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Sierra AA, Loureiro ME, Esperante S, Borkosky SS, Gallo GL, de Prat Gay G, Lopez N. Nuclease Activity of the Junín Virus Nucleoprotein C-Terminal Domain. Viruses 2023; 15:1818. [PMID: 37766225 PMCID: PMC10535676 DOI: 10.3390/v15091818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The mammarenavirus Junín (JUNV) is the causative agent of Argentine hemorrhagic fever, a severe disease of public health concern. The most abundant viral protein is the nucleoprotein (NP), a multifunctional, two-domain protein with the primary role as structural component of the viral nucleocapsids, used as template for viral polymerase RNA synthesis activities. Here, we report that the C-terminal domain (CTD) of the attenuated Candid#1 strain of the JUNV NP can be purified as a stable soluble form with a secondary structure in line with known NP structures from other mammarenaviruses. We show that the JUNV NP CTD interacts with the viral matrix protein Z in vitro, and that the full-length NP and Z interact with each other in cellulo, suggesting that the NP CTD is responsible for this interaction. This domain comprises an arrangement of four acidic residues and a histidine residue conserved in the active site of exoribonucleases belonging to the DEDDh family. We show that the JUNV NP CTD displays metal-ion-dependent nuclease activity against DNA and single- and double-stranded RNA, and that this activity is impaired by the mutation of a catalytic residue within the DEDDh motif. These results further support this activity, not previously observed in the JUNV NP, which could impact the mechanism of the cellular immune response modulation of this important pathogen.
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Affiliation(s)
- Alicia Armella Sierra
- Centro de Virología Humana y Animal (CEVHAN), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Abierta Interamericana, Buenos Aires C1287, Argentina; (A.A.S.); (M.E.L.); (G.L.G.)
| | - María Eugenia Loureiro
- Centro de Virología Humana y Animal (CEVHAN), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Abierta Interamericana, Buenos Aires C1287, Argentina; (A.A.S.); (M.E.L.); (G.L.G.)
| | - Sebastián Esperante
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires C1405, Argentina; (S.E.); (S.S.B.); (G.d.P.G.)
| | - Silvia Susana Borkosky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires C1405, Argentina; (S.E.); (S.S.B.); (G.d.P.G.)
| | - Giovanna L. Gallo
- Centro de Virología Humana y Animal (CEVHAN), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Abierta Interamericana, Buenos Aires C1287, Argentina; (A.A.S.); (M.E.L.); (G.L.G.)
| | - Gonzalo de Prat Gay
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET, Buenos Aires C1405, Argentina; (S.E.); (S.S.B.); (G.d.P.G.)
| | - Nora Lopez
- Centro de Virología Humana y Animal (CEVHAN), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad Abierta Interamericana, Buenos Aires C1287, Argentina; (A.A.S.); (M.E.L.); (G.L.G.)
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2
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Nguyen THV, Yekwa E, Selisko B, Canard B, Alvarez K, Ferron F. Inhibition of Arenaviridae nucleoprotein exonuclease by bisphosphonate. IUCRJ 2022; 9:468-479. [PMID: 35844481 PMCID: PMC9252148 DOI: 10.1107/s2052252522005061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Arenaviruses are emerging enveloped negative-sense RNA viruses that cause neurological and hemorrhagic diseases in humans. Currently, no FDA-approved vaccine or therapeutic agent is available except for ribavirin, which must be administered early during infection for optimum efficacy. A hallmark of arenavirus infection is rapid and efficient immune suppression mediated by the exonuclease domain encoded by the nucleoprotein. This exonuclease is therefore an attractive target for the design of novel antiviral drugs since exonuclease inhibitors might not only have a direct effect on the enzyme but could also boost viral clearance through stimulation of the innate immune system of the host cell. Here, in silico screening and an enzymatic assay were used to identify a novel, specific but weak inhibitor of the arenavirus exonuclease, with IC50 values of 65.9 and 68.6 µM for Mopeia virus and Lymphocytic choriomeningitis virus, respectively. This finding was further characterized using crystallographic and docking approaches. This study serves as a proof of concept and may have assigned a new therapeutic purpose for the bisphosphonate family, therefore paving the way for the development of inhibitors against Arenaviridae.
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Affiliation(s)
- Thi Hong Van Nguyen
- Aix-Marseille Université and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS – UMR-7257, 13288 Marseille, France
| | - Elsie Yekwa
- Aix-Marseille Université and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS – UMR-7257, 13288 Marseille, France
| | - Barbara Selisko
- Aix-Marseille Université and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS – UMR-7257, 13288 Marseille, France
| | - Bruno Canard
- Aix-Marseille Université and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS – UMR-7257, 13288 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Karine Alvarez
- Aix-Marseille Université and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS – UMR-7257, 13288 Marseille, France
| | - François Ferron
- Aix-Marseille Université and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS – UMR-7257, 13288 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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3
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Hemphill WO, Simpson SR, Liu M, Salsbury FR, Hollis T, Grayson JM, Perrino FW. TREX1 as a Novel Immunotherapeutic Target. Front Immunol 2021; 12:660184. [PMID: 33868310 PMCID: PMC8047136 DOI: 10.3389/fimmu.2021.660184] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in the TREX1 3' → 5' exonuclease are associated with a spectrum of autoimmune disease phenotypes in humans and mice. Failure to degrade DNA activates the cGAS-STING DNA-sensing pathway signaling a type-I interferon (IFN) response that ultimately drives immune system activation. TREX1 and the cGAS-STING DNA-sensing pathway have also been implicated in the tumor microenvironment, where TREX1 is proposed to degrade tumor-derived DNA that would otherwise activate cGAS-STING. If tumor-derived DNA were not degraded, the cGAS-STING pathway would be activated to promote IFN-dependent antitumor immunity. Thus, we hypothesize TREX1 exonuclease inhibition as a novel immunotherapeutic strategy. We present data demonstrating antitumor immunity in the TREX1 D18N mouse model and discuss theory surrounding the best strategy for TREX1 inhibition. Potential complications of TREX1 inhibition as a therapeutic strategy are also discussed.
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Affiliation(s)
- Wayne O. Hemphill
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Sean R. Simpson
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Mingyong Liu
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC, United States
| | - Thomas Hollis
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Jason M. Grayson
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Fred W. Perrino
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, United States
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4
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Cheng HL, Lin CT, Huang KW, Wang S, Lin YT, Toh SI, Hsiao YY. Structural insights into the duplex DNA processing of TREX2. Nucleic Acids Res 2019; 46:12166-12176. [PMID: 30357414 PMCID: PMC6294518 DOI: 10.1093/nar/gky970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023] Open
Abstract
The three prime repair exonuclease 2 (TREX2) is an essential 3′-to-5′ exonuclease that functions in cell proliferation, genome integrity and skin homeostasis maintenance. The abnormal expression level of TREX2 can result in broken chromosome, increased susceptibility to skin carcinogenesis and Psoriasis. However, the molecular mechanisms of how TREX2 binds and processes its natural substrates, dsDNA or chromosomal DNA, to maintain genome stability remain unclear. In this study, we present four new crystal structures: apo-TREX2, TREX2 in complex with two different dsDNA substrates, and TREX2 in complex with a processed dsDNA product. Analysis of the structures reveals that TREX2 stacks with the 5′-terminal of dsDNA by a Leu20-Pro21-Asn22 cluster for precisely trimming the 3′-overhang. In addition, TREX2 specifically interacts with the non-scissile strand of dsDNA by an α-helix-loop region. The unique interaction patterns of the TREX2–dsDNA complex highlight the requirement of long double-stranded region for TREX2 binding and provide evidence of the functional role of TREX2 in processing chromosomal DNA. Moreover, the non-processive property of TREX2 is elucidated by the structure of TREX2–product complex. Our work discloses the first structural basis of the molecular interactions between TREX2 and its substrates and unravels the mechanistic actions of TREX2.
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Affiliation(s)
- Hiu-Lo Cheng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan 30050, ROC
| | - Chun-Ting Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
| | - Kuan-Wei Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
| | - Shuying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan 70101, ROC.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan 70101, ROC
| | - Yeh-Tung Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
| | - Shu-Ing Toh
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC.,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
| | - Yu-Yuan Hsiao
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan 30050, ROC.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC.,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan 30068, ROC
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5
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Manils J, Casas E, Viña-Vilaseca A, López-Cano M, Díez-Villanueva A, Gómez D, Marruecos L, Ferran M, Benito C, Perrino FW, Vavouri T, de Anta JM, Ciruela F, Soler C. The Exonuclease Trex2 Shapes Psoriatic Phenotype. J Invest Dermatol 2016; 136:2345-2355. [DOI: 10.1016/j.jid.2016.05.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/10/2016] [Accepted: 05/31/2016] [Indexed: 02/07/2023]
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6
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Multifaceted role of TREX2 in the skin defense against UV-induced skin carcinogenesis. Oncotarget 2016; 6:22375-96. [PMID: 26090614 PMCID: PMC4673170 DOI: 10.18632/oncotarget.4296] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/02/2015] [Indexed: 01/05/2023] Open
Abstract
TREX2 is a 3′-DNA exonuclease specifically expressed in keratinocytes. Here, we investigated the relevance and mechanisms of TREX2 in ultraviolet (UV)-induced skin carcinogenesis. TREX2 expression was up-regulated by chronic UV exposure whereas it was de-regulated or lost in human squamous cell carcinomas (SCCs). Moreover, we identified SNPs in the TREX2 gene that were more frequent in patients with head and neck SCCs than in healthy individuals. In mice, TREX2 deficiency led to enhanced susceptibility to UVB-induced skin carcinogenesis which was preceded by aberrant DNA damage removal and degradation as well as reduced inflammation. Specifically, TREX2 loss diminished the up-regulation of IL12 and IFNγ, key cytokines related to DNA repair and antitumor immunity. In UV-treated keratinocytes, TREX2 promoted DNA repair and passage to late apoptotic stages. Notably, TREX2 was recruited to low-density nuclear chromatin and micronuclei, where it interacted with phosphorylated H2AX histone, which is a critical player in both DNA repair and cell death. Altogether, our data provide new insights in the molecular mechanisms of TREX2 activity and establish cell autonomous and non-cell autonomous functions of TREX2 in the UVB-induced skin response.
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Hsiao YY, Fang WH, Lee CC, Chen YP, Yuan HS. Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways. PLoS Biol 2014; 12:e1001803. [PMID: 24594808 PMCID: PMC3942315 DOI: 10.1371/journal.pbio.1001803] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
DNA repair mechanisms are essential for preservation of genome integrity. However, it is not clear how DNA are selected and processed at broken ends by exonucleases during repair pathways. Here we show that the DnaQ-like exonuclease RNase T is critical for Escherichia coli resistance to various DNA-damaging agents and UV radiation. RNase T specifically trims the 3' end of structured DNA, including bulge, bubble, and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3' end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3' overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V-dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DnaQ-like exonucleases in DNA 3'-end processing.
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Affiliation(s)
- Yu-Yuan Hsiao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Woei-Horng Fang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Chia-Chia Lee
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Yi-Ping Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Hanna S. Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan, Republic of China
- * E-mail:
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8
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Dickey TH, Altschuler SE, Wuttke DS. Single-stranded DNA-binding proteins: multiple domains for multiple functions. Structure 2014; 21:1074-84. [PMID: 23823326 DOI: 10.1016/j.str.2013.05.013] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/15/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
The recognition of single-stranded DNA (ssDNA) is integral to myriad cellular functions. In eukaryotes, ssDNA is present stably at the ends of chromosomes and at some promoter elements. Furthermore, it is formed transiently by several cellular processes including telomere synthesis, transcription, and DNA replication, recombination, and repair. To coordinate these diverse activities, a variety of proteins have evolved to bind ssDNA in a manner specific to their function. Here, we review the recognition of ssDNA through the analysis of high-resolution structures of proteins in complex with ssDNA. This functionally diverse set of proteins arises from a limited set of structural motifs that can be modified and arranged to achieve distinct activities, including a range of ligand specificities. We also investigate the ways in which these domains interact in the context of large multidomain proteins/complexes. These comparisons reveal the structural features that define the range of functions exhibited by these proteins.
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Affiliation(s)
- Thayne H Dickey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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Jiang X, Huang Q, Wang W, Dong H, Ly H, Liang Y, Dong C. Structures of arenaviral nucleoproteins with triphosphate dsRNA reveal a unique mechanism of immune suppression. J Biol Chem 2013; 288:16949-16959. [PMID: 23615902 PMCID: PMC3675627 DOI: 10.1074/jbc.m112.420521] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A hallmark of severe Lassa fever is the generalized immune suppression, the mechanism of which is poorly understood. Lassa virus (LASV) nucleoprotein (NP) is the only known 3′-5′ exoribonuclease that can suppress type I interferon (IFN) production possibly by degrading immune-stimulatory RNAs. How this unique enzymatic activity of LASV NP recognizes and processes RNA substrates is unknown. We provide an atomic view of a catalytically active exoribonuclease domain of LASV NP (LASV NP-C) in the process of degrading a 5′ triphosphate double-stranded (ds) RNA substrate, a typical pathogen-associated molecular pattern molecule, to induce type I IFN production. Additionally, we provide for the first time a high-resolution crystal structure of an active exoribonuclease domain of Tacaribe arenavirus (TCRV) NP. Coupled with the in vitro enzymatic and cell-based interferon suppression assays, these structural analyses strongly support a unified model of an exoribonuclease-dependent IFN suppression mechanism shared by all known arenaviruses. New knowledge learned from these studies should aid the development of therapeutics against pathogenic arenaviruses that can infect hundreds of thousands of individuals and kill thousands annually.
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Affiliation(s)
- Xue Jiang
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Qinfeng Huang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota 55108
| | - Wenjian Wang
- Laboratory of Department of Surgery, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Haohao Dong
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom; Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, United Kingdom
| | - Hinh Ly
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota 55108.
| | - Yuying Liang
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota 55108.
| | - Changjiang Dong
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom.
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Yu M, Yu Q, Rutledge PJ, Todd MH. A fluorescent "allosteric scorpionand" complex visualizes a biological recognition event. Chembiochem 2013; 14:224-9. [PMID: 23303717 DOI: 10.1002/cbic.201200637] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Indexed: 12/31/2022]
Abstract
We describe a new class of fluorescent reporter and its employment to visualize the biotin/avidin binding interaction. Derivatives of the azamacrocycle cyclam that contain a pendant naphthalimide dye are inherently fluorescent when zinc(II) is coordinated. Introducing a second pendant group--biotin--affords an unsymmetrical bis-triazole-scorpionand ligand that interacts specifically with avidin. This ligand has been assembled by using a one-pot "double-click" strategy and complexed with copper(II) and zinc(II). The zinc(II) complex is fluorescent, and its fluorescence output changes in the presence of avidin. Upon avidin binding, the fluorescence output is diminished by interaction with the protein, at [complex]/[avidin] ratios of up to 4:1. The observed change might arise from a specific quenching effect in the biotin binding pocket or from a binding-induced change in the coordination geometry of the complex.
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Affiliation(s)
- Mingfeng Yu
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
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11
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Hastie KM, King LB, Zandonatti MA, Saphire EO. Structural basis for the dsRNA specificity of the Lassa virus NP exonuclease. PLoS One 2012; 7:e44211. [PMID: 22937163 PMCID: PMC3429428 DOI: 10.1371/journal.pone.0044211] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 07/30/2012] [Indexed: 01/13/2023] Open
Abstract
Lassa virus causes hemorrhagic fever characterized by immunosuppression. The nucleoprotein of Lassa virus, termed NP, binds the viral genome. It also has an additional enzymatic activity as an exonuclease that specifically digests double-stranded RNA (dsRNA). dsRNA is a strong signal to the innate immune system of viral infection. Digestion of dsRNA by the NP exonuclease activity appears to cause suppression of innate immune signaling in the infected cell. Although the fold of the NP enzyme is conserved and the active site completely conserved with other exonucleases in its DEDDh family, NP is atypical among exonucleases in its preference for dsRNA and its strict specificity for one substrate. Here, we present the crystal structure of Lassa virus NP in complex with dsRNA. We find that unlike the exonuclease in Klenow fragment, the double-stranded nucleic acid in complex with Lassa NP remains base-paired instead of splitting, and that binding of the paired complementary strand is achieved by “relocation” of a basic loop motif from its typical exonuclease position. Further, we find that just one single glycine that contacts the substrate strand and one single tyrosine that stacks with a base of the complementary, non-substrate strand are responsible for the unique substrate specificity. This work thus provides templates for development of antiviral drugs that would be specific for viral, rather than host exonucleases of similar fold and active site, and illustrates how a very few amino acid changes confer alternate specificity and biological phenotype to an enzyme.
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Affiliation(s)
- Kathryn M. Hastie
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Liam B. King
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Michelle A. Zandonatti
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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Shimada A, Masui R, Nakagawa N, Takahata Y, Kim K, Kuramitsu S, Fukui K. A novel single-stranded DNA-specific 3'-5' exonuclease, Thermus thermophilus exonuclease I, is involved in several DNA repair pathways. Nucleic Acids Res 2010; 38:5692-705. [PMID: 20457749 PMCID: PMC2943613 DOI: 10.1093/nar/gkq350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Single-stranded DNA (ssDNA)-specific exonucleases (ssExos) are expected to be involved in a variety of DNA repair pathways corresponding to their cleavage polarities; however, the relationship between the cleavage polarity and the respective DNA repair pathways is only partially understood. To understand the cellular function of ssExos in DNA repair better, genes encoding ssExos were disrupted in Thermus thermophilus HB8 that seems to have only a single set of 5'-3' and 3'-5' ssExos unlike other model organisms. Disruption of the tthb178 gene, which was expected to encode a 3'-5' ssExo, resulted in significant increase in the sensitivity to H(2)O(2) and frequency of the spontaneous mutation rate, but scarcely affected the sensitivity to ultraviolet (UV) irradiation. In contrast, disruption of the recJ gene, which encodes a 5'-3' ssExo, showed little effect on the sensitivity to H(2)O(2), but caused increased sensitivity to UV irradiation. In vitro characterization revealed that TTHB178 possessed 3'-5' ssExo activity that degraded ssDNAs containing deaminated and methylated bases, but not those containing oxidized bases or abasic sites. Consequently, we concluded that TTHB178 is a novel 3'-5' ssExo that functions in various DNA repair systems in cooperation with or independently of RecJ. We named TTHB178 as T. thermophilus exonuclease I.
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Affiliation(s)
- Atsuhiro Shimada
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043 and RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
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13
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