1
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Zhao Y, Zhou C, Guo B, Yang X, Wang H. Pyrococcus furiosus Argonaute-mediated porcine epidemic diarrhea virus detection. Appl Microbiol Biotechnol 2024; 108:137. [PMID: 38229331 DOI: 10.1007/s00253-023-12919-0] [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: 07/21/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/18/2024]
Abstract
Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, induces severe vomiting and acute watery diarrhea in unweaned piglets. The pig industry has suffered tremendous financial losses due to the high mortality rate of piglets caused by PEDV. Consequently, a simple and rapid on-site diagnostic technology is crucial for preventing and controlling PEDV. This study established a detection method for PEDV using recombinase-aided amplification (RAA) and Pyrococcus furiosus Argonaute (PfAgo), which can detect 100 copies of PEDV without cross-reactivity with other pathogens. The entire reaction of RAA and PfAgo to detect PEDV does not require sophisticated instruments, and the reaction results can be observed with the naked eye. Overall, this integrated RAA-PfAgo cleavage assay is a practical tool for accurately and quickly detecting PEDV. KEY POINTS: • PfAgo has the potential to serve as a viable molecular diagnostic tool for the detection and diagnosis of viral genomes • The RAA-PfAgo detection technique has a remarkable level of sensitivity and specificity • The RAA-PfAgo detection system can identify PEDV without needing advanced equipment.
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Affiliation(s)
- Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Boyan Guo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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2
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Zhao Y, Yang M, Zhou C, Guo B, Wang K, Song C, Wang H. Establishment of a simple, sensitive, and specific ASFV detection method based on Pyrococcus furiosus argonaute. Biosens Bioelectron 2024; 254:116230. [PMID: 38520983 DOI: 10.1016/j.bios.2024.116230] [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: 11/28/2023] [Revised: 02/25/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024]
Abstract
African swine fever (ASF), which is casued by African swine fever virus (ASFV), is a fatal infectious disease of pigs that results in significant losses to the breeding industry. Therefore, screening and detection are crucial for the control and prevention of the ASFV. Argonaute is a new detection tool that is being extensively used due to its high specificity and programmability. This study reports on a new nucleic acid assay method, termed REPD, which uses recombinase-aided amplification and restriction endonuclease-assisted Pyrococcus furiosus argonaute (PfAgo) detection. One-pot REPD was developed for the detection of ASFV. The one-pot REPD could detect a single copy of ASFV nucleic acid and showed no cross-reactivity with other pathogens. Detection in clinical samples was 100% consistent with the results of real-time PCR analysis. The results showed that the one-pot REPD assay is convenient, sensitive, specific, and potentially adaptable to the detection of ASFV. In summary, this study highlights a novel method that can be employed for the detection of pathogens.
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Affiliation(s)
- Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ming Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Boyan Guo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Kailu Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Cailiang Song
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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3
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Lin L, Luo Q, Li L, Zheng Y, Wei H, Liao J, Liu Y, Liu M, Wang Z, Lin W, Zou X, Zhu H, Lin M. Recombinase polymerase amplification combined with Pyrococcus furiosus Argonaute for fast Salmonella spp. testing in food safety. Int J Food Microbiol 2024; 417:110697. [PMID: 38642433 DOI: 10.1016/j.ijfoodmicro.2024.110697] [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: 10/29/2023] [Revised: 02/24/2024] [Accepted: 04/10/2024] [Indexed: 04/22/2024]
Abstract
Foodborne illness caused by Salmonella spp. is one of the most prevalent public health problems globally, which have brought immeasurable economic burden and social impact to countries around the world. Neither current nucleic acid amplification detection method nor standard culture method (2-3 days) are suitable for field detection in areas with a heavy burden of Salmonella spp. Here, we developed a highly sensitive and accurate assay for Salmonella spp. detection in less than 40 min. Specifically, the invA gene of Salmonella spp. was amplified by recombinase polymerase amplification (RPA), followed by Pyrococcus furiosus Argonaute (PfAgo)-based target sequence cleavage, which could be observed by a fluorescence reader or the naked eye. The assay offered the lowest detectable concentration of 1.05 × 101 colony forming units/mL (CFU/mL). This assay had strong specificity and high sensitivity for the detection of Salmonella spp. in field samples, which indicated the feasibility of this assay.
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Affiliation(s)
- Liyun Lin
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Qiulan Luo
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Liejun Li
- Guangdong Hybribio Biotech Co., Ltd., Chaozhou, Guangdong, China
| | - Yuzhong Zheng
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Huagui Wei
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Jiayu Liao
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Yaqun Liu
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Mouquan Liu
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Zhonghe Wang
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Wanling Lin
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Xianghui Zou
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Hui Zhu
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China
| | - Min Lin
- School of Biotechnology and Food Engineering, Hanshan Normal University, Chaozhou, Guangdong Province, China.
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4
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Shi Y, Tan Z, Wu D, Wu Y, Li G. Pyrococcus furiosus argonaute based Alicyclobacillus acidoterrestrsis detection in fruit juice. Food Microbiol 2024; 120:104475. [PMID: 38431321 DOI: 10.1016/j.fm.2024.104475] [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: 11/29/2023] [Revised: 12/28/2023] [Accepted: 01/09/2024] [Indexed: 03/05/2024]
Abstract
Alicyclobacillus acidoterrestris is the major threat to fruit juice for its off-odor producing characteristic. In this study, Pyrococcus furiosus Argonaute (PfAgo), a novel endonuclease with precise DNA cleavage activity, was used for A. acidoterrestrisdetection, termed as PAD. The partially amplified 16 S rRNA gene of A. acidoterrestris can be cleaved by PfAgo activated by a short 5'-phosphorylated single strand DNA, producing a new guide DNA (gDNA). Then, PfAgo was activated by the new gDNA to cut a molecular beacon (MB) with fluorophore-quencher reporter, resulting in the recovery of fluorescence. The fluorescent intensity is positively related with the concentration of A. acidoterrestris. The PAD assay showed excellent specificity and sensitivity as low as 101 CFU/mL, which can be a powerful tool for on-site detection of A. acidoterrestris in fruit juice industry in the future, reducing the economic loss.
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Affiliation(s)
- Yiheng Shi
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Zishan Tan
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, United Kingdom
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China; NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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5
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Han R, Wang F, Chen W, Ma L. A Fast and Sensitive One-Tube SARS-CoV-2 Detection Platform Based on RTX-PCR and Pyrococcus furiosus Argonaute. BIOSENSORS 2024; 14:245. [PMID: 38785719 PMCID: PMC11118887 DOI: 10.3390/bios14050245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/29/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
Since SARS-CoV-2 is a highly transmissible virus, alternative reliable, fast, and cost-effective methods are still needed to prevent virus spread that can be applied in the laboratory and for point-of-care testing. Reverse transcription real-time fluorescence quantitative PCR (RT-qPCR) is currently the gold criteria for detecting RNA viruses, which requires reverse transcriptase to reverse transcribe viral RNA into cDNA, and fluorescence quantitative PCR detection was subsequently performed. The frequently used reverse transcriptase is thermolabile; the detection process is composed of two steps: the reverse transcription reaction at a relatively low temperature, and the qPCR performed at a relatively high temperature, moreover, the RNA to be detected needs to pretreated if they had advanced structure. Here, we develop a fast and sensitive one-tube SARS-CoV-2 detection platform based on Ultra-fast RTX-PCR and Pyrococcus furiosus Argonaute-mediated Nucleic acid Detection (PAND) technology (URPAND). URPAND was achieved ultra-fast RTX-PCR process based on a thermostable RTX (exo-) with both reverse transcriptase and DNA polymerase activity. The URPAND can be completed RT-PCR and PAND to detect nucleic acid in one tube within 30 min. This method can specifically detect SARS-CoV-2 with a low detection limit of 100 copies/mL. The diagnostic results of clinical samples with one-tube URPAND displayed 100% consistence with RT-qPCR test. Moreover, URPAND was also applied to identify SARS-CoV-2 D614G mutant due to its single-nucleotide specificity. The URPAND platform is rapid, accurate, tube closed, one-tube, easy-to-operate and free of large instruments, which provides a new strategy to the detection of SARS-CoV-2 and other RNA viruses.
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Affiliation(s)
- Rui Han
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China; (R.H.); (F.W.)
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China; (R.H.); (F.W.)
| | - Wanping Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China; (R.H.); (F.W.)
- School of Pharmacy, Qingdao University, Qingdao 266071, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China; (R.H.); (F.W.)
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6
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Lu Y, Wen J, Wang C, Wang M, Jiang F, Miao L, Xu M, Li Y, Chen X, Chen Y. Mesophilic Argonaute-Based Single Polystyrene Sphere Aptamer Fluorescence Platform for the Multiplexed and Ultrasensitive Detection of Non-Nucleic Acid Targets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308424. [PMID: 38081800 DOI: 10.1002/smll.202308424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Indexed: 01/04/2024]
Abstract
The rapid, simultaneous, and accurate identification of multiple non-nucleic acid targets in clinical or food samples at room temperature is essential for public health. Argonautes (Agos) are guided, programmable, target-activated, next-generation nucleic acid endonucleases that could realize one-pot and multiplexed detection using a single enzyme, which cannot be achieved with CRISPR/Cas. However, currently reported thermophilic Ago-based multi-detection sensors are mainly employed in the detection of nucleic acids. Herein, this work proposes a Mesophilic Argonaute Report-based single millimeter Polystyrene Sphere (MARPS) multiplex detection platform for the simultaneous analysis of non-nucleic acid targets. The aptamer is utilized as the recognition element, and a single millimeter-sized polystyrene sphere (PSmm) with a large concentration of guide DNA on the surface served as the microreactor. These are combined with precise Clostridium butyricum Ago (CbAgo) cleavage and exonuclease I (Exo I) signal amplification to achieve the efficient and sensitive recognition of non-nucleic acid targets, such as mycotoxins (<60 pg mL-1) and pathogenic bacteria (<102 cfu mL-1). The novel MARPS platform is the first to use mesophilic Agos for the multiplex detection of non-nucleic acid targets, overcoming the limitations of CRISPR/Cas in this regard and representing a major advancement in non-nucleic acid target detection using a gene-editing-based system.
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Affiliation(s)
- Yingying Lu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junping Wen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chengming Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mengjiao Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Feng Jiang
- Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Hubei Provincial Institute for Food Supervision and Test, Wuhan, 430075, China
| | - Lin Miao
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Minggao Xu
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaohua Chen
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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7
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Prostova M, Kanevskaya A, Panteleev V, Lisitskaya L, Perfilova Tugaeva KV, Sluchanko NN, Esyunina D, Kulbachinskiy A. DNA-targeting short Argonautes complex with effector proteins for collateral nuclease activity and bacterial population immunity. Nat Microbiol 2024; 9:1368-1381. [PMID: 38622379 DOI: 10.1038/s41564-024-01654-5] [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: 11/25/2023] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
Two prokaryotic defence systems, prokaryotic Argonautes (pAgos) and CRISPR-Cas, detect and cleave invader nucleic acids using complementary guides and the nuclease activities of pAgo or Cas proteins. However, not all pAgos are active nucleases. A large clade of short pAgos bind nucleic acid guides but lack nuclease activity, suggesting a different mechanism of action. Here we investigate short pAgos associated with a putative effector nuclease, NbaAgo from Novosphingopyxis baekryungensis and CmeAgo from Cupriavidus metallidurans. We show that these pAgos form a heterodimeric complex with co-encoded effector nucleases (short prokaryotic Argonaute, DNase and RNase associated (SPARDA)). RNA-guided target DNA recognition unleashes the nuclease activity of SPARDA leading to indiscriminate collateral cleavage of DNA and RNA. Activation of SPARDA by plasmids or phages results in degradation of cellular DNA and cell death or dormancy, conferring target-specific population protection and expanding the range of known prokaryotic immune systems.
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Affiliation(s)
- Maria Prostova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Anna Kanevskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | | | - Lidia Lisitskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kristina V Perfilova Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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8
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Zhao Y, Zhang T, Zhou C, Guo B, Wang H. Pyrococcus furiosus Argonaute Based Detection Assays for Porcine Deltacoronavirus. ACS Synth Biol 2024; 13:1323-1331. [PMID: 38567812 DOI: 10.1021/acssynbio.4c00045] [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: 04/20/2024]
Abstract
Porcine deltacoronavirus (PDCoV) is a major cause of diarrhea and diarrhea-related deaths among piglets and results in massive losses to the overall porcine industry. The clinical manifestations of porcine diarrhea brought on by the porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), and PDCoV are oddly similar to each other. Hence, the identification of different pathogens through molecular diagnosis and serological techniques is crucial. Three novel detection methods for identifying PDCoV have been developed utilizing recombinase-aided amplification (RAA) or reverse transcription recombinase-aided amplification (RT-RAA) in conjunction with Pyrococcus furiosus Argonaute (PfAgo): RAA-PfAgo, one-pot RT-RAA-PfAgo, and one-pot RT-RAA-PfAgo-LFD. The indicated approaches have a detection limit of around 60 copies/μL of PDCoV and do not cross-react with other viruses including PEDV, TGEV, RVA, PRV, PCV2, or PCV3. The applicability of one-pot RT-RAA-PfAgo and one-pot RT-RAA-PfAgo-LFD were examined using clinical samples and showed a positive rate comparable to the qPCR method. These techniques offer cutting-edge technical assistance for identifying, stopping, and managing PDCoV.
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Affiliation(s)
- Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Tiejun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Boyan Guo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
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9
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Zheng L, Zhou B, Yang Y, Zan B, Zhong B, Wu B, Feng Y, Liu Q, Hong L. Mn 2+-induced structural flexibility enhances the entire catalytic cycle and the cleavage of mismatches in prokaryotic argonaute proteins. Chem Sci 2024; 15:5612-5626. [PMID: 38638240 PMCID: PMC11023060 DOI: 10.1039/d3sc06221j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/01/2024] [Indexed: 04/20/2024] Open
Abstract
Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid-based biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+ in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicate that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+ in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.
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Affiliation(s)
- Lirong Zheng
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- Department of Cell and Developmental Biology & Michigan Neuroscience Institute, University of Michigan Medical School 48105 Ann Arbor MI USA
| | - Bingxin Zhou
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University Shanghai 200240 China
| | - Yu Yang
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Bing Zan
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
| | - Bozitao Zhong
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Banghao Wu
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Yan Feng
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Liu
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University Shanghai 200240 China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University Shanghai 200240 China
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10
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Fu R, Hou J, Wang Z, Xianyu Y. Mn 2+-Mediated Modulation of PfAgo Activity for Biosensing. Adv Healthc Mater 2024:e2304484. [PMID: 38530141 DOI: 10.1002/adhm.202304484] [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: 12/15/2023] [Revised: 03/01/2024] [Indexed: 03/27/2024]
Abstract
Argonaute (Ago) as a powerful enzyme has provided new insights into biosensing due to its programmability, high sensitivity, and user-friendly operation. However, current strategies mainly rely on phosphorylated guide DNA to modulate the cleavage activity of Ago, which is limited in versatility and simplicity. Herein, the authors report the Mn2+-enhanced cleavage activity of Ago and employ Mn-ions with variable valence to regulate the activity of Pyrococcus furiosus Ago (PfAgo) for biosensing applications. The conversion of Mn ions with different valence states through MnO2 nanoflowers enables the sensitive detection of ascorbic acid, alkaline phosphatase, and arsenic with limits of detection of 2.5 nmol L-1, 0.009 U L-1, and 0.4 ng mL-1, respectively. A PfAgo-based immunoassay is further developed that allows for the detection of diverse targets, thus providing a promising toolbox to broaden PfAgo-based sensors into versatile bioanalytical and biomedical applications.
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Affiliation(s)
- Ruijie Fu
- College of Biosystems Engineering and Food Science, Zhejiang University, Zhejiang, 310058, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang, 310058, China
| | - Jinjie Hou
- College of Biosystems Engineering and Food Science, Zhejiang University, Zhejiang, 310058, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang, 310058, China
| | - Zexiang Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Zhejiang, 310058, China
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang, 310058, China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Zhejiang, 310058, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang, 310058, China
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310058, China
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11
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Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M. The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res 2024; 52:2530-2545. [PMID: 38197228 PMCID: PMC10954474 DOI: 10.1093/nar/gkad1241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.
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Affiliation(s)
- Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Edvardas Golovinas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Reda Pocevičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Danielis Rutkauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, LT-02300, Vilnius, Lithuania
| | - Marija Jankunec
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Evelina Zagorskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Edvinas Jurgelaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Algirdas Grybauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
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12
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Kou J, Li Y, Zhao Z, Qiao J, Zhang Q, Han X, Cheng X, Man S, Ma L. Simultaneous Dual-Gene Test of Methicillin-Resistant Staphylococcus Aureus using an Argonaute-Centered Portable and Visual Biosensor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311764. [PMID: 38506607 DOI: 10.1002/smll.202311764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Indexed: 03/21/2024]
Abstract
The development of novel method for drug-resistant bacteria detection is imperative. A simultaneous dual-gene Test of methicillin-resistant Staphylococcus aureus (MRSA) is developed using an Argonaute-centered portable biosensor (STAR). This is the first report concerning Argonaute-based pathogenic bacteria detection. Simply, the species-specific mecA and nuc gene are isothermally amplified using loop-mediated isothermal amplification (LAMP) technique, followed by Argonaute-based detection enabled by its programmable, guided, sequence-specific recognition and cleavage. With the strategy, the targeted nucleic acid signals gene are dexterously converted into fluorescent signals. STAR is capable of detecting the nuc gene and mecA gene simultaneously in a single reaction. The limit of detection is 10 CFU/mL with a dynamic range from 10 to 107 CFU/mL. The sample-to-result time is <65 min. This method is successfully adapted to detect clinical samples, contaminated foods, and MRSA-infected animals. This work broadens the reach of Argonaute-based biosensing and presents a novel bacterial point-of-need (PON) detection platform.
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Affiliation(s)
- Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Qiang Zhang
- Branch of Tianjin Third Central Hospital, Tianjin, 300250, China
| | - Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xinkuan Cheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
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13
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Zhao J, Han M, Ma A, Jiang F, Chen R, Dong Y, Wang X, Ruan S, Chen Y. A machine vision-assisted Argonaute-mediated fluorescence biosensor for the detection of viable Salmonella in food without convoluted DNA extraction and amplification procedures. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133648. [PMID: 38306835 DOI: 10.1016/j.jhazmat.2024.133648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/04/2024]
Abstract
The precise identification viable pathogens hold paramount significance in the prevention of foodborne diseases outbreaks. In this study, we integrated machine vision and learning with single microsphere to develop a phage and Clostridium butyricum Argonaute (CbAgo)-mediated fluorescence biosensor for detecting viable Salmonella typhimurium (S. typhimurium) without convoluted DNA extraction and amplification procedures. Phage and lysis buffer was utilized to capture and lyse viable S. typhimurium, respectively. Subsequently, CbAgo can cleave the bacterial DNA to obtain target DNA that guides a newly targeted cleavage of fluorescent probes. After that, the resulting fluorescent signal accumulates on the streptavidin-modified single microsphere. The overall detection process is then analyzed and interpreted by machine vision and learning algorithms, achieving highly sensitive detection of S. typhimurium with a limit of detection at 40.5 CFU/mL and a linear range of 50-107 CFU/mL. Furthermore, the proposed biosensor demonstrates standard recovery rates and coefficients of variation at 93.22% - 106.02% and 1.47% - 12.75%, respectively. This biosensor exhibits exceptional sensitivity and selectivity, presenting a promising method for the rapid and effective detection of foodborne pathogens. ENVIRONMENTAL IMPLICATION: Bacterial pathogens exist widely in the environment and seriously threaten the safety of human life. In this study, we developed a phage and Clostridium butyricum Argonaute-mediated fluorescence biosensor for the detection of viable Salmonella typhimurium in environmental water and food samples. Compared with other Salmonella detection methods, this method does not need complex DNA extraction and amplification steps, which reduces the use of chemical reagents and experimental consumables in classic DNA extraction kit methods.
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Affiliation(s)
- Junpeng Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Minjie Han
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Feng Jiang
- Key Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Wuhan 430075, Hubei, China
| | - Rui Chen
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Yongzhen Dong
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Xufeng Wang
- College of Food Science and Technology, Huazhong Agricultural University, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Shilong Ruan
- Daye Public Inspection and Test Center, Daye 435100, Hubei, China
| | - Yiping Chen
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, Liaoning, China.
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14
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Yang B, Wang H, Kong J, Fang X. Long-term monitoring of ultratrace nucleic acids using tetrahedral nanostructure-based NgAgo on wearable microneedles. Nat Commun 2024; 15:1936. [PMID: 38431675 PMCID: PMC10908814 DOI: 10.1038/s41467-024-46215-w] [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: 11/08/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Real-time and continuous monitoring of nucleic acid biomarkers with wearable devices holds potential for personal health management, especially in the context of pandemic surveillance or intensive care unit disease. However, achieving high sensitivity and long-term stability remains challenging. Here, we report a tetrahedral nanostructure-based Natronobacterium gregoryi Argonaute (NgAgo) for long-term stable monitoring of ultratrace unamplified nucleic acids (cell-free DNAs and RNAs) in vivo for sepsis on wearable device. This integrated wireless wearable consists of a flexible circuit board, a microneedle biosensor, and a stretchable epidermis patch with enrichment capability. We comprehensively investigate the recognition mechanism of nucleic acids by NgAgo/guide DNA and signal transformation within the Debye distance. In vivo experiments demonstrate the suitability for real-time monitoring of cell-free DNA and RNA with a sensitivity of 0.3 fM up to 14 days. These results provide a strategy for highly sensitive molecular recognition in vivo and for on-body detection of nucleic acid.
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Affiliation(s)
- Bin Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Haonan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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15
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Zhao Y, Zhang Y, Wu W, Kang T, Sun J, Jiang H. Rapid and sensitive detection of Mycoplasma synoviae using RPA combined with Pyrococcus furiosus Argonaute. Poult Sci 2024; 103:103244. [PMID: 38194834 PMCID: PMC10792625 DOI: 10.1016/j.psj.2023.103244] [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: 07/30/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 01/11/2024] Open
Abstract
Mycoplasma synoviae (MS) is an important pathogen in laying hens and causes serious economic losses in poultry production. Rapid, accurate and specific detection is important for the prevention and control of MS. Argonaute from Pyrococcus furiosus (PfAgo) is emerging as a nucleic acid detector that works via "dual-step" sequence-specific cleavage. In this study, an MS detection method combining recombinase polymerase amplification (RPA) and PfAgo was established. Through elaborate design and screening of RPA primers and PfAgo gDNA and condition optimization, amplification and detection procedures can be completed within 40 min, whereas the results were superficially interpreted under UV and blue light. The sensitivity for MS detection was 2 copies/µL, and the specificity results showed no cross reaction with other pathogens. For the detection of 31 clinical samples, the results of this method and qPCR were completely consistent. This method provides a reliable and convenient method for the on-site detection of MS that is easy to operate without complex instruments and equipment.
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Affiliation(s)
- Yanli Zhao
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Yuhua Zhang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Weiqing Wu
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Tianhao Kang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jian Sun
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Hongxia Jiang
- Guangdong Key Laboratory for Veterinary Pharmaceutics Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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16
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He P, Zhou W, Wei H, Yu J. Fast and Ultrasensitive Detection of Monkeypox by a Pyrococcus furiosus Argonaute System Coupled with a Short Amplification. Viruses 2024; 16:382. [PMID: 38543748 PMCID: PMC10975468 DOI: 10.3390/v16030382] [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: 01/18/2024] [Revised: 02/17/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Monkeypox virus (MPXV), the pathogen responsible for the infectious disease monkeypox, causes lesions on the skin, lymphadenopathy, and fever. It has posed a global public health threat since May 2022. Highly sensitive and specific detection of MPXV is crucial for preventing the spread of the disease. Pyrococcus furiosus Argonaute (PfAgo) is an artificial DNA-guided restriction cleavage enzyme programmable with 5'-phosphorylated ssDNA sequences, which can be developed to specifically detect nucleic acids of pathogens. Here, a PfAgo-based system was established for the detection of MPXV-specific DNA targeting the F3L gene. A short amplicon of 79 bp could be obtained through a fast PCR procedure, which was completed within 45 min. Two 5'-phosphorylation guide DNAs were designed to guide PfAgo to cleave the amplicon to obtain an 18 bp 5'-phosphorylation sequence specific to MPXV, not to other orthopoxviruses (cowpox, variola, and vaccinia viruses). The 18 bp sequence guided PfAgo to cleave a designed probe specific to MPXV to emit fluorescence. With optimized conditions for the PfAgo-MPXV system, it could be completed in 60 min for the detection of the extracted MPXV DNA with the limit of detection (LOD) of 1.1 copies/reaction and did not depend on expensive instruments. Successful application of the PfAgo-MPXV system in sensitively detecting MPXV in simulated throat swabs, skin swabs, sera, and wastewater demonstrated the system's good performance. The PfAgo platform, with high sensitivity and specificity established here, has the potential to prevent the spread of MPXV.
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Affiliation(s)
- Ping He
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhao Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Finocchio G, Koopal B, Potocnik A, Heijstek C, Westphal AH, Jinek M, Swarts DC. Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA. Nucleic Acids Res 2024; 52:2012-2029. [PMID: 38224450 PMCID: PMC10899771 DOI: 10.1093/nar/gkad1248] [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: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
In both prokaryotic and eukaryotic innate immune systems, TIR domains function as NADases that degrade the key metabolite NAD+ or generate signaling molecules. Catalytic activation of TIR domains requires oligomerization, but how this is achieved varies in distinct immune systems. In the Short prokaryotic Argonaute (pAgo)/TIR-APAZ (SPARTA) immune system, TIR NADase activity is triggered upon guide RNA-mediated recognition of invading DNA by an unknown mechanism. Here, we describe cryo-EM structures of SPARTA in the inactive monomeric and target DNA-activated tetrameric states. The monomeric SPARTA structure reveals that in the absence of target DNA, a C-terminal tail of TIR-APAZ occupies the nucleic acid binding cleft formed by the pAgo and TIR-APAZ subunits, inhibiting SPARTA activation. In the active tetrameric SPARTA complex, guide RNA-mediated target DNA binding displaces the C-terminal tail and induces conformational changes in pAgo that facilitate SPARTA-SPARTA dimerization. Concurrent release and rotation of one TIR domain allow it to form a composite NADase catalytic site with the other TIR domain within the dimer, and generate a self-complementary interface that mediates cooperative tetramerization. Combined, this study provides critical insights into the structural architecture of SPARTA and the molecular mechanism underlying target DNA-dependent oligomerization and catalytic activation.
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Affiliation(s)
- Giada Finocchio
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Balwina Koopal
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Ana Potocnik
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Clint Heijstek
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Daan C Swarts
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
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18
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Oh C, Xun G, Lane ST, Petrov VA, Zhao H, Nguyen TH. Portable, single nucleotide polymorphism-specific duplex assay for virus surveillance in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168701. [PMID: 37992833 DOI: 10.1016/j.scitotenv.2023.168701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
The Argonaute protein from the archaeon Pyrococcus furiosus (PfAgo) is a DNA-guided nuclease that targets DNA with any sequence. We designed a virus detection assay in which the PfAgo enzyme cleaves the reporter probe, thus generating fluorescent signals when amplicons from a reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay contain target sequences. We confirmed that the RT-LAMP-PfAgo assay for the SARS-CoV-2 Delta variant produced significantly higher fluorescent signals (p < 0.001) when a single nucleotide polymorphism (SNP), exclusive to the Delta variant, was present, compared to the samples without the SNP. Additionally, the duplex assay for Pepper mild mottle virus (PMMOV) and SARS-CoV-2 detection produced specific fluorescent signals (FAM or ROX) only when the corresponding sequences were present. Furthermore, the RT-LAMP-PfAgo assay does not require dilution to reduce the impact of environmental inhibitors. The limit of detection of the PMMOV assay, determined with 30 wastewater samples, was 28 gc/μL, with a 95 % confidence interval of [11,103]. Finally, using a point-of-use device, the RT-LAMP-PfAgo assay successfully detected PMMOV in wastewater samples. Based on our findings, we conclude that the RT-LAMP-PfAgo assay can be used as a portable, SNP-specific duplex assay, which will significantly improve virus surveillance in wastewater.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Department of Environmental Engineering Sciences, University of Florida, Gainesville, FL, USA.
| | - Guanhua Xun
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stephan Thomas Lane
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
| | - Vassily Andrew Petrov
- Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States
| | - Huimin Zhao
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States; Departments of Chemical and Biomolecular Engineering, Chemistry, and Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, United States; Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
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19
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Wang L, Chen W, Zhang C, Xie X, Huang F, Chen M, Mao W, Yu N, Wei Q, Ma L, Li Z. Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute. Mol Cell 2024; 84:675-686.e4. [PMID: 38295801 DOI: 10.1016/j.molcel.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/15/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
The Argonaute nuclease from the thermophilic archaeon Pyrococcus furiosus (PfAgo) contributes to host defense and represents a promising biotechnology tool. Here, we report the structure of a PfAgo-guide DNA-target DNA ternary complex at the cleavage-compatible state. The ternary complex is predominantly dimerized, and the dimerization is solely mediated by PfAgo at PIWI-MID, PIWI-PIWI, and PAZ-N interfaces. Additionally, PfAgo accommodates a short 14-bp guide-target DNA duplex with a wedge-type N domain and specifically recognizes 5'-phosphorylated guide DNA. In contrast, the PfAgo-guide DNA binary complex is monomeric, and the engagement of target DNA with 14-bp complementarity induces sufficient dimerization and activation of PfAgo, accompanied by movement of PAZ and N domains. A closely related Argonaute from Thermococcus thioreducens adopts a similar dimerization configuration with an additional zinc finger formed at the dimerization interface. Dimerization of both Argonautes stabilizes the catalytic loops, highlighting the important role of Argonaute dimerization in the activation and target cleavage.
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Affiliation(s)
- Longyu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wanping Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Chendi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xiaochen Xie
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Fuyong Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Miaomiao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wuxiang Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Na Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qiang Wei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
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20
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Lan Y, Xu B, Xi Y, Luo Y, Guo X, Huang Z, Luo D, Zhu A, He P, Li C, Huang Q, Li Q. Accurate Detection of Multiple Tumor Mutations in Formalin-Fixed Paraffin-Embedded Tissues by Coupling Sequence Artifacts Elimination and Mutation Enrichment With MeltArray. J Transl Med 2024; 104:100300. [PMID: 38042496 DOI: 10.1016/j.labinv.2023.100300] [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: 09/07/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are the primary source of DNA for companion diagnostics (CDx) of cancers. Degradation of FFPE tissue DNA and inherent tumor heterogeneity constitute serious challenges in current CDx assays. To address these limitations, we introduced sequence artifact elimination and mutation enrichment to MeltArray, a highly multiplexed PCR approach, to establish an integrated protocol that provides accuracy, ease of use, and rapidness. Using PIK3CA mutations as a model, we established a MeltArray protocol that could eliminate sequence artifacts completely and enrich mutations from 23.5- to 59.4-fold via a single-reaction pretreatment step comprising uracil-DNA-glycosylase excision and PCR clamping. The entire protocol could identify 13 PIK3CA hotspot mutations of 0.05% to 0.5% mutant allele fractions within 5 hours. Evaluation of 106 breast cancer and 40 matched normal FFPE tissue samples showed that all 47 PIK3CA mutant samples were from the cancer tissue, and no false-positive results were detected in the normal samples. Further evaluation of 105 colorectal and 40 matched normal FFPE tissue samples revealed that 11 PIK3CA mutants were solely from the cancer sample. The detection results of our protocol were consistent with those of the droplet digital PCR assays that underwent sequence artifact elimination. Of the 60 colorectal samples with next-generation sequencing results, the MeltArray protocol detected 2 additional mutant samples with low mutant allele fractions. We conclude that the new protocol provides an improved alternative to current CDx assays for detecting tumor mutations in FFPE tissue DNA.
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Affiliation(s)
- Yanping Lan
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Boheng Xu
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, China
| | - Yuxin Xi
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yi Luo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China; School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiaoxia Guo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zhibin Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Danjiao Luo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Anqi Zhu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Pujing He
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Changxing Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China; School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Qiuying Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
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21
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Zhang Y, Gong B, Lin Y, Zhu Y, Su G, Yu Y. Split G-quadruplex based PfAgo sensing platform for nucleotide mutation discrimination and human genotyping. Analyst 2024; 149:707-711. [PMID: 38230655 DOI: 10.1039/d3an02090h] [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: 01/18/2024]
Abstract
A PfAgo-G4 sensing platform exploiting G4 as a signal reporter was proposed, validated, and optimized. By introducing two mismatches at the Link strand, a universal nucleotide design rule was established for accurate single nucleotide polymorphism discrimination with PfAgo-G4. The FUT2 gene was then successfully and accurately genotyped using human buccal swab samples.
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Affiliation(s)
- Yan Zhang
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
| | - Bin Gong
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
| | - Yanan Lin
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
| | - Yuedong Zhu
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
| | - Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
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22
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Lu X, Xiao J, Wang L, Zhu B, Huang F. The nuclease-associated short prokaryotic Argonaute system nonspecifically degrades DNA upon activation by target recognition. Nucleic Acids Res 2024; 52:844-855. [PMID: 38048327 PMCID: PMC10810196 DOI: 10.1093/nar/gkad1145] [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: 05/05/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023] Open
Abstract
Prokaryotic Argonautes (pAgos) play a vital role in host defense by utilizing short nucleic acid guides to recognize and target complementary nucleic acids. Despite being the majority of pAgos, short pAgos have only recently received attention. Short pAgos are often associated with proteins containing an APAZ domain and a nuclease domain including DUF4365, SMEK, or HNH domain. In contrast to long pAgos that specifically cleave the target DNA, our study demonstrates that the short pAgo from Thermocrispum municipal, along with its associated DUF4365-APAZ protein, forms a heterodimeric complex. Upon RNA-guided target DNA recognition, this complex is activated to nonspecifically cleave DNA. Additionally, we found that the TmuRE-Ago complex shows a preference for 5'-OH guide RNA, specifically requires a uridine nucleotide at the 5' end of the guide RNA, and is sensitive to single-nucleotide mismatches between the guide RNA and target DNA. Based on its catalytic properties, our study has established a novel nucleic acid detection method and demonstrated its feasibility. This study not only expands our understanding of the defense mechanism employed by short pAgo systems but also suggests their potential applications in nucleic acid detection.
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Affiliation(s)
- Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jun Xiao
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Longfei Wang
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518063, China
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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23
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Li Y, Tang X, Wang N, Zhao Z, Man S, Zhu L, Ma L. Argonaute-DNAzyme tandem biosensing for highly sensitive and simultaneous dual-gene detection of methicillin-resistant Staphylococcus aureus. Biosens Bioelectron 2024; 244:115758. [PMID: 37931440 DOI: 10.1016/j.bios.2023.115758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), a common zoonotic multidrug-resistant bacterium, puts a great threat to public health and food safety. Rapid and reliable detection of MRSA is crucial to guide effective patient treatment at early stages of infection and control the spread of MRSA infections. Herein, we developed a Simultaneous dual-gene and ulTra-sensitive detection for methicillin-resistant Staphylococcus aureus using Argonaute-DNAzyme tandem Detection (STAND). Simply, loop-mediated isothermal amplification (LAMP) was used for the amplification of the species-specific mecA and nuc gene, followed by STAND enabled by the site-specific cleavage of programable Argonaute. The Argonaute-DNAzyme tandem reaction rendered a conceptually novel signal amplification and transduction module that was more sensitive (1 or 2 order of magnitude higher) than the original Argonaute-based biosensing. With the strategy, the target nucleic acid signals gene were dexterously converted into fluorescent signals. STAND could detect the nuc gene and mecA gene simultaneously in a single reaction with 1 CFU/mL MRSA and a dynamic range from 1 to 108 CFU/mL. This method was confirmed by clinical samples and challenged by identifying contaminated foods and MRSA-infected animals. This work enriches the arsenal of Argonaute-mediated biosensing and presents a novel biosensing strategy to detect pathogenic bacteria with ultra-sensitivity, specificity and on-site capability.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Nan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Lei Zhu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
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24
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Graver BA, Chakravarty N, Solomon KV. Prokaryotic Argonautes for in vivo biotechnology and molecular diagnostics. Trends Biotechnol 2024; 42:61-73. [PMID: 37451948 DOI: 10.1016/j.tibtech.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
Prokaryotic Argonautes (pAgos) are an emerging class of programmable endonucleases that are believed to be more flexible than existing CRISPR-Cas systems and have significant potential for biotechnology. Current applications of pAgos include a myriad of molecular diagnostics and in vitro DNA assembly tools. However, efforts have historically been centered on thermophilic pAgo variants. To enable in vivo biotechnological applications such as gene editing, focus has shifted to pAgos from mesophilic organisms. We discuss what is known of pAgos, how they are being developed for various applications, and strategies to overcome current challenges to in vivo applications in prokaryotes and eukaryotes.
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Affiliation(s)
- Brett A Graver
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Namrata Chakravarty
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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25
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Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S. Nucleic-acid-triggered NADase activation of a short prokaryotic Argonaute. Nature 2024; 625:822-831. [PMID: 37783228 DOI: 10.1038/s41586-023-06665-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Argonaute (Ago) proteins mediate RNA- or DNA-guided inhibition of nucleic acids1,2. Although the mechanisms used by eukaryotic Ago proteins and long prokaryotic Ago proteins (pAgos) are known, that used by short pAgos remains elusive. Here we determined the cryo-electron microscopy structures of a short pAgo and the associated TIR-APAZ proteins (SPARTA) from Crenotalea thermophila (Crt): a free-state Crt-SPARTA; a guide RNA-target DNA-loaded Crt-SPARTA; two Crt-SPARTA dimers with distinct TIR organization; and a Crt-SPARTA tetramer. These structures reveal that Crt-SPARTA is composed of a bilobal-fold Ago lobe that connects with a TIR lobe. Whereas the Crt-Ago contains a MID and a PIWI domain, Crt-TIR-APAZ has a TIR domain, an N-like domain, a linker domain and a trigger domain. The bound RNA-DNA duplex adopts a B-form conformation that is recognized by base-specific contacts. Nucleic acid binding causes conformational changes because the trigger domain acts as a 'roadblock' that prevents the guide RNA 5' ends and the target DNA 3' ends from reaching their canonical pockets; this disorders the MID domain and promotes Crt-SPARTA dimerization. Two RNA-DNA-loaded Crt-SPARTA dimers form a tetramer through their TIR domains. Four Crt-TIR domains assemble into two parallel head-to-tail-organized TIR dimers, indicating an NADase-active conformation, which is supported by our mutagenesis study. Our results reveal the structural basis of short-pAgo-mediated defence against invading nucleic acids, and provide insights for optimizing the detection of SPARTA-based programmable DNA sequences.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Kun Shang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- Medical School, Yan'an University, Yan'an, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Zhixia Mu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Xingke Fu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Hongtao Zhu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
| | - Wei Ding
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China.
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26
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Beskrovnaia M, Agapov A, Makasheva K, Zharkov DO, Esyunina D, Kulbachinskiy A. Sensing of DNA modifications by pAgo proteins in vitro. Biochimie 2023; 220:39-47. [PMID: 38128776 DOI: 10.1016/j.biochi.2023.12.006] [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: 10/11/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Many prokaryotic Argonaute (pAgo) proteins act as programmable nucleases that use small guide DNAs for recognition and cleavage of complementary target DNA. Recent studies suggested that pAgos participate in cell defense against invader DNA and may also be involved in other genetic processes, including DNA replication and repair. The ability of pAgos to recognize specific targets potentially make them an invaluable tool for DNA manipulations. Here, we demonstrate that DNA-guided DNA-targeting pAgo nucleases from three bacterial species, DloAgo from Dorea longicatena, CbAgo from Clostridium butyricum and KmAgo from Kurthia massiliensis, can sense site-specific modifications in the target DNA, including 8-oxoguanine, thymine glycol, ethenoadenine and pyrimidine dimers. The effects of DNA modifications on the activity of pAgos strongly depend on their positions relative to the site of cleavage and are comparable to or exceed the effects of guide-target mismatches at corresponding positions. For all tested pAgos, the strongest effects are observed when DNA lesions are located at the cleavage position. The results demonstrate that DNA cleavage by pAgos is strongly affected by DNA modifications, thus making possible their use as sensors of DNA damage.
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Affiliation(s)
| | - Aleksei Agapov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Kristina Makasheva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, 630090, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, 630090, Russia
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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27
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Jang H, Song J, Kim S, Byun JH, Lee KG, Park KH, Woo E, Lim EK, Jung J, Kang T. ANCA: artificial nucleic acid circuit with argonaute protein for one-step isothermal detection of antibiotic-resistant bacteria. Nat Commun 2023; 14:8033. [PMID: 38052830 DOI: 10.1038/s41467-023-43899-4] [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: 06/15/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
Endonucleases have recently widely used in molecular diagnostics. Here, we report a strategy to exploit the properties of Argonaute (Ago) proteins for molecular diagnostics by introducing an artificial nucleic acid circuit with Ago protein (ANCA) method. The ANCA is designed to perform a continuous autocatalytic reaction through cross-catalytic cleavage of the Ago protein, enabling one-step, amplification-free, and isothermal DNA detection. Using the ANCA method, carbapenemase-producing Klebsiella pneumoniae (CPKP) are successfully detected without DNA extraction and amplification steps. In addition, we demonstrate the detection of carbapenem-resistant bacteria in human urine and blood samples using the method. We also demonstrate the direct identification of CPKP swabbed from surfaces using the ANCA method in conjunction with a three-dimensional nanopillar structure. Finally, the ANCA method is applied to detect CPKP in rectal swab specimens from infected patients, achieving sensitivity and specificity of 100% and 100%, respectively. The developed method can contribute to simple, rapid and accurate diagnosis of CPKP, which can help prevent nosocomial infections.
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Affiliation(s)
- Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital Research Institute, 175 Cambridge Street, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA, 02114, USA
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Kyoung G Lee
- Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kwang-Hyun Park
- Disease Target Structure Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Euijeon Woo
- Disease Target Structure Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea.
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28
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Wang Y, Chen Y, Tang Y, Wang Y, Gao S, Yang L, Wang P. A recombinase polymerase amplification and Pyrococcus furiosus Argonaute combined method for ultra-sensitive detection of white spot syndrome virus in shrimp. JOURNAL OF FISH DISEASES 2023; 46:1357-1365. [PMID: 37635423 DOI: 10.1111/jfd.13853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023]
Abstract
White spot disease (WSD) in shrimp is an acute infectious disease caused by white spot syndrome virus (WSSV). WSD has seriously threatened the security of shrimp farming, causing huge economic losses worldwide. As there is currently no effective treatment for WSD, developing early detection technologies for WSSV is of great significance for the prevention. In this study, we have established a detection method for WSSV using a combination of recombinase polymerase amplification (RPA) and Pyrococcus furiosus Argonaute (PfAgo). We have achieved a detection sensitivity of single copy per reaction, which is more sensitive than the previously reported detection methods. Additionally, we have demonstrated high specificity. The entire detection process can be completed within 75 min without the need for precise thermal cyclers, making it suitable for on-site testing. The fluorescence signal generated by the reaction can be quantified using a portable fluorescence detector or observed with the naked eye under a blue light background. This study provides an ultrasensitive on-site detection method for WSSV in shrimp aquaculture and expands the application of PfAgo in the field of aquatic disease diagnosis.
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Affiliation(s)
- Yu Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Yukang Chen
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Yixin Tang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Yue Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Lihong Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Ocean University, Lianyungang, China
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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Chen R, Zhao J, Han M, Dong Y, Jiang F, Chen Y. DNA Extraction- and Amplification-Free Nucleic Acid Biosensor for the Detection of Foodborne Pathogens Based on CRISPR/Cas12a and Argonaute Protein-Mediated Cascade Signal Amplification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18037-18045. [PMID: 37947312 DOI: 10.1021/acs.jafc.3c06530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
A novel method for detecting low levels of viable foodborne pathogens, specifically Salmonella typhimurium (S. typhimurium), has been developed. Traditional nucleic acid assay, such as polymerase chain reaction (PCR), often requires complex DNA extraction and amplification, making it challenging to differentiate between viable and nonviable pathogens. This assay employed a phage as the recognition element to precisely identify and lyse viable S. typhimurium that can undergo DNA extraction. It combined the efficient trans-cleavage activities of CRISPR/Cas12a with the specific cleavage advantages of Argonaute proteins, enabling ultrasensitive detection. This double-enzyme-mediated nucleic acid test can accurately distinguish viable and nonviable S. typhimurium with a detection limit of 23 CFU/mL without DNA amplification. The method was successfully applied to common food samples, producing results consistent with quantitative PCR tests. This work provides a promising platform for easily detecting viable foodborne pathogens with high sensitivity without the need for DNA extraction and amplification.
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Affiliation(s)
- Rui Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junpeng Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Minjie Han
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yongzhen Dong
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian, Liaoning 116034, China
| | - Feng Jiang
- Key Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Wuhan 430075, China
| | - Yiping Chen
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian, Liaoning 116034, China
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30
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Song X, Lei S, Liu S, Liu Y, Fu P, Zeng Z, Yang K, Chen Y, Li M, She Q, Han W. Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection. Nat Commun 2023; 14:6970. [PMID: 37914725 PMCID: PMC10620215 DOI: 10.1038/s41467-023-42793-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Diverse prokaryotic Agos (pAgos) play potential functions in microbial defense. The functions and mechanisms of a group of full-length yet catalytically inactive pAgos, long-B pAgos, remain unclear. Here, we show that most long-B pAgos are functionally connected with distinct associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. The long-B pAgo-nuclease system (BPAN) is activated by guide RNA-directed target DNA recognition and performs collateral DNA degradation in vitro. In vivo, the system mediates genomic DNA degradation after sensing invading plasmid, which kills the infected cells and results in the depletion of the invader from the cell population. Together, the BPAN system provides immunoprotection via abortive infection. Our data also suggest that the defense strategy is employed by other long-B pAgos equipped with distinct associated proteins.
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Affiliation(s)
- Xinmi Song
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Sheng Lei
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shunhang Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yanqiu Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Pan Fu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ke Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ming Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, 266237, Jimo, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China.
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31
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Sun K, Liu Y, Zhao W, Ma B, Zhang M, Yu X, Ye Z. Prokaryotic Argonaute Proteins: A New Frontier in Point-of-Care Viral Diagnostics. Int J Mol Sci 2023; 24:14987. [PMID: 37834437 PMCID: PMC10573157 DOI: 10.3390/ijms241914987] [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: 08/09/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
The recent pandemic of SARS-CoV-2 has underscored the critical need for rapid and precise viral detection technologies. Point-of-care (POC) technologies, which offer immediate and accurate testing at or near the site of patient care, have become a cornerstone of modern medicine. Prokaryotic Argonaute proteins (pAgo), proficient in recognizing target RNA or DNA with complementary sequences, have emerged as potential game-changers. pAgo present several advantages over the currently popular CRISPR/Cas systems-based POC diagnostics, including the absence of a PAM sequence requirement, the use of shorter nucleic acid molecules as guides, and a smaller protein size. This review provides a comprehensive overview of pAgo protein detection platforms and critically assesses their potential in the field of viral POC diagnostics. The objective is to catalyze further research and innovation in pAgo nucleic acid detection and diagnostics, ultimately facilitating the creation of enhanced diagnostic tools for clinic viral infections in POC settings.
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Affiliation(s)
| | | | | | | | | | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (K.S.); (Y.L.); (W.Z.); (B.M.); (M.Z.)
| | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China; (K.S.); (Y.L.); (W.Z.); (B.M.); (M.Z.)
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32
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Marsic T, Gundra SR, Wang Q, Aman R, Mahas A, Mahfouz M. Programmable site-specific DNA double-strand breaks via PNA-assisted prokaryotic Argonautes. Nucleic Acids Res 2023; 51:9491-9506. [PMID: 37560931 PMCID: PMC10516665 DOI: 10.1093/nar/gkad655] [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: 05/05/2023] [Revised: 07/14/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Programmable site-specific nucleases promise to unlock myriad applications in basic biology research, biotechnology and gene therapy. Gene-editing systems have revolutionized our ability to engineer genomes across diverse eukaryotic species. However, key challenges, including delivery, specificity and targeting organellar genomes, pose barriers to translational applications. Here, we use peptide nucleic acids (PNAs) to facilitate precise DNA strand invasion and unwinding, enabling prokaryotic Argonaute (pAgo) proteins to specifically bind displaced single-stranded DNA and introduce site-specific double-strand breaks (DSBs) independent of the target sequence. We named this technology PNA-assisted pAgo editing (PNP editing) and determined key parameters for designing PNP editors to efficiently generate programable site-specific DSBs. Our design allows the simultaneous use of multiple PNP editors to generate multiple site-specific DSBs, thereby informing design considerations for potential in vitro and in vivo applications, including genome editing.
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Affiliation(s)
- Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Sivakrishna Rao Gundra
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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33
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Lin Q, Cao Y, Han G, Sun W, Weng W, Chen H, Wang H, Kong J. Programmable Clostridium perfringens Argonaute-Based, One-Pot Assay for the Multiplex Detection of miRNAs. Anal Chem 2023; 95:13401-13406. [PMID: 37565811 DOI: 10.1021/acs.analchem.3c01990] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Assays for the molecular detection of miRNAs are typically constrained by the level of multiplexing, especially in a single tube. Here, we report a general and programmable diagnostic platform by combining mesophilic Clostridium perfringens Argonaute (CpAgo) with exponential isothermal amplification (EXPAR), which is a dual-signal amplification strategy, allowing for the rapid and sensitive detection of multiple miRNAs with single-nucleotide discrimination in one pot. The CpAgo-based One-Pot (COP) assay achieved a limit of detection of 1 zM miRNA within 30 min of turnaround time and a wide concentration range. This COP assay was applied to simultaneously detect four miRNAs in a single tube from clinical serum samples, showing superior analytical performance in distinguishing colorectal cancer patients from healthy individuals. This programmable, one-pot, multiplex, rapid, and specific strategy offers great promise in scientific research and clinical applications.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry, Fudan University, 200438 Shanghai, China
| | - Yuanwei Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Guobin Han
- Department of Chemistry, Fudan University, 200438 Shanghai, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Wenhao Weng
- Department of Clinical Laboratory Yangpu Hospital, Tongji University School of Medicine, 200090 Shanghai, China
| | - Hui Chen
- Department of Chemistry, Fudan University, 200438 Shanghai, China
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, 200438 Shanghai, China
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34
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Wu Z, Yu L, Shi W, Ma J. Argonaute protein-based nucleic acid detection technology. Front Microbiol 2023; 14:1255716. [PMID: 37744931 PMCID: PMC10515653 DOI: 10.3389/fmicb.2023.1255716] [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: 07/09/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023] Open
Abstract
It is vital to diagnose pathogens quickly and effectively in the research and treatment of disease. Argonaute (Ago) proteins are recently discovered nucleases with nucleic acid shearing activity that exhibit specific recognition properties beyond CRISPR-Cas nucleases, which are highly researched but restricted PAM sequence recognition. Therefore, research on Ago protein-mediated nucleic acid detection technology has attracted significant attention from researchers in recent years. Using Ago proteins in developing nucleic acid detection platforms can enable efficient, convenient, and rapid nucleic acid detection and pathogen diagnosis, which is of great importance for human life and health and technological development. In this article, we introduce the structure and function of Argonaute proteins and discuss the latest advances in their use in nucleic acid detection.
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Affiliation(s)
- Zhiyun Wu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Li Yu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Institute of Stem Cell, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Weifeng Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Jinhong Ma
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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35
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Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM. Oligomerization-mediated activation of a short prokaryotic Argonaute. Nature 2023; 621:154-161. [PMID: 37494956 DOI: 10.1038/s41586-023-06456-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
Although eukaryotic and long prokaryotic Argonaute proteins (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyse NAD(P)+ to induce bacterial cell death1. Here we present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Argonaute (Ago) protein and TIR-APAZ, an associated protein2. SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA-DNA-bound state, two dimeric RNA-DNA-bound states and a tetrameric RNA-DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. The RNA-DNA-binding channel of apo inactive SPARTA is occupied by an auto-inhibitory motif in TIR-APAZ. After the binding of RNA-DNA, SPARTA transitions from a monomer to a symmetric dimer and then an asymmetric dimer, in which two TIR domains interact through charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolysing NAD(P)+. In addition, we observe unique features of interactions between SPARTA and RNA-DNA, including competition between the DNA 3' end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings provide a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily.
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Affiliation(s)
- Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center and Center for Cancer Metabolism, The Ohio State University, Columbus, OH, USA
| | - Xiao-Yuan Yang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center and Center for Cancer Metabolism, The Ohio State University, Columbus, OH, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Shiyu Xia
- Divison of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- Comprehensive Cancer Center and Center for Cancer Metabolism, The Ohio State University, Columbus, OH, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA.
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36
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Wang Y, Wang Y, Chen Y, Yan Q, Lin A. Research progress in mitochondrial gene editing technology. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:460-472. [PMID: 37643980 PMCID: PMC10495247 DOI: 10.3724/zdxbyxb-2023-0129] [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: 03/17/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations result in a variety of genetic diseases. As an emerging therapeutic method, mtDNA editing technology recognizes targets more based on the protein and less on the nucleic acid. Although the protein recognition type mtDNA editing technology represented by zinc finger nuclease technology, transcription activator like effector nuclease technology and base editing technology has made some progress, the disadvantages of complex recognition sequence design hinder further popularization. Gene editing based on nucleic acid recognition by the CRISPR system shows superiority due to the simple structure, easy design and modification. However, the lack of effective means to deliver nucleic acids into mitochondria limits application in the field of mtDNA editing. With the advances in the study of endogenous and exogenous import pathways and the deepening understanding of DNA repair mechanisms, growing evidence shows the feasibility of nucleic acid delivery and the broad application prospects of nucleic acid recognition type mtDNA editing technology. Based on the classification of recognition elements, this article summarizes the current principles and development of mitochondrial gene editing technology, and discusses its application prospects.
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Affiliation(s)
- Yichen Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Zhejiang University Cancer Center, Hangzhou 310058, China.
| | - Ying Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Yu Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Qingfeng Yan
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Zhejiang University Cancer Center, Hangzhou 310058, China.
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Center for RNA Medicine, International Institutes of Medicine, Zhejiang University, Jinhua 322000, Zhejiang Province, China.
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37
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Liu Q, Chen W, Zhang Y, Hu F, Jiang X, Wang F, Liu Y, Ma L. A programmable pAgo nuclease with RNA target-cleavage specificity from the mesophilic bacterium Verrucomicrobia. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1204-1212. [PMID: 37431184 PMCID: PMC10448046 DOI: 10.3724/abbs.2023110] [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: 10/15/2022] [Accepted: 02/10/2023] [Indexed: 07/12/2023] Open
Abstract
Argonaute (Ago) proteins are conserved programmable nucleases present in eukaryotes and prokaryotes and provide defense against mobile genetic elements. Almost all characterized pAgos prefer to cleave DNA targets. Here, we describe a novel pAgo from Verrucomicrobia bacterium (VbAgo) that can specifically cleave RNA targets rather than DNA targets at 37°C and function as a multiple-turnover enzyme showing prominent catalytic capacity. VbAgo utilizes DNA guides (gDNAs) to cleave RNA targets at the canonical cleavage site. Meanwhile, the cleavage activity is remarkably strengthened at low concentrations of NaCl. In addition, VbAgo presents a weak tolerance for mismatches between gDNAs and RNA targets, and single-nucleotide mismatches at positions 11‒12 and dinucleotide mismatches at positions 3‒15 dramatically reduce target cleavage. Moreover, VbAgo can efficiently cleave highly structured RNA targets at 37°C. These properties of VbAgo broaden our understanding of Ago proteins and expand the pAgo-based RNA manipulation toolbox.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China
| | - Wanping Chen
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China
- School of PharmacyQingdao UniversityQingdao266071China
| | - Yue Zhang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China
| | - Fengyang Hu
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China
| | - Xiaoman Jiang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China
- Hubei Jiangxia LaboratoryWuhan430200China
| | - Yang Liu
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan430062China
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38
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Wang S, Sun E, Liu Y, Yin B, Zhang X, Li M, Huang Q, Tan C, Qian P, Rao VB, Tao P. Landscape of New Nuclease-Containing Antiphage Systems in Escherichia coli and the Counterdefense Roles of Bacteriophage T4 Genome Modifications. J Virol 2023; 97:e0059923. [PMID: 37306585 PMCID: PMC10308915 DOI: 10.1128/jvi.00599-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 05/19/2023] [Indexed: 06/13/2023] Open
Abstract
Many phages, such as T4, protect their genomes against the nucleases of bacterial restriction-modification (R-M) and CRISPR-Cas systems through covalent modification of their genomes. Recent studies have revealed many novel nuclease-containing antiphage systems, raising the question of the role of phage genome modifications in countering these systems. Here, by focusing on phage T4 and its host Escherichia coli, we depicted the landscape of the new nuclease-containing systems in E. coli and demonstrated the roles of T4 genome modifications in countering these systems. Our analysis identified at least 17 nuclease-containing defense systems in E. coli, with type III Druantia being the most abundant system, followed by Zorya, Septu, Gabija, AVAST type 4, and qatABCD. Of these, 8 nuclease-containing systems were found to be active against phage T4 infection. During T4 replication in E. coli, 5-hydroxymethyl dCTP is incorporated into the newly synthesized DNA instead of dCTP. The 5-hydroxymethylcytosines (hmCs) are further modified by glycosylation to form glucosyl-5-hydroxymethylcytosine (ghmC). Our data showed that the ghmC modification of the T4 genome abolished the defense activities of Gabija, Shedu, Restriction-like, type III Druantia, and qatABCD systems. The anti-phage T4 activities of the last two systems can also be counteracted by hmC modification. Interestingly, the Restriction-like system specifically restricts phage T4 containing an hmC-modified genome. The ghmC modification cannot abolish the anti-phage T4 activities of Septu, SspBCDE, and mzaABCDE, although it reduces their efficiency. Our study reveals the multidimensional defense strategies of E. coli nuclease-containing systems and the complex roles of T4 genomic modification in countering these defense systems. IMPORTANCE Cleavage of foreign DNA is a well-known mechanism used by bacteria to protect themselves from phage infections. Two well-known bacterial defense systems, R-M and CRISPR-Cas, both contain nucleases that cleave the phage genomes through specific mechanisms. However, phages have evolved different strategies to modify their genomes to prevent cleavage. Recent studies have revealed many novel nuclease-containing antiphage systems from various bacteria and archaea. However, no studies have systematically investigated the nuclease-containing antiphage systems of a specific bacterial species. In addition, the role of phage genome modifications in countering these systems remains unknown. Here, by focusing on phage T4 and its host Escherichia coli, we depicted the landscape of the new nuclease-containing systems in E. coli using all 2,289 genomes available in NCBI. Our studies reveal the multidimensional defense strategies of E. coli nuclease-containing systems and the complex roles of genomic modification of phage T4 in countering these defense systems.
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Affiliation(s)
- Shuangshuang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Erchao Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Yuepeng Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Baoqi Yin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Xueqi Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Mengling Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Ping Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Pan Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
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Olina A, Agapov A, Yudin D, Sutormin D, Galivondzhyan A, Kuzmenko A, Severinov K, Aravin AA, Kulbachinskiy A. Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli. Microbiol Spectr 2023; 11:e0414622. [PMID: 37102866 PMCID: PMC10269773 DOI: 10.1128/spectrum.04146-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/29/2023] [Indexed: 04/28/2023] Open
Abstract
Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we show that two pAgos from cyanobacteria Synechococcus elongatus (SeAgo) and Limnothrix rosea (LrAgo) are active in heterologous Escherichia coli and aid cell division in the presence of the gyrase inhibitor ciprofloxacin, depending on the host double-strand break repair machinery. Both pAgos are preferentially loaded with small guide DNAs (smDNAs) derived from the sites of replication termination. Ciprofloxacin increases the amounts of smDNAs from the termination region and from the sites of genomic DNA cleavage by gyrase, suggesting that smDNA biogenesis depends on DNA replication and is stimulated by gyrase inhibition. Ciprofloxacin enhances asymmetry in the distribution of smDNAs around Chi sites, indicating that it induces double-strand breaks that serve as a source of smDNA during their processing by RecBCD. While active in E. coli, SeAgo does not protect its native host S. elongatus from ciprofloxacin. These results suggest that pAgo nucleases may help to complete replication of chromosomal DNA by promoting chromosome decatenation or participating in the processing of gyrase cleavage sites, and may switch their functional activities depending on the host species. IMPORTANCE Prokaryotic Argonautes (pAgos) are programmable nucleases with incompletely understood functions in vivo. In contrast to eukaryotic Argonautes, most studied pAgos recognize DNA targets. Recent studies suggested that pAgos can protect bacteria from invader DNA and counteract phage infection and may also have other functions including possible roles in DNA replication, repair, and gene regulation. Here, we have demonstrated that two cyanobacterial pAgos, SeAgo and LrAgo, can assist DNA replication and facilitate cell division in the presence of topoisomerase inhibitors in Escherichia coli. They are specifically loaded with small guide DNAs from the region of replication termination and protect the cells from the action of the gyrase inhibitor ciprofloxacin, suggesting that they help to complete DNA replication and/or repair gyrase-induced breaks. The results show that pAgo proteins may serve as a backup to topoisomerases under conditions unfavorable for DNA replication and may modulate the resistance of host bacterial strains to antibiotics.
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Affiliation(s)
- Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Denis Yudin
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Dmitry Sutormin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Anton Kuzmenko
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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40
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Lisitskaya L, Kropocheva E, Agapov A, Prostova M, Panteleev V, Yudin D, Ryazansky S, Kuzmenko A, Aravin A, Esyunina D, Kulbachinskiy A. Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo. Nucleic Acids Res 2023; 51:5106-5124. [PMID: 37094066 PMCID: PMC10250240 DOI: 10.1093/nar/gkad290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Prokaryotic Argonaute proteins (pAgos) are homologs of eukaryotic Argonautes (eAgos) and are also thought to play a role in cell defense against invaders. However, pAgos are much more diverse than eAgos and little is known about their functional activities and target specificities in vivo. Here, we describe five pAgos from mesophilic bacteria that act as programmable DNA endonucleases and analyze their ability to target chromosomal and invader DNA. In vitro, the analyzed proteins use small guide DNAs for precise cleavage of single-stranded DNA at a wide range of temperatures. Upon their expression in Escherichia coli, all five pAgos are loaded with small DNAs preferentially produced from plasmids and chromosomal regions of replication termination. One of the tested pAgos, EmaAgo from Exiguobacterium marinum, can induce DNA interference between homologous sequences resulting in targeted processing of multicopy plasmid and genomic elements. EmaAgo also protects bacteria from bacteriophage infection, by loading phage-derived guide DNAs and decreasing phage DNA content and phage titers. Thus, the ability of pAgos to target multicopy elements may be crucial for their protective function. The wide spectrum of pAgo activities suggests that they may have diverse functions in vivo and paves the way for their use in biotechnology.
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Affiliation(s)
- Lidiya Lisitskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Ekaterina Kropocheva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Maria Prostova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Vladimir Panteleev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny141700, Russia
| | - Denis Yudin
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Anton Kuzmenko
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow123182, Russia
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41
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Boyle TA, Hatoum-Aslan A. Recurring and emerging themes in prokaryotic innate immunity. Curr Opin Microbiol 2023; 73:102324. [PMID: 37163858 PMCID: PMC10360293 DOI: 10.1016/j.mib.2023.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/12/2023]
Abstract
A resurgence of interest in the pathways that bacteria use to protect against their viruses (i.e. phages) has led to the discovery of dozens of new antiphage defenses. Given the sheer abundance and diversity of phages - the ever-evolving targets of immunity - it is not surprising that these newly described defenses are also remarkably diverse. However, as their mechanisms slowly come into focus, some common strategies and themes are also beginning to emerge. This review highlights recurring and emerging themes in the mechanisms of innate immunity in bacteria and archaea, with an emphasis on recently described systems that have undergone more thorough mechanistic characterization.
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Affiliation(s)
- Tori A Boyle
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL 61801, USA
| | - Asma Hatoum-Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL 61801, USA.
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42
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Li Y, Kou J, Han X, Qiao J, Zhang W, Man S, Ma L. Argonaute-triggered visual and rebuilding-free foodborne pathogenic bacteria detection. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131485. [PMID: 37149945 DOI: 10.1016/j.jhazmat.2023.131485] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/15/2023] [Accepted: 04/23/2023] [Indexed: 05/09/2023]
Abstract
Foodborne pathogenic bacteria are recognized as the main causes of microbial contamination in food safety. Early screening and ultrasensitive detection of foodborne pathogenic bacteria is critical procedure to guarantee food safety. Argonaute is emerging as a new tool for detection owing to the programmability and high specificity. We reported a Novel and One-step cleavage method based on Argonaute by integrating Tag-specific primer extension and Exonuclease I (Exo I) for the first time, termed as NOTE-Ago. In this method, the invA of Salmonella typhi and nuc gene of Staphylococcus aureus were amplified using Tag-specific primer and the remaining primers were digested by Exo I. Then amplicons were served as the guide DNA for PfAgo. Consequently, the fluorophore-quencher reporter could be cleaved via PfAgo, resulting in changes in fluorescent intensity. With this strategy, target nucleic acid could be dexterously converted into fluorescent signals. The NOTE-Ago assay could detect 1 CFU/mL with a dynamic range from 1 to 108 CFU/mL. The satisfactory selectivity of NOTE-Ago assay further facilitated its application for detecting S. typhi- and S. aureus-contaminated food samples. This work enriches the toolbox of Argonaute-based detection and provides a one-step cleavage and rebuilding-free method for ultrasensitive detection of bacteria.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Wenlu Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China.
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China.
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43
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Dong Z, Chen X, Zhuo R, Li Y, Zhou Z, Sun Y, Liu Y, Liu M. Efficient manipulation of gene expression using Natronobacterium gregoryi Argonaute in zebrafish. BMC Biol 2023; 21:95. [PMID: 37095525 PMCID: PMC10127001 DOI: 10.1186/s12915-023-01599-x] [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: 01/12/2022] [Accepted: 04/13/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Natronobacterium gregoryi Argonaute (NgAgo) was found to reduce mRNA without generating detectable DNA double-strand breaks in a couple of endogenous genes in zebrafish, suggesting its potential as a tool for gene knockdown. However, little is known about how it interacts with nucleic acid molecules to interfere with gene expression. RESULTS In this study, we first confirmed that coinjection of NgAgo and gDNA downregulated target genes, generated gene-specific phenotypes and verified some factors (including 5' phosphorylation, GC ratio, and target positions) of gDNAs affecting gene downregulation. Therein, the sense and antisense gDNAs were equally effective, suggesting that NgAgo possibly binds to DNA. NgAgo-VP64 with gDNAs targeting promoters upregulated the target genes, further providing evidence that NgAgo interacts with genomic DNA and controls gene transcription. Finally, we explain the downregulation of NgAgo/gDNA target genes by interference with the process of gene transcription, which differs from that of morpholino oligonucleotides. CONCLUSIONS The present study provides conclusions that NgAgo may target genomic DNA and that target positions and the gDNA GC ratio influence its regulation efficiency.
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Affiliation(s)
- Zhangji Dong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong Jiangsu, 226001, China.
| | - Xu Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong Jiangsu, 226001, China
| | - Run Zhuo
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong Jiangsu, 226001, China
| | - Yuanyuan Li
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong Jiangsu, 226001, China
| | - Zhihao Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong Jiangsu, 226001, China
| | - Ying Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong Jiangsu, 226001, China
| | - Yan Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong Jiangsu, 226001, China
| | - Mei Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong Jiangsu, 226001, China.
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44
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Bobadilla Ugarte P, Barendse P, Swarts DC. Argonaute proteins confer immunity in all domains of life. Curr Opin Microbiol 2023; 74:102313. [PMID: 37023508 DOI: 10.1016/j.mib.2023.102313] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 04/08/2023]
Abstract
Both eukaryotes and prokaryotes (archaea and bacteria) encode an arsenal of immune systems that protect the host against mobile genetic elements (MGEs) including viruses, plasmids, and transposons. Whereas Argonaute proteins (Agos) are best known for post-transcriptional gene silencing in eukaryotes, in all domains of life, members from the highly diverse Argonaute protein family act as programmable immune systems. To this end, Agos are programmed with small single-stranded RNA or DNA guides to detect and silence complementary MGEs. Across and within the different domains of life, Agos function in distinct pathways and MGE detection can trigger various mechanisms that provide immunity. In this review, we delineate the diverse immune pathways and underlying mechanisms for both eukaryotic Argonautes (eAgos) and prokaryotic Argonautes (pAgos).
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Affiliation(s)
| | - Patrick Barendse
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Daan C Swarts
- Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, The Netherlands.
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45
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Chen Y, Zeng Z, She Q, Han W. The abortive infection functions of CRISPR-Cas and Argonaute. Trends Microbiol 2023; 31:405-418. [PMID: 36463018 DOI: 10.1016/j.tim.2022.11.005] [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: 09/15/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
CRISPR-Cas and prokaryotic Argonaute (pAgo) are nucleic acid (NA)-guided defense systems that protect prokaryotes against the invasion of mobile genetic elements. Previous studies established that they are directed by NA fragments (guides) to recognize invading complementary NA (targets), and that they cleave the targets to silence the invaders. Nevertheless, growing evidence indicates that many CRISPR-Cas and pAgo systems exploit the abortive infection (Abi) strategy to confer immunity. The CRISPR-Cas and pAgo Abi systems typically sense invaders using the NA recognition ability and activate various toxic effectors to kill the infected cells to prevent the invaders from spreading. This review summarizes the diverse mechanisms of these CRISPR-Cas and pAgo systems, and highlights their critical roles in the arms race between microbes and invaders.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, 266237, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China.
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46
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Panteleev V, Kropocheva E, Esyunina D, Kulbachinskiy A. Strong temperature effects on the fidelity of target DNA recognition by a thermophilic pAgo nuclease. Biochimie 2023; 209:142-149. [PMID: 36804511 DOI: 10.1016/j.biochi.2023.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/22/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
Prokaryotic Argonaute (pAgo) proteins are programmable nucleases with great promise in genetic engineering and biotechnology. Previous studies identified several DNA-targeting pAgo nucleases from mesophilic and thermophilic prokaryotic species that are active in various temperature ranges. However, the effects of temperature on the specificity of target recognition and cleavage by pAgos have not been studied. Here, we describe a thermostable pAgo nuclease from the thermophilic bacterium Thermobrachium celere, TceAgo. We show that TceAgo preferentially uses 5'-phosphorylated small DNA guides and can perform specific cleavage of both single-stranded and double-stranded DNA substrates in a wide range of temperatures. Single-nucleotide mismatches between guide and target molecules differently change the reaction efficiency depending on the mismatch position, with the fidelity of target recognition greatly increased at elevated temperatures. Thus, TceAgo can serve as a tool to allow specific detection and cleavage of DNA targets in a temperature-dependent manner. The results demonstrate that the specificity of programmable nucleases can be strongly affected by the reaction conditions, which should be taken into account when using these nucleases in various in vitro and in vivo applications.
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Affiliation(s)
- Vladimir Panteleev
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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47
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Xie X, Wang L, Ma L. A bacterial Argonaute from Tepiditoga spiralis with the ability of RNA guided plasmid cleavage. Biochem Biophys Res Commun 2023; 640:157-163. [PMID: 36512847 DOI: 10.1016/j.bbrc.2022.11.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022]
Abstract
The eukaryotic Argonaute proteins (eAgos) play an important role in the RNA interference pathway. The function and mechanism of prokaryotic Argonaute proteins (pAgos) in vivo are still unclear although the structure of pAgos and eAgos are highly homologous. Most of the reported pAgos have a preference for 5'P-gDNA, but MpAgo originated from bacteria Marinitoga piezophila preferentially uses 5'OH-gRNA to target DNA and RNA. To enrich our knowledge of this type of Argonaute proteins, here we report an Argonaute protein derived from Tepiditoga spiralis (TsAgo). Like MpAgo, TsAgo has a preference for 5'OH-gRNA. Meanwhile, TsAgo has DNA and RNA cleavage activity in presence of Mn2+ and Mg2+, and TsAgo has catalytic activity at 37-70 °C. In addition, TsAgo can tolerate mismatches in the 5'-end and 3'-tail regions of guides but is sensitive to mismatches in the 5'-seed and central regions of guides, especially the central region. Furthermore, the EMSA assay reveals that TsAgo exhibits a stronger binding affinity for 5'OH-gRNA than 5'P-gRNA which is consistent with its cleavage activity. Moreover, the structural modeling analysis demonstrates that like MpAgo, TsAgo has an ordered α5 at the C terminus of the PIWI domain which may hinder to binding of 5' phosphate. Importantly, we find that TsAgo can target and cut plasmid DNA in vitro at 60 °C under the direction of RNA guides. These studies broaden our understanding of pAgos, and demonstrate that TsAgo can be regarded as an RNA-guided programmable nuclease for cleaving plasmids.
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Affiliation(s)
- Xiaochen Xie
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
| | - Longyu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
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48
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Yang L, Guo B, Wang Y, Zhao C, Zhang X, Wang Y, Tang Y, Shen H, Wang P, Gao S. Pyrococcus furiosus Argonaute Combined with Recombinase Polymerase Amplification for Rapid and Sensitive Detection of Enterocytozoon hepatopenaei. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:944-951. [PMID: 36548210 DOI: 10.1021/acs.jafc.2c06582] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Enterocytozoon hepatopenaei (EHP) is one of the most serious pathogens in shrimp farming. This study combines recombinase polymerase amplification (RPA) with the Argonaute from Pyrococcus furiosus (PfAgo) and establishes a sensitive and reliable method for on-site detection of EHP. With careful screening of gDNA and optimization of the reaction, the method shows a good specificity and reaches a sensitivity of single copy per reaction, which is higher than the sensitivity of the currently available molecular assays. The whole procedure can be finished within 1.5 h including the sample processing time and only requires minimum laboratory support, which is user-friendly for on-site environments. This is the first application of PfAgo for the diagnosis of infectious diseases in seafood supply chains. It provides a reliable method for on-site detection of EHP in shrimp farms and establishes a groundwork for multiplex detection of important pathogens in seafood farming using PfAgo.
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Affiliation(s)
- Lihong Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Bo Guo
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yu Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Chenjie Zhao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xue Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yue Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Yixin Tang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong 226007, China
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
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49
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Tang Y, Wang F, Wang Y, Wang Y, Liu Y, Chen Z, Li W, Yang S, Ma L. In vitro characterization of a pAgo nuclease TtdAgo from Thermococcus thioreducens and evaluation of its effect in vivo. Front Bioeng Biotechnol 2023; 11:1142637. [PMID: 36937752 PMCID: PMC10017986 DOI: 10.3389/fbioe.2023.1142637] [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: 01/11/2023] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
In spite of the development of genome-editing tools using CRISPR-Cas systems, highly efficient and effective genome-editing tools are still needed that use novel programmable nucleases such as Argonaute (Ago) proteins to accelerate the construction of microbial cell factories. In this study, a prokaryotic Ago (pAgo) from a hyperthermophilic archaeon Thermococcus thioreducens (TtdAgo) was characterized in vitro. Our results showed that TtdAgo has a typical DNA-guided DNA endonuclease activity, and the efficiency and accuracy of cleavage are modulated by temperature, divalent ions, and the phosphorylation and length of gDNAs and their complementarity to the DNA targets. TtdAgo can utilize 5'-phosphorylated (5'-P) or 5'- hydroxylated (5'-OH) DNA guides to cleave single-stranded DNA (ssDNA) at temperatures ranging from 30°C to 95°C in the presence of Mn2+ or Mg2+ and displayed no obvious preference for the 5'-end-nucleotide of the guide. In addition, single-nucleotide mismatches had little effects on cleavage efficiency, except for mismatches at position 4 or 8 that dramatically reduced target cleavage. Moreover, TtdAgo performed programmable cleavage of double-stranded DNA at 75°C. We further introduced TtdAgo into an industrial ethanologenic bacterium Zymomonas mobilis to evaluate its effect in vivo. Our preliminary results indicated that TtdAgo showed cell toxicity toward Z. mobilis, resulting in a reduced growth rate and final biomass. In conclusion, we characterized TtdAgo in vitro and investigated its effect on Z. mobilis in this study, which lays a foundation to develop Ago-based genome-editing tools for recalcitrant industrial microorganisms in the future.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lixin Ma
- *Correspondence: Shihui Yang, ; Lixin Ma,
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50
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Zhao C, Yang L, Zhang X, Tang Y, Wang Y, Shao X, Gao S, Liu X, Wang P. Rapid and Sensitive Genotyping of SARS-CoV-2 Key Mutation L452R with an RPA- PfAgo Method. Anal Chem 2022; 94:17151-17159. [PMID: 36459151 PMCID: PMC9743015 DOI: 10.1021/acs.analchem.2c03563] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022]
Abstract
In the two years of COVID-19 pandemic, the SARS-CoV-2 variants have caused waves of infections one after another, and the pandemic is not ending. The key mutations on the S protein enable the variants with enhanced viral infectivity, immune evasion, and/or antibody neutralization resistance, bringing difficulties to epidemic prevention and control. In support of precise epidemic control and precision medicine of the virus, a fast and simple genotyping method for the key mutations of SARS-CoV-2 variants needs to be developed. By utilizing the specific recognition and cleavage property of the nuclease Argonaute from Pyrococcus furiosus (PfAgo), we developed a recombinase polymerase amplification (RPA) and PfAgo combined method for a rapid and sensitive genotyping of SARS-CoV-2 key mutation L452R. With a delicate design of the strategy, careful screening of the RPA primers and PfAgo gDNA, and optimization of the reaction, the method achieves a high sensitivity of a single copy per reaction, which is validated with the pseudovirus. This is the highest sensitivity that can be achieved theoretically and the highest sensitivity as compared to the available SARS-CoV-2 genotyping assays. Using RPA, the procedure of the method is finished within 1.5 h and only needs a minimum laboratorial support, suggesting that the method can be easily applied locally or on-site. The RPA-PfAgo method established in this study provides a strong support to the precise epidemic control and precision medicine of SARS-CoV-2 variants and can be readily developed for the simultaneous genotyping of multiple SARS-CoV-2 mutations.
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Affiliation(s)
- Chenjie Zhao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Lihong Yang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xue Zhang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yixin Tang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yue Wang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiaofu Shao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Song Gao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xin Liu
- Key
Laboratory of Molecular Biophysics of Ministry of Education, College
of Life Science and Technology, Huazhong
University of Science and Technology, Wuhan 430074, China
| | - Pei Wang
- School
of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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