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Kim DY, Lee SY, Ha HJ, Park HH. Structural basis of Cas3 activation in type I-C CRISPR-Cas system. Nucleic Acids Res 2024:gkae723. [PMID: 39180405 DOI: 10.1093/nar/gkae723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/29/2024] [Accepted: 08/07/2024] [Indexed: 08/26/2024] Open
Abstract
CRISPR-Cas systems function as adaptive immune mechanisms in bacteria and archaea and offer protection against phages and other mobile genetic elements. Among many types of CRISPR-Cas systems, Type I CRISPR-Cas systems are most abundant, with target interference depending on a multi-subunit, RNA-guided complex known as Cascade that recruits a transacting helicase nuclease, Cas3, to degrade the target. While structural studies on several other types of Cas3 have been conducted long ago, it was only recently that the structural study of Type I-C Cas3 in complex with Cascade was revealed, shedding light on how Cas3 achieve its activity in the Cascade complex. In the present study, we elucidated the first structure of standalone Type I-C Cas3 from Neisseria lactamica (NlaCas3). Structural analysis revealed that the histidine-aspartate (HD) nuclease active site of NlaCas3 was bound to two Fe2+ ions that inhibited its activity. Moreover, NlaCas3 could cleave both single-stranded and double-stranded DNA in the presence of Ni2+ or Co2+, showing the highest activity in the presence of both Ni2+ and Mg2+ ions. By comparing the structural studies of various Cas3 proteins, we determined that our NlaCas3 stays in an inactive conformation, allowing us to understand the structural changes associated with its activation and their implication.
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Affiliation(s)
- Do Yeon Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - So Yeon Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul 06974, Republic of Korea
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Roberts A, Spang D, Sanozky-Dawes R, Nethery MA, Barrangou R. Characterization of Ligilactobacillus salivarius CRISPR-Cas systems. mSphere 2024; 9:e0017124. [PMID: 38990000 PMCID: PMC11288051 DOI: 10.1128/msphere.00171-24] [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: 02/28/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Ligilactobacillus is a diverse genus among lactobacilli with phenotypes that reflect adaptation to various hosts. CRISPR-Cas systems are highly prevalent within lactobacilli, and Ligilactobacillus salivarius, the most abundant species of Ligilactobacillus, possesses both DNA- and RNA-targeting CRISPR-Cas systems. In this study, we explore the presence and functional properties of I-B, I-C, I-E, II-A, and III-A CRISPR-Cas systems in over 500 Ligilactobacillus genomes, emphasizing systems found in L. salivarius. We examined the I-E, II-A, and III-A CRISPR-Cas systems of two L. salivarius strains and observed occurrences of split cas genes and differences in CRISPR RNA maturation in native hosts. This prompted testing of the single Cas9 and multiprotein Cascade and Csm CRISPR-Cas effector complexes in a cell-free context to demonstrate the functionality of these systems. We also predicted self-targeting spacers within L. salivarius CRISPR-Cas systems and found that nearly a third of L. salivarius genomes possess unique self-targeting spacers that generally target elements other than prophages. With these two L. salivarius strains, we performed prophage induction coupled with RNA sequencing and discovered that the prophages residing within these strains are inducible and likely active elements, despite targeting by CRISPR-Cas systems. These findings deepen our comprehension of CRISPR-Cas systems in L. salivarius, further elucidating their relationship with associated prophages and providing a functional basis for the repurposing of these Cas effectors for bacterial manipulation. IMPORTANCE Ligilactobacillus salivarius is a diverse bacterial species widely used in the food and dietary supplement industries. In this study, we investigate the occurrence and diversity of their adaptive immune systems, CRISPR-Cas, in over 500 genomes. We establish their function and provide insights into their role in the interplay between the bacterial host and the predatory phages that infect them. Such findings expand our knowledge about these important CRISPR-Cas immune systems widespread across the bacterial tree of life and also provide a technical basis for the repurposing of these molecular machines for the development of molecular biology tools and the manipulation and engineering of bacteria and other life forms.
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Affiliation(s)
- Avery Roberts
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Daniel Spang
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Rosemary Sanozky-Dawes
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
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3
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Choi W, Cha S, Kim K. Navigating the CRISPR/Cas Landscape for Enhanced Diagnosis and Treatment of Wilson's Disease. Cells 2024; 13:1214. [PMID: 39056796 PMCID: PMC11274827 DOI: 10.3390/cells13141214] [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: 05/27/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system continues to evolve, thereby enabling more precise detection and repair of mutagenesis. The development of CRISPR/Cas-based diagnosis holds promise for high-throughput, cost-effective, and portable nucleic acid screening and genetic disease diagnosis. In addition, advancements in transportation strategies such as adeno-associated virus (AAV), lentiviral vectors, nanoparticles, and virus-like vectors (VLPs) offer synergistic insights for gene therapeutics in vivo. Wilson's disease (WD), a copper metabolism disorder, is primarily caused by mutations in the ATPase copper transporting beta (ATP7B) gene. The condition is associated with the accumulation of copper in the body, leading to irreversible damage to various organs, including the liver, nervous system, kidneys, and eyes. However, the heterogeneous nature and individualized presentation of physical and neurological symptoms in WD patients pose significant challenges to accurate diagnosis. Furthermore, patients must consume copper-chelating medication throughout their lifetime. Herein, we provide a detailed description of WD and review the application of novel CRISPR-based strategies for its diagnosis and treatment, along with the challenges that need to be overcome.
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Affiliation(s)
- Woong Choi
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
| | - Seongkwang Cha
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
- Neuroscience Research Institute, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul 02841, Republic of Korea;
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
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Yu T, Huang J, Huang X, Hao J, Zhang P, Guo T, Bao G, Li G. Sub-MIC antibiotics increased the fitness cost of CRISPR-Cas in Acinetobacter baumannii. Front Microbiol 2024; 15:1381749. [PMID: 39011146 PMCID: PMC11246858 DOI: 10.3389/fmicb.2024.1381749] [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: 02/05/2024] [Accepted: 06/04/2024] [Indexed: 07/17/2024] Open
Abstract
Introduction The escalating prevalence of bacterial resistance, particularly multidrug-resistant bacteria like Acinetobacter baumannii, has become a significant global public health concern. The CRISPR-Cas system, a crucial defense mechanism in bacteria against foreign genetic elements, provides a competitive advantage. Type I-Fb and Type I-Fa are two subtypes of CRISPR-Cas systems that were found in A. baumannii, and the I-Fb CRISPR-Cas system regulates antibiotic resistance in A. baumannii. However, it is noteworthy that a majority of clinical isolates of A. baumannii lack or have incomplete CRISPR-Cas systems and most of them are multidrug-resistant. In light of this, our study aimed to examine the impact of antibiotic pressure on the fitness cost of the I-Fb CRISPR-Cas system in A. baumannii. Methods and Results In the study, we conducted in vitro competition experiments to investigate the influence of sub-minimum inhibitory concentration (sub-MIC) on the CRISPR-Cas systems' fitness cost in A. baumannii. We found that the fitness cost of the CRISPR-Cas system was increased under sub-MIC conditions. The expression of CRISPR-Cas-related genes was decreased, while the conjugation frequency was increased in AB43 under sub-MIC conditions. Through metabolomic analysis, we identified that sub-MIC conditions primarily affected energy metabolism pathways. In particular, we observed increased carbon metabolism, nitrogen metabolism, and intracellular ATP. Notably, the CRISPR-Cas system demonstrated resistance to the efflux pump-mediated resistance. Furthermore, the expression of efflux pump-related genes was increased under sub-MIC conditions. Conclusion Our findings suggest that the I-Fb CRISPR-Cas system confers a significant competitive advantage in A. baumanni. However, under sub-MIC conditions, its function and the ability to inhibit the energy required for efflux pumps are reduced, resulting in an increased fitness cost and loss of competitive advantage.
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Affiliation(s)
- Ting Yu
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Department of Laboratory Medicine, Affiliated Hospital, Yangzhou University, Yangzhou, China
| | - Jiayuan Huang
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Xinyue Huang
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Jingchen Hao
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Pengyu Zhang
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Tingting Guo
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Department of Laboratory Medicine, Affiliated Hospital, Yangzhou University, Yangzhou, China
| | - Guangyu Bao
- Department of Laboratory Medicine, Affiliated Hospital, Yangzhou University, Yangzhou, China
| | - Guocai Li
- Department of Microbiology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Department of Laboratory Medicine, Affiliated Hospital, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Medical College/Guangling College, Yangzhou University, Yangzhou, China
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Wang S, Zeng X, Jiang Y, Wang W, Bai L, Lu Y, Zhang L, Tan GY. Unleashing the potential: type I CRISPR-Cas systems in actinomycetes for genome editing. Nat Prod Rep 2024. [PMID: 38888887 DOI: 10.1039/d4np00010b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Covering: up to the end of 2023Type I CRISPR-Cas systems are widely distributed, found in over 40% of bacteria and 80% of archaea. Among genome-sequenced actinomycetes (particularly Streptomyces spp.), 45.54% possess type I CRISPR-Cas systems. In comparison to widely used CRISPR systems like Cas9 or Cas12a, these endogenous CRISPR-Cas systems have significant advantages, including better compatibility, wide distribution, and ease of operation (since no exogenous Cas gene delivery is needed). Furthermore, type I CRISPR-Cas systems can simultaneously edit and regulate genes by adjusting the crRNA spacer length. Meanwhile, most actinomycetes are recalcitrant to genetic manipulation, hindering the discovery and engineering of natural products (NPs). The endogenous type I CRISPR-Cas systems in actinomycetes may offer a promising alternative to overcome these barriers. This review summarizes the challenges and recent advances in CRISPR-based genome engineering technologies for actinomycetes. It also presents and discusses how to establish and develop genome editing tools based on type I CRISPR-Cas systems in actinomycetes, with the aim of their future application in gene editing and the discovery of NPs in actinomycetes.
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Affiliation(s)
- Shuliu Wang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Xiaoqian Zeng
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Yue Jiang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering (SKLBE), School of Biotechnology, East China University of Science and Technology (ECUST), Shanghai 200237, China.
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Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024; 300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA-cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
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Affiliation(s)
- Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Kole Long
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Swarmistha Devi Aribam
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.
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Rafiq MS, Shabbir MA, Raza A, Irshad S, Asghar A, Maan MK, Gondal MA, Hao H. CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance. BioDrugs 2024; 38:387-404. [PMID: 38605260 DOI: 10.1007/s40259-024-00656-3] [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] [Accepted: 03/08/2024] [Indexed: 04/13/2024]
Abstract
Antimicrobial resistance (AMR) can potentially harm global public health. Horizontal gene transfer (HGT), which speeds up the emergence of AMR and increases the burden of drug resistance in mobile genetic elements (MGEs), is the primary method by which AMR genes are transferred across bacterial pathogens. New approaches are urgently needed to halt the spread of bacterial diseases and antibiotic resistance. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), an RNA-guided adaptive immune system, protects prokaryotes from foreign DNA like plasmids and phages. This approach may be essential in limiting horizontal gene transfer and halting the spread of antibiotic resistance. The CRISPR-Cas system has been crucial in identifying and understanding resistance mechanisms and developing novel therapeutic approaches. This review article investigates the CRISPR-Cas system's potential as a tool to combat bacterial AMR. Antibiotic-resistant bacteria can be targeted and eliminated by the CRISPR-Cas system. It has been proven to be an efficient method for removing carbapenem-resistant plasmids and regaining antibiotic susceptibility. The CRISPR-Cas system has enormous potential as a weapon against bacterial AMR. It precisely targets and eliminates antibiotic-resistant bacteria, facilitates resistance mechanism identification, and offers new possibilities in diagnostics and therapeutics.
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Affiliation(s)
- Muhammad Shahzad Rafiq
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Ahmed Raza
- Livestock and Dairy Development Department, Punjab, Pakistan
| | - Shoaib Irshad
- Livestock and Dairy Development Department, Punjab, Pakistan
| | - Andleeb Asghar
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Kashif Maan
- Department of Veterinary Surgery and Pet Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Mushtaq Ahmed Gondal
- Institute of Continuing Education and Extension, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, China.
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Sultana S, Azlan A, Mohd Desa MN, Mahyudin NA, Anburaj A. A review of CRISPR-Cas and PCR-based methods for the detection of animal species in the food chain-current challenges and future prospects. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2024; 41:213-227. [PMID: 38284970 DOI: 10.1080/19440049.2024.2304577] [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: 10/26/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024]
Abstract
Regular testing and systematic investigation play a vital role to ensure product safety. Until now, the existing food authentication techniques have been based on proteins, lipids, and nucleic acid-based assays. Among various deoxyribonucleic acid (DNA)-based methods, the recently developed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based bio-sensing is an innovative and fast-expanding technology. The CRISPR/Cas-9 is known as Clustered Regularly Interspaced Short Palindromic Repeats due to the flexibility and simplicity of the CRISPR/Cas9 site-specific editing tool has been applied in many biological research areas such as Gene therapy, cell line development, discovering mechanisms of disease, and drug discovery. Nowadays, the CRISPR-Cas system has also been introduced into food authentication via detecting DNA barcodes of poultry and livestock both in processed and unprocessed food samples. This review documents various DNA based approaches, in an accessible format. Future CRISPR technologies are forecast while challenges are outlined.
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Affiliation(s)
- Sharmin Sultana
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Azrina Azlan
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Nutrition, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- Research Centre of Excellence for Nutrition and Non-Communicable Diseases, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | | | - Nor Ainy Mahyudin
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Amaladoss Anburaj
- Centre for Aquaculture and Veterinary Science (CAVS), School of Applied Science, Temasek Polytechnic, Singapore, Singapore
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9
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Cui Y, Qu X. CRISPR-Cas systems of lactic acid bacteria and applications in food science. Biotechnol Adv 2024; 71:108323. [PMID: 38346597 DOI: 10.1016/j.biotechadv.2024.108323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/29/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) systems are widely distributed in lactic acid bacteria (LAB), contributing to their RNA-mediated adaptive defense immunity. The CRISPR-Cas-based genetic tools have exhibited powerful capability. It has been highly utilized in different organisms, accelerating the development of life science. The review summarized the components, adaptive immunity mechanisms, and classification of CRISPR-Cas systems; analyzed the distribution and characteristics of CRISPR-Cas system in LAB. The review focuses on the development of CRISPR-Cas-based genetic tools in LAB for providing latest development and future trend. The diverse and broad applications of CRISPR-Cas systems in food/probiotic industry are introduced. LAB harbor a plenty of CRISPR-Cas systems, which contribute to generate safer and more robust strains with increased resistance against bacteriophage and prevent the dissemination of plasmids carrying antibiotic-resistance markers. Furthermore, the CRISPR-Cas system from LAB could be used to exploit novel, flexible, programmable genome editing tools of native host and other organisms, resolving the limitation of genetic operation of some LAB species, increasing the important biological functions of probiotics, improving the adaptation of probiotics in complex environments, and inhibiting the growth of foodborne pathogens. The development of the genetic tools based on CRISPR-Cas system in LAB, especially the endogenous CRISPR-Cas system, will open new avenues for precise regulation, rational design, and flexible application of LAB.
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Affiliation(s)
- Yanhua Cui
- Department of Food Nutrition and Health, School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
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10
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Liu S, Liu H, Wang X, Shi L. The immune system of prokaryotes: potential applications and implications for gene editing. Biotechnol J 2024; 19:e2300352. [PMID: 38403433 DOI: 10.1002/biot.202300352] [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: 07/19/2023] [Revised: 11/30/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
Gene therapy has revolutionized the treatment of genetic diseases. Spearheading this revolution are sophisticated genome editing methods such as TALENs, ZFNs, and CRISPR-Cas, which trace their origins back to prokaryotic immune systems. Prokaryotes have developed various antiviral defense systems to combat viral attacks and the invasion of genetic elements. The comprehension of these defense mechanisms has paved the way for the development of indispensable tools in molecular biology. Among them, restriction endonuclease originates from the innate immune system of bacteria. The CRISPR-Cas system, a widely applied genome editing technology, is derived from the prokaryotic adaptive immune system. Single-base editing is a precise editing tool based on CRISPR-Cas system that involves deamination of target base. It is worth noting that prokaryotes possess deamination enzymes as part of their defense arsenal over foreign genetic material. Furthermore, prokaryotic Argonauts (pAgo) proteins, also function in anti-phage defense, play an important role in complementing the CRISPR-Cas system by addressing certain limitations it may have. Recent studies have also shed light on the significance of Retron, a reverse transcription transposon previously showed potential in genome editing, has also come to light in the realm of prokaryotic immunity. These noteworthy findings highlight the importance of studying prokaryotic immune system for advancing genome editing techniques. Here, both the origin of prokaryotic immunity underlying aforementioned genome editing tools, and potential applications of deaminase, pAgo protein and reverse transcriptase in genome editing among prokaryotes were introduced, thus emphasizing the fundamental mechanism and significance of prokaryotic immunity.
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Affiliation(s)
- Siyang Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hongling Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lei Shi
- School of Life Sciences, Chongqing University, Chongqing, China
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11
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Gencay YE, Jasinskytė D, Robert C, Semsey S, Martínez V, Petersen AØ, Brunner K, de Santiago Torio A, Salazar A, Turcu IC, Eriksen MK, Koval L, Takos A, Pascal R, Schou TS, Bayer L, Bryde T, Johansen KC, Bak EG, Smrekar F, Doyle TB, Satlin MJ, Gram A, Carvalho J, Jessen L, Hallström B, Hink J, Damholt B, Troy A, Grove M, Clube J, Grøndahl C, Haaber JK, van der Helm E, Zdravkovic M, Sommer MOA. Engineered phage with antibacterial CRISPR-Cas selectively reduce E. coli burden in mice. Nat Biotechnol 2024; 42:265-274. [PMID: 37142704 PMCID: PMC10869271 DOI: 10.1038/s41587-023-01759-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/22/2023] [Indexed: 05/06/2023]
Abstract
Antibiotic treatments have detrimental effects on the microbiome and lead to antibiotic resistance. To develop a phage therapy against a diverse range of clinically relevant Escherichia coli, we screened a library of 162 wild-type (WT) phages, identifying eight phages with broad coverage of E. coli, complementary binding to bacterial surface receptors, and the capability to stably carry inserted cargo. Selected phages were engineered with tail fibers and CRISPR-Cas machinery to specifically target E. coli. We show that engineered phages target bacteria in biofilms, reduce the emergence of phage-tolerant E. coli and out-compete their ancestral WT phages in coculture experiments. A combination of the four most complementary bacteriophages, called SNIPR001, is well tolerated in both mouse models and minipigs and reduces E. coli load in the mouse gut better than its constituent components separately. SNIPR001 is in clinical development to selectively kill E. coli, which may cause fatal infections in hematological cancer patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Lev Koval
- SNIPR BIOME ApS, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | | | | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, New York City, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Morten Otto Alexander Sommer
- SNIPR BIOME ApS, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Biosustainability, DTU Biosustain, Kongens Lyngby, Denmark.
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12
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Xu Z, Chen S, Wu W, Wen Y, Cao H. Type I CRISPR-Cas-mediated microbial gene editing and regulation. AIMS Microbiol 2023; 9:780-800. [PMID: 38173969 PMCID: PMC10758571 DOI: 10.3934/microbiol.2023040] [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: 09/10/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
There are six major types of CRISPR-Cas systems that provide adaptive immunity in bacteria and archaea against invasive genetic elements. The discovery of CRISPR-Cas systems has revolutionized the field of genetics in many organisms. In the past few years, exploitations of the most abundant class 1 type I CRISPR-Cas systems have revealed their great potential and distinct advantages to achieve gene editing and regulation in diverse microorganisms in spite of their complicated structures. The widespread and diversified type I CRISPR-Cas systems are becoming increasingly attractive for the development of new biotechnological tools, especially in genetically recalcitrant microbial strains. In this review article, we comprehensively summarize recent advancements in microbial gene editing and regulation by utilizing type I CRISPR-Cas systems. Importantly, to expand the microbial host range of type I CRISPR-Cas-based applications, these structurally complicated systems have been improved as transferable gene-editing tools with efficient delivery methods for stable expression of CRISPR-Cas elements, as well as convenient gene-regulation tools with the prevention of DNA cleavage by obviating deletion or mutation of the Cas3 nuclease. We envision that type I CRISPR-Cas systems will largely expand the biotechnological toolbox for microbes with medical, environmental and industrial importance.
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Affiliation(s)
- Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Weiyan Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yongqi Wen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Huiluo Cao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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13
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Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
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Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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14
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Santiago-Frangos A, Henriques WS, Wiegand T, Gauvin CC, Buyukyoruk M, Graham AB, Wilkinson RA, Triem L, Neselu K, Eng ET, Lander GC, Wiedenheft B. Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays. Nat Struct Mol Biol 2023; 30:1675-1685. [PMID: 37710013 PMCID: PMC10872659 DOI: 10.1038/s41594-023-01097-2] [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: 03/22/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023]
Abstract
Bacteria and archaea acquire resistance to viruses and plasmids by integrating fragments of foreign DNA into the first repeat of a CRISPR array. However, the mechanism of site-specific integration remains poorly understood. Here, we determine a 560-kDa integration complex structure that explains how Pseudomonas aeruginosa Cas (Cas1-Cas2/3) and non-Cas proteins (for example, integration host factor) fold 150 base pairs of host DNA into a U-shaped bend and a loop that protrude from Cas1-2/3 at right angles. The U-shaped bend traps foreign DNA on one face of the Cas1-2/3 integrase, while the loop places the first CRISPR repeat in the Cas1 active site. Both Cas3 proteins rotate 100 degrees to expose DNA-binding sites on either side of the Cas2 homodimer, which each bind an inverted repeat motif in the leader. Leader sequence motifs direct Cas1-2/3-mediated integration to diverse repeat sequences that have a 5'-GT. Collectively, this work reveals new DNA-binding surfaces on Cas2 that are critical for DNA folding and site-specific delivery of foreign DNA.
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Affiliation(s)
| | - William S Henriques
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Colin C Gauvin
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Murat Buyukyoruk
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Ava B Graham
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Royce A Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Lenny Triem
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Kasahun Neselu
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY, USA
| | - Edward T Eng
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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15
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Li D, Chen Y, Huang F, Wang J, Li X, Yang Y. CRISPRe: An innate transcriptional enhancer for endogenous genes in CRISPR-Cas immunity. iScience 2023; 26:107814. [PMID: 37766991 PMCID: PMC10520945 DOI: 10.1016/j.isci.2023.107814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/20/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
CRISPR-Cas system has been repurposed to the promising strategy of CRISPR-based transcriptional interference/activation (CRISPRi/CRISPRa) without eliciting DNA breaks that enables Cas complex a block for transcription initiation or elongation, which greatly expands its application fields and values. However, loss of Cas nuclease ability, especially the endogenous nuclease, may affect genome stability seriously. Here, we found a transcriptional enhancer for genes (CRISPRe) in type I-C system of industrial strain Ketogulonicigenium vulgare by maintaining the natural activity of Cas3 nuclease and introducing the specific motifs that do not trigger immunity. CRISPRe greatly improved the expression of heterologous and endogenous genes and the biosynthesis of products by facilitating transcriptional elongation. Besides, the mechanism for pyrroloquinoline quinone (PQQ) biosynthesis regulated by coupling transcriptional-translational elongation in operon was elucidated. Hence, we enrich the toolbox for CRISPR-Cas system and provide a new framework for gene regulation at transcription.
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Affiliation(s)
- Dan Li
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
- School of Liquor-making Engineering, Sichuan University Jinjiang College, Meishan 620680, China
| | - Yihong Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Fei Huang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Jianmei Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Xufeng Li
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Yi Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, China
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16
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Volke DC, Orsi E, Nikel PI. Emergent CRISPR-Cas-based technologies for engineering non-model bacteria. Curr Opin Microbiol 2023; 75:102353. [PMID: 37413959 DOI: 10.1016/j.mib.2023.102353] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) technologies brought a transformative change in the way bacterial genomes are edited, and a plethora of studies contributed to developing multiple tools based on these approaches. Prokaryotic biotechnology benefited from the implementation of such genome engineering strategies, with an increasing number of non-model bacterial species becoming genetically tractable. In this review, we summarize the recent trends in engineering non-model microbes using CRISPR-Cas technologies, discussing their potential in supporting cell factory design towards biotechnological applications. These efforts include, among other examples, genome modifications as well as tunable transcriptional regulation (both positive and negative). Moreover, we examine how CRISPR-Cas toolkits for engineering non-model organisms enabled the exploitation of emergent biotechnological processes (e.g. native and synthetic assimilation of one-carbon substrates). Finally, we discuss our slant on the future of bacterial genome engineering for domesticating non-model organisms in light of the most recent advances in the ever-expanding CRISPR-Cas field.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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17
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Domgaard H, Cahoon C, Armbrust MJ, Redman O, Jolley A, Thomas A, Jackson R. CasDinG is a 5'-3' dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity. Nucleic Acids Res 2023; 51:8115-8132. [PMID: 37395408 PMCID: PMC10450177 DOI: 10.1093/nar/gkad546] [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: 08/17/2022] [Revised: 06/05/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
CRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. Here, we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP-dependent 5'-3' DNA translocase that unwinds double-stranded (ds)DNA and RNA/DNA hybrids. The crystal structure of CasDinG reveals a superfamily 2 helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these domains, we identified the preferred PAM sequence for the type IV-A system (5'-GNAWN-3' on the 5'-side of the target) with a plasmid library and performed plasmid clearance assays with domain deletion mutants. Plasmid clearance assays demonstrated that all three domains are essential for type IV-A immunity. Protein expression and biochemical assays suggested the vFeS domain is needed for protein stability and the arch for helicase activity. However, deletion of the N-terminal domain did not impair ATPase, ssDNA binding, or helicase activities, indicating a role distinct from canonical helicase activities that structure prediction tools suggest involves interaction with dsDNA. This work demonstrates CasDinG helicase activity is essential for type IV-A CRISPR immunity as well as the yet undetermined activity of the CasDinG N-terminal domain.
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Affiliation(s)
- Hannah Domgaard
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Christian Cahoon
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Matthew J Armbrust
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Olivine Redman
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Alivia Jolley
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Aaron Thomas
- Center for Integrated Biosystems, Utah State University, Logan, UT, USA
| | - Ryan N Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
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18
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Shangguan Q, White MF. Repurposing the atypical type I-G CRISPR system for bacterial genome engineering. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001373. [PMID: 37526970 PMCID: PMC10482374 DOI: 10.1099/mic.0.001373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
The CRISPR-Cas system functions as a prokaryotic immune system and is highly diverse, with six major types and numerous sub-types. The most abundant are type I CRISPR systems, which utilize a multi-subunit effector, Cascade, and a CRISPR RNA (crRNA) to detect invading DNA species. Detection leads to DNA loading of the Cas3 helicase-nuclease, leading to long-range deletions in the targeted DNA, thus providing immunity against mobile genetic elements (MGE). Here, we focus on the type I-G system, a streamlined, 4-subunit complex with an atypical Cas3 enzyme. We demonstrate that Cas3 helicase activity is not essential for immunity against MGE in vivo and explore applications of the Thioalkalivibrio sulfidiphilus Cascade effector for genome engineering in Escherichia coli. Long-range, bidirectional deletions were observed when the lacZ gene was targeted. Deactivation of the Cas3 helicase activity dramatically altered the types of deletions observed, with small deletions flanked by direct repeats that are suggestive of microhomology mediated end joining. When donor DNA templates were present, both the wild-type and helicase-deficient systems promoted homology-directed repair (HDR), with the latter system providing improvements in editing efficiency, suggesting that a single nick in the target site may promote HDR in E. coli using the type I-G system. These findings open the way for further application of the type I-G CRISPR systems in genome engineering.
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Affiliation(s)
- Qilin Shangguan
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Malcolm F. White
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
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19
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Yigider E, Taspinar MS, Agar G. Advances in bread wheat production through CRISPR/Cas9 technology: a comprehensive review of quality and other aspects. PLANTA 2023; 258:55. [PMID: 37522927 DOI: 10.1007/s00425-023-04199-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]
Abstract
MAIN CONCLUSION This review provides a comprehensive overview of the CRISPR/Cas9 technique and the research areas of this gene editing tool in improving wheat quality. Wheat (Triticum aestivum L.), the basic nutrition for most of the human population, contributes 20% of the daily energy needed because of its, carbohydrate, essential amino acids, minerals, protein, and vitamin content. Wheat varieties that produce high yields and have enhanced nutritional quality will be required to fulfill future demands. Hexaploid wheat has A, B, and D genomes and includes three like but not identical copies of genes that influence important yield and quality. CRISPR/Cas9, which allows multiplex genome editing provides major opportunities in genome editing studies of plants, especially complicated genomes such as wheat. In this overview, we discuss the CRISPR/Cas9 technique, which is credited with bringing about a paradigm shift in genome editing studies. We also provide a summary of recent research utilizing CRISPR/Cas9 to investigate yield, quality, resistance to biotic/abiotic stress, and hybrid seed production. In addition, we provide a synopsis of the laboratory experience-based solution alternatives as well as the potential obstacles for wheat CRISPR studies. Although wheat's extensive genome and complicated polyploid structure previously slowed wheat genetic engineering and breeding progress, effective CRISPR/Cas9 systems are now successfully used to boost wheat development.
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Affiliation(s)
- Esma Yigider
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, 25240, Erzurum, Turkey
| | - Mahmut Sinan Taspinar
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, 25240, Erzurum, Turkey.
| | - Guleray Agar
- Faculty of Science, Department of Biology, Atatürk University, 25240, Erzurum, Turkey
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20
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Alkompoz AK, Hamed SM, Zaid ASA, Almangour TA, Al-Agamy MH, Aboshanab KM. Correlation of CRISPR/Cas and Antimicrobial Resistance in Klebsiella pneumoniae Clinical Isolates Recovered from Patients in Egypt Compared to Global Strains. Microorganisms 2023; 11:1948. [PMID: 37630508 PMCID: PMC10459600 DOI: 10.3390/microorganisms11081948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
The CRISPR/Cas system has been long known to interfere with the acquisition of foreign genetic elements and was recommended as a tool for fighting antimicrobial resistance. The current study aimed to explore the prevalence of the CRISPR/Cas system in Klebsiella pneumoniae isolates recovered from patients in Egypt in comparison to global strains and correlate the CRISPR/Cas to susceptibility to antimicrobial agents. A total of 181 clinical isolates were PCR-screened for cas and selected antimicrobial resistance genes (ARGs). In parallel, 888 complete genome sequences were retrieved from the NCBI database for in silico analysis. CRISPR/Cas was found in 46 (25.4%) isolates, comprising 18.8% type I-E and 6.6% type I-E*. Multidrug resistance (MDR) and extensive drug resistance (XDR) were found in 73.5% and 25.4% of the isolates, respectively. More than 95% of the CRISPR/Cas-bearing isolates were MDR (65.2%) or XDR (32.6%). No significant difference was found in the susceptibility to the tested antimicrobial agents among the CRISPR/Cas-positive and -negative isolates. The same finding was obtained for the majority of the screened ARGs. Among the published genomes, 23.2% carried CRISPR/Cas, with a higher share of I-E* (12.8%). They were confined to specific sequence types (STs), most commonly ST147, ST23, ST15, and ST14. More plasmids and ARGs were carried by the CRISPR/Cas-negative group than others, but their distribution in the two groups was not significantly different. The prevalence of some ARGs, such as blaKPC, blaTEM, and rmtB, was significantly higher among the genomes of the CRISPR/Cas-negative strains. A weak, nonsignificant positive correlation was found between the number of spacers and the number of resistance plasmids and ARGs. In conclusion, the correlation between CRISPR/Cas and susceptibility to antimicrobial agents or bearing resistance plasmids and ARGs was found to be nonsignificant. Plasmid-targeting spacers might not be naturally captured by CRISPR/Cas. Spacer match analysis is recommended to provide a clearer image of the exact behavior of CRISPR/Cas towards resistance plasmids.
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Affiliation(s)
| | - Samira M. Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October, Giza 12451, Egypt;
| | - Ahmed S. Abu Zaid
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
| | - Thamer A. Almangour
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohamed H. Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
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21
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Kauert DJ, Madariaga-Marcos J, Rutkauskas M, Wulfken A, Songailiene I, Sinkunas T, Siksnys V, Seidel R. The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex. Nat Struct Mol Biol 2023:10.1038/s41594-023-01019-2. [PMID: 37415009 DOI: 10.1038/s41594-023-01019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/11/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) sequences and CRISPR-associated (Cas) genes comprise CIRSPR-Cas effector complexes, which have revolutionized gene editing with their ability to target specific genomic loci using CRISPR RNA (crRNA) complementarity. Recognition of double-stranded DNA targets proceeds via DNA unwinding and base pairing between crRNA and the DNA target strand, forming an R-loop structure. Full R-loop extension is a prerequisite for subsequent DNA cleavage. However, the recognition of unintended sequences with multiple mismatches has limited therapeutic applications and is still poorly understood on a mechanistic level. Here we set up ultrafast DNA unwinding experiments on the basis of plasmonic DNA origami nanorotors to study R-loop formation by the Cascade effector complex in real time, close to base-pair resolution. We resolve a weak global downhill bias of the forming R-loop, followed by a steep uphill bias for the final base pairs. We also show that the energy landscape is modulated by base flips and mismatches. These findings suggest that Cascade-mediated R-loop formation occurs on short timescales in submillisecond single base-pair steps, but on longer timescales in six base-pair intermediate steps, in agreement with the structural periodicity of the crRNA-DNA hybrid.
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Affiliation(s)
- Dominik J Kauert
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | | | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Alexander Wulfken
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany.
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22
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Aldag P, Rutkauskas M, Madariaga-Marcos J, Songailiene I, Sinkunas T, Kemmerich F, Kauert D, Siksnys V, Seidel R. Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system. Nat Commun 2023; 14:3654. [PMID: 37339984 DOI: 10.1038/s41467-023-38790-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/16/2023] [Indexed: 06/22/2023] Open
Abstract
CRISPR-Cas effector complexes enable the defense against foreign nucleic acids and have recently been exploited as molecular tools for precise genome editing at a target locus. To bind and cleave their target, the CRISPR-Cas effectors have to interrogate the entire genome for the presence of a matching sequence. Here we dissect the target search and recognition process of the Type I CRISPR-Cas complex Cascade by simultaneously monitoring DNA binding and R-loop formation by the complex. We directly quantify the effect of DNA supercoiling on the target recognition probability and demonstrate that Cascade uses facilitated diffusion for its target search. We show that target search and target recognition are tightly linked and that DNA supercoiling and limited 1D diffusion need to be considered when understanding target recognition and target search by CRISPR-Cas enzymes and engineering more efficient and precise variants.
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Affiliation(s)
- Pierre Aldag
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | | | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekis ave. 7, Vilnius, 10257, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekis ave. 7, Vilnius, 10257, Lithuania
| | - Felix Kemmerich
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Dominik Kauert
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekis ave. 7, Vilnius, 10257, Lithuania.
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany.
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23
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Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N. Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment. Mol Cell 2023:S1097-2765(23)00420-3. [PMID: 37343553 DOI: 10.1016/j.molcel.2023.05.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/19/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023]
Abstract
Type IV CRISPR-Cas systems, which are primarily found on plasmids and exhibit a strong plasmid-targeting preference, are the only one of the six known CRISPR-Cas types for which the mechanistic details of their function remain unknown. Here, we provide high-resolution functional snapshots of type IV-A Csf complexes before and after target dsDNA binding, either in the absence or presence of CasDinG, revealing the mechanisms underlying CsfcrRNA complex assembly, "DWN" PAM-dependent dsDNA targeting, R-loop formation, and CasDinG recruitment. Furthermore, we establish that CasDinG, a signature DinG family helicase, harbors ssDNA-stimulated ATPase activity and ATP-dependent 5'-3' DNA helicase activity. In addition, we show that CasDinG unwinds the non-target strand (NTS) and target strand (TS) of target dsDNA from the CsfcrRNA complex. These molecular details advance our mechanistic understanding of type IV-A CRISPR-Csf function and should enable Csf complexes to be harnessed as genome-engineering tools for biotechnological applications.
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Affiliation(s)
- Ning Cui
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun-Tao Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yongrui Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yanhong Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiao-Yu Liu
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chongyuan Wang
- Faculty of Pharmaceutical Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518055, China; Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518055, China
| | - Hongda Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Ning Jia
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China.
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24
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Zimmermann A, Prieto-Vivas JE, Cautereels C, Gorkovskiy A, Steensels J, Van de Peer Y, Verstrepen KJ. A Cas3-base editing tool for targetable in vivo mutagenesis. Nat Commun 2023; 14:3389. [PMID: 37296137 PMCID: PMC10256805 DOI: 10.1038/s41467-023-39087-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
The generation of genetic diversity via mutagenesis is routinely used for protein engineering and pathway optimization. Current technologies for random mutagenesis often target either the whole genome or relatively narrow windows. To bridge this gap, we developed CoMuTER (Confined Mutagenesis using a Type I-E CRISPR-Cas system), a tool that allows inducible and targetable, in vivo mutagenesis of genomic loci of up to 55 kilobases. CoMuTER employs the targetable helicase Cas3, signature enzyme of the class 1 type I-E CRISPR-Cas system, fused to a cytidine deaminase to unwind and mutate large stretches of DNA at once, including complete metabolic pathways. The tool increases the number of mutations in the target region 350-fold compared to the rest of the genome, with an average of 0.3 mutations per kilobase. We demonstrate the suitability of CoMuTER for pathway optimization by doubling the production of lycopene in Saccharomyces cerevisiae after a single round of mutagenesis.
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Affiliation(s)
- Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Julian E Prieto-Vivas
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
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25
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Wu J, Tao Y, Deng D, Meng Z, Zhao Y. The applications of CRISPR/Cas-mediated genome editing in genetic hearing loss. Cell Biosci 2023; 13:93. [PMID: 37210555 DOI: 10.1186/s13578-023-01021-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/25/2023] [Indexed: 05/22/2023] Open
Abstract
Hearing loss (HL) can be caused by a number of different genetic factors. Non-syndromic HL refers that HL occurs as an isolated symptom in an individual, whereas syndromic HL refers that HL is associated with other symptoms or abnormalities. To date, more than 140 genes have been identified as being associated with non-syndromic HL, and approximately 400 genetic syndromes can include HL as one of the clinical symptoms. However, no gene therapeutic approaches are currently available to restore or improve hearing. Therefore, there is an urgent necessity to elucidate the possible pathogenesis of specific mutations in HL-associated genes and to investigate the promising therapeutic strategies for genetic HL. The development of the CRISPR/Cas system has revolutionized the field of genome engineering, which has become an efficacious and cost-effective tool to foster genetic HL research. Moreover, several in vivo studies have demonstrated the therapeutic efficacy of the CRISPR/Cas-mediated treatments for specific genetic HL. In this review, we briefly introduce the progress in CRISPR/Cas technique as well as the understanding of genetic HL, and then we detail the recent achievements of CRISPR/Cas technique in disease modeling and therapeutic strategies for genetic HL. Furthermore, we discuss the challenges for the application of CRISPR/Cas technique in future clinical treatments.
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Affiliation(s)
- Junhao Wu
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Yong Tao
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Di Deng
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Zhaoli Meng
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China.
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China.
| | - Yu Zhao
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital of Sichuan University, Chengdu, 610041, China.
- Department of Audiology and Speech Language Pathology, West China Hospital of Sichuan University, Chengdu, China.
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26
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McBride TM, Cameron SC, Fineran PC, Fagerlund RD. The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems. Biochem J 2023; 480:471-488. [PMID: 37052300 DOI: 10.1042/bcj20220073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 04/14/2023]
Abstract
Prokaryotes have adaptive defence mechanisms that protect them from mobile genetic elements and viral infection. One defence mechanism is called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins). There are six different types of CRISPR-Cas systems and multiple subtypes that vary in composition and mode of action. Type I and III CRISPR-Cas systems utilise multi-protein complexes, which differ in structure, nucleic acid binding and cleaving preference. The type I-D system is a chimera of type I and III systems. Recently, there has been a burst of research on the type I-D CRISPR-Cas system. Here, we review the mechanism, evolution and biotechnological applications of the type I-D CRISPR-Cas system.
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Affiliation(s)
- Tess M McBride
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Shaharn C Cameron
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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27
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Sufyan M, Daraz U, Hyder S, Zulfiqar U, Iqbal R, Eldin SM, Rafiq F, Mahmood N, Shahzad K, Uzair M, Fiaz S, Ali I. An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges. Funct Integr Genomics 2023; 23:119. [PMID: 37022538 DOI: 10.1007/s10142-023-01036-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Genome editing is a useful, adaptable, and favored technique for both functional genomics and crop enhancement. Over the years, rapidly evolving genome editing technologies, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas), transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs), have shown broad application prospects in gene function research and improvement of critical agronomic traits in many crops. These technologies have also opened up opportunities for plant breeding. These techniques provide excellent chances for the quick modification of crops and the advancement of plant science in the future. The current review describes various genome editing techniques and how they function, particularly CRISPR/Cas9 systems, which can contribute significantly to the most accurate characterization of genomic rearrangement and plant gene functions as well as the enhancement of critical traits in field crops. To accelerate the use of gene-editing technologies for crop enhancement, the speed editing strategy of gene-family members was designed. As it permits genome editing in numerous biological systems, the CRISPR technology provides a valuable edge in this regard that particularly captures the attention of scientists.
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Affiliation(s)
- Muhammad Sufyan
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Umar Daraz
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Sajjad Hyder
- Department of Botant, Government College Women University, Sialkot, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Sayed M Eldin
- Center of Research, Faculty of Engineering, Future University in Egypt, New Cairo, 11835, Egypt
| | - Farzana Rafiq
- School of Environmental Sciences and Engineering, NCEPU, Beijing, China
| | - Naveed Mahmood
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Khurram Shahzad
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Iftikhar Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh, 19120, Pakistan.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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28
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Bhatia S, Pooja, Yadav SK. CRISPR-Cas for genome editing: Classification, mechanism, designing and applications. Int J Biol Macromol 2023; 238:124054. [PMID: 36933595 DOI: 10.1016/j.ijbiomac.2023.124054] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/24/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Clustered regularly interspersed short pallindromic repeats (CRISPR) and CRISPR associated proteins (Cas) system (CRISPR-Cas) came into light as prokaryotic defence mechanism for adaptive immune response. CRISPR-Cas works by integrating short sequences of the target genome (spacers) into the CRISPR locus. The locus containing spacers interspersed repeats is further expressed into small guide CRISPR RNA (crRNA) which is then deployed by the Cas proteins to evade the target genome. Based on the Cas proteins CRISPR-Cas is classified according to polythetic system of classification. The characteristic of the CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new arenas due to which today CRISPR-Cas has evolved as cutting end technique in the field of genome editing. Here, we discuss about the evolution of CRISPR, its classification and various Cas systems including the designing and molecular mechanism of CRISPR-Cas. Applications of CRISPR-Cas as a genome editing tools are also highlighted in the areas such as agriculture, and anticancer therapy. Briefly discuss the role of CRISPR and its Cas systems in the diagnosis of COVID-19 and its possible preventive measures. The challenges in existing CRISP-Cas technologies and their potential solutions are also discussed briefly.
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Affiliation(s)
- Simran Bhatia
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India; Regional Center for Biotechnology, Faridabad, India
| | - Pooja
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India
| | - Sudesh Kumar Yadav
- Center of Innovative and applied Bioprocessing, Sector-81, Knowledge City, Mohali, India; Regional Center for Biotechnology, Faridabad, India.
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29
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Sather LM, Zamani M, Muhammed Z, Kearsley JVS, Fisher GT, Jones KM, Finan TM. A broadly distributed predicted helicase/nuclease confers phage resistance via abortive infection. Cell Host Microbe 2023; 31:343-355.e5. [PMID: 36893733 DOI: 10.1016/j.chom.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/16/2022] [Accepted: 01/11/2023] [Indexed: 03/11/2023]
Abstract
There is strong selection for the evolution of systems that protect bacterial populations from viral attack. We report a single phage defense protein, Hna, that provides protection against diverse phages in Sinorhizobium meliloti, a nitrogen-fixing alpha-proteobacterium. Homologs of Hna are distributed widely across bacterial lineages, and a homologous protein from Escherichia coli also confers phage defense. Hna contains superfamily II helicase motifs at its N terminus and a nuclease motif at its C terminus, with mutagenesis of these motifs inactivating viral defense. Hna variably impacts phage DNA replication but consistently triggers an abortive infection response in which infected cells carrying the system die but do not release phage progeny. A similar host cell response is triggered in cells containing Hna upon expression of a phage-encoded single-stranded DNA binding protein (SSB), independent of phage infection. Thus, we conclude that Hna limits phage spread by initiating abortive infection in response to a phage protein.
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Affiliation(s)
- Leah M Sather
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Maryam Zamani
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Zahed Muhammed
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Jason V S Kearsley
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
| | - Gabrielle T Fisher
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Kathryn M Jones
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Turlough M Finan
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada.
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30
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CRISPR-Cas assisted diagnostics: A broad application biosensing approach. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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31
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The genome editing revolution. Trends Biotechnol 2023; 41:396-409. [PMID: 36709094 DOI: 10.1016/j.tibtech.2022.12.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/28/2023]
Abstract
A series of spectacular scientific discoveries and technological advances in the second half of the 20th century have provided the basis for the ongoing genome editing revolution. The elucidation of structural and functional features of DNA and RNA was followed by pioneering studies on genome editing: Molecular biotechnology was born. Since then, four decades followed during which progress of scientific insights and technological methods continued at an overwhelming pace. Fundamental insights into microbial host-virus interactions led to the development of tools for genome editing using restriction enzymes or the revolutionary CRISPR-Cas technology. In this review, we provide a historical overview of milestones that led to the genome editing revolution and speculate about future trends in biotechnology.
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32
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Yang H, Zhang Y, Teng X, Hou H, Deng R, Li J. CRISPR-based nucleic acid diagnostics for pathogens. Trends Analyt Chem 2023; 160:116980. [PMID: 36818498 PMCID: PMC9922438 DOI: 10.1016/j.trac.2023.116980] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/28/2022] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
Pathogenic infection remains the primary threat to human health, such as the global COVID-19 pandemic. It is important to develop rapid, sensitive and multiplexed tools for detecting pathogens and their mutated variants, particularly the tailor-made strategies for point-of-care diagnosis allowing for use in resource-constrained settings. The rapidly evolving CRISPR/Cas systems have provided a powerful toolbox for pathogenic diagnostics via nucleic acid tests. In this review, we firstly describe the resultant promising class 2 (single, multidomain effector) and recently explored class 1 (multisubunit effector complexes) CRISPR tools. We present diverse engineering nucleic acid diagnostics based on CRISPR/Cas systems for pathogenic viruses, bacteria and fungi, and highlight the application for detecting viral variants and drug-resistant bacteria enabled by CRISPR-based mutation profiling. Finally, we discuss the challenges involved in on-site diagnostic assays and present emerging CRISPR systems and CRISPR cascade that potentially enable multiplexed and preamplification-free pathogenic diagnostics.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, 610065, China,Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China,Beijing Institute of Life Science and Technology, Beijing, 102206, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, 610065, China,Corresponding author
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China,Corresponding author
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33
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Sen D, Mukhopadhyay P. Application of CRISPR Cas systems in DNA recorders and writers. Biosystems 2023; 225:104870. [PMID: 36842456 DOI: 10.1016/j.biosystems.2023.104870] [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: 12/04/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 02/26/2023]
Abstract
The necessity to record and store biological data is increasing in due course of time. However, it is quite difficult to understand biological mechanisms and keep a track of these events in some storage mediums. DNA (deoxyribonucleic acid) is the best candidate for the storage of cellular events in the biological system. It is energy efficient as well as stable at the same time. DNA-based writers and memory devices are continually evolving and finding new avenues in terms of their wide range of applications. Among all the DNA-based storage devices that employ enzymes like recombinases, nucleases, integrases, and polymerases, one of the most popular tools used for these devices is the emerging and versatile CRISPR Cas technology. CRISPR Cas is a prokaryotic immune system that keeps a memory of viral attacks and protects prokaryotes from potential future infections. The main aim of this short review is to study such molecular recorders and writers that employ CRISPR Cas technologies and obtain an in-depth overview of the mechanisms involved and the applications of these molecular devices.
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Affiliation(s)
- Debmitra Sen
- Department of Microbiology, University of Kalyani, Nadia, West Bengal, 741235, India.
| | - Poulami Mukhopadhyay
- Department of Microbiology, Barrackpore Rastraguru Surendranath College, Barrackpore, Kolkata, West Bengal, 700120, India.
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34
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Malla RR, Middela K. CRISPR-Based Approaches for Cancer Immunotherapy. Crit Rev Oncog 2023; 28:1-14. [PMID: 38050977 DOI: 10.1615/critrevoncog.2023048723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) technology is a powerful gene editing tool that has the potential to revolutionize cancer treatment. It allows for precise and efficient editing of specific genes that drive cancer growth and progression. CRISPR-based approaches gene knock-out, which deletes specific genes or sequences of DNA within a cancer cell, and gene knock-in, which inserts new sequences of DNA into a cancer cell to identify potential targets for cancer therapy. Further, genome-wide CRISPR-Cas9-based screens identify specific markers for diagnosis of cancers. Recently, immunotherapy has become a highly efficient strategy for the treatment of cancer. The use of CRISPR in cancer immunotherapy is focused on enhancing the function of T cells, making them more effective at attacking cancer cells and inactivating the immune evasion mechanisms of cancer cells. It has the potential to generate CAR-T cells, which are T cells that have been genetically engineered to target and attack cancer cells specifically. This review uncovers the latest developments in CRISPR-based gene editing strategies and delivery of their components in cancer cells. In addition, the applications of CRISPR in cancer immune therapy are discussed. Overall, this review helps to explore the potential of CRISPR-based strategies in cancer immune therapy in clinical settings.
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Affiliation(s)
- Rama Rao Malla
- Cancer Biology Laboratory, Department of Biochemistry and Bioinformatics, School of Science, Gandhi Institute of Technology and Management (GITAM) (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India; Department of Biochemistry and Bioinformatics, School of Science, GITAM (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India
| | - Keerthana Middela
- Department of Biochemistry and Bioinformatics, School of Science, GITAM (Deemed to be University), Visakhapatnam-530045, Andhra Pradesh, India
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35
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Maloshenok LG, Abushinova GA, Ryazanova AY, Bruskin SA, Zherdeva VV. Visualizing the Nucleome Using the CRISPR–Cas9 System: From in vitro to in vivo. BIOCHEMISTRY (MOSCOW) 2023; 88:S123-S149. [PMID: 37069118 PMCID: PMC9940691 DOI: 10.1134/s0006297923140080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
One of the latest methods in modern molecular biology is labeling genomic loci in living cells using fluorescently labeled Cas protein. The NIH Foundation has made the mapping of the 4D nucleome (the three-dimensional nucleome on a timescale) a priority in the studies aimed to improve our understanding of chromatin organization. Fluorescent methods based on CRISPR-Cas are a significant step forward in visualization of genomic loci in living cells. This approach can be used for studying epigenetics, cell cycle, cellular response to external stimuli, rearrangements during malignant cell transformation, such as chromosomal translocations or damage, as well as for genome editing. In this review, we focused on the application of CRISPR-Cas fluorescence technologies as components of multimodal imaging methods for in vivo mapping of chromosomal loci, in particular, attribution of fluorescence signal to morphological and anatomical structures in a living organism. The review discusses the approaches to the highly sensitive, high-precision labeling of CRISPR-Cas components, delivery of genetically engineered constructs into cells and tissues, and promising methods for molecular imaging.
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Affiliation(s)
- Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Gerel A Abushinova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center for Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
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36
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Flusche T, Rajan R. Molecular Details of DNA Integration by CRISPR-Associated Proteins During Adaptation in Bacteria and Archaea. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1414:27-43. [PMID: 35852729 DOI: 10.1007/5584_2022_730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in bacteria and archaea, where immunological memory is retained in the CRISPR locus as short pieces of the intruding nucleic acid, termed spacers. The adaptation to new infections occurs through the integration of a new spacer into the CRISPR array. For immune protection, spacers are transcribed into CRISPR RNAs (crRNA) that are used to guide the effector nuclease of the system in sequence-dependent target cleavage. Spacers originate as a prespacer from either DNA or RNA depending on the CRISPR-Cas system being observed, and the nearly universal Cas proteins, Cas1 and Cas2, insert the prespacer into the CRISPR locus during adaptation in all systems that contain them. The mechanism of site-specific prespacer integration varies across CRISPR classes and types, and distinct differences can even be found within the same subtype. In this review, the current knowledge on the mechanisms of prespacer integration in type II-A CRISPR-Cas systems will be described. Comparisons of the currently characterized type II-A systems show that distinct mechanisms exist within different members of this subtype and are correlated to sequence-specific interactions of Cas proteins and the DNA elements present in the CRISPR array. These observations indicate that nature has fine-tuned the mechanistic details while performing the basic step of DNA integration by Cas proteins, which offers unique advantages to develop Cas1-Cas2-based biotechnology.
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Affiliation(s)
- Tamara Flusche
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, USA.
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Roberts A, Nethery MA, Barrangou R. Functional characterization of diverse type I-F CRISPR-associated transposons. Nucleic Acids Res 2022; 50:11670-11681. [PMID: 36384163 PMCID: PMC9723613 DOI: 10.1093/nar/gkac985] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/07/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
CRISPR-Cas systems generally provide adaptive immunity in prokaryotes through RNA-guided degradation of foreign genetic elements like bacteriophages and plasmids. Recently, however, transposon-encoded and nuclease-deficient CRISPR-Cas systems were characterized and shown to be co-opted by Tn7-like transposons for CRISPR RNA-guided DNA transposition. As a genome engineering tool, these CRISPR-Cas systems and their associated transposon proteins can be deployed for programmable, site-specific integration of sizable cargo DNA, circumventing the need for DNA cleavage and homology-directed repair involving endogenous repair machinery. Here, we selected a diverse set of type I-F3 CRISPR-associated transposon systems derived from Gammaproteobacteria, predicted all components essential for transposition activity, and deployed them for functionality testing within Escherichia coli. Our results demonstrate that these systems possess a significant range of integration efficiencies with regards to temperature, transposon size, and flexible PAM requirements. Additionally, our findings support the categorization of these systems into functional compatibility groups for efficient and orthogonal RNA-guided DNA integration. This work expands the CRISPR-based toolbox with new CRISPR RNA-guided DNA integrases that can be applied to complex and extensive genome engineering efforts.
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Affiliation(s)
- Avery Roberts
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC 27695, USA,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, NC 27695, USA,Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
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Patterson A, White A, Waymire E, Fleck S, Golden S, Wilkinson RA, Wiedenheft B, Bothner B. Anti-CRISPR proteins function through thermodynamic tuning and allosteric regulation of CRISPR RNA-guided surveillance complex. Nucleic Acids Res 2022; 50:11243-11254. [PMID: 36215034 DOI: 10.1093/nar/gkac841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/14/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR RNA-guided detection and degradation of foreign DNA is a dynamic process. Viruses can interfere with this cellular defense by expressing small proteins called anti-CRISPRs. While structural models of anti-CRISPRs bound to their target complex provide static snapshots that inform mechanism, the dynamics and thermodynamics of these interactions are often overlooked. Here, we use hydrogen deuterium exchange-mass spectrometry (HDX-MS) and differential scanning fluorimetry (DSF) experiments to determine how anti-CRISPR binding impacts the conformational landscape of the type IF CRISPR RNA guided surveillance complex (Csy) upon binding of two different anti-CRISPR proteins (AcrIF9 and AcrIF2). The results demonstrate that AcrIF2 binding relies on enthalpic stabilization, whereas AcrIF9 uses an entropy driven reaction to bind the CRISPR RNA-guided surveillance complex. Collectively, this work reveals the thermodynamic basis and mechanistic versatility of anti-CRISPR-mediated immune suppression. More broadly, this work presents a striking example of how allosteric effectors are employed to regulate nucleoprotein complexes.
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Affiliation(s)
- Angela Patterson
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Aidan White
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Elizabeth Waymire
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Sophie Fleck
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
| | - Sarah Golden
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Royce A Wilkinson
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Microbiology and Cell Biology Department, Montana State University, Bozeman, MT 59717, USA
| | - Brian Bothner
- Chemistry and Biochemistry Department, Montana State University, Bozeman, MT 59717, USA
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Khurana A, Sayed N, Singh V, Khurana I, Allawadhi P, Rawat PS, Navik U, Pasumarthi SK, Bharani KK, Weiskirchen R. A comprehensive overview of CRISPR/Cas 9 technology and application thereof in drug discovery. J Cell Biochem 2022; 123:1674-1698. [PMID: 36128934 DOI: 10.1002/jcb.30329] [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: 04/24/2022] [Revised: 08/13/2022] [Accepted: 09/01/2022] [Indexed: 11/07/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas technology possesses revolutionary potential to positively affect various domains of drug discovery. It has initiated a rise in the area of genetic engineering and its advantages range from classical science to translational medicine. These genome editing systems have given a new dimension to our capabilities to alter, detect and annotate specified gene sequences. Moreover, the ease, robustness and adaptability of the CRISPR/Cas9 technology have led to its extensive utilization in research areas in such a short period of time. The applications include the development of model cell lines, understanding disease mechanisms, discovering disease targets, developing transgenic animals and plants, and transcriptional modulation. Further, the technology is rapidly growing; hence, an overlook of progressive success is crucial. This review presents the current status of the CRISPR-Cas technology in a tailor-made format from its discovery to several advancements for drug discovery alongwith future trends associated with possibilities and hurdles including ethical concerns.
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Affiliation(s)
- Amit Khurana
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Hyderabad, Telangana, India
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Nilofer Sayed
- Department of Pharmacy, Pravara Rural Education Society's (P.R.E.S.'s) College of Pharmacy, Shreemati Nathibai Damodar Thackersey (SNDT) Women's University, Nashik, Maharashtra, India
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Isha Khurana
- Department of Pharmaceutical Chemistry, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh, India
| | - Prince Allawadhi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pushkar Singh Rawat
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | | | - Kala Kumar Bharani
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal, Telangana, India
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Aachen, Germany
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Yoshimi K, Takeshita K, Kodera N, Shibumura S, Yamauchi Y, Omatsu M, Umeda K, Kunihiro Y, Yamamoto M, Mashimo T. Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3. Nat Commun 2022; 13:4917. [PMID: 36042215 PMCID: PMC9427990 DOI: 10.1038/s41467-022-32618-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Type I CRISPR-Cas3 uses an RNA-guided multi Cas-protein complex, Cascade, which detects and degrades foreign nucleic acids via the helicase-nuclease Cas3 protein. Despite many studies using cryoEM and smFRET, the precise mechanism of Cas3-mediated cleavage and degradation of target DNA remains elusive. Here we reconstitute the CRISPR-Cas3 system in vitro to show how the Escherichia coli Cas3 (EcoCas3) with EcoCascade exhibits collateral non-specific single-stranded DNA (ssDNA) cleavage and target specific DNA degradation. Partial binding of EcoCascade to target DNA with tolerated mismatches within the spacer sequence, but not the PAM, elicits collateral ssDNA cleavage activity of recruited EcoCas3. Conversely, stable binding with complete R-loop formation drives EcoCas3 to nick the non-target strand (NTS) in the bound DNA. Helicase-dependent unwinding then combines with trans ssDNA cleavage of the target strand and repetitive cis cleavage of the NTS to degrade the target double-stranded DNA (dsDNA) substrate. High-speed atomic force microscopy demonstrates that EcoCas3 bound to EcoCascade repeatedly reels and releases the target DNA, followed by target fragmentation. Together, these results provide a revised model for collateral ssDNA cleavage and target dsDNA degradation by CRISPR-Cas3, furthering understanding of type I CRISPR priming and interference and informing future genome editing tools.
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Affiliation(s)
- Kazuto Yoshimi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.,Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Kohei Takeshita
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | | | - Yuko Yamauchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Mine Omatsu
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Laboratory of Macromolecular Dynamics and X-ray Crystallography, Department of Life Science, University of Hyogo, Hyogo, 678-1297, Japan
| | - Kenichi Umeda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | | | - Masaki Yamamoto
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Laboratory of Macromolecular Dynamics and X-ray Crystallography, Department of Life Science, University of Hyogo, Hyogo, 678-1297, Japan
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan. .,Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
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CRISPR-Cas in Acinetobacter baumannii Contributes to Antibiotic Susceptibility by Targeting Endogenous AbaI. Microbiol Spectr 2022; 10:e0082922. [PMID: 35938813 PMCID: PMC9430643 DOI: 10.1128/spectrum.00829-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Acinetobacter baumannii is a well-known human opportunistic pathogen in nosocomial infections, and the emergence of multidrug-resistant Acinetobacter baumannii has become a complex problem for clinical anti-infective treatments. The ways this organism obtains multidrug resistance phenotype include horizontal gene transfer and other mechanisms, such as altered targets, decreased permeability, increased enzyme production, overexpression of efflux pumps, metabolic changes, and biofilm formation. A CRISPR-Cas system generally consists of a CRISPR array and one or more operons of cas genes, which can restrict horizontal gene transfer in bacteria. Nevertheless, it is unclear how CRISPR-Cas systems regulate antibiotic resistance in Acinetobacter baumannii. Thus, we sought to assess how CRISPR-Cas affects biofilm formation, membrane permeability, efflux pump, reactive oxygen species, and quorum sensing to clarify further the mechanism of CRISPR-Cas regulation of Acinetobacter baumannii antibiotic resistance. In the clinical isolate AB43, which has a complete I-Fb CRISPR-Cas system, we discovered that the Cas3 nuclease of this type I-F CRISPR-Cas system regulates Acinetobacter baumannii quorum sensing and has a unique function in changing drug resistance. As a result of quorum sensing, synthase abaI is reduced, allowing efflux pumps to decrease, biofilm formation to become weaker, reactive oxygen species to generate, and drug resistance to decrease in response to CRISPR-Cas activity. These observations suggest that the CRISPR-Cas system targeting endogenous abaI may boost bacterial antibiotic sensitivity. IMPORTANCE CRISPR-Cas systems are vital for genome editing, bacterial virulence, and antibiotic resistance. How CRISPR-Cas systems regulate antibiotic resistance in Acinetobacter baumannii is almost wholly unknown. In this study, we reveal that the quorum sensing regulator abaI mRNA was a primary target of the I-Fb CRISPR-Cas system and the cleavage activity of Cas3 was the most critical factor in regulating abaI mRNA degradation. These results advance our understanding of how CRISPR-Cas systems inhibit drug resistance. However, the mechanism of endogenous targeting of abaI by CRISPR-Cas needs to be further explored.
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42
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Verma MK, Roychowdhury S, Sahu BD, Mishra A, Sethi KK. CRISPR-based point-of-care diagnostics incorporating Cas9, Cas12, and Cas13 enzymes advanced for SARS-CoV-2 detection. J Biochem Mol Toxicol 2022; 36:e23113. [PMID: 35642647 PMCID: PMC9347549 DOI: 10.1002/jbt.23113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022]
Abstract
An outbreak of the novel beta coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first came to light in December 2019, which has unfolded rapidly and turned out to be a global pandemic. Early prognosis of viral contamination involves speedy intervention, disorder control, and good-sized management of the spread of disease. Reverse transcription-polymerase chain reaction, considered the gold standard test for detecting nucleic acids and pathogen diagnosis, provides high sensitivity and specificity. However, reliance on high-priced equipped kits, associated reagents, and skilled personnel slow down sickness detection. Lately, the improvement of clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated protein)-based diagnostic systems has reshaped molecular diagnosis due to their low cost, simplicity, speed, efficiency, high sensitivity, specificity, and versatility, which is vital for accomplishing point-of-care diagnostics. We reviewed and summarized CRISPR-Cas-based point-of-care diagnostic strategies and research in these paintings while highlighting their characteristics and challenges for identifying SARS-CoV-2.
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Affiliation(s)
- Monika K. Verma
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Sanjana Roychowdhury
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Bidya Dhar Sahu
- Department of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Awanish Mishra
- Department of Pharmacology and ToxicologyNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
| | - Kalyan K. Sethi
- Department of Medicinal ChemistryNational Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, KamrupGuwahatiAssamIndia
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43
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Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium. Proc Natl Acad Sci U S A 2022; 119:e2205068119. [PMID: 35857876 PMCID: PMC9335239 DOI: 10.1073/pnas.2205068119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Bifidobacterium is a commensal bacterial genus ubiquitous in the human gastrointestinal tract, which is associated with a range of health benefits. The advent of CRISPR-based genome editing technologies provides opportunities to investigate the genetics of important bacteria and transcend the lack of genetic tools in bifidobacteria to study the basis for their health-promoting attributes. Here, we repurpose the endogenous type I-G CRISPR-Cas system and adopt an exogenous CRISPR base editor for genome engineering in B. animalis subsp. lactis, demonstrating that both genomic and epigenetic contexts drive editing outcomes across strains. We reprogrammed the endogenous type I-G system to screen for naturally occurring large deletions up to 27 kb and to generate a 500-bp deletion in tetW to abolish tetracycline resistance. A CRISPR-cytosine base editor was optimized to install C•G-to-T•A amber mutations to resensitize multiple B. lactis strains to tetracycline. Remarkably, we uncovered epigenetic patterns that are distributed unevenly among B. lactis strains, despite their genomic homogeneity, that may contribute to editing efficiency variability. Insights were also expanded to Bifidobacterium longum subsp. infantis to emphasize the broad relevance of these findings. This study highlights the need to develop individualized CRISPR-based genome engineering approaches for distinct bacterial strains and opens avenues for engineering of next generation probiotics.
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44
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Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin. Arch Microbiol 2022; 204:461. [DOI: 10.1007/s00203-022-03085-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/08/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
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45
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Happi Mbakam C, Lamothe G, Tremblay G, Tremblay JP. CRISPR-Cas9 Gene Therapy for Duchenne Muscular Dystrophy. Neurotherapeutics 2022; 19:931-941. [PMID: 35165856 PMCID: PMC9294086 DOI: 10.1007/s13311-022-01197-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 12/26/2022] Open
Abstract
Discovery of the CRISPR-Cas (clustered regularly interspaced short palindromic repeat, CRISPR-associated) system a decade ago has opened new possibilities in the field of precision medicine. CRISPR-Cas was initially identified in bacteria and archaea to play a protective role against foreign genetic elements during viral infections. The application of this technique for the correction of different mutations found in the Duchenne muscular dystrophy (DMD) gene led to the development of several potential therapeutic approaches for DMD patients. The mutations responsible for Duchenne muscular dystrophy mainly include exon deletions (70% of patients) and point mutations (about 30% of patients). The CRISPR-Cas 9 technology is becoming increasingly precise and is acquiring diverse functions through novel innovations such as base editing and prime editing. However, questions remain about its translation to the clinic. Current research addressing off-target editing, efficient muscle-specific delivery, immune response to nucleases, and vector challenges may eventually lead to the clinical use of the CRISPR-Cas9 technology. In this review, we present recent CRISPR-Cas9 strategies to restore dystrophin expression in vitro and in animal models of DMD.
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Affiliation(s)
- Cedric Happi Mbakam
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Gabriel Lamothe
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Guillaume Tremblay
- CHU de Québec Research Center - Laval University, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada
| | - Jacques P Tremblay
- CHU de Québec Research Center - Laval University, Québec, Canada.
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec City, Québec, Canada.
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46
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Jiang D, Zhang D, Li S, Liang Y, Zhang Q, Qin X, Gao J, Qiu J. Highly efficient genome editing in Xanthomonas oryzae pv. oryzae through repurposing the endogenous type I-C CRISPR-Cas system. MOLECULAR PLANT PATHOLOGY 2022; 23:583-594. [PMID: 34954876 PMCID: PMC8916207 DOI: 10.1111/mpp.13178] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Efficient and modular genome editing technologies that manipulate the genome of bacterial pathogens will facilitate the study of pathogenesis mechanisms. However, such methods are yet to be established for Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight. We identified a single type I-C CRISPR-Cas system in the Xoo genome and leveraged this endogenous defence system for high-efficiency genome editing in Xoo. Specifically, we developed plasmid components carrying a mini-CRISPR array, donor DNA, and a phage-derived recombination system to enable the efficient and programmable genome editing of precise deletions, insertions, base substitutions, and gene replacements. Furthermore, the type I-C CRISPR-Cas system of Xoo cleaves target DNA unidirectionally, and this can be harnessed to generate large genomic deletions up to 212 kb efficiently. Therefore, the genome-editing strategy we have developed can serve as an excellent tool for functional genomics of Xoo, and should also be applicable to other CRISPR-harbouring bacterial plant pathogens.
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Affiliation(s)
- Dandan Jiang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
| | - Dandan Zhang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Shengnan Li
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yueting Liang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
| | - Qianwei Zhang
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
| | - Xu Qin
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
| | - Jinlan Gao
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jin‐Long Qiu
- State Key Laboratory of Plant GenomicsInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijingChina
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Sun S, He Z, Jiang P, Baral R, Pandelia ME. Metal Dependence and Functional Diversity of Type I Cas3 Nucleases. Biochemistry 2022; 61:327-338. [PMID: 35184547 DOI: 10.1021/acs.biochem.1c00779] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Type I CRISPR-Cas systems provide prokaryotes with protection from parasitic genetic elements by cleaving foreign DNA. In addition, they impact bacterial physiology by regulating pathogenicity and virulence, making them key players in adaptability and evolution. The signature nuclease Cas3 is a phosphodiesterase belonging to the HD-domain metalloprotein superfamily. By directing specific metal incorporation, we map a promiscuous metal ion cofactor profile for Cas3 from Thermobifida fusca (Tf). Tf Cas3 affords significant ssDNA cleavage with four homo-dimetal centers (Fe2+, Co2+, Mn2+, and Ni2+), while the diferrous form is the most active and likely biologically relevant in vivo. Electron paramagnetic resonance (EPR) spectroscopy and Mössbauer spectroscopy show that the diiron cofactor can access three redox forms, while the diferrous form can be readily obtained with mild reductants. We further employ EPR and Mössbauer on Fe-enriched proteins to establish that Cas3″ enzymes harbor a dinuclear cofactor, which was not previously confirmed. We demonstrate that the ancillary His ligand is critical for efficient ssDNA cleavage but not for diiron assembly or small molecule hydrolysis. We further explore the ability of Cas3 to hydrolyze cyclic mononucleotides and show that Tf Cas3 hydrolyzes 2'3'-cAMP with catalytic efficiency comparable to that of the conserved virulence factor A (CvfA), an HD-domain protein hydrolyzing 2'3'-cylic phosphodiester bonds at RNA 3'-termini. Because this CvfA activity is linked to virulence regulation, Cas3 may also utilize 2'3'-cAMP hydrolysis as a possible molecular route to control virulence.
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Affiliation(s)
- Sining Sun
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Zunyu He
- Yale University, New Haven, Connecticut 06520-8055, United States
| | - Paul Jiang
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Rishika Baral
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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Yoshimi K, Takeshita K, Yamayoshi S, Shibumura S, Yamauchi Y, Yamamoto M, Yotsuyanagi H, Kawaoka Y, Mashimo T. CRISPR-Cas3-based diagnostics for SARS-CoV-2 and influenza virus. iScience 2022; 25:103830. [PMID: 35128347 PMCID: PMC8801231 DOI: 10.1016/j.isci.2022.103830] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/21/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
CRISPR-based diagnostics (CRISPR-dx), including the Cas12-based DETECTR and Cas13-based SHERLOCK Class 2 CRISPRs, have been used to detect the presence of DNA or RNA from pathogens, such as the 2009 pandemic influenza virus A (IAV) and the 2019 novel coronavirus SARS-CoV-2. Here, we describe the collateral single-stranded DNA cleavage with Class 1 type I CRISPR-Cas3 and highlight its potential for development as a Cas3-mediated rapid (within 40 min), low-cost, instrument-free detection method for SARS-CoV-2. This assay, which we call Cas3-Operated Nucleic Acid detectioN (CONAN), not only detects SARS-CoV-2 in clinical samples, but also offers specific detection of single-base-pair mutations in IAV variants. This tool allows rapid and accurate point-of-care testing for patients with suspected SARS-CoV-2 or drug-resistant IAV infections in hospitals.
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Affiliation(s)
- Kazuto Yoshimi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kohei Takeshita
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | | | - Yuko Yamauchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases and Applied Immunology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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Tan R, Krueger RK, Gramelspacher MJ, Zhou X, Xiao Y, Ke A, Hou Z, Zhang Y. Cas11 enables genome engineering in human cells with compact CRISPR-Cas3 systems. Mol Cell 2022; 82:852-867.e5. [PMID: 35051351 PMCID: PMC8964063 DOI: 10.1016/j.molcel.2021.12.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/09/2021] [Accepted: 12/21/2021] [Indexed: 11/28/2022]
Abstract
Leading CRISPR-Cas technologies employ Cas9 and Cas12 enzymes that generate RNA-guided dsDNA breaks. Yet, the most abundant microbial adaptive immune systems, Type I CRISPRs, are under-exploited for eukaryotic applications. Here, we report the adoption of a minimal CRISPR-Cas3 from Neisseria lactamica (Nla) type I-C system to create targeted large deletions in the human genome. RNP delivery of its processive Cas3 nuclease and target recognition complex Cascade can confer ∼95% editing efficiency. Unexpectedly, NlaCascade assembly in bacteria requires internal translation of a hidden component Cas11 from within the cas8 gene. Furthermore, expressing a separately encoded NlaCas11 is the key to enable plasmid- and mRNA-based editing in human cells. Finally, we demonstrate that supplying cas11 is a universal strategy to systematically implement divergent I-C, I-D, and I-B CRISPR-Cas3 editors with compact sizes, distinct PAM preferences, and guide orthogonality. These findings greatly expand our ability to engineer long-range genome edits.
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Affiliation(s)
- Renke Tan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA,These authors contributed equally
| | - Ryan K Krueger
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA,These authors contributed equally
| | - Max J Gramelspacher
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Xufei Zhou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Wentz TG, Tremblay BJM, Bradshaw M, Doxey AC, Sharma SK, Sauer JD, Pellett S. Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster. Front Microbiol 2022; 12:787726. [PMID: 35222299 PMCID: PMC8865420 DOI: 10.3389/fmicb.2021.787726] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/27/2021] [Indexed: 12/28/2022] Open
Abstract
Most strains of proteolytic group I Clostridium botulinum (G1 C. botulinum) and some strains of Clostridium sporogenes possess genes encoding botulinum neurotoxin (BoNT), a potent neuroparalytic agent. Within G1 C. botulinum, conserved bont gene clusters of three major toxin serotypes (bont/A/B/F) can be found on conjugative plasmids and/or within chromosomal pathogenicity islands. CRISPR-Cas systems enable site-specific targeting of previously encountered mobile genetic elements (MGE) such as plasmids and bacteriophage through the creation of a spacer library complementary to protospacers within the MGEs. To examine whether endogenous CRISPR-Cas systems restrict the transfer of bont gene clusters across strains we conducted a bioinformatic analysis profiling endogenous CRISPR-Cas systems from 241 G1 C. botulinum and C. sporogenes strains. Approximately 6,200 CRISPR spacers were identified across the strains and Type I-B, III-A/B/D cas genes and CRISPR array features were identified in 83% of the strains. Mapping the predicted spacers against the masked strain and RefSeq plasmid dataset identified 56,000 spacer-protospacer matches. While spacers mapped heavily to targets within bont(+) plasmids, no protospacers were identified within the bont gene clusters. These results indicate the toxin is not a direct target of CRISPR-Cas but the plasmids predominantly responsible for its mobilization are. Finally, while the presence of a CRISPR-Cas system did not reliably indicate the presence or absence of a bont gene cluster, comparative genomics across strains indicates they often occupy the same hypervariable loci common to both species, potentially suggesting similar mechanisms are involved in the acquisition and curation of both genomic features.
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Affiliation(s)
- Travis G. Wentz
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, United States,Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States,Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | | | - Marite Bradshaw
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Shashi K. Sharma
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, United States
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States,*Correspondence: Sabine Pellett,
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