1
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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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2
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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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3
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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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4
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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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5
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Guo L, Huang P, Li Z, Shin YC, Yan P, Lu M, Chen M, Xiao Y. Auto-inhibition and activation of a short Argonaute-associated TIR-APAZ defense system. Nat Chem Biol 2024; 20:512-520. [PMID: 37932527 DOI: 10.1038/s41589-023-01478-0] [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: 05/20/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Short prokaryotic Ago accounts for most prokaryotic Argonaute proteins (pAgos) and is involved in defending bacteria against invading nucleic acids. Short pAgo associated with TIR-APAZ (SPARTA) has been shown to oligomerize and deplete NAD+ upon guide-mediated target DNA recognition. However, the molecular basis of SPARTA inhibition and activation remains unknown. In this study, we determined the cryogenic electron microscopy structures of Crenotalea thermophila SPARTA in its inhibited, transient and activated states. The SPARTA monomer is auto-inhibited by its acidic tail, which occupies the guide-target binding channel. Guide-mediated target binding expels this acidic tail and triggers substantial conformational changes to expose the Ago-Ago dimerization interface. As a result, SPARTA assembles into an active tetramer, where the four TIR domains are rearranged and packed to form NADase active sites. Together with biochemical evidence, our results provide a panoramic vision explaining SPARTA auto-inhibition and activation and expand understanding of pAgo-mediated bacterial defense systems.
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Affiliation(s)
- Lijie Guo
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Pingping Huang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhaoxing Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Young-Cheul Shin
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Purui Yan
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Meiling Lu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Meirong Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, China.
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6
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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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7
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Lin Q, Ye X, Chen H, Fang X, Chen H, Kong J. Binding Activity of Prokaryotic Argonaute for Background-Suppressed Exponential Isothermal Amplification. Anal Chem 2024; 96:620-623. [PMID: 38170960 DOI: 10.1021/acs.analchem.3c05263] [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: 01/05/2024]
Abstract
Prokaryotic Argonautes (pAgos) have been recently used in many nucleic acid biosensing applications but have rarely been used for regulating the isothermal amplification system. Herein, we reported Thermus thermophilus Argonaute (TtAgo)-mediated background-suppressed exponential isothermal amplification (EXPAR) as the first example to explore the binding activity of pAgos toward regulation of the amplification template. It was demonstrated that thermophilic pAgos efficiently eliminated nonspecific hybridization between templates by their binding affinity with the template, resulting in greatly enhancing the specificity of EXPAR. TtAgo-mediated, background-suppressed EXPAR was employed to detect miRNA with a detection limit of 10-15 M, which was 1000 times and 100 times more sensitive than that of traditional RT-PCR and EXPAR, respectively. This method further showed good performance in discriminating cancer patients from healthy individuals, indicating its potential for practical clinical applications.
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Affiliation(s)
- Qiuyuan Lin
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Technology for Precision Medicine, School of Medical Technology and Engineering Fujian Medical University, Fuzhou 350005, China
| | - Xin Ye
- Department of Laboratory Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, Shaanxi PR China
| | - Hongyuan Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200437, China
| | - Xueen Fang
- Department of Chemistry, Fudan University, Shanghai 200437, China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai 200437, China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai 200437, China
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8
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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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9
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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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10
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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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11
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Mercier C, Thies D, Zhong L, Raftery MJ, Erdmann S. Characterization of an archaeal virus-host system reveals massive genomic rearrangements in a laboratory strain. Front Microbiol 2023; 14:1274068. [PMID: 37789858 PMCID: PMC10544981 DOI: 10.3389/fmicb.2023.1274068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
Halophilic archaea (haloarchaea) are known to exhibit multiple chromosomes, with one main chromosome and one or several smaller secondary chromosomes or megaplasmids. Halorubrum lacusprofundi, a model organism for studying cold adaptation, exhibits one secondary chromosome and one megaplasmid that include a large arsenal of virus defense mechanisms. We isolated a virus (Halorubrum tailed virus DL1, HRTV-DL1) infecting Hrr. lacusprofundi, and present an in-depth characterization of the virus and its interactions with Hrr. lacusprofundi. While studying virus-host interactions between Hrr. lacusprofundi and HRTV-DL1, we uncover that the strain in use (ACAM34_UNSW) lost the entire megaplasmid and about 38% of the secondary chromosome. The loss included the majority of virus defense mechanisms, making the strain sensitive to HRTV-DL1 infection, while the type strain (ACAM34_DSMZ) appears to prevent virus replication. Comparing infection of the type strain ACAM34_DSMZ with infection of the laboratory derived strain ACAM34_UNSW allowed us to identify host responses to virus infection that were only activated in ACAM34_UNSW upon the loss of virus defense mechanisms. We identify one of two S-layer proteins as primary receptor for HRTV-DL1 and conclude that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Additionally, we identify archaeal homologs to eukaryotic proteins potentially being involved in the defense against virus infection.
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Affiliation(s)
- Coraline Mercier
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
| | - Daniela Thies
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW, Australia
| | - Susanne Erdmann
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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12
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Olina A, Agapov A, Yudin D, Sutormin D, Galivondzhyan A, Kuzmenko A, Severinov K, Aravin AA, Kulbachinskiy A. Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli. Microbiol Spectr 2023; 11:e0414622. [PMID: 37102866 PMCID: PMC10269773 DOI: 10.1128/spectrum.04146-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/29/2023] [Indexed: 04/28/2023] Open
Abstract
Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we show that two pAgos from cyanobacteria Synechococcus elongatus (SeAgo) and Limnothrix rosea (LrAgo) are active in heterologous Escherichia coli and aid cell division in the presence of the gyrase inhibitor ciprofloxacin, depending on the host double-strand break repair machinery. Both pAgos are preferentially loaded with small guide DNAs (smDNAs) derived from the sites of replication termination. Ciprofloxacin increases the amounts of smDNAs from the termination region and from the sites of genomic DNA cleavage by gyrase, suggesting that smDNA biogenesis depends on DNA replication and is stimulated by gyrase inhibition. Ciprofloxacin enhances asymmetry in the distribution of smDNAs around Chi sites, indicating that it induces double-strand breaks that serve as a source of smDNA during their processing by RecBCD. While active in E. coli, SeAgo does not protect its native host S. elongatus from ciprofloxacin. These results suggest that pAgo nucleases may help to complete replication of chromosomal DNA by promoting chromosome decatenation or participating in the processing of gyrase cleavage sites, and may switch their functional activities depending on the host species. IMPORTANCE Prokaryotic Argonautes (pAgos) are programmable nucleases with incompletely understood functions in vivo. In contrast to eukaryotic Argonautes, most studied pAgos recognize DNA targets. Recent studies suggested that pAgos can protect bacteria from invader DNA and counteract phage infection and may also have other functions including possible roles in DNA replication, repair, and gene regulation. Here, we have demonstrated that two cyanobacterial pAgos, SeAgo and LrAgo, can assist DNA replication and facilitate cell division in the presence of topoisomerase inhibitors in Escherichia coli. They are specifically loaded with small guide DNAs from the region of replication termination and protect the cells from the action of the gyrase inhibitor ciprofloxacin, suggesting that they help to complete DNA replication and/or repair gyrase-induced breaks. The results show that pAgo proteins may serve as a backup to topoisomerases under conditions unfavorable for DNA replication and may modulate the resistance of host bacterial strains to antibiotics.
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Affiliation(s)
- Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Denis Yudin
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Dmitry Sutormin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Anton Kuzmenko
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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13
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Panteleev V, Kropocheva E, Esyunina D, Kulbachinskiy A. Strong temperature effects on the fidelity of target DNA recognition by a thermophilic pAgo nuclease. Biochimie 2023; 209:142-149. [PMID: 36804511 DOI: 10.1016/j.biochi.2023.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/22/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
Prokaryotic Argonaute (pAgo) proteins are programmable nucleases with great promise in genetic engineering and biotechnology. Previous studies identified several DNA-targeting pAgo nucleases from mesophilic and thermophilic prokaryotic species that are active in various temperature ranges. However, the effects of temperature on the specificity of target recognition and cleavage by pAgos have not been studied. Here, we describe a thermostable pAgo nuclease from the thermophilic bacterium Thermobrachium celere, TceAgo. We show that TceAgo preferentially uses 5'-phosphorylated small DNA guides and can perform specific cleavage of both single-stranded and double-stranded DNA substrates in a wide range of temperatures. Single-nucleotide mismatches between guide and target molecules differently change the reaction efficiency depending on the mismatch position, with the fidelity of target recognition greatly increased at elevated temperatures. Thus, TceAgo can serve as a tool to allow specific detection and cleavage of DNA targets in a temperature-dependent manner. The results demonstrate that the specificity of programmable nucleases can be strongly affected by the reaction conditions, which should be taken into account when using these nucleases in various in vitro and in vivo applications.
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Affiliation(s)
- Vladimir Panteleev
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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14
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Koopal B, Mutte SK, Swarts DC. A long look at short prokaryotic Argonautes. Trends Cell Biol 2022:S0962-8924(22)00239-2. [DOI: 10.1016/j.tcb.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/23/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
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15
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Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD + depletion. Nat Microbiol 2022; 7:1857-1869. [PMID: 36192537 DOI: 10.1038/s41564-022-01239-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/26/2022] [Indexed: 02/02/2023]
Abstract
Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). The majority (~60%) of pAgos identified bioinformatically are shorter (comprising only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here we show that Geobacter sulfurreducens short pAgo and the NAD+-bound Sir2 protein form a stable heterodimeric complex. The GsSir2/Ago complex presumably recognizes invading plasmid or phage DNA and activates the Sir2 subunit, which triggers endogenous NAD+ depletion and cell death, and prevents the propagation of invading DNA. We reconstituted NAD+ depletion activity in vitro and showed that activated GsSir2/Ago complex functions as a NADase that hydrolyses NAD+ to ADPR. Thus, short Sir2-associated pAgos provide defence against phages and plasmids, underscoring the diversity of mechanisms of prokaryotic Agos.
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16
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Sun S, Xu D, Zhu L, Hu B, Huang Z. A Programmable, DNA-Exclusively-Guided Argonaute DNase and Its Higher Cleavage Specificity Achieved by 5′-Hydroxylated Guide. Biomolecules 2022; 12:biom12101340. [PMID: 36291549 PMCID: PMC9599953 DOI: 10.3390/biom12101340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/17/2022] [Accepted: 09/18/2022] [Indexed: 12/03/2022] Open
Abstract
Argonaute proteins exist widely in eukaryotes and prokaryotes, and they are of great potential for molecular cloning, nucleic acid detection, DNA assembly, and gene editing. However, their overall properties are not satisfactory and hinder their broad applications. Herein, we investigated a prokaryotic Argonaute nuclease from a mesophilic bacterium Clostridium disporicum (CdAgo) and explored its overall properties, especially with 5′-hydroxylated (5′-OH) guides. We found that CdAgo can exclusively use single-stranded DNA (ssDNA) as guide to cleave ssDNA and plasmid targets. Further, we found the length of the efficient guide is narrower for the 5′-OH guide (17–20 nt) than for the 5′-phosphorylated guide (5′-P, 14–21 nt). Furthermore, we discovered that the 5′-OH guides can generally offer stronger mismatch discrimination than the 5′-P ones. The 5′-OH guides offer the narrower length range, higher mismatch discrimination and more accurate cleavage than the 5′-P guides. Therefore, 5′-OH-guide-directed CdAgo has great potential in biological and biomedical applications.
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Affiliation(s)
- Shichao Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Dejin Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Lin Zhu
- Study on the Structure-Specific Small Molecule Drug in Sichuan Province College Key Laboratory, Department of Pharmacy, Chengdu Medical College, Chengdu 610500, China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- Correspondence: (B.H.); (Z.H.)
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu 610041, China
- Correspondence: (B.H.); (Z.H.)
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17
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Lisitskaya L, Shin Y, Agapov A, Olina A, Kropocheva E, Ryazansky S, Aravin AA, Esyunina D, Murakami KS, Kulbachinskiy A. Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity. Nat Commun 2022; 13:4624. [PMID: 35941106 PMCID: PMC9360449 DOI: 10.1038/s41467-022-32079-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 12/26/2022] Open
Abstract
Argonaute proteins are programmable nucleases that have defense and regulatory functions in both eukaryotes and prokaryotes. All known prokaryotic Argonautes (pAgos) characterized so far act on DNA targets. Here, we describe a new class of pAgos that uniquely use DNA guides to process RNA targets. The biochemical and structural analysis of Pseudooceanicola lipolyticus pAgo (PliAgo) reveals an unusual organization of the guide binding pocket that does not rely on divalent cations and the canonical set of contacts for 5'-end interactions. Unconventional interactions of PliAgo with the 5'-phosphate of guide DNA define its new position within pAgo and shift the site of target RNA cleavage in comparison with known Argonautes. The specificity for RNA over DNA is defined by ribonucleotide residues at the cleavage site. The analysed pAgos sense mismatches and modifications in the RNA target. The results broaden our understanding of prokaryotic defense systems and extend the spectrum of programmable nucleases with potential use in RNA technology.
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Affiliation(s)
- Lidiya Lisitskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, Russia.
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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18
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Nakanishi K. Anatomy of four human Argonaute proteins. Nucleic Acids Res 2022; 50:6618-6638. [PMID: 35736234 PMCID: PMC9262622 DOI: 10.1093/nar/gkac519] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) bind to complementary target RNAs and regulate their gene expression post-transcriptionally. These non-coding regulatory RNAs become functional after loading into Argonaute (AGO) proteins to form the effector complexes. Humans have four AGO proteins, AGO1, AGO2, AGO3 and AGO4, which share a high sequence identity. Since most miRNAs are found across the four AGOs, it has been thought that they work redundantly, and AGO2 has been heavily studied as the exemplified human paralog. Nevertheless, an increasing number of studies have found that the other paralogs play unique roles in various biological processes and diseases. In the last decade, the structural study of the four AGOs has provided the field with solid structural bases. This review exploits the completed structural catalog to describe common features and differences in target specificity across the four AGOs.
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Affiliation(s)
- Kotaro Nakanishi
- To whom correspondence should be addressed. Tel: +1 614 688 2188;
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19
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Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems. Microorganisms 2022; 10:microorganisms10050914. [PMID: 35630358 PMCID: PMC9148166 DOI: 10.3390/microorganisms10050914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023] Open
Abstract
Xylella fastidiosa causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, X. fastidiosa has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various X. fastidiosa strains to successfully colonize the xylem tissue and cause disease in specific plant hosts, but the mechanisms by which this happens have not been fully elucidated. Here we present thorough comparative analyses of 94 whole-genome sequences of X. fastidiosa strains from diverse plant hosts and geographic regions. Core-genome phylogeny revealed clades with members sharing mostly a geographic region rather than a host plant of origin. Phylogenetic trees for 1605 orthologous CDSs were explored for potential candidates related to host specificity using a score of mapping metrics. However, no candidate host-specificity determinants were strongly supported using this approach. We also show that X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, including a diversity of prophage regions. Our findings provide a better understanding of the diversity of phylogenetically close genomes and expand the knowledge of X. fastidiosa mobile genetic elements and immunity systems.
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20
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Prokaryotic Argonaute Protein from Natronobacterium gregoryi Requires RNAs To Activate for DNA Interference In Vivo. mBio 2022; 13:e0365621. [PMID: 35343788 PMCID: PMC9040764 DOI: 10.1128/mbio.03656-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Argonaute proteins are present in all three domains of life, which are archaea, bacteria, and eukarya. Unlike the eukaryotic Argonaute proteins, which use small RNA guides to target mRNAs, some prokaryotic Argonaute proteins (pAgos) use a small DNA guide to interfere with DNA and/or RNA targets. However, the mechanisms of pAgo natural function remain unknown. Here, we investigate the mechanism by which pAgo from Natronobacterium gregoryi (NgAgo) targets plasmid and bacteriophage T7 DNA using a heterologous Escherichia coli-based model system. We show that NgAgo expressed from a plasmid linearizes its expression vector. Cotransformation assays demonstrate that NgAgo requires an RNA in trans that is transcribed from the bacteriophage T7 promoter to activate cleavage of a cotransformed plasmid, reminiscent of the trans-RNA function in CRISPR/Cas9. We propose a mechanism to explain how NgAgo eliminates invading foreign DNA and bacteriophage. By leveraging this discovery, we show that NgAgo can be programmed to target a plasmid or a chromosome locus.
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21
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Characterization of a Programmable Argonaute Nuclease from the Mesophilic Bacterium Rummeliibacillus suwonensis. Biomolecules 2022; 12:biom12030355. [PMID: 35327547 PMCID: PMC8945025 DOI: 10.3390/biom12030355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/08/2022] [Accepted: 02/18/2022] [Indexed: 12/26/2022] Open
Abstract
Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo from Kurthia massiliensis can utilize DNA and RNA guide of any sequence to effectively cleave DNA and RNA targets. Here we find that three active pAgos, which have about 50% sequence identity with KmAgo, possess typical DNA-guided DNA target cleavage ability. Among them, RsuAgo from Rummeliibacillus suwonensis is mainly explored for which can cleave both DNA and RNA targets. Interestingly, RsuAgo-mediated RNA target cleavage occurs only with short guide DNAs in a narrow length range (16–20 nt), and mismatches between the guide and target sequence greatly affect the efficiency of RNA target cleavage. RsuAgo-mediated target cleavage shows a preference for a guide strand with a 5′-terminal A residue. Furthermore, we have found that RsuAgo can cleave double-stranded DNA in a low-salt buffer at 37 °C. These properties of RsuAgo provide a new tool for DNA and RNA manipulation at moderate temperatures.
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22
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Kropocheva EV, Lisitskaya LA, Agapov AA, Musabirov AA, Kulbachinskiy AV, Esyunina DM. Prokaryotic Argonaute Proteins as a Tool for Biotechnology. Mol Biol 2022; 56:854-873. [PMID: 36060308 PMCID: PMC9427165 DOI: 10.1134/s0026893322060103] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/20/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
Abstract
Programmable nucleases are the most important tool for manipulating the genes and genomes of both prokaryotes and eukaryotes. Since the end of the 20th century, many approaches were developed for specific modification of the genome. The review briefly considers the advantages and disadvantages of the main genetic editors known to date. The main attention is paid to programmable nucleases from the family of prokaryotic Argonaute proteins. Argonaute proteins can recognize and cleave DNA sequences using small complementary guide molecules and play an important role in protecting prokaryotic cells from invading DNA. Argonaute proteins have already found applications in biotechnology for targeted cleavage and detection of nucleic acids and can potentially be used for genome editing.
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Affiliation(s)
- E. V. Kropocheva
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - L. A. Lisitskaya
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - A. A. Agapov
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - A. A. Musabirov
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - A. V. Kulbachinskiy
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - D. M. Esyunina
- Institute of Molecular Genetics, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
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23
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Egido JE, Costa AR, Aparicio-Maldonado C, Haas PJ, Brouns SJJ. Mechanisms and clinical importance of bacteriophage resistance. FEMS Microbiol Rev 2021; 46:6374866. [PMID: 34558600 PMCID: PMC8829019 DOI: 10.1093/femsre/fuab048] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022] Open
Abstract
We are in the midst of a golden age of uncovering defense systems against bacteriophages. Apart from the fundamental interest in these defense systems, and revolutionary applications that have been derived from them (e.g. CRISPR-Cas9 and restriction endonucleases), it is unknown how defense systems contribute to resistance formation against bacteriophages in clinical settings. Bacteriophages are now being reconsidered as therapeutic agents against bacterial infections due the emergence of multidrug resistance. However, bacteriophage resistance through defense systems and other means could hinder the development of successful phage-based therapies. Here, we review the current state of the field of bacteriophage defense, highlight the relevance of bacteriophage defense for potential clinical use of bacteriophages as therapeutic agents and suggest new directions of research.
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Affiliation(s)
- Julia E Egido
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands.,Fagenbank, Delft, Netherlands
| | - Cristian Aparicio-Maldonado
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands.,Fagenbank, Delft, Netherlands
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24
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Isaev AB, Musharova OS, Severinov KV. Microbial Arsenal of Antiviral Defenses. Part II. BIOCHEMISTRY (MOSCOW) 2021; 86:449-470. [PMID: 33941066 DOI: 10.1134/s0006297921040064] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). The constant threat of phage infection is a major force that shapes evolution of microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering had been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection. In the first part defense associated with cell surface, roles of small molecules, and innate immunity systems relying on DNA modification were discussed. The second part focuses on adaptive immunity systems, abortive infection mechanisms, defenses associated with mobile genetic elements, and novel systems discovered in recent years through metagenomic mining.
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Affiliation(s)
- Artem B Isaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia.
| | - Olga S Musharova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia. .,Institute of Molecular Genetics, Moscow, 119334, Russia
| | - Konstantin V Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143028, Russia. .,Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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25
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Kropocheva E, Kuzmenko A, Aravin AA, Esyunina D, Kulbachinskiy A. A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis. Nucleic Acids Res 2021; 49:4054-4065. [PMID: 33744962 PMCID: PMC8053121 DOI: 10.1093/nar/gkab182] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/02/2021] [Accepted: 03/06/2021] [Indexed: 01/20/2023] Open
Abstract
Argonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some prokaryotic argonautes (pAgos) were shown to recognize RNA targets in vitro, the majority of studied pAgos have strict specificity toward DNA, which limits their practical use in RNA-centric applications. Here, we describe a unique pAgo nuclease, KmAgo, from the mesophilic bacterium Kurthia massiliensis that can be programmed with either DNA or RNA guides and can precisely cleave both DNA and RNA targets. KmAgo binds 16–20 nt long 5′-phosphorylated guide molecules with no strict specificity for their sequence and is active in a wide range of temperatures. In bacterial cells, KmAgo is loaded with small DNAs with no obvious sequence preferences suggesting that it can uniformly target genomic sequences. Mismatches between the guide and target sequences greatly affect the efficiency and precision of target cleavage, depending on the mismatch position and the nature of the reacting nucleic acids. Target RNA cleavage by KmAgo depends on the formation of secondary structure indicating that KmAgo can be used for structural probing of RNA. These properties of KmAgo open the way for its use for highly specific nucleic acid detection and cleavage.
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Affiliation(s)
- Ekaterina Kropocheva
- Institute of Molecular Genetics, National Research Centre 'Kurchatov Institute', Moscow 123182, Russia
| | - Anton Kuzmenko
- Institute of Molecular Genetics, National Research Centre 'Kurchatov Institute', Moscow 123182, Russia.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Centre 'Kurchatov Institute', Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Centre 'Kurchatov Institute', Moscow 123182, Russia
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26
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Expression and Functional Analysis of the Argonaute Protein of Thermus thermophilus (TtAgo) in E. coli BL21(DE3). Biomolecules 2021; 11:biom11040524. [PMID: 33807395 PMCID: PMC8067300 DOI: 10.3390/biom11040524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/24/2022] Open
Abstract
The prokaryotic Argonaute proteins (pAgos) have been reported to cleave or interfere with DNA targets in a guide-dependent or independent manner. It is often difficult to characterize pAgos in vivo due to the extreme environments favored by their hosts. In the present study, we expressed functional Thermus thermophilus pAgo (TtAgo) in E. coli BL21 (DE3) cells at 37 °C. Initial attempts to express TtAgo in BL21(DE3) cells at 37 °C failed. This was not because of TtAgo mediated general toxicity to the host cells, but instead because of TtAgo-induced loss of its expression plasmid. We employed this discovery to establish a screening system for isolating loss-of-function mutants of TtAgo. The E. colifabI gene was used to help select for full-length TtAgo loss of function mutants, as overexpression of fabI renders the cell to be resistant to the triclosan. We isolated and characterized eight mutations in TtAgo that abrogated function. The ability of TtAgo to induce loss of its expression vector in vivo at 37 °C is an unreported function that is mechanistically different from its reported in vitro activity. These results shed light on the mechanisms by which TtAgo functions as a defense against foreign DNA invasion.
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27
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Liu M, Huang M, Wang M, Zhu D, Jia R, Chen S, Zhang L, Pan L, Cheng A. The Clustered Regularly Interspaced Short Palindromic Repeat System and Argonaute: An Emerging Bacterial Immunity System for Defense Against Natural Transformation? Front Microbiol 2020; 11:593301. [PMID: 33193265 PMCID: PMC7642515 DOI: 10.3389/fmicb.2020.593301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/23/2020] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) systems and prokaryotic Argonaute proteins (Agos) have been shown to defend bacterial and archaeal cells against invading nucleic acids. Indeed, they are important elements for inhibiting horizontal gene transfer between bacterial and archaeal cells. The CRISPR system employs an RNA-guide complex to target invading DNA or RNA, while Agos target DNA using single stranded DNA or RNA as guides. Thus, the CRISPR and Agos systems defend against exogenous nucleic acids by different mechanisms. It is not fully understood how antagonization of these systems occurs during natural transformation, wherein exogenous DNA enters a host cell as single stranded DNA and is then integrated into the host genome. In this review, we discuss the functions and mechanisms of the CRISPR system and Agos in cellular defense against natural transformation.
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Affiliation(s)
- Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mi Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Research Centre of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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28
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Kuzmenko A, Oguienko A, Esyunina D, Yudin D, Petrova M, Kudinova A, Maslova O, Ninova M, Ryazansky S, Leach D, Aravin AA, Kulbachinskiy A. DNA targeting and interference by a bacterial Argonaute nuclease. Nature 2020; 587:632-637. [PMID: 32731256 DOI: 10.1038/s41586-020-2605-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/24/2020] [Indexed: 12/21/2022]
Abstract
Members of the conserved Argonaute protein family use small RNA guides to locate their mRNA targets and regulate gene expression and suppress mobile genetic elements in eukaryotes1,2. Argonautes are also present in many bacterial and archaeal species3-5. Unlike eukaryotic proteins, several prokaryotic Argonaute proteins use small DNA guides to cleave DNA, a process known as DNA interference6-10. However, the natural functions and targets of DNA interference are poorly understood, and the mechanisms of DNA guide generation and target discrimination remain unknown. Here we analyse the activity of a bacterial Argonaute nuclease from Clostridium butyricum (CbAgo) in vivo. We show that CbAgo targets multicopy genetic elements and suppresses the propagation of plasmids and infection by phages. CbAgo induces DNA interference between homologous sequences and triggers DNA degradation at double-strand breaks in the target DNA. The loading of CbAgo with locus-specific small DNA guides depends on both its intrinsic endonuclease activity and the cellular double-strand break repair machinery. A similar interaction was reported for the acquisition of new spacers during CRISPR adaptation, and prokaryotic genomes that encode Ago nucleases are enriched in CRISPR-Cas systems. These results identify molecular mechanisms that generate guides for DNA interference and suggest that the recognition of foreign nucleic acids by prokaryotic defence systems involves common principles.
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Affiliation(s)
- Anton Kuzmenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Anastasiya Oguienko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Denis Yudin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Mayya Petrova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alina Kudinova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Olga Maslova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria Ninova
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - David Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alexei A Aravin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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29
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Makarova KS, Karamycheva S, Shah SA, Vestergaard G, Garrett RA, Koonin EV. Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array. FEMS Microbiol Lett 2020; 366:5472869. [PMID: 30993331 DOI: 10.1093/femsle/fnz079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022] Open
Abstract
Screening of genomic and metagenomic databases for new variants of CRISPR-Cas systems increasingly results in the discovery of derived variants that do not seem to possess the interference capacity and are implicated in functions distinct from adaptive immunity. We describe an extremely derived putative class 1 CRISPR-Cas system that is present in many Halobacteria and consists of distant homologs of the Cas5 and Cas7 protein along with an uncharacterized conserved protein and various nucleases. We hypothesize that, although this system lacks typical CRISPR effectors or a CRISPR array, it functions as a RNA-dependent defense mechanism that, unlike other derived CRISPR-Cas, utilizes alternative nucleases to cleave invader genomes.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Shiraz A Shah
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Danish Archaea Centre, Ole Maaloes Vej 5, Copenhagen , DK-2200 Denmark
| | - Gisle Vestergaard
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 1, 2800 Kgs. Lyngby, Denmark
| | - Roger A Garrett
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Danish Archaea Centre, Ole Maaloes Vej 5, Copenhagen , DK-2200 Denmark
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
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30
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Olina A, Kuzmenko A, Ninova M, Aravin AA, Kulbachinskiy A, Esyunina D. Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus. RNA Biol 2020; 17:677-688. [PMID: 32013676 PMCID: PMC7237159 DOI: 10.1080/15476286.2020.1724716] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/03/2020] [Accepted: 01/12/2020] [Indexed: 12/17/2022] Open
Abstract
Members of the conserved Argonaute (Ago) protein family provide defence against invading nucleic acids in eukaryotes in the process of RNA interference. Many prokaryotes also contain Ago proteins that are predicted to be active nucleases; however, their functional activities in host cells remain poorly understood. Here, we characterize the in vitro and in vivo properties of the SeAgo protein from the mesophilic cyanobacterium Synechococcus elongatus. We show that SeAgo is a DNA-guided nuclease preferentially acting on single-stranded DNA targets, with non-specific guide-independent activity observed for double-stranded substrates. The SeAgo gene is steadily expressed in S. elongatus; however, its deletion or overexpression does not change the kinetics of cell growth. When purified from its host cells or from heterologous E. coli, SeAgo is loaded with small guide DNAs whose formation depends on the endonuclease activity of the argonaute protein. SeAgo co-purifies with SSB proteins suggesting that they may also be involved in DNA processing. The SeAgo-associated small DNAs are derived from diverse genomic locations, with certain enrichment for the proposed sites of chromosomal replication initiation and termination, but show no preference for an endogenous plasmid. Therefore, promiscuous genome sampling by SeAgo does not have great effects on cell physiology and plasmid maintenance.
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Affiliation(s)
- Anna Olina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anton Kuzmenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria Ninova
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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31
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Wu J, Yang J, Cho WC, Zheng Y. Argonaute proteins: Structural features, functions and emerging roles. J Adv Res 2020; 24:317-324. [PMID: 32455006 PMCID: PMC7235612 DOI: 10.1016/j.jare.2020.04.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/23/2020] [Accepted: 04/26/2020] [Indexed: 02/07/2023] Open
Abstract
Argonaute proteins are highly conserved in almost all organisms. They not only involve in the biogenesis of small regulatory RNAs, but also regulate gene expression and defend against foreign pathogen invasion via small RNA-mediated gene silencing pathways. As a key player in these pathways, the abnormal expression and/or mis-modifications of Argonaute proteins lead to the disorder of small RNA biogenesis and functions, thus influencing multiply biological processes and disease development, especially cancer. In this review, we focus on the post-translational modifications and novel functions of Argonaute proteins in alternative splicing, host defense and genome editing.
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Key Words
- AKT3, AKT serine/threonine kinase 3
- Argonaute protein
- CCR4-NOT, carbon catabolite repressor 4-negative on TATA
- CRISPR-Cas9, clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (cas9)
- DGCR8, DiGeorge syndrome critical region gene 8
- EGFR, epidermal growth factor receptor
- GW182 protein, glycine/tryptophan repeats-containing protein with molecular weight of 182 kDa
- H3K9, histone H3 lysine 9
- Hsp70/90, heat shock proteins 70/90
- JEV, Japanese encephalitis virus
- KRAS, Kirsten rat sarcoma oncogene
- P4H, prolyl 4-hydroxylase
- PAM, protospacer adjacent motif
- PAZ, PIWI-argonaute-zwille
- PIWI, P-element-induced wimpy testis
- Post-translational modification
- RISCs, small RNA-induced silencing complexes
- Small RNA
- TRBP, the transactivating response (TAR) RNA-binding protein
- TRIM71/LIN41, tripartite motif-containing 71, known as Lin41
- WSSV, white spot syndrome virus
- miRNAs
- piRNAs
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Affiliation(s)
- Jin'en Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China
| | - Jing Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong Special Administrative Region
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
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32
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The arms race between bacteria and their phage foes. Nature 2020; 577:327-336. [PMID: 31942051 DOI: 10.1038/s41586-019-1894-8] [Citation(s) in RCA: 403] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/13/2019] [Indexed: 12/26/2022]
Abstract
Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.
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33
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Tai HC, Lim C. Gene Silencing Mechanisms Revealed by Dynamics of Guide, Target, and Duplex Binding to Argonaute. J Chem Theory Comput 2019; 16:688-699. [PMID: 31751512 DOI: 10.1021/acs.jctc.9b00546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Argonaute (Ago) protein plays a central role in silencing gene expression by binding a "guide" strand to the base-pair with a complementary mRNA and degrading the mRNA. The current understanding of how Ago-guide and Ago-guide-mRNA complexes assemble is based mainly on static crystal structures; the associated kinetic pathways remain unknown/unclear. By simulating the successive binding of guide/target strand to Thermus thermophilus Ago (TtAgo) and computing the respective free energy landscapes, we directly visualize how TtAgo silencing complexes form and function. We show that the guide binding rate depends on its initial loading position onto TtAgo. Subsequent target recognition beyond the scissile 10-11 nucleotides must overcome a substantial energy barrier for TtAgo's nucleotide-binding groove to expand widely. This work reveals novel roles for the core TtAgo domains and shows how the kinetic barriers that must be overcome for critical structural changes to occur lead to target repression/cleavage.
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Affiliation(s)
- Hui-Chung Tai
- Institute of Biomedical Sciences , Academia Sinica , Taipei 115 , Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences , Academia Sinica , Taipei 115 , Taiwan.,Department of Chemistry , National Tsing Hua University , Hsinchu 300 , Taiwan
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34
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Chen J, Kuhn LA. Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation. J Mol Graph Model 2019; 90:59-76. [PMID: 31026779 PMCID: PMC6657700 DOI: 10.1016/j.jmgm.2019.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 12/22/2022]
Abstract
Schlafen proteins are important in cell differentiation and defense against viruses, and yet this family of vertebrate proteins is just beginning to be understood at the molecular level. Here, the three-dimensional architecture and molecular interfaces of human schlafen12 (hSLFN12), which promotes intestinal stem cell differentiation, are analyzed by sequence conservation and structural modeling in light of the functions of its homologs and binding partners. Our analysis shows that the schlafen or divergent AAA ATPase domain described in the N-terminal region of schlafens in databases and the literature is a misannotation. This N-terminal region is conclusively an AlbA_2 DNA/RNA binding domain, forming the conserved core of schlafens and their sequence homologs from bacteria through mammals. Group III schlafens additionally contain a AAA NTPase domain in their C-terminal helicase region. In hSLFN12, we have uncovered a domain matching rho GTPases, which directly follows the AlbA_2 domain in all group II-III schlafens. Potential roles for the GTPase-like domain include antiviral activity and cytoskeletal interactions that contribute to nucleocytoplasmic shuttling and cell polarization during differentiation. Based on features conserved with rSlfn13, the AlbA_2 region in hSLFN12 is likely to bind RNA, possibly as a ribonuclease. We hypothesize that RNA binding by hSLFN12 contributes to an RNA-induced transcriptional silencing/E3 ligase complex, given the functions of hSLFN12's partners, SUV39H1, JMJD6, and PDLIM7. hSLFN12's partner hSerpinB12 may contribute to heterochromatin formation, based on its homology to MENT, or directly regulate transcription via its binding to RNA polymerase II. The analysis presented here provides clear architectural and transcriptional regulation hypotheses to guide experimental design for hSLFN12 and the thousands of schlafens that share its motifs.
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Affiliation(s)
- Jiaxing Chen
- Protein Structural Analysis and Design Lab, Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824-1319, USA
| | - Leslie A Kuhn
- Protein Structural Analysis and Design Lab, Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824-1319, USA.
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35
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Hegge JW, Swarts DC, Chandradoss SD, Cui T, Kneppers J, Jinek M, Joo C, van der Oost J. DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute. Nucleic Acids Res 2019; 47:5809-5821. [PMID: 31069393 PMCID: PMC6582352 DOI: 10.1093/nar/gkz306] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/05/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022] Open
Abstract
Prokaryotic Argonaute proteins (pAgos) constitute a diverse group of endonucleases of which some mediate host defense by utilizing small interfering DNA guides (siDNA) to cleave complementary invading DNA. This activity can be repurposed for programmable DNA cleavage. However, currently characterized DNA-cleaving pAgos require elevated temperatures (≥65°C) for their activity, making them less suitable for applications that require moderate temperatures, such as genome editing. Here, we report the functional and structural characterization of the siDNA-guided DNA-targeting pAgo from the mesophilic bacterium Clostridium butyricum (CbAgo). CbAgo displays a preference for siDNAs that have a deoxyadenosine at the 5'-end and thymidines at nucleotides 2-4. Furthermore, CbAgo mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at moderate temperatures (37°C). This study demonstrates that certain pAgos are capable of programmable DNA cleavage at moderate temperatures and thereby expands the scope of the potential pAgo-based applications.
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Affiliation(s)
- Jorrit W Hegge
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Daan C Swarts
- Laboratory of Biochemistry, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Stanley D Chandradoss
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Tao Ju Cui
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jeroen Kneppers
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
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36
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Pohlschroder M, Albers SV. Editorial: Editorial for thematic issue on Archaea. FEMS Microbiol Rev 2019; 42:719-720. [PMID: 30137299 DOI: 10.1093/femsre/fuy032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/25/2018] [Indexed: 11/13/2022] Open
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Bacteriophage-host arm race: an update on the mechanism of phage resistance in bacteria and revenge of the phage with the perspective for phage therapy. Appl Microbiol Biotechnol 2019; 103:2121-2131. [PMID: 30680434 DOI: 10.1007/s00253-019-09629-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/25/2018] [Accepted: 12/27/2018] [Indexed: 12/20/2022]
Abstract
Due to a constant attack by phage, bacteria in the environment have evolved diverse mechanisms to defend themselves. Several reviews on phage resistance mechanisms have been published elsewhere. Thanks to the advancement of molecular techniques, several new phage resistance mechanisms were recently identified. For the practical phage therapy, the emergence of phage-resistant bacteria could be an obstacle. However, unlike antibiotic, phages could evolve a mechanism to counter-adapt against phage-resistant bacteria. In this review, we summarized the most recent studies of the phage-bacteria arm race with the perspective of future applications of phages as antimicrobial agents.
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Abstract
The eukaryotic Ago proteins and the RNA interference pathways they are involved in are widely used as a powerful tool in research and as potential therapeutics. In contrast, the properties and functions of prokaryotic Ago (pAgo) proteins have remained poorly understood. Understanding the diversity and functions of pAgos holds a huge potential for discovery of new cellular pathways and novel tools for genome manipulations. Only few pAgos have been characterized by structural or biochemical approaches, while previous genomic studies discovered about 300 proteins in archaeal and eubacterial genomes. Since that time the number of bacterial strains with sequenced genomes has greatly expanded, and many previously sequenced genomes have been revised. We undertook comprehensive analysis of pAgo proteins in sequenced genomes and almost tripled the number of known genes of this family. Our research thus forms a foundation for further experimental characterization of pAgo functions that will be important for understanding of the basic biology of these proteins and their adoption as a potential tool for genome engineering in the future. Members of the ancient family of Argonaute (Ago) proteins are present in all domains of life. The common feature of Ago proteins is the ability to bind small nucleic acid guides and use them for sequence-specific recognition—and sometimes cleavage—of complementary targets. While eukaryotic Ago (eAgo) proteins are key players in RNA interference and related pathways, the properties and functions of these proteins in archaeal and bacterial species have just started to emerge. We undertook comprehensive exploration of prokaryotic Ago (pAgo) proteins in sequenced genomes and revealed their striking diversity in comparison with eAgos. Many pAgos contain divergent variants of the conserved domains involved in interactions with nucleic acids, while having extra domains that are absent in eAgos, suggesting that they might have unusual specificities in the nucleic acid recognition and cleavage. Many pAgos are associated with putative nucleases, helicases, and DNA binding proteins in the same gene or operon, suggesting that they are involved in target processing. The great variability of pAgos revealed by our analysis opens new ways for exploration of their functions in host cells and for their use as potential tools in genome editing.
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Lisitskaya L, Aravin AA, Kulbachinskiy A. DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins. Nat Commun 2018; 9:5165. [PMID: 30514832 PMCID: PMC6279821 DOI: 10.1038/s41467-018-07449-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/26/2018] [Indexed: 12/14/2022] Open
Abstract
Recognition and repression of RNA targets by Argonaute proteins guided by small RNAs is the essence of RNA interference in eukaryotes. Argonaute proteins with diverse structures are also found in many bacterial and archaeal genomes. Recent studies revealed that, similarly to their eukaryotic counterparts, prokaryotic Argonautes (pAgos) may function in cell defense against foreign genetic elements but, in contrast, preferably act on DNA targets. Many crucial details of the pAgo action, and the roles of a plethora of pAgos with non-conventional architecture remain unknown. Here, we review available structural and biochemical data on pAgos and discuss their possible functions in host defense and other genetic processes in prokaryotic cells. In this review, Aravin and colleagues examine bacterial and archaeal Argonaute proteins, discuss their diverse architectures and their possible roles in host defense, proposing additional functions for Argonaute proteins in prokaryotic cells.
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Affiliation(s)
- Lidiya Lisitskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Alexei A Aravin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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