antidefense and interviral conflicts. Additionally, multiple highly derived CRISPR variants of yet unknown functions have been discovered. A major route of innovation in CRISPR evolution is the repurposing of diverged repeat variants encoded outside CRISPR arrays for various structural and regulatory functions. The evolutionary plasticity and functional versatility of CRISPR systems are striking manifestations of the ubiquitous interplay between defense and “normal” cellular functions. The CRISPR systems show remarkable functional versatility beyond their principal function as an adaptive immune mechanism. This Essay discusses how derived CRISPR systems have been recruited by transposons on multiple occasions and mediate RNA-guided transposition; derived CRISPR RNAs are frequently recruited for regulatory functions.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Grüschow S, Adamson CS, White MF. Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector. Nucleic Acids Res 2021; 49:13122-13134. [PMID: 34871408 PMCID: PMC8682760 DOI: 10.1093/nar/gkab1190] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Type III CRISPR systems detect invading RNA, resulting in the activation of the enzymatic Cas10 subunit. The Cas10 cyclase domain generates cyclic oligoadenylate (cOA) second messenger molecules, activating a variety of effector nucleases that degrade nucleic acids to provide immunity. The prophage-encoded Vibrio metoecus type III-B (VmeCmr) locus is uncharacterised, lacks the HD nuclease domain in Cas10 and encodes a NucC DNA nuclease effector that is also found associated with Cyclic-oligonucleotide-based anti-phage signalling systems (CBASS). Here we demonstrate that VmeCmr is activated by target RNA binding, generating cyclic-triadenylate (cA3) to stimulate a robust NucC-mediated DNase activity. The specificity of VmeCmr is probed, revealing the importance of specific nucleotide positions in segment 1 of the RNA duplex and the protospacer flanking sequence (PFS). We harness this programmable system to demonstrate the potential for a highly specific and sensitive assay for detection of the SARS-CoV-2 virus RNA with a limit of detection (LoD) of 2 fM using a commercial plate reader without any extrinsic amplification step. The sensitivity is highly dependent on the guide RNA used, suggesting that target RNA secondary structure plays an important role that may also be relevant in vivo.
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Affiliation(s)
- Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Catherine S Adamson
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, KY16 9ST, UK
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Dixit B, Prakash A, Kumar P, Gogoi P, Kumar M. The core Cas1 protein of CRISPR-Cas I-B in Leptospira shows metal-tunable nuclease activity. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100059. [PMID: 34841349 PMCID: PMC8610301 DOI: 10.1016/j.crmicr.2021.100059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/26/2022] Open
Abstract
Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 is the causative agent of leptospirosis in animals and humans. This organism carries a functional cas1 gene classified under CRISPR-Cas I-B. In this study, using various nuclease assays and bioinformatics analysis, we report that the recombinant Cas1 (LinCas1) possesses metal-ion dependent DNase activity, which is inhibited upon substitution or chelation of metal-ion and/or interaction with recombinant Cas2 (LinCas2) of L. interrogans. Model of LinCas1 structure shows a shorter N-terminal domain unlike other Cas1 orthologs reported to date. The C-terminal domain of LinCas1 contains conserved divalent-metal binding residues (Glu108, His176, and Glu191) and the mutation of these residues leads to abolition in DNase activity. Immunoassay using anti-LinCas2 demonstrates that LinCas1 interacts with LinCas2 and attains a saturation point. Moreover, the nuclease activity of the LinCas1-Cas2 mixture on ds-DNA displayed a reduction in activity compared to the pure core LinCas proteins under in vitro condition. The DNase activity for LinCas1 is consistent with a role for this protein in the recognition/cleavage of foreign DNA and integration of foreign DNA as spacer into the CRISPR array.
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Affiliation(s)
- Bhuvan Dixit
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Aman Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Pankaj Kumar
- Division of Livestock and Fisheries Management, ICAR Research Complex for Eastern Region, Patna, Bihar 800014, India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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Kong H, Ju E, Yi K, Xu W, Lao Y, Cheng D, Zhang Q, Tao Y, Li M, Ding J. Advanced Nanotheranostics of CRISPR/Cas for Viral Hepatitis and Hepatocellular Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102051. [PMID: 34665528 PMCID: PMC8693080 DOI: 10.1002/advs.202102051] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/25/2021] [Indexed: 05/08/2023]
Abstract
Liver disease, particularly viral hepatitis and hepatocellular carcinoma (HCC), is a global healthcare burden and leads to more than 2 million deaths per year worldwide. Despite some success in diagnosis and vaccine development, there are still unmet needs to improve diagnostics and therapeutics for viral hepatitis and HCC. The emerging clustered regularly interspaced short palindromic repeat/associated proteins (CRISPR/Cas) technology may open up a unique avenue to tackle these two diseases at the genetic level in a precise manner. Especially, liver is a more accessible organ over others from the delivery point of view, and many advanced strategies applied for nanotheranostics can be adapted in CRISPR-mediated diagnostics or liver gene editing. In this review, the focus is on these two aspects of viral hepatitis and HCC applications. An overview on CRISPR editor development and current progress in clinical trials is first given, followed by highlighting the recent advances integrating the merits of gene editing and nanotheranostics. The promising systems that are used in other applications but may hold potentials in liver gene editing are also discussed. This review concludes with the perspectives on rationally designing the next-generation CRISPR approaches and improving the editing performance.
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Affiliation(s)
- Huimin Kong
- Laboratory of Biomaterials and Translational MedicineCenter for Nanomedicine and Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen University600 Tianhe RoadGuangzhou510630P. R. China
| | - Enguo Ju
- Laboratory of Biomaterials and Translational MedicineCenter for Nanomedicine and Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen University600 Tianhe RoadGuangzhou510630P. R. China
| | - Ke Yi
- Laboratory of Biomaterials and Translational MedicineCenter for Nanomedicine and Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen University600 Tianhe RoadGuangzhou510630P. R. China
| | - Weiguo Xu
- Key Laboratory of Polymer EcomaterialsChangchun Institute of Applied ChemistryChinese Academy of Sciences5625 Renmin StreetChangchun130022P. R. China
| | - Yeh‐Hsing Lao
- Department of Biomedical EngineeringColumbia University3960 Broadway Lasker Room 450New YorkNY10032USA
| | - Du Cheng
- PCFM Lab of Ministry of EducationSchool of Materials Science and EngineeringSun Yat‐sen University135 Xingangxi RoadGuangzhou510275P. R. China
| | - Qi Zhang
- Laboratory of Biomaterials and Translational MedicineCenter for Nanomedicine and Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen University600 Tianhe RoadGuangzhou510630P. R. China
- Guangdong Provincial Key Laboratory of Liver Disease Research600 Tianhe RoadGuangzhou510630P. R. China
| | - Yu Tao
- Laboratory of Biomaterials and Translational MedicineCenter for Nanomedicine and Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen University600 Tianhe RoadGuangzhou510630P. R. China
- Guangdong Provincial Key Laboratory of Liver Disease Research600 Tianhe RoadGuangzhou510630P. R. China
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational MedicineCenter for Nanomedicine and Biotherapy CenterThe Third Affiliated HospitalSun Yat‐sen University600 Tianhe RoadGuangzhou510630P. R. China
| | - Jianxun Ding
- Key Laboratory of Polymer EcomaterialsChangchun Institute of Applied ChemistryChinese Academy of Sciences5625 Renmin StreetChangchun130022P. R. China
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Li JJ, Shi Y, Wu JN, Li H, Smagghe G, Liu TX. CRISPR/Cas9 in lepidopteran insects: Progress, application and prospects. JOURNAL OF INSECT PHYSIOLOGY 2021; 135:104325. [PMID: 34743972 DOI: 10.1016/j.jinsphys.2021.104325] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/26/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Clustered regularly spaced short palindrome repeats (CRISPR) structure family forms the acquired immune system in bacteria and archaea. Recent advances in CRISPR/Cas genome editing as derived from prokaryotes, confirmed the characteristics of robustness, high target specificity and programmability, and also revolutionized the insect sciences field. The successful application of CRISPR in a wide variety of lepidopteran insects, with a high genetic diversity, provided opportunities to explore gene functions, insect modification and pest control. In this review, we present a detailed overview on the recent progress of CRISPR in lepidopteran insects, and described the basic principles of the system and its application. Major interest is on wing development, pigmentation, mating, reproduction, sex determination, metamorphosis, resistance and silkworm breeding innovation. Finally, we outlined the limitations of CRISPR/Cas system and discussed its application prospects in lepidopteran insects.
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Affiliation(s)
- Jiang-Jie Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China; Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Yan Shi
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China; Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Ji-Nan Wu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China
| | - Hao Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Tong-Xian Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, PR China.
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Kolesnik MV, Fedorova I, Karneyeva KA, Artamonova DN, Severinov KV. Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1301-1314. [PMID: 34903162 PMCID: PMC8527444 DOI: 10.1134/s0006297921100114] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022]
Abstract
The emergence and persistence of selfish genetic elements is an intrinsic feature of all living systems. Cellular organisms have evolved a plethora of elaborate defense systems that limit the spread of such genetic parasites. CRISPR-Cas are RNA-guided defense systems used by prokaryotes to recognize and destroy foreign nucleic acids. These systems acquire and store fragments of foreign nucleic acids and utilize the stored sequences as guides to recognize and destroy genetic invaders. CRISPR-Cas systems have been extensively studied, as some of them are used in various genome editing technologies. Although Type III CRISPR-Cas systems are among the most common CRISPR-Cas systems, they are also some of the least investigated ones, mostly due to the complexity of their action compared to other CRISPR-Cas system types. Type III effector complexes specifically recognize and cleave RNA molecules. The recognition of the target RNA activates the effector large subunit - the so-called CRISPR polymerase - which cleaves DNA and produces small cyclic oligonucleotides that act as signaling molecules to activate auxiliary effectors, notably non-specific RNases. In this review, we provide a historical overview of the sometimes meandering pathway of the Type III CRISPR research. We also review the current data on the structures and activities of Type III CRISPR-Cas systems components, their biological roles, and evolutionary history. Finally, using structural modeling with AlphaFold2, we show that the archaeal HRAMP signature protein, which heretofore has had no assigned function, is a degenerate relative of Type III CRISPR-Cas signature protein Cas10, suggesting that HRAMP systems have descended from Type III CRISPR-Cas systems or their ancestors.
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Affiliation(s)
- Matvey V Kolesnik
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Iana Fedorova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Karyna A Karneyeva
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Daria N Artamonova
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Konstantin V Severinov
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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Xu M, Weng Q, Ji J. Applications and advances of CRISPR/Cas9 in animal cancer model. Brief Funct Genomics 2021; 19:235-241. [PMID: 32124927 DOI: 10.1093/bfgp/elaa002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/07/2020] [Indexed: 01/18/2023] Open
Abstract
The recent developments of clustered regularly interspaced short palindromic repeats(CRISPR)/-associate protein 9 (CRISPR/Cas9) have got scientific interests due to the straightforward, efficient and versatile talents of it. Furthermore, the CRISPR/Cas9 system has democratized access to gene editing in many biological fields, including cancer. Cancer development is a multistep process caused by innate and acquired mutations and leads to the initiation and progression of tumorigenesis. It is obvious that establishing appropriate animal cancer models which can simulate human cancers is crucial for cancer research currently. Since the emergence of CRISPR/Cas9, considerable efforts have been taken by researchers to apply this technology in generating animal cancer models. Although there is still a long way to go we are happy to see the achievements we have made and the promising future we have.
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Butiuc-Keul A, Farkas A, Carpa R, Iordache D. CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes. Microb Physiol 2021; 32:2-17. [PMID: 34192695 DOI: 10.1159/000516643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/16/2021] [Indexed: 11/19/2022]
Abstract
Being frequently exposed to foreign nucleic acids, bacteria and archaea have developed an ingenious adaptive defense system, called CRISPR-Cas. The system is composed of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) array, together with CRISPR (cas)-associated genes. This system consists of a complex machinery that integrates fragments of foreign nucleic acids from viruses and mobile genetic elements (MGEs), into CRISPR arrays. The inserted segments (spacers) are transcribed and then used by cas proteins as guide RNAs for recognition and inactivation of the targets. Different types and families of CRISPR-Cas systems consist of distinct adaptation and effector modules with evolutionary trajectories, partially independent. The origin of the effector modules and the mechanism of spacer integration/deletion is far less clear. A review of the most recent data regarding the structure, ecology, and evolution of CRISPR-Cas systems and their role in the modulation of accessory genomes in prokaryotes is proposed in this article. The CRISPR-Cas system's impact on the physiology and ecology of prokaryotes, modulation of horizontal gene transfer events, is also discussed here. This system gained popularity after it was proposed as a tool for plant and animal embryo editing, in cancer therapy, as antimicrobial against pathogenic bacteria, and even for combating the novel coronavirus - SARS-CoV-2; thus, the newest and promising applications are reviewed as well.
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Affiliation(s)
- Anca Butiuc-Keul
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Anca Farkas
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Rahela Carpa
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania.,Center of Systems Biology, Biodiversity and Bioresources, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Dumitrana Iordache
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
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Botella L, Jung T. Multiple Viral Infections Detected in Phytophthora condilina by Total and Small RNA Sequencing. Viruses 2021; 13:v13040620. [PMID: 33916635 PMCID: PMC8067226 DOI: 10.3390/v13040620] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 12/13/2022] Open
Abstract
Marine oomycetes have recently been shown to be concurrently infected by (−)ssRNA viruses of the order Bunyavirales. In this work, even higher virus variability was found in a single isolate of Phytophthora condilina, a recently described member of Phytophthora phylogenetic Clade 6a, which was isolated from brackish estuarine waters in southern Portugal. Using total and small RNA-seq the full RdRp of 13 different potential novel bunya-like viruses and two complete toti-like viruses were detected. All these viruses were successfully confirmed by reverse transcription polymerase chain reaction (RT-PCR) using total RNA as template, but complementarily one of the toti-like and five of the bunya-like viruses were confirmed when dsRNA was purified for RT-PCR. In our study, total RNA-seq was by far more efficient for de novo assembling of the virus sequencing but small RNA-seq showed higher read numbers for most viruses. Two main populations of small RNAs (21 nts and 25 nts-long) were identified, which were in accordance with other Phytophthora species. To the best of our knowledge, this is the first study using small RNA sequencing to identify viruses in Phytophthora spp.
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Affiliation(s)
- Leticia Botella
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic;
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, Na Sadkach 1780, 37005 Ceske Budejovice, Czech Republic
- Correspondence: ; Tel.: +420-389-032-942
| | - Thomas Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 1, 61300 Brno, Czech Republic;
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Nidhi S, Anand U, Oleksak P, Tripathi P, Lal JA, Thomas G, Kuca K, Tripathi V. Novel CRISPR-Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives. Int J Mol Sci 2021; 22:3327. [PMID: 33805113 PMCID: PMC8036902 DOI: 10.3390/ijms22073327] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
According to Darwin's theory, endless evolution leads to a revolution. One such example is the Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-Cas system, an adaptive immunity system in most archaea and many bacteria. Gene editing technology possesses a crucial potential to dramatically impact miscellaneous areas of life, and CRISPR-Cas represents the most suitable strategy. The system has ignited a revolution in the field of genetic engineering. The ease, precision, affordability of this system is akin to a Midas touch for researchers editing genomes. Undoubtedly, the applications of this system are endless. The CRISPR-Cas system is extensively employed in the treatment of infectious and genetic diseases, in metabolic disorders, in curing cancer, in developing sustainable methods for fuel production and chemicals, in improving the quality and quantity of food crops, and thus in catering to global food demands. Future applications of CRISPR-Cas will provide benefits for everyone and will save countless lives. The technology is evolving rapidly; therefore, an overview of continuous improvement is important. In this review, we aim to elucidate the current state of the CRISPR-Cas revolution in a tailor-made format from its discovery to exciting breakthroughs at the application level and further upcoming trends related to opportunities and challenges including ethical concerns.
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Affiliation(s)
- Sweta Nidhi
- Department of Genomics and Bioinformatics, Aix-Marseille University, 13007 Marseille, France;
| | - Uttpal Anand
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel;
| | - Patrik Oleksak
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Pooja Tripathi
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India;
| | - Jonathan A. Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
| | - George Thomas
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
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Survival of Salmonella Under Heat Stress is Associated with the Presence/Absence of CRISPR Cas Genes and Iron Levels. Curr Microbiol 2021; 78:1741-1751. [PMID: 33738531 DOI: 10.1007/s00284-021-02443-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) cas genes have been linked to stress response in Salmonella. Our aim was to identify the presence of CRISPR cas in Salmonella and its response to heat in the presence of iron. Whole genomes of Salmonella (n = 50) of seven serovars were compared to identify the presence of CRISPR cas genes, direct-repeats and spacers. All Salmonella genomes had all cas genes present except S. Newport 2393 which lacked these genes. Gene-specific primers were used to confirm the absence of these genes in S. Newport 2393. The presence/absence of CRISPR cas genes was further investigated among 469 S. Newport genomes from PATRIC with 283 genomes selected for pan-genome analysis. The response of eleven Salmonella strains of various serovars to gradual heat in ferrous and ferric forms of iron was investigated. A total of 32/283 S. Newport genomes that lacked all CRISPR cas genes clustered together. S. Newport 2393 was the most heat-sensitive strain at higher iron levels (200 and 220 pm) in ferrous and ferric forms of iron. The absence of CRISPR cas genes in S. Newport 2393 may contribute to its increase in heat sensitivity and iron may play a role in this. The high reduction in numbers of most Salmonella strains exposed to heat makes it unfeasible to extract RNA and conduct transcription studies. Further studies should be conducted to validate the survival of Salmonella when exposed to heat in the presence/absence of CRISPR cas genes and different iron levels.
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Sharma P, Sharma BS, Verma RJ. CRISPR-based genome editing of zebrafish. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:69-84. [PMID: 33934838 DOI: 10.1016/bs.pmbts.2021.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9, once discovered as an adaptive immune system in bacteria, has emerged as a disruptive technology in the field of genetic engineering. Technological advancements in the recent past has enhanced the applicability of CRISPR/Cas9 tool for gene editing, gene therapies, developmental studies and mutational analysis in various model organisms. Zebrafish, one of the excellent animal models, is preferred for conducting CRISPR/Cas9 studies to assess the functional implication of specific genes of interest. CRISPR/Cas9 mediated gene editing techniques, such as, knock-out and knock-in approaches, provide evidences to identify the role of different genes through loss-of-function studies. Also, CRISPR/Cas9 has been proved to be an efficient tool for designing disease models for gene expression studies based on phenotypic screening. The present chapter provides an overview of CRISPR/Cas9 mechanism, different strategies for DNA modifications and gene function analysis, highlighting the translational applications for future prospects, such as screening of drug toxicity and efficacy.
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Affiliation(s)
- Preeti Sharma
- Department of Zoology, Biomedical Technology & Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India; PanGenomics International Pvt Ltd, Sterling Accuris Diagnostics, Ellis Bridge, Ahmedabad, Gujarat, India.
| | - B Sharan Sharma
- Rivaara Labs Pvt Ltd, KD Hospital, Vaishnodevi Circle, Ahmedabad, Gujarat, India
| | - Ramtej J Verma
- Department of Zoology, Biomedical Technology & Human Genetics, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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History, evolution and classification of CRISPR-Cas associated systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 179:11-76. [PMID: 33785174 DOI: 10.1016/bs.pmbts.2020.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This chapter provides a detailed description of the history of CRISPR-Cas and its evolution into one of the most efficient genome-editing strategies. The chapter begins by providing information on early findings that were critical in deciphering the role of CRISPR-Cas associated systems in prokaryotes. It then describes how CRISPR-Cas had been evolved into an efficient genome-editing strategy. In the subsequent section, latest developments in the genome-editing approaches based on CRISPR-Cas are discussed. The chapter ends with the recent classification and possible evolution of CRISPR-Cas systems.
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Huang F, Zhu B. The Cyclic Oligoadenylate Signaling Pathway of Type III CRISPR-Cas Systems. Front Microbiol 2021; 11:602789. [PMID: 33552016 PMCID: PMC7854544 DOI: 10.3389/fmicb.2020.602789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/11/2020] [Indexed: 12/24/2022] Open
Abstract
Type III CRISPR-Cas systems, which are widespread in both bacteria and archaea, provide immunity against DNA viruses and plasmids in a transcription-dependent manner. Since an unprecedented cyclic oligoadenylate (cOA) signaling pathway was discovered in type III systems in 2017, the cOA signaling has been extensively studied in recent 3 years, which has expanded our understanding of type III systems immune defense and also its counteraction by viruses. In this review, we summarized recent advances in cOA synthesis, cOA-activated effector protein, cOA signaling-mediated immunoprotection, and cOA signaling inhibition, and highlighted the crosstalk between cOA signaling and other cyclic oligonucleotide-mediated immunity discovered very recently.
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Affiliation(s)
- Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
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Newsom S, Parameshwaran HP, Martin L, Rajan R. The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies. Front Cell Infect Microbiol 2021; 10:619763. [PMID: 33585286 PMCID: PMC7876343 DOI: 10.3389/fcimb.2020.619763] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Bacterial and archaeal CRISPR-Cas systems offer adaptive immune protection against foreign mobile genetic elements (MGEs). This function is regulated by sequence specific binding of CRISPR RNA (crRNA) to target DNA/RNA, with an additional requirement of a flanking DNA motif called the protospacer adjacent motif (PAM) in certain CRISPR systems. In this review, we discuss how the same fundamental mechanism of RNA-DNA and/or RNA-RNA complementarity is utilized by bacteria to regulate two distinct functions: to ward off intruding genetic materials and to modulate diverse physiological functions. The best documented examples of alternate functions are bacterial virulence, biofilm formation, adherence, programmed cell death, and quorum sensing. While extensive complementarity between the crRNA and the targeted DNA and/or RNA seems to constitute an efficient phage protection system, partial complementarity seems to be the key for several of the characterized alternate functions. Cas proteins are also involved in sequence-specific and non-specific RNA cleavage and control of transcriptional regulator expression, the mechanisms of which are still elusive. Over the past decade, the mechanisms of RNA-guided targeting and auxiliary functions of several Cas proteins have been transformed into powerful gene editing and biotechnological tools. We provide a synopsis of CRISPR technologies in this review. Even with the abundant mechanistic insights and biotechnology tools that are currently available, the discovery of new and diverse CRISPR types holds promise for future technological innovations, which will pave the way for precision genome medicine.
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Affiliation(s)
- Sydney Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Lindsie Martin
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
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Singh V. An introduction and use of the CRISPR-Cas systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 179:1-10. [PMID: 33785173 DOI: 10.1016/bs.pmbts.2020.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Clusters of regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated proteins (Cas) system (CRISPR-Cas) is a rapidly evolving field of targeted genome engineering. The type II CRISPR-Cas9 is used for genome editing of many organisms. Single guide RNA (sgRNA) can bind to Cas9 protein that can target desired sequences in presence of protospacer adjacent motif (PAM) sequences. This complex binds and generate a DSB that is repaired by NHEJ or HDR pathways, subsequently gene insertion/deletion (Indels) is generated that leads to change in the organism's genotype followed by its phenotype. In this chapter, CRISPR-mediated targeted genome editing in different lower organisms has been highlighted to promote its basic understanding to be applied for biotechnological, biomedical and therapeutic applications.
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Affiliation(s)
- Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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48
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Xu CF, Chen GJ, Luo YL, Zhang Y, Zhao G, Lu ZD, Czarna A, Gu Z, Wang J. Rational designs of in vivo CRISPR-Cas delivery systems. Adv Drug Deliv Rev 2021; 168:3-29. [PMID: 31759123 DOI: 10.1016/j.addr.2019.11.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/09/2019] [Accepted: 11/19/2019] [Indexed: 02/08/2023]
Abstract
The CRISPR-Cas system initiated a revolution in genome editing when it was, for the first time, demonstrated success in the mammalian cells. Today, scientists are able to readily edit genomes, regulate gene transcription, engineer posttranscriptional events, and image nucleic acids using CRISPR-Cas-based tools. However, to efficiently transport CRISPR-Cas into target tissues/cells remains challenging due to many extra- and intra-cellular barriers, therefore largely limiting the applications of CRISPR-based therapeutics in vivo. In this review, we summarize the features of plasmid-, RNA- and ribonucleoprotein (RNP)-based CRISPR-Cas therapeutics. Then, we survey the current in vivo delivery systems. We specify the requirements for efficient in vivo delivery in clinical settings, and highlight both efficiency and safety for different CRISPR-Cas tools.
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Mycobacterium tuberculosis CRISPR/Cas system Csm1 holds clues to the evolutionary relationship between DNA polymerase and cyclase activity. Int J Biol Macromol 2020; 170:140-149. [PMID: 33352158 DOI: 10.1016/j.ijbiomac.2020.12.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 10/22/2022]
Abstract
Prokaryotic CRISPR/Cas systems confer immunity against invading nucleic acids through effector complexes. Csm1, the signature protein of Type III effector complexes, catalyses cyclic oligoadenylate synthesis when in the effector complex, but not when alone, activating the Csm6 nuclease and switching on the antiviral response. Here, we provide biochemical evidence that M. tuberculosis Csm1 (MtbCsm1) has ion-dependent polymerase activity when independent of the effector complex. Structural studies provide supporting evidence that the catalytic core of the MtbCsm1 palm2 domain is almost identical to that of classical DNA polymerase Pol IV, and that the palm1 and B domains function as the other structural elements required (thumb and fingers) for DNA polymerase activity. MtbCsm1 polymerase activity is relatively weak in vitro and its functional relevance in vivo is unknown. Our structural and mutagenesis data suggest that residue K692 in the palm2 domain has been significant in the evolution of Csm1 from a polymerase to a cyclase, and support the notion that the cyclase activity of Csm1 requires the presence of other elements provided by the CRISPR/Cas effector complex. This structural rationale for Csm1 polymerase (alone) and cyclase (within the effector complex) activity should benefit future functional investigations and engineering.
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50
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Manav MC, Van LB, Lin J, Fuglsang A, Peng X, Brodersen DE. Structural basis for inhibition of an archaeal CRISPR-Cas type I-D large subunit by an anti-CRISPR protein. Nat Commun 2020; 11:5993. [PMID: 33239638 PMCID: PMC7689449 DOI: 10.1038/s41467-020-19847-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
A hallmark of type I CRISPR-Cas systems is the presence of Cas3, which contains both the nuclease and helicase activities required for DNA cleavage during interference. In subtype I-D systems, however, the histidine-aspartate (HD) nuclease domain is encoded as part of a Cas10-like large effector complex subunit and the helicase activity in a separate Cas3' subunit, but the functional and mechanistic consequences of this organisation are not currently understood. Here we show that the Sulfolobus islandicus type I-D Cas10d large subunit exhibits an unusual domain architecture consisting of a Cas3-like HD nuclease domain fused to a degenerate polymerase fold and a C-terminal domain structurally similar to Cas11. Crystal structures of Cas10d both in isolation and bound to S. islandicus rod-shaped virus 3 AcrID1 reveal that the anti-CRISPR protein sequesters the large subunit in a non-functional state unable to form a cleavage-competent effector complex. The architecture of Cas10d suggests that the type I-D effector complex is similar to those found in type III CRISPR-Cas systems and that this feature is specifically exploited by phages for anti-CRISPR defence.
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Affiliation(s)
- M Cemre Manav
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Lan B Van
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark
| | - Jinzhong Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Anders Fuglsang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark.
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark.
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