1
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Xiang Y, Ke W, Qin Y, Zhou B, Hu Y. PfAgo-based dual signal amplification biosensor for rapid and highly sensitive detection of alkaline phosphatase activity. Mikrochim Acta 2024; 191:439. [PMID: 38954110 DOI: 10.1007/s00604-024-06516-9] [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: 04/26/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
A Pyrococcus furiosus Argonaute (PfAgo)-based biosensor is presented for alkaline phosphatase (ALP) activity detection in which the ALP-catalyzed hydrolysis of 3'-phosphate-modified functional DNA activates the strand displacement amplification, and the amplicon mediates the fluorescent reporter cleavage as a guide sequence of PfAgo. Under the dual amplification mode of PfAgo-catalyzed multiple-turnover cleavage activity and pre-amplification technology, the developed method was successfully applied to ALP activity determination with a detection limit (LOD) of 0.0013 U L-1 (3σ) and a detection range of 0.0025 to 1 U L-1 within 90 min. The PfAgo-based method exhibits satisfactory analytic performance in the presence of potential interferents and in complex human serum samples. The proposed method shows several advantages, such as rapid analysis, high sensitivity, low-cost, and easy operation, and has great potential in disease evolution fundamental studies and clinical diagnosis applications.
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Affiliation(s)
- YuQiang Xiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Weikang Ke
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, 430070, People's Republic of China
| | - Yuqing Qin
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, 430070, People's Republic of China
| | - Bosheng Zhou
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, 430070, People's Republic of China
| | - Yonggang Hu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
- Hubei Hongshan Laboratory, Wuhan, 430070, People's Republic of China.
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2
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Bastiaanssen C, Bobadilla Ugarte P, Kim K, Finocchio G, Feng Y, Anzelon TA, Köstlbacher S, Tamarit D, Ettema TJG, Jinek M, MacRae IJ, Joo C, Swarts DC, Wu F. RNA-guided RNA silencing by an Asgard archaeal Argonaute. Nat Commun 2024; 15:5499. [PMID: 38951509 PMCID: PMC11217426 DOI: 10.1038/s41467-024-49452-1] [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: 03/26/2024] [Accepted: 06/04/2024] [Indexed: 07/03/2024] Open
Abstract
Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are subdivided into two clades: AGOs generally facilitate miRNA- or siRNA-mediated silencing, while PIWIs generally facilitate piRNA-mediated silencing. It is currently unclear when and how Argonaute-based RNA silencing mechanisms arose and diverged during the emergence and early evolution of eukaryotes. Here, we show that in Asgard archaea, the closest prokaryotic relatives of eukaryotes, an evolutionary expansion of Argonaute proteins took place. In particular, a deep-branching PIWI protein (HrAgo1) encoded by the genome of the Lokiarchaeon 'Candidatus Harpocratesius repetitus' shares a common origin with eukaryotic PIWI proteins. Contrasting known prokaryotic Argonautes that use single-stranded DNA as guides and/or targets, HrAgo1 mediates RNA-guided RNA cleavage, and facilitates gene silencing when expressed in human cells and supplied with miRNA precursors. A cryo-EM structure of HrAgo1, combined with quantitative single-molecule experiments, reveals that the protein displays structural features and target-binding modes that are a mix of those of eukaryotic AGO and PIWI proteins. Thus, this deep-branching archaeal PIWI may have retained an ancestral molecular architecture that preceded the functional and mechanistic divergence of eukaryotic AGOs and PIWIs.
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Affiliation(s)
- Carolien Bastiaanssen
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Kijun Kim
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Giada Finocchio
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Yanlei Feng
- School of Life Sciences, College of Science, Eastern Institute of Technology, Ningbo, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Todd A Anzelon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stephan Köstlbacher
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Daniel Tamarit
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
- Department of Physics, Ewha Womans University, Seoul, Korea.
| | - Daan C Swarts
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.
| | - Fabai Wu
- School of Life Sciences, College of Science, Eastern Institute of Technology, Ningbo, China.
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3
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Sun D, Zhu K, Wang L, Mu Z, Wu K, Hua L, Qin B, Gao X, Wang Y, Cui S. Nucleic acid-induced NADase activation of a short Sir2-associated prokaryotic Argonaute system. Cell Rep 2024; 43:114391. [PMID: 38923459 DOI: 10.1016/j.celrep.2024.114391] [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: 09/06/2023] [Revised: 04/25/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Inhibition of nucleic acid targets is mediated by Argonaute (Ago) proteins guided by RNA or DNA. Although the mechanisms underpinning the functions of eukaryotic and "long" prokaryotic Ago proteins (pAgos) are well understood, those for short pAgos remain enigmatic. Here, we determine two cryoelectron microscopy structures of short pAgos in association with the NADase-domain-containing protein Sir2-APAZ from Geobacter sulfurreducens (GsSir2/Ago): the guide RNA-target DNA-loaded GsSir2/Ago quaternary complex (2.58 Å) and the dimer of the quaternary complex (2.93Å). These structures show that the nucleic acid binding causes profound conformational changes that result in disorder or partial dissociation of the Sir2 domain, suggesting that it adopts a NADase-active conformation. Subsequently, two RNA-/DNA-loaded GsSir2/Ago complexes form a dimer through their MID domains, further enhancing NADase activity through synergistic effects. The findings provide a structural basis for short-pAgo-mediated defense against invading nucleic acids.
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Affiliation(s)
- Dapeng Sun
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Zhixia Mu
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Kang Wu
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Lei Hua
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Medical School, Yan'an University, Yan'an, Shaanxi 716000, China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China.
| | - Yumei Wang
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China; Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China.
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4
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Agapov A, Panteleev V, Kropocheva E, Kanevskaya A, Esyunina D, Kulbachinskiy A. Prokaryotic Argonaute nuclease cooperates with co-encoded RNase to acquire guide RNAs and target invader DNA. Nucleic Acids Res 2024; 52:5895-5911. [PMID: 38716875 PMCID: PMC11162769 DOI: 10.1093/nar/gkae345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 06/11/2024] Open
Abstract
Argonautes are an evolutionary conserved family of programmable nucleases that identify target nucleic acids using small guide oligonucleotides. In contrast to eukaryotic Argonautes (eAgos) that act on RNA, most studied prokaryotic Argonautes (pAgos) recognize DNA targets. Similarly to eAgos, pAgos can protect prokaryotic cells from invaders, but the biogenesis of guide oligonucleotides that confer them specificity to their targets remains poorly understood. Here, we have identified a new group of RNA-guided pAgo nucleases and demonstrated that a representative pAgo from this group, AmAgo from the mesophilic bacterium Alteromonas macleodii, binds guide RNAs of varying lengths for specific DNA targeting. Unlike most pAgos and eAgos, AmAgo is strictly specific to hydroxylated RNA guides containing a 5'-adenosine. AmAgo and related pAgos are co-encoded with a conserved RNA endonuclease from the HEPN superfamily (Ago-associated protein, Agap-HEPN). In vitro, Agap cleaves RNA between guanine and adenine nucleotides producing hydroxylated 5'-A guide oligonucleotides bound by AmAgo. In vivo, Agap cooperates with AmAgo in acquiring guide RNAs and counteracting bacteriophage infection. The AmAgo-Agap pair represents the first example of a pAgo system that autonomously produces RNA guides for DNA targeting and antiviral defense, which holds promise for programmable DNA targeting in biotechnology.
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Affiliation(s)
- Aleksei Agapov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladimir Panteleev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | | | - Anna Kanevskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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5
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Gómez‐Campo CL, Abdelmoteleb A, Pulido V, Gost M, Sánchez‐Hevia DL, Berenguer J, Mencía M. Differential requirement for RecFOR pathway components in Thermus thermophilus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13269. [PMID: 38822640 PMCID: PMC11143384 DOI: 10.1111/1758-2229.13269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/06/2024] [Indexed: 06/03/2024]
Abstract
Recombinational repair is an important mechanism that allows DNA replication to overcome damaged templates, so the DNA is duplicated timely and correctly. The RecFOR pathway is one of the common ways to load RecA, while the RuvABC complex operates in the resolution of DNA intermediates. We have generated deletions of recO, recR and ruvB genes in Thermus thermophilus, while a recF null mutant could not be obtained. The recO deletion was in all cases accompanied by spontaneous loss of function mutations in addA or addB genes, which encode a helicase-exonuclease also key for recombination. The mutants were moderately affected in viability and chromosome segregation. When we generated these mutations in a Δppol/addAB strain, we observed that the transformation efficiency was maintained at the typical level of Δppol/addAB, which is 100-fold higher than that of the wild type. Most mutants showed increased filamentation phenotypes, especially ruvB, which also had DNA repair defects. These results suggest that in T. thermophilus (i) the components of the RecFOR pathway have differential roles, (ii) there is an epistatic relationship of the AddAB complex over the RecFOR pathway and (iii) that neither of the two pathways or their combination is strictly required for viability although they are necessary for normal DNA repair and chromosome segregation.
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Affiliation(s)
- Cristina L. Gómez‐Campo
- Center for Plant Biotechnology and Genomics (CBGP)Polytechnic University of MadridMadridSpain
| | - Ali Abdelmoteleb
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
- Department of Botany, Faculty of AgricultureMenoufia UniversityShebin El‐KomEgypt
| | - Verónica Pulido
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | - Marc Gost
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | | | - José Berenguer
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
| | - Mario Mencía
- Department of Molecular BiologyScience Faculty, Center for Molecular Biology Severo Ochoa (CBM), Autonomous University of Madrid‐Higher Council of Scientific Research (CSIC)MadridSpain
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6
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Kou J, Li Y, Zhao Z, Qiao J, Zhang Q, Han X, Cheng X, Man S, Ma L. Simultaneous Dual-Gene Test of Methicillin-Resistant Staphylococcus Aureus using an Argonaute-Centered Portable and Visual Biosensor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311764. [PMID: 38506607 DOI: 10.1002/smll.202311764] [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: 12/17/2023] [Indexed: 03/21/2024]
Abstract
The development of novel method for drug-resistant bacteria detection is imperative. A simultaneous dual-gene Test of methicillin-resistant Staphylococcus aureus (MRSA) is developed using an Argonaute-centered portable biosensor (STAR). This is the first report concerning Argonaute-based pathogenic bacteria detection. Simply, the species-specific mecA and nuc gene are isothermally amplified using loop-mediated isothermal amplification (LAMP) technique, followed by Argonaute-based detection enabled by its programmable, guided, sequence-specific recognition and cleavage. With the strategy, the targeted nucleic acid signals gene are dexterously converted into fluorescent signals. STAR is capable of detecting the nuc gene and mecA gene simultaneously in a single reaction. The limit of detection is 10 CFU/mL with a dynamic range from 10 to 107 CFU/mL. The sample-to-result time is <65 min. This method is successfully adapted to detect clinical samples, contaminated foods, and MRSA-infected animals. This work broadens the reach of Argonaute-based biosensing and presents a novel bacterial point-of-need (PON) detection platform.
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Affiliation(s)
- Jun Kou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Qiang Zhang
- Branch of Tianjin Third Central Hospital, Tianjin, 300250, China
| | - Xiao Han
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xinkuan Cheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
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7
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Pal A, Vasudevan V, Houle F, Lantin M, Maniates K, Huberdeau MQ, Abbott A, Simard M. Defining the contribution of microRNA-specific Argonautes with slicer capability in animals. Nucleic Acids Res 2024; 52:5002-5015. [PMID: 38477356 PMCID: PMC11109967 DOI: 10.1093/nar/gkae173] [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: 01/19/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
microRNAs regulate gene expression through interaction with an Argonaute protein. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicer residues in the canonical microRNA pathway is still unclear in animals. To address this, we created Caenorhabditis elegans strains with mutated slicer residues in the endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the mutation in ALG-1 and ALG-2 catalytic residues affects overall animal fitness and causes phenotypes reminiscent of miRNA defects only when grown and maintained at restrictive temperature. Furthermore, the analysis of global miRNA expression shows that the slicer residues of ALG-1 and ALG-2 contribute differentially to regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the catalytic tetrad of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicer residues of miRNA-specific Argonautes contribute to maintaining levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.
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Affiliation(s)
- Anisha Pal
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - Vaishnav Vasudevan
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - François Houle
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - Michael Lantin
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - Katherine A Maniates
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, USA
| | - Miguel Quévillon Huberdeau
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - Allison L Abbott
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Martin J Simard
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
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8
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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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9
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Zheng L, Zhou B, Yang Y, Zan B, Zhong B, Wu B, Feng Y, Liu Q, Hong L. Mn 2+-induced structural flexibility enhances the entire catalytic cycle and the cleavage of mismatches in prokaryotic argonaute proteins. Chem Sci 2024; 15:5612-5626. [PMID: 38638240 PMCID: PMC11023060 DOI: 10.1039/d3sc06221j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/01/2024] [Indexed: 04/20/2024] Open
Abstract
Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid-based biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+ in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicate that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+ in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.
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Affiliation(s)
- Lirong Zheng
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- Department of Cell and Developmental Biology & Michigan Neuroscience Institute, University of Michigan Medical School 48105 Ann Arbor MI USA
| | - Bingxin Zhou
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University Shanghai 200240 China
| | - Yu Yang
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Bing Zan
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
| | - Bozitao Zhong
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Banghao Wu
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Yan Feng
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Liu
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University Shanghai 200240 China
- State Key Laboratory for Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong University Shanghai 200240 China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University Shanghai 200240 China
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10
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Fu R, Hou J, Wang Z, Xianyu Y. Mn 2+-Mediated Modulation of PfAgo Activity for Biosensing. Adv Healthc Mater 2024:e2304484. [PMID: 38530141 DOI: 10.1002/adhm.202304484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/01/2024] [Indexed: 03/27/2024]
Abstract
Argonaute (Ago) as a powerful enzyme has provided new insights into biosensing due to its programmability, high sensitivity, and user-friendly operation. However, current strategies mainly rely on phosphorylated guide DNA to modulate the cleavage activity of Ago, which is limited in versatility and simplicity. Herein, the authors report the Mn2+-enhanced cleavage activity of Ago and employ Mn-ions with variable valence to regulate the activity of Pyrococcus furiosus Ago (PfAgo) for biosensing applications. The conversion of Mn ions with different valence states through MnO2 nanoflowers enables the sensitive detection of ascorbic acid, alkaline phosphatase, and arsenic with limits of detection of 2.5 nmol L-1, 0.009 U L-1, and 0.4 ng mL-1, respectively. A PfAgo-based immunoassay is further developed that allows for the detection of diverse targets, thus providing a promising toolbox to broaden PfAgo-based sensors into versatile bioanalytical and biomedical applications.
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Affiliation(s)
- Ruijie Fu
- College of Biosystems Engineering and Food Science, Zhejiang University, Zhejiang, 310058, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang, 310058, China
| | - Jinjie Hou
- College of Biosystems Engineering and Food Science, Zhejiang University, Zhejiang, 310058, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang, 310058, China
| | - Zexiang Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Zhejiang, 310058, China
- Institute of Pesticide and Environmental Toxicology, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang, 310058, China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Zhejiang, 310058, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang, 310058, China
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310058, China
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11
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Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M. The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res 2024; 52:2530-2545. [PMID: 38197228 PMCID: PMC10954474 DOI: 10.1093/nar/gkad1241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.
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Affiliation(s)
- Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Edvardas Golovinas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Reda Pocevičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Danielis Rutkauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, LT-02300, Vilnius, Lithuania
| | - Marija Jankunec
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Evelina Zagorskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Edvinas Jurgelaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Algirdas Grybauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
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12
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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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13
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Yang B, Wang H, Kong J, Fang X. Long-term monitoring of ultratrace nucleic acids using tetrahedral nanostructure-based NgAgo on wearable microneedles. Nat Commun 2024; 15:1936. [PMID: 38431675 PMCID: PMC10908814 DOI: 10.1038/s41467-024-46215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Real-time and continuous monitoring of nucleic acid biomarkers with wearable devices holds potential for personal health management, especially in the context of pandemic surveillance or intensive care unit disease. However, achieving high sensitivity and long-term stability remains challenging. Here, we report a tetrahedral nanostructure-based Natronobacterium gregoryi Argonaute (NgAgo) for long-term stable monitoring of ultratrace unamplified nucleic acids (cell-free DNAs and RNAs) in vivo for sepsis on wearable device. This integrated wireless wearable consists of a flexible circuit board, a microneedle biosensor, and a stretchable epidermis patch with enrichment capability. We comprehensively investigate the recognition mechanism of nucleic acids by NgAgo/guide DNA and signal transformation within the Debye distance. In vivo experiments demonstrate the suitability for real-time monitoring of cell-free DNA and RNA with a sensitivity of 0.3 fM up to 14 days. These results provide a strategy for highly sensitive molecular recognition in vivo and for on-body detection of nucleic acid.
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Affiliation(s)
- Bin Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Haonan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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14
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Li Y, Shen Z, Zhang M, Yang XY, Cleary SP, Xie J, Marathe IA, Kostelic M, Greenwald J, Rish AD, Wysocki VH, Chen C, Chen Q, Fu TM, Yu Y. PtuA and PtuB assemble into an inflammasome-like oligomer for anti-phage defense. Nat Struct Mol Biol 2024; 31:413-423. [PMID: 38177683 DOI: 10.1038/s41594-023-01172-8] [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: 02/22/2023] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Escherichia coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB. PtuA contains an ATPase domain, while PtuB is predicted to function as a nuclease. Here we show that PtuA and PtuB form a stable complex with a 6:2 stoichiometry. Cryo-electron microscopy structure of PtuAB reveals a distinctive horseshoe-like configuration. PtuA adopts a hexameric arrangement, organized as an asymmetric trimer of dimers, contrasting the ring-like structure by other ATPases. Notably, the three pairs of PtuA dimers assume distinct conformations and fulfill unique roles in recruiting PtuB. Our functional assays have further illuminated the importance of the oligomeric assembly of PtuAB in anti-phage defense. Moreover, we have uncovered that ATP molecules can directly bind to PtuA and inhibit the activities of PtuAB. Together, the assembly and function of the Septu system shed light on understanding other ATPase-containing systems in bacterial immunity.
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Affiliation(s)
- Yuanyuan Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Mengyuan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Xiao-Yuan Yang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Sean P Cleary
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Jiale Xie
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Ila A Marathe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Marius Kostelic
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Jacelyn Greenwald
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Anthony D Rish
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Chong Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
| | - Qiang Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China.
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA.
| | - Yamei Yu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China.
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15
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He P, Zhou W, Wei H, Yu J. Fast and Ultrasensitive Detection of Monkeypox by a Pyrococcus furiosus Argonaute System Coupled with a Short Amplification. Viruses 2024; 16:382. [PMID: 38543748 PMCID: PMC10975468 DOI: 10.3390/v16030382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/17/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Monkeypox virus (MPXV), the pathogen responsible for the infectious disease monkeypox, causes lesions on the skin, lymphadenopathy, and fever. It has posed a global public health threat since May 2022. Highly sensitive and specific detection of MPXV is crucial for preventing the spread of the disease. Pyrococcus furiosus Argonaute (PfAgo) is an artificial DNA-guided restriction cleavage enzyme programmable with 5'-phosphorylated ssDNA sequences, which can be developed to specifically detect nucleic acids of pathogens. Here, a PfAgo-based system was established for the detection of MPXV-specific DNA targeting the F3L gene. A short amplicon of 79 bp could be obtained through a fast PCR procedure, which was completed within 45 min. Two 5'-phosphorylation guide DNAs were designed to guide PfAgo to cleave the amplicon to obtain an 18 bp 5'-phosphorylation sequence specific to MPXV, not to other orthopoxviruses (cowpox, variola, and vaccinia viruses). The 18 bp sequence guided PfAgo to cleave a designed probe specific to MPXV to emit fluorescence. With optimized conditions for the PfAgo-MPXV system, it could be completed in 60 min for the detection of the extracted MPXV DNA with the limit of detection (LOD) of 1.1 copies/reaction and did not depend on expensive instruments. Successful application of the PfAgo-MPXV system in sensitively detecting MPXV in simulated throat swabs, skin swabs, sera, and wastewater demonstrated the system's good performance. The PfAgo platform, with high sensitivity and specificity established here, has the potential to prevent the spread of MPXV.
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Affiliation(s)
- Ping He
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhao Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, China; (P.H.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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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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17
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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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18
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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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19
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Liu S, Liu H, Wang X, Shi L. The immune system of prokaryotes: potential applications and implications for gene editing. Biotechnol J 2024; 19:e2300352. [PMID: 38403433 DOI: 10.1002/biot.202300352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/30/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
Gene therapy has revolutionized the treatment of genetic diseases. Spearheading this revolution are sophisticated genome editing methods such as TALENs, ZFNs, and CRISPR-Cas, which trace their origins back to prokaryotic immune systems. Prokaryotes have developed various antiviral defense systems to combat viral attacks and the invasion of genetic elements. The comprehension of these defense mechanisms has paved the way for the development of indispensable tools in molecular biology. Among them, restriction endonuclease originates from the innate immune system of bacteria. The CRISPR-Cas system, a widely applied genome editing technology, is derived from the prokaryotic adaptive immune system. Single-base editing is a precise editing tool based on CRISPR-Cas system that involves deamination of target base. It is worth noting that prokaryotes possess deamination enzymes as part of their defense arsenal over foreign genetic material. Furthermore, prokaryotic Argonauts (pAgo) proteins, also function in anti-phage defense, play an important role in complementing the CRISPR-Cas system by addressing certain limitations it may have. Recent studies have also shed light on the significance of Retron, a reverse transcription transposon previously showed potential in genome editing, has also come to light in the realm of prokaryotic immunity. These noteworthy findings highlight the importance of studying prokaryotic immune system for advancing genome editing techniques. Here, both the origin of prokaryotic immunity underlying aforementioned genome editing tools, and potential applications of deaminase, pAgo protein and reverse transcriptase in genome editing among prokaryotes were introduced, thus emphasizing the fundamental mechanism and significance of prokaryotic immunity.
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Affiliation(s)
- Siyang Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hongling Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lei Shi
- School of Life Sciences, Chongqing University, Chongqing, China
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20
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Lu X, Xiao J, Wang L, Zhu B, Huang F. The nuclease-associated short prokaryotic Argonaute system nonspecifically degrades DNA upon activation by target recognition. Nucleic Acids Res 2024; 52:844-855. [PMID: 38048327 PMCID: PMC10810196 DOI: 10.1093/nar/gkad1145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023] Open
Abstract
Prokaryotic Argonautes (pAgos) play a vital role in host defense by utilizing short nucleic acid guides to recognize and target complementary nucleic acids. Despite being the majority of pAgos, short pAgos have only recently received attention. Short pAgos are often associated with proteins containing an APAZ domain and a nuclease domain including DUF4365, SMEK, or HNH domain. In contrast to long pAgos that specifically cleave the target DNA, our study demonstrates that the short pAgo from Thermocrispum municipal, along with its associated DUF4365-APAZ protein, forms a heterodimeric complex. Upon RNA-guided target DNA recognition, this complex is activated to nonspecifically cleave DNA. Additionally, we found that the TmuRE-Ago complex shows a preference for 5'-OH guide RNA, specifically requires a uridine nucleotide at the 5' end of the guide RNA, and is sensitive to single-nucleotide mismatches between the guide RNA and target DNA. Based on its catalytic properties, our study has established a novel nucleic acid detection method and demonstrated its feasibility. This study not only expands our understanding of the defense mechanism employed by short pAgo systems but also suggests their potential applications in nucleic acid detection.
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Affiliation(s)
- Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jun Xiao
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Longfei Wang
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518063, China
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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21
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Li Y, Tang X, Wang N, Zhao Z, Man S, Zhu L, Ma L. Argonaute-DNAzyme tandem biosensing for highly sensitive and simultaneous dual-gene detection of methicillin-resistant Staphylococcus aureus. Biosens Bioelectron 2024; 244:115758. [PMID: 37931440 DOI: 10.1016/j.bios.2023.115758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), a common zoonotic multidrug-resistant bacterium, puts a great threat to public health and food safety. Rapid and reliable detection of MRSA is crucial to guide effective patient treatment at early stages of infection and control the spread of MRSA infections. Herein, we developed a Simultaneous dual-gene and ulTra-sensitive detection for methicillin-resistant Staphylococcus aureus using Argonaute-DNAzyme tandem Detection (STAND). Simply, loop-mediated isothermal amplification (LAMP) was used for the amplification of the species-specific mecA and nuc gene, followed by STAND enabled by the site-specific cleavage of programable Argonaute. The Argonaute-DNAzyme tandem reaction rendered a conceptually novel signal amplification and transduction module that was more sensitive (1 or 2 order of magnitude higher) than the original Argonaute-based biosensing. With the strategy, the target nucleic acid signals gene were dexterously converted into fluorescent signals. STAND could detect the nuc gene and mecA gene simultaneously in a single reaction with 1 CFU/mL MRSA and a dynamic range from 1 to 108 CFU/mL. This method was confirmed by clinical samples and challenged by identifying contaminated foods and MRSA-infected animals. This work enriches the arsenal of Argonaute-mediated biosensing and presents a novel biosensing strategy to detect pathogenic bacteria with ultra-sensitivity, specificity and on-site capability.
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Affiliation(s)
- Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiaoqin Tang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Nan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Lei Zhu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
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22
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Pal A, Vasudevan V, Houle F, Lantin M, Maniates KA, Quevillon Huberdeau M, Abbott A, Simard MJ. Defining the contribution of microRNA-specific slicing Argonautes in animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.19.524781. [PMID: 36711744 PMCID: PMC9882343 DOI: 10.1101/2023.01.19.524781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
microRNAs regulate gene expression through interaction with an Argonaute protein family member. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicing activity in the canonical microRNA pathway is still unclear in animals. To address the importance of slicing Argonautes in animals, we created Caenorhabditis elegans strains, carrying catalytically dead endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the loss of ALG-1 and ALG-2 slicing activity affects overall animal fitness and causes phenotypes, reminiscent of miRNA defects, only when grown and maintained at restrictive temperature. Furthermore, the analysis of global miRNA expression shows that the catalytic activity of ALG-1 and ALG-2 differentially regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the slicing activity of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicing activity of miRNA-specific Argonautes function to maintain the levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.
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23
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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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24
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Graver BA, Chakravarty N, Solomon KV. Prokaryotic Argonautes for in vivo biotechnology and molecular diagnostics. Trends Biotechnol 2024; 42:61-73. [PMID: 37451948 DOI: 10.1016/j.tibtech.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
Prokaryotic Argonautes (pAgos) are an emerging class of programmable endonucleases that are believed to be more flexible than existing CRISPR-Cas systems and have significant potential for biotechnology. Current applications of pAgos include a myriad of molecular diagnostics and in vitro DNA assembly tools. However, efforts have historically been centered on thermophilic pAgo variants. To enable in vivo biotechnological applications such as gene editing, focus has shifted to pAgos from mesophilic organisms. We discuss what is known of pAgos, how they are being developed for various applications, and strategies to overcome current challenges to in vivo applications in prokaryotes and eukaryotes.
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Affiliation(s)
- Brett A Graver
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Namrata Chakravarty
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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25
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Nakanishi K. When Argonaute takes out the ribonuclease sword. J Biol Chem 2024; 300:105499. [PMID: 38029964 PMCID: PMC10772731 DOI: 10.1016/j.jbc.2023.105499] [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: 07/10/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023] Open
Abstract
Argonaute (AGO) proteins in all three domains of life form ribonucleoprotein or deoxyribonucleoprotein complexes by loading a guide RNA or DNA, respectively. Since all AGOs retain a PIWI domain that takes an RNase H fold, the ancestor was likely an endoribonuclease (i.e., a slicer). In animals, most miRNA-mediated gene silencing occurs slicer independently. However, the slicer activity of AGO is indispensable in specific events, such as development and differentiation, which are critical for vertebrates and thus cannot be replaced by the slicer-independent regulation. This review highlights the distinctions in catalytic activation mechanisms among slicing-competent AGOs, shedding light on the roles of two metal ions in target recognition and cleavage. The precision of the target specificity by the RNA-induced silencing complexes is reevaluated and redefined. The possible coevolutionary relationship between slicer-independent gene regulation and AGO-binding protein, GW182, is also explored. These discussions reveal that numerous captivating questions remain unanswered regarding the timing and manner in which AGOs employ their slicing activity.
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Affiliation(s)
- Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.
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26
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Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S. Nucleic-acid-triggered NADase activation of a short prokaryotic Argonaute. Nature 2024; 625:822-831. [PMID: 37783228 DOI: 10.1038/s41586-023-06665-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Argonaute (Ago) proteins mediate RNA- or DNA-guided inhibition of nucleic acids1,2. Although the mechanisms used by eukaryotic Ago proteins and long prokaryotic Ago proteins (pAgos) are known, that used by short pAgos remains elusive. Here we determined the cryo-electron microscopy structures of a short pAgo and the associated TIR-APAZ proteins (SPARTA) from Crenotalea thermophila (Crt): a free-state Crt-SPARTA; a guide RNA-target DNA-loaded Crt-SPARTA; two Crt-SPARTA dimers with distinct TIR organization; and a Crt-SPARTA tetramer. These structures reveal that Crt-SPARTA is composed of a bilobal-fold Ago lobe that connects with a TIR lobe. Whereas the Crt-Ago contains a MID and a PIWI domain, Crt-TIR-APAZ has a TIR domain, an N-like domain, a linker domain and a trigger domain. The bound RNA-DNA duplex adopts a B-form conformation that is recognized by base-specific contacts. Nucleic acid binding causes conformational changes because the trigger domain acts as a 'roadblock' that prevents the guide RNA 5' ends and the target DNA 3' ends from reaching their canonical pockets; this disorders the MID domain and promotes Crt-SPARTA dimerization. Two RNA-DNA-loaded Crt-SPARTA dimers form a tetramer through their TIR domains. Four Crt-TIR domains assemble into two parallel head-to-tail-organized TIR dimers, indicating an NADase-active conformation, which is supported by our mutagenesis study. Our results reveal the structural basis of short-pAgo-mediated defence against invading nucleic acids, and provide insights for optimizing the detection of SPARTA-based programmable DNA sequences.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Kun Shang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- Medical School, Yan'an University, Yan'an, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Zhixia Mu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Xingke Fu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China
| | - Hongtao Zhu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
| | - Wei Ding
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Key Laboratory of Pathogen Infection Prevention and Control, Peking Union Medical College, Ministry of Education, Beijing, China.
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27
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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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28
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Koonin EV, Krupovic M. New faces of prokaryotic mobile genetic elements: guide RNAs link transposition with host defense mechanisms. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 36:100473. [PMID: 37779558 PMCID: PMC10538440 DOI: 10.1016/j.coisb.2023.100473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Most life forms harbor multiple, diverse mobile genetic elements (MGE) that widely differ in their rates and mechanisms of mobility. Recent findings on two classes of MGE in prokaryotes revealed a novel mechanism, RNA-guided transposition, where a transposon-encoded guide RNA directs the transposase to a unique site in the host genome. Tn7-like transposons, on multiple occasions, recruited CRISPR systems that lost the capacity to cleave target DNA and instead mediate RNA-guided transposition via CRISPR RNA. Conversely, the abundant transposon-associated, RNA-guided nucleases IscB and TnpB that appear to promote proliferation of IS200/IS605 and IS607 transposons were the likely evolutionary ancestors of type II and type V CRISPR systems, respectively. Thus, RNA-guided target recognition is a major biological phenomenon that connects MGE with host defense mechanisms. More RNA-guided defensive and MGE-associated functionalities are likely to be discovered.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, 75015 Paris
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29
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Chen R, Zhao J, Han M, Dong Y, Jiang F, Chen Y. DNA Extraction- and Amplification-Free Nucleic Acid Biosensor for the Detection of Foodborne Pathogens Based on CRISPR/Cas12a and Argonaute Protein-Mediated Cascade Signal Amplification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18037-18045. [PMID: 37947312 DOI: 10.1021/acs.jafc.3c06530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
A novel method for detecting low levels of viable foodborne pathogens, specifically Salmonella typhimurium (S. typhimurium), has been developed. Traditional nucleic acid assay, such as polymerase chain reaction (PCR), often requires complex DNA extraction and amplification, making it challenging to differentiate between viable and nonviable pathogens. This assay employed a phage as the recognition element to precisely identify and lyse viable S. typhimurium that can undergo DNA extraction. It combined the efficient trans-cleavage activities of CRISPR/Cas12a with the specific cleavage advantages of Argonaute proteins, enabling ultrasensitive detection. This double-enzyme-mediated nucleic acid test can accurately distinguish viable and nonviable S. typhimurium with a detection limit of 23 CFU/mL without DNA amplification. The method was successfully applied to common food samples, producing results consistent with quantitative PCR tests. This work provides a promising platform for easily detecting viable foodborne pathogens with high sensitivity without the need for DNA extraction and amplification.
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Affiliation(s)
- Rui Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junpeng Zhao
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Minjie Han
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yongzhen Dong
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian, Liaoning 116034, China
| | - Feng Jiang
- Key Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Wuhan 430075, China
| | - Yiping Chen
- State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian, Liaoning 116034, China
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30
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Song X, Lei S, Liu S, Liu Y, Fu P, Zeng Z, Yang K, Chen Y, Li M, She Q, Han W. Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection. Nat Commun 2023; 14:6970. [PMID: 37914725 PMCID: PMC10620215 DOI: 10.1038/s41467-023-42793-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Diverse prokaryotic Agos (pAgos) play potential functions in microbial defense. The functions and mechanisms of a group of full-length yet catalytically inactive pAgos, long-B pAgos, remain unclear. Here, we show that most long-B pAgos are functionally connected with distinct associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. The long-B pAgo-nuclease system (BPAN) is activated by guide RNA-directed target DNA recognition and performs collateral DNA degradation in vitro. In vivo, the system mediates genomic DNA degradation after sensing invading plasmid, which kills the infected cells and results in the depletion of the invader from the cell population. Together, the BPAN system provides immunoprotection via abortive infection. Our data also suggest that the defense strategy is employed by other long-B pAgos equipped with distinct associated proteins.
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Affiliation(s)
- Xinmi Song
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Sheng Lei
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shunhang Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yanqiu Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Pan Fu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ke Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ming Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, 266237, Jimo, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China.
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31
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Taton A, Gilderman TS, Ernst DC, Omaga CA, Cohen LA, Rey-Bedon C, Golden JW, Golden SS. Synechococcus elongatus Argonaute reduces natural transformation efficiency and provides immunity against exogenous plasmids. mBio 2023; 14:e0184323. [PMID: 37791787 PMCID: PMC10653904 DOI: 10.1128/mbio.01843-23] [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: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE S. elongatus is an important cyanobacterial model organism for the study of its prokaryotic circadian clock, photosynthesis, and other biological processes. It is also widely used for genetic engineering to produce renewable biochemicals. Our findings reveal an SeAgo-based defense mechanism in S. elongatus against the horizontal transfer of genetic material. We demonstrate that deletion of the ago gene facilitates genetic studies and genetic engineering of S. elongatus.
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Affiliation(s)
- Arnaud Taton
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Tami S. Gilderman
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Dustin C. Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Carla A. Omaga
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Lucas A. Cohen
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Camilo Rey-Bedon
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - James W. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Susan S. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
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32
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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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33
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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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34
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Chen Q, Zhou T. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. J Biol Chem 2023; 299:105225. [PMID: 37673341 PMCID: PMC10562873 DOI: 10.1016/j.jbc.2023.105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Recent advancements in small RNA sequencing have unveiled a previously hidden world of regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small interfering RNAs, microRNAs, and piwi-interacting RNAs. This exploration, starting with tRNA-derived small RNAs, has led to the discovery of a diverse universe of sncRNAs derived from various longer structured RNAs such as rRNAs, small nucleolar RNAs, small nuclear RNAs, Y RNAs, and vault RNAs, with exciting uncharted functional possibilities. In this perspective, we discuss the emerging functional principles of sncRNAs beyond the well-known RNAi-like mechanisms, focusing on those that operate independent of linear sequence complementarity but rather function in an aptamer-like fashion. Aptamers use 3D structure for specific interactions with ligands and are modulated by RNA modifications and subcellular environments. Given that aptamer-like sncRNA functions are widespread and present in species lacking RNAi, they may represent an ancient functional principle that predates RNAi. We propose a rethinking of the origin of RNAi and its relationship with these aptamer-like functions in sncRNAs and how these complementary mechanisms shape biological processes. Lastly, the aptamer-like function of sncRNAs highlights the need for caution in using small RNA mimics in research and therapeutics, as their specificity is not restricted solely to linear sequence.
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Affiliation(s)
- Qi Chen
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah, USA; Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.
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35
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Akritidou K, Thurtle-Schmidt BH. OLD family nuclease function across diverse anti-phage defense systems. Front Microbiol 2023; 14:1268820. [PMID: 37840731 PMCID: PMC10568477 DOI: 10.3389/fmicb.2023.1268820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Bacteriophages constitute a ubiquitous threat to bacteria, and bacteria have evolved numerous anti-phage defense systems to protect themselves. These systems include well-studied phenomena such as restriction endonucleases and CRISPR, while emerging studies have identified many new anti-phage defense systems whose mechanisms are unknown or poorly understood. Some of these systems involve overcoming lysogenization defect (OLD) nucleases, a family of proteins comprising an ABC ATPase domain linked to a Toprim nuclease domain. Despite being discovered over 50 years ago, OLD nuclease function remained mysterious until recent biochemical, structural, and bioinformatic studies revealed that OLD nucleases protect bacteria by functioning in diverse anti-phage defense systems including the Gabija system and retrons. In this review we will highlight recent discoveries in OLD protein function and their involvement in multiple discrete anti-phage defense systems.
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36
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Wang S, Wang S, Hao T, Zhu S, Qiu X, Li Y, Yang X, Wu S. Detection of Salmonella DNA and drug-resistance mutation by PCR-based CRISPR-lbCas12a system. AMB Express 2023; 13:100. [PMID: 37750967 PMCID: PMC10522547 DOI: 10.1186/s13568-023-01588-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: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 09/27/2023] Open
Abstract
Salmonella is an important foodborne pathogen, which can cause serious public health problems. Rapid and accurate detection of Salmonella infection and drug resistance mutations in patients will provide timely guidance for clinical treatment and avoid disease progression and other related clinical problems. Here, we established a highly sensitive and quick method for Salmonella and drug resistance mutation detection based on polymerase chain reaction (PCR) and CRISPR-lbCas12a system and evaluated its practicability with clinical samples.Specific CRISPR RNAs (crRNAs) and primers are designed for Salmonella DNA and parC gene S80I mutation diagnosis. CrRNAs with and without phosphorylated modification and different crRNA preparation methods are used to assess the effect on the detection system. After optimization, we detected as low as one copy of Salmonella DNA and drug resistance mutation parC S80I with the Salmonella DNA standard. For 94 clinical samples, this method also showed high sensitivity (100%, 95% CI: 84.98-100%) and specificity (98.48%, 95% CI: 90.73-99.92%) with less time (3 h) than plate culture (16 h) and conventional antimicrobial susceptibility testing (over 16 h). Besides, one parC S80I mutant strain was detected, which is consistent with the result of DNA sequencing. Taken together, we established a highly sensitive and specific method for Salmonella infection and parC S80I drug resistance mutation detection with fewer reagents and ordinary instruments. This assay has wide application prospects for fast detection of pathogen (bacterium and virus) infection, drug resistance determination, and proper treatment guidance.
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Affiliation(s)
- Shan Wang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shang Wang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Tongyu Hao
- Medical Laboratory of Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Shimao Zhu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
- South China Hospital of Shenzhen University, Shenzhen, China
| | - Xinying Qiu
- Medical Laboratory of Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China
- South China Hospital of Shenzhen University, Shenzhen, China
| | - Xiaoxu Yang
- Department of Biology and Genetics, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518000, China.
- South China Hospital of Shenzhen University, Shenzhen, China.
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37
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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: 2] [Impact Index Per Article: 2.0] [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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38
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [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: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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39
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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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40
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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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41
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Guo M, Zhu Y, Lin Z, Yang D, Zhang A, Guo C, Huang Z. Cryo-EM structure of the ssDNA-activated SPARTA complex. Cell Res 2023; 33:731-734. [PMID: 37491603 PMCID: PMC10474254 DOI: 10.1038/s41422-023-00850-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/30/2023] [Indexed: 07/27/2023] Open
Affiliation(s)
- Minghui Guo
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zhiying Lin
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Dehui Yang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Anqi Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Changyou Guo
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- New Cornerstone Science Laboratory, Shenzhen, Guangdong, China.
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42
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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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43
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Liu Y, Chen X, Zhao Y, Wang XY, Luo YW, Chen L, Wang W, Zhong S, Hu M, Dai Z, Jiang J, Wang X, Ji H, Cheng XX, Zheng A, Zuo J, Liu H, Ma D, Luo Z, Cao F, Hu S, Huang AL, Tang KF. Small cytosolic double-stranded DNA represses cyclic GMP-AMP synthase activation and induces autophagy. Cell Rep 2023; 42:112852. [PMID: 37481718 DOI: 10.1016/j.celrep.2023.112852] [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: 01/22/2023] [Revised: 04/28/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023] Open
Abstract
The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway is a major mediator of inflammation following stimulation with >45 bp double-stranded DNA (dsDNA). Herein, we identify a class of ∼20-40 bp small cytosolic dsDNA (scDNA) molecules that compete with long dsDNA (200-1,500 bp herring testis [HT]-DNA) for binding to cGAS, thus repressing HT-DNA-induced cGAS activation. The scDNA promotes cGAS and Beclin-1 interaction, releasing Rubicon, a negative regulator of phosphatidylinositol 3-kinase class III (PI3KC3), from the Beclin-1-PI3KC3 complex. This leads to PI3KC3 activation and induces autophagy, causing degradation of STING and long cytosolic dsDNA. Moreover, DNA damage decreases, and autophagy inducers increase scDNA levels. scDNA transfection and treatment with autophagy inducers attenuate DNA damage-induced cGAS activation. Thus, scDNA molecules serve as effective brakes for cGAS activation, preventing excessive inflammatory cytokine production following DNA damage. Our findings may have therapeutic implications for cytosolic DNA-associated inflammatory diseases.
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Affiliation(s)
- Yao Liu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xiao Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yuemei Zhao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Xing-Yue Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Yu-Wei Luo
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lina Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Weiyun Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Shouhui Zhong
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Meizhen Hu
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Zhizheng Dai
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jiayu Jiang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Xin Wang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Hongyu Ji
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xiao-Xiao Cheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Anqi Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Jiwei Zuo
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Hui Liu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Di Ma
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Zhicheng Luo
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Fang Cao
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shanshan Hu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325015, P.R. China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China.
| | - Kai-Fu Tang
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, P.R. China.
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44
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Wang Y, Wang Y, Chen Y, Yan Q, Lin A. Research progress in mitochondrial gene editing technology. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:460-472. [PMID: 37643980 PMCID: PMC10495247 DOI: 10.3724/zdxbyxb-2023-0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations result in a variety of genetic diseases. As an emerging therapeutic method, mtDNA editing technology recognizes targets more based on the protein and less on the nucleic acid. Although the protein recognition type mtDNA editing technology represented by zinc finger nuclease technology, transcription activator like effector nuclease technology and base editing technology has made some progress, the disadvantages of complex recognition sequence design hinder further popularization. Gene editing based on nucleic acid recognition by the CRISPR system shows superiority due to the simple structure, easy design and modification. However, the lack of effective means to deliver nucleic acids into mitochondria limits application in the field of mtDNA editing. With the advances in the study of endogenous and exogenous import pathways and the deepening understanding of DNA repair mechanisms, growing evidence shows the feasibility of nucleic acid delivery and the broad application prospects of nucleic acid recognition type mtDNA editing technology. Based on the classification of recognition elements, this article summarizes the current principles and development of mitochondrial gene editing technology, and discusses its application prospects.
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Affiliation(s)
- Yichen Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Zhejiang University Cancer Center, Hangzhou 310058, China.
| | - Ying Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Yu Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Qingfeng Yan
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Zhejiang University Cancer Center, Hangzhou 310058, China.
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Center for RNA Medicine, International Institutes of Medicine, Zhejiang University, Jinhua 322000, Zhejiang Province, China.
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45
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Rousset F, Yirmiya E, Nesher S, Brandis A, Mehlman T, Itkin M, Malitsky S, Millman A, Melamed S, Sorek R. A conserved family of immune effectors cleaves cellular ATP upon viral infection. Cell 2023; 186:3619-3631.e13. [PMID: 37595565 DOI: 10.1016/j.cell.2023.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/18/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023]
Abstract
During viral infection, cells can deploy immune strategies that deprive viruses of molecules essential for their replication. Here, we report a family of immune effectors in bacteria that, upon phage infection, degrade cellular adenosine triphosphate (ATP) and deoxyadenosine triphosphate (dATP) by cleaving the N-glycosidic bond between the adenine and sugar moieties. These ATP nucleosidase effectors are widely distributed within multiple bacterial defense systems, including cyclic oligonucleotide-based antiviral signaling systems (CBASS), prokaryotic argonautes, and nucleotide-binding leucine-rich repeat (NLR)-like proteins, and we show that ATP and dATP degradation during infection halts phage propagation. By analyzing homologs of the immune ATP nucleosidase domain, we discover and characterize Detocs, a family of bacterial defense systems with a two-component phosphotransfer-signaling architecture. The immune ATP nucleosidase domain is also encoded within diverse eukaryotic proteins with immune-like architectures, and we show biochemically that eukaryotic homologs preserve the ATP nucleosidase activity. Our findings suggest that ATP and dATP degradation is a cell-autonomous innate immune strategy conserved across the tree of life.
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Affiliation(s)
- Francois Rousset
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Erez Yirmiya
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shahar Nesher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tevie Mehlman
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Millman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarah Melamed
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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46
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Gu Y, Li H, Deep A, Enustun E, Zhang D, Corbett KD. Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552793. [PMID: 37609250 PMCID: PMC10441436 DOI: 10.1101/2023.08.10.552793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Prokaryotes encode diverse anti-bacteriophage immune systems, including the single-protein Shedu nuclease. Here we reveal the structural basis for activation of Bacillus cereus Shedu. In the inactive homotetramer, a key catalytic residue in Shedu's nuclease domain is sequestered away from the catalytic site. Activation involves a conformational change that completes the active site and promotes assembly of a homo-octamer for coordinated double-strand DNA cleavage. Removal of Shedu's N-terminal domain ectopically activates the enzyme, suggesting that this domain allosterically inhibits Shedu in the absence of infection. Bioinformatic analysis of nearly 8,000 Shedu homologs reveals remarkable diversity in their N-terminal regulatory domains: we identify 79 domain families falling into eight functional classes, including diverse nucleic acid binding, enzymatic, and other domains. Together, these data reveal Shedu as a broad family of immune nucleases with a common nuclease core regulated by diverse N-terminal domains that likely respond to a range of infection-related signals.
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Affiliation(s)
- Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA 92093
| | - Huan Li
- Department of Biology, Saint Louis University, Saint Louis, MO 63103
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA 92093
| | - Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla CA 92093
| | - Dapeng Zhang
- Department of Biology, Saint Louis University, Saint Louis, MO 63103
| | - Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA 92093
- Department of Molecular Biology, University of California San Diego, La Jolla CA 92093
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47
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Wang Z, Wang Z, Zhang F, Wu L. Thermus thermophilus Argonaute-based signal amplifier for highly sensitive and specific microRNA detection. Front Bioeng Biotechnol 2023; 11:1221943. [PMID: 37583711 PMCID: PMC10424790 DOI: 10.3389/fbioe.2023.1221943] [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: 05/13/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
The prokaryote-derived gene defense system as a new generation of nucleic acid detection tool exhibits impressive performance in the field of molecular diagnosis. Prokaryotic Argonaute (Ago) is a CRISPR-associated protein that is guided by a short DNA (gDNA) and then efficiently cleaves gDNA-complementary nucleic acids and presents unique characteristics that are different from the CRISPR/Cas system. However, the application of Ago in biosensing is still relatively scarce, and many properties of Ago need to be further clarified. In this study, we aim to systematically explore the properties of Thermus thermophilus Argonaute (TtAgo), including the dependence of TtAgo activity on guide DNA (gDNA) length, substrates' length, and the position of gDNA complementary region on the substrate. Based on these properties, we constructed an exonuclease III-assisted target-recycled amplification system (exoAgo) for sensitive miRNA detection. The result showed that exoAgo can be used for miRNA profiling with a detection limit of 12.2 pM and single-base-resolution and keep good performance for the detection of complex samples, which indicates that Ago has great application potential in the detection of nucleic acids. In conclusion, this study will provide guidance for further development and utilization of Ago in the field of biosensing.
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Affiliation(s)
- Ziqi Wang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Haikou, China
| | - Zitong Wang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Haikou, China
| | - Fan Zhang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Haikou, China
| | - Lingyi Wu
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Haikou, China
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48
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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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49
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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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50
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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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