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Mishra G, Srivastava K, Rais J, Dixit M, Kumari Singh V, Chandra Mishra L. CRISPR-Cas9: A Potent Gene-editing Tool for the Treatment of Cancer. Curr Mol Med 2024; 24:191-204. [PMID: 36788695 DOI: 10.2174/1566524023666230213094308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 02/16/2023]
Abstract
The prokaryotic adaptive immune system has clustered regularly interspaced short palindromic repeat. CRISPR-associated protein (CRISPR-Cas) genome editing systems have been harnessed. A robust programmed technique for efficient and accurate genome editing and gene targeting has been developed. Engineered cell therapy, in vivo gene therapy, animal modeling, and cancer diagnosis and treatment are all possible applications of this ground-breaking approach. Multiple genetic and epigenetic changes in cancer cells induce malignant cell growth and provide chemoresistance. The capacity to repair or ablate such mutations has enormous potential in the fight against cancer. The CRISPR-Cas9 genome editing method has recently become popular in cancer treatment research due to its excellent efficiency and accuracy. The preceding study has shown therapeutic potential in expanding our anticancer treatments by using CRISPR-Cas9 to directly target cancer cell genomic DNA in cellular and animal cancer models. In addition, CRISPR-Cas9 can combat oncogenic infections and test anticancer medicines. It may design immune cells and oncolytic viruses for cancer immunotherapeutic applications. In this review, these preclinical CRISPRCas9- based cancer therapeutic techniques are summarised, along with the hurdles and advancements in converting therapeutic CRISPR-Cas9 into clinical use. It will increase their applicability in cancer research.
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Affiliation(s)
- Gauri Mishra
- Department of Zoology, Swami Shraddhanand College, University of Delhi-110036, Delhi, India
- Division Radiopharmaceuticals and Radiation Biology, Institute of Nuclear Medicine and Allied Sciences, Brig SK Mazumdar Road, Delhi-110054, India
| | - Kamakshi Srivastava
- Department of Zoology, Swami Shraddhanand College, University of Delhi-110036, Delhi, India
| | - Juhi Rais
- Department of Nuclear Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow-226014, India
| | - Manish Dixit
- Department of Nuclear Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow-226014, India
| | - Vandana Kumari Singh
- Department of Zoology, Hansraj College, University of Delhi- 110007, Dehli, India
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Basu S, Bhattacharya D, Pramanik A, Saha M, Mukherjee J. In-silico whole-genome sequence analysis of a halotolerant filamentous mangrove cyanobacterium revealed CRISPR-Cas systems with unique properties. JOURNAL OF PHYCOLOGY 2023; 59:1339-1346. [PMID: 37795780 DOI: 10.1111/jpy.13393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Abstract
Novel CRISPR systems capable of cleaving both DNA and RNA are progressively emerging as attractive tools for genome manipulation of prokaryotic and eukaryotic organisms. We report specific characteristics of CRISPR systems present in Oxynema aestuarii AP17, a halotolerant, filamentous cyanobacterium and the second known member of the Oxynema genus. In-silico analyses of its whole-genome sequence revealed the presence of multiple Type I and Type III CRISPR loci with one Type I-G system previously unreported in cyanobacteria. We further identified the leader sequences at the 5' end of multiple CRISPR loci, many of which were distinct from previously reported cyanobacterial CRISPR leaders. Phylogenetic analyses of the O. aestuarii AP17 Cas1 proteins revealed two protein sequences that were unique and distantly related to other cyanobacterial Cas1 protein sequences. Our findings are significant because novel Class 1 CRISPR systems possess multi-subunit effectors and are highly flexible for repurposing by protein domain fusions made to the effector complex. Additionally, Type III CRISPRs are particularly useful for genome editing in certain extremophiles for which mesophilic Type II CRISPRs are ineffective.
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Affiliation(s)
- Shayontani Basu
- School of Environmental Studies, Jadavpur University, Kolkata, India
| | | | - Arnab Pramanik
- Jagadis Bose National Science Talent Search, Kolkata, India
| | - Malay Saha
- Department of Botany, Sovarani Memorial College, Howrah, India
| | - Joydeep Mukherjee
- School of Environmental Studies, Jadavpur University, Kolkata, India
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3
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Liu Z, Liu J, Yang Z, Zhu L, Zhu Z, Huang H, Jiang L. Endogenous CRISPR-Cas mediated in situ genome editing: State-of-the-art and the road ahead for engineering prokaryotes. Biotechnol Adv 2023; 68:108241. [PMID: 37633620 DOI: 10.1016/j.biotechadv.2023.108241] [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: 04/18/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
The CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing in various prokaryotes. However, the perturbation of DNA homeostasis and the inherent toxicity of Cas9/12a proteins could easily lead to cell death, which led to the development of endogenous CRISPR-Cas systems. Programming the widespread endogenous CRISPR-Cas systems for in situ genome editing represents a promising tool in prokaryotes, especially in genetically intractable species. Here, this review briefly summarizes the advances of endogenous CRISPR-Cas-mediated genome editing, covering aspects of establishing and optimizing the genetic tools. In particular, this review presents the application of different types of endogenous CRISPR-Cas tools for strain engineering, including genome editing and genetic regulation. Notably, this review also provides a detailed discussion of the transposon-associated CRISPR-Cas systems, and the programmable RNA-guided transposition using endogenous CRISPR-Cas systems to enable editing of microbial communities for understanding and control. Therefore, they will be a powerful tool for targeted genetic manipulation. Overall, this review will not only facilitate the development of standard genetic manipulation tools for non-model prokaryotes but will also enable more non-model prokaryotes to be genetically tractable.
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Affiliation(s)
- Zhenlei Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jiayu Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Zhihan Yang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Liying Zhu
- College of Chemical and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Zhengming Zhu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China.
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
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Watts EA, Garrett SC, Catchpole RJ, Clark LM, Sanders TJ, Marshall CJ, Wenck BR, Vickerman RL, Santangelo TJ, Fuchs R, Robb B, Olson S, Graveley BR, Terns MP. Histones direct site-specific CRISPR spacer acquisition in model archaeon. Nat Microbiol 2023; 8:1682-1694. [PMID: 37550505 PMCID: PMC10823912 DOI: 10.1038/s41564-023-01446-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
CRISPR-Cas systems provide heritable immunity against viruses and other mobile genetic elements by incorporating fragments of invader DNA into the host CRISPR array as spacers. Integration of new spacers is localized to the 5' end of the array, and in certain Gram-negative Bacteria this polarized localization is accomplished by the integration host factor. For most other Bacteria and Archaea, the mechanism for 5' end localization is unknown. Here we show that archaeal histones play a key role in directing integration of CRISPR spacers. In Pyrococcus furiosus, deletion of either histone A or B impairs integration. In vitro, purified histones are sufficient to direct integration to the 5' end of the CRISPR array. Archaeal histone tetramers and bacterial integration host factor induce similar U-turn bends in bound DNA. These findings indicate a co-evolution of CRISPR arrays with chromosomal DNA binding proteins and a widespread role for binding and bending of DNA to facilitate accurate spacer integration.
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Kumar R, Sinha NR, Mohan RR. Corneal gene therapy: Structural and mechanistic understanding. Ocul Surf 2023; 29:279-297. [PMID: 37244594 DOI: 10.1016/j.jtos.2023.05.007] [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: 03/31/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Cornea, a dome-shaped and transparent front part of the eye, affords 2/3rd refraction and barrier functions. Globally, corneal diseases are the leading cause of vision impairment. Loss of corneal function including opacification involve the complex crosstalk and perturbation between a variety of cytokines, chemokines and growth factors generated by corneal keratocytes, epithelial cells, lacrimal tissues, nerves, and immune cells. Conventional small-molecule drugs can treat mild-to-moderate traumatic corneal pathology but requires frequent application and often fails to treat severe pathologies. The corneal transplant surgery is a standard of care to restore vision in patients. However, declining availability and rising demand of donor corneas are major concerns to maintain ophthalmic care. Thus, the development of efficient and safe nonsurgical methods to cure corneal disorders and restore vision in vivo is highly desired. Gene-based therapy has huge potential to cure corneal blindness. To achieve a nonimmunogenic, safe and sustained therapeutic response, the selection of a relevant genes, gene editing methods and suitable delivery vectors are vital. This article describes corneal structural and functional features, mechanistic understanding of gene therapy vectors, gene editing methods, gene delivery tools, and status of gene therapy for treating corneal disorders, diseases, and genetic dystrophies.
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Affiliation(s)
- Rajnish Kumar
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow campus, UP, 226028, India
| | - Nishant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Rajiv R Mohan
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
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Poulalier-Delavelle M, Baker JP, Millard J, Winzer K, Minton NP. Endogenous CRISPR/Cas systems for genome engineering in the acetogens Acetobacterium woodii and Clostridium autoethanogenum. Front Bioeng Biotechnol 2023; 11:1213236. [PMID: 37425362 PMCID: PMC10328091 DOI: 10.3389/fbioe.2023.1213236] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Acetogenic bacteria can play a major role in achieving Net Zero through their ability to convert CO2 into industrially relevant chemicals and fuels. Full exploitation of this potential will be reliant on effective metabolic engineering tools, such as those based on the Streptococcus pyogenes CRISPR/Cas9 system. However, attempts to introduce cas9-containing vectors into Acetobacterium woodii were unsuccessful, most likely as a consequence of Cas9 nuclease toxicity and the presence of a recognition site for an endogenous A. woodii restriction-modification (R-M) system in the cas9 gene. As an alternative, this study aims to facilitate the exploitation of CRISPR/Cas endogenous systems as genome engineering tools. Accordingly, a Python script was developed to automate the prediction of protospacer adjacent motif (PAM) sequences and used to identify PAM candidates of the A. woodii Type I-B CRISPR/Cas system. The identified PAMs and the native leader sequence were characterized in vivo by interference assay and RT-qPCR, respectively. Expression of synthetic CRISPR arrays, consisting of the native leader sequence, direct repeats, and adequate spacer, along with an editing template for homologous recombination, successfully led to the creation of 300 bp and 354 bp in-frame deletions of pyrE and pheA, respectively. To further validate the method, a 3.2 kb deletion of hsdR1 was also generated, as well as the knock-in of the fluorescence-activating and absorption-shifting tag (FAST) reporter gene at the pheA locus. Homology arm length, cell density, and the amount of DNA used for transformation were found to significantly impact editing efficiencies. The devised workflow was subsequently applied to the Type I-B CRISPR/Cas system of Clostridium autoethanogenum, enabling the generation of a 561 bp in-frame deletion of pyrE with 100% editing efficiency. This is the first report of genome engineering of both A. woodii and C. autoethanogenum using their endogenous CRISPR/Cas systems.
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Affiliation(s)
| | | | | | | | - Nigel P. Minton
- *Correspondence: Margaux Poulalier-Delavelle, ; Nigel P. Minton,
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Salvà-Serra F, Pérez-Pantoja D, Donoso RA, Jaén-Luchoro D, Fernández-Juárez V, Engström-Jakobsson H, Moore ERB, Lalucat J, Bennasar-Figueras A. Comparative genomics of Stutzerimonas balearica ( Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds. Front Microbiol 2023; 14:1159176. [PMID: 37275147 PMCID: PMC10234333 DOI: 10.3389/fmicb.2023.1159176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.
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Affiliation(s)
- Francisco Salvà-Serra
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Raúl A. Donoso
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Víctor Fernández-Juárez
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Hedvig Engström-Jakobsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antoni Bennasar-Figueras
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
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Kushwaha SK, Kumar AA, Gupta H, Marathe SA. The Phylogenetic Study of the CRISPR-Cas System in Enterobacteriaceae. Curr Microbiol 2023; 80:196. [PMID: 37118221 DOI: 10.1007/s00284-023-03298-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/07/2023] [Indexed: 04/30/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) system is a bacterial and archaeal adaptive immune system undergoing rapid multifaceted evolution. This evolution plausibly occurs due to the genetic exchanges of complete loci or individual entities. Here, we systematically investigate the evolutionary framework of the CRISPR-Cas system in six Enterobacteriaceae species and its evolutionary association with housekeeping genes as determined by the gyrB phenogram. The strains show high variability in the cas3 gene and the CRISPR1 locus among the closely related Enterobacteriaceae species, hinting at a series of genetic exchanges. The CRISPR leader is conserved, especially toward the distal end, and could be a core region of the leader. The spacers are conserved within the strains of most species, while some strains show unique sets of spacers. However, inter-species spacer conservation was rarely observed. For a considerable proportion of these spacers, protospacer sources were not detected. These results advance our understanding of the dynamics of the CRISPR-Cas system; however, the biological functions are yet to be characterised.
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Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Aryahi A Kumar
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Hardik Gupta
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India.
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Zhang T, Jia Y, Li H, Xu D, Zhou J, Wang G. CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins. Brief Bioinform 2022; 23:6674167. [PMID: 35998924 DOI: 10.1093/bib/bbac335] [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: 05/03/2022] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 11/12/2022] Open
Abstract
CRISPR-Cas system is an adaptive immune system widely found in most bacteria and archaea to defend against exogenous gene invasion. One of the most critical steps in the study of exploring and classifying novel CRISPR-Cas systems and their functional diversity is the identification of Cas proteins in CRISPR-Cas systems. The discovery of novel Cas proteins has also laid the foundation for technologies such as CRISPR-Cas-based gene editing and gene therapy. Currently, accurate and efficient screening of Cas proteins from metagenomic sequences and proteomic sequences remains a challenge. For Cas proteins with low sequence conservation, existing tools for Cas protein identification based on homology cannot guarantee identification accuracy and efficiency. In this paper, we have developed a novel stacking-based ensemble learning framework for Cas protein identification, called CRISPRCasStack. In particular, we applied the SHAP (SHapley Additive exPlanations) method to analyze the features used in CRISPRCasStack. Sufficient experimental validation and independent testing have demonstrated that CRISPRCasStack can address the accuracy deficiencies and inefficiencies of the existing state-of-the-art tools. We also provide a toolkit to accurately identify and analyze potential Cas proteins, Cas operons, CRISPR arrays and CRISPR-Cas locus in prokaryotic sequences. The CRISPRCasStack toolkit is available at https://github.com/yrjia1015/CRISPRCasStack.
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Affiliation(s)
- Tianjiao Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Yuran Jia
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Hongfei Li
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Dali Xu
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Jie Zhou
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
| | - Guohua Wang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, 150040, China
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Tao S, Chen H, Li N, Liang W. The Application of the CRISPR-Cas System in Antibiotic Resistance. Infect Drug Resist 2022; 15:4155-4168. [PMID: 35942309 PMCID: PMC9356603 DOI: 10.2147/idr.s370869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
The emergence and global epidemic of antimicrobial resistance (AMR) poses a serious threat to global public health in recent years. AMR genes are shared between bacterial pathogens mainly via horizontal gene transfer (HGT) on mobile genetic elements (MGEs), thereby accelerating the spread of antimicrobial resistance (AMR) and increasing the burden of drug resistance. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance. The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are an RNA-guided adaptive immune system in prokaryotes that recognizes and defends against invasive genetic elements such as phages and plasmids. Because of its specifically target and cleave DNA sequences encoding antibiotic resistance genes, CRISPR/Cas system has been developed into a new gene-editing tool for the prevention and control of bacterial drug resistance. CRISPR-Cas plays a potentially important role in controlling horizontal gene transfer and limiting the spread of antibiotic resistance. In this review, we will introduce the structure and working mechanism of CRISPR-Cas systems, followed by delivery strategies, and then focus on the relationship between antimicrobial resistance and CRISPR-Cas. Moreover, the challenges and prospects of this research field are discussed, thereby providing a reference for the prevention and control of the spread of antibiotic resistance.
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Affiliation(s)
- Shuan Tao
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
| | - Huimin Chen
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
| | - Na Li
- Bengbu Medical College, Bengbu, Anhui Province, 233030, People’s Republic of China
| | - Wei Liang
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
- Correspondence: Wei Liang, Lianyungang Clinical College of Jiangsu University, No. 161. Xingfu Road, Haizhou District, Lianyungang, Jiangsu Province, 222023, People’s Republic of China, Tel/Fax +86-51885213100; Tel/Fax +86 15351883016, Email
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Baci GM, Cucu AA, Giurgiu AI, Muscă AS, Bagameri L, Moise AR, Bobiș O, Rațiu AC, Dezmirean DS. Advances in Editing Silkworms ( Bombyx mori) Genome by Using the CRISPR-Cas System. INSECTS 2021; 13:28. [PMID: 35055871 PMCID: PMC8777690 DOI: 10.3390/insects13010028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) represents a powerful genome editing technology that revolutionized in a short period of time numerous natural sciences branches. Therefore, extraordinary progress was made in various fields, such as entomology or biotechnology. Bombyx mori is one of the most important insects, not only for the sericulture industry, but for numerous scientific areas. The silkworms play a key role as a model organism, but also as a bioreactor for the recombinant protein production. Nowadays, the CRISPR-Cas genome editing system is frequently used in order to perform gene analyses, to increase the resistance against certain pathogens or as an imaging tool in B. mori. Here, we provide an overview of various studies that made use of CRISPR-Cas for B. mori genome editing, with a focus on emphasizing the high applicability of this system in entomology and biological sciences.
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Affiliation(s)
- Gabriela-Maria Baci
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Alexandra-Antonia Cucu
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Alexandru-Ioan Giurgiu
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Adriana-Sebastiana Muscă
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Lilla Bagameri
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Adela Ramona Moise
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Otilia Bobiș
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | | | - Daniel Severus Dezmirean
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
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12
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Wu Y, Battalapalli D, Hakeem MJ, Selamneni V, Zhang P, Draz MS, Ruan Z. Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections. J Nanobiotechnology 2021; 19:401. [PMID: 34863214 PMCID: PMC8642896 DOI: 10.1186/s12951-021-01132-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is spreading rapidly around the world and seriously impeding efforts to control microbial infections. Although nucleic acid testing is widely deployed for the detection of antibiotic resistant bacteria, the current techniques-mainly based on polymerase chain reaction (PCR)-are time-consuming and laborious. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance (AMR). The CRISPR-Cas system is an adaptive immune system found in many prokaryotes that presents attractive opportunities to target and edit nucleic acids with high precision and reliability. Engineered CRISPR-Cas systems are reported to effectively kill bacteria or even revert bacterial resistance to antibiotics (resensitizing bacterial cells to antibiotics). Strategies for combating antimicrobial resistance using CRISPR (i.e., Cas9, Cas12, Cas13, and Cas14) can be of great significance in detecting bacteria and their resistance to antibiotics. This review discusses the structures, mechanisms, and detection methods of CRISPR-Cas systems and how these systems can be engineered for the rapid and reliable detection of bacteria using various approaches, with a particular focus on nanoparticles. In addition, we summarize the most recent advances in applying the CRISPR-Cas system for virulence modulation of bacterial infections and combating antimicrobial resistance.
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Affiliation(s)
- Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Mohammed J Hakeem
- Department of Food Science and Human Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Venkatarao Selamneni
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pengfei Zhang
- Department of Central Laboratory, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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13
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Vink JNA, Baijens JHL, Brouns SJJ. PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems. Genome Biol 2021; 22:281. [PMID: 34593010 PMCID: PMC8482600 DOI: 10.1186/s13059-021-02495-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR-Cas biology, including target requirements such as the protospacer adjacent motif (PAM). However, studies have so far been limited by a low number of mapped spacers in the database. RESULTS By using vast metagenomic sequence databases, we map approximately one-third of more than 200,000 unique CRISPR spacers from a variety of microbes and derive a catalog of more than two hundred unique PAM sequences associated with specific CRISPR-Cas subtypes. These PAMs are further used to correctly assign the orientation of CRISPR arrays, revealing conserved patterns between the last nucleotides of the CRISPR repeat and PAM. We could also deduce CRISPR-Cas subtype-specific preferences for targeting either template or coding strand of open reading frames. While some DNA-targeting systems (type I-E and type II systems) prefer the template strand and avoid mRNA, other DNA- and RNA-targeting systems (types I-A and I-B and type III systems) prefer the coding strand and mRNA. In addition, we find large-scale evidence that both CRISPR-Cas adaptation machinery and CRISPR arrays are shared between different CRISPR-Cas systems. This could lead to simultaneous DNA and RNA targeting of invaders, which may be effective at combating mobile genetic invaders. CONCLUSIONS This study has broad implications for our understanding of how CRISPR-Cas systems work in a wide range of organisms for which only the genome sequence is known.
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Affiliation(s)
- Jochem N A Vink
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Jan H L Baijens
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.
- Kavli Institute of Nanoscience, Delft, The Netherlands.
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14
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Alkhnbashi OS, Mitrofanov A, Bonidia R, Raden M, Tran V, Eggenhofer F, Shah S, Öztürk E, Padilha V, Sanches D, de Carvalho A, Backofen R. CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. Nucleic Acids Res 2021; 49:W125-W130. [PMID: 34133710 PMCID: PMC8265192 DOI: 10.1093/nar/gkab456] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/28/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
CRISPR–Cas systems are adaptive immune systems in prokaryotes, providing resistance against invading viruses and plasmids. The identification of CRISPR loci is currently a non-standardized, ambiguous process, requiring the manual combination of multiple tools, where existing tools detect only parts of the CRISPR-systems, and lack quality control, annotation and assessment capabilities of the detected CRISPR loci. Our CRISPRloci server provides the first resource for the prediction and assessment of all possible CRISPR loci. The server integrates a series of advanced Machine Learning tools within a seamless web interface featuring: (i) prediction of all CRISPR arrays in the correct orientation; (ii) definition of CRISPR leaders for each locus; and (iii) annotation of cas genes and their unambiguous classification. As a result, CRISPRloci is able to accurately determine the CRISPR array and associated information, such as: the Cas subtypes; cassette boundaries; accuracy of the repeat structure, orientation and leader sequence; virus-host interactions; self-targeting; as well as the annotation of cas genes, all of which have been missing from existing tools. This annotation is presented in an interactive interface, making it easy for scientists to gain an overview of the CRISPR system in their organism of interest. Predictions are also rendered in GFF format, enabling in-depth genome browser inspection. In summary, CRISPRloci constitutes a full suite for CRISPR–Cas system characterization that offers annotation quality previously available only after manual inspection.
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Affiliation(s)
- Omer S Alkhnbashi
- To whom correspondence should be addressed. Tel: +49 761 2037460; Fax: +49 761 2037462;
| | | | | | - Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Van Dinh Tran
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Ekrem Öztürk
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Victor A Padilha
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, SP, Brazil
| | - Danilo S Sanches
- Universidade Tecnológica Federal do Paraná, Campus Cornélio Procópio, 86300000 Cornélio Procópio, PR, Brazil
| | | | - Rolf Backofen
- Correspondence may also be addressed to Rolf Backofen.
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15
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Padilha VA, Alkhnbashi OS, Tran VD, Shah SA, Carvalho ACPLF, Backofen R. Casboundary: automated definition of integral Cas cassettes. Bioinformatics 2021; 37:1352-1359. [PMID: 33226067 PMCID: PMC8208735 DOI: 10.1093/bioinformatics/btaa984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION CRISPR-Cas are important systems found in most archaeal and many bacterial genomes, providing adaptive immunity against mobile genetic elements in prokaryotes. The CRISPR-Cas systems are encoded by a set of consecutive cas genes, here termed cassette. The identification of cassette boundaries is key for finding cassettes in CRISPR research field. This is often carried out by using Hidden Markov Models and manual annotation. In this article, we propose the first method able to automatically define the cassette boundaries. In addition, we present a Cas-type predictive model used by the method to assign each gene located in the region defined by a cassette's boundaries a Cas label from a set of pre-defined Cas types. Furthermore, the proposed method can detect potentially new cas genes and decompose a cassette into its modules. RESULTS We evaluate the predictive performance of our proposed method on data collected from the two most recent CRISPR classification studies. In our experiments, we obtain an average similarity of 0.86 between the predicted and expected cassettes. Besides, we achieve F-scores above 0.9 for the classification of cas genes of known types and 0.73 for the unknown ones. Finally, we conduct two additional study cases, where we investigate the occurrence of potentially new cas genes and the occurrence of module exchange between different genomes. AVAILABILITY AND IMPLEMENTATION https://github.com/BackofenLab/Casboundary. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Victor A Padilha
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, SP 13566-590, Brazil
| | - Omer S Alkhnbashi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Van Dinh Tran
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Shiraz A Shah
- COPSAC, Copenhagen University Hospitals Herlev and Gentofte, DK-2820 Gentofte, Denmark
| | - André C P L F Carvalho
- Institute of Mathematics and Computer Sciences, University of São Paulo, São Carlos, SP 13566-590, Brazil
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
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16
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CRISPR-Cas systems in Proteus mirabilis. INFECTION GENETICS AND EVOLUTION 2021; 92:104881. [PMID: 33905883 DOI: 10.1016/j.meegid.2021.104881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 02/14/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a bacterial defense mechanism against bacteriophages composed of two different parts: the CRISPR array and the Cas genes. The spacer acquisition is done by the adaptation module consisting of the hallmark Cas1 Cas2 proteins, which inserts new spacers into the CRISPR array. Here we aimed to describe the CRISPR-Cas system in Proteus mirabilis (P. mirabilis) isolates. CRISPR loci was observed in 30 genomic contents of 109 P. mirabilis isolates that each locus was consisted of two CRISPR arrays and each array had a different preserved leader sequences. Only the type I-E CRISPR-Cas system was common in these isolates. The source of the spacers was identified, including phages and prophages. CRISPR spacer origin analysis also identified a conserved PAM sequence of 5'-AAG-3' nucleotide stretch. Through collecting spacers, CRISPR arrays of P. mirabilis isolates were expanded mostly by integration of bacteriophageal source of spacers. This study shows novel findings in the area of the P-mirabilis CRISPR-Cas system. In this regard, among analyzed genome of P. mirabilis isolates, Class I CRISR-Cas systems were dominant, and all belonged to type I-E. In the flanks of the CRISPR, some other elements with regulatory role were also found. A motif of 11 nt size was found to be preserved among the analyzed genome. We believe that it might has a CRISPR-Cas system transcription facilitator by targeting the Rho element.
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17
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Garrett SC. Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array. Front Microbiol 2021; 12:664299. [PMID: 33868219 PMCID: PMC8047081 DOI: 10.3389/fmicb.2021.664299] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/12/2021] [Indexed: 01/22/2023] Open
Abstract
CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes) is a type of prokaryotic immune system that is unique in its ability to provide sequence-specific adaptive protection, which can be updated in response to new threats. CRISPR-Cas does this by storing fragments of DNA from invading genetic elements in an array interspersed with short repeats. The CRISPR array can be continuously updated through integration of new DNA fragments (termed spacers) at one end, but over time existing spacers become obsolete. To optimize immunity, spacer uptake, residency, and loss must be regulated. This mini-review summarizes what is known about how spacers are organized, maintained, and lost from CRISPR arrays.
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Affiliation(s)
- Sandra C Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, United States
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18
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Abstract
CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, bacteriophages. Immunity is achieved through the acquisition of short DNA fragments from the viral invader’s genome. CRISPR-Cas immune systems adapt to new threats by acquiring new spacers from invading nucleic acids such as phage genomes. However, some CRISPR-Cas loci lack genes necessary for spacer acquisition despite variation in spacer content between microbial strains. It has been suggested that such loci may use acquisition machinery from cooccurring CRISPR-Cas systems within the same strain. Here, following infection by a virulent phage with a double-stranded DNA (dsDNA) genome, we observed spacer acquisition in the native host Flavobacterium columnare that carries an acquisition-deficient CRISPR-Cas subtype VI-B system and a complete subtype II-C system. We show that the VI-B locus acquires spacers from both the bacterial and phage genomes, while the newly acquired II-C spacers mainly target the viral genome. Both loci preferably target the terminal end of the phage genome, with priming-like patterns around a preexisting II-C protospacer. Through gene deletion, we show that the RNA-cleaving VI-B system acquires spacers in trans using acquisition machinery from the DNA-cleaving II-C system. Our observations support the concept of cross talk between CRISPR-Cas systems and raise further questions regarding the plasticity of adaptation modules.
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19
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Nidhi S, Anand U, Oleksak P, Tripathi P, Lal JA, Thomas G, Kuca K, Tripathi V. Novel CRISPR-Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives. Int J Mol Sci 2021; 22:3327. [PMID: 33805113 PMCID: PMC8036902 DOI: 10.3390/ijms22073327] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
According to Darwin's theory, endless evolution leads to a revolution. One such example is the Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-Cas system, an adaptive immunity system in most archaea and many bacteria. Gene editing technology possesses a crucial potential to dramatically impact miscellaneous areas of life, and CRISPR-Cas represents the most suitable strategy. The system has ignited a revolution in the field of genetic engineering. The ease, precision, affordability of this system is akin to a Midas touch for researchers editing genomes. Undoubtedly, the applications of this system are endless. The CRISPR-Cas system is extensively employed in the treatment of infectious and genetic diseases, in metabolic disorders, in curing cancer, in developing sustainable methods for fuel production and chemicals, in improving the quality and quantity of food crops, and thus in catering to global food demands. Future applications of CRISPR-Cas will provide benefits for everyone and will save countless lives. The technology is evolving rapidly; therefore, an overview of continuous improvement is important. In this review, we aim to elucidate the current state of the CRISPR-Cas revolution in a tailor-made format from its discovery to exciting breakthroughs at the application level and further upcoming trends related to opportunities and challenges including ethical concerns.
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Affiliation(s)
- Sweta Nidhi
- Department of Genomics and Bioinformatics, Aix-Marseille University, 13007 Marseille, France;
| | - Uttpal Anand
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel;
| | - Patrik Oleksak
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Pooja Tripathi
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India;
| | - Jonathan A. Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
| | - George Thomas
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
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20
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Mitrofanov A, Alkhnbashi OS, Shmakov SA, Makarova K, Koonin E, Backofen R. CRISPRidentify: identification of CRISPR arrays using machine learning approach. Nucleic Acids Res 2021; 49:e20. [PMID: 33290505 PMCID: PMC7913763 DOI: 10.1093/nar/gkaa1158] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 02/02/2023] Open
Abstract
CRISPR–Cas are adaptive immune systems that degrade foreign genetic elements in archaea and bacteria. In carrying out their immune functions, CRISPR–Cas systems heavily rely on RNA components. These CRISPR (cr) RNAs are repeat-spacer units that are produced by processing of pre-crRNA, the transcript of CRISPR arrays, and guide Cas protein(s) to the cognate invading nucleic acids, enabling their destruction. Several bioinformatics tools have been developed to detect CRISPR arrays based solely on DNA sequences, but all these tools employ the same strategy of looking for repetitive patterns, which might correspond to CRISPR array repeats. The identified patterns are evaluated using a fixed, built-in scoring function, and arrays exceeding a cut-off value are reported. Here, we instead introduce a data-driven approach that uses machine learning to detect and differentiate true CRISPR arrays from false ones based on several features. Our CRISPR detection tool, CRISPRidentify, performs three steps: detection, feature extraction and classification based on manually curated sets of positive and negative examples of CRISPR arrays. The identified CRISPR arrays are then reported to the user accompanied by detailed annotation. We demonstrate that our approach identifies not only previously detected CRISPR arrays, but also CRISPR array candidates not detected by other tools. Compared to other methods, our tool has a drastically reduced false positive rate. In contrast to the existing tools, our approach not only provides the user with the basic statistics on the identified CRISPR arrays but also produces a certainty score as a practical measure of the likelihood that a given genomic region is a CRISPR array.
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Affiliation(s)
| | | | - Sergey A Shmakov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rolf Backofen
- To whom correspondence should be addressed. Tel: +49 761/203 7461; Fax: +49 761/203 7462;
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21
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Affiliation(s)
- Christine Pourcel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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22
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Ding C, Adrian L. Comparative genomics in "Candidatus Kuenenia stuttgartiensis" reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins. BMC Genomics 2020; 21:851. [PMID: 33261555 PMCID: PMC7709395 DOI: 10.1186/s12864-020-07242-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/18/2020] [Indexed: 11/10/2022] Open
Abstract
Background Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the databases, little is known about the stability and variability of their genomes and how the genomes evolve in response to changing environments. Results Here we report the complete genome of the anammox bacterium “Candidatus Kuenenia stuttgartiensis” strain CSTR1 which was enriched planktonically in a semi-continuous stirred-tank reactor. A comparison of the genome of strain CSTR1 with the genome of “Ca. Kuenenia stuttgartiensis” MBR1 and the draft genome of KUST showed > 99% average nucleotide identity among all. Rearrangements of large genomic regions were observed, most of which were associated with transposase genes. Phylogenetic analysis suggests that strain MBR1 is more distantly related to the other two strains. Proteomic analysis of actively growing cells of strain CSTR1 (growth rate ~ 0.33 d− 1) failed to detect the annotated cytochrome cd1-type nitrite reductase (NirS) although in total 1189 proteins were found in the proteome. Yet, this NirS was expressed when strain CSTR1 was under stress or starvation (growth rate < 0.06 d− 1). We also observed large sequence shifts in the strongly expressed S-layer protein compared to other “Ca. Kuenenia” strains, indicating the formation of hybrids of genes encoding the surface proteins. Conclusions “Ca. Kuenenia” strains appear to be relatively stable in their basic physiological traits, but show high variability in overall genome structure and surface proteins.
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Affiliation(s)
- Chang Ding
- Helmholtz Centre for Environmental Research - UFZ, Environmental Biotechnology, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research - UFZ, Environmental Biotechnology, Permoserstraße 15, 04318, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355, Berlin, Germany
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23
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Shmakov SA, Utkina I, Wolf YI, Makarova KS, Severinov KV, Koonin EV. CRISPR Arrays Away from cas Genes. CRISPR J 2020; 3:535-549. [PMID: 33346707 PMCID: PMC7757702 DOI: 10.1089/crispr.2020.0062] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
CRISPR-Cas systems typically consist of a CRISPR array and cas genes that are organized in one or more operons. However, a substantial fraction of CRISPR arrays are not adjacent to cas genes. Definitive identification of such isolated CRISPR arrays runs into the problem of false-positives, with unrelated types of repetitive sequences mimicking CRISPR. We developed a computational pipeline to eliminate false CRISPR predictions and found that up to 25% of the CRISPR arrays in complete bacterial and archaeal genomes are located away from cas genes. Most of the repeats in these isolated arrays are identical to repeats in cas-adjacent CRISPR arrays in the same or closely related genomes, indicating an evolutionary relationship between isolated arrays and arrays in typical CRISPR-cas loci. The spacers in isolated CRISPR arrays show nearly as many matches to viral genomes as spacers from complete CRISPR-cas loci, suggesting that the isolated arrays were either functionally active recently or continue to function. Reconstruction of evolutionary events in closely related bacterial genomes suggests three routes of evolution of isolated CRISPR arrays: (1) loss of cas genes in a CRISPR-cas locus, (2) de novo generation of arrays from off-target spacer integration into sequences resembling the corresponding repeats, and (3) transfer by mobile genetic elements. Both combination of de novo emerging arrays with cas genes and regain of cas genes by isolated arrays via recombination likely contribute to functional diversification in CRISPR-Cas evolution.
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Affiliation(s)
- Sergey A. Shmakov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA; Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Irina Utkina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA; Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
- The Hospital for Sick Children, University of Toronto, Toronto, Canada; Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA; Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA; Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Konstantin V. Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia; and Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
- Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA; Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
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24
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Zhang Y, Zhao G, Ahmed FYH, Yi T, Hu S, Cai T, Liao Q. In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster. Front Oncol 2020; 10:584404. [PMID: 33123486 PMCID: PMC7567020 DOI: 10.3389/fonc.2020.584404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
The CRISPR/Cas system has stood in the center of attention in the last few years as a revolutionary gene editing tool with a wide application to investigate gene functions. However, the labor-intensive workflow requires a sophisticated pre-experimental and post-experimental analysis, thus becoming one of the hindrances for the further popularization of practical applications. Recently, the increasing emergence and advancement of the in silico methods play a formidable role to support and boost experimental work. However, various tools based on distinctive design principles and frameworks harbor unique characteristics that are likely to confuse users about how to choose the most appropriate one for their purpose. In this review, we will present a comprehensive overview and comparisons on the in silico methods from the aspects of CRISPR/Cas system identification, guide RNA design, and post-experimental assistance. Furthermore, we establish the hypotheses in light of the new trends around the technical optimization and hope to provide significant clues for future tools development.
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Affiliation(s)
- Yuwei Zhang
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, China.,Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Guofang Zhao
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Fatma Yislam Hadi Ahmed
- Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China
| | - Tianfei Yi
- Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China
| | - Shiyun Hu
- Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China
| | - Ting Cai
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Qi Liao
- Hwa Mei Hospital, University of Chinese Academy of Science, Ningbo, China.,Zhejiang Key Laboratory of Pathophysiology, Department of Preventative Medicine, Medical School of Ningbo University, Ningbo, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
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25
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Garrett S, Shiimori M, Watts EA, Clark L, Graveley BR, Terns MP. Primed CRISPR DNA uptake in Pyrococcus furiosus. Nucleic Acids Res 2020; 48:6120-6135. [PMID: 32421777 PMCID: PMC7293040 DOI: 10.1093/nar/gkaa381] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/15/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas adaptive immune systems are used by prokaryotes to defend against invaders like viruses and other mobile genetic elements. Immune memories are stored in the form of 'spacers' which are short DNA sequences that are captured from invaders and added to the CRISPR array during a process called 'adaptation'. Spacers are transcribed and the resulting CRISPR (cr)RNAs assemble with different Cas proteins to form effector complexes that recognize matching nucleic acid and destroy it ('interference'). Adaptation can be 'naïve', i.e. independent of any existing spacer matches, or it can be 'primed', i.e. spurred by the crRNA-mediated detection of a complete or partial match to an invader sequence. Here we show that primed adaptation occurs in Pyrococcus furiosus. Although P. furiosus has three distinct CRISPR-Cas interference systems (I-B, I-A and III-B), only the I-B system and Cas3 were necessary for priming. Cas4, which is important for selection and processing of new spacers in naïve adaptation, was also essential for priming. Loss of either the I-B effector proteins or Cas3 reduced naïve adaptation. However, when Cas3 and all crRNP genes were deleted, uptake of correctly processed spacers was observed, indicating that none of these interference proteins are necessary for naïve adaptation.
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Affiliation(s)
- Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Masami Shiimori
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Elizabeth A Watts
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Landon Clark
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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26
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Kieper SN, Almendros C, Brouns SJJ. Conserved motifs in the CRISPR leader sequence control spacer acquisition levels in Type I-D CRISPR-Cas systems. FEMS Microbiol Lett 2020; 366:5525085. [PMID: 31252430 PMCID: PMC6607411 DOI: 10.1093/femsle/fnz129] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022] Open
Abstract
Integrating short DNA fragments at the correct leader-repeat junction is key to successful CRISPR-Cas memory formation. The Cas1-2 proteins are responsible to carry out this process. However, the CRISPR adaptation process additionally requires a DNA element adjacent to the CRISPR array, called leader, to facilitate efficient localization of the correct integration site. In this work, we introduced the core CRISPR adaptation genes cas1 and cas2 from the Type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and assessed spacer integration efficiency. Truncation of the leader resulted in a significant reduction of spacer acquisition levels and revealed the importance of different conserved regions for CRISPR adaptation rates. We found three conserved sequence motifs in the leader of I-D CRISPR arrays that each affected spacer acquisition rates, including an integrase anchoring site. Our findings support the model in which the leader sequence is an integral part of type I-D adaptation in Synechocystis sp. acting as a localization signal for the adaptation complex to drive CRISPR adaptation at the first repeat of the CRISPR array.
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Affiliation(s)
- Sebastian N Kieper
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cristóbal Almendros
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Stan J J Brouns
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.,Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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27
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Padilha VA, Alkhnbashi OS, Shah SA, de Carvalho ACPLF, Backofen R. CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems. Gigascience 2020; 9:giaa062. [PMID: 32556168 PMCID: PMC7298778 DOI: 10.1093/gigascience/giaa062] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/27/2020] [Accepted: 05/15/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR-Cas genes are extraordinarily diverse and evolve rapidly when compared to other prokaryotic genes. With the rapid increase in newly sequenced archaeal and bacterial genomes, manual identification of CRISPR-Cas systems is no longer viable. Thus, an automated approach is required for advancing our understanding of the evolution and diversity of these systems and for finding new candidates for genome engineering in eukaryotic models. RESULTS We introduce CRISPRcasIdentifier, a new machine learning-based tool that combines regression and classification models for the prediction of potentially missing proteins in instances of CRISPR-Cas systems and the prediction of their respective subtypes. In contrast to other available tools, CRISPRcasIdentifier can both detect cas genes and extract potential association rules that reveal functional modules for CRISPR-Cas systems. In our experimental benchmark on the most recently published and comprehensive CRISPR-Cas system dataset, CRISPRcasIdentifier was compared with recent and state-of-the-art tools. According to the experimental results, CRISPRcasIdentifier presented the best Cas protein identification and subtype classification performance. CONCLUSIONS Overall, our tool greatly extends the classification of CRISPR cassettes and, for the first time, predicts missing Cas proteins and association rules between Cas proteins. Additionally, we investigated the properties of CRISPR subtypes. The proposed tool relies not only on the knowledge of manual CRISPR annotation but also on models trained using machine learning.
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Affiliation(s)
- Victor A Padilha
- Institute of Mathematics and Computer Sciences, University of São Paulo, Av. Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Omer S Alkhnbashi
- Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Shiraz A Shah
- COPSAC, Copenhagen University Hospitals Herlev and Gentofte, Ledreborg Alle 34, DK-2820 Gentofte, Denmark
| | - André C P L F de Carvalho
- Institute of Mathematics and Computer Sciences, University of São Paulo, Av. Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Rolf Backofen
- Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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28
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Alkhnbashi OS, Meier T, Mitrofanov A, Backofen R, Voß B. CRISPR-Cas bioinformatics. Methods 2020; 172:3-11. [PMID: 31326596 DOI: 10.1016/j.ymeth.2019.07.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/19/2019] [Accepted: 07/15/2019] [Indexed: 02/07/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) are essential genetic elements in many archaeal and bacterial genomes, playing a key role in a prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas system has also been engineered to facilitate target gene editing in eukaryotic genomes. Bioinformatics played an essential role in the detection and analysis of CRISPR systems and here we review the bioinformatics-based efforts that pushed the field of CRISPR-Cas research further. We discuss the bioinformatics tools that have been published over the last few years and, finally, present the most popular tools for the design of CRISPR-Cas9 guides.
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Affiliation(s)
| | - Tobias Meier
- Computational Biology, Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany.
| | | | - Rolf Backofen
- Chair of Bioinformatics, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Germany.
| | - Björn Voß
- Computational Biology, Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany.
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29
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Hickman AB, Kailasan S, Genzor P, Haase AD, Dyda F. Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas. eLife 2020; 9:50004. [PMID: 31913120 PMCID: PMC6977970 DOI: 10.7554/elife.50004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/08/2020] [Indexed: 12/17/2022] Open
Abstract
Key to CRISPR-Cas adaptive immunity is maintaining an ongoing record of invading nucleic acids, a process carried out by the Cas1-Cas2 complex that integrates short segments of foreign genetic material (spacers) into the CRISPR locus. It is hypothesized that Cas1 evolved from casposases, a novel class of transposases. We show here that the Methanosarcina mazei casposase can integrate varied forms of the casposon end in vitro, and recapitulates several properties of CRISPR-Cas integrases including site-specificity. The X-ray structure of the casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. The differences between transposase and CRISPR-Cas integrase are largely architectural, and it appears that evolutionary change involved changes in protein-protein interactions to favor Cas2 binding over tetramerization; this in turn led to preferred integration of single spacers over two transposon ends.
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Affiliation(s)
- Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Shweta Kailasan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Pavol Genzor
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Astrid D Haase
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
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30
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Grainy J, Garrett S, Graveley BR, P Terns M. CRISPR repeat sequences and relative spacing specify DNA integration by Pyrococcus furiosus Cas1 and Cas2. Nucleic Acids Res 2019; 47:7518-7531. [PMID: 31219587 PMCID: PMC6698737 DOI: 10.1093/nar/gkz548] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/26/2022] Open
Abstract
Acquiring foreign spacer DNA into the CRISPR locus is an essential primary step of the CRISPR-Cas pathway in prokaryotes for developing host immunity to mobile genetic elements. Here, we investigate spacer integration in vitro using proteins from Pyrococcus furiosus and demonstrate that Cas1 and Cas2 are sufficient to accurately integrate spacers into a minimal CRISPR locus. Using high-throughput sequencing, we identified high frequency spacer integration occurring at the same CRISPR repeat border sites utilized in vivo, as well as at several non-CRISPR plasmid sequences which share features with repeats. Analysis of non-CRISPR integration sites revealed that Cas1 and Cas2 are directed to catalyze full-site spacer integration at specific DNA stretches where guanines and/or cytosines are 30 base pairs apart and the intervening sequence harbors several positionally conserved bases. Moreover, assaying a series of CRISPR repeat mutations, followed by sequencing of the integration products, revealed that the specificity of integration is primarily directed by sequences at the leader-repeat junction as well as an adenine-rich sequence block in the mid-repeat. Together, our results indicate that P. furiosus Cas1 and Cas2 recognize multiple sequence features distributed over a 30 base pair DNA region for accurate spacer integration at the CRISPR repeat.
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Affiliation(s)
- Julie Grainy
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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31
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Konstantinov YM, Petrushin IS. Detection of CRISPR cassettes and cas genes in the Arabidopsis thaliana genome. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The state of the art in the evolution of plant viruses allows the genetic foundations of antiviral immunity in higher (including the most important crops) plants to be categorized as one of the most pressing issues of genetics and selection. According to the endosymbiotic theory, mitochondria descended from alphaproteobacteria that had been absorbed but not degraded by the host cell. The discovery of CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins), which implement the adaptive immunity function in prokaryotes, raises the question whether such a mechanism of antiviral protection could be caught up by evolution and used by representatives of eukaryotes (in particular, plants). The purpose of this work was to analyze the complete sequences of nuclear, mitochondrial, and chloroplast genomes of Arabidopsis thaliana in order to search for genetic elements similar to those in CRISPR-Cas systems of bacteria and archaea. As a result, in silico methods helped us to detect a locus of regularly intermittent short direct repeats in the mitochondrial genome of A. thaliana ecotypes. The structure of this locus corresponds to the CRISPR locus of the prokaryotic adaptive antiviral immune system. The probable connection between the locus found in the mitochondrial genome of the higher plant and the function of adaptive immunity is indicated by a similarity between the spacer sequences in the CRISPR cassette found and the genome of Cauliflower mosaic virus affecting Arabidopsis plants. Sequences of repeats and spacers of CRISPR cassettes in Arabidopsis C24 and Ler lines are perfectly identical. However, the locations of the CRISPR locus in the mitochondrial genomes of these lines differ significantly. The CRISPR cassette in the Col-0 line was found to be completely broken as a result of four deletions and one insertion. Although cas genes were not detected in the mitochondrial genome of the studied Arabidopsis ecotypes, their presence was detected in the nuclear genome. Both cas genes and numerous CRISPR cassettes were found on all the five chromosomes in the nuclear genome of the Col-0 ecotype. The results suggest the existence of a system of adaptive immunity in plants, which is similar to the CRISPR immunity of bacteria and archaea.
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Affiliation(s)
- Yu. M. Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS; Irkutsk State University
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32
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Garcia-Robledo JE, Barrera MC, Tobón GJ. CRISPR/Cas: from adaptive immune system in prokaryotes to therapeutic weapon against immune-related diseases. Int Rev Immunol 2019; 39:11-20. [PMID: 31625429 DOI: 10.1080/08830185.2019.1677645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CRISPR/Cas evolved as an adaptive immune system in bacteria and archaea to inactivate foreign viral and plasmid DNA. However, the capacities of various CRISPR/Cas systems for precise genome editing based on sequence homology also allow their use as tools for genomic and epigenomic modification in eukaryotes. Indeed, these genetic characteristics have proven useful for disease modeling and testing the specific functions of target genes under pathological conditions. Moreover, recent studies provide compelling evidence that CRISPR/Cas systems could be useful therapeutic tools against human diseases, including cancer, monogenic disorders, and autoimmune disorders.HighlightsCRISPR/Cas evolved as an adaptive immune system in bacteria and archaea.CRISPR/Cas systems are nowadays used as tools for genomic modification.CRISPR/Cas systems could be useful therapeutic tools against human disease, including autoimmune conditions.
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Affiliation(s)
| | - María Claudia Barrera
- Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional; Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
| | - Gabriel J Tobón
- Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional; Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
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33
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Scrascia M, D'Addabbo P, Roberto R, Porcelli F, Oliva M, Calia C, Dionisi AM, Pazzani C. Characterization of CRISPR-Cas Systems in Serratia marcescens Isolated from Rhynchophorus ferrugineus (Olivier, 1790) (Coleoptera: Curculionidae). Microorganisms 2019; 7:microorganisms7090368. [PMID: 31546915 PMCID: PMC6780938 DOI: 10.3390/microorganisms7090368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
The CRISPR-Cas adaptive immune system has been attracting increasing scientific interest for biological functions and biotechnological applications. Data on the Serratia marcescens system are scarce. Here, we report a comprehensive characterisation of CRISPR-Cas systems identified in S. marcescens strains isolated as secondary symbionts of Rhynchophorus ferrugineus, also known as Red Palm Weevil (RPW), one of the most invasive pests of major cultivated palms. Whole genome sequencing was performed on four strains (S1, S5, S8, and S13), which were isolated from the reproductive apparatus of RPWs. Subtypes I-F and I-E were harboured by S5 and S8, respectively. No CRISPR-Cas system was detected in S1 or S13. Two CRISPR arrays (4 and 51 spacers) were detected in S5 and three arrays (11, 31, and 30 spacers) were detected in S8. The CRISPR-Cas systems were located in the genomic region spanning from ybhR to phnP, as if this were the only region where CRISPR-Cas loci were acquired. This was confirmed by analyzing the S. marcescens complete genomes available in the NCBI database. This region defines a genomic hotspot for horizontally acquired genes and/or CRISPR-Cas systems. This study also supplies the first identification of subtype I-E in S. marcescens.
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Affiliation(s)
- Maria Scrascia
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Pietro D'Addabbo
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Roberta Roberto
- Department of Plants, Food, and Soil Sciences, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Francesco Porcelli
- Department of Plants, Food, and Soil Sciences, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Marta Oliva
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Carla Calia
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
| | - Anna Maria Dionisi
- Department of Infectious diseases, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Carlo Pazzani
- Department of Biology, University of Bari Aldo Moro, 70124 Bari, Italy.
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34
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Milicevic O, Repac J, Bozic B, Djordjevic M, Djordjevic M. A Simple Criterion for Inferring CRISPR Array Direction. Front Microbiol 2019; 10:2054. [PMID: 31551987 PMCID: PMC6737040 DOI: 10.3389/fmicb.2019.02054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022] Open
Abstract
Inferring transcriptional direction (orientation) of the CRISPR array is essential for many applications, including systematically investigating non-canonical CRISPR/Cas functions. The standard method, CRISPRDirection (embedded within CRISPRCasFinder), fails to predict the orientation (ND predictions) for ∼37% of the classified CRISPR arrays (>2200 loci); this goes up to >70% for the II-B subtype where non-canonical functions were first experimentally discovered. Alternatively, Potential Orientation (also embedded within CRISPRCasFinder), has a much smaller frequency of ND predictions but might have significantly lower accuracy. We propose a novel simple criterion, where the CRISPR array direction is assigned according to the direction of its associated cas genes (Cas Orientation). We systematically assess the performance of the three methods (Cas Orientation, CRISPRDirection, and Potential Orientation) across all CRISPR/Cas subtypes, by a mutual crosscheck of their predictions, and by comparing them to the experimental dataset. Interestingly, CRISPRDirection agrees much better with Cas Orientation than with Potential Orientation, despite CRISPRDirection and Potential Orientation being mutually related – Potential Orientation corresponding to one of six (heterogeneous) predictors employed by CRISPRDirection – and being unrelated to Cas Orientation. We find that Cas Orientation has much higher accuracy compared to Potential Orientation and comparable accuracy to CRISPRDirection – while accurately assigning an orientation to ∼95% of the CRISPR arrays that are non-determined by CRISPRDirection. Cas Orientation is, at the same time, simple to employ, requiring only (routine for prokaryotes) the prediction of the associated protein coding gene direction.
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Affiliation(s)
- Ognjen Milicevic
- School of Medicine, University of Belgrade, Belgrade, Serbia.,Multidisciplinary Ph.D. Program in Biophysics, University of Belgrade, Belgrade, Serbia
| | - Jelena Repac
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
| | - Bojan Bozic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
| | | | - Marko Djordjevic
- Faculty of Biology, Institute of Physiology and Biochemistry, University of Belgrade, Belgrade, Serbia
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35
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Long J, Xu Y, Ou L, Yang H, Xi Y, Chen S, Duan G. Polymorphism of Type I-F CRISPR/Cas system in Escherichia coli of phylogenetic group B2 and its application in genotyping. INFECTION GENETICS AND EVOLUTION 2019; 74:103916. [PMID: 31195154 DOI: 10.1016/j.meegid.2019.103916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/22/2019] [Accepted: 06/07/2019] [Indexed: 12/26/2022]
Abstract
E. coli of phylogenetic group B2 is responsible for many extraintestinal infections, posing a great threat to health. The relatively polymorphic nature of CRISPR in phylogenetically related E. coli strains makes them potential markers for bacterial typing and evolutionary studies. In the current work, we investigated the occurrence and diversity of CRISPR/Cas system and explored its potential for genotyping. Type I-F CRISPR/Cas systems were found in 413 of 1190 strains of E. coli and exhibited the clustering within certain CCs and STs. And CRISPR spacer contents correlated well with MLST types. The divergence analysis of CRISPR showed stronger discriminatory power than MLST, and CRISPR polymorphism was instrumental for differentiating highly closely related strains. The timeline of spacer acquisition and deletion provided important information for inferring the evolution model between distinct serotypes. Identical spacer sequences were shared by strains with the same H-antigen type but not strains with the same O-antigen type. The homology between spacers and antibiotic-resistant plasmids demonstrated the role of Type I-F system in limiting the acquisition of antimicrobial resistance. Collectively, our data presents the dynamic nature of Type I-F CRISPR in E. coli of phylogenetic group B2 and provides new insights into the application of CRISPR-based typing in the species.
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Affiliation(s)
- Jinzhao Long
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yake Xu
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China; School Hospital, Henan University of Science and Technology, Luoyang, Henan, China
| | - Liuyang Ou
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuanlin Xi
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuaiyin Chen
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
| | - Guangcai Duan
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China; Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China.
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36
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Crawley AB, Henriksen JR, Barrangou R. CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems. CRISPR J 2019. [PMID: 31021201 DOI: 10.1089/crispr.2017.0022.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas adaptive immune systems of bacteria and archaea have catapulted into the scientific spotlight as genome editing tools. To aid researchers in the field, we have developed an automated pipeline, named CRISPRdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness. All six major types and 23 currently recognized subtypes and novel putative V-U types are detected. Here, we use the pipeline to identify and classify putative CRISPR-Cas systems in 2,777 complete genomes from the NCBI RefSeq database. This allows comparison to previous publications and investigation of the occurrence and size of CRISPR-Cas systems. Software available at http://github.com/crisprlab/CRISPRdisco provides reproducible, standardized, accessible, transparent, and high-throughput analysis methods available to all researchers in and beyond the CRISPR-Cas research community. This tool opens new avenues to enable classification within a complex nomenclature and provides analytical methods in a field that has evolved rapidly.
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Affiliation(s)
- Alexandra B Crawley
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
| | | | - Rodolphe Barrangou
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
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37
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Abstract
Pervasive application of CRISPR-Cas systems in genome editing has prompted an increase in both interest and necessity to further elucidate existing systems as well as discover putative novel systems. The ubiquity and power of current computational platforms have made in silico approaches to CRISPR-Cas identification and characterization accessible to a wider audience and increasingly amenable for processing extensive data sets. Here, we describe in silico methods for predicting and visualizing notable features of CRISPR-Cas systems, including Cas domain determination, CRISPR array visualization, and inference of the protospacer-adjacent motif. The efficiency of these tools enables rapid exploration of CRISPR-Cas diversity across prokaryotic genomes and supports scalable analysis of large genomic data sets.
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Affiliation(s)
- Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States; Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, NC, United States.
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38
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Nickel L, Ulbricht A, Alkhnbashi OS, Förstner KU, Cassidy L, Weidenbach K, Backofen R, Schmitz RA. Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1. RNA Biol 2018; 16:492-503. [PMID: 30153081 DOI: 10.1080/15476286.2018.1514234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) system is a prokaryotic adaptive defense system against foreign nucleic acids. In the methanoarchaeon Methanosarcina mazei Gö1, two types of CRISPR-Cas systems are present (type I-B and type III-C). Both loci encode a Cas6 endonuclease, Cas6b-IB and Cas6b-IIIC, typically responsible for maturation of functional short CRISPR RNAs (crRNAs). To evaluate potential cross cleavage activity, we biochemically characterized both Cas6b proteins regarding their crRNA binding behavior and their ability to process pre-crRNA from the respective CRISPR array in vivo. Maturation of crRNA was studied in the respective single deletion mutants by northern blot and RNA-Seq analysis demonstrating that in vivo primarily Cas6b-IB is responsible for crRNA processing of both CRISPR arrays. Tentative protein level evidence for the translation of both Cas6b proteins under standard growth conditions was detected, arguing for different activities or a potential non-redundant role of Cas6b-IIIC within the cell. Conservation of both Cas6 endonucleases was observed in several other M. mazei isolates, though a wide variety was displayed. In general, repeat and leader sequence conservation revealed a close correlation in the M. mazei strains. The repeat sequences from both CRISPR arrays from M. mazei Gö1 contain the same sequence motif with differences only in two nucleotides. These data stand in contrast to all other analyzed M. mazei isolates, which have at least one additional CRISPR array with repeats belonging to another sequence motif. This conforms to the finding that Cas6b-IB is the crucial and functional endonuclease in M. mazei Gö1. Abbreviations: sRNA: small RNA; crRNA: CRISPR RNA; pre-crRNAs: Precursor CRISPR RNA; CRISPR: clustered regularly interspaced short palindromic repeats; Cas: CRISPR associated; nt: nucleotide; RNP: ribonucleoprotein; RBS: ribosome binding site.
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Affiliation(s)
- Lisa Nickel
- a Institute of General Microbiology , Christian-Albrechts-University of Kiel , Kiel , Germany
| | - Andrea Ulbricht
- a Institute of General Microbiology , Christian-Albrechts-University of Kiel , Kiel , Germany
| | - Omer S Alkhnbashi
- b Bioinformatics Group, Department of Computer Science , University of Freiburg , Freiburg , Germany
| | - Konrad U Förstner
- c Core Unit Systems Medicine , Institute of Molecular Infection Biology, University of Würzburg , Würzburg , Germany
| | - Liam Cassidy
- d Institute for Experimental Medicine , Christian-Albrechts-University of Kiel , Kiel , Germany
| | - Katrin Weidenbach
- a Institute of General Microbiology , Christian-Albrechts-University of Kiel , Kiel , Germany
| | - Rolf Backofen
- b Bioinformatics Group, Department of Computer Science , University of Freiburg , Freiburg , Germany.,e BIOSS Centre for Biological Signaling Studies , University of Freiburg , Freiburg , Germany
| | - Ruth A Schmitz
- a Institute of General Microbiology , Christian-Albrechts-University of Kiel , Kiel , Germany
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39
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Abstract
Rathayibacter toxicus is a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makes R. toxicus a highly regulated species. This work provides novel insights into the evolution of R. toxicus. R. toxicus is the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of the R. toxicus genome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria. Rathayibacter toxicus is a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution of R. toxicus to explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy of Rathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequenced Rathayibacter genomes indicated that Rathayibacter forms nine species-level groups. R. toxicus is the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover, R. toxicus has low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates. R. toxicus is the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of the R. toxicus species.
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40
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Hou S, Brenes-Álvarez M, Reimann V, Alkhnbashi OS, Backofen R, Muro-Pastor AM, Hess WR. CRISPR-Cas systems in multicellular cyanobacteria. RNA Biol 2018; 16:518-529. [PMID: 29995583 DOI: 10.1080/15476286.2018.1493330] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor > 40 different putative CRISPR repeat-spacer cassettes, while the number of cas gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium Anabaena sp. PCC 7120 contains only three cas1 genes but hosts three Class 1, possibly one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the Anabaena sp. PCC 7120 fdxN gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-cas systems and points to a previously not recognized connection. The gene all3613 resembling a possible Class 2 effector protein is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity and presence of numerous CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study. Abbreviations: Cas: CRISPR associated sequences; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; C2c: Class 2 candidate; SDR: small dispersed repeat; TSS: transcriptional start site; UTR: untranslated region.
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Affiliation(s)
- Shengwei Hou
- a Faculty of Biology, Genetics and Experimental Bioinformatics , University of Freiburg , Freiburg , Germany
| | - Manuel Brenes-Álvarez
- b Instituto de Bioquímica Vegetal y Fotosíntesis , Consejo Superior de Investigaciones Científicas and Universidad de Sevilla , Seville , Spain
| | - Viktoria Reimann
- a Faculty of Biology, Genetics and Experimental Bioinformatics , University of Freiburg , Freiburg , Germany
| | - Omer S Alkhnbashi
- c Bioinformatics group, Department of Computer Science , University of Freiburg , Freiburg , Germany
| | - Rolf Backofen
- c Bioinformatics group, Department of Computer Science , University of Freiburg , Freiburg , Germany.,d Center for Biological Systems Analysis (ZBSA) , University of Freiburg , Freiburg , Germany.,e BIOSS Centre for Biological Signaling Studies , University of Freiburg , Freiburg , Germany
| | - Alicia M Muro-Pastor
- c Bioinformatics group, Department of Computer Science , University of Freiburg , Freiburg , Germany
| | - Wolfgang R Hess
- a Faculty of Biology, Genetics and Experimental Bioinformatics , University of Freiburg , Freiburg , Germany.,f Freiburg Institute for Advanced Studies,University of Freiburg, Freiburg, Germany
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41
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Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 2018; 46:W246-W251. [PMID: 29790974 PMCID: PMC6030898 DOI: 10.1093/nar/gky425] [Citation(s) in RCA: 718] [Impact Index Per Article: 119.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/09/2018] [Indexed: 12/25/2022] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.
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Affiliation(s)
- David Couvin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Aude Bernheim
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France
- CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France
| | - Claire Toffano-Nioche
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France
- CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France
| | - Juraj Michalik
- Université Lille 1, CRIStAL, équipe Bonsai, Cité Scientifique Bat M3, 59655 Villeneuve d'Ascq Cedex, France
| | - Bertrand Néron
- Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue du Docteur Roux, 75015, Paris, France
- CNRS, UMR3525, 25-28 rue du Docteur Roux, 75015, Paris, France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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42
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Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR, Backofen R. Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Res 2018; 46:W25-W29. [PMID: 29788132 PMCID: PMC6030932 DOI: 10.1093/nar/gky329] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/03/2018] [Accepted: 05/18/2018] [Indexed: 12/20/2022] Open
Abstract
The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.
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Affiliation(s)
- Martin Raden
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Syed M Ali
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Omer S Alkhnbashi
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Fabrizio Costa
- Department of Computer Science, University of Exeter, Exeter EX4 4QF, UK
| | - Jason A Davis
- Coreva Scientific, Kaiser-Joseph-Str 198-200, 79098 Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rick Gelhausen
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Jens Georg
- Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1HH, UK
| | - Robert Kleinkauf
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Steffen C Lott
- Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Mostafa M Mohamed
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Alexander Mattheis
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Milad Miladi
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | | | - Sebastian Will
- Theoretical Biochemistry Group, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria
| | - Joachim Wolff
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Patrick R Wright
- Department of Clinical Research, Clinical Trial Unit, University of Basel Hospital, Schanzenstrasse 55, 4031 Basel, Switzerland
| | - Rolf Backofen
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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43
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Shah SA, Alkhnbashi OS, Behler J, Han W, She Q, Hess WR, Garrett RA, Backofen R. Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families. RNA Biol 2018; 16:530-542. [PMID: 29911924 PMCID: PMC6546367 DOI: 10.1080/15476286.2018.1483685] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in Synechocystis confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk.
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Affiliation(s)
- Shiraz A Shah
- a Copenhagen Prospective Studies on Asthma in Childhood , Herlev and Gentofte Hospital, University of Copenhagen , Denmark.,d Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
| | - Omer S Alkhnbashi
- b Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Freiburg , Germany
| | - Juliane Behler
- c Genetics and Experimental Bioinformatics, Faculty of Biology , University of Freiburg, Freiburg , Germany
| | - Wenyuan Han
- d Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
| | - Qunxin She
- d Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
| | - Wolfgang R Hess
- c Genetics and Experimental Bioinformatics, Faculty of Biology , University of Freiburg, Freiburg , Germany.,e Freiburg Institute for Advanced Studies , University of Freiburg , Freiburg , Germany
| | - Roger A Garrett
- d Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
| | - Rolf Backofen
- b Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Freiburg , Germany.,f BIOSS Centre for Biological Signaling Studies , University of Freiburg , Freiburg , Germany
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44
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Crawley AB, Henriksen JR, Barrangou R. CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems. CRISPR J 2018; 1:171-181. [PMID: 31021201 PMCID: PMC6636876 DOI: 10.1089/crispr.2017.0022] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas adaptive immune systems of bacteria and archaea have catapulted into the scientific spotlight as genome editing tools. To aid researchers in the field, we have developed an automated pipeline, named CRISPRdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness. All six major types and 23 currently recognized subtypes and novel putative V-U types are detected. Here, we use the pipeline to identify and classify putative CRISPR-Cas systems in 2,777 complete genomes from the NCBI RefSeq database. This allows comparison to previous publications and investigation of the occurrence and size of CRISPR-Cas systems. Software available at http://github.com/crisprlab/CRISPRdisco provides reproducible, standardized, accessible, transparent, and high-throughput analysis methods available to all researchers in and beyond the CRISPR-Cas research community. This tool opens new avenues to enable classification within a complex nomenclature and provides analytical methods in a field that has evolved rapidly.
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Affiliation(s)
- Alexandra B Crawley
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
| | | | - Rodolphe Barrangou
- 1 Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University , Raleigh, North Carolina
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45
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Teikari JE, Hou S, Wahlsten M, Hess WR, Sivonen K. Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity. Front Microbiol 2018; 9:356. [PMID: 29568283 PMCID: PMC5853447 DOI: 10.3389/fmicb.2018.00356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/14/2018] [Indexed: 11/13/2022] Open
Abstract
Salinity is an important abiotic factor controlling the distribution and abundance of Nodularia spumigena, the dominating diazotrophic and toxic phototroph, in the brackish water cyanobacterial blooms of the Baltic Sea. To expand the available genomic information for brackish water cyanobacteria, we sequenced the isolate Nodularia spumigena UHCC 0039 using an Illumina-SMRT hybrid sequencing approach, revealing a chromosome of 5,294,286 base pairs (bp) and a single plasmid of 92,326 bp. Comparative genomics in Nostocales showed pronounced genetic similarity among Nodularia spumigena strains evidencing their short evolutionary history. The studied Baltic Sea strains share similar sets of CRISPR-Cas cassettes and a higher number of insertion sequence (IS) elements compared to Nodularia spumigena CENA596 isolated from a shrimp production pond in Brazil. Nodularia spumigena UHCC 0039 proliferated similarly at three tested salinities, whereas the lack of salt inhibited its growth and triggered transcriptome remodeling, including the up-regulation of five sigma factors and the down-regulation of two other sigma factors, one of which is specific for strain UHCC 0039. Down-regulated genes additionally included a large genetic region for the synthesis of two yet unidentified natural products. Our results indicate a remarkable plasticity of the Nodularia salinity acclimation, and thus salinity strongly impacts the intensity and distribution of cyanobacterial blooms in the Baltic Sea.
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Affiliation(s)
- Jonna E Teikari
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Matti Wahlsten
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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46
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Rollie C, Graham S, Rouillon C, White MF. Prespacer processing and specific integration in a Type I-A CRISPR system. Nucleic Acids Res 2018; 46:1007-1020. [PMID: 29228332 PMCID: PMC5815122 DOI: 10.1093/nar/gkx1232] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 12/15/2022] Open
Abstract
The CRISPR-Cas system for prokaryotic adaptive immunity provides RNA-mediated protection from viruses and mobile genetic elements. Adaptation is dependent on the Cas1 and Cas2 proteins along with varying accessory proteins. Here we analyse the process in Sulfolobus solfataricus, showing that while Cas1 and Cas2 catalyze spacer integration in vitro, host factors are required for specificity. Specific integration also requires at least 400 bp of the leader sequence, and is dependent on the presence of hydrolysable ATP, suggestive of an active process that may involve DNA remodelling. Specific spacer integration is associated with processing of prespacer 3' ends in a PAM-dependent manner. This is reflected in PAM-dependent processing of prespacer 3' ends in vitro in the presence of cell lysate or the Cas4 nuclease, in a reaction consistent with PAM-directed binding and protection of prespacer DNA. These results highlight the diverse interplay between CRISPR-Cas elements and host proteins across CRISPR types.
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Affiliation(s)
- Clare Rollie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Christophe Rouillon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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47
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Shakya M, Soucy SM, Zhaxybayeva O. Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evol 2017; 3:vex036. [PMID: 29250433 PMCID: PMC5721377 DOI: 10.1093/ve/vex036] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized that the GTA ancestor was a virus. Whether GTAs represent an atypical virus, a defective virus, or a virus co-opted by the prokaryotes for some function, remains to be elucidated. To evaluate these possibilities, we examined the distribution and evolutionary histories of genes that encode a GTA in the α-proteobacterium Rhodobacter capsulatus (RcGTA). We report that although homologs of many individual RcGTA genes are abundant across bacteria and their viruses, RcGTA-like genomes are mainly found in one subclade of α-proteobacteria. When compared with the viral homologs, genes of the RcGTA-like genomes evolve significantly slower, and do not have higher %A+T nucleotides than their host chromosomes. Moreover, they appear to reside in stable regions of the bacterial chromosomes that are generally conserved across taxonomic orders. These findings argue against RcGTA being an atypical or a defective virus. Our phylogenetic analyses suggest that RcGTA ancestor likely originated in the lineage that gave rise to contemporary α-proteobacterial orders Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Sphingomonadales, and since that time the RcGTA-like element has co-evolved with its host chromosomes. Such evolutionary history is compatible with maintenance of these elements by bacteria due to some selective advantage. As for many other prokaryotic traits, horizontal gene transfer played a substantial role in the evolution of RcGTA-like elements, not only in shaping its genome components within the orders, but also in occasional dissemination of RcGTA-like regions across the orders and even to different bacterial phyla.
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Affiliation(s)
- Migun Shakya
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Shannon M Soucy
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA.,Department of Computer Science, Dartmouth College, 6211 Sudikoff Lab, Hanover, NH 03755, USA
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Tajkarimi M, Wexler HM. CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome. Front Microbiol 2017; 8:2234. [PMID: 29218031 PMCID: PMC5704556 DOI: 10.3389/fmicb.2017.02234] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/31/2017] [Indexed: 12/29/2022] Open
Abstract
Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved. The CRISPR-Cas system is a multi-functional system described in prokaryotes that may be involved in control both of HGT and of gene regulation. Results: Clustered regularly interspaced short palindromic repeats (CRISPR) elements in all strains of B. fragilis (n = 109) with publically available genomes were identified. Three different CRISPR-Cas types, corresponding most closely to Type IB, Type IIIB, and Type IIC, were identified. Thirty-five strains had two CRISPR-Cas types, and three strains included all three CRISPR-Cas types in their respective genomes. The cas1 gene in the Type IIIB system encoded a reverse-transcriptase/Cas1 fusion protein rarely found in prokaryotes. We identified a short CRISPR (3 DR) with no associated cas genes present in most of the isolates; these CRISPRs were found immediately upstream of a hipA/hipB operon and we speculate that this element may be involved in regulation of this operon related to formation of persister cells during antimicrobial exposure. Also, blood isolates of B. fragilis did not have Type IIC CRISPR-Cas systems and had atypical Type IIIB CRISPR-Cas systems that were lacking adjacent cas genes. Conclusions: This is the first systematic report of CRISPR-Cas systems in a wide range of B. fragilis strains from a variety of sources. There are four apparent CRISPR-Cas systems in B. fragilis-three systems have adjacent cas genes. Understanding CRISPR/Cas function in B. fragilis will elucidate their role in gene expression, DNA repair and ability to survive exposure to antibiotics. Also, based on their unique CRISPR-Cas arrays, their phylogenetic clustering and their virulence potential, we are proposing that blood isolates of B. fragilis be viewed a separate subgroup.
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Affiliation(s)
- Mehrdad Tajkarimi
- Brentwood Biomedical Research Institute, Los Angeles, CA, United States
| | - Hannah M Wexler
- Brentwood Biomedical Research Institute, Los Angeles, CA, United States.,University of California, Los Angeles, Los Angeles, CA, United States.,GLAVA Health Care System, Los Angeles, CA, United States
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Liu T, Liu Z, Ye Q, Pan S, Wang X, Li Y, Peng W, Liang Y, She Q, Peng N. Coupling transcriptional activation of CRISPR-Cas system and DNA repair genes by Csa3a in Sulfolobus islandicus. Nucleic Acids Res 2017; 45:8978-8992. [PMID: 28911114 PMCID: PMC5587795 DOI: 10.1093/nar/gkx612] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 07/05/2017] [Indexed: 12/16/2022] Open
Abstract
CRISPR-Cas system provides the adaptive immunity against invading genetic elements in prokaryotes. Recently, we demonstrated that Csa3a regulator mediates spacer acquisition in Sulfolobus islandicus by activating the expression of Type I-A adaptation cas genes. However, links between the activation of spacer adaptation and CRISPR transcription/processing, and the requirement for DNA repair genes during spacer acquisition remained poorly understood. Here, we demonstrated that de novo spacer acquisition required Csa1, Cas1, Cas2 and Cas4 proteins of the Sulfolobus Type I-A system. Disruption of genes implicated in crRNA maturation or DNA interference led to a significant accumulation of acquired spacers, mainly derived from host genomic DNA. Transcriptome and proteome analyses showed that Csa3a activated expression of adaptation cas genes, CRISPR RNAs, and DNA repair genes, including herA helicase, nurA nuclease and DNA polymerase II genes. Importantly, Csa3a specifically bound the promoters of the above DNA repair genes, suggesting that they were directly activated by Csa3a for adaptation. The Csa3a regulator also specifically bound to the leader sequence to activate CRISPR transcription in vivo. Our data indicated that the Csa3a regulator couples transcriptional activation of the CRISPR-Cas system and DNA repair genes for spacer adaptation and efficient interference of invading genetic elements.
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Affiliation(s)
- Tao Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Zhenzhen Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qing Ye
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Saifu Pan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaodi Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China.,Archaeal Centre, Department of Biology, University of Copenhagen, Ole Maal⊘es Vej 5, DK-2200 Copenhagen N, Denmark
| | - Wenfang Peng
- Archaeal Centre, Department of Biology, University of Copenhagen, Ole Maal?es Vej 5, DK-2200 Copenhagen N, Denmark
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qunxin She
- Archaeal Centre, Department of Biology, University of Copenhagen, Ole Maal?es Vej 5, DK-2200 Copenhagen N, Denmark
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
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Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia. PLoS One 2017; 12:e0185234. [PMID: 28934361 PMCID: PMC5608340 DOI: 10.1371/journal.pone.0185234] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/09/2017] [Indexed: 12/18/2022] Open
Abstract
Prevotella intermedia, a major periodontal pathogen, is increasingly implicated in human respiratory tract and cystic fibrosis lung infections. Nevertheless, the specific mechanisms employed by this pathogen remain only partially characterized and poorly understood, largely due to its total lack of genetic accessibility. Here, using Single Molecule, Real-Time (SMRT) genome and methylome sequencing, bisulfite sequencing, in addition to cloning and restriction analysis, we define the specific genetic barriers to exogenous DNA present in two of the most widespread laboratory strains, P. intermedia ATCC 25611 and P. intermedia Strain 17. We identified and characterized multiple restriction-modification (R-M) systems, some of which are considerably divergent between the two strains. We propose that these R-M systems are the root cause of the P. intermedia transformation barrier. Additionally, we note the presence of conserved Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) systems in both strains, which could provide a further barrier to exogenous DNA uptake and incorporation. This work will provide a valuable resource during the development of a genetic system for P. intermedia, which will be required for fundamental investigation of this organism’s physiology, metabolism, and pathogenesis in human disease.
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