1
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Liu Q, Zeng H, Wang T, Ni H, Li Y, Qian W, Fang T, Xu G. Development of RPA-Cas12a assay for rapid and sensitive detection of Pneumocystis jirovecii. BMC Microbiol 2024; 24:314. [PMID: 39187803 PMCID: PMC11345955 DOI: 10.1186/s12866-024-03440-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024] Open
Abstract
Pneumocystis jirovecii is a prevalent opportunistic fungal pathogen that can lead to life-threatening Pneumocystis pneumonia in immunocompromised individuals. Given that timely and accurate diagnosis is essential for initiating prompt treatment and enhancing patient outcomes, it is vital to develop a rapid, simple, and sensitive method for P. jirovecii detection. Herein, we exploited a novel detection method for P. jirovecii by combining recombinase polymerase amplification (RPA) of nucleic acids isothermal amplification and the trans cleavage activity of Cas12a. The factors influencing the efficiency of RPA and Cas12a-mediated trans cleavage reaction, such as RPA primer, crRNA, the ratio of crRNA to Cas12a and ssDNA reporter concentration, were optimized. Our RPA-Cas12a-based fluorescent assay can be completed within 30-40 min, comprising a 25-30 min RPA reaction and a 5-10 min trans cleavage reaction. It can achieve a lower detection threshold of 0.5 copies/µL of target DNA with high specificity. Moreover, our RPA-Cas12a-based fluorescent method was examined using 30 artificial samples and demonstrated high accuracy with a diagnostic accuracy of 93.33%. In conclusion, a novel, rapid, sensitive, and cost-effective RPA-Cas12a-based detection method was developed and demonstrates significant potential for on-site detection of P. jirovecii in resource-limited settings.
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Affiliation(s)
- Qiming Liu
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Hao Zeng
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Ting Wang
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - HongXia Ni
- Ningbo Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, China
| | - Yongdong Li
- Ningbo Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, China
| | - Weidong Qian
- School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an, 710021, China.
| | - Ting Fang
- Department of Epidemiology and Biostatistics, School of Public Health Health Science Center of Ningbo University, Ningbo, 315211, China.
| | - Guozhang Xu
- Department of Epidemiology and Biostatistics, School of Public Health Health Science Center of Ningbo University, Ningbo, 315211, China.
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2
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Jung H, Inaba Y, Banta S. CRISPR/dCas12a knock-down of Acidithiobacillus ferrooxidans electron transport chain bc 1 complexes enables enhanced metal sulfide bioleaching. J Biol Chem 2024:107703. [PMID: 39173952 DOI: 10.1016/j.jbc.2024.107703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024] Open
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that plays an important role in biogeochemical iron and sulfur cycling and is a member of the consortia used in industrial hydrometallurgical processing of copper. Metal sulfide bioleaching is catalyzed by the regeneration of ferric iron, however, bioleaching of chalcopyrite, the dominant unmined form of copper on Earth, is inhibited by surface passivation. Here, we report the implementation of CRISPR interference (CRISPRi) using the catalytically inactive Cas12a (dCas12a) in A. ferrooxidans to knockdown the expression of genes in the petI and petII operons. These operons encode bc1 complex proteins and knockdown of these genes enabled the manipulation (enhancement or repression) of iron oxidation. The petB2 gene knockdown strain enhanced iron oxidation, leading to enhanced pyrite and chalcopyrite oxidation, which correlated with reduced biofilm formation and decreased surface passivation of the minerals. These findings highlight the utility of CRISPRi/dCas12a technology for engineering A. ferrooxidans while unveiling a new strategy to manipulate and improve bioleaching efficiency.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, New York, New York
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, New York, New York
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York.
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3
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Wang Y, Xu X, Que J, Wang X, Ni W, Wu Y, Yang L, Li Y. Ratiometric Readout of Bacterial Infections via a Lyophilized CRISPR-Cas12a Sensor with Color-Changeable Bioluminescence. Anal Chem 2024; 96:12776-12783. [PMID: 39047235 DOI: 10.1021/acs.analchem.4c02114] [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: 07/27/2024]
Abstract
The healthcare burden imposed by bacterial infections demands robust and accessible diagnostic methods that can be performed outside hospitals and centralized laboratories. Here, we report Pathogen Assay with Ratiometric Luminescence (PEARL), a sensitive and easy-to-operate platform for detecting pathogenic bacteria. The PEARL leveraged a color-changeable CRISPR-Cas12a sensor and recombinase polymerase amplification to elicit ratiometric bioluminescence responses to target inputs. This platform enabled robust and visualized identification of attomolar bacteria genome deoxyribonucleic acid according to the color changes of the reactions. In addition, the components of the color-changeable Cas12a sensor could be lyophilized for 3 month storage at ambient temperature and then be fully activated with the amplicons derived from crude bacterial lysates, reducing the requirements for cold-chain storage and tedious handling steps. We demonstrated that the PEARL assay is applicable for identifying the infections caused by Pseudomonas aeruginosa in different clinical specimens, including sputa, urines, and swabs derived from wounds. These results revealed the potential of PEARL to be used by untrained personnel, which will facilitate decentralized pathogen diagnosis in community- and resource-limited regions.
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Affiliation(s)
- Yu Wang
- College of Life Sciences, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Xiaoning Xu
- College of Life Sciences, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Jinqi Que
- College of Life Sciences, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Xinyu Wang
- College of Life Sciences, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Wei Ni
- Hubei Provincial Hospital of Traditional Chinese Medicine, Hubei Province Academy of Traditional Chinese Medicine, Wuhan 430061, P. R. China
| | - Yunhua Wu
- College of Life Sciences, South-Central Minzu University, Wuhan 430074, P. R. China
| | - Liu Yang
- Hubei Provincial Hospital of Traditional Chinese Medicine, Hubei Province Academy of Traditional Chinese Medicine, Wuhan 430061, P. R. China
| | - Yong Li
- College of Life Sciences, South-Central Minzu University, Wuhan 430074, P. R. China
- Hubei Jiangxia Laboratory, Wuhan 430200, P. R. China
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4
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Vialetto E, Miele S, Goren MG, Yu J, Yu Y, Collias D, Beamud B, Osbelt L, Lourenço M, Strowig T, Brisse S, Barquist L, Qimron U, Bikard D, Beisel C. Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity. Nucleic Acids Res 2024; 52:6079-6091. [PMID: 38661215 PMCID: PMC11162776 DOI: 10.1093/nar/gkae281] [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: 07/14/2023] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials using multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae as models. Comparing different Cas nucleases, DNA-targeting nucleases outperformed RNA-targeting nucleases based on the tested targets. Focusing on AsCas12a that exhibited robust targeting across different strains, we found that the elucidated modes of escape varied widely, restraining opportunities to enhance killing. We also encountered individual guide RNAs yielding different extents of clearance across strains, which were linked to an interplay between improper gRNA folding and strain-specific DNA repair and survival. To explore features that could improve targeting across strains, we performed a genome-wide screen in different K. pneumoniae strains that yielded guide design rules and trained an algorithm for predicting guide efficiency. Finally, we showed that Cas12a antimicrobials can be exploited to eliminate K. pneumoniae when encoded in phagemids delivered by T7-like phages. Altogether, our results highlight the importance of evaluating antimicrobial activity of CRISPR antimicrobials across relevant strains and define critical parameters for efficient CRISPR-based targeting.
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Affiliation(s)
- Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Solange Miele
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Moran G Goren
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Daphne Collias
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Beatriz Beamud
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Lisa Osbelt
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
| | - Udi Qimron
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - David Bikard
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
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5
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Mohammad N, Talton L, Dalgan S, Hetzler Z, Steksova A, Wei Q. Ratiometric nonfluorescent CRISPR assay utilizing Cas12a-induced plasmid supercoil relaxation. Commun Chem 2024; 7:130. [PMID: 38851849 PMCID: PMC11162422 DOI: 10.1038/s42004-024-01214-2] [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: 12/08/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Most CRISPR-based biosensors rely on labeled reporter molecules and expensive equipment for signal readout. A recent approach quantifies analyte concentration by sizing λ DNA reporters via gel electrophoresis, providing a simple solution for label-free detection. Here, we report an alternative strategy for label-free CRISPR-Cas12a, which relies on Cas12a trans-nicking induced supercoil relaxation of dsDNA plasmid reporters to generate a robust and ratiometric readout. The ratiometric CRISPR (rCRISPR) measures the relative percentage of supercoiled plasmid DNA to the relaxed circular DNA by gel electrophoresis for more accurate target concentration quantification. This simple method is two orders of magnitude more sensitive than the typical fluorescent reporter. This self-referenced strategy solves the potential application limitations of previously demonstrated DNA sizing-based CRISPR-Dx without compromising the sensitivity. Finally, we demonstrated the applicability of rCRISPR for detecting various model DNA targets such as HPV 16 and real AAV samples, highlighting its feasibility for point-of-care CRISPR-Dx applications.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Logan Talton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Selen Dalgan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Zach Hetzler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Anastasiia Steksova
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA.
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6
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Nalefski EA, Kooistra RM, Parikh I, Hedley S, Rajaraman K, Madan D. Determinants of CRISPR Cas12a nuclease activation by DNA and RNA targets. Nucleic Acids Res 2024; 52:4502-4522. [PMID: 38477377 PMCID: PMC11077072 DOI: 10.1093/nar/gkae152] [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: 05/31/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The RNA-guided CRISPR-associated (Cas) enzyme Cas12a cleaves specific double-stranded (ds-) or single-stranded (ss-) DNA targets (in cis), unleashing non-specific ssDNA cleavage (in trans). Though this trans-activity is widely coopted for diagnostics, little is known about target determinants promoting optimal enzyme performance. Using quantitative kinetics, we show formation of activated nuclease proceeds via two steps whereby rapid binding of Cas12a ribonucleoprotein to target is followed by a slower allosteric transition. Activation does not require a canonical protospacer-adjacent motif (PAM), nor is utilization of such PAMs predictive of high trans-activity. We identify several target determinants that can profoundly impact activation times, including bases within the PAM (for ds- but not ssDNA targets) and sequences within and outside those complementary to the spacer, DNA topology, target length, presence of non-specific DNA, and ribose backbone itself, uncovering previously uncharacterized cleavage of and activation by RNA targets. The results provide insight into the mechanism of Cas12a activation, with direct implications on the role of Cas12a in bacterial immunity and for Cas-based diagnostics.
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Affiliation(s)
| | | | | | | | | | - Damian Madan
- Global Health Labs, Inc, Bellevue, WA 98007, USA
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7
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Rananaware SR, Meister KS, Shoemaker GM, Vesco EK, Sandoval LSW, Lewis JG, Bodin AP, Karalkar VN, Lange IH, Pizzano BLM, Chang M, Ahmadimashhadi MR, Flannery SJ, Nguyen LT, Wang GP, Jain PK. PAM-free diagnostics with diverse type V CRISPR-Cas systems. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24306194. [PMID: 38746294 PMCID: PMC11092703 DOI: 10.1101/2024.05.02.24306194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Type V CRISPR-Cas effectors have revolutionized molecular diagnostics by facilitating the detection of nucleic acid biomarkers. However, their dependence on the presence of protospacer adjacent motif (PAM) sites on the target double-stranded DNA (dsDNA) greatly limits their flexibility as diagnostic tools. Here we present a novel method named PICNIC that solves the PAM problem for CRISPR-based diagnostics with just a simple ∼10-min modification to contemporary CRISPR-detection protocols. Our method involves the separation of dsDNA into individual single-stranded DNA (ssDNA) strands through a high- temperature and high-pH treatment. We then detect the released ssDNA strands with diverse Cas12 enzymes in a PAM-free manner. We show the utility of PICNIC by successfully applying it for PAM-free detection with three different subtypes of the Cas12 family- Cas12a, Cas12b, and Cas12i. Notably, by combining PICNIC with a truncated 15-nucleotide spacer containing crRNA, we demonstrate PAM-independent detection of clinically important single- nucleotide polymorphisms with CRISPR. We apply this approach to detect the presence of a drug-resistant variant of HIV-1, specifically the K103N mutant, that lacks a PAM site in the vicinity of the mutation. Additionally, we successfully translate our approach to clinical samples by detecting and genotyping HCV-1a and HCV-1b variants with 100% specificity at a PAM-less site within the HCV genome. In summary, PICNIC is a simple yet groundbreaking method that enhances the flexibility and precision of CRISPR-Cas12-based diagnostics by eliminating the restriction of the PAM sequence.
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8
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Feng X, Xu R, Liao J, Zhao J, Zhang B, Xu X, Zhao P, Wang X, Yao J, Wang P, Wang X, Han W, She Q. Flexible TAM requirement of TnpB enables efficient single-nucleotide editing with expanded targeting scope. Nat Commun 2024; 15:3464. [PMID: 38658536 PMCID: PMC11043419 DOI: 10.1038/s41467-024-47697-4] [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: 07/02/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
TnpBs encoded by the IS200/IS605 family transposon are among the most abundant prokaryotic proteins from which type V CRISPR-Cas nucleases may have evolved. Since bacterial TnpBs can be programmed for RNA-guided dsDNA cleavage in the presence of a transposon-adjacent motif (TAM), these nucleases hold immense promise for genome editing. However, the activity and targeting specificity of TnpB in homology-directed gene editing remain unknown. Here we report that a thermophilic archaeal TnpB enables efficient gene editing in the natural host. Interestingly, the TnpB has different TAM requirements for eliciting cell death and for facilitating gene editing. By systematically characterizing TAM variants, we reveal that the TnpB recognizes a broad range of TAM sequences for gene editing including those that do not elicit apparent cell death. Importantly, TnpB shows a very high targeting specificity on targets flanked by a weak TAM. Taking advantage of this feature, we successfully leverage TnpB for efficient single-nucleotide editing with templated repair. The use of different weak TAM sequences not only facilitates more flexible gene editing with increased cell survival, but also greatly expands targeting scopes, and this strategy is probably applicable to diverse CRISPR-Cas systems.
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Affiliation(s)
- Xu Feng
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Ruyi Xu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jianglan Liao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jingyu Zhao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Baochang Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiaoxiao Xu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Pengpeng Zhao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiaoning Wang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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9
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Sun K, Pu L, Chen C, Chen M, Li K, Li X, Li H, Geng J. An autocatalytic CRISPR-Cas amplification effect propelled by the LNA-modified split activators for DNA sensing. Nucleic Acids Res 2024; 52:e39. [PMID: 38477342 DOI: 10.1093/nar/gkae176] [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: 08/10/2023] [Revised: 01/25/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
CRISPR-Cas systems with dual functions offer precise sequence-based recognition and efficient catalytic cleavage of nucleic acids, making them highly promising in biosensing and diagnostic technologies. However, current methods encounter challenges of complexity, low turnover efficiency, and the necessity for sophisticated probe design. To better integrate the dual functions of Cas proteins, we proposed a novel approach called CRISPR-Cas Autocatalysis Amplification driven by LNA-modified Split Activators (CALSA) for the highly efficient detection of single-stranded DNA (ssDNA) and genomic DNA. By introducing split ssDNA activators and the site-directed trans-cleavage mediated by LNA modifications, an autocatalysis-driven positive feedback loop of nucleic acids based on the LbCas12a system was constructed. Consequently, CALSA enabled one-pot and real-time detection of genomic DNA and cell-free DNA (cfDNA) from different tumor cell lines. Notably, CALSA achieved high sensitivity, single-base specificity, and remarkably short reaction times. Due to the high programmability of nucleic acid circuits, these results highlighted the immense potential of CALSA as a powerful tool for cascade signal amplification. Moreover, the sensitivity and specificity further emphasized the value of CALSA in biosensing and diagnostics, opening avenues for future clinical applications.
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Affiliation(s)
- Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 641400, China
| | - Lei Pu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
- School of Pharmacy, North Sichuan Medical College, 637000 Nanchong, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Huanqing Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Chengdu, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 641400, China
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10
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Zhang F, Wang JY, Li CL, Zhang WG. HyCas9-12aGEP: an efficient genome editing platform for Corynebacterium glutamicum. Front Bioeng Biotechnol 2024; 12:1327172. [PMID: 38532881 PMCID: PMC10963414 DOI: 10.3389/fbioe.2024.1327172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Corynebacterium glutamicum plays a crucial role as a significant industrial producer of metabolites. Despite the successful development of CRISPR-Cas9 and CRISPR-Cas12a-assisted genome editing technologies in C. glutamicum, their editing resolution and efficiency are hampered by the diverse on-target activities of guide RNAs (gRNAs). To address this problem, a hybrid CRISPR-Cas9-Cas12a genome editing platform (HyCas9-12aGEP) was developed in C. glutamicum in this study to co-express sgRNA (corresponding to SpCas9 guide RNA), crRNA (corresponding to FnCas12a guide RNA), or hfgRNA (formed by the fusion of sgRNA and crRNA). HyCas9-12aGEP improves the efficiency of mapping active gRNAs and outperforms both CRISPR-Cas9 and CRISPR-Cas12a in genome editing resolution and efficiency. In the experiment involving the deletion of the cg0697-0740 gene segment, an unexpected phenotype was observed, and HyCas9-12aGEP efficiently identified the responsible genotype from more than 40 genes. Here, HyCas9-12aGEP greatly improve our capability in terms of genome reprogramming in C. glutamicum.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | | | | | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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11
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Hsiung CC, Wilson CM, Sambold NA, Dai R, Chen Q, Misiukiewicz S, Arab A, Teyssier N, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Higher-order combinatorial chromatin perturbations by engineered CRISPR-Cas12a for functional genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.18.558350. [PMID: 37781594 PMCID: PMC10541102 DOI: 10.1101/2023.09.18.558350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting 1-3 genomic sites per cell. To develop a tool for higher-order ( > 3) combinatorial targeting of genomic sites with CRISPRi in functional genomics screens, we engineered an Acidaminococcus Cas12a variant -- referred to as mul tiplexed transcriptional interference AsCas12a (multiAsCas12a). multiAsCas12a incorporates a key mutation, R1226A, motivated by the hypothesis of nicking-induced stabilization of the ribonucleoprotein:DNA complex for improving CRISPRi activity. multiAsCas12a significantly outperforms prior state-of-the-art Cas12a variants in combinatorial CRISPRi targeting using high-order multiplexed arrays of lentivirally transduced CRISPR RNAs (crRNA), including in high-throughput pooled screens using 6-plex crRNA array libraries. Using multiAsCas12a CRISPRi, we discover new enhancer elements and dissect the combinatorial function of cis-regulatory elements. These results instantiate a group testing framework for efficiently surveying potentially numerous combinations of chromatin perturbations for biological discovery and engineering.
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12
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Zhang F, Liu ZY, Liu S, Zhang WG, Wang BB, Li CL, Xu JZ. Rapid screening of point mutations by mismatch amplification mutation assay PCR. Appl Microbiol Biotechnol 2024; 108:190. [PMID: 38305911 PMCID: PMC10837254 DOI: 10.1007/s00253-024-13036-2] [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: 02/22/2023] [Revised: 08/18/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Metabolic engineering frequently makes use of point mutation and saturation mutation library creation. At present, sequencing is the only reliable and direct technique to detect point mutation and screen saturation mutation library. In this study, mismatch amplification mutation assay (MAMA) PCR was used to detect point mutation and screen saturation mutation library. In order to fine-tune the expression of odhA encoding 2-oxoglutarate dehydrogenase E1 component, a saturating mutant library of the RBS of odhA was created in Corynebacterium glutamicum P12 based on the CRISPR-Cas2a genome editing system, which increased the L-proline production by 81.3%. MAMA PCR was used to filter out 42% of the non-mutant transformants in the mutant library, which effectively reduced the workload of the subsequent fermentation test and the number of sequenced samples. The rapid and sensitive MAMA-PCR method established in this study provides a general strategy for detecting point mutations and improving the efficiency of mutation library screening. KEY POINTS: • MAMA PCR was optimized and developed to detect point mutation. • MAMA PCR greatly improves the screening efficiency of point mutation. • Attenuation of odhA expression in P12 effectively improves proline production.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Zhen Yang Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Wei Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.
| | - Bing Bing Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Chang Lon Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Jian Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
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13
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Kruglova N, Shepelev M. Increasing Gene Editing Efficiency via CRISPR/Cas9- or Cas12a-Mediated Knock-In in Primary Human T Cells. Biomedicines 2024; 12:119. [PMID: 38255224 PMCID: PMC10813735 DOI: 10.3390/biomedicines12010119] [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: 11/27/2023] [Revised: 12/22/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
T lymphocytes represent a promising target for genome editing. They are primarily modified to recognize and kill tumor cells or to withstand HIV infection. In most studies, T cell genome editing is performed using the CRISPR/Cas technology. Although this technology is easily programmable and widely accessible, its efficiency of T cell genome editing was initially low. Several crucial improvements were made in the components of the CRISPR/Cas technology and their delivery methods, as well as in the culturing conditions of T cells, before a reasonable editing level suitable for clinical applications was achieved. In this review, we summarize and describe the aforementioned parameters that affect human T cell editing efficiency using the CRISPR/Cas technology, with a special focus on gene knock-in.
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Affiliation(s)
- Natalia Kruglova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia;
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14
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Ramesh A, Lee S, Wheeldon I. Genome Editing, Transcriptional Regulation, and Forward Genetic Screening Using CRISPR-Cas12a Systems in Yarrowia lipolytica. Methods Mol Biol 2024; 2760:169-198. [PMID: 38468089 DOI: 10.1007/978-1-0716-3658-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Class II Type V endonucleases have increasingly been adapted to develop sophisticated and easily accessible synthetic biology tools for genome editing, transcriptional regulation, and functional genomic screening in a wide range of organisms. One such endonuclease, Cas12a, presents itself as an attractive alternative to Cas9-based systems. The ability to mature its own guide RNAs (gRNAs) from a single transcript has been leveraged for easy multiplexing, and its lack of requirement of a tracrRNA element, also allows for short gRNA expression cassettes. To extend these functionalities into the industrially relevant oleaginous yeast Yarrowia lipolytica, we developed a set of CRISPR-Cas12a vectors for easy multiplexed gene knockout, repression, and activation. We further extended the utility of this CRISPR-Cas12a system to functional genomic screening by constructing a genome-wide guide library targeting every gene with an eightfold coverage. Pooled CRISPR screens conducted with this library were used to profile Cas12a guide activities and develop a machine learning algorithm that could accurately predict highly efficient Cas12a gRNA. In this protocols chapter, we first present a method by which protein coding genes may be functionally disrupted via indel formation with CRISPR-Cas12a systems. Further, we describe how Cas12a fused to a transcriptional regulator can be used in conjunction with shortened gRNA to achieve transcriptional repression or activation. Finally, we describe the design, cloning, and validation of a genome-wide library as well as a protocol for the execution of a pooled CRISPR screen, to determine guide activity profiles in a genome-wide context in Y. lipolytica. The tools and strategies discussed here expand the list of available synthetic biology tools for facile genome engineering in this industrially important host.
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Affiliation(s)
- Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Sangcheon Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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15
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Zhang Y, Kubiak AM, Bailey TS, Claessen L, Hittmeyer P, Dubois L, Theys J, Lambin P. Development of a CRISPR-Cas12a system for efficient genome engineering in clostridia. Microbiol Spectr 2023; 11:e0245923. [PMID: 37947521 PMCID: PMC10715149 DOI: 10.1128/spectrum.02459-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Continued efforts in developing the CRISPR-Cas systems will further enhance our understanding and utilization of Clostridium species. This study demonstrates the development and application of a genome-engineering tool in two Clostridium strains, Clostridium butyricum and Clostridium sporogenes, which have promising potential as probiotics and oncolytic agents. Particular attention was given to the folding of precursor crRNA and the role of this process in off-target DNA cleavage by Cas12a. The results provide the guidelines necessary for efficient genome engineering using this system in clostridia. Our findings not only expand our fundamental understanding of genome-engineering tools in clostridia but also improve this technology to allow use of its full potential in a plethora of biotechnological applications.
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Affiliation(s)
- Yanchao Zhang
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Aleksandra M. Kubiak
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Exomnis Biotech BV, Maastricht, The Netherlands
| | - Tom S. Bailey
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Luuk Claessen
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- LivingMed Biotech SRL, Liège, Belgium
| | - Philip Hittmeyer
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- LivingMed Biotech SRL, Liège, Belgium
| | - Ludwig Dubois
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Jan Theys
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Philippe Lambin
- M-Lab, Department of Precision Medicine, GROW - School of Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
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16
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Lei Z, Lian L, Zhang L, Liu C, Zhai S, Yuan X, Wei J, Liu H, Liu Y, Du Z, Gul I, Zhang H, Qin Z, Zeng S, Jia P, Du K, Deng L, Yu D, He Q, Qin P. Detection of Frog Virus 3 by Integrating RPA-CRISPR/Cas12a-SPM with Deep Learning. ACS OMEGA 2023; 8:32555-32564. [PMID: 37720737 PMCID: PMC10500685 DOI: 10.1021/acsomega.3c02929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A fast, easy-to-implement, highly sensitive, and point-of-care (POC) detection system for frog virus 3 (FV3) is proposed. Combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a, a limit of detection (LoD) of 100 aM (60.2 copies/μL) is achieved by optimizing RPA primers and CRISPR RNAs (crRNAs). For POC detection, smartphone microscopy is implemented, and an LoD of 10 aM is achieved in 40 min. The proposed system detects four positive animal-derived samples with a quantitation cycle (Cq) value of quantitative PCR (qPCR) in the range of 13 to 32. In addition, deep learning models are deployed for binary classification (positive or negative samples) and multiclass classification (different concentrations of FV3 and negative samples), achieving 100 and 98.75% accuracy, respectively. Without temperature regulation and expensive equipment, the proposed RPA-CRISPR/Cas12a combined with smartphone readouts and artificial-intelligence-assisted classification showcases the great potential for FV3 detection, specifically POC detection of DNA virus.
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Affiliation(s)
- Zhengyang Lei
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Lijin Lian
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Likun Zhang
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Changyue Liu
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Shiyao Zhai
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Xi Yuan
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Jiazhang Wei
- Department
of Otolaryngology & Head and Neck, The
People’s Hospital of Guangxi Zhuang Autonomous Region, Guangxi
Academy of Medical Sciences, 6 Taoyuan Road, Nanning, 530021, China
| | - Hong Liu
- Animal
and Plant Inspection and Quarantine Technical Centre, Shenzhen Exit and Entry Inspection and Quarantine Bureau, Shenzhen, Guangdong Province 518045, China
| | - Ying Liu
- Animal
and Plant Inspection and Quarantine Technical Centre, Shenzhen Exit and Entry Inspection and Quarantine Bureau, Shenzhen, Guangdong Province 518045, China
| | - Zhicheng Du
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Ijaz Gul
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Haihui Zhang
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Zhifeng Qin
- Animal
and Plant Inspection and Quarantine Technology Center, Shenzhen Customs, Shenzhen, Guangdong Province 518033, China
| | - Shaoling Zeng
- Animal
and Plant Inspection and Quarantine Technology Center, Shenzhen Customs, Shenzhen, Guangdong Province 518033, China
| | - Peng Jia
- Quality and
Standards Academy, Shenzhen Technology University, Shenzhen 518118, China
| | - Ke Du
- Department
of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Lin Deng
- Shenzhen
Bay Laboratory, Shenzhen 518132, China
| | - Dongmei Yu
- School
of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, Shandong 264209, China
| | - Qian He
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
| | - Peiwu Qin
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
- Tsinghua
Shenzhen International Graduate School, Institute of Biopharmaceutics and Health Engineering, Shenzhen, Guangdong Province 518055, China
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17
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Rananaware SR, Vesco EK, Shoemaker GM, Anekar SS, Sandoval LSW, Meister KS, Macaluso NC, Nguyen LT, Jain PK. Programmable RNA detection with CRISPR-Cas12a. Nat Commun 2023; 14:5409. [PMID: 37669948 PMCID: PMC10480431 DOI: 10.1038/s41467-023-41006-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Cas12a, a CRISPR-associated protein complex, has an inherent ability to cleave DNA substrates and is utilized in diagnostic tools to identify DNA molecules. We demonstrate that multiple orthologs of Cas12a activate trans-cleavage in the presence of split activators. Specifically, the PAM-distal region of the crRNA recognizes RNA targets provided that the PAM-proximal seed region has a DNA target. Our method, Split Activator for Highly Accessible RNA Analysis (SAHARA), detects picomolar concentrations of RNA without sample amplification, reverse-transcription, or strand-displacement by simply supplying a short DNA sequence complementary to the seed region. Beyond RNA detection, SAHARA outperforms wild-type CRISPR-Cas12a in specificity towards point-mutations and can detect multiple RNA and DNA targets in pooled crRNA/Cas12a arrays via distinct PAM-proximal seed DNAs. In conclusion, SAHARA is a simple, yet powerful nucleic acid detection platform based on Cas12a that can be applied in a multiplexed fashion and potentially be expanded to other CRISPR-Cas enzymes.
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Affiliation(s)
| | - Emma K Vesco
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Grace M Shoemaker
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Swapnil S Anekar
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | | | - Katelyn S Meister
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Nicolas C Macaluso
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Long T Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA
| | - Piyush K Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA.
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18
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Fei X, Lei C, Ren W, Liu X, Liu C. Regulating the trans-Cleavage Activity of CRISPR/Cas12a by Using an Elongation-Caged Single-Stranded DNA Activator and the Biosensing Applications. Anal Chem 2023; 95:12169-12176. [PMID: 37531567 DOI: 10.1021/acs.analchem.3c02471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
The CRISPR/Cas12a system exhibits extraordinary capability in the field of biosensing and molecular diagnosis due to its trans-cleavage ability. However, it is still desirable for precise control and programmable regulation of Cas12a trans-cleavage activity to promote the in-depth studies and application expansion of Cas12a-based sensing platforms. In this work, we have developed a new and robust CRISPR/Cas12a regulation mechanism by endowing the activator with the function of caging crRNA ingeniously. Specifically, we constructed an integrated elongation-caged activator (EL-activator) by extending the ssDNA activator on the 3'-end. We found that appending only about 8 nt that is complementary to the crRNA repeat region is enough to cage the crRNA spacer/repeat region, thus effectively inhibiting Cas12a trans-cleavage activity. The inner inhibition mechanism was further uncovered after a thorough investigation, demonstrating that the EL-activator works by impeding the conformation of crRNA required for Cas12a recognition and destroying its affinity with Cas12a. By further switching on the elongated moiety on the EL-activator using target biomarkers, the blocked trans-cleavage activity of Cas12a can be rapidly recovered. Finally, a versatile sensing platform was established based on the EL-activator regulation mechanism, expanding the conventional Cas12a system that only directly recognizes DNA to the direct detection of enzymes and RNA biomarkers. This work has enriched the CRISPR/Cas12a regulation toolbox and expanded its sensing applications.
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Affiliation(s)
- Xinrui Fei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Chao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Xiaoling Liu
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
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19
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Sinan S, Appleby NM, Russell R. Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550589. [PMID: 37546762 PMCID: PMC10402064 DOI: 10.1101/2023.07.25.550589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a in vitro, and we measured the contributions of distinct regions of the pre-crRNA to this reaction. We find that the pre-crRNA binds rapidly and extraordinarily tightly to Cas12a (Kd = 0.6 pM), such that pre-crRNA binding is fully rate limiting for processing and therefore determines the specificity of Cas12a for different pre-crRNAs. The guide sequence contributes 10-fold to the affinities of both the precursor and mature forms of the crRNA, while deletion of an upstream sequence had no significant effect on affinity of the pre-crRNA. After processing, the mature crRNA remains very tightly bound to Cas12a, with a half-life of ~1 day and a Kd value of 60 pM. Addition of a 5'-phosphoryl group, which is normally lost during the processing reaction as the scissile phosphate, tightens binding of the mature crRNA by ~10-fold by accelerating binding and slowing dissociation. Using a direct competition assay, we found that pre-crRNA binding specificity is robust to other changes in RNA sequence, including tested changes in the guide sequence, addition of a 3' extension, and secondary structure within the guide region. Together our results provide a quantitative framework for pre-crRNA binding and processing by Cas12a and suggest strategies for optimizing crRNA design in some genome editing applications.
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Affiliation(s)
- Selma Sinan
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| | - Nathan M. Appleby
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712
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20
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Patinios C, de Vries ST, Diallo M, Lanza L, Verbrugge PLJVQ, López-Contreras AM, van der Oost J, Weusthuis RA, Kengen SWM. Multiplex genome engineering in Clostridium beijerinckii NCIMB 8052 using CRISPR-Cas12a. Sci Rep 2023; 13:10153. [PMID: 37349508 PMCID: PMC10287719 DOI: 10.1038/s41598-023-37220-y] [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: 02/15/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023] Open
Abstract
Clostridium species are re-emerging as biotechnological workhorses for industrial acetone-butanol-ethanol production. This re-emergence is largely due to advances in fermentation technologies but also due to advances in genome engineering and re-programming of the native metabolism. Several genome engineering techniques have been developed including the development of numerous CRISPR-Cas tools. Here, we expanded the CRISPR-Cas toolbox and developed a CRISPR-Cas12a genome engineering tool in Clostridium beijerinckii NCIMB 8052. By controlling the expression of FnCas12a with the xylose-inducible promoter, we achieved efficient (25-100%) single-gene knockout of five C. beijerinckii NCIMB 8052 genes (spo0A, upp, Cbei_1291, Cbei_3238, Cbei_3832). Moreover, we achieved multiplex genome engineering by simultaneously knocking out the spo0A and upp genes in a single step with an efficiency of 18%. Finally, we showed that the spacer sequence and position in the CRISPR array can affect the editing efficiency outcome.
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Affiliation(s)
- Constantinos Patinios
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Stijn T de Vries
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Mamou Diallo
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Bioconversion Group, Wageningen Food and Biobased Research, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Lucrezia Lanza
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Pepijn L J V Q Verbrugge
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ana M López-Contreras
- Bioconversion Group, Wageningen Food and Biobased Research, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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21
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Xu J, Bai X, Zhang X, Yuan B, Lin L, Guo Y, Cui Y, Liu J, Cui H, Ren X, Wang J, Yuan Y. Development and application of DETECTR-based rapid detection for pathogenic Bacillusanthracis. Anal Chim Acta 2023; 1247:340891. [PMID: 36781250 DOI: 10.1016/j.aca.2023.340891] [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: 10/26/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/02/2023]
Abstract
Bacillus anthracis (B. anthracis) is a gram-positive bacterium responsible for the acute disease anthrax. Rapid and reliable identification of pathogenic B. anthracis is important in the detection of natural infectious disease cases or bio-threats. Herein, a DNA endonuclease targeted CRISPR trans reporter (DETECTR) detection platform based on recombinase polymerase amplification (RPA) was studied. The DETECTR system targeted three sequences from B. anthracis (the BA_5345 chromosomal specific marker, the protective antigen gene pag A from pXO1 plasmid and the capsule-biosynthesis-related gene cap A from pXO2 plasmid). We developed a rapid (<40 min), easy-to-implement and accurate identification method for of B. anthracis nucleic acid with near two-copies sensitivity. The combination of tripartite primer sets is effective for the reliable identification of B. anthracis but also for fast screening of pathogenic strains. More importantly, DETECTR correctly detected simulated clinical blood samples and firstly detected positive samples collected from the location of world War-II site, preserved at north-east China (45°36'55.940″ N, 126°38'33.738″ E) with high sensitivity and specificity. Our study provides insight into the DETECTR-based detection of B. anthracis. We present a novel screening and diagnostic option for pathogenic B. anthracis that can be performed on a user-friendly portable device. Based on its proven reliability, sensitivity, specificity and simplicity, our proposed method can be readily adapted to detect pathogenic B. anthracis, anthrax and biothreats.
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Affiliation(s)
- Jianhao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Xinru Bai
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Lei Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Jinxiong Liu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Hongyu Cui
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Xiangang Ren
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150009, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
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22
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Collias D, Vialetto E, Yu J, Co K, Almási ÉDH, Rüttiger AS, Achmedov T, Strowig T, Beisel CL. Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria. Nat Commun 2023; 14:680. [PMID: 36754958 PMCID: PMC9908933 DOI: 10.1038/s41467-023-36283-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
Bacterial genome editing commonly relies on chromosomal cleavage with Cas nucleases to counter-select against unedited cells. However, editing normally requires efficient recombination and high transformation efficiencies, which are unavailable in most strains. Here, we show that systematically attenuating DNA targeting activity enables RecA-mediated repair in different bacteria, allowing chromosomal cleavage to drive genome editing. Attenuation can be achieved by altering the format or expression strength of guide (g)RNAs; using nucleases with reduced cleavage activity; or engineering attenuated gRNAs (atgRNAs) with disruptive hairpins, perturbed nuclease-binding scaffolds, non-canonical PAMs, or guide mismatches. These modifications greatly increase cell counts and even improve the efficiency of different types of edits for Cas9 and Cas12a in Escherichia coli and Klebsiella oxytoca. We further apply atgRNAs to restore ampicillin sensitivity in Klebsiella pneumoniae, establishing a resistance marker for genetic studies. Attenuating DNA targeting thus offers a counterintuitive means to achieve CRISPR-driven editing across bacteria.
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Affiliation(s)
- Daphne Collias
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 27695, Raleigh, NC, USA
| | - Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Khoa Co
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Éva D H Almási
- Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - Ann-Sophie Rüttiger
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Tatjana Achmedov
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany.
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 27695, Raleigh, NC, USA.
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany.
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23
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Bennis NX, Anderson JP, Kok SMC, Daran JMG. Expanding the genome editing toolbox of Saccharomyces cerevisiae with the endonuclease ErCas12a. FEMS Yeast Res 2023; 23:foad043. [PMID: 37791490 PMCID: PMC10583194 DOI: 10.1093/femsyr/foad043] [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: 07/04/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023] Open
Abstract
ErCas12a is a class 2 type V CRISPR-Cas nuclease isolated from Eubacterium rectale with attractive fundamental characteristics, such as RNA self-processing capability, and lacks reach-through royalties typical for Cas nucleases. This study aims to develop a ErCas12a-mediated genome editing tool applicable in the model yeast Saccharomyces cerevisiae. The optimal design parameters for ErCas12a editing in S. cerevisiae were defined as a 21-nt spacer flanked by 19 nt direct repeats expressed from either RNApolII or III promoters, achieving near 100% editing efficiencies in commonly targeted genomic locations. To be able to transfer the ErCas12a genome editing tool to different strain lineages, a transportable platform plasmid was constructed and evaluated for its genome editing efficiency. Using an identical crRNA expression design, the transportable ErCas12a genome editing tool showed lower efficiency when targeting the ADE2 gene. In contrast to genomic Ercas12a expression, episomal expression of Ercas12a decreases maximum specific growth rate on glucose, indicating ErCas12a toxicity at high expression levels. Moreover, ErCas12a processed a multispacer crRNA array using the RNA self-processing capability, which allowed for simultaneous editing of multiple chromosomal locations. ErCas12a is established as a valuable addition to the genetic toolbox for S. cerevisiae.
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Affiliation(s)
- Nicole X Bennis
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627 HZ Delft, The Netherlands
| | - Jonah P Anderson
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627 HZ Delft, The Netherlands
| | - Siebe M C Kok
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627 HZ Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2627 HZ Delft, The Netherlands
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24
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Qian W, Wang X, Huang J, Liu J, Chen S, Wang T, Zhang D, Li Y. Sensitive and rapid RT-RPA-Cas12a-mediated detection method capable of human rhinovirus A and/or C species by targeting VP4. Virus Res 2023; 323:199001. [PMID: 36375713 PMCID: PMC10194307 DOI: 10.1016/j.virusres.2022.199001] [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: 08/27/2022] [Revised: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Human rhinovirus (HRV), the main etiologic agent of the common cold, is responsible for significant morbidity, medical costs, and the loss of productivity in the workplace and school. To prevent the spread of HRV, accurate, low-cost and rapid diagnostics of HRV is crucial for identifying those at-risk for the illness associated with HRV, with the most frequently detected species, including HRV species A (HRV-A) and C (HRV-C). Here, a novel HRV-A and/or HRV-C molecular diagnostic assay that integrates reverse-transcription recombinase polymerase amplification assay (RT-RPA) amplification with CRISPR/Cas12a detection, with the result readout using a fluorescence detector or lateral flow strip (LFS). The established assay could be completed within 50 min without complex instruments and skilled technicians. The limit of detection of the RT-RPA-Cas12a-mediated real-time fluorescence or LFS assay could reach 0.1 copy/μl, and 0.5 copy/μl for the end-point fluorescence assay with a UV light illuminator readout, respectively. Meanwhile, the assay demonstrates excellent specificity without cross-reactivity to non-target viruses. Furthermore, they were appraised using 80 clinical samples, and RT-RPA-Cas12a-mediated fluorescence or LFS assay displayed high-accuracy with positive and negative predictive agreement of 96.7%, 95% and 100%, respectively. Taken together, the RT-RPA-Cas12a-mediated assay is a rapid, sensitive, and specific detection tool for routine and on-site detection method for HRV-A and/or HRV-C infections, and shows great promise for use in resource-poor or constrained settings.
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Affiliation(s)
- Weidong Qian
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, PR China
| | - Xuefei Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, PR China
| | - Jie Huang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, PR China
| | - Jian Liu
- Shanghai Animal Disease Prevention and Control Center, Shanghai 201103, PR China
| | - Si Chen
- University of Shenzhen, Shenzhen 518052, PR China
| | - Ting Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, PR China
| | - Dandan Zhang
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China.
| | - Yongdong Li
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo 315010, PR China.
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25
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Gawlitt S, Liao C, Achmedov T, Beisel CL. Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint. RNA Biol 2023; 20:666-680. [PMID: 37654098 PMCID: PMC10478742 DOI: 10.1080/15476286.2023.2247247] [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] [Revised: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
CRISPR technologies comprising a Cas nuclease and a guide RNA (gRNA) can utilize multiple gRNAs to enact multi-site editing or regulation in the same cell. Nature devised a highly compact means of encoding gRNAs in the form of CRISPR arrays composed of conserved repeats separated by targeting spacers. However, the capacity to acquire new spacers keeps the arrays longer than necessary for CRISPR technologies. Here, we show that CRISPR arrays utilized by the Cas9 nuclease can be shortened without compromising and sometimes even enhancing targeting activity. Using multiplexed gene repression in E. coli, we found that each region could be systematically shortened to varying degrees before severely compromising targeting activity. Surprisingly, shortening some spacers yielded enhanced targeting activity, which was linked to folding of the transcribed array prior to processing. Overall, shortened CRISPR-Cas9 arrays can facilitate multiplexed editing and gene regulation from a smaller DNA footprint across many bacterial applications of CRISPR technologies.
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Affiliation(s)
- Sandra Gawlitt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Tatjana Achmedov
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Chase L. Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
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26
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Kuzmin AA, Tomilin AN. Building Blocks of Artificial CRISPR-Based Systems beyond Nucleases. Int J Mol Sci 2022; 24:ijms24010397. [PMID: 36613839 PMCID: PMC9820447 DOI: 10.3390/ijms24010397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Tools developed in the fields of genome engineering, precise gene regulation, and synthetic gene networks have an increasing number of applications. When shared with the scientific community, these tools can be used to further unlock the potential of precision medicine and tissue engineering. A large number of different genetic elements, as well as modifications, have been used to create many different systems and to validate some technical concepts. New studies have tended to optimize or improve existing elements or approaches to create complex synthetic systems, especially those based on the relatively new CRISPR technology. In order to maximize the output of newly developed approaches and to move from proof-of-principle experiments to applications in regenerative medicine, it is important to navigate efficiently through the vast number of genetic elements to choose those most suitable for specific needs. In this review, we have collected information regarding the main genetic elements and their modifications, which can be useful in different synthetic systems with an emphasis of those based on CRISPR technology. We have indicated the most suitable elements and approaches to choose or combine in planning experiments, while providing their deeper understanding, and have also stated some pitfalls that should be avoided.
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27
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Wu WY, Mohanraju P, Liao C, Adiego-Pérez B, Creutzburg SCA, Makarova KS, Keessen K, Lindeboom TA, Khan TS, Prinsen S, Joosten R, Yan WX, Migur A, Laffeber C, Scott DA, Lebbink JHG, Koonin EV, Beisel CL, van der Oost J. The miniature CRISPR-Cas12m effector binds DNA to block transcription. Mol Cell 2022; 82:4487-4502.e7. [PMID: 36427491 DOI: 10.1016/j.molcel.2022.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 08/01/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022]
Abstract
CRISPR-Cas are prokaryotic adaptive immune systems. Cas nucleases generally use CRISPR-derived RNA guides to specifically bind and cleave DNA or RNA targets. Here, we describe the experimental characterization of a bacterial CRISPR effector protein Cas12m representing subtype V-M. Despite being less than half the size of Cas12a, Cas12m catalyzes auto-processing of a crRNA guide, recognizes a 5'-TTN' protospacer-adjacent motif (PAM), and stably binds a guide-complementary double-stranded DNA (dsDNA). Cas12m has a RuvC domain with a non-canonical catalytic site and accordingly is incapable of guide-dependent cleavage of target nucleic acids. Despite lacking target cleavage activity, the high binding affinity of Cas12m to dsDNA targets allows for interference as demonstrated by its ability to protect bacteria against invading plasmids through silencing invader transcription and/or replication. Based on these molecular features, we repurposed Cas12m by fusing it to a cytidine deaminase that resulted in base editing within a distinct window.
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Affiliation(s)
- Wen Y Wu
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Belén Adiego-Pérez
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Sjoerd C A Creutzburg
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Kira S Makarova
- National Centre for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Karlijn Keessen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Timon A Lindeboom
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Tahseen S Khan
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Stijn Prinsen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Rob Joosten
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | | | - Anzhela Migur
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Charlie Laffeber
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | | | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands; Department of Radiation Oncology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Eugene V Koonin
- National Centre for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
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28
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Naranitus P, Aiamsa-At P, Sukonta T, Hannanta-Anan P, Chaijarasphong T. Smartphone-compatible, CRISPR-based platforms for sensitive detection of acute hepatopancreatic necrosis disease in shrimp. JOURNAL OF FISH DISEASES 2022; 45:1805-1816. [PMID: 35946585 DOI: 10.1111/jfd.13702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Acute Hepatopancreatic Necrosis Disease (AHPND), caused by bacterial isolates expressing PirAB binary toxins, represents the severest and most economically destructive disease affecting penaeid shrimp. Its rapid disease progression and associated massive mortalities call for vigilant monitoring and early diagnosis, but molecular detection methods that simultaneously satisfy the requirements of sensitivity, specificity, and portability are still scarce. In this work, the CRISPR-Cas12a technology was harnessed for the development of two fluorescent assays compatible with naked-eye visualization. The first assay, AP4-Cas12a, was based on the OIE-recommended AP4 two-tubed nested PCR method and was designed to bypass the time-consuming and potentially hazardous agarose gel electrophoresis step. Using AP4-Cas12a, the detection limit of 10 copies per reaction could be achieved within less than 30 minutes post-PCR. The second assay, RPA-Cas12a, utilized recombinase polymerase amplification (RPA) to rapidly and isothermally amplify the target DNA, followed by amplicon detection by Cas12a, resulting in a protocol that can be completed in less than an hour at a constant temperature of 37°C. The detection limit of RPA-Cas12a is 100 copies of plasmid DNA or 100 fg of bacterial genomic DNA per reaction. Importantly, we validated that both assays are compatible with a previously reported smartphone-based device for facile visualization of fluorescence, thereby providing an affordable option that requires less consumables than lateral flow detection. Using this portable device for readouts, the AP4-Cas12a and RPA-Cas12a methods showed excellent concordance with the AP4-agarose gel electrophoresis approach in the evaluation of clinical samples. Therefore, the developed Cas12a assays have the potential to streamline both in-laboratory and onsite diagnosis of AHPND.
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Affiliation(s)
- Punyaporn Naranitus
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Praphutson Aiamsa-At
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanwarat Sukonta
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimkhuan Hannanta-Anan
- Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Thawatchai Chaijarasphong
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
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29
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CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae. Nat Commun 2022; 13:7168. [PMID: 36418866 PMCID: PMC9684475 DOI: 10.1038/s41467-022-34736-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR-Cas mediated genome engineering has revolutionized functional genomics. However, understanding of DNA repair following Cas-mediated DNA cleavage remains incomplete. Using Cas12a ribonucleoprotein genome editing in the fungal pathogen, Magnaporthe oryzae, we detail non-canonical DNA repair outcomes from hundreds of transformants. Sanger and nanopore sequencing analysis reveals significant variation in DNA repair profiles, ranging from small INDELs to kilobase size deletions and insertions. Furthermore, we find the frequency of DNA repair outcomes varies between loci. The results are not specific to the Cas-nuclease or selection procedure. Through Ku80 deletion analysis, a key protein required for canonical non-homologous end joining, we demonstrate activity of an alternative end joining mechanism that creates larger DNA deletions, and uses longer microhomology compared to C-NHEJ. Together, our results suggest preferential DNA repair pathway activity in the genome that can create different mutation profiles following repair, which could create biased genome variation and impact genome engineering and genome evolution.
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30
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Wu L, Wang X, Wu X, Xu S, Liu M, Cao X, Tang T, Huang X, Huang H. MnO 2 Nanozyme-Mediated CRISPR-Cas12a System for the Detection of SARS-CoV-2. ACS APPLIED MATERIALS & INTERFACES 2022; 14:50534-50542. [PMID: 36301087 PMCID: PMC9631339 DOI: 10.1021/acsami.2c14497] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
The CRISPR-Cas system was developed into a molecular diagnostic tool with high sensitivity, low cost, and high specificity in recent years. Colorimetric assays based on nanozymes offer an attractive point-of-care testing method for their low cost of use and user-friendly operation. Here, a MnO2 nanozyme-mediated CRISPR-Cas12a system was instituted to detect SARS-CoV-2. MnO2 nanorods linked to magnetic beads via a single-stranded DNA (ssDNA) linker used as an oxidase-like nanozyme inducing the color change of 3,3',5,5'-tetramethylbenzidine, which can be distinguished by the naked eye. The detection buffer color will change when the Cas12a is activated by SARS-CoV-2 and indiscriminately cleave the linker ssDNA. The detection limit was 10 copies per microliter and showed no cross-reaction with other coronaviruses. The nanozyme-mediated CRISPR-Cas12a system shows high selectivity and facile operation, with great potential for molecular diagnosis in point-of-care testing applications.
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Affiliation(s)
- Lina Wu
- School of Food Science and Pharmaceutical Engineering,
Nanjing Normal University, Nanjing210023,
People’s Republic of China
- Zhejiang Laboratory,
Hangzhou311100, People’s Republic of China
| | - Xinjie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern
Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs,
Agricultural Genomics Institute at Shenzhen, Chinese Academy of
Agricultural Sciences, Shenzhen, 518120, People’s Republic
of China
| | - Xiangchuan Wu
- School of Food Science and Pharmaceutical Engineering,
Nanjing Normal University, Nanjing210023,
People’s Republic of China
| | - Shiqi Xu
- School of Food Science and Pharmaceutical Engineering,
Nanjing Normal University, Nanjing210023,
People’s Republic of China
| | - Ming Liu
- State Key Laboratory of Respiratory Disease, National
Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory
Health, The First Affiliated Hospital, Guangzhou Medical
University, Guangzhou510120, China
| | - Xizhong Cao
- State Key Laboratory of Respiratory Disease, National
Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory
Health, The First Affiliated Hospital, Guangzhou Medical
University, Guangzhou510120, China
| | - Taishan Tang
- State Key Laboratory of Respiratory Disease, National
Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory
Health, The First Affiliated Hospital, Guangzhou Medical
University, Guangzhou510120, China
| | - Xingxu Huang
- Zhejiang Laboratory,
Hangzhou311100, People’s Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering,
Nanjing Normal University, Nanjing210023,
People’s Republic of China
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31
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Hang XM, Wang HY, Liu PF, Zhao KR, Wang L. Cas12a-assisted RTF-EXPAR for accurate, rapid and simple detection of SARS-CoV-2 RNA. Biosens Bioelectron 2022; 216:114683. [PMID: 36088673 PMCID: PMC9444317 DOI: 10.1016/j.bios.2022.114683] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/09/2022] [Accepted: 08/31/2022] [Indexed: 11/02/2022]
Abstract
Developing highly accurate and simple approaches to rapidly identify and isolate SARS-CoV-2 infected patients is important for the control of the COVID-19 pandemic. We, herein, reported the performance of a Cas12a-assisted RTF-EXPAR strategy for the identification of SARS-CoV-2 RNA. This assay combined the advantages of RTF-EXPAR with CRISPR-Cas12a can detect SARS-CoV-2 within 40 min, requiring only isothermal control. Particularly, the simultaneous use of EXPAR amplification and CRISPR improved the detection sensitivity, thereby realizing ultrasensitive SARS-CoV-2 RNA detection with a detection limit of 3.77 aM (∼2 copies/μL) in an end-point fluorescence read-out fashion, and at 4.81 aM (∼3 copies/μL) level via a smartphone-assisted analysis system (RGB analysis). Moreover, Cas12a increases the specificity by intrinsic sequence-specific template recognition. Overall, this method is fast, sensitive, and accurate, needing minimal equipment, which holds great promise to meet the requirements of point-of-care molecular detection of SARS-CoV-2.
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Affiliation(s)
- Xiao-Min Hang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Hui-Yi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Peng-Fei Liu
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, PR China
| | - Kai-Ren Zhao
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Li Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China.
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32
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Spangler JR, Leski TA, Schultzhaus Z, Wang Z, Stenger DA. Large scale screening of CRISPR guide RNAs using an optimized high throughput robotics system. Sci Rep 2022; 12:13953. [PMID: 35977955 PMCID: PMC9385653 DOI: 10.1038/s41598-022-17474-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
All CRISPR/CAS systems utilize CRISPR guide RNAs (crRNAs), the design of which depend on the type of CAS protein, genetic target and the environment/matrix. While machine learning approaches have recently been developed to optimize some crRNA designs, candidate crRNAs must still be screened for efficacy under relevant conditions. Here, we demonstrate a high-throughput method to screen hundreds of candidate crRNAs for activation of Cas13a collateral RNA cleavage. Entire regions of a model gene transcript (Y. pestis lcrV gene) were tiled to produce overlapping crRNA sets. We tested for possible effects that included crRNA/target sequence, size and secondary structures, and the commercial source of DNA oligomers used to generate crRNAs. Detection of a 981 nt target RNA was initially successful with 271 out of 296 tested guide RNAs, and that was improved to 287 out of 296 (97%) after protocol optimizations. For this specific example, we determined that crRNA efficacy did not strongly depend on the target region or crRNA physical properties, but was dependent on the source of DNA oligomers used for RNA preparation. Our high-throughput methods for screening crRNAs has general applicability to the optimization of Cas12 and Cas13 guide RNA designs.
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Affiliation(s)
- J R Spangler
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA.
| | - T A Leski
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - Z Schultzhaus
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Z Wang
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
| | - D A Stenger
- Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington, DC, USA
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33
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Wu L, Wang X, Wu C, Cao X, Tang T, Huang H, Huang X. Ultrasensitive SARS-CoV-2 diagnosis by CRISPR-based screen-printed carbon electrode. Anal Chim Acta 2022; 1221:340120. [PMID: 35934402 PMCID: PMC9249825 DOI: 10.1016/j.aca.2022.340120] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 12/15/2022]
Abstract
Early and accurate diagnosis of SARS-CoV-2 was crucial for COVID-19 control and urgently required ultra-sensitive and rapid detection methods. CRISPR-based detection systems have great potential for rapid SARS-CoV-2 detection, but detecting ultra-low viral loads remains technically challenging. Here, we report an ultrasensitive CRISPR/Cas12a-based electrochemical detection system with an electrochemical biosensor, dubbed CRISPR-SPCE, in which the CRISPR ssDNA reporter was immobilized onto a screen-printed carbon electrode. Electrochemical signals are detected due to CRISPR cleavage, giving enhanced detection sensitivity. CRISPR-SPCE enables ultrasensitive SARS-CoV-2 detection, reaching as few as 0.27 copies μL-1. Moreover, CRISPR-SPCE is also highly specific and inexpensive, providing a fast and simple SARS-CoV-2 assay.
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Affiliation(s)
- Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, PR China; Zhejiang Laboratory, Hangzhou, 311100, PR China.
| | - Xinjie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, PR China
| | - Chengyuan Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, PR China
| | - Xizhong Cao
- Animal, Plant and Food Inspection Center of Nanjing Customs District, Nanjing, 210023, PR China
| | - Taishan Tang
- Animal, Plant and Food Inspection Center of Nanjing Customs District, Nanjing, 210023, PR China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, PR China; College of Pharmaceutical Science, Nanjing Tech University, Nanjing, 211816, PR China.
| | - Xingxu Huang
- Zhejiang Laboratory, Hangzhou, 311100, PR China.
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34
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Xu JH, Kang L, Yuan B, Feng ZH, Li SQ, Wang J, Wang YR, Xin WW, Gao S, Li JX, Sun YS, Wang JL, Yuan Y. Development and evaluation of a rapid RPA/CRISPR-based detection of Francisella tularensis. Front Microbiol 2022; 13:901520. [PMID: 36033876 PMCID: PMC9399789 DOI: 10.3389/fmicb.2022.901520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Francisella tularensis is a dangerous pathogen that causes an extremely contagious zoonosis in humans named tularemia. Given its low-dose morbidity, the potential to be fatal, and aerosol spread, it is regarded as a severe threat to public health. The US Centers for Disease Control and Prevention (CDC) has classified it as a category A potential agent for bioterrorism and a Tier 1 Select Agent. Herein, we combined recombinase polymerase amplification (RPA) with CRISPR/Cas12a system to select the F. tularensis target gene (TUL4), creating a two-pronged rapid and ultrasensitive diagnostic method for detecting F. tularensis. The real-time RPA (RT-RPA) assay detected F. tularensis within 10 min at a sensitivity of 5 copies/reaction, F. tularensis genomic DNA of 5 fg, and F. tularensis of 2 × 102 CFU/ml; the RPA-CRISPR/Cas12a assay detects F. tularensis within 40 min at a sensitivity of 0.5 copies/reaction, F. tularensis genomic DNA of 1 fg, and F. tularensis of 2 CFU/ml. Furthermore, the evaluation of specificity showed that both assays were highly specific to F. tularensis. More importantly, in a test of prepared simulated blood and sewage samples, the RT-RPA assay results were consistent with RT-PCR assay results, and the RPA-CRISPR/Cas12a assay could detect a minute amount of F. tularensis genomic DNA (2.5 fg). There was no nonspecific detection with blood samples and sewage samples, giving the tests a high practical application value. For example, in on-site and epidemic areas, the RT-RPA was used for rapid screening and the RPA-CRISPR/Cas12a assay was used for more accurate diagnosis.
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Affiliation(s)
- Jian-Hao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zi-Han Feng
- Department of Disease Control and Prevention, The No. 96609 Hospital of Chinese People's Liberation Army, Yinchuan, China
| | - Shi-Qing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Ya-Ru Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Wen-Wen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jia-Xin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yan-Song Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- *Correspondence: Yan-Song Sun
| | - Jing-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Jing-Lin Wang
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- Yuan Yuan
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Zhang A, Sun B, Zhang J, Cheng C, Zhou J, Niu F, Luo Z, Yu L, Yu C, Dai Y, Xie K, Hu Q, Qiu Y, Cao L, Chu H. CRISPR/Cas12a Coupled With Recombinase Polymerase Amplification for Sensitive and Specific Detection of Aphelenchoides besseyi. Front Bioeng Biotechnol 2022; 10:912959. [PMID: 35845427 PMCID: PMC9279656 DOI: 10.3389/fbioe.2022.912959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/17/2022] [Indexed: 12/26/2022] Open
Abstract
Aphelenchoides besseyi (A. besseyi), a seed-borne parasitic nematode, is the causal agent of rice white tip disease (RWTD), which may result in a drastic loss of rice yield. Seed treatments are currently considered to be the most effective means of preventing the spread of RWTD. Therefore, the rapid, highly specific, and accurate detection of A. besseyi from rice seeds is crucial for the surveillance, prevention, and control of RWTD. Here, we describe a novel detection assay that combines recombinase polymerase amplification (RPA) and CRISPR/Cas12a to detect A. besseyi (termed RPA-Cas12a-Ab), with a low limit of detection (LOD) of 1 copy/μl of plasmid or 1:107 diluted DNA extracted from individual nematodes. To improve the user-friendliness, lateral flow strip assay (LFA) was adopted to visualize the detection result. The LOD of the RPA-Cas12a-Ab LFA assay was 1,000 copies/μl plasmid or 1:10 diluted DNA extracted from individual nematodes. The assay developed in this study was able to identify A. besseyi in 45 min with high accuracy and sensitivity without cross reaction with three closely related non-A. besseyi species. Thus, RPA-Cas12a-Ab is a rapid, sensitive, and specific detection system that requires no sophisticated equipment and shows promise for on-site surveillance of A. besseyi.
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Affiliation(s)
- Anpeng Zhang
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Bin Sun
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jianming Zhang
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Can Cheng
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jihua Zhou
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Fuan Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhongyong Luo
- Shanghai Agricultural Science and Technology Seed Co., Ltd., Shanghai, China
| | - Luzhen Yu
- Technical Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Cui Yu
- Technical Center for Animal Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Yuting Dai
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Kaizhen Xie
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qiyan Hu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yue Qiu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liming Cao
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Liming Cao, ; Huangwei Chu,
| | - Huangwei Chu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Liming Cao, ; Huangwei Chu,
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Lin H, Liang Y, Zou L, Li B, Zhao J, Wang H, Sun J, Deng X, Tang S. Combination of Isothermal Recombinase-Aided Amplification and CRISPR-Cas12a-Mediated Assay for Rapid Detection of Major Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern. Front Microbiol 2022; 13:945133. [PMID: 35836420 PMCID: PMC9274097 DOI: 10.3389/fmicb.2022.945133] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 variants is a new and unsolved threat; therefore, it is an urgent and unmet need to develop a simple and rapid method for detecting and tracking SARS-CoV-2 variants. The spike gene of SARS-CoV-2 was amplified by isothermal recombinase-aided amplification (RAA) followed by the cleavage of CRISPR-Cas12a in which five allele-specific crRNAs and two Omicron-specific crRNAs were designed to detect and distinguish major SARS-CoV-2 variants of concerns (VOCs), including alpha, beta, delta variants, and Omicron sublineages BA.1 and BA.2. The whole reaction can be carried out in one tube at 39°C within 1.5–2 h, and the results can be read out by a fluorescence meter or naked eyes. Our results show that the RAA/CRISPR-Cas12a-based assay could readily distinguish the signature mutations, i.e., K417N, T478K, E484K, N501Y, and D614G, with a sensitivity of 100.0% and a specificity of 94.9–100.0%, respectively. The assay had a low limit of detection (LOD) of 104 copies/reaction and a concordance of 92.59% with Sanger sequencing results when detecting 54 SARS-CoV-2 positive clinical samples. The two Omicron-specific crRNAs can readily and correctly distinguish Omicron BA.1 and BA.2 sublineages with a LOD of as low as 20 copies/reaction. Furthermore, no cross-reaction was observed for all crRNAs analyzed when detecting clinical samples infected with 11 common respiratory pathogens. The combination of isothermal amplification and CRISPR-Cas12a-mediated assay is suitable for rapid detection of major SARS-CoV-2 variants in point-of-care testing and in resource-limiting settings. This simple assay could be quickly updated for emerging variants and implemented to routinely monitor and track the spread of SARS-CoV-2 variants.
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Affiliation(s)
- Hongqing Lin
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuanhao Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Lirong Zou
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Baisheng Li
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Jianhui Zhao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Haiying Wang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jiufeng Sun
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
| | - Xiaoling Deng
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Xiaoling Deng,
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Shixing Tang,
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Mattiello L, Rütgers M, Sua-Rojas MF, Tavares R, Soares JS, Begcy K, Menossi M. Molecular and Computational Strategies to Increase the Efficiency of CRISPR-Based Techniques. FRONTIERS IN PLANT SCIENCE 2022; 13:868027. [PMID: 35712599 PMCID: PMC9194676 DOI: 10.3389/fpls.2022.868027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The prokaryote-derived Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas mediated gene editing tools have revolutionized our ability to precisely manipulate specific genome sequences in plants and animals. The simplicity, precision, affordability, and robustness of this technology have allowed a myriad of genomes from a diverse group of plant species to be successfully edited. Even though CRISPR/Cas, base editing, and prime editing technologies have been rapidly adopted and implemented in plants, their editing efficiency rate and specificity varies greatly. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9-derived technologies and their implications on enhancing editing efficiency. We highlight the major efforts of engineering Cas9, Cas12a, Cas12b, and Cas12f proteins aiming to improve their efficiencies. We also provide a perspective on the global future of agriculturally based products using DNA-free CRISPR/Cas techniques. The improvement of CRISPR-based technologies efficiency will enable the implementation of genome editing tools in a variety of crop plants, as well as accelerate progress in basic research and molecular breeding.
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Affiliation(s)
- Lucia Mattiello
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Mark Rütgers
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Maria Fernanda Sua-Rojas
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Rafael Tavares
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - José Sérgio Soares
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, FL, United States
| | - Marcelo Menossi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, Brazil
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38
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Liu X, Li Y, Wang X, Song Y, Wu L, Yu B, Ma X, Ma P, Liu M, Huang X, Wang X. Rapid and Specific Detection of Active SARS-CoV-2 With CRISPR/Cas12a. Front Microbiol 2022; 12:820698. [PMID: 35154046 PMCID: PMC8832066 DOI: 10.3389/fmicb.2021.820698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Rapid and sensitive nucleic acid detection of SARS-CoV-2 has contributed to the clinical diagnosis and control of COVID-19. Although detection of virus genomic RNA (gRNA) has been commonly used in clinical diagnosis, SARS-CoV-2 gRNA detection could not discriminate between active infectious virus with remnant viral RNA. In contrast to genomic RNA, subgenomic RNAs (sgRNAs) are only produced when the virus is actively replicating and transcription, detection of sgRNA could be an indication to evaluate infectivity. CRISPR/Cas-based nucleic acid detection methods have been considered potential diagnostic tools due to their intrinsic sensitivity, specificity and simplicity. In this study, to specifically detect active virus replication, we developed a CRISPR-based active SARS-CoV-2 (CRISPR-actCoV) detection strategy by detecting sgRNAs of SARS-CoV-2. CRISPR-actCoV with CRISPR Cas12a-assisted fluorescence reporter system enables detection of sgRNAs at 10 copies in 35 min with high specificity and can be read out with naked eyes. Further, we performed CRISPR-actCoV mediated sgRNA detection in 30 SARS-CoV-2 potentially infected clinical samples, and 21 samples were SARS-CoV-2 sgRNA positive. A quantitative RT-PCR assay was also performed to detect gRNA of SARS-CoV-2 in parallel. Among the 30 clinical samples, 27 samples were gRNA positive. Taken together, CRISPR-actCoV provides an alternative for rapid and accurate detection of active SARS-CoV-2 and has great significance in better response of coronavirus causing epidemic disease.
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Affiliation(s)
- Xinyi Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Yanhua Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xin Wang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Yifan Song
- School of Life Sciences, Fudan University, Shanghai, China
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Benyuan Yu
- Animal, Plant and Food Inspection Center of Nanjing Customs District, Nanjing, China
| | - Xiaodong Ma
- Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, South China Normal University, Guangzhou, China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Liu
- State Key Laboratory of Respiratory Disease/National Clinical Research Center for Respiratory Disease/National Center for Respiratory Medicine/Guangzhou Institute of Respiratory Health/The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Ming Liu,
| | - Xingxu Huang
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
- Xingxu Huang,
| | - Xinjie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
- Xinjie Wang,
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39
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Lewis IC, Yan Y, Finnigan GC. Analysis of a Cas12a-based gene-drive system in budding yeast. Access Microbiol 2022; 3:000301. [PMID: 35024561 PMCID: PMC8749140 DOI: 10.1099/acmi.0.000301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022] Open
Abstract
The discovery and adaptation of CRISPR/Cas systems within molecular biology has provided advances across biological research, agriculture and human health. Genomic manipulation through use of a CRISPR nuclease and programmed guide RNAs has become a common and widely accessible practice. The identification and introduction of new engineered variants and orthologues of Cas9 as well as alternative CRISPR systems such as the type V group have provided additional molecular options for editing. These include distinct PAM requirements, staggered DNA double-strand break formation, and the ability to multiplex guide RNAs from a single expression construct. Use of CRISPR/Cas has allowed for the construction and testing of a powerful genetic architecture known as a gene drive within eukaryotic model systems. Our previous work developed a drive within budding yeast using Streptococcus pyogenes Cas9. Here, we installed the type V Francisella novicida Cas12a (Cpf1) nuclease gene and its corresponding guide RNA to power a highly efficient artificial gene drive in diploid yeast. We examined the consequence of altering guide length or introduction of individual mutational substitutions to the crRNA sequence. Cas12a-dependent gene-drive function required a guide RNA of at least 18 bp and could not tolerate most changes within the 5' end of the crRNA.
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Affiliation(s)
- Isabel C Lewis
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA.,Present address: School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yao Yan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Gregory C Finnigan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
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40
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Bryson JW, Auxillos JY, Rosser SJ. Multiplexed activation in mammalian cells using a split-intein CRISPR/Cas12a based synthetic transcription factor. Nucleic Acids Res 2022; 50:549-560. [PMID: 34908140 PMCID: PMC8754635 DOI: 10.1093/nar/gkab1191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/15/2021] [Accepted: 11/26/2021] [Indexed: 01/09/2023] Open
Abstract
The adoption of CRISPR systems for the generation of synthetic transcription factors has greatly simplified the process for upregulating endogenous gene expression, with a plethora of applications in cell biology, bioproduction and cell reprogramming. The recently discovered CRISPR/Cas12a (Cas12a) systems offer extended potential, as Cas12a is capable of processing its own crRNA array, to provide multiple individual crRNAs for subsequent targeting from a single transcript. Here we show the application of dFnCas12a-VPR in mammalian cells, with the Francisella novicida Cas12a (FnCas12a) possessing a shorter PAM sequence than Acidaminococcus sp. (As) or Lachnospiraceae bacterium (Lb) variants, enabling denser targeting of genomic loci, while performing just as well or even better than the other variants. We observe that synergistic activation and multiplexing can be achieved using crRNA arrays but also show that crRNAs expressed towards the 5' of 6-crRNA arrays show evidence of enhanced activity. This not only represents a more flexible tool for transcriptional modulation but further expands our understanding of the design capabilities and limitations when considering longer crRNA arrays for multiplexed targeting.
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Affiliation(s)
- James W Bryson
- Department of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jamie Y Auxillos
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan J Rosser
- Department of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, UK
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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41
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Abstract
CRISPR-Cas adaptive immune systems in bacteria and archaea utilize short CRISPR RNAs (crRNAs) to guide sequence-specific recognition and clearance of foreign genetic material. Multiple crRNAs are stored together in a compact format called a CRISPR array that is transcribed and processed into the individual crRNAs. While the exact processing mechanisms vary widely, some CRISPR-Cas systems, including those encoding the Cas9 nuclease, rely on a trans-activating crRNA (tracrRNA). The tracrRNA was discovered in 2011 and was quickly co-opted to create single-guide RNAs as core components of CRISPR-Cas9 technologies. Since then, further studies have uncovered processes extending beyond the traditional role of tracrRNA in crRNA biogenesis, revealed Cas nucleases besides Cas9 that are dependent on tracrRNAs, and established new applications based on tracrRNA engineering. In this review, we describe the biology of the tracrRNA and how its ongoing characterization has garnered new insights into prokaryotic immune defense and enabled key technological advances.
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Affiliation(s)
- Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany;
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany;
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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42
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Hu M, Zhu D, Zhou X. M-CDC: Magnetic pull-down-assisted colorimetric method based on the CRISPR/Cas12a system. Methods 2021; 203:259-267. [PMID: 34813932 DOI: 10.1016/j.ymeth.2021.11.009] [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: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022] Open
Abstract
The construction of a rapid, simple, and specific nucleic acid detection platform is of great significance to the control of the large-scale spread of infectious diseases. We have recently established a magnetic pull-down-assisted colorimetric method based on the CRISPR/Cas12a system (termed M-CDC), which effectively integrates the advantages of CRISPR/Cas12a, magnetic beads-based separation, and AuNP bioprobe to provide a simple and specific biosensing platform for nucleic acid assay. The M-CDC method is compatible with point-of-care testing and enables the detection of nucleic acid samples in less than an hour without relying on expensive and complex instruments. In this paper, step-by-step instructions for M-CDC assay, including recombinase polymerase amplification (RPA)/reverse transcription-polymerase chain reaction (RT-RPA) of DNA or RNA, Cas12a-mediated target recognition and cleavage, and subsequent magnetic beads-mediated colorimetric readouts are provided. In addition, the protocol for the expression and purification of Lachnospiraceae bacterium-Cas12a (LbCas12a) protein, the design and synthesis of high-efficient crRNA, and the preparation of AuNP bioprobe are also offered.
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Affiliation(s)
- Menglu Hu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Debin Zhu
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry, South China Normal University, Guangzhou 510006, PR China.
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China.
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43
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Yuan M, Ding R, Chen S, Duan G. Advances in Field Detection Based on CRISPR/Cas System. ACS Synth Biol 2021; 10:2824-2832. [PMID: 34714068 DOI: 10.1021/acssynbio.1c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid and accurate diagnostic methods are essential to interrupt outbreaks of infectious diseases such as COVID-19. However, the most commonly used nucleic acid detection method, qPCR or RT-qPCR, takes several hours to complete and requires highly sophisticated equipment. Recently, an emerging nucleic acid detection method based on the CRISPR/Cas system has reduced the reliance on qPCR. It has several important features that make it suitable for on-site POCT (point-of-care testing), including short detection cycles, low cost, high sensitivity, and the ability to be combined with different readout methods. This review briefly introduces the steps of CRISPR/Cas detection and then summarizes the current advances of CRISPR/Cas-based POCT from four steps: nucleic acid extraction, target amplification, CRISPR/Cas-based signal generation, and signal output. Finally, we discuss the advantages and challenges of CRISPR-based POCT and describe the future research perspectives for CRISPR.
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Affiliation(s)
- Mingzhu Yuan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Ronghua Ding
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
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44
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Liu Y, Chen Y, Huang S, Ma X, Huang X, Wang X, Zhou F. Rapid and Sensitive Diagnosis of Drug-Resistant FLT3-F691L Mutation by CRISPR Detection. Front Mol Biosci 2021; 8:753276. [PMID: 34760927 PMCID: PMC8574994 DOI: 10.3389/fmolb.2021.753276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/11/2021] [Indexed: 12/26/2022] Open
Abstract
Sensitive and efficient detection of drug-resistant mutations is essential in cancer precision medicine. In treating acute myeloid leukemia (AML), FLT3 gene F691L mutation shows universal resistance to all currently available FLT3 inhibitors. However, there is no particular detection method for FLT3-F691L. Commonly-used first-generation sequencing (FGS) approaches have low sensitivity, and next-generation sequencing (NGS) is time-consuming. Herein, we developed an accurate and sensitive FLT3-F691L diagnostic method by CRISPR detection. Briefly, the FLT3-691 region is amplified by recombinase polymerase amplification (RPA) and detected by L691-crRNA induced Cas12a reaction, and finally the result can be directly observed under a blue lamp or analyzed by a fluorescence reader. Confirmed by the tests on diluted plasmids and 120 AML patient samples, this method can achieve a sensitivity of 0.1% and complete the whole diagnosis process within 40 min. Potentially, this method will play an important role in point-of-care applications and guidance of AML treatment.
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Affiliation(s)
- Yin Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanling Chen
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiaodong Ma
- Key Laboratory of Brain, Cognition and Education Sciences, Institute for Brain Research and Rehabilitation, South China Normal University, Ministry of Education, Guangzhou, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xinjie Wang
- Key Laboratory of Brain, Cognition and Education Sciences, Institute for Brain Research and Rehabilitation, South China Normal University, Ministry of Education, Guangzhou, China.,Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciencesn, Shenzhen, China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
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45
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Xiao X, Lin Z, Huang X, Lu J, Zhou Y, Zheng L, Lou Y. Rapid and Sensitive Detection of Vibrio vulnificus Using CRISPR/Cas12a Combined With a Recombinase-Aided Amplification Assay. Front Microbiol 2021; 12:767315. [PMID: 34745075 PMCID: PMC8566878 DOI: 10.3389/fmicb.2021.767315] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/04/2021] [Indexed: 12/19/2022] Open
Abstract
Vibrio vulnificus is an important zoonotic and aquatic pathogen and can cause vibriosis in humans and aquatic animals (especially farmed fish and shrimp species). Rapid and sensitive detection methods for V. vulnificus are still required to diagnose human vibriosis early and reduce aquaculture losses. Herein, we developed a rapid and sensitive diagnostic method comprising a recombinase-aided amplification (RAA) assay and the CRISPR/Cas12a system (named RAA-CRISPR/Cas12a) to detect V. vulnificus. The RAA-CRISPR/Cas12a method allows rapid and sensitive detection of V. vulnificus in 40 min without a sophisticated instrument, and the limit of detection is two copies of V. vulnificus genomic DNA per reaction. Meanwhile, the method shows satisfactory specificity toward non-target bacteria and high accuracy in the spiked blood, stool, and shrimp samples. Therefore, our proposed rapid and sensitive V. vulnificus detection method, RAA-CRISPR/Cas12a, has great potential for early diagnosis of human vibriosis and on-site V. vulnificus detection in aquaculture and food safety control.
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Affiliation(s)
- Xingxing Xiao
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Ziqin Lin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Xianhui Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Jinfang Lu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yan Zhou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Laibao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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46
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Asin-Garcia E, Martin-Pascual M, Garcia-Morales L, van Kranenburg R, Martins dos Santos VAP. ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida. ACS Synth Biol 2021; 10:2672-2688. [PMID: 34547891 PMCID: PMC8524654 DOI: 10.1021/acssynbio.1c00297] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 12/11/2022]
Abstract
Genome recoding enables incorporating new functions into the DNA of microorganisms. By reassigning codons to noncanonical amino acids, the generation of new-to-nature proteins offers countless opportunities for bioproduction and biocontainment in industrial chassis. A key bottleneck in genome recoding efforts, however, is the low efficiency of recombineering, which hinders large-scale applications at acceptable speed and cost. To relieve this bottleneck, we developed ReScribe, a highly optimized recombineering tool enhanced by CRISPR-Cas9-mediated counterselection built upon the minimal PAM 5'-NNG-3' of the Streptococcus canis Cas9 (ScCas9). As a proof of concept, we used ReScribe to generate a minimally recoded strain of the industrial chassis Pseudomonas putida by replacing TAG stop codons (functioning as PAMs) of essential metabolic genes with the synonymous TAA. We showed that ReScribe enables nearly 100% engineering efficiency of multiple loci in P. putida, opening promising avenues for genome editing and applications thereof in this bacterium and beyond.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Maria Martin-Pascual
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Luis Garcia-Morales
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem 4206 AC, The Netherlands
- Laboratory
of Microbiology, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
| | - Vitor A. P. Martins dos Santos
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
- LifeGlimmer
GmbH, Berlin 12163, Germany
- Bioprocess
Engineering Group, Wageningen University
& Research, Wageningen 6700 AA, The Netherlands
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47
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Magnusson JP, Rios AR, Wu L, Qi LS. Enhanced Cas12a multi-gene regulation using a CRISPR array separator. eLife 2021; 10:e66406. [PMID: 34499031 PMCID: PMC8478413 DOI: 10.7554/elife.66406] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
The type V-A Cas12a protein can process its CRISPR array, a feature useful for multiplexed gene editing and regulation. However, CRISPR arrays often exhibit unpredictable performance due to interference between multiple guide RNA (gRNAs). Here, we report that Cas12a array performance is hypersensitive to the GC content of gRNA spacers, as high-GC spacers can impair activity of the downstream gRNA. We analyze naturally occurring CRISPR arrays and observe that natural repeats always contain an AT-rich fragment that separates gRNAs, which we term a CRISPR separator. Inspired by this observation, we design short, AT-rich synthetic separators (synSeparators) that successfully remove the disruptive effects between gRNAs. We further demonstrate enhanced simultaneous activation of seven endogenous genes in human cells using an array containing the synSeparator. These results elucidate a previously underexplored feature of natural CRISPR arrays and demonstrate how nature-inspired engineering solutions can improve multi-gene control in mammalian cells.
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Affiliation(s)
- Jens P Magnusson
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Antonio Ray Rios
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Lingling Wu
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Lei S Qi
- Department of Bioengineering, Stanford UniversityStanfordUnited States
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
- Stanford ChEM-H Institute, Stanford UniversityStanfordUnited States
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48
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Wörle E, Jakob L, Schmidbauer A, Zinner G, Grohmann D. Decoupling the bridge helix of Cas12a results in a reduced trimming activity, increased mismatch sensitivity and impaired conformational transitions. Nucleic Acids Res 2021; 49:5278-5293. [PMID: 34009379 PMCID: PMC8136826 DOI: 10.1093/nar/gkab286] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/26/2022] Open
Abstract
The widespread and versatile prokaryotic CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats and associated Cas proteins) constitute powerful weapons against foreign nucleic acids. Recently, the single-effector nuclease Cas12a that belongs to the type V CRISPR-Cas system was added to the Cas enzymes repertoire employed for gene editing purposes. Cas12a is a bilobal enzyme composed of the REC and Nuc lobe connected by the wedge, REC1 domain and bridge helix (BH). We generated BH variants and integrated biochemical and single-molecule FRET (smFRET) studies to elucidate the role of the BH for the enzymatic activity and conformational flexibility of Francisella novicida Cas12a. We demonstrate that the BH impacts the trimming activity and mismatch sensitivity of Cas12a resulting in Cas12a variants with improved cleavage accuracy. smFRET measurements reveal the hitherto unknown open and closed state of apo Cas12a. BH variants preferentially adopt the open state. Transition to the closed state of the Cas12a-crRNA complex is inefficient in BH variants but the semi-closed state of the ternary complex can be adopted even if the BH is deleted in its entirety. Taken together, these insights reveal that the BH is a structural element that influences the catalytic activity and impacts conformational transitions of FnCas12a.
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Affiliation(s)
- Elisabeth Wörle
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Leonhard Jakob
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Andreas Schmidbauer
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Gabriel Zinner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, 93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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49
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Randazzo P, Bennis NX, Daran JM, Daran-Lapujade P. gEL DNA: A Cloning- and Polymerase Chain Reaction-Free Method for CRISPR-Based Multiplexed Genome Editing. CRISPR J 2021; 4:896-913. [PMID: 33900846 DOI: 10.1089/crispr.2020.0028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Even for the genetically accessible yeast Saccharomyces cerevisiae, the CRISPR-Cas DNA editing technology has strongly accelerated and facilitated strain construction. Several methods have been validated for fast and highly efficient single editing events, and diverse approaches for multiplex genome editing have been described in the literature by means of SpCas9 or FnCas12a endonucleases and their associated guide RNAs (gRNAs). The gRNAs used to guide the Cas endonuclease to the editing site are typically expressed from plasmids using native Pol II or Pol III RNA polymerases. These gRNA expression plasmids require laborious, time-consuming cloning steps, which hampers their implementation for academic and applied purposes. In this study, we explore the potential of expressing gRNA from linear DNA fragments using the T7 RNA polymerase (T7RNAP) for single and multiplex genome editing in Saccharomyces cerevisiae. Using FnCas12a, this work demonstrates that transforming short, linear DNA fragments encoding gRNAs in yeast strains expressing T7RNAP promotes highly efficient single and duplex DNA editing. These DNA fragments can be custom ordered, which makes this approach highly suitable for high-throughput strain construction. This work expands the CRISPR toolbox for large-scale strain construction programs in S. cerevisiae and promises to be relevant for other less genetically accessible yeast species.
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Affiliation(s)
- Paola Randazzo
- Department of Biotechnology, Delft University of Biotechnology, Delft, Netherlands
| | - Nicole Xanthe Bennis
- Department of Biotechnology, Delft University of Biotechnology, Delft, Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Biotechnology, Delft, Netherlands
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50
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Yu L, Marchisio MA. Saccharomyces cerevisiae Synthetic Transcriptional Networks Harnessing dCas12a and Type V-A anti-CRISPR Proteins. ACS Synth Biol 2021; 10:870-883. [PMID: 33819020 DOI: 10.1021/acssynbio.1c00006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Type V-A anti-CRISPR proteins (AcrVAs) represent the response from phages to the CRISPR-Cas12a prokaryotic immune system. CRISPR-Cas12a was repurposed, in high eukaryotes, to carry out gene editing and transcription regulation, the latter via a nuclease-dead Cas12a (dCas12a). Consequently, AcrVAs were adopted to regulate (d)Cas12a activity. However, the usage of both dCas12a-based transcription factors and AcrVAs in the yeast Saccharomyces cerevisiae has not been explored. In this work, we show that, in the baker's yeast, two dCas12a proteins (denAsCas12a and dLbCas12a) work both as activators (upon fusion to a strong activation domain) and repressors, whereas dMbCa12a is nonfunctional. The activation efficiency of dCas12a-ADs manifests a dependence on the number of crRNA binding sites, whereas it is not directly correlated to the amount of crRNA in the cells. Moreover, AcrVA1, AcrVA4, and AcrVA5 are able to inhibit dLbCa12a in yeast, and denAsCas12a is only inhibited by AcrVA1. However, AcrVA1 performs well at high concentration only. Coexpression of two or three AcrVAs does not enhance inhibition of dCas12a(-AD), suggesting a competition between different AcrVAs. Further, AcrVA4 significantly limits gene editing by LbCas12a. Overall, our results indicate that dCas12a:crRNA and AcrVA proteins are highly performant components in S. cerevisiae synthetic transcriptional networks.
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Affiliation(s)
- Lifang Yu
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China
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