1
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Kottur J, Malik R, Aggarwal AK. Nucleic acid mediated activation of a short prokaryotic Argonaute immune system. Nat Commun 2024; 15:4852. [PMID: 38844755 DOI: 10.1038/s41467-024-49271-4] [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: 09/20/2023] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P)+ hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15-3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.
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Affiliation(s)
- Jithesh Kottur
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Antiviral Drug Research, Institute of Advanced Virology, Thiruvananthapuram, Kerala, 695317, India.
| | - Radhika Malik
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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2
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Zhang J, Chen M, Jiang H, Sun H, Ren J, Yang X, Liu S, Wang D, Liu J, Ma D, Guo X, Luo G. Atom-Modified gDNA Enhances Cleavage Activity of TtAgo Enabling Ultra-Sensitive Nucleic Acid Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403120. [PMID: 38728591 DOI: 10.1002/advs.202403120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/02/2024] [Indexed: 05/12/2024]
Abstract
The DNA-guided (gDNA) Argonaute from Thermus thermophilus (TtAgo) has little potential for nucleic acid detection and gene editing due to its poor dsDNA cleavage activity at relatively low temperature. Herein, the dsDNA cleavage activity of TtAgo is enhanced by using 2'-fluorine (2'F)-modified gDNA and developes a novel nucleic acid testing strategy. This study finds that the gDNA with 2'F-nucleotides at the 3'-end (2'F-gDNA) can promote the assembly of the TtAgo-guide-target ternary complex significantly by increasing its intermolecular force to target DNA and TtAgo, thereby providing ≈40-fold activity enhancement and decreasing minimum reaction temperature from 65 to 60°C. Based on this outstanding advance, a novel nucleic acid testing strategy is proposed, termed FAST, which is performed by using the 2'F-gDNA/TtAgo for target recognition and combining it with Bst DNA polymerase for nucleic acid amplification. By integrating G-quadruplex and Thioflavin T, the FAST assay achieves one-pot real-time fluorescence analysis with ultra-sensitivity, providing a limit of detection up to 5 copies (20 µL reaction mixture) for miR-21 detection. In summary, an atom-modification-based strategy has been developed for enhancing the cleavage activity of TtAgo efficiently, thereby improving its practicability and establishing a TtAgo-based nucleic acid testing technology with ultra-sensitivity and high-specificity.
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Affiliation(s)
- Jun Zhang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Miaomiao Chen
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Huan Jiang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Huifang Sun
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Jianing Ren
- Department of Oncology & Department of Rheumatology and Immunology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Xin Yang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Shanshan Liu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Cancer Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Jianping Liu
- Department of Oncology & Department of Rheumatology and Immunology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Daiyuan Ma
- Department of Oncology & Department of Rheumatology and Immunology, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, School of Laboratory Medicine & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, China
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3
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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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4
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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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5
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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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6
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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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7
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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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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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9
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Wang Z, Feng N, Zhou Y, Cheng X, Zhou C, Ma A, Wang Q, Li Y, Chen Y. Mesophilic Argonaute-Mediated Polydisperse Droplet Biosensor for Amplification-Free, One-Pot, and Multiplexed Nucleic Acid Detection Using Deep Learning. Anal Chem 2024; 96:2068-2077. [PMID: 38259216 DOI: 10.1021/acs.analchem.3c04426] [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: 01/24/2024]
Abstract
Detection of nucleic acids from a single multiplexed and amplification-free test is critical for ensuring food safety, clinical diagnostics, and environmental monitoring. In this study, we introduced a mesophilic Argonaute protein from Clostridium butyricum (CbAgo), which exhibits nucleic acid endonuclease activity, to achieve a programmable, amplification-free system (PASS) for rapid nucleic acid quantification at ambient temperatures in one pot. By using CbAgo-mediated binding with specific guide DNA (gDNA) and subsequent targeted cleavage of wild-type target DNAs complementary to gDNA, PASS can detect multiple foodborne pathogen DNA (<102 CFU/mL) simultaneously. The fluorescence signals were then transferred to polydisperse emulsions and analyzed by using deep learning. This simplifies the process and increases the suitability of polydisperse emulsions compared to traditional digital PCR, which requires homogeneous droplets for accurate detection. We believe that PASS has the potential to become a next-generation point-of-care digital nucleic acid detection method.
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Affiliation(s)
- Zhipan Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Niu Feng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yanan Zhou
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xinrui Cheng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Cuiyun Zhou
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qinyu Wang
- Department of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430000, Hubei China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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10
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Zhen X, Xu X, Ye L, Xie S, Huang Z, Yang S, Wang Y, Li J, Long F, Ouyang S. Structural basis of antiphage immunity generated by a prokaryotic Argonaute-associated SPARSA system. Nat Commun 2024; 15:450. [PMID: 38200015 PMCID: PMC10781750 DOI: 10.1038/s41467-023-44660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Argonaute (Ago) proteins are ubiquitous across all kingdoms of life. Eukaryotic Agos (eAgos) use small RNAs to recognize transcripts for RNA silencing in eukaryotes. In contrast, the functions of prokaryotic counterparts (pAgo) are less well known. Recently, short pAgos in conjunction with the associated TIR or Sir2 (SPARTA or SPARSA) were found to serve as antiviral systems to combat phage infections. Herein, we present the cryo-EM structures of nicotinamide adenine dinucleotide (NAD+)-bound SPARSA with and without nucleic acids at resolutions of 3.1 Å and 3.6 Å, respectively. Our results reveal that the APAZ (Analogue of PAZ) domain and the short pAgo form a featured architecture similar to the long pAgo to accommodate nucleic acids. We further identified the key residues for NAD+ binding and elucidated the structural basis for guide RNA and target DNA recognition. Using structural comparisons, molecular dynamics simulations, and biochemical experiments, we proposed a putative mechanism for NAD+ hydrolysis in which an H186 loop mediates nucleophilic attack by catalytic water molecules. Overall, our study provides mechanistic insight into the antiphage role of the SPARSA system.
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Affiliation(s)
- Xiangkai Zhen
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xiaolong Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China
| | - Le Ye
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Song Xie
- College of Chemistry, Fuzhou University, 350116, Fuzhou, China
| | - Zhijie Huang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Sheng Yang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Yanhui Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, 350116, Fuzhou, China.
| | - Feng Long
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China Wuhan University, Wuhan, 430071, China.
| | - Songying Ouyang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
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11
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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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12
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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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13
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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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14
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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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15
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Yang Z, Mao S, Wang L, Fu S, Dong Y, Jaffrezic-Renault N, Guo Z. CRISPR/Cas and Argonaute-Based Biosensors for Pathogen Detection. ACS Sens 2023; 8:3623-3642. [PMID: 37819690 DOI: 10.1021/acssensors.3c01232] [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: 10/13/2023]
Abstract
Over the past few decades, pathogens have posed a threat to human security, and rapid identification of pathogens should be one of the ideal methods to prevent major public health security outbreaks. Therefore, there is an urgent need for highly sensitive and specific approaches to identify and quantify pathogens. Clustered Regularly Interspaced Short Palindromic Repeats CRISPR/Cas systems and Argonaute (Ago) belong to the Microbial Defense Systems (MDS). The guided, programmable, and targeted activation of nucleases by both of them is leading the way to a new generation of pathogens detection. We compare these two nucleases in terms of similarities and differences. In addition, we discuss future challenges and prospects for the development of the CRISPR/Cas systems and Argonaute (Ago) biosensors, especially electrochemical biosensors. This review is expected to afford researchers entering this multidisciplinary field useful guidance and to provide inspiration for the development of more innovative electrochemical biosensors for pathogens detection.
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Affiliation(s)
- Zhiruo Yang
- Hubei Province Key Laboratory of Occupational Hazard identification and Control, School of Medicine, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, PR China
| | - Siying Mao
- Hubei Province Key Laboratory of Occupational Hazard identification and Control, School of Medicine, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, PR China
| | - Lu Wang
- Hubei Province Key Laboratory of Occupational Hazard identification and Control, School of Medicine, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, PR China
| | - Sinan Fu
- Hubei Province Key Laboratory of Occupational Hazard identification and Control, School of Medicine, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, PR China
| | - Yanming Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Nicole Jaffrezic-Renault
- University of Lyon, Institute of Analytical Sciences, UMR-CNRS 5280, 5, La Doua Street, Villeurbanne 69100, France
| | - Zhenzhong Guo
- Hubei Province Key Laboratory of Occupational Hazard identification and Control, School of Medicine, School of Public Health, Wuhan University of Science and Technology, Wuhan 430065, PR China
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16
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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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17
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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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18
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Kottur J, Malik R, Aggarwal AK. Nucleic Acid Mediated Activation of a Short Prokaryotic Argonaute Immune System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.17.558117. [PMID: 37745538 PMCID: PMC10516056 DOI: 10.1101/2023.09.17.558117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The continual pressure of invading DNA has led bacteria to develop numerous immune systems, including a short prokaryotic Argonaute (pAgo) TIR-APAZ system (SPARTA) that is activated by invading DNA to unleash its TIR domain for NAD(P)+ hydrolysis. To gain a molecular understanding of this activation process, we resolved a crystal structure of SPARTA heterodimer in the absence of guide RNA/target ssDNA at 2.66Å resolution and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide RNA/target ssDNA at nominal 3.15-3.35Å resolution. The crystal structure provides a high-resolution view of the TIR-APAZ protein and the MID-PIWI domains of short pAgo - wherein, the APAZ domain emerges as equivalent to the N, L1 and L2 regions of long pAgos and the MID domain has a unique insertion (insert57). A comparison to cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure to relieve auto-inhibition to permit nucleic acid binding and transition to an active oligomer. Oligomerization is accompanied by the nucleation of the TIR domains in a parallel-strands arrangement for catalysis. Together, the structures provide a visualization of SPARTA before and after RNA/ssDNA binding and reveal the basis of SPARTA's active assembly leading to NAD(P)+ degradation and abortive infection.
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Affiliation(s)
- Jithesh Kottur
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Radhika Malik
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aneel K. Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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19
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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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20
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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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21
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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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22
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Ni D, Lu X, Stahlberg H, Ekundayo B. Activation mechanism of a short argonaute-TIR prokaryotic immune system. SCIENCE ADVANCES 2023; 9:eadh9002. [PMID: 37467330 PMCID: PMC10355822 DOI: 10.1126/sciadv.adh9002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/08/2023] [Indexed: 07/21/2023]
Abstract
Short prokaryotic argonaute (pAgo) and toll/interleukin-1 receptor/resistance protein (TIR)-analog of PAZ (APAZ) form a heterodimeric SPARTA complex that provides immunity to its prokaryotic host through an abortive infection mechanism. Monomeric SPARTA senses foreign RNA/DNA duplexes to assemble an active tetramer resulting in cell death by nicotinamide adenine dinucleotide (oxidized form) (NAD) depletion via an unknown mechanism. We report nine structures of SPARTA in different functional states at a resolution range of 4.2 to 2.9 angstroms, revealing its activation mechanism. Inactive SPARTA monomers bind to RNA/DNA duplexes to form symmetric dimers mediated by the association of Ago subunits. The initiation of tetramer assembly induces flexibility of the TIR domains enabling a symmetry-breaking rotational movement of a TIR domain in the dimer units which facilitates the TIR oligomerization, resulting in the formation of the substrate binding pocket and the activation of the SPARTA complex's NADase activity. Our findings provide detailed structural and mechanistic insights into activating a short argonaute defense system.
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Affiliation(s)
- Dongchun Ni
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL, and Dept. Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Cubotron, Rt. de la Sorge, 1015 Lausanne, Switzerland
| | - Xuhang Lu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL, and Dept. Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Cubotron, Rt. de la Sorge, 1015 Lausanne, Switzerland
| | - Babatunde Ekundayo
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL, and Dept. Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Cubotron, Rt. de la Sorge, 1015 Lausanne, Switzerland
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23
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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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24
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Xiong X, Lu Z, Ma L, Zhai C. Applications of Programmable Endonucleases in Sequence- and Ligation-Independent Seamless DNA Assembly. Biomolecules 2023; 13:1022. [PMID: 37509059 PMCID: PMC10377497 DOI: 10.3390/biom13071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Programmable endonucleases, such as Cas (Clustered Regularly-Interspaced Short Repeats-associated proteins) and prokaryotic Argonaute (pAgo), depend on base pairing of the target DNA with the guide RNA or DNA to cleave DNA strands. Therefore, they are capable of recognizing and cleaving DNA sequences at virtually any arbitrary site. The present review focuses on the commonly used in vivo and in vitro recombination-based gene cloning methods and the application of programmable endonucleases in these sequence- and ligation-independent DNA assembly methods. The advantages and shortcomings of the programmable endonucleases utilized as tools for gene cloning are also discussed in this review.
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Affiliation(s)
- Xingchen Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiwen Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
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25
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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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26
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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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27
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Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Grybauskas A, Gražulis S, Zaremba M. Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein. Sci Rep 2023; 13:6123. [PMID: 37059709 PMCID: PMC10104839 DOI: 10.1038/s41598-023-32600-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
Argonaute (Ago) proteins are found in all three domains of life. The best-characterized group is eukaryotic Argonautes (eAgos). Being the structural core of RNA interference machinery, they use guide RNA molecules for RNA targeting. Prokaryotic Argonautes (pAgos) are more diverse, both in terms of structure (there are eAgo-like 'long' and truncated 'short' pAgos) and mechanism, as many pAgos are specific for DNA, not RNA guide and/or target strands. Some long pAgos act as antiviral defence systems. Their defensive role was recently demonstrated for short pAgo-encoding systems SPARTA and GsSir2/Ago, but the function and action mechanisms of all other short pAgos remain unknown. In this work, we focus on the guide and target strand preferences of AfAgo, a truncated long-B Argonaute protein encoded by an archaeon Archaeoglobus fulgidus. We demonstrate that AfAgo associates with small RNA molecules carrying 5'-terminal AUU nucleotides in vivo, and characterize its affinity to various RNA and DNA guide/target strands in vitro. We also present X-ray structures of AfAgo bound to oligoduplex DNAs that provide atomic details for base-specific AfAgo interactions with both guide and target strands. Our findings broaden the range of currently known Argonaute-nucleic acid recognition mechanisms.
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Affiliation(s)
- Elena Manakova
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Edvardas Golovinas
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Reda Pocevičiūtė
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Algirdas Grybauskas
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Saulius Gražulis
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania.
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28
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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: 12] [Impact Index Per Article: 12.0] [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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29
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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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30
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The genome editing revolution. Trends Biotechnol 2023; 41:396-409. [PMID: 36709094 DOI: 10.1016/j.tibtech.2022.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/28/2023]
Abstract
A series of spectacular scientific discoveries and technological advances in the second half of the 20th century have provided the basis for the ongoing genome editing revolution. The elucidation of structural and functional features of DNA and RNA was followed by pioneering studies on genome editing: Molecular biotechnology was born. Since then, four decades followed during which progress of scientific insights and technological methods continued at an overwhelming pace. Fundamental insights into microbial host-virus interactions led to the development of tools for genome editing using restriction enzymes or the revolutionary CRISPR-Cas technology. In this review, we provide a historical overview of milestones that led to the genome editing revolution and speculate about future trends in biotechnology.
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31
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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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32
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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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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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Zhuang H, Ji D, Fan J, Li M, Tao R, Du K, Lu S, Chai Z, Fan X. Mechanistic Insights into the Protection Effect of Argonaute-RNA Complex on the HCV Genome. Biomolecules 2022; 12:1631. [PMID: 36358979 PMCID: PMC9687641 DOI: 10.3390/biom12111631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 11/14/2023] Open
Abstract
While host miRNA usually plays an antiviral role, the relentless tides of viral evolution have carved out a mechanism to recruit host miRNA as a viral protector. By complementing miR-122 at the 5' end of the genome, the hepatitis C virus (HCV) gene can form a complex with Argonaute 2 (Ago2) protein to protect the 5' end of HCV RNA from exonucleolytic attacks. Experiments showed that the disruption of the stem-loop 1(SL1) structure and the 9th nucleotide (T9) of HCV site 1 RNA could enhance the affinity of the Ago2 protein to the HCV site 1 RNA (target RNA). However, the underlying mechanism of how the conformation and dynamics of the Ago2: miRNA: target RNA complex is affected by the SL1 and T9 remains unclear. To address this, we performed large-scale molecular dynamics simulations on the AGO2-miRNA complex binding with the WT target, T9-abasic target and SL1-disruption target, respectively. The results revealed that the T9 and SL1 structures could induce the departing motion of the PAZ, PIWI and N domains, propping up the mouth of the central groove which accommodates the target RNA, causing the instability of the target RNA and disrupting the Ago2 binding. The coordinated motion among the PAZ, PIWI and N domains were also weakened by the T9 and SL1 structures. Moreover, we proposed a new model wherein the Ago2 protein could adopt a more constraint conformation with the proximity and more correlated motions of the PAZ, N and PIWI domains to protect the target RNA from dissociation. These findings reveal the mechanism of the Ago2-miRNA complex's protective effect on the HCV genome at the atomic level, which will offer guidance for the design of drugs to confront the protection effect and engineering of Ago2 as a gene-regulation tool.
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Affiliation(s)
- Haiming Zhuang
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Jigang Fan
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Mingyu Li
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Ran Tao
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, China
| | - Kui Du
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing 312000, China
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Zongtao Chai
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Hepatic Surgery, Shanghai Geriatric Cancer, Shanghai 201104, China
| | - Xiaohua Fan
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
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Koopal B, Mutte SK, Swarts DC. A long look at short prokaryotic Argonautes. Trends Cell Biol 2022:S0962-8924(22)00239-2. [DOI: 10.1016/j.tcb.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/23/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
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Wang L, Xie X, Lv B, Liu Y, Li W, Zhang Z, Yang J, Yan G, Chen W, Zhang C, Wang F, Li C, Ma L. A bacterial Argonaute with efficient DNA and RNA cleavage activity guided by small DNA and RNA. Cell Rep 2022; 41:111533. [PMID: 36288702 DOI: 10.1016/j.celrep.2022.111533] [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: 04/25/2022] [Revised: 08/18/2022] [Accepted: 09/29/2022] [Indexed: 11/03/2022] Open
Abstract
Argonaute proteins are widespread in prokaryotes and eukaryotes with diversified catalytic activities. Here, we describe an Argonaute from Marinitoga hydrogenitolerans (MhAgo) with all eight cleavage activities. Utilization of all four types of guides and efficient cleavage of single-stranded DNA (ssDNA) and RNA targets are revealed. The preference for the 5'-terminus nucleotides of 5'P guides, but no obvious preferences for that in 5'OH guides, is further uncovered. Moreover, the cleavage efficiency is heavily impaired by mismatches in the central and 3'-supplementary regions of guides, and the affinity between guides or guides/target duplex and MhAgo is proved as one of the factors affecting cleavage efficiency. Structural and mutational analyses imply some unknown distinctive structural features behind the cleavage activity of MhAgo. Meanwhile, 5'OH-guide RNA (gRNA)-mediated plasmid cleavage activity is unveiled. Conclusively, MhAgo is versatile, and its biochemical characteristics improve our understanding of pAgos and the pAgo-based techniques.
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Affiliation(s)
- 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
| | - 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
| | - Bin Lv
- 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
| | - Yang Liu
- 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
| | - Wenqiang Li
- 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
| | - Zhiwei Zhang
- 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
| | - Jun Yang
- 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
| | - Guangbo Yan
- 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
| | - Wanping Chen
- 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
| | - Cheng Zhang
- 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
| | - Fei 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
| | - Chunhua Li
- 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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Sun S, Xu D, Zhu L, Hu B, Huang Z. A Programmable, DNA-Exclusively-Guided Argonaute DNase and Its Higher Cleavage Specificity Achieved by 5′-Hydroxylated Guide. Biomolecules 2022; 12:biom12101340. [PMID: 36291549 PMCID: PMC9599953 DOI: 10.3390/biom12101340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 12/03/2022] Open
Abstract
Argonaute proteins exist widely in eukaryotes and prokaryotes, and they are of great potential for molecular cloning, nucleic acid detection, DNA assembly, and gene editing. However, their overall properties are not satisfactory and hinder their broad applications. Herein, we investigated a prokaryotic Argonaute nuclease from a mesophilic bacterium Clostridium disporicum (CdAgo) and explored its overall properties, especially with 5′-hydroxylated (5′-OH) guides. We found that CdAgo can exclusively use single-stranded DNA (ssDNA) as guide to cleave ssDNA and plasmid targets. Further, we found the length of the efficient guide is narrower for the 5′-OH guide (17–20 nt) than for the 5′-phosphorylated guide (5′-P, 14–21 nt). Furthermore, we discovered that the 5′-OH guides can generally offer stronger mismatch discrimination than the 5′-P ones. The 5′-OH guides offer the narrower length range, higher mismatch discrimination and more accurate cleavage than the 5′-P guides. Therefore, 5′-OH-guide-directed CdAgo has great potential in biological and biomedical applications.
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Affiliation(s)
- Shichao Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Dejin Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Lin Zhu
- Study on the Structure-Specific Small Molecule Drug in Sichuan Province College Key Laboratory, Department of Pharmacy, Chengdu Medical College, Chengdu 610500, China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- Correspondence: (B.H.); (Z.H.)
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu 610041, China
- Correspondence: (B.H.); (Z.H.)
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38
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Nye DB, Tanner NA. Chimeric DNA byproducts in strand displacement amplification using the T7 replisome. PLoS One 2022; 17:e0273979. [PMID: 36121810 PMCID: PMC9484634 DOI: 10.1371/journal.pone.0273979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/19/2022] [Indexed: 11/30/2022] Open
Abstract
Recent advances in next generation sequencing technologies enable reading DNA molecules hundreds of kilobases in length and motivate development of DNA amplification methods capable of producing long amplicons. In vivo, DNA replication is performed not by a single polymerase enzyme, but multiprotein complexes called replisomes. Here, we investigate strand-displacement amplification reactions using the T7 replisome, a macromolecular complex of a helicase, a single-stranded DNA binding protein, and a DNA polymerase. The T7 replisome may initiate processive DNA synthesis from DNA nicks, and the reaction of a 48 kilobase linear double stranded DNA substrate with the T7 replisome and nicking endonucleases is shown to produce discrete DNA amplicons. To gain a mechanistic understanding of this reaction, we utilized Oxford Nanopore long-read sequencing technology. Sequence analysis of the amplicons revealed chimeric DNA reads and uncovered a connection between template switching and polymerase exonuclease activity. Nanopore sequencing provides insight to guide the further development of isothermal amplification methods for long DNA, and our results highlight the need for high-specificity, high-turnover nicking endonucleases to initiate DNA amplification without thermal denaturation.
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Affiliation(s)
- Dillon B. Nye
- Nucleic Acid Replication Division, New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Nathan A. Tanner
- Nucleic Acid Replication Division, New England Biolabs Inc., Ipswich, Massachusetts, United States of America
- * E-mail:
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39
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Li B, Yang S, Long J, Chen X, Zhang Q, Ning L, He B, Chen H, Huang J. AGODB: a comprehensive domain annotation database of argonaute proteins. Database (Oxford) 2022; 2022:6693399. [PMID: 36068786 PMCID: PMC9448894 DOI: 10.1093/database/baac078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 07/18/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
Abstract
Argonaute (Ago) proteins are widely expressed in almost all organisms. Eukaryotic Ago (eAgo) proteins bind small RNA guides forming RNA-induced silencing complex that silence gene expression, and prokaryotic Ago (pAgo) proteins defend against invading nucleic acids via binding small RNAs or DNAs. pAgo proteins have shown great potential as a candidate ‘scissors’ for gene editing. Protein domains are fundamental units of protein structure, function and evolution; however, the domains of Ago proteins are not well annotated/curated currently. Therefore, full functional domain annotation of Ago proteins is urgently needed for researchers to understand the function and mechanism of Ago proteins. Herein, we constructed the first comprehensive domain annotation database of Ago proteins (AGODB). The database curates detailed information of 1902 Ago proteins, including 1095 eAgos and 807 pAgos. Especially for long pAgo proteins, all six domains are annotated and curated. Gene Ontology (GO) enrichment analysis revealed that Ago genes in different species were enriched in the following GO terms: biological processes (BPs), molecular function and cellular compartment. GO enrichment analysis results were integrated into AGODB, which provided insights into the BP that Ago genes may participate in. AGODB also allows users to search the database with a variety of options and download the search results. We believe that the AGODB will be a useful resource for understanding the function and domain components of Ago proteins. This database is expected to cater to the needs of scientific community dedicated to the research of Ago proteins.
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Affiliation(s)
- Bowen Li
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Shanshan Yang
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Jinjin Long
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Xue Chen
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Qianyue Zhang
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Lin Ning
- School of Health Care Technology, Chengdu Neusoft University , Chengdu, Sichuan 611844, China
| | - Bifang He
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Heng Chen
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China , Chengdu, Sichuan 611731, China
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40
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Santiago-Frangos A, Nemudryi A, Nemudraia A, Wiegand T, Nichols JE, Krishna P, Scherffius AM, Zahl TR, Wilkinson RA, Wiedenheft B. CRISPR-Cas, Argonaute proteins and the emerging landscape of amplification-free diagnostics. Methods 2022; 205:1-10. [PMID: 35690249 PMCID: PMC9181078 DOI: 10.1016/j.ymeth.2022.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/06/2022] [Accepted: 06/04/2022] [Indexed: 01/04/2023] Open
Abstract
Polymerase Chain Reaction (PCR) is the reigning gold standard for molecular diagnostics. However, the SARS-CoV-2 pandemic reveals an urgent need for new diagnostics that provide users with immediate results without complex procedures or sophisticated equipment. These new demands have stimulated a tsunami of innovations that improve turnaround times without compromising the specificity and sensitivity that has established PCR as the paragon of diagnostics. Here we briefly introduce the origins of PCR and isothermal amplification, before turning to the emergence of CRISPR-Cas and Argonaute proteins, which are being coupled to fluorimeters, spectrometers, microfluidic devices, field-effect transistors, and amperometric biosensors, for a new generation of nucleic acid-based diagnostics.
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Affiliation(s)
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Anna Nemudraia
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Joseph E Nichols
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Pushya Krishna
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Andrew M Scherffius
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Trevor R Zahl
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Royce A Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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Lisitskaya L, Shin Y, Agapov A, Olina A, Kropocheva E, Ryazansky S, Aravin AA, Esyunina D, Murakami KS, Kulbachinskiy A. Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity. Nat Commun 2022; 13:4624. [PMID: 35941106 PMCID: PMC9360449 DOI: 10.1038/s41467-022-32079-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 12/26/2022] Open
Abstract
Argonaute proteins are programmable nucleases that have defense and regulatory functions in both eukaryotes and prokaryotes. All known prokaryotic Argonautes (pAgos) characterized so far act on DNA targets. Here, we describe a new class of pAgos that uniquely use DNA guides to process RNA targets. The biochemical and structural analysis of Pseudooceanicola lipolyticus pAgo (PliAgo) reveals an unusual organization of the guide binding pocket that does not rely on divalent cations and the canonical set of contacts for 5'-end interactions. Unconventional interactions of PliAgo with the 5'-phosphate of guide DNA define its new position within pAgo and shift the site of target RNA cleavage in comparison with known Argonautes. The specificity for RNA over DNA is defined by ribonucleotide residues at the cleavage site. The analysed pAgos sense mismatches and modifications in the RNA target. The results broaden our understanding of prokaryotic defense systems and extend the spectrum of programmable nucleases with potential use in RNA technology.
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Affiliation(s)
- Lidiya Lisitskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 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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42
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Li X, Dong H, Guo X, Huang F, Xu X, Li N, Yang Y, Yao T, Feng Y, Liu Q. Mesophilic Argonaute-based isothermal detection of SARS-CoV-2. Front Microbiol 2022; 13:957977. [PMID: 35966688 PMCID: PMC9363790 DOI: 10.3389/fmicb.2022.957977] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
Coronavirus disease (COVID-19), caused by SARS-CoV-2 infection and its mutations, has spread rapidly all over the world and still requires sensitive detection to distinguish mutations. CRISPR-based diagnosis has been regarded as a next-generation detection method; however, it has some limitations, such as the need for specific recognition sequences and multiple enzymes for multiplex detection. Therefore, research on the exploration and development of novel nucleases helps to promote specific and sensitive diagnoses. Prokaryotic Argonaute (Ago) proteins exert directed nuclease activity that can target any sequence. Recently, thermophilic Agos have been developed as new detection techniques achieving multiplexity for multiple targets using a single enzyme, as well as accurate recognition of single-base differential sequences. In this study, to overcome the requirement for high reaction temperature of thermophilic Ago-based methods, we expanded the mining of mesophilic Agos to achieve CRISPR-like isothermal detection, named mesophilic Ago-based isothermal detection method (MAIDEN). The principle of MAIDEN uses mesophilic Ago cleavage combined with reverse transcription, which can provide single-strand DNA as a substrate and allow cleavage of fluorescence probes to sense SARS-CoV-2 at moderate temperature. We first mined and optimized the mesophilic Ago and the fluorescence reporter system and then selected a compatible reverse transcription reaction. Furthermore, we optimized MAIDEN into a one-step reaction that can detect SARS-CoV-2 RNA at the nanomolar concentration at a constant temperature of 42°C within 60 min. Therefore, MAIDEN shows advantageous portability and easy-to-implement operation, avoiding the possibility of open-lid contamination. Our study was the first attempt to demonstrate that mesophilic Agos can be harnessed as diagnostic tools, and MAIDEN was easily extended to detect other pathogens in a rapid and efficient manner.
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Affiliation(s)
- Xiao Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Huarong Dong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyi Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nuolan Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tianbao Yao
- Department of Cardiology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Qian Liu
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Zheng L, Lu H, Zan B, Li S, Liu H, Liu Z, Huang J, Liu Y, Jiang F, Liu Q, Feng Y, Hong L. Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity. Nucleic Acids Res 2022; 50:7529-7544. [PMID: 35766425 PMCID: PMC9303296 DOI: 10.1093/nar/gkac565] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Prokaryotic Argonaute proteins (pAgos) widely participate in hosts to defend against the invasion of nucleic acids. Compared with the CRISPR-Cas system, which requires a specific motif on the target and can only use RNA as guide, pAgos exhibit precise endonuclease activity on any arbitrary target sequence and can use both RNA and DNA as guide, thus rendering great potential for genome editing applications. Hitherto, most in-depth studies on the structure-function relationship of pAgos were conducted on thermophilic ones, functioning at ∼60 to 100°C, whose structures were, however, determined experimentally at much lower temperatures (20–33°C). It remains unclear whether these low-temperature structures can represent the true conformations of the thermophilic pAgos under their physiological conditions. The present work studied three pAgos, PfAgo, TtAgo and CbAgo, whose physiological temperatures differ significantly (95, 75 and 37°C). By conducting thorough experimental and simulation studies, we found that thermophilic pAgos (PfAgo and TtAgo) adopt a loosely-packed structure with a partially-melted surface at the physiological temperatures, largely different from the compact crystalline structures determined at moderate temperatures. In contrast, the mesophilic pAgo (CbAgo) assumes a compact crystalline structure at its optimal function temperature. Such a partially-disrupted structure endows thermophilic pAgos with great flexibility both globally and locally at the catalytic sites, which is crucial for them to achieve high DNA-cleavage activity. To further prove this, we incubated thermophilic pAgos with urea to purposely disrupt their structures, and the resulting cleavage activity was significantly enhanced below the physiological temperature, even at human body temperature. Further testing of many thermophilic Agos present in various thermophilic prokaryotes demonstrated that their structures are generally disrupted under physiological conditions. Therefore, our findings suggest that the highly dynamical structure with a partially-melted surface, distinct from the low-temperature crystalline structure, could be a general strategy assumed by thermophilic pAgos to achieve the high DNA-cleavage activity.
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Affiliation(s)
- Lirong Zheng
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui Lu
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Song Li
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Liu
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yongjia Liu
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, 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
| | - Yan Feng
- State Key laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Institute of Natural Sciences, School of Medicine, Shanghai National Center for Applied Mathematics (SJTU center), Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
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Fang M, Xu Z, Huang D, Naeem M, Zhu X, Xu Z. Characterization and application of a thermophilic Argonaute from archaeon
Thermococcus thioreducens. Biotechnol Bioeng 2022; 119:2388-2398. [DOI: 10.1002/bit.28153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/13/2022] [Accepted: 05/28/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Mengjun Fang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
- Institute of Biological Engineering, College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
| | - Zhipeng Xu
- The First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Di Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
- Institute of Biological Engineering, College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
| | - Muhammad Naeem
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
- Institute of Biological Engineering, College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine at Central South UniversityChangshaHunanChina
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
- Institute of Biological Engineering, College of Chemical and Biological EngineeringZhejiang UniversityHangzhouChina
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Sun Y, Guo X, Lu H, Chen L, Huang F, Liu Q, Feng Y. An Argonaute from Thermus parvatiensis exhibits endonuclease activity mediated by 5' chemically modified DNA guides. Acta Biochim Biophys Sin (Shanghai) 2022; 54:686-695. [PMID: 35643958 PMCID: PMC9828299 DOI: 10.3724/abbs.2022047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Prokaryotic Argonaute (pAgo) nucleases with precise DNA cleavage activity show great potential for gene manipulation. Extensive biochemical studies have revealed that recognition of guides with different 5' groups by Ago is important for biocatalysis. Here, we identified an Ago from the thermophilic Thermus parvatiensis ( TpsAgo) and analyzed the regulatory effect of 5'-modified guides on TpsAgo cleavage activity. Recombinant TpsAgo cleaves single-stranded DNA and RNA targets at 65-90°C, which is mediated by a 5' hydroxyl or phosphate DNA guide. Notably, TpsAgo can utilize various 5'-modified DNA guides for catalysis, including 5'-NH 2C 6, 5'-Biotin, 5'-FAM and 5'-SHC 6 guides. Moreover, TpsAgo performs programmable cleavage of double-stranded DNA at temperatures over 80°C and strongly tolerates NaCl concentrations up to 3.2 M. These results provide insight into the catalytic performance of Agos by guide regulation, which may facilitate their biotechnological applications.
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Affiliation(s)
- Yingying Sun
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Xiang Guo
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Hui Lu
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Liuqing Chen
- Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055China
| | - Fei Huang
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Qian Liu
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China
| | - Yan Feng
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200240China,Correspondence address. Tel: +86-21-34207189; E-mail:
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Huang F, Xu X, Dong H, Li N, Zhong B, Lu H, Liu Q, Feng Y. Catalytic properties and biological function of a PIWI-RE nuclease from Pseudomonas stutzeri. BIORESOUR BIOPROCESS 2022; 9:57. [PMID: 38647609 PMCID: PMC10991935 DOI: 10.1186/s40643-022-00539-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: 02/17/2022] [Accepted: 04/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prokaryotic Argonaute (pAgo) proteins are well-known oligonucleotide-directed endonucleases, which contain a conserved PIWI domain required for endonuclease activity. Distantly related to pAgos, PIWI-RE family, which is defined as PIWI with conserved R and E residues, has been suggested to exhibit divergent activities. The distinctive biochemical properties and physiological functions of PIWI-RE family members need to be elucidated to explore their applications in gene editing. RESULTS Here, we describe the catalytic performance and cellular functions of a PIWI-RE family protein from Pseudomonas stutzeri (PsPIWI-RE). Structural modelling suggests that the protein possesses a PIWI structure similar to that of pAgo, but with different PAZ-like and N-terminal domains. Unlike previously reported pAgos, recombinant PsPIWI-RE acts as an RNA-guided DNA nuclease, as well as a DNA-guided RNA nuclease. It cleaves single-stranded DNA at temperatures ranging from 20 to 65 °C, with an optimum temperature of 45 °C. Mutation at D525 or D610 significantly reduced its endonuclease activity, confirming that both residues are key for catalysis. Comparing with wild-type, mutant with PIWI-RE knockout is more sensitive to ciprofloxacin as DNA replication inhibitor, suggesting PIWI-RE may potentially be involved in DNA replication. CONCLUSION Our study provides the first insights into the programmable nuclease activity and biological function of the unknown PIWI-RE family of proteins, emphasizing their important role in vivo and potential application in genomic DNA modification.
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Affiliation(s)
- Fei Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyi Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huarong Dong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Nuolan Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bozitao Zhong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction. Nat Commun 2022; 13:2697. [PMID: 35577775 PMCID: PMC9110713 DOI: 10.1038/s41467-022-30355-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/28/2022] [Indexed: 01/01/2023] Open
Abstract
Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments. PlasmidMaker should greatly expand the potential of synthetic biology. Despite their broad utility, design and construction of plasmids remains laborious and time-consuming. Here the authors report a robust, versatile, and automated end-to-end platform that enables scarless construction of virtually any plasmid.
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Zeng Z, Chen Y, Pinilla-Redondo R, Shah SA, Zhao F, Wang C, Hu Z, Wu C, Zhang C, Whitaker RJ, She Q, Han W. A short prokaryotic Argonaute activates membrane effector to confer antiviral defense. Cell Host Microbe 2022; 30:930-943.e6. [PMID: 35594868 DOI: 10.1016/j.chom.2022.04.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/25/2022] [Accepted: 04/26/2022] [Indexed: 11/03/2022]
Abstract
Argonaute (Ago) proteins are widespread nucleic-acid-guided enzymes that recognize targets through complementary base pairing. Although, in eukaryotes, Agos are involved in RNA silencing, the functions of prokaryotic Agos (pAgos) remain largely unknown. In particular, a clade of truncated and catalytically inactive pAgos (short pAgos) lacks characterization. Here, we reveal that a short pAgo protein in the archaeon Sulfolobus islandicus, together with its two genetically associated proteins, Aga1 and Aga2, provide robust antiviral protection via abortive infection. Aga2 is a toxic transmembrane effector that binds anionic phospholipids via a basic pocket, resulting in membrane depolarization and cell killing. Ago and Aga1 form a stable complex that exhibits nucleic-acid-directed nucleic-acid-recognition ability and directly interacts with Aga2, pointing to an immune sensing mechanism. Together, our results highlight the cooperation between pAgos and their widespread associated proteins, suggesting an uncharted diversity of pAgo-derived immune systems.
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Affiliation(s)
- Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Fen Zhao
- Hubei Hongshan Laboratory, 430070 Wuhan, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070 Wuhan, China
| | - Chen Wang
- Hubei Hongshan Laboratory, 430070 Wuhan, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zeyu Hu
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Chang Wu
- State Key Laboratory of Agricultural Microbiology and College of Life Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Rachel J Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - 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 Sciences and Technology, Huazhong Agricultural University, 430070 Wuhan, China; Hubei Hongshan Laboratory, 430070 Wuhan, China.
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Li W, Liu Y, He R, Wang L, Wang Y, Zeng W, Zhang Z, Wang F, Ma L. A programmable pAgo nuclease with RNA target preference from the psychrotolerant bacterium Mucilaginibacter paludis. Nucleic Acids Res 2022; 50:5226-5238. [PMID: 35524569 PMCID: PMC9122594 DOI: 10.1093/nar/gkac315] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Argonaute (Ago) proteins are programmable nucleases found in eukaryotes and prokaryotes. Prokaryotic Agos (pAgos) share a high degree of structural homology with eukaryotic Agos (eAgos), and eAgos originate from pAgos. Although eAgos exclusively cleave RNA targets, most characterized pAgos cleave DNA targets. This study characterized a novel pAgo, MbpAgo, from the psychrotolerant bacterium Mucilaginibacter paludis which prefers to cleave RNA targets rather than DNA targets. Compared to previously studied Agos, MbpAgo can utilize both 5′phosphorylated(5′P) and 5′hydroxylated(5′OH) DNA guides (gDNAs) to efficiently cleave RNA targets at the canonical cleavage site if the guide is between 15 and 17 nt long. Furthermore, MbpAgo is active at a wide range of temperatures (4–65°C) and displays no obvious preference for the 5′-nucleotide of a guide. Single-nucleotide and most dinucleotide mismatches have no or little effects on cleavage efficiency, except for dinucleotide mismatches at positions 11–13 that dramatically reduce target cleavage. MbpAgo can efficiently cleave highly structured RNA targets using both 5′P and 5′OH gDNAs in the presence of Mg2+ or Mn2+. The biochemical characterization of MbpAgo paves the way for its use in RNA manipulations such as nucleic acid detection and clearance of RNA viruses.
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Affiliation(s)
- Wenqiang Li
- 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
| | - Yang Liu
- 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
| | - Ruyi He
- 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
| | - Yaping 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
| | - Wanting Zeng
- 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
| | - Zhiwei Zhang
- 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
| | - Fei 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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50
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Vaiskunaite R, Vainauskas J, Morris JJL, Potapov V, Bitinaite J. Programmable cleavage of linear double-stranded DNA by combined action of Argonaute CbAgo from Clostridium butyricum and nuclease deficient RecBC helicase from E.coli. Nucleic Acids Res 2022; 50:4616-4629. [PMID: 35420131 PMCID: PMC9071414 DOI: 10.1093/nar/gkac229] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 03/18/2022] [Accepted: 03/24/2022] [Indexed: 01/04/2023] Open
Abstract
Prokaryotic Argonautes (pAgos) use small nucleic acids as specificity guides to cleave single-stranded DNA at complementary sequences. DNA targeting function of pAgos creates attractive opportunities for DNA manipulations that require programmable DNA cleavage. Currently, the use of mesophilic pAgos as programmable endonucleases is hampered by their limited action on double-stranded DNA (dsDNA). We demonstrate here that efficient cleavage of linear dsDNA by mesophilic Argonaute CbAgo from Clostridium butyricum can be activated in vitro via the DNA strand unwinding activity of nuclease deficient mutant of RecBC DNA helicase from Escherichia coli (referred to as RecBexo–C). Properties of CbAgo and characteristics of simultaneous cleavage of DNA strands in concurrence with DNA strand unwinding by RecBexo–C were thoroughly explored using 0.03–25 kb dsDNAs. When combined with RecBexo–C, CbAgo could cleave targets located 11–12.5 kb from the ends of linear dsDNA at 37°C. Our study demonstrates that CbAgo with RecBexo–C can be programmed to generate DNA fragments with custom-designed single-stranded overhangs suitable for ligation with compatible DNA fragments. The combination of CbAgo and RecBexo–C represents the most efficient mesophilic DNA-guided DNA-cleaving programmable endonuclease for in vitro use in diagnostic and synthetic biology methods that require sequence-specific nicking/cleavage of linear dsDNA at any desired location.
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Affiliation(s)
- Rita Vaiskunaite
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | | | - Janna J L Morris
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
| | - Jurate Bitinaite
- Research Department, New England Biolabs, Ipswich, MA 01938, USA
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