1
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Chhipa AS, Radadiya E, Patel S. CRISPR-Cas based diagnostic tools: Bringing diagnosis out of labs. Diagn Microbiol Infect Dis 2024; 109:116252. [PMID: 38479094 DOI: 10.1016/j.diagmicrobio.2024.116252] [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: 08/31/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/30/2024]
Abstract
Timely detection is important for the effective management of infectious diseases. Reverse Transcription Polymerase Chain Reaction (RT-PCR) stands as the prime nucleic acid based test that is employed for the detection of infectious diseases. The method ensures sensitivity and specificity. However, RT-PCR is a relatively expensive technique due to the requirement of costly equipment and reagents. Further, it requires skilled personnel and established laboratories that are usually inaccessible in underdeveloped areas. On the other hand, rapid antigen based techniques are cost effective and easily accessible, but are less effective in terms of sensitivity and specificity. CRISPR-Cas systems are advanced diagnostic tools that combine the advantages of both PCR and antigen based detection techniques, and allows the rapid detection with high sensitivity/specificity. The present review aims to discuss the applicability of CRISPR-Cas based diagnostic tools for the infectious disease detection. The review further attempts to highlight the current limitations and future research directions to improve the CRISPR based diagnostic tools for rapid and effective disease detection.
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Affiliation(s)
- Abu Sufiyan Chhipa
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India
| | - Ekta Radadiya
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India
| | - Snehal Patel
- Department of Pharmacology, Institute of Pharmacy, Nirma University, India.
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2
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Tavakolidakhrabadi N, Aulicino F, May CJ, Saleem MA, Berger I, Welsh GI. Genome editing and kidney health. Clin Kidney J 2024; 17:sfae119. [PMID: 38766272 PMCID: PMC11099665 DOI: 10.1093/ckj/sfae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Indexed: 05/22/2024] Open
Abstract
Genome editing technologies, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas in particular, have revolutionized the field of genetic engineering, providing promising avenues for treating various genetic diseases. Chronic kidney disease (CKD), a significant health concern affecting millions of individuals worldwide, can arise from either monogenic or polygenic mutations. With recent advancements in genomic sequencing, valuable insights into disease-causing mutations can be obtained, allowing for the development of new treatments for these genetic disorders. CRISPR-based treatments have emerged as potential therapies, especially for monogenic diseases, offering the ability to correct mutations and eliminate disease phenotypes. Innovations in genome editing have led to enhanced efficiency, specificity and ease of use, surpassing earlier editing tools such as zinc-finger nucleases and transcription activator-like effector nucleases (TALENs). Two prominent advancements in CRISPR-based gene editing are prime editing and base editing. Prime editing allows precise and efficient genome modifications without inducing double-stranded DNA breaks (DSBs), while base editing enables targeted changes to individual nucleotides in both RNA and DNA, promising disease correction in the absence of DSBs. These technologies have the potential to treat genetic kidney diseases through specific correction of disease-causing mutations, such as somatic mutations in PKD1 and PKD2 for polycystic kidney disease; NPHS1, NPHS2 and TRPC6 for focal segmental glomerulosclerosis; COL4A3, COL4A4 and COL4A5 for Alport syndrome; SLC3A1 and SLC7A9 for cystinuria and even VHL for renal cell carcinoma. Apart from editing the DNA sequence, CRISPR-mediated epigenome editing offers a cost-effective method for targeted treatment providing new avenues for therapeutic development, given that epigenetic modifications are associated with the development of various kidney disorders. However, there are challenges to overcome, including developing efficient delivery methods, improving safety and reducing off-target effects. Efforts to improve CRISPR-Cas technologies involve optimizing delivery vectors, employing viral and non-viral approaches and minimizing immunogenicity. With research in animal models providing promising results in rescuing the expression of wild-type podocin in mouse models of nephrotic syndrome and successful clinical trials in the early stages of various disorders, including cancer immunotherapy, there is hope for successful translation of genome editing to kidney diseases.
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Affiliation(s)
| | - Francesco Aulicino
- BrisSynBio Bristol Synthetic Biology Centre, Biomedical Sciences, School of Biochemistry, Bristol Royal Hospital for Children
| | - Carl J May
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
| | - Moin A Saleem
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
- Department of Paediatric Nephrology, Bristol Royal Hospital for Children, Bristol, UK
| | - Imre Berger
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Gavin I Welsh
- Bristol Renal, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, UK
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3
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Zheng C, Liang H, Dai L, Yu J, Long C. Dissecting the CRISPR Cas1-Cas2 Protospacer Binding and Selection Mechanism by Using Molecular Dynamics Simulations. J Phys Chem B 2024; 128:3563-3574. [PMID: 38573978 DOI: 10.1021/acs.jpcb.3c07320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Cas1 and Cas2 are highly conserved proteins among the clustered regularly interspaced short palindromic repeat Cas (CRISPR-Cas) systems and play a crucial role in protospacer selection and integration. According to the double-forked CRISPR Cas1-Cas2 complex, we conducted extensive all-atom molecular dynamics simulations to investigate the protospacer DNA binding and recognition. Our findings revealed that single-point amino acid mutations in Cas1 or in Cas2 had little impact on the binding of the protospacer, both in the binding and precatalytic states. In contrast, multiple-point amino acid mutations, particularly G74A, P80L, and V89A mutations on Cas2 and Cas2' proteins (m-multiple1 system), significantly affected the protospacer binding and selection. Notably, mutations on Cas2 and Cas2' led to an increased number of hydrogen bonds (#HBs) between Cas2&Cas2' and the dsDNA in the m-multiple1 system compared with the wild-type system. And the strong electrostatic interactions between Cas1-Cas2 and the protospacer DNA (psDNA) in the m-multiple1 system again suggested the increase in the binding affinity of protospacer acquisition. Specifically, mutations in Cas2 and Cas2' can remotely make the protospacer adjacent motif complementary (PAMc) sequences better in recognition by the two active sites, while multiple mutations K211E, P202Q, P212L, R138L, V134A, A286T, P282H, and P294H on Cas1a/Cas1b&Cas1a'/Cas1b' (m-multiple2 system) decrease the #HBs and the electrostatic interactions and make the PAMc worse in recognition compared with the wild-type system.
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Affiliation(s)
- Chuanbo Zheng
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Hongqiong Liang
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Liqiang Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California 92697, United States
| | - Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
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4
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Pradeu T, Thomma BPHJ, Girardin SE, Lemaitre B. The conceptual foundations of innate immunity: Taking stock 30 years later. Immunity 2024; 57:613-631. [PMID: 38599162 DOI: 10.1016/j.immuni.2024.03.007] [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: 01/14/2024] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
While largely neglected over decades during which adaptive immunity captured most of the attention, innate immune mechanisms have now become central to our understanding of immunology. Innate immunity provides the first barrier to infection in vertebrates, and it is the sole mechanism of host defense in invertebrates and plants. Innate immunity also plays a critical role in maintaining homeostasis, shaping the microbiota, and in disease contexts such as cancer, neurodegeneration, metabolic syndromes, and aging. The emergence of the field of innate immunity has led to an expanded view of the immune system, which is no longer restricted to vertebrates and instead concerns all metazoans, plants, and even prokaryotes. The study of innate immunity has given rise to new concepts and language. Here, we review the history and definition of the core concepts of innate immunity, discussing their value and fruitfulness in the long run.
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Affiliation(s)
- Thomas Pradeu
- CNRS UMR 5164 ImmunoConcept, University of Bordeaux, Bordeaux, France; Department of Biological and Medical Sciences, University of Bordeaux, Bordeaux, France; Presidential Fellow, Chapman University, Orange, CA, USA.
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Bruno Lemaitre
- Global Health Institute, School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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5
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Oh GS, An S, Kim S. Harnessing CRISPR-Cas adaptation for RNA recording and beyond. BMB Rep 2024; 57:40-49. [PMID: 38053290 PMCID: PMC10828431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 12/07/2023] Open
Abstract
Prokaryotes encode clustered regularly interspaced short palindromic repeat (CRISPR) arrays and CRISPR-associated (Cas) genes as an adaptive immune machinery. CRISPR-Cas systems effectively protect hosts from the invasion of foreign enemies, such as bacteriophages and plasmids. During a process called 'adaptation', non-self-nucleic acid fragments are acquired as spacers between repeats in the host CRISPR array, to establish immunological memory. The highly conserved Cas1-Cas2 complexes function as molecular recorders to integrate spacers in a time course manner, which can subsequently be expressed as crRNAs complexed with Cas effector proteins for the RNAguided interference pathways. In some of the RNA-targeting type III systems, Cas1 proteins are fused with reverse transcriptase (RT), indicating that RT-Cas1-Cas2 complexes can acquire RNA transcripts for spacer acquisition. In this review, we summarize current studies that focus on the molecular structure and function of the RT-fused Cas1-Cas2 integrase, and its potential applications as a directional RNA-recording tool in cells. Furthermore, we highlight outstanding questions for RT-Cas1-Cas2 studies and future directions for RNA-recording CRISPR technologies. [BMB Reports 2024; 57(1): 40-49].
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Affiliation(s)
- Gyeong-Seok Oh
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Seongjin An
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- Department of Life Sciences, School of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Sungchul Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
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6
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Bost J, Recalde A, Waßmer B, Wagner A, Siebers B, Albers SV. Application of the endogenous CRISPR-Cas type I-D system for genetic engineering in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Front Microbiol 2023; 14:1254891. [PMID: 37849926 PMCID: PMC10577407 DOI: 10.3389/fmicb.2023.1254891] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems are widely distributed among bacteria and archaea. In this study, we demonstrate the successful utilization of the type I-D CRISPR-Cas system for genetic engineering in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Given its extreme growth conditions characterized by a temperature of 75°C and pH 3, an uracil auxotrophic selection system was previously established, providing a basis for our investigations. We developed a novel plasmid specifically designed for genome editing, which incorporates a mini-CRISPR array that can be induced using xylose, resulting in targeted DNA cleavage. Additionally, we integrated a gene encoding the β-galactosidase of Saccharolobus solfataricus into the plasmid, enabling blue-white screening and facilitating the mutant screening process. Through the introduction of donor DNA containing genomic modifications into the plasmid, we successfully generated deletion mutants and point mutations in the genome of S. acidocaldarius. Exploiting the PAM (protospacer adjacent motif) dependence of type I systems, we experimentally confirmed the functionality of three different PAMs (CCA, GTA, and TCA) through a self-targeting assessment assay and the gene deletion of upsE. Our findings elucidate the application of the endogenous Type I-D CRISPR-Cas system for genetic engineering in S. acidocaldarius, thus expanding its genetic toolbox.
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Affiliation(s)
- Jan Bost
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Alejandra Recalde
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bianca Waßmer
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Alexander Wagner
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
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7
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Lin YQ, Feng KK, Lu JY, Le JQ, Li WL, Zhang BC, Li CL, Song XH, Tong LW, Shao JW. CRISPR/Cas9-based application for cancer therapy: Challenges and solutions for non-viral delivery. J Control Release 2023; 361:727-749. [PMID: 37591461 DOI: 10.1016/j.jconrel.2023.08.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/04/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023]
Abstract
CRISPR/Cas9 genome editing is a promising therapeutic technique, which makes precise and rapid gene editing technology possible on account of its high sensitivity and efficiency. CRISPR/Cas9 system has been proved to able to effectively disrupt and modify genes, which shows great potential for cancer treatment. Current researches proves that virus vectors are capable of effectively delivering the CRISPR/Cas9 system, but immunogenicity and carcinogenicity caused by virus transmission still trigger serious consequences. Therefore, the greatest challenge of CRISPR/Cas9 for cancer therapy lies on how to deliver it to the target tumor site safely and effectively. Non-viral delivery systems with specific targeting, high loading capacity, and low immune toxicity are more suitable than viral vectors, which limited by uncontrollable side effects. Their medical advances and applications have been widely concerned. Herein, we present the molecule mechanism and different construction strategies of CRISPR/Cas9 system for editing genes at the beginning of this research. Subsequently, several common CRISPR/Cas9 non-viral deliveries for cancer treatment are introduced. Lastly, based on the main factors limiting the delivery efficiency of non-viral vectors proposed in the existing researches and literature, we summarize and discuss the main methods to solve these limitations in the existing tumor treatment system, aiming to introduce further optimization and innovation of the CRISPR/Cas9 non-viral delivery system suitable for cancer treatment.
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Affiliation(s)
- Ying-Qi Lin
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ke-Ke Feng
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Jie-Ying Lu
- Faculty of Foreign Studies, Guangdong Baiyun University, Guangzhou 510450, China
| | - Jing-Qing Le
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Wu-Lin Li
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Bing-Chen Zhang
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Cheng-Lei Li
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Xun-Huan Song
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ling-Wu Tong
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Jing-Wei Shao
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, College of Chemistry, Fuzhou University, Fuzhou 350108, China.
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8
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Chakrabarty P, Sen R, Sengupta S. From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution. Funct Integr Genomics 2023; 23:278. [PMID: 37610667 DOI: 10.1007/s10142-023-01206-w] [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: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.
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Affiliation(s)
- Prayas Chakrabarty
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
| | - Raneet Sen
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
- Institute of Bioorganic Chemistry, Department of RNA Metabolism, Polish Academy of Sciences, Poznan, Poland
| | - Sugopa Sengupta
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India.
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9
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Zheng Q, Wang W, Zhou Y, Mo J, Chang X, Zha Z, Zha L. Synthetic nanoparticles for the delivery of CRISPR/Cas9 gene editing system: classification and biomedical applications. Biomater Sci 2023; 11:5361-5389. [PMID: 37381725 DOI: 10.1039/d3bm00788j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Gene editing has great potential in biomedical research including disease diagnosis and treatment. Clustered regularly interspaced short palindromic repeats (CRISPR) is the most straightforward and cost-effective method. The efficient and precise delivery of CRISPR can impact the specificity and efficacy of gene editing. In recent years, synthetic nanoparticles have been discovered as effective CRISPR/Cas9 delivery vehicles. We categorized synthetic nanoparticles for CRISPR/Cas9 delivery and discribed their advantages and disadvantages. Further, the building blocks of different kinds of nanoparticles and their applications in cells/tissues, cancer and other diseases were described in detail. Finally, the challenges encountered in the clinical application of CRISPR/Cas9 delivery materials were discussed, and potential solutions were provided regarding efficiency and biosafety issues.
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Affiliation(s)
- Qi Zheng
- International Immunology Centre, Anhui Agricultural University, Hefei 230036, P. R. China.
| | - Weitao Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China.
| | - Yuhang Zhou
- International Immunology Centre, Anhui Agricultural University, Hefei 230036, P. R. China.
| | - Jiayin Mo
- International Immunology Centre, Anhui Agricultural University, Hefei 230036, P. R. China.
| | - Xinyue Chang
- International Immunology Centre, Anhui Agricultural University, Hefei 230036, P. R. China.
| | - Zhengbao Zha
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, P. R. China.
| | - Lisha Zha
- International Immunology Centre, Anhui Agricultural University, Hefei 230036, P. R. China.
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10
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McBride TM, Cameron SC, Fineran PC, Fagerlund RD. The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems. Biochem J 2023; 480:471-488. [PMID: 37052300 DOI: 10.1042/bcj20220073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 04/14/2023]
Abstract
Prokaryotes have adaptive defence mechanisms that protect them from mobile genetic elements and viral infection. One defence mechanism is called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins). There are six different types of CRISPR-Cas systems and multiple subtypes that vary in composition and mode of action. Type I and III CRISPR-Cas systems utilise multi-protein complexes, which differ in structure, nucleic acid binding and cleaving preference. The type I-D system is a chimera of type I and III systems. Recently, there has been a burst of research on the type I-D CRISPR-Cas system. Here, we review the mechanism, evolution and biotechnological applications of the type I-D CRISPR-Cas system.
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Affiliation(s)
- Tess M McBride
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Shaharn C Cameron
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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11
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CRISPR-Cas adaptation in Escherichia coli. Biosci Rep 2023; 43:232582. [PMID: 36809461 PMCID: PMC10011333 DOI: 10.1042/bsr20221198] [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: 11/28/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/23/2023] Open
Abstract
Prokaryotes use the adaptive immunity mediated via the Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated (CRISPR-Cas) system for protection against invading elements such as phages and plasmids. The immunity is achieved by capturing small DNA fragments or spacers from foreign nucleic acids (protospacers) and integrating them into the host CRISPR locus. This step of CRISPR-Cas immunity called 'naïve CRISPR adaptation' requires the conserved Cas1-Cas2 complex and is often supported by variable host proteins that assist in spacer processing and integration. Bacteria that have acquired new spacers become immune to the same invading elements when reinfected. CRISPR-Cas immunity can also be updated by integrating new spacers from the same invading elements, a process called 'primed adaptation'. Only properly selected and integrated spacers are functional in the next steps of CRISPR immunity when their processed transcripts are used for RNA-guided target recognition and interference (target degradation). Capturing, trimming, and integrating new spacers in the correct orientation are universal steps of adaptation to all CRISPR-Cas systems, but some details are CRISPR-Cas type-specific and species-specific. In this review, we provide an overview of the mechanisms of CRISPR-Cas class 1 type I-E adaptation in Escherichia coli as a general model for adaptation processes (DNA capture and integration) that have been studied in detail. We focus on the role of host non-Cas proteins involved in adaptation, particularly on the role of homologous recombination.
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12
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Karamali F, Behtaj S, Babaei-Abraki S, Hadady H, Atefi A, Savoj S, Soroushzadeh S, Najafian S, Nasr Esfahani MH, Klassen H. Potential therapeutic strategies for photoreceptor degeneration: the path to restore vision. J Transl Med 2022; 20:572. [PMID: 36476500 PMCID: PMC9727916 DOI: 10.1186/s12967-022-03738-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/29/2022] [Indexed: 12/12/2022] Open
Abstract
Photoreceptors (PRs), as the most abundant and light-sensing cells of the neuroretina, are responsible for converting light into electrical signals that can be interpreted by the brain. PR degeneration, including morphological and functional impairment of these cells, causes significant diminution of the retina's ability to detect light, with consequent loss of vision. Recent findings in ocular regenerative medicine have opened promising avenues to apply neuroprotective therapy, gene therapy, cell replacement therapy, and visual prostheses to the challenge of restoring vision. However, successful visual restoration in the clinical setting requires application of these therapeutic approaches at the appropriate stage of the retinal degeneration. In this review, firstly, we discuss the mechanisms of PR degeneration by focusing on the molecular mechanisms underlying cell death. Subsequently, innovations, recent developments, and promising treatments based on the stage of disorder progression are further explored. Then, the challenges to be addressed before implementation of these therapies in clinical practice are considered. Finally, potential solutions to overcome the current limitations of this growing research area are suggested. Overall, the majority of current treatment modalities are still at an early stage of development and require extensive additional studies, both pre-clinical and clinical, before full restoration of visual function in PR degeneration diseases can be realized.
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Affiliation(s)
- Fereshteh Karamali
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Sanaz Behtaj
- grid.1022.10000 0004 0437 5432Clem Jones Centre for Neurobiology and Stem Cell Research, Griffith University, Queensland, Australia ,grid.1022.10000 0004 0437 5432Menzies Health Institute Queensland, Griffith University, Southport, QLD 4222 Australia
| | - Shahnaz Babaei-Abraki
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Hanieh Hadady
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Atefeh Atefi
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Soraya Savoj
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Sareh Soroushzadeh
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Najafian
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr Esfahani
- grid.417689.5Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Henry Klassen
- grid.266093.80000 0001 0668 7243Gavin Herbert Eye Institute, Irvine, CA USA
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13
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Dela Ahator S, Liu Y, Wang J, Zhang LH. The virulence factor regulator and quorum sensing regulate the type I-F CRISPR-Cas mediated horizontal gene transfer in Pseudomonas aeruginosa. Front Microbiol 2022; 13:987656. [PMID: 36246261 PMCID: PMC9563714 DOI: 10.3389/fmicb.2022.987656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is capable of thriving in diverse environments due to its network of regulatory components for effective response to stress factors. The survival of the bacteria is also dependent on the ability to discriminate between the acquisition of beneficial and non-beneficial genetic materials via horizontal gene transfer (HGT). Thus, bacteria have evolved the CRISPR-Cas adaptive immune system for defense against the deleterious effect of phage infection and HGT. By using the transposon mutagenesis approach, we identified the virulence factor regulator (Vfr) as a key regulator of the type I-F CRISPR-Cas system in P. aeruginosa. We showed that Vfr influences the expression of the CRISPR-Cas system through two signaling pathways in response to changes in calcium levels. Under calcium-rich conditions, Vfr indirectly regulates the CRISPR-Cas system via modulation of the AHL-QS gene expression, which could be vital for defense against phage infection at high cell density. When encountering calcium deficiency, however, Vfr can directly regulate the CRISPR-Cas system via a cAMP-dependent pathway. Furthermore, we provide evidence that mutation of vfr reduces the CRISPR-Cas spacer acquisition and interference of HGT. The results from this study add to the regulatory network of factors controlling the CRISPR-Cas system in response to abiotic factors in the environment. The findings may facilitate the design of effective and reliable phage therapies against P. aeruginosa infections, as targeting Vfr could prevent the development of the CRISPR-Cas mediated phage resistance.
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Affiliation(s)
- Stephen Dela Ahator
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
- Research Group for Host Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Yang Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Jianhe Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
- *Correspondence: Lian-Hui Zhang,
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14
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Riaz A, Kanwal F, Ahmad I, Ahmad S, Farooq A, Madsen CK, Brinch-Pedersen H, Bekalu ZE, Dai F, Zhang G, Alqudah AM. New Hope for Genome Editing in Cultivated Grasses: CRISPR Variants and Application. Front Genet 2022; 13:866121. [PMID: 35923689 PMCID: PMC9340155 DOI: 10.3389/fgene.2022.866121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
With the advent of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) mediated genome editing, crop improvement has progressed significantly in recent years. In this genome editing tool, CRISPR-associated Cas nucleases are restricted to their target of DNA by their preferred protospacer adjacent motifs (PAMs). A number of CRISPR-Cas variants have been developed e.g. CRISPR-Cas9, -Cas12a and -Cas12b, with different PAM requirements. In this mini-review, we briefly explain the components of the CRISPR-based genome editing tool for crop improvement. Moreover, we intend to highlight the information on the latest development and breakthrough in CRISPR technology, with a focus on a comparison of major variants (CRISPR-Cas9, -Cas12a, and -Cas12b) to the newly developed CRISPR-SpRY that have nearly PAM-less genome editing ability. Additionally, we briefly explain the application of CRISPR technology in the improvement of cultivated grasses with regard to biotic and abiotic stress tolerance as well as improving the quality and yield.
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Affiliation(s)
- Asad Riaz
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Farah Kanwal
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Iqrar Ahmad
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Shakeel Ahmad
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ayesha Farooq
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Claus Krogh Madsen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Zelalem Eshetu Bekalu
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Guoping Zhang, ; Ahmad M. Alqudah, ,
| | - Ahmad M. Alqudah
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
- *Correspondence: Guoping Zhang, ; Ahmad M. Alqudah, ,
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15
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Schwarz C, Mathieu J, Laverde Gomez JA, Yu P, Alvarez PJJ. Renaissance for Phage-Based Bacterial Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4691-4701. [PMID: 34793127 DOI: 10.1021/acs.est.1c06232] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jenny A Laverde Gomez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
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16
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Wang SW, Gao C, Zheng YM, Yi L, Lu JC, Huang XY, Cai JB, Zhang PF, Cui YH, Ke AW. Current applications and future perspective of CRISPR/Cas9 gene editing in cancer. Mol Cancer 2022; 21:57. [PMID: 35189910 PMCID: PMC8862238 DOI: 10.1186/s12943-022-01518-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) system provides adaptive immunity against plasmids and phages in prokaryotes. This system inspires the development of a powerful genome engineering tool, the CRISPR/CRISPR-associated nuclease 9 (CRISPR/Cas9) genome editing system. Due to its high efficiency and precision, the CRISPR/Cas9 technique has been employed to explore the functions of cancer-related genes, establish tumor-bearing animal models and probe drug targets, vastly increasing our understanding of cancer genomics. Here, we review current status of CRISPR/Cas9 gene editing technology in oncological research. We first explain the basic principles of CRISPR/Cas9 gene editing and introduce several new CRISPR-based gene editing modes. We next detail the rapid progress of CRISPR screening in revealing tumorigenesis, metastasis, and drug resistance mechanisms. In addition, we introduce CRISPR/Cas9 system delivery vectors and finally demonstrate the potential of CRISPR/Cas9 engineering to enhance the effect of adoptive T cell therapy (ACT) and reduce adverse reactions.
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17
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Brackett NF, Pomés A, Chapman MD. New Frontiers: Precise Editing of Allergen Genes Using CRISPR. FRONTIERS IN ALLERGY 2022; 2:821107. [PMID: 35386981 PMCID: PMC8974684 DOI: 10.3389/falgy.2021.821107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/24/2021] [Indexed: 11/14/2022] Open
Abstract
Genome engineering with clustered regularly interspaced short palindromic repeats (CRISPR) technology offers the unique potential for unequivocally deleting allergen genes at the source. Compared to prior gene editing approaches, CRISPR boasts substantial improvements in editing efficiency, throughput, and precision. CRISPR has demonstrated success in several clinical applications such as sickle cell disease and β-thalassemia, and preliminary knockout studies of allergenic proteins using CRISPR editing show promise. Given the advantages of CRISPR, as well as specific DNA targets in the allergen genes, CRISPR gene editing is a viable approach for tackling allergy, which may lead to significant disease improvement. This review will highlight recent applications of CRISPR editing of allergens, particularly cat allergen Fel d 1, and will discuss the advantages and limitations of this approach compared to existing treatment options.
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18
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Wimmer T, Bonthu D, Moeschl V, Kleekamp P, Thiel C, Lytvynchuk L, Ellinwood M, Stieger K. A Bioluminescence Resonance Energy Transfer-Based Reporter System: Characterization and Applications. CRISPR J 2021; 4:884-895. [PMID: 34847743 DOI: 10.1089/crispr.2021.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome editing strategies and DNA repair research need powerful analytical tools. We generated a bioluminescence resonance energy transfer (BRET)-based reporter for the quantification of indel frequencies induced by DNA repair. The BRET reporter, expressed as a single molecule, consists of a mutated Renilla reniformis luciferase domain and a GFP2 domain separated by a shuttle-cloning box for the integration of any given endonuclease target sequence. The luciferase activity acts both as energy donor and as the internal standard, while the loss of GFP2 fluorescence acts as a reporter for the out-of-frame sequence alterations that result from the DNA repair via the non-homologous end joining/microhomology-mediated end joining DNA repair pathways of the endonuclease-mediated DNA double-strand break. This results in a decrease of the fluorescence/luminescence ratio. Employing this reporter in different experimental scenarios, using different cell lines and diseases targeted, we quantified the influence of both protein knockdown of DNA repair pathways as well as guide RNA mismatches on CRISPR-mediated nuclease activity and subsequent repair based on mutagenic repair on the reporter. In conclusion, we demonstrated this BRET-based reporter to be a robust and sensitive analytical tool for assessment of variety of different genome editing-based approaches.
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Affiliation(s)
- Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Dileep Bonthu
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Vincent Moeschl
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Philip Kleekamp
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Christian Thiel
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Lyubomyr Lytvynchuk
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
| | | | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany
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19
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Jensen TL, Gøtzsche CR, Woldbye DPD. Current and Future Prospects for Gene Therapy for Rare Genetic Diseases Affecting the Brain and Spinal Cord. Front Mol Neurosci 2021; 14:695937. [PMID: 34690692 PMCID: PMC8527017 DOI: 10.3389/fnmol.2021.695937] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
In recent years, gene therapy has been raising hopes toward viable treatment strategies for rare genetic diseases for which there has been almost exclusively supportive treatment. We here review this progress at the pre-clinical and clinical trial levels as well as market approvals within diseases that specifically affect the brain and spinal cord, including degenerative, developmental, lysosomal storage, and metabolic disorders. The field reached an unprecedented milestone when Zolgensma® (onasemnogene abeparvovec) was approved by the FDA and EMA for in vivo adeno-associated virus-mediated gene replacement therapy for spinal muscular atrophy. Shortly after EMA approved Libmeldy®, an ex vivo gene therapy with lentivirus vector-transduced autologous CD34-positive stem cells, for treatment of metachromatic leukodystrophy. These successes could be the first of many more new gene therapies in development that mostly target loss-of-function mutation diseases with gene replacement (e.g., Batten disease, mucopolysaccharidoses, gangliosidoses) or, less frequently, gain-of-toxic-function mutation diseases by gene therapeutic silencing of pathologic genes (e.g., amyotrophic lateral sclerosis, Huntington's disease). In addition, the use of genome editing as a gene therapy is being explored for some diseases, but this has so far only reached clinical testing in the treatment of mucopolysaccharidoses. Based on the large number of planned, ongoing, and completed clinical trials for rare genetic central nervous system diseases, it can be expected that several novel gene therapies will be approved and become available within the near future. Essential for this to happen is the in depth characterization of short- and long-term effects, safety aspects, and pharmacodynamics of the applied gene therapy platforms.
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Affiliation(s)
- Thomas Leth Jensen
- Department of Neurology, Rigshospitalet University Hospital, Copenhagen, Denmark
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20
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Kordyś M, Sen R, Warkocki Z. Applications of the versatile CRISPR-Cas13 RNA targeting system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1694. [PMID: 34553495 DOI: 10.1002/wrna.1694] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas are adaptable natural prokaryotic defense systems that act against invading viruses and plasmids. Among the six currently known major CRISPR-Cas types, the type VI CRISPR-Cas13 is the only one known to exclusively bind and cleave foreign RNA. Within the last couple of years, this system has been adapted to serve numerous, and sometimes not obvious, applications, including some that might be developed as effective molecular therapies. Indeed, Cas13 has been adapted to kill antibiotic-resistant bacteria. In a cell-free environment, Cas13 has been used in the development of highly specific, sensitive, multiplexing-capable, and field-adaptable detection tools. Importantly, Cas13 can be reprogrammed and applied to eukaryotes to either combat pathogenic RNA viruses or in the regulation of gene expression, facilitating the knockdown of mRNA, circular RNA, and noncoding RNA. Furthermore, Cas13 has been harnessed for in vivo RNA modifications including programmable regulation of alternative splicing, A-to-I and C to U editing, and m6A modifications. Finally, approaches allowing for the detection and characterization of RNA-interacting proteins have also been demonstrated. Here, we provide a comprehensive overview of the applications utilizing CRISPR-Cas13 that illustrate its versatility. We also discuss the most important limitations of the CRISPR-Cas13-based technologies, and controversies regarding them. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Martyna Kordyś
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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21
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Singh P, Ali SA. Impact of CRISPR-Cas9-Based Genome Engineering in Farm Animals. Vet Sci 2021; 8:122. [PMID: 34209174 PMCID: PMC8309983 DOI: 10.3390/vetsci8070122] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022] Open
Abstract
Humans are sorely over-dependent on livestock for their daily basic need of food in the form of meat, milk, and eggs. Therefore, genetic engineering and transgenesis provide the opportunity for more significant gains and production in a short span of time. One of the best strategies is the genetic alteration of livestock to enhance the efficiency of food production (e.g., meat and milk), animal health, and welfare (animal population and disease). Moreover, genome engineering in the bovine is majorly focused on subjects such as disease resistance (e.g., tuberculosis), eradicate allergens (e.g., beta-lactoglobulin knock-out), products generation (e.g., meat from male and milk from female), male or female birth specifically (animal sexing), the introduction of valuable traits (e.g., stress tolerance and disease resistance) and their wellbeing (e.g., hornlessness). This review addressed the impressive genome engineering method CRISPR, its fundamental principle for generating highly efficient target-specific guide RNA, and the accompanying web-based tools. However, we have covered the remarkable roadmap of the CRISPR method from its conception to its use in cattle. Additionally, we have updated the comprehensive information on CRISPR-based gene editing in cattle.
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Affiliation(s)
| | - Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, ICAR-National Dairy Research Institute, Karnal 132001, India;
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22
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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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23
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Long C, Dai L, E C, Da LT, Yu J. Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2. Biophys J 2021; 120:3126-3137. [PMID: 34197800 PMCID: PMC8390960 DOI: 10.1016/j.bpj.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/10/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cas1 and Cas2 are highly conserved proteins across clustered-regularly-interspaced-short-palindromic-repeat-Cas systems and play a significant role in protospacer acquisition. Based on crystal structure of twofold symmetric Cas1-Cas2 in complex with dual-forked protospacer DNA (psDNA), we conducted all-atom molecular dynamics simulations to study the psDNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence, or PAMc, of Cas1-Cas2. In the simulation, we noticed that two active sites of Cas1 and Cas1’ bind asymmetrically to two identical PAMc on the psDNA captured from the crystal structure. For the modified psDNA containing only one PAMc, as that to be recognized by Cas1-Cas2 in general, our simulations show that the non-PAMc association site of Cas1-Cas2 remains destabilized until after the stably bound PAMc being cleaved at the corresponding association site. Thus, long-range correlation appears to exist upon the PAMc cleavage between the two active sites (∼10 nm apart) on Cas1-Cas2, which can be allosterically mediated by psDNA and Cas2 and Cas2’ in bridging. To substantiate such findings, we conducted repeated runs and further simulated Cas1-Cas2 in complex with synthesized psDNA sequences psL and psH, which have been measured with low and high frequency in acquisition, respectively. Notably, such intersite correlation becomes even more pronounced for the Cas1-Cas2 in complex with psH but remains low for the Cas1-Cas2 in complex with psL. Hence, our studies demonstrate that PAMc recognition and cleavage at one active site of Cas1-Cas2 may allosterically regulate non-PAMc association or even cleavage at the other site, and such regulation can be mediated by noncatalytic Cas2 and DNA protospacer to possibly support the ensued psDNA acquisition.
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Affiliation(s)
- Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Liqiang Dai
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China; Beijing Computational Science Research Center, Beijing, China
| | - Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai, China
| | - Jin Yu
- Departments of Physics and Astronomy and Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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24
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CRISPR-mediated host genomic DNA damage is efficiently repaired through microhomology-mediated end joining in Zymomonas mobilis. J Genet Genomics 2021; 48:115-122. [PMID: 33958317 DOI: 10.1016/j.jgg.2021.02.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/07/2021] [Accepted: 02/21/2021] [Indexed: 02/07/2023]
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against mobile genetic elements (MGEs) through uptake of invader-derived spacers. De novo adaptation samples spacers from both invaders and hosts, whereas primed adaptation shows higher specificity to sample spacers from invaders in many model systems as well as in the subtype I-F system of Zymomonas mobilis. Self-derived spacers will lead to CRISPR self-interference. However, our in vivo study demonstrated that this species used the microhomology-mediated end joining (MMEJ) pathway to efficiently repair subtype I-F CRISPR-Cas system-mediated DNA breaks guided by the self-targeting spacers. MMEJ repair of DNA breaks requires direct microhomologous sequences flanking the protospacers and leads to DNA deletions covering the protospacers. Importantly, CRISPR-mediated genomic DNA breaks failed to be repaired via MMEJ pathway in presence of higher copies of short homologous DNA. Moreover, CRISPR-cleaved exogenous plasmid DNA was failed to be repaired through MMEJ pathway, probably due to the inhibition of MMEJ by the presence of higher copies of the plasmid DNA in Z. mobilis. Our results infer that MMEJ pathway discriminates DNA damages between in the host chromosome versus mobile genetic element (MGE) DNA, and maintains genome stability post CRISPR immunity in Z. mobilis.
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25
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Duarte F, Déglon N. Genome Editing for CNS Disorders. Front Neurosci 2020; 14:579062. [PMID: 33192264 PMCID: PMC7642486 DOI: 10.3389/fnins.2020.579062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Central nervous system (CNS) disorders have a social and economic burden on modern societies, and the development of effective therapies is urgently required. Gene editing may prevent or cure a disease by inducing genetic changes at endogenous loci. Genome editing includes not only the insertion, deletion or replacement of nucleotides, but also the modulation of gene expression and epigenetic editing. Emerging technologies based on ZFs, TALEs, and CRISPR/Cas systems have extended the boundaries of genome manipulation and promoted genome editing approaches to the level of promising strategies for counteracting genetic diseases. The parallel development of efficient delivery systems has also increased our access to the CNS. In this review, we describe the various tools available for genome editing and summarize in vivo preclinical studies of CNS genome editing, whilst considering current limitations and alternative approaches to overcome some bottlenecks.
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Affiliation(s)
- Fábio Duarte
- Laboratory of Neurotherapies and NeuroModulation, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland.,Laboratory of Neurotherapies and NeuroModulation, Neuroscience Research Center, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Nicole Déglon
- Laboratory of Neurotherapies and NeuroModulation, Department of Clinical Neurosciences, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland.,Laboratory of Neurotherapies and NeuroModulation, Neuroscience Research Center, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
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26
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Mohammadinejad R, Dehshahri A, Sagar Madamsetty V, Zahmatkeshan M, Tavakol S, Makvandi P, Khorsandi D, Pardakhty A, Ashrafizadeh M, Ghasemipour Afshar E, Zarrabi A. In vivo gene delivery mediated by non-viral vectors for cancer therapy. J Control Release 2020; 325:249-275. [PMID: 32634464 PMCID: PMC7334939 DOI: 10.1016/j.jconrel.2020.06.038] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022]
Abstract
Gene therapy by expression constructs or down-regulation of certain genes has shown great potential for the treatment of various diseases. The wide clinical application of nucleic acid materials dependents on the development of biocompatible gene carriers. There are enormous various compounds widely investigated to be used as non-viral gene carriers including lipids, polymers, carbon materials, and inorganic structures. In this review, we will discuss the recent discoveries on non-viral gene delivery systems. We will also highlight the in vivo gene delivery mediated by non-viral vectors to treat cancer in different tissue and organs including brain, breast, lung, liver, stomach, and prostate. Finally, we will delineate the state-of-the-art and promising perspective of in vivo gene editing using non-viral nano-vectors.
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Affiliation(s)
- Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Dehshahri
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Vijay Sagar Madamsetty
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Jacksonville, FL 32224, USA
| | - Masoumeh Zahmatkeshan
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shima Tavakol
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Pooyan Makvandi
- Institute for Polymers, Composites and Biomaterials, National Research Council, IPCB-CNR, Naples, Italy; Chemistry Department, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6153753843, Iran
| | - Danial Khorsandi
- Department of Medical Nanotechnology, Faculty of Advanced, Technologies in Medicine, Iran University of Medical Sciences, Tehran 14496-14535, Iran; Department of Biotechnology-Biomedicine, University of Barcelona, Barcelona 08028, Spain
| | - Abbas Pardakhty
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Elham Ghasemipour Afshar
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, Istanbul 34956, Turkey; Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla, Istanbul 34956, Turkey.
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27
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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review. Gene 2020; 753:144813. [DOI: 10.1016/j.gene.2020.144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/26/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
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28
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Bezuidt OKI, Lebre PH, Pierneef R, León-Sobrino C, Adriaenssens EM, Cowan DA, Van de Peer Y, Makhalanyane TP. Phages Actively Challenge Niche Communities in Antarctic Soils. mSystems 2020; 5:e00234-20. [PMID: 32371471 PMCID: PMC7205518 DOI: 10.1128/msystems.00234-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 12/22/2022] Open
Abstract
By modulating the structure, diversity, and trophic outputs of microbial communities, phages play crucial roles in many biomes. In oligotrophic polar deserts, the effects of katabatic winds, constrained nutrients, and low water availability are known to limit microbial activity. Although phages may substantially govern trophic interactions in cold deserts, relatively little is known regarding the precise ecological mechanisms. Here, we provide the first evidence of widespread antiphage innate immunity in Antarctic environments using metagenomic sequence data from hypolith communities as model systems. In particular, immunity systems such as DISARM and BREX are shown to be dominant systems in these communities. Additionally, we show a direct correlation between the CRISPR-Cas adaptive immunity and the metavirome of hypolith communities, suggesting the existence of dynamic host-phage interactions. In addition to providing the first exploration of immune systems in cold deserts, our results suggest that phages actively challenge niche communities in Antarctic polar deserts. We provide evidence suggesting that the regulatory role played by phages in this system is an important determinant of bacterial host interactions in this environment.IMPORTANCE In Antarctic environments, the combination of both abiotic and biotic stressors results in simple trophic levels dominated by microbiomes. Although the past two decades have revealed substantial insights regarding the diversity and structure of microbiomes, we lack mechanistic insights regarding community interactions and how phages may affect these. By providing the first evidence of widespread antiphage innate immunity, we shed light on phage-host dynamics in Antarctic niche communities. Our analyses reveal several antiphage defense systems, including DISARM and BREX, which appear to dominate in cold desert niche communities. In contrast, our analyses revealed that genes which encode antiphage adaptive immunity were underrepresented in these communities, suggesting lower infection frequencies in cold edaphic environments. We propose that by actively challenging niche communities, phages play crucial roles in the diversification of Antarctic communities.
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Affiliation(s)
- Oliver K I Bezuidt
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Pedro Humberto Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rian Pierneef
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
| | - Carlos León-Sobrino
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Yves Van de Peer
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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29
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Abstract
Some bacteria possess an adaptive immune system that maintains a memory of past viral infections in the CRISPR loci of their genomes. This memory is used to mount targeted responses against later threats but is remarkably shallow: it remembers only a few dozen to a few hundred viruses. We present a statistical theory of CRISPR-based immunity that quantitatively predicts the depth of bacterial immune memory in terms of a tradeoff with fundamental constraints of the cellular biochemical machinery. Some bacteria and archaea possess an immune system, based on the CRISPR-Cas mechanism, that confers adaptive immunity against viruses. In such species, individual prokaryotes maintain cassettes of viral DNA elements called spacers as a memory of past infections. Typically, the cassettes contain several dozen expressed spacers. Given that bacteria can have very large genomes and since having more spacers should confer a better memory, it is puzzling that so little genetic space would be devoted by prokaryotes to their adaptive immune systems. Here, assuming that CRISPR functions as a long-term memory-based defense against a diverse landscape of viral species, we identify a fundamental tradeoff between the amount of immune memory and effectiveness of response to a given threat. This tradeoff implies an optimal size for the prokaryotic immune repertoire in the observational range.
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30
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Cas3 Protein-A Review of a Multi-Tasking Machine. Genes (Basel) 2020; 11:genes11020208. [PMID: 32085454 PMCID: PMC7074321 DOI: 10.3390/genes11020208] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 01/20/2023] Open
Abstract
Cas3 has essential functions in CRISPR immunity but its other activities and roles, in vitro and in cells, are less widely known. We offer a concise review of the latest understanding and questions arising from studies of Cas3 mechanism during CRISPR immunity, and highlight recent attempts at using Cas3 for genetic editing. We then spotlight involvement of Cas3 in other aspects of cell biology, for which understanding is lacking—these focus on CRISPR systems as regulators of cellular processes in addition to defense against mobile genetic elements.
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31
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Calvo-Villamañán A, Bernheim A, Bikard D. Methods for the Analysis and Characterization of Defense Mechanisms Against Horizontal Gene Transfer: CRISPR Systems. Methods Mol Biol 2020; 2075:235-249. [PMID: 31584167 DOI: 10.1007/978-1-4939-9877-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CRISPR-Cas systems provide RNA-guided adaptive immunity to the majority of archaea and many bacteria. They are able to capture pieces of invading genetic elements in the form of novel spacers in an array of repeats. These elements can then be used as a memory to destroy incoming DNA through the action of RNA-guided nucleases. This chapter describes general procedures to determine the ability of CRISPR-Cas systems to capture novel sequences and to use them to block phages and horizontal gene transfer. All protocols are performed in Staphylococcus aureus using Type II-A CRISPR-Cas systems. Nonetheless, the protocols provided can be adapted to work with other bacteria and other types of CRISPR-Cas systems.
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Affiliation(s)
- Alicia Calvo-Villamañán
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- École Doctorale FIRE-Programme Bettencourt, Centre de Recherches Interdisciplinaires, Paris, France
| | - Aude Bernheim
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France
- École Doctorale FIRE-Programme Bettencourt, Centre de Recherches Interdisciplinaires, Paris, France
- Microbial Evolutionary Genomics, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- AgroParisTech, Paris, France
| | - David Bikard
- Synthetic Biology Group, Microbiology Department, Institut Pasteur, Paris, France.
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32
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Crystal structure of Cas1 in complex with branched DNA. SCIENCE CHINA-LIFE SCIENCES 2019; 63:516-528. [DOI: 10.1007/s11427-019-9827-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/02/2019] [Indexed: 01/18/2023]
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33
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Xu X, Wan T, Xin H, Li D, Pan H, Wu J, Ping Y. Delivery of CRISPR/Cas9 for therapeutic genome editing. J Gene Med 2019; 21:e3107. [PMID: 31237055 DOI: 10.1002/jgm.3107] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/25/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
The clustered, regularly-interspaced, short palindromic repeat (CRISPR)-associated nuclease 9 (CRISPR/Cas9) is emerging as a promising genome-editing tool for treating diseases in a precise way, and has been applied to a wide range of research in the areas of biology, genetics, and medicine. Delivery of therapeutic genome-editing agents provides a promising platform for the treatment of genetic disorders. Although viral vectors are widely used to deliver CRISPR/Cas9 elements with high efficiency, they suffer from several drawbacks, such as mutagenesis, immunogenicity, and off-target effects. Recently, non-viral vectors have emerged as another class of delivery carriers in terms of their safety, simplicity, and flexibility. In this review, we discuss the modes of CRISPR/Cas9 delivery, the barriers to the delivery process and the application of CRISPR/Cas9 system for the treatment of genetic disorders. We also highlight several representative types of non-viral vectors, including polymers, liposomes, cell-penetrating peptides, and other synthetic vectors, for the therapeutic delivery of CRISPR/Cas9 system. The applications of CRISPR/Cas9 in treating genetic disorders mediated by the non-viral vectors are also discussed.
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Affiliation(s)
- Xiaojie Xu
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Tao Wan
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Huhu Xin
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Da Li
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Jun Wu
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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34
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Estève J, Blouin JM, Lalanne M, Azzi-Martin L, Dubus P, Bidet A, Harambat J, Llanas B, Moranvillier I, Bedel A, Moreau-Gaudry F, Richard E. Generation of induced pluripotent stem cells-derived hepatocyte-like cells for ex vivo gene therapy of primary hyperoxaluria type 1. Stem Cell Res 2019; 38:101467. [PMID: 31151050 DOI: 10.1016/j.scr.2019.101467] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/30/2019] [Accepted: 05/19/2019] [Indexed: 12/17/2022] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare autosomal recessive disorder of the liver metabolism due to functional deficiency of the peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT). AGT deficiency results in overproduction of oxalate which complexes with calcium to form insoluble calcium-oxalate salts in urinary tracts, ultimately leading to end-stage renal disease. Currently, the only curative treatment for PH1 is combined liver-kidney transplantation, which is limited by donor organ shortage and lifelong requirement for immunosuppression. Transplantation of genetically modified autologous hepatocytes is an attractive therapeutic option for PH1. However, the use of fresh primary hepatocytes suffers from limitations such as organ availability, insufficient cell proliferation, loss of function, and the risk of immune rejection. We developed patient-specific induced pluripotent stem cells (PH1-iPSCs) free of reprogramming factors as a source of renewable and genetically defined autologous PH1-hepatocytes. We then investigated additive gene therapy using a lentiviral vector encoding wild-type AGT under the control of the liver-specific transthyretin promoter. Genetically modified PH1-iPSCs successfully provided hepatocyte-like cells (HLCs) that exhibited significant AGT expression at both RNA and protein levels after liver-specific differentiation process. These results pave the way for cell-based therapy of PH1 by transplantation of genetically modified autologous HLCs derived from patient-specific iPSCs.
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Affiliation(s)
- Julie Estève
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France
| | - Jean-Marc Blouin
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France
| | - Magalie Lalanne
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France
| | | | - Pierre Dubus
- Univ.Bordeaux, INSERM, BARITON, U1053, CHU Bordeaux, 33076, France
| | - Audrey Bidet
- Laboratoire d'hématologie, CHU Bordeaux, Bordeaux, France
| | - Jérôme Harambat
- Service de Néphrologie pédiatrique, Centre de Référence Maladies Rénales Rares du Sud-Ouest, CHU Bordeaux, 33000 Bordeaux, France
| | - Brigitte Llanas
- Service de Néphrologie pédiatrique, Centre de Référence Maladies Rénales Rares du Sud-Ouest, CHU Bordeaux, 33000 Bordeaux, France
| | | | - Aurélie Bedel
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France
| | | | - Emmanuel Richard
- Univ.Bordeaux, INSERM, BMGIC, U1035, CHU Bordeaux, 33076 Bordeaux, France.
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35
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Fineran PC. Resistance is not futile: bacterial 'innate' and CRISPR-Cas 'adaptive' immune systems. MICROBIOLOGY-SGM 2019; 165:834-841. [PMID: 30958259 DOI: 10.1099/mic.0.000802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria are under a constant pressure from their viruses (phages) and other mobile genetic elements. They protect themselves through a range of defence strategies, which can be broadly classified as 'innate' and 'adaptive'. The bacterial innate immune systems include defences provided by restriction modification and abortive infection, among others. Bacterial adaptive immunity is elicited by a diverse range of CRISPR-Cas systems. Here, I discuss our research on both innate and adaptive phage resistance mechanisms and some of the evasion strategies employed by phages.
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Affiliation(s)
- Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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36
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Musharova O, Sitnik V, Vlot M, Savitskaya E, Datsenko KA, Krivoy A, Fedorov I, Semenova E, Brouns SJJ, Severinov K. Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation. Mol Microbiol 2019; 111:1558-1570. [PMID: 30875129 PMCID: PMC6568314 DOI: 10.1111/mmi.14237] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2019] [Indexed: 01/05/2023]
Abstract
CRISPR interference occurs when a protospacer recognized by the CRISPR RNA is destroyed by Cas effectors. In Type I CRISPR‐Cas systems, protospacer recognition can lead to «primed adaptation» – acquisition of new spacers from in cis located sequences. Type I CRISPR‐Cas systems require the presence of a trinucleotide protospacer adjacent motif (PAM) for efficient interference. Here, we investigated the ability of each of 64 possible trinucleotides located at the PAM position to induce CRISPR interference and primed adaptation by the Escherichia coli Type I‐E CRISPR‐Cas system. We observed clear separation of PAM variants into three groups: those unable to cause interference, those that support rapid interference and those that lead to reduced interference that occurs over extended periods of time. PAM variants unable to support interference also did not support primed adaptation; those that supported rapid interference led to no or low levels of adaptation, while those that caused attenuated levels of interference consistently led to highest levels of adaptation. The results suggest that primed adaptation is fueled by the products of CRISPR interference. Extended over time interference with targets containing «attenuated» PAM variants provides a continuous source of new spacers leading to high overall level of spacer acquisition.
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Affiliation(s)
- Olga Musharova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Vasily Sitnik
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Ekaterina Savitskaya
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Kirill A Datsenko
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Andrey Krivoy
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Ivan Fedorov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Ekaterina Semenova
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.,Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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37
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Porter SN, Levine RM, Pruett-Miller SM. A Practical Guide to Genome Editing Using Targeted Nuclease Technologies. Compr Physiol 2019; 9:665-714. [PMID: 30873595 DOI: 10.1002/cphy.c180022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering using programmable nucleases is a rapidly evolving technique that enables precise genetic manipulations within complex genomes. Although this technology first surfaced with the creation of meganucleases, zinc finger nucleases, and transcription activator-like effector nucleases, CRISPR-Cas9 has been the most widely adopted platform because of its ease of use. This comprehensive review presents a basic overview of genome engineering and discusses the major technological advances in the field. In addition to nucleases, we discuss CRISPR-derived base editors and epigenetic modifiers. We also delve into practical applications of these tools, including creating custom-edited cell and animal models as well as performing genetic screens. Finally, we discuss the potential for therapeutic applications and ethical considerations related to employing this technology in humans. © 2019 American Physiological Society. Compr Physiol 9:665-714, 2019.
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Affiliation(s)
- Shaina N Porter
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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38
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Abstract
The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.
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Affiliation(s)
- Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany
| | - Andrés Escalera-Maurer
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Majda Bratovič
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
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39
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Abstract
Immunological memory is one of the core topics of contemporary immunology. Yet there are many discussions about what this concept precisely means, which components of the immune system display it, and in which phyla it exists. Recent years have seen the multiplication of claims that immunological memory can be found in "innate" immune cells and in many phyla beyond vertebrates (including invertebrates, plants, but also bacteria and archaea), as well as the multiplication of concepts to account for these phenomena, such as "innate immune memory" or "trained immunity". The aim of this critical review is to analyze these recent claims and concepts, and to distinguish ideas that have often been misleadingly associated, such as memory, adaptive immunity, and specificity. We argue that immunological memory is a gradual and multidimensional phenomenon, irreducible to any simple dichotomy, and we show why adopting this new view matters from an experimental and therapeutic point of view.
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Affiliation(s)
- Thomas Pradeu
- ImmunoConcept, CNRS & University of Bordeaux, Bordeaux, France
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40
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Xia Y, Liang TJ. Development of Direct-acting Antiviral and Host-targeting Agents for Treatment of Hepatitis B Virus Infection. Gastroenterology 2019; 156:311-324. [PMID: 30243618 PMCID: PMC6340783 DOI: 10.1053/j.gastro.2018.07.057] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/13/2018] [Accepted: 07/23/2018] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) infection affects approximately 300 million people worldwide. Although antiviral therapies have improved the long-term outcomes, patients often require life-long treatment and there is no cure for HBV infection. New technologies can help us learn more about the pathogenesis of HBV infection and develop therapeutic agents to reduce its burden. We review recent advances in development of direct-acting antiviral and host-targeting agents, some of which have entered clinical trials. We also discuss strategies for unbiased high-throughput screens to identify compounds that inhibit HBV and for repurposing existing drugs.
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Affiliation(s)
- Yuchen Xia
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892.
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41
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Ahmed W, Hafeez MA, Ahmad R, Mahmood S. CRISPR-Cas system in regulation of immunity and virulence of bacterial pathogens. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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42
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Zhu Y, Huang Z. Recent advances in structural studies of the CRISPR-Cas-mediated genome editing tools. Natl Sci Rev 2018; 6:438-451. [PMID: 34691893 PMCID: PMC8291651 DOI: 10.1093/nsr/nwy150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and accompanying CRISPR-associated (Cas) proteins provide RNA-guided adaptive immunity for prokaryotes to defend themselves against viruses. The CRISPR-Cas systems have attracted much attention in recent years for their power in aiding the development of genome editing tools. Based on the composition of the CRISPR RNA-effector complex, the CRISPR-Cas systems can be divided into two classes and six types. In this review, we summarize recent advances in the structural biology of the CRISPR-Cas-mediated genome editing tools, which helps us to understand the mechanism of how the guide RNAs assemble with diverse Cas proteins to cleave target nucleic acids.
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Affiliation(s)
- Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
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Nicholson TJ, Jackson SA, Croft BI, Staals RHJ, Fineran PC, Brown CM. Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems. RNA Biol 2018; 16:566-576. [PMID: 30157725 DOI: 10.1080/15476286.2018.1509662] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against invading genetic elements, such as plasmids, bacteriophages and archaeal viruses. They consist of cas genes and CRISPR loci, which store genetic memories of previously encountered invaders as short sequences termed spacers. Spacers determine the specificity of CRISPR-Cas defence and immunity can be gained or updated by the addition of new spacers into CRISPR loci. There are two main routes to spacer acquisition, which are known as naïve and primed CRISPR adaptation. Naïve CRISPR adaptation involves the de novo formation of immunity, independent of pre-existing spacers. In contrast, primed CRISPR adaptation (priming) uses existing spacers to enhance the acquisition of new spacers. Priming typically results in spacer acquisition from locations near the site of target recognition by the existing (priming) spacer. Primed CRISPR adaptation has been observed in several type I CRISPR-Cas systems and it is potentially widespread. However, experimental evidence is unavailable for some subtypes, and for most systems, priming has only been shown in a small number of hosts. There is also no current evidence of priming by other CRISPR-Cas types. Here, we used a bioinformatic approach to search for evidence of priming in diverse CRISPR-Cas systems. By analysing the clustering of spacers acquired from phages, prophages and archaeal viruses, including strand and directional biases between subsequently acquired spacers, we demonstrate that two patterns of primed CRISPR adaptation dominate in type I systems. In addition, we find evidence of a priming-like pathway in type II CRISPR-Cas systems.
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Affiliation(s)
- Thomas J Nicholson
- a Department of Biochemistry , University of Otago , Dunedin , New Zealand.,b Genetics Otago , University of Otago , Dunedin , New Zealand
| | - Simon A Jackson
- b Genetics Otago , University of Otago , Dunedin , New Zealand.,c Department of Microbiology and Immunology , University of Otago , Dunedin , New Zealand
| | - Bradley I Croft
- a Department of Biochemistry , University of Otago , Dunedin , New Zealand
| | - Raymond H J Staals
- c Department of Microbiology and Immunology , University of Otago , Dunedin , New Zealand.,d Laboratory of Microbiology, Department of Agrotechnology and Food Sciences , Wageningen University , Wageningen , The Netherlands
| | - Peter C Fineran
- b Genetics Otago , University of Otago , Dunedin , New Zealand.,c Department of Microbiology and Immunology , University of Otago , Dunedin , New Zealand
| | - Chris M Brown
- a Department of Biochemistry , University of Otago , Dunedin , New Zealand.,b Genetics Otago , University of Otago , Dunedin , New Zealand
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Molenda O, Tang S, Lomheim L, Gautam VK, Lemak S, Yakunin AF, Maxwell KL, Edwards EA. Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes. ISME JOURNAL 2018; 13:24-38. [PMID: 30104577 DOI: 10.1038/s41396-018-0254-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 01/12/2023]
Abstract
Dehalococcoides mccartyi are obligate organohalide-respiring bacteria that play an important detoxifying role in the environment. They have small genomes (~1.4 Mb) with a core region interrupted by two high plasticity regions (HPRs) containing dozens of genes encoding reductive dehalogenases involved in organohalide respiration. The genomes of eight new strains of D. mccartyi were closed from metagenomic data from a related set of enrichment cultures, bringing the total number of genomes to 24. Two of the newly sequenced strains and three previously sequenced strains contain CRISPR-Cas systems. These D. mccartyi CRISPR-Cas systems were found to primarily target prophages and genomic islands. The genomic islands were identified either as integrated into D. mccartyi genomes or as circular extrachromosomal elements. We observed active circularization of the integrated genomic island containing vcrABC operon encoding the dehalogenase (VcrA) responsible for the transformation of vinyl chloride to non-toxic ethene. We interrogated archived DNA from established enrichment cultures and found that the CRISPR array acquired three new spacers in 11 years. These data provide a glimpse into dynamic processes operating on the genomes distinct to D. mccartyi strains found in enrichment cultures and provide the first insights into possible mechanisms of lateral DNA exchange in D. mccartyi.
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Affiliation(s)
- Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Vasu K Gautam
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada. .,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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45
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Shu M, Fu R, Wang W. A bacteriophage model based on CRISPR/Cas immune system in a chemostat. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2018; 14:1361-1377. [PMID: 29161865 DOI: 10.3934/mbe.2017070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Clustered regularly interspaced short palindromic repeats(CRISPRs) along with Cas proteins are a widespread immune system across bacteria and archaea. In this paper, a mathematical model in a chemostat is proposed to investigate the effect of CRISPR/Cas on the bacteriophage dynamics. It is shown that the introduction of CRISPR/Cas can induce a backward bifurcation and transcritical bifurcation. Numerical simulations reveal the coexistence of a stable infection-free equilibrium with an infection equilibrium, or a stable infection-free equilibrium with a stable periodic solution.
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Affiliation(s)
- Mengshi Shu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, School of Mathematics and Statistics, Southwest University, Chongqing 400715, China
| | - Rui Fu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, School of Mathematics and Statistics, Southwest University, Chongqing 400715, China
| | - Wendi Wang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, School of Mathematics and Statistics, Southwest University, Chongqing, 400715, China
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46
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) constitute a multi-functional, constantly evolving immune system in bacteria and archaea cells. A heritable, molecular memory is generated of phage, plasmids, or other mobile genetic elements that attempt to attack the cell. This memory is used to recognize and interfere with subsequent invasions from the same genetic elements. This versatile prokaryotic tool has also been used to advance applications in biotechnology. Here we review a large body of CRISPR-Cas research to explore themes of evolution and selection, population dynamics, horizontal gene transfer, specific and cross-reactive interactions, cost and regulation, non-immunological CRISPR functions that boost host cell robustness, as well as applicable mechanisms for efficient and specific genetic engineering. We offer future directions that can be addressed by the physics community. Physical understanding of the CRISPR-Cas system will advance uses in biotechnology, such as developing cell lines and animal models, cell labeling and information storage, combatting antibiotic resistance, and human therapeutics.
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Affiliation(s)
- Melia E Bonomo
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, United States of America. Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America
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Li L, Hu S, Chen X. Non-viral delivery systems for CRISPR/Cas9-based genome editing: Challenges and opportunities. Biomaterials 2018; 171:207-218. [PMID: 29704747 DOI: 10.1016/j.biomaterials.2018.04.031] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 02/06/2023]
Abstract
In recent years, CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) genome editing systems have become one of the most robust platforms in basic biomedical research and therapeutic applications. To date, efficient in vivo delivery of the CRISPR/Cas9 system to the targeted cells remains a challenge. Although viral vectors have been widely used in the delivery of the CRISPR/Cas9 system in vitro and in vivo, their fundamental shortcomings, such as the risk of carcinogenesis, limited insertion size, immune responses and difficulty in large-scale production, severely limit their further applications. Alternative non-viral delivery systems for CRISPR/Cas9 are urgently needed. With the rapid development of non-viral vectors, lipid- or polymer-based nanocarriers have shown great potential for CRISPR/Cas9 delivery. In this review, we analyze the pros and cons of delivering CRISPR/Cas9 systems in the form of plasmid, mRNA, or protein and then discuss the limitations and challenges of CRISPR/Cas9-based genome editing. Furthermore, current non-viral vectors that have been applied for CRISPR/Cas9 delivery in vitro and in vivo are outlined in details. Finally, critical obstacles for non-viral delivery of CRISPR/Cas9 system are highlighted and promising strategies to overcome these barriers are proposed.
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Affiliation(s)
- Ling Li
- Department of PET Center, Xiangya Hospital, Central South University, Changsha, 410008, China; Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Shuo Hu
- Department of PET Center, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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48
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Zhu Y, Zhang F, Huang Z. Structural insights into the inactivation of CRISPR-Cas systems by diverse anti-CRISPR proteins. BMC Biol 2018; 16:32. [PMID: 29554913 PMCID: PMC5859409 DOI: 10.1186/s12915-018-0504-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A molecular arms race is progressively being unveiled between prokaryotes and viruses. Prokaryotes utilize CRISPR-mediated adaptive immune systems to kill the invading phages and mobile genetic elements, and in turn, the viruses evolve diverse anti-CRISPR proteins to fight back. The structures of several anti-CRISPR proteins have now been reported, and here we discuss their structural features, with a particular emphasis on topology, to discover their similarities and differences. We summarize the CRISPR-Cas inhibition mechanisms of these anti-CRISPR proteins in their structural context. Considering anti-CRISPRs in this way will provide important clues for studying their origin and evolution.
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Affiliation(s)
- Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
| | - Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
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49
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Gao B, Bian X, Chi L, Tu P, Ru H, Lu K. Editor's Highlight: OrganophosphateDiazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome. Toxicol Sci 2018; 157:354-364. [PMID: 28369659 DOI: 10.1093/toxsci/kfx053] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome plays a key role in energy production, immune system development, and host resistance against invading pathogens, etc. Disruption of gut bacterial homeostasis is associated with a number of human diseases. Several environmental chemicals have been reported to induce alterations of the gut microbiome. Diazinon, one of important organophosphate insecticides, has been widely used in agriculture. Diazinon and its metabolites are readily detected in different environmental settings and human urine. The toxicity of organophosphates has been a long-standing public health concern. We recently demonstrated that organophosphate insecticide diazinon perturbed the gut microbiome composition of mice. However, the functional impact of exposure on the gut microbiome has not been adequately assessed yet. In particular, the molecular mechanism responsible for exposure-induced microbial profile and community structure changes has not been identified. Therefore, in this study, we used metatranscriptomics to examine the effects of diazinon exposure on the gut metatranscriptome in C57BL/6 mice. Herein, we demonstrated for the first time that organophosphate diazinon modulated quorum sensing, which may serve as a key mechanism to regulate bacterial population, composition, and more importantly, their functional genes. In addition, we also found that diazinon exposure activated diverse stress response pathways and profoundly impaired energy metabolism of gut bacteria. These findings provide new understandings of the functional interplay between the gut microbiome and environmental chemicals, such as organophosphates.
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Affiliation(s)
- Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602.,Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Xiaoming Bian
- Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602.,Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina 27607
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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Uppada V, Gokara M, Rasineni GK. Diagnosis and therapy with CRISPR advanced CRISPR based tools for point of care diagnostics and early therapies. Gene 2018; 656:22-29. [PMID: 29496558 DOI: 10.1016/j.gene.2018.02.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/14/2018] [Accepted: 02/24/2018] [Indexed: 12/26/2022]
Abstract
Molecular diagnostics is of critical importance to public health worldwide. It facilitates not only detection and characterization of diseases, but also monitors drug responses, assists in the identification of genetic modifiers and disease susceptibility. Based upon DNA variation, a wide range of molecular-based tests are available to assess/diagnose diseases. The CRISPR-Cas9 system has recently emerged as a versatile tool for biological and medical research. In this system, a single guide RNA (sgRNA) directs the endonuclease Cas9 to a targeted DNA sequence for site-specific manipulation. As designing CRISPR-guided nucleases can be done easily and relatively fast, the CRISPR/Cas9 system has evolved as widely used DNA editing tool. This technique led to a large number of gene editing studies in variety of organisms. CRISPR/Cas9-mediated diagnosis and therapy has picked up pace due to specificity and accuracy of CRISPR. The aim is not only to identify specific pathogens, especially virus but also to repair disease-causing alleles by changing the DNA sequence at the exact location on the chromosome. At present, PCR-based molecular diagnostic testing predominates; however, alternative technologies aimed at reducing genome complexity without PCR are anticipated to gain momentum in the coming years. Furthermore, development of integrated chip devices should allow point-of-care testing and facilitate genetic readouts from single cells and molecules. Together with molecular based therapy CRISPR based diagnostic testing will be a revolution in modern health care settings. In this review, we emphasize on current developing diagnostic techniques based upon CRISPR Cas approach along with short insights on its therapeutic usage.
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Affiliation(s)
- Vanita Uppada
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Mahesh Gokara
- Department of Biochemistry, University of Hyderabad, Hyderabad 500046, Telangana, India
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