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Gao R, Liu X, Xiong Z, Wang G, Ai L. Research progress on detection of foodborne pathogens: The more rapid and accurate answer to food safety. Food Res Int 2024; 193:114767. [PMID: 39160035 DOI: 10.1016/j.foodres.2024.114767] [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: 05/21/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 08/21/2024]
Abstract
In recent years, foodborne diseases have posed a serious threat to human health, and rapid detection of foodborne pathogens is particularly crucial for the prevention and control of such diseases. This article offers a detailed overview of the development of detection techniques for foodborne pathogens, transitioning from traditional microbiological culture methods to the current array of techniques, including immunological, molecular biological, and biosensor-based methods. It summarizes the technical principles, advantages, disadvantages, and research progress of these diverse methods. Furthermore, the article demonstrates that the combination of different methods enhances the efficiency and accuracy of pathogens detection. Specifically, the article focuses on the application and advantages of combining CRISPR/Cas systems with other detection methods in the detection of foodborne pathogens. CRISPR/Cas systems, with their high specificity, sensitivity, and ease of operation, show great potential in the field of foodborne pathogens detection. When integrated with other detection techniques such as immunological detection techniques, molecular biology detection techniques, and biosensors, the accuracy and efficiency of detection can be further improved. By fully utilizing these tools, early detection and control of foodborne diseases can be achieved, enhancing public health and preventing disease outbreaks. This article serves as a valuable reference for exploring more convenient, accurate, and sensitive field detection methods for foodborne pathogens, promoting the application of rapid detection techniques, and ensuring food safety and human health.
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Affiliation(s)
- Ruoxuan Gao
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xinxin Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Guangqiang Wang
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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2
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Alalmaie A, Diaf S, Khashan R. Insight into the molecular mechanism of the transposon-encoded type I-F CRISPR-Cas system. J Genet Eng Biotechnol 2023; 21:60. [PMID: 37191877 DOI: 10.1186/s43141-023-00507-8] [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: 07/05/2022] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
CRISPR-Cas9 is a popular gene-editing tool that allows researchers to introduce double-strand breaks to edit parts of the genome. CRISPR-Cas9 system is used more than other gene-editing tools because it is simple and easy to customize. However, Cas9 may produce unintended double-strand breaks in DNA, leading to off-target effects. There have been many improvements in the CRISPR-Cas system to control the off-target effect and improve the efficiency. The presence of a nuclease-deficient CRISPR-Cas system in several bacterial Tn7-like transposons inspires researchers to repurpose to direct the insertion of Tn7-like transposons instead of cleaving the target DNA, which will eventually limit the risk of off-target effects. Two transposon-encoded CRISPR-Cas systems have been experimentally confirmed. The first system, found in Tn7 like-transposon (Tn6677), is associated with the variant type I-F CRISPR-Cas system. The second one, found in Tn7 like-transposon (Tn5053), is related to the variant type V-K CRISPR-Cas system. This review describes the molecular and structural mechanisms of DNA targeting by the transposon-encoded type I-F CRISPR-Cas system, from assembly around the CRISPR-RNA (crRNA) to the initiation of transposition.
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Affiliation(s)
- Amnah Alalmaie
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Saint Joseph University, Philadelphia, PA, 19131, USA
| | - Saousen Diaf
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Saint Joseph University, Philadelphia, PA, 19131, USA
| | - Raed Khashan
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Sciences, Long Island University, Brooklyn, NY, 11201, USA.
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3
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Liu J, Wu D, Chen J, Jia S, Chen J, Wu Y, Li G. CRISPR-Cas systems mediated biosensing and applications in food safety detection. Crit Rev Food Sci Nutr 2022; 64:2960-2985. [PMID: 36218189 DOI: 10.1080/10408398.2022.2128300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Food safety, closely related to economic development of food industry and public health, has become a global concern and gained increasing attention worldwide. Effective detection technology is of great importance to guarantee food safety. Although several classical detection methods have been developed, they have some limitations in portability, selectivity, and sensitivity. The emerging CRISPR-Cas systems, uniquely integrating target recognition specificity, signal transduction, and efficient signal amplification abilities, possess superior specificity and sensitivity, showing huge potential to address aforementioned challenges and develop next-generation techniques for food safety detection. In this review, we focus on recent progress of CRISPR-Cas mediated biosensing and their applications in food safety monitoring. The properties and principles of commonly used CRISPR-Cas systems are highlighted. Notably, the frequently coupled nucleic acid amplification strategies to enhance their selectivity and sensitivity, especially isothermal amplification methods, as well as various signal output modes are also systematically summarized. Meanwhile, the application of CRISPR-Cas systems-based biosensors in food safety detection including foodborne virus, foodborne bacteria, food fraud, genetically modified organisms (GMOs), toxins, heavy metal ions, antibiotic residues, and pesticide residues is comprehensively described. Furthermore, the current challenges and future prospects in this field are tentatively discussed.
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Affiliation(s)
- Jianghua Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Jiahui Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Shijie Jia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Jian Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
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4
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Disarming of type I-F CRISPR-Cas surveillance complex by anti-CRISPR proteins AcrIF6 and AcrIF9. Sci Rep 2022; 12:15548. [PMID: 36109551 PMCID: PMC9478129 DOI: 10.1038/s41598-022-19797-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immune systems that protect against phages and other invading nucleic acids. The evolutionary arms race between prokaryotes and phages gave rise to phage anti-CRISPR (Acr) proteins that act as a counter defence against CRISPR-Cas systems by inhibiting the effector complex. Here, we used a combination of bulk biochemical experiments, X-ray crystallography and single-molecule techniques to explore the inhibitory activity of AcrIF6 and AcrIF9 proteins against the type I-F CRISPR-Cas system from Aggregatibacter actinomycetemcomitans (Aa). We showed that AcrIF6 and AcrIF9 proteins hinder Aa-Cascade complex binding to target DNA. We solved a crystal structure of Aa1-AcrIF9 protein, which differ from other known AcrIF9 proteins by an additional structurally important loop presumably involved in the interaction with Cascade. We revealed that AcrIF9 association with Aa-Cascade promotes its binding to off-target DNA sites, which facilitates inhibition of CRISPR-Cas protection.
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Sun W, Guo W, Liu Z, Qiao S, Wang Z, Wang J, Qu L, Shan L, Sun F, Xu S, Bai O, Liang C. Direct MYD88 L265P gene detection for diffuse large B-cell lymphoma (DLBCL) via a miniaturised CRISPR/dCas9-based sensing chip. LAB ON A CHIP 2022; 22:768-776. [PMID: 35073397 DOI: 10.1039/d1lc01055g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Traditional methods for single-nucleotide variants based on amplification and fluorescence signals require expensive reagents and cumbersome instruments, and they are time-consuming for each trial. Here, a porous anodised aluminium (PAA)-based sensing chip modified with deactivated Cas9 (dCas9) proteins and synthetic guide RNA (sgRNA) as the biorecognition receptor is developed, which can be used for the label-free sensing of the diffuse large B-cell lymphoma (DLBCL) MYD88L265P gene by integrating with electrochemical ionic current rectification (ICR) measurement. The sgRNA that can specifically identify and capture the MYD88L265P gene was screened, which has been proved to be workable to activate dCas9 for the target MYD88L265P. In the sensing process, the dCas9 proteins can capture the genome sequence, thus bringing negative charges over the PAA chip and correspondingly resulting in a variation in the ICR value due to the uneven transport of potassium anions through the ion channels of the PAA chip. The whole sensing can be finished within 40 min, and there is no need for gene amplification. The CRISPR/dCas9-based sensor demonstrates ultrasensitive detection performance in the concentration range of 50 to 200 ng μL-1 and it has been proved to be feasible for the genome sequence of patient tissues. This sensor shows the potential of targeting other mutations by designing the corresponding sgRNAs and expands the applications of CRISPR/dCas9 technology to the on-chip electrical detection of nucleic acids, which will be very valuable for rapid diagnosis of clinically mutated genes. This makes the hybrid CRISPR-PAA chip an ideal candidate for next-generation nucleic acid biosensors.
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Affiliation(s)
- Weihan Sun
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Wei Guo
- Department of Hematology, The First Hospital of Jilin University, Jilin University, 71 Xinmin Street, 130021 Changchun, China.
| | - Zhiyi Liu
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Sennan Qiao
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Ziming Wang
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
| | - Jiayu Wang
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Lingxuan Qu
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Liang Shan
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
| | - Fei Sun
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
| | - Shuping Xu
- State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2699 Qianjin Ave., 130012 Changchun, China.
| | - Ou Bai
- Department of Hematology, The First Hospital of Jilin University, Jilin University, 71 Xinmin Street, 130021 Changchun, China.
| | - Chongyang Liang
- Department of Biopharmacy, School of Pharmaceutical Sciences, Jilin University, 1266 Fujin Road, 130021 Changchun, China.
- Institute of Frontier Medical Science, Jilin University, 1163 Xinmin Street, 130021 Changchun, China
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6
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Klompe SE, Jaber N, Beh LY, Mohabir JT, Bernheim A, Sternberg SH. Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons. Mol Cell 2022; 82:616-628.e5. [PMID: 35051352 PMCID: PMC8849592 DOI: 10.1016/j.molcel.2021.12.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/20/2021] [Accepted: 12/16/2021] [Indexed: 02/05/2023]
Abstract
Canonical CRISPR-Cas systems utilize RNA-guided nucleases for targeted cleavage of foreign nucleic acids, whereas some nuclease-deficient CRISPR-Cas complexes have been repurposed to direct the insertion of Tn7-like transposons. Here, we established a bioinformatic and experimental pipeline to comprehensively explore the diversity of Type I-F CRISPR-associated transposons. We report DNA integration for 20 systems and identify a highly active subset that exhibits complete orthogonality in transposon DNA mobilization. We reveal the modular nature of CRISPR-associated transposons by exploring the horizontal acquisition of targeting modules and by characterizing a system that encodes both a programmable, RNA-dependent pathway, and a fixed, RNA-independent pathway. Finally, we analyzed transposon-encoded cargo genes and found the striking presence of anti-phage defense systems, suggesting a role in transmitting innate immunity between bacteria. Collectively, this study substantially advances our biological understanding of CRISPR-associated transposon function and expands the suite of RNA-guided transposases for programmable, large-scale genome engineering.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA Transposable Elements/genetics
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Escherichia coli/genetics
- Escherichia coli/immunology
- Escherichia coli/metabolism
- Evolution, Molecular
- Gene Editing
- Gene Expression Regulation, Bacterial
- Genetic Variation
- Immunity, Innate
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Transposases/genetics
- Transposases/metabolism
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Affiliation(s)
- Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Nora Jaber
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Leslie Y Beh
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jason T Mohabir
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Aude Bernheim
- French National Institute of Health and Medical Research (INSERM), University of Paris, Paris, France
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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7
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Qian S, Chen Y, Xu X, Peng C, Wang X, Wu H, Liu Y, Zhong X, Xu J, Wu J. Advances in amplification-free detection of nucleic acid: CRISPR/Cas system as a powerful tool. Anal Biochem 2022; 643:114593. [DOI: 10.1016/j.ab.2022.114593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/28/2022] [Accepted: 02/05/2022] [Indexed: 12/26/2022]
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8
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Efficient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant. Sci Rep 2021; 11:9586. [PMID: 33953310 PMCID: PMC8100143 DOI: 10.1038/s41598-021-89029-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/20/2021] [Indexed: 02/03/2023] Open
Abstract
Thermophilic organisms are extensively studied in industrial biotechnology, for exploration of the limits of life, and in other contexts. Their optimal growth at high temperatures presents a challenge for the development of genetic tools for their genome editing, since genetic markers and selection substrates are often thermolabile. We sought to develop a thermostable CRISPR-Cas9 based system for genome editing of thermophiles. We identified CaldoCas9 and designed an associated guide RNA and showed that the pair have targetable nuclease activity in vitro at temperatures up to 65 °C. We performed a detailed characterization of the protospacer adjacent motif specificity of CaldoCas9, which revealed a preference for 5'-NNNNGNMA. We constructed a plasmid vector for the delivery and use of the CaldoCas9 based genome editing system in the extreme thermophile Thermus thermophilus at 65 °C. Using the vector, we generated gene knock-out mutants of T. thermophilus, targeting genes on the bacterial chromosome and megaplasmid. Mutants were obtained at a frequency of about 90%. We demonstrated that the vector can be cured from mutants for a subsequent round of genome editing. CRISPR-Cas9 based genome editing has not been reported previously in the extreme thermophile T. thermophilus. These results may facilitate development of genome editing tools for other extreme thermophiles and to that end, the vector has been made available via the plasmid repository Addgene.
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9
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Chuang YF, Phipps AJ, Lin FL, Hecht V, Hewitt AW, Wang PY, Liu GS. Approach for in vivo delivery of CRISPR/Cas system: a recent update and future prospect. Cell Mol Life Sci 2021; 78:2683-2708. [PMID: 33388855 PMCID: PMC11072787 DOI: 10.1007/s00018-020-03725-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/19/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system provides a groundbreaking genetic technology that allows scientists to modify genes by targeting specific genomic sites. Due to the relative simplicity and versatility of the CRISPR/Cas system, it has been extensively applied in human genetic research as well as in agricultural applications, such as improving crops. Since the gene editing activity of the CRISPR/Cas system largely depends on the efficiency of introducing the system into cells or tissues, an efficient and specific delivery system is critical for applying CRISPR/Cas technology. However, there are still some hurdles remaining for the translatability of CRISPR/Cas system. In this review, we summarized the approaches used for the delivery of the CRISPR/Cas system in mammals, plants, and aquacultures. We further discussed the aspects of delivery that can be improved to elevate the potential for CRISPR/Cas translatability.
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Affiliation(s)
- Yu-Fan Chuang
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, 518055, China
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Andrew J Phipps
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Fan-Li Lin
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, 518055, China
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Valerie Hecht
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
| | - Peng-Yuan Wang
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, 518055, China.
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC, Australia.
| | - Guei-Sheung Liu
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia.
- Aier Eye Institute, Changsha, Hunan, China.
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Bayarsaikhan D, Bayarsaikhan G, Lee B. Recent advances in stem cells and gene editing: Drug discovery and therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:231-269. [PMID: 34127195 DOI: 10.1016/bs.pmbts.2021.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recently introduced genome editing technology has had a remarkable impact on genetic medicine. Zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas nucleases are the three major platforms used for priming of stem cells or correction of mutated genes. Among these nucleases, CRISPR/Cas is the most easily applicable. Various CRISPR/Cas variants such as base editors, prime editors, mad7 nucleases, RESCUE, REPAIR, digenome sequencing, and SHERLOCK are being developed and considered as a promising tool for gene therapy and drug discovery. These advances in the CRISPR/Cas platform have enabled the correction of gene mutations from DNA to RNA level and validation of the safety of genome editing performance at a very precise level by allowing the detection of one base-pair mismatch. These promising alternatives of the CRISPR/Cas system can benefit millions of patients with intractable diseases. Although the therapeutic effects of stem cells have been confirmed in a wide range of disease models, their safety still remains an issue. Hence, scientists are concentrating on generating functionally improved stem cells by using programmable nucleases such as CRISPR. Therefore, in this chapter, we have summarized the applicable options of the CRISPR/Cas platforms by weighing their advantages and limitations in drug discovery and gene therapy.
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Affiliation(s)
- Delger Bayarsaikhan
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea
| | - Govigerel Bayarsaikhan
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea
| | - Bonghee Lee
- Lee Gil Ya Cancer and Diabetes Institute, School of Medicine, Gachon University, Incheon City, Republic of Korea.
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The evolution and history of gene editing technologies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:1-62. [PMID: 33685594 DOI: 10.1016/bs.pmbts.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Scientific enquiry must be the driving force of research. This sentiment is manifested as the profound impact gene editing technologies are having in our current world. There exist three main gene editing technologies today: Zinc Finger Nucleases, TALENs and the CRISPR-Cas system. When these systems were being uncovered, none of the scientists set out to design tools to engineer genomes. They were simply trying to understand the mechanisms existing in nature. If it was not for this simple sense of wonder, we probably would not have these breakthrough technologies. In this chapter, we will discuss the history, applications and ethical issues surrounding these technologies, focusing on the now predominant CRISPR-Cas technology. Gene editing technologies, as we know them now, are poised to have an overwhelming impact on our world. However, it is impossible to predict the route they will take in the future or to comprehend the full impact of its repercussions.
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12
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Wu H, Chen X, Zhang M, Wang X, Chen Y, Qian C, Wu J, Xu J. Versatile detection with CRISPR/Cas system from applications to challenges. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116150] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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Petris G. Preface. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:xvii-xxii. [PMID: 34175053 DOI: 10.1016/s1877-1173(21)00133-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana. Genes (Basel) 2020; 11:genes11121504. [PMID: 33327465 PMCID: PMC7764966 DOI: 10.3390/genes11121504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (Pscore ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.
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15
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Wiegand T, Semenova E, Shiriaeva A, Fedorov I, Datsenko K, Severinov K, Wiedenheft B. Reproducible Antigen Recognition by the Type I-F CRISPR-Cas System. CRISPR J 2020; 3:378-387. [PMID: 33095052 PMCID: PMC7580607 DOI: 10.1089/crispr.2020.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CRISPR-associated proteins 1 and 2 (Cas1-2) are necessary and sufficient for new spacer acquisition in some CRISPR-Cas systems (e.g., type I-E), but adaptation in other systems (e.g., type II-A) involves the crRNA-guided surveillance complex. Here we show that the type I-F Cas1-2/3 proteins are necessary and sufficient to produce low levels of spacer acquisition, but the presence of the type I-F crRNA-guided surveillance complex (Csy) improves the efficiency of adaptation and significantly increases the fidelity of protospacer adjacent motif selection. Sequences selected for integration are preferentially derived from specific regions of extrachromosomal DNA, and patterns of spacer selection are highly reproducible between independent biological replicates. This work helps define the role of the Csy complex in I-F adaptation and reveals that actively replicating mobile genetic elements have antigenic signatures that facilitate their integration during CRISPR adaptation.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA; Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
| | - Anna Shiriaeva
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Microbiology, Peter the Great St. Petersburg Polytechnic University, Saint-Petersburg, Russia; Russian Academy of Sciences, Moscow, Russia
| | - Ivan Fedorov
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
| | - Kirill Datsenko
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia; Russian Academy of Sciences, Moscow, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia; and Russian Academy of Sciences, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA; Russian Academy of Sciences, Moscow, Russia
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16
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Karvelis T, Bigelyte G, Young JK, Hou Z, Zedaveinyte R, Budre K, Paulraj S, Djukanovic V, Gasior S, Silanskas A, Venclovas Č, Siksnys V. PAM recognition by miniature CRISPR-Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Res 2020; 48:5016-5023. [PMID: 32246713 PMCID: PMC7229846 DOI: 10.1093/nar/gkaa208] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 12/26/2022] Open
Abstract
In recent years, CRISPR-associated (Cas) nucleases have revolutionized the genome editing field. Being guided by an RNA to cleave double-stranded (ds) DNA targets near a short sequence termed a protospacer adjacent motif (PAM), Cas9 and Cas12 offer unprecedented flexibility, however, more compact versions would simplify delivery and extend application. Here, we present a collection of 10 exceptionally compact (422–603 amino acids) CRISPR–Cas12f nucleases that recognize and cleave dsDNA in a PAM dependent manner. Categorized as class 2 type V-F, they originate from the previously identified Cas14 family and distantly related type V-U3 Cas proteins found in bacteria. Using biochemical methods, we demonstrate that a 5′ T- or C-rich PAM sequence triggers dsDNA target cleavage. Based on this discovery, we evaluated whether they can protect against invading dsDNA in Escherichia coli and find that some but not all can. Altogether, our findings show that miniature Cas12f nucleases can protect against invading dsDNA like much larger class 2 CRISPR effectors and have the potential to be harnessed as programmable nucleases for genome editing.
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Affiliation(s)
- Tautvydas Karvelis
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Greta Bigelyte
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | | | | | | | - Karolina Budre
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | | | | | | | - Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
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17
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Wiegand T, Karambelkar S, Bondy-Denomy J, Wiedenheft B. Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression. Annu Rev Microbiol 2020; 74:21-37. [PMID: 32503371 DOI: 10.1146/annurev-micro-020518-120107] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
More than 50 protein families have been identified that inhibit CRISPR (clustered regularly interspaced short palindromic repeats)-Cas-mediated adaptive immune systems. Here, we analyze the available anti-CRISPR (Acr) structures and describe common themes and unique mechanisms of stoichiometric and enzymatic suppressors of CRISPR-Cas. Stoichiometric inhibitors often function as molecular decoys of protein-binding partners or nucleic acid targets, while enzymatic suppressors covalently modify Cas ribonucleoprotein complexes or degrade immune signaling molecules. We review mechanistic insights that have been revealed by structures of Acrs, discuss some of the trade-offs associated with each of these strategies, and highlight how Acrs are regulated and deployed in the race to overcome adaptive immunity.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA;
| | - Shweta Karambelkar
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, California 94143, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, Berkeley, California 94720, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA;
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18
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Hirschi M, Lu WT, Santiago-Frangos A, Wilkinson R, Golden SM, Davidson AR, Lander GC, Wiedenheft B. AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex. Nat Commun 2020; 11:2730. [PMID: 32483187 PMCID: PMC7264359 DOI: 10.1038/s41467-020-16512-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/07/2020] [Indexed: 11/09/2022] Open
Abstract
Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of anti-CRISPRs that suppress these immune systems. Here we report structures of anti-CRISPR protein IF9 (AcrIF9) in complex with the type I-F CRISPR RNA-guided surveillance complex (Csy). In addition to sterically blocking the hybridization of complementary dsDNA to the CRISPR RNA, our results show that AcrIF9 binding also promotes non-sequence-specific engagement with dsDNA, potentially sequestering the complex from target DNA. These findings highlight the versatility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems.
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Affiliation(s)
- Marscha Hirschi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92121, USA
| | - Wang-Ting Lu
- Department of Molecular Genetics, and Department of Biochemistry, University of Toronto, 661 University Avenue, Room 1634, Toronto, ON, M5G 1M1, Canada
| | - Andrew Santiago-Frangos
- Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA
| | - Royce Wilkinson
- Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA
| | - Sarah M Golden
- Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA
| | - Alan R Davidson
- Department of Molecular Genetics, and Department of Biochemistry, University of Toronto, 661 University Avenue, Room 1634, Toronto, ON, M5G 1M1, Canada.
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92121, USA.
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA.
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19
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Liu Z, Schiel JA, Maksimova E, Strezoska Ž, Zhao G, Anderson EM, Wu Y, Warren J, Bartels A, van Brabant Smith A, Lowe CE, Forbes KP. ErCas12a CRISPR-MAD7 for Model Generation in Human Cells, Mice, and Rats. CRISPR J 2020; 3:97-108. [PMID: 32315227 PMCID: PMC7194332 DOI: 10.1089/crispr.2019.0068] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MAD7 is an engineered class 2 type V-A CRISPR-Cas (Cas12a/Cpf1) system isolated from Eubacterium rectale. Analogous to Cas9, it is an RNA-guided nuclease with demonstrated gene editing activity in Escherichia coli and yeast cells. Here, we report that MAD7 is capable of generating indels and fluorescent gene tagging of endogenous genes in human HCT116 and U2OS cancer cell lines, respectively. In addition, MAD7 is highly proficient in generating indels, small DNA insertions (23 bases), and larger integrations ranging from 1 to 14 kb in size in mouse and rat embryos, resulting in live-born transgenic animals. Due to the different protospacer adjacent motif requirement, small-guide RNA, and highly efficient targeted gene disruption and insertions, MAD7 can expand the CRISPR toolbox for genome enginnering across different systems and model organisms.
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Affiliation(s)
- Zhenyi Liu
- ENVIGO Research Model Services (Formerly Horizon Discovery Group), St. Louis, Missouri, USA
| | - John A. Schiel
- Horizon Discovery Group Company, Lafayette, Colorado, USA
| | | | | | - Guojun Zhao
- ENVIGO Research Model Services (Formerly Horizon Discovery Group), St. Louis, Missouri, USA
| | | | - Yumei Wu
- ENVIGO Research Model Services (Formerly Horizon Discovery Group), St. Louis, Missouri, USA
| | - Joe Warren
- ENVIGO Research Model Services (Formerly Horizon Discovery Group), St. Louis, Missouri, USA
| | - Angela Bartels
- ENVIGO Research Model Services (Formerly Horizon Discovery Group), St. Louis, Missouri, USA
| | | | | | - Kevin P. Forbes
- ENVIGO Research Model Services (Formerly Horizon Discovery Group), St. Louis, Missouri, USA
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20
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Zhang F. Harnessing Nature’s Diversity for Developing New Biotechnologies. MOLECULAR FRONTIERS JOURNAL 2020. [DOI: 10.1142/s2529732519400169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular biologists today make use of a number of technologies based on natural products or systems, essentially using the wonders of life to further discover wonderous things about life. This cycle is powered by the immense amount of natural diversity. Here I highlight how one natural system, CRISPR, has been engineered for a range of applications aimed at improving human health and discuss possible ways natural diversity may be leveraged in the future.
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Affiliation(s)
- Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
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21
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Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 2019; 18:67-83. [DOI: 10.1038/s41579-019-0299-x] [Citation(s) in RCA: 797] [Impact Index Per Article: 159.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/16/2022]
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22
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Abstract
While humans have made enormous progress in the exploration and exploitation of Earth, exploration of outer space remains beyond current human capabilities. The principal challenges lie in current space technology and engineering which includes the protection of astronauts from the hazards of working and living in the space environment. These challenges may lead to a paradoxical situation where progress in space technology and the ability to ensure acceptable risk/benefit for human space exploration becomes dissociated and the rate of scientific discovery declines. In this paper, we discuss the predominant challenges of the space environment for human health and argue that development and deployment of a human enhancement policy, initially confined to astronauts - for the purpose of future human space programmes is a rational solution to these challenges.
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Affiliation(s)
- Konrad Szocik
- Department of Social Sciences, University of Information Technology, and Management, Rzeszow, Poland
| | - Martin Braddock
- Sherwood Observatory, Mansfield and Sutton Astronomical Society, England, UK
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23
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Young JK, Gasior SL, Jones S, Wang L, Navarro P, Vickroy B, Barrangou R. The repurposing of type I-E CRISPR-Cascade for gene activation in plants. Commun Biol 2019; 2:383. [PMID: 31646186 PMCID: PMC6802105 DOI: 10.1038/s42003-019-0637-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
CRISPR-Cas systems are robust and facile tools for manipulating the genome, epigenome and transcriptome of eukaryotic organisms. Most groups use class 2 effectors, such as Cas9 and Cas12a, however, other CRISPR-Cas systems may provide unique opportunities for genome engineering. Indeed, the multi-subunit composition of class 1 systems offers to expand the number of domains and functionalities that may be recruited to a genomic target. Here we report DNA targeting in Zea mays using a class 1 type I-E CRISPR-Cas system from S. thermophilus. First, we engineer its Cascade complex to modulate gene expression by tethering a plant transcriptional activation domain to 3 different subunits. Next, using an immunofluorescent assay, we confirm Cascade cellular complex formation and observe enhanced gene activation when multiple subunits tagged with the transcriptional activator are combined. Finally, we examine Cascade mediated gene activation at chromosomal DNA targets by reprogramming Zea mays cells to change color.
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Affiliation(s)
- Joshua K. Young
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA 50131 USA
| | - Stephen L. Gasior
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA 50131 USA
| | - Spencer Jones
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA 50131 USA
| | - Lijuan Wang
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA 50131 USA
| | - Pedro Navarro
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA 50131 USA
| | - Becca Vickroy
- Department of Molecular Engineering, Corteva Agriscience™, Johnston, IA 50131 USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695 USA
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24
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Amoako DG, Somboro AM, Abia ALK, Allam M, Ismail A, Bester LA, Essack SY. Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa. Pathogens 2019; 8:E166. [PMID: 31569754 PMCID: PMC6963616 DOI: 10.3390/pathogens8040166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/19/2022] Open
Abstract
This study undertook genome mining and comparative genomics to gain genetic insights into the dominance of the methicillin-resistant Staphylococcus aureus (MRSA) endemic clone ST612-CC8-t1257-SCCmec_IVd(2B), obtained from the poultry food chain in South Africa. Functional annotation of the genome revealed a vast array of similar central metabolic, cellular and biochemical networks within the endemic clone crucial for its survival in the microbial community. In-silico analysis of the clone revealed the possession of uniform defense systems, restriction-modification system (type I and IV), accessory gene regulator (type I), arginine catabolic mobile element (type II), and type 1 clustered, regularly interspaced, short palindromic repeat (CRISPR)Cas array (N = 7 ± 1), which offer protection against exogenous attacks. The estimated pathogenic potential predicted a higher probability (average Pscore ≈ 0.927) of the clone being pathogenic to its host. The clone carried a battery of putative virulence determinants whose expression are critical for establishing infection. However, there was a slight difference in their possession of adherence factors (biofilm operon system) and toxins (hemolysins and enterotoxins). Further analysis revealed a conserved environmental tolerance and persistence mechanisms related to stress (oxidative and osmotic), heat shock, sporulation, bacteriocins, and detoxification, which enable it to withstand lethal threats and contribute to its success in diverse ecological niches. Phylogenomic analysis with close sister lineages revealed that the clone was closely related to the MRSA isolate SHV713 from Australia. The results of this bioinformatic analysis provide valuable insights into the biology of this endemic clone.
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Affiliation(s)
- Daniel Gyamfi Amoako
- Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
| | - Anou M Somboro
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa.
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa.
| | - Linda A Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal; Durban 4000, South Africa.
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa.
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25
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Nasef M, Muffly MC, Beckman AB, Rowe SJ, Walker FC, Hatoum-Aslan A, Dunkle JA. Regulation of cyclic oligoadenylate synthesis by the Staphylococcus epidermidis Cas10-Csm complex. RNA (NEW YORK, N.Y.) 2019; 25:948-962. [PMID: 31076459 PMCID: PMC6633199 DOI: 10.1261/rna.070417.119] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
CRISPR-Cas systems are a class of adaptive immune systems in prokaryotes that use small CRISPR RNAs (crRNAs) in conjunction with CRISPR-associated (Cas) nucleases to recognize and degrade foreign nucleic acids. Recent studies have revealed that Type III CRISPR-Cas systems synthesize second messenger molecules previously unknown to exist in prokaryotes, cyclic oligoadenylates (cOA). These molecules activate the Csm6 nuclease to promote RNA degradation and may also coordinate additional cellular responses to foreign nucleic acids. Although cOA production has been reconstituted and characterized for a few bacterial and archaeal Type III systems, cOA generation and its regulation have not been explored for the Staphylococcus epidermidis Type III-A CRISPR-Cas system, a longstanding model for CRISPR-Cas function. Here, we demonstrate that this system performs Mg2+-dependent synthesis of 3-6 nt cOA. We show that activation of cOA synthesis is perturbed by single nucleotide mismatches between the crRNA and target RNA at discrete positions, and that synthesis is antagonized by Csm3-mediated target RNA cleavage. Altogether, our results establish the requirements for cOA production in a model Type III CRISPR-Cas system and suggest a natural mechanism to dampen immunity once the foreign RNA is destroyed.
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Affiliation(s)
- Mohamed Nasef
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Mary C Muffly
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Andrew B Beckman
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Sebastian J Rowe
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Forrest C Walker
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Asma Hatoum-Aslan
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Jack A Dunkle
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
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26
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Chou-Zheng L, Hatoum-Aslan A. A type III-A CRISPR-Cas system employs degradosome nucleases to ensure robust immunity. eLife 2019; 8:e45393. [PMID: 30942690 PMCID: PMC6447361 DOI: 10.7554/elife.45393] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/15/2019] [Indexed: 12/16/2022] Open
Abstract
CRISPR-Cas systems provide sequence-specific immunity against phages and mobile genetic elements using CRISPR-associated nucleases guided by short CRISPR RNAs (crRNAs). Type III systems exhibit a robust immune response that can lead to the extinction of a phage population, a feat coordinated by a multi-subunit effector complex that destroys invading DNA and RNA. Here, we demonstrate that a model type III system in Staphylococcus epidermidis relies upon the activities of two degradosome-associated nucleases, PNPase and RNase J2, to mount a successful defense. Genetic, molecular, and biochemical analyses reveal that PNPase promotes crRNA maturation, and both nucleases are required for efficient clearance of phage-derived nucleic acids. Furthermore, functional assays show that RNase J2 is essential for immunity against diverse mobile genetic elements originating from plasmid and phage. Altogether, our observations reveal the evolution of a critical collaboration between two nucleic acid degrading machines which ensures cell survival when faced with phage attack.
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Affiliation(s)
- Lucy Chou-Zheng
- Department of Biological SciencesThe University of AlabamaTuscaloosaUnited States
| | - Asma Hatoum-Aslan
- Department of Biological SciencesThe University of AlabamaTuscaloosaUnited States
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27
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Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV, Cheng DR, Scott DA. Functionally diverse type V CRISPR-Cas systems. Science 2019; 363:88-91. [PMID: 30523077 PMCID: PMC11258546 DOI: 10.1126/science.aav7271] [Citation(s) in RCA: 287] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 11/20/2018] [Indexed: 01/05/2024]
Abstract
Type V CRISPR-Cas systems are distinguished by a single RNA-guided RuvC domain-containing effector, Cas12. Although effectors of subtypes V-A (Cas12a) and V-B (Cas12b) have been studied in detail, the distinct domain architectures and diverged RuvC sequences of uncharacterized Cas12 proteins suggest unexplored functional diversity. Here, we identify and characterize Cas12c, -g, -h, and -i. Cas12c, -h, and -i demonstrate RNA-guided double-stranded DNA (dsDNA) interference activity. Cas12i exhibits markedly different efficiencies of CRISPR RNA spacer complementary and noncomplementary strand cleavage resulting in predominant dsDNA nicking. Cas12g is an RNA-guided ribonuclease (RNase) with collateral RNase and single-strand DNase activities. Our study reveals the functional diversity emerging along different routes of type V CRISPR-Cas evolution and expands the CRISPR toolbox.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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28
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Foss DV, Hochstrasser ML, Wilson RC. Clinical applications of CRISPR-based genome editing and diagnostics. Transfusion 2019; 59:1389-1399. [PMID: 30600536 DOI: 10.1111/trf.15126] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-driven genome editing has rapidly transformed preclinical biomedical research by eliminating the underlying genetic basis of many diseases in model systems and facilitating the study of disease etiology. Translation to the clinic is under way, with announced or impending clinical trials utilizing ex vivo strategies for anticancer immunotherapy or correction of hemoglobinopathies. These exciting applications represent just a fraction of what is theoretically possible for this emerging technology, but many technical hurdles must be overcome before CRISPR-based genome editing technology can reach its full potential. One exciting recent development is the use of CRISPR systems for diagnostic detection of genetic sequences associated with pathogens or cancer. We review the biologic origins and functional mechanism of CRISPR systems and highlight several current and future clinical applications of genome editing.
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Affiliation(s)
- Dana V Foss
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California
| | - Megan L Hochstrasser
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California
| | - Ross C Wilson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California
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29
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Abstract
In recent years, Cas9 has revolutionized the genome-editing field and enabled a broad range of applications from basic biology to biotechnology and medicine. Cas9 specificity is dictated by base pairing of the guide RNA to the complementary DNA strand, however to initiate hybridization, a short protospacer adjacent motif (PAM) sequence is required in the vicinity of the target sequence. The PAM is recognized by the Cas9 protein and varies between Cas9s. There are thousands of type II CRISPR-Cas9 sequences available in sequence databases. To characterize the PAM recognition diversity provided by Cas9 orthologs, we developed a phylogeny-guided bioinformatics approach and streamlined our experimental procedures for Cas9 expression and RNP complex assembly using cell lysates and in vitro translation mixtures. This approach could be easily adapted for the characterization of other CRISPR-Cas nucleases that require PAM sequences and generate double-strand breaks following target recognition.
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Affiliation(s)
| | - Joshua K Young
- Department of Molecular Engineering, Corteva Agriscience™ Agriculture Division of DowDuPont™, Johnston, IA, United States
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30
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Hatoum-Aslan A. CRISPR Methods for Nucleic Acid Detection Herald the Future of Molecular Diagnostics. Clin Chem 2018; 64:1681-1683. [DOI: 10.1373/clinchem.2018.295485] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Asma Hatoum-Aslan
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL
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31
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Klotz C, Barrangou R. Engineering Components of the Lactobacillus S-Layer for Biotherapeutic Applications. Front Microbiol 2018; 9:2264. [PMID: 30333802 PMCID: PMC6176008 DOI: 10.3389/fmicb.2018.02264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/05/2018] [Indexed: 02/06/2023] Open
Abstract
Lactic acid bacteria (LAB) are frequently harnessed for the delivery of biomolecules to mucosal tissues. Several species of Lactobacillus are commonly employed for this task, of which a subset are known to possess surface-layers (S-layers). S-layers are two-dimensional crystalline arrays of repeating proteinaceous subunits that form the outermost coating of many prokaryotic cell envelopes. Their periodicity and abundance have made them a target for numerous biotechnological applications. In the following review, we examine the multi-faceted S-layer protein (Slp), and its use in both heterologous protein expression systems and mucosal vaccine delivery frameworks, through its diverse genetic components: the strong native promoter, capable of synthesizing as many as 500 Slp subunits per second; the signal peptide that stimulates robust secretion of recombinant proteins; and the structural domains, which can be harnessed for both cell surface display of foreign peptides or adhesion enhancement of a host bacterium. Although numerous studies have established vaccine platforms based on one or more components of the Lactobacillus S-layer, this area of research still remains largely in its infancy, thus this review is meant to not only highlight past works, but also advocate for the future usage of Slps in biotherapeutic research.
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Affiliation(s)
- Courtney Klotz
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC, United States
- Department of Food, Bioprocessing and 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 and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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Raper AT, Stephenson AA, Suo Z. Sharpening the Scissors: Mechanistic Details of CRISPR/Cas9 Improve Functional Understanding and Inspire Future Research. J Am Chem Soc 2018; 140:11142-11152. [PMID: 30160947 DOI: 10.1021/jacs.8b05469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interest in CRISPR/Cas9 remains high level as new applications of the revolutionary gene-editing tool continue to emerge. While key structural and biochemical findings have illuminated major steps in the enzymatic mechanism of Cas9, several important details remain unidentified or poorly characterized that may contribute to known functional limitations. Here we describe the foundation of research that has led to a fundamental understanding of Cas9 and address mechanistic uncertainties that restrict continued development of this gene-editing platform, including specificity for the protospacer adjacent motif, propensity for off-target binding and cleavage, as well as interactions with cellular components during gene editing. Discussion of these topics and considerations should inspire future research to hone this remarkable technology and advance CRISPR/Cas9 to new heights.
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Affiliation(s)
- Austin T Raper
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Anthony A Stephenson
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Zucai Suo
- Ohio State Biochemistry Program , The Ohio State University , Columbus , Ohio 43210 , United States.,The James Comprehensive Cancer Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Department of Biomedical Sciences , College of Medicine, Florida State University , Tallahassee , Florida 32306 , United States
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