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Kuzikov M, Reinshagen J, Wycisk K, Corona A, Esposito F, Malune P, Manelfi C, Iaconis D, Beccari A, Tramontano E, Nowotny M, Windshügel B, Gribbon P, Zaliani A. Drug repurposing screen to identify inhibitors of the RNA polymerase (nsp12) and helicase (nsp13) from SARS-CoV-2 replication and transcription complex. Virus Res 2024; 343:199356. [PMID: 38490582 PMCID: PMC10958470 DOI: 10.1016/j.virusres.2024.199356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Coronaviruses contain one of the largest genomes among the RNA viruses, coding for 14-16 non-structural proteins (nsp) that are involved in proteolytic processing, genome replication and transcription, and four structural proteins that build the core of the mature virion. Due to conservation across coronaviruses, nsps form a group of promising drug targets as their inhibition directly affects viral replication and, therefore, progression of infection. A minimal but fully functional replication and transcription complex was shown to be formed by one RNA-dependent RNA polymerase (nsp12), one nsp7, two nsp8 accessory subunits, and two helicase (nsp13) enzymes. Our approach involved, targeting nsp12 and nsp13 to allow multiple starting point to interfere with virus infection progression. Here we report a combined in-vitro repurposing screening approach, identifying new and confirming reported SARS-CoV-2 nsp12 and nsp13 inhibitors.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany.
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Krzysztof Wycisk
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Paolo Malune
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Daniela Iaconis
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Andrea Beccari
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Marcin Nowotny
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
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2
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He YN, Han XR, Wang D, Hou JL, Hou XM. Dual mode of DDX3X as an ATP-dependent RNA helicase and ATP-independent nucleic acid chaperone. Biochem Biophys Res Commun 2024; 714:149964. [PMID: 38669753 DOI: 10.1016/j.bbrc.2024.149964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
Human DDX3X, an important member of the DEAD-box family RNA helicases, plays a crucial role in RNA metabolism and is involved in cancer development, viral infection, and neurodegenerative disease. Although there have been many studies on the physiological functions of human DDX3X, issues regarding its exact targets and mechanisms of action remain unclear. In this study, we systematically characterized the biochemical activities and substrate specificity of DDX3X. The results demonstrate that DDX3X is a bidirectional RNA helicase to unwind RNA duplex and RNA-DNA hybrid driven by ATP. DDX3X also has nucleic acid annealing activity, especially for DNA. More importantly, it can function as a typical nucleic acid chaperone which destabilizes highly structured DNA and RNA in an ATP-independent manner and promotes their annealing to form a more stable structure. Further truncation mutations confirmed that the highly disordered N-tail and C-tail are critical for the biochemical activities of DDX3X. They are functionally complementary, with the N-tail being crucial. These results will shed new light on our understanding of the molecular mechanism of DDX3X in RNA metabolism and DNA repair, and have potential significance for the development of antiviral/anticancer drugs targeting DDX3X.
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Affiliation(s)
- Yi-Ning He
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiao-Rui Han
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dong Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jia-Li Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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3
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Inniss NL, Rzhetskaya M, Ling-Hu T, Lorenzo-Redondo R, Bachta KE, Satchell KJF, Hultquist JF. Activity and inhibition of the SARS-CoV-2 Omicron nsp13 R392C variant using RNA duplex unwinding assays. SLAS Discov 2024; 29:100145. [PMID: 38301954 DOI: 10.1016/j.slasd.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
SARS-CoV-2 nsp13 helicase is an essential enzyme for viral replication and a promising target for antiviral drug development. This study compares the double-stranded RNA (dsRNA) unwinding activity of nsp13 and the Omicron nsp13R392C variant, which is predominant in currently circulating lineages. Using in vitro gel- and fluorescence-based assays, we found that both nsp13 and nsp13R392C have dsRNA unwinding activity with equivalent kinetics. Furthermore, the R392C mutation had no effect on the efficiency of the nsp13-specific helicase inhibitor SSYA10-001. We additionally confirmed the activity of several other helicase inhibitors against nsp13, including punicalagin that inhibited dsRNA unwinding at nanomolar concentrations. Overall, this study reveals the utility of using dsRNA unwinding assays to screen small molecules for antiviral activity against nsp13 and the Omicron nsp13R392C variant. Continual monitoring of newly emergent variants will be essential for considering resistance profiles of lead compounds as they are advanced towards next-generation therapeutic development.
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Affiliation(s)
- Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Margarita Rzhetskaya
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ted Ling-Hu
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Kelly E Bachta
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA.
| | - Judd F Hultquist
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA.
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Vadla GP, Singh K, Lorson CL, Lorson MA. The contribution and therapeutic implications of IGHMBP2 mutations on IGHMBP2 biochemical activity and ABT1 association. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167091. [PMID: 38403020 PMCID: PMC10999323 DOI: 10.1016/j.bbadis.2024.167091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/27/2024]
Abstract
Mutations within immunoglobulin mu DNA binding protein (IGHMBP2), an RNA-DNA helicase, result in SMA with respiratory distress type I (SMARD1) and Charcot Marie Tooth type 2S (CMT2S). The underlying biochemical mechanism of IGHMBP2 is unknown as well as the functional significance of IGHMBP2 mutations in disease severity. Here we report the biochemical mechanisms of IGHMBP2 disease-causing mutations D565N and H924Y, and their potential impact on therapeutic strategies. The IGHMBP2-D565N mutation has been identified in SMARD1 patients, while the IGHMBP2-H924Y mutation has been identified in CMT2S patients. For the first time, we demonstrate a correlation between the altered IGHMBP2 biochemical activity associated with the D565N and H924Y mutations and disease severity and pathology in patients and our Ighmbp2 mouse models. We show that IGHMBP2 mutations that alter the association with activator of basal transcription (ABT1) impact the ATPase and helicase activities of IGHMBP2 and the association with the 47S pre-rRNA 5' external transcribed spacer. We demonstrate that the D565N mutation impairs IGHMBP2 ATPase and helicase activities consistent with disease pathology. The H924Y mutation alters IGHMBP2 activity to a lesser extent while maintaining association with ABT1. In the context of the compound heterozygous patient, we demonstrate that the total biochemical activity associated with IGHMBP2-D565N and IGHMBP2-H924Y proteins is improved over IGHMBP2-D565N alone. Importantly, we demonstrate that the efficacy of therapeutic applications may vary based on the underlying IGHMBP2 mutations and the relative biochemical activity of the mutant IGHMBP2 protein.
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Affiliation(s)
- Gangadhar P Vadla
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Kamal Singh
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Christian L Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Monique A Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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5
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Messmer M, Pierson L, Pasquier C, Djordjevic N, Chicher J, Hammann P, Pfeffer S, Girardi E. DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection. Virol J 2024; 21:76. [PMID: 38553727 PMCID: PMC10981342 DOI: 10.1186/s12985-024-02349-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/20/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND RNA helicases are emerging as key factors regulating host-virus interactions. The DEAD-box ATP-dependent RNA helicase DDX5, which plays an important role in many aspects of cellular RNA biology, was also found to either promote or inhibit viral replication upon infection with several RNA viruses. Here, our aim is to examine the impact of DDX5 on Sindbis virus (SINV) infection. METHODS We analysed the interaction between DDX5 and the viral RNA using imaging and RNA-immunoprecipitation approaches. The interactome of DDX5 in mock- and SINV-infected cells was determined by mass spectrometry. We validated the interaction between DDX17 and the viral capsid by co- immunoprecipitation in the presence or absence of an RNase treatment. We determined the subcellular localization of DDX5, its cofactor DDX17 and the viral capsid protein by co-immunofluorescence. Finally, we investigated the impact of DDX5 depletion and overexpression on SINV infection at the viral protein, RNA and infectious particle accumulation level. The contribution of DDX17 was also tested by knockdown experiments. RESULTS In this study we demonstrate that DDX5 interacts with the SINV RNA during infection. Furthermore, the proteomic analysis of the DDX5 interactome in mock and SINV-infected HCT116 cells identified new cellular and viral partners and confirmed the interaction between DDX5 and DDX17. Both DDX5 and DDX17 re-localize from the nucleus to the cytoplasm upon SINV infection and interact with the viral capsid protein. We also show that DDX5 depletion negatively impacts the viral replication cycle, while its overexpression has a pro-viral effect. Finally, we observed that DDX17 depletion reduces SINV infection, an effect which is even more pronounced in a DDX5-depleted background, suggesting a synergistic pro-viral effect of the DDX5 and DDX17 proteins on SINV. CONCLUSIONS These results not only shed light on DDX5 as a novel and important host factor to the SINV life cycle, but also expand our understanding of the roles played by DDX5 and DDX17 as regulators of viral infections.
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Affiliation(s)
- Mélanie Messmer
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, Strasbourg, 67084, France
| | - Louison Pierson
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, Strasbourg, 67084, France
| | - Charline Pasquier
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, Strasbourg, 67084, France
| | - Nikola Djordjevic
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, Strasbourg, 67084, France
| | - Johana Chicher
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg - Esplanade, Université de Strasbourg, 2 allée Konrad Roentgen, Strasbourg, 67084, France
| | - Philippe Hammann
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg - Esplanade, Université de Strasbourg, 2 allée Konrad Roentgen, Strasbourg, 67084, France
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, Strasbourg, 67084, France
| | - Erika Girardi
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, Strasbourg, 67084, France.
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6
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Di Paco G, Macchiagodena M, Procacci P. Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations. ChemMedChem 2024:e202400095. [PMID: 38456332 DOI: 10.1002/cmdc.202400095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
We have assembled a computational pipeline based on virtual screening, docking techniques, and nonequilibrium molecular dynamics simulations, with the goal of identifying possible inhibitors of the SARS-CoV-2 NSP13 helicase, catalyzing by ATP hydrolysis the unwinding of double or single-stranded RNA in the viral replication process inside the host cell. The druggable sites for broad-spectrum inhibitors are represented by the RNA binding sites at the 5' entrance and 3' exit of the central channel, a structural motif that is highly conserved across coronaviruses. Potential binders were first generated using structure-based ligand techniques. Their potency was estimated by using four popular docking scoring functions. Common docking hits for NSP13 were finally tested using advanced nonequilibrium alchemical techniques for binding free energy calculations on a high-performing parallel cluster. Four potential NSP13 inhibitors with potency from submicrimolar to nanomolar were finally identified.
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Affiliation(s)
- Giorgio Di Paco
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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7
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Winstone L, Jung Y, Wu Y. DDX41: exploring the roles of a versatile helicase. Biochem Soc Trans 2024; 52:395-405. [PMID: 38348889 PMCID: PMC10903454 DOI: 10.1042/bst20230725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 02/29/2024]
Abstract
DDX41 is a DEAD-box helicase and is conserved across species. Mutations in DDX41 have been associated with myeloid neoplasms, including myelodysplastic syndrome and acute myeloid leukemia. Though its pathogenesis is not completely known, DDX41 has been shown to have many cellular roles, including in pre-mRNA splicing, innate immune sensing, ribosome biogenesis, translational regulation, and R-loop metabolism. In this review, we will summarize the latest understandings regarding the various roles of DDX41, as well as highlight challenges associated with drug development to target DDX41. Overall, understanding the molecular and cellular mechanisms of DDX41 could help develop novel therapeutic options for DDX41 mutation-related hematologic malignancies.
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Affiliation(s)
- Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yohan Jung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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8
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Kulikowicz T, Sommers JA, Fuchs KF, Wu Y, Brosh RM. Purification and biochemical characterization of the G4 resolvase and DNA helicase FANCJ. Methods Enzymol 2024; 695:1-27. [PMID: 38521581 DOI: 10.1016/bs.mie.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
G-quadruplex (G4) DNA or RNA poses a unique nucleic acid structure in genomic transactions. Because of the unique topology presented by G4, cells have exquisite mechanisms and pathways to metabolize G4 that arise in guanine-rich regions of the genome such as telomeres, promoter regions, ribosomal DNA, and other chromosomal elements. G4 resolvases are often represented by a class of molecular motors known as helicases that disrupt the Hoogsteen hydrogen bonds in G4 by harnessing the chemical energy of nucleoside triphosphate hydrolysis. Of special interest to researchers in the field, including us, is the human FANCJ DNA helicase that efficiently resolves G4 DNA structures. Notably, FANCJ mutations are linked to Fanconi Anemia and are prominent in breast and ovarian cancer. Since our discovery that FANCJ efficiently resolves G4 DNA structures 15 years ago, we and other labs have characterized mechanistic aspects of FANCJ-catalyzed G4 resolution and its biological importance in genomic integrity and cellular DNA replication. In addition to its G4 resolvase function, FANCJ is also a classic DNA helicase that acts on conventional duplex DNA structures, which are relevant to the enzyme's role in interstrand cross link repair, double-strand break repair via homologous recombination, and response to replication stress. Here, we describe detailed procedures for the purification of recombinant FANCJ protein and characterization of its G4 resolvase and duplex DNA helicase activity.
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Affiliation(s)
- Tomasz Kulikowicz
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Joshua A Sommers
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, United States.
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9
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Akbari B, Ahmadi E, Zabihi MR, Zamir MR, Shaker MS, Noorbakhsh F. SARS-CoV-2 helicase might interfere with cellular nonsense-mediated RNA decay: insights from a bioinformatics study. BMC Genom Data 2023; 24:68. [PMID: 37980504 PMCID: PMC10657555 DOI: 10.1186/s12863-023-01173-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND Viruses employ diverse strategies to interfere with host defense mechanisms, including the production of proteins that mimic or resemble host proteins. This study aimed to analyze the similarities between SARS-CoV-2 and human proteins, investigate their impact on virus-host interactions, and elucidate underlying mechanisms. RESULTS Comparing the proteins of SARS-CoV-2 with human and mammalian proteins revealed sequence and structural similarities between viral helicase with human UPF1. The latter is a protein that is involved in nonsense-mediated RNA decay (NMD), an mRNA surveillance pathway which also acts as a cellular defense mechanism against viruses. Protein sequence similarities were also observed between viral nsp3 and human Poly ADP-ribose polymerase (PARP) family of proteins. Gene set enrichment analysis on transcriptomic data derived from SARS-CoV-2 positive samples illustrated the enrichment of genes belonging to the NMD pathway compared with control samples. Moreover, comparing transcriptomic data from SARS-CoV-2-infected samples with transcriptomic data derived from UPF1 knockdown cells demonstrated a significant overlap between datasets. CONCLUSIONS These findings suggest that helicase/UPF1 sequence and structural similarity might have the ability to interfere with the NMD pathway with pathogenic and immunological implications.
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Affiliation(s)
- Behnia Akbari
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Ahmadi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zabihi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Roshan Zamir
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Sadeghi Shaker
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran.
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10
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Appel CD, Bermek O, Dandey VP, Wood M, Viverette E, Williams JG, Bouvette J, Riccio AA, Krahn JM, Borgnia MJ, Williams RS. Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2. Mol Cell 2023; 83:3692-3706.e5. [PMID: 37832548 PMCID: PMC10629462 DOI: 10.1016/j.molcel.2023.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/25/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for Sen1 activities is ill defined. Here, Sen1 cryoelectron microscopy (cryo-EM) reconstructions reveal an elongated inchworm-like architecture. Sen1 is composed of an amino terminal helical repeat Sen1 N-terminal (Sen1N) regulatory domain that is flexibly linked to its C-terminal SF1B helicase motor core (Sen1Hel) via an intrinsically disordered tether. In an autoinhibited state, the Sen1Sen1N domain regulates substrate engagement by promoting occlusion of the RNA substrate-binding cleft. The X-ray structure of an activated Sen1Hel engaging single-stranded RNA and ADP-SO4 shows that the enzyme encircles RNA and implicates a single-nucleotide power stroke in the Sen1 RNA translocation mechanism. Together, our data unveil dynamic protein-protein and protein-RNA interfaces underpinning helicase regulation and inactivation of human SETX activity by RNA-binding-deficient mutants in ataxia with oculomotor apraxia 2 neurodegenerative disease.
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Affiliation(s)
- C Denise Appel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Oya Bermek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Venkata P Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Makayla Wood
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Elizabeth Viverette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jonathan Bouvette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
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11
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Saifi SK, Passricha N, Tuteja R, Nath M, Gill R, Gill SS, Tuteja N. OsRuvBL1a DNA helicase boost salinity and drought tolerance in transgenic indica rice raised by in planta transformation. Plant Sci 2023; 335:111786. [PMID: 37419328 DOI: 10.1016/j.plantsci.2023.111786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
RuvBL, is a member of SF6 superfamily of helicases and is conserved among the various model systems. Recently, rice (Oryza sativa L.) homolog of RuvBL has been biochemically characterized for its ATPase and DNA helicase activities; however its involvement in stress has not been studied so far. Present investigation reports the detailed functional characterization of OsRuvBL under abiotic stresses through genetic engineering. An efficient Agrobacterium-mediated in planta transformation protocol was developed in indica rice to generate the transgenic lines and study was focused on optimization of factors to achieve maximum transformation efficiency. Overexpressing OsRuvBL1a transgenic lines showed enhanced tolerance under in vivo salinity stress as compared to WT plants. The physiological and biochemical analysis of the OsRuvBL1a transgenic lines showed better performance under salinity and drought stresses. Several stress responsive interacting partners of OsRuvBL1a were identified using Y2H system revealed to its role in stress tolerance. Functional mechanism for boosting stress tolerance by OsRuvBL1a has been proposed in this study. This integration of OsRuvBL1a gene in rice genome using in planta transformation method helped to achieve the abiotic stress resilient smart crop. This study is the first direct evidence to show the novel function of RuvBL in boosting abiotic stress tolerance in plants.
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Affiliation(s)
- Shabnam K Saifi
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nishat Passricha
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Renu Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Nath
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; ICAR-Directorate of Mushroom Research, Chambaghat, Solan, Himachal Pradesh 173213, India
| | - Ritu Gill
- Stress Physiology and Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak 124 001, Haryana, India
| | - Sarvajeet Singh Gill
- Stress Physiology and Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak 124 001, Haryana, India.
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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12
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Perumal SK. A real-time fluorescent gp32 probe-based assay for monitoring single-stranded DNA-dependent DNA processing enzymes. Biochem Biophys Rep 2023; 35:101518. [PMID: 37534323 PMCID: PMC10391720 DOI: 10.1016/j.bbrep.2023.101518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
Single-stranded DNA (ssDNA) generated during DNA replication, recombination and damage repair reactions is an important intermediate and ssDNA-binding proteins that binds these intermediates coordinate various DNA metabolic processes. Mechanistic details of these ssDNA-dependent processes can be explored by monitoring the generation and consumption of ssDNA in real time. In this work, a fluorescein-labeled gp32-based sensor was employed to continuously monitor various aspects of ssDNA-dependent DNA replication and recombination processes in real time. The gp32 protein probe displayed high sensitivity and specificity to a variety of ssDNA-dependent processes of T4 phage. Several applications of the probe are illustrated here: the solution dynamics of ssDNA-binding protein, protein-protein and protein-DNA interactions involving gp32 protein and its mode of interaction, ssDNA translocation and protein displacement activities of helicases, primer extension activity of DNA polymerase holoenzyme and nucleoprotein filament formation during DNA recombination. The assay has identified new protein-protein interactions of gp32 during T4 replication and recombination. The fluorescent probe described here can thus be used as a universal probe for monitoring in real time various ssDNA-dependent processes, which is based on a well-characterized and easy-to-express bacteriophage T4 gene 32 protein, gp32.
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13
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Corona A, Madia VN, De Santis R, Manelfi C, Emmolo R, Ialongo D, Patacchini E, Messore A, Amatore D, Faggioni G, Artico M, Iaconis D, Talarico C, Di Santo R, Lista F, Costi R, Tramontano E. Diketo acid inhibitors of nsp13 of SARS-CoV-2 block viral replication. Antiviral Res 2023; 217:105697. [PMID: 37562607 DOI: 10.1016/j.antiviral.2023.105697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
For RNA viruses, RNA helicases have long been recognized to play critical roles during virus replication cycles, facilitating proper folding and replication of viral RNAs, therefore representing an ideal target for drug discovery. SARS-CoV-2 helicase, the non-structural protein 13 (nsp13) is a highly conserved protein among all known coronaviruses, and, at the moment, is one of the most explored viral targets to identify new possible antiviral agents. In the present study, we present six diketo acids (DKAs) as nsp13 inhibitors able to block both SARS-CoV-2 nsp13 enzymatic functions. Among them four compounds were able to inhibit viral replication in the low micromolar range, being active also on other human coronaviruses such as HCoV229E and MERS CoV. The experimental investigation of the binding mode revealed ATP-non-competitive kinetics of inhibition, not affected by substrate-displacement effect, suggesting an allosteric binding mode that was further supported by molecular modelling calculations predicting the binding into an allosteric conserved site located in the RecA2 domain.
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Affiliation(s)
- Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente. Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Riccardo De Santis
- Defense Institute for Biomedical Sciences, Via Santo Stefano Rotondo 4, 00184, Rome, Italy
| | - Candida Manelfi
- EXSCALATE - Dompé Farmaceutici SpA, via Tommaso De Amicis 95, 80131, Napoli, Italy
| | - Roberta Emmolo
- Dipartimento di Scienze della vita e dell'ambiente. Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Davide Ialongo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Elisa Patacchini
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Donatella Amatore
- Defense Institute for Biomedical Sciences, Via Santo Stefano Rotondo 4, 00184, Rome, Italy
| | - Giovanni Faggioni
- Defense Institute for Biomedical Sciences, Via Santo Stefano Rotondo 4, 00184, Rome, Italy
| | - Marco Artico
- Department of Sensory Organs, "Sapienza" Università di Roma, V.le Regina Elena 324, I-00161, Rome, Italy
| | - Daniela Iaconis
- EXSCALATE - Dompé Farmaceutici SpA, via Tommaso De Amicis 95, 80131, Napoli, Italy
| | - Carmine Talarico
- EXSCALATE - Dompé Farmaceutici SpA, via Tommaso De Amicis 95, 80131, Napoli, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy
| | - Florigio Lista
- Defense Institute for Biomedical Sciences, Via Santo Stefano Rotondo 4, 00184, Rome, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci-Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185, Rome, Italy.
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente. Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy.
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14
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Yu J, Im H, Lee G. Unwinding mechanism of SARS-CoV helicase (nsp13) in the presence of Ca 2+, elucidated by biochemical and single-molecular studies. Biochem Biophys Res Commun 2023; 668:35-41. [PMID: 37235917 PMCID: PMC10193821 DOI: 10.1016/j.bbrc.2023.05.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
The recent outbreak of COVID-19 has created a serious health crisis with fatFal infectious viral diseases, such as Severe Acute Respiratory Syndrome (SARS). The nsp13, a helicase of coronaviruses is an essential element for viral replication that unwinds secondary structures of DNA and RNA, and is thus considered a major therapeutic target for treatment. The replication of coronaviruses and other retroviruses occurs in the cytoplasm of infected cells, in association with viral replication organelles, called virus-induced cytosolic double-membrane vesicles (DMVs). In addition, an increase in cytosolic Ca2+ concentration accelerates viral replication. However, the molecular mechanism of nsp13 in the presence of Ca2+ is not well understood. In this study, we applied biochemical methods and single-molecule techniques to demonstrate how nsp13 achieves its unwinding activity while performing ATP hydrolysis in the presence of Ca2+. Our study found that nsp13 could efficiently unwind double stranded (ds) DNA under physiological concentration of Ca2+ of cytosolic DMVs. These findings provide new insights into the properties of nsp13 in the range of calcium in cytosolic DMVs.
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Affiliation(s)
- Jeongmin Yu
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Hyeryeon Im
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Gwangrog Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
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15
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Incicco JJ, Cababie LA, Sarto C, Adler NS, Amrein F, Mikkelsen E, Arrar M, Kaufman SB. Thermodynamic and mechanistic analysis of the functional properties of dengue virus NS3 helicase. Biophys Rev 2023; 15:591-600. [PMID: 37681085 PMCID: PMC10480135 DOI: 10.1007/s12551-023-01101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023] Open
Abstract
The Dengue Virus (DENV) non-structural protein 3 (NS3) is a multi-functional protein critical in the viral life cycle. The DENV NS3 is comprised of a serine protease domain and a helicase domain. The helicase domain itself acts as a molecular motor, either translocating in a unidirectional manner along single-stranded RNA or unwinding double-stranded RNA, processes fueled by the hydrolysis of nucleoside triphosphates. In this brief review, we summarize our contributions and ongoing efforts to uncover the thermodynamic and mechanistic functional properties of the DENV NS3 as an NTPase and helicase.
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Affiliation(s)
- J. Jeremías Incicco
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| | - Leila A. Cababie
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| | - Carolina Sarto
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires. CONICET, Intendente Güiraldes 2160, Caba, 1428 Argentina
| | - Natalia S. Adler
- CONICET. Centro de Investigaciones en Bionanociencias (CIBION), Godoy Cruz 2390, Caba, 1425 Argentina
| | - Fernando Amrein
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| | - Evelyn Mikkelsen
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
| | - Mehrnoosh Arrar
- Instituto de Cálculo, Universidad de Buenos Aires. CONICET, Intendente Güiraldes 2160, Caba, 1428 Argentina
| | - Sergio B. Kaufman
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, CONICET, Junín 956, Caba, 1113 Argentina
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Caba, 1113 Argentina
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16
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Chaudhary J, Gautam T, Gahlaut V, Singh K, Kumar S, Batra R, Gupta PK. Identification and characterization of RuvBL DNA helicase genes for tolerance against abiotic stresses in bread wheat (Triticum aestivum L.) and related species. Funct Integr Genomics 2023; 23:255. [PMID: 37498392 DOI: 10.1007/s10142-023-01177-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
Recombination UVB (sensitivity) like (RuvBL) helicase genes represent a conserved family of genes, which are known to be involved in providing tolerance against abiotic stresses like heat and drought. We identified nine wheat RuvBL genes, one each on nine different chromosomes, belonging to homoeologous groups 2, 3, and 4. The lengths of genes ranged from 1647 to 2197 bp and exhibited synteny with corresponding genes in related species including Ae. tauschii, Z. mays, O. sativa, H. vulgare, and B. distachyon. The gene sequences were associated with regulatory cis-elements and transposable elements. Two genes, namely TaRuvBL1a-4A and TaRuvBL1a-4B, also carried targets for a widely known miRNA, tae-miR164. Gene ontology revealed that these genes were closely associated with ATP-dependent formation of histone acetyltransferase complex. Analysis of the structure and function of RuvBL proteins revealed that the proteins were localized mainly in the cytoplasm. A representative gene, namely TaRuvBL1a-4A, was also shown to be involved in protein-protein interactions with ten other proteins. On the basis of phylogeny, RuvBL proteins were placed in two sub-divisions, namely RuvBL1 and RuvBL2, which were further classified into clusters and sub-clusters. In silico studies suggested that these genes were differentially expressed under heat/drought. The qRT-PCR analysis confirmed that expression of TaRuvBL genes differed among wheat cultivars, which differed in the level of thermotolerance. The present study advances our understanding of the biological role of wheat RuvBL genes and should help in planning future studies on RuvBL genes in wheat including use of RuvBL genes in breeding thermotolerant wheat cultivars.
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Affiliation(s)
- Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Vijay Gahlaut
- Council of Scientific & Industrial Research-Institute of Himalayan Bioresource Technology, Palampur, India
- Department of Biotechnology, University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Kalpana Singh
- Department of Bioinformatics, College of animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Sourabh Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
| | - Ritu Batra
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
- IIMT University, 'O' Pocket, Ganga Nagar, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India.
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17
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Mehyar N. Coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2 helicase inhibitors: A systematic review of in vitro studies. J Virus Erad 2023:100327. [PMID: 37363132 PMCID: PMC10214743 DOI: 10.1016/j.jve.2023.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/11/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction The recent outbreak of SARS-CoV-2 significantly increased the need to find inhibitors that target the essential enzymes for virus replication in the host cells. This systematic review was conducted to identify potential inhibitors of SARS-CoV, MERS-CoV, and SARS-CoV-2 helicases that have been tested by in vitro methods. The inhibition mechanisms of these compounds were discussed in this review, in addition to their cytotoxic and viral infection protection properties. Methods The databases PUBMED/MEDLINE, EMBASE, SCOPUS, and Web of Science were searched using different combinations of the keywords "helicase", "nsp13", "inhibitors", "coronaviridae", "coronaviruses", "virus replication", "replication", and "antagonists and inhibitors". Results By the end of this search, a total of 6854 articles had been identified. Thirty-one articles were included in this review. These studies reported the inhibitory effects of 309 compounds on SARS-CoV, MERS-CoV, and SARS-CoV-2 helicase activities measured by in vitro methods. Helicase inhibitors were categorized according to the type of coronavirus and the type of tested enzymatic activity, nature, approval, inhibition level, cytotoxicity, and viral infection protection effects. These inhibitors are classified according to the site of their interaction with the coronavirus helicases into four types: zinc-binding site inhibitors, nucleic acid binding site inhibitors, nucleotide-binding site inhibitors, and inhibitors with no clear interaction site. Conclusion Evidence from in vitro studies suggests that helicase inhibitors have a high potential as antiviral agents. Several helicase inhibitors tested in vitro showed good antiviral activities while maintaining moderate cytotoxicity. These inhibitors should be clinically investigated to determine their efficiency in treating different coronavirus infections, particularly COVID-19.
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Affiliation(s)
- Nimer Mehyar
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
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18
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Datta A, Sommers JA, Jhujh SS, Harel T, Stewart GS, Brosh RM. Discovery of a new hereditary RECQ helicase disorder RECON syndrome positions the replication stress response and genome homeostasis as centrally important processes in aging and age-related disease. Ageing Res Rev 2023; 86:101887. [PMID: 36805074 PMCID: PMC10018417 DOI: 10.1016/j.arr.2023.101887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
Characterizing the molecular deficiencies underlying human aging has been a formidable challenge as it is clear that a complex myriad of factors including genetic mutations, environmental influences, and lifestyle choices influence the deterioration responsible for human pathologies. In addition, the common denominators of human aging, exemplified by the newly updated hallmarks of aging (López-Otín et al., 2023), suggest multiple avenues and layers of crosstalk between pathways important for genome and cellular homeostasis, both of which are major determinants of both good health and lifespan. In this regard, we postulate that hereditary disorders characterized by chromosomal instability offer a unique window of insight into aging and age-related disease processes. Recently, we discovered a new RECQ helicase disorder, designated RECON syndrome attributed to bi-allelic mutations in the RECQL1 gene (Abu-Libdeh et al., 2022). Cells deficient in RECQL1 exhibit genomic instability and a compromised response to replication stress, providing further evidence for the significance of genome homeostasis to suppress disease phenotypes. Here we provide a perspective on the pathology of RECON syndrome to inform the reader as to how molecular defects in the RECQL1 gene contribute to underlying deficiencies in nucleic acid metabolism often seen in certain aging or age-related diseases.
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Affiliation(s)
- Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Joshua A Sommers
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Satpal S Jhujh
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Grant S Stewart
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA.
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Ahire MS, Nagar SR, D’souza ZI, Tupkari JV, Dalvi SM. Expression of Minichromosome Maintenance Protein 2 (MCM2) in Oral Epithelial Dysplasia and Oral Squamous Cell Carcinoma: A Systematic Review. Indian J Otolaryngol Head Neck Surg 2023; 75:183-192. [PMID: 37007886 PMCID: PMC10050670 DOI: 10.1007/s12070-022-03296-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 11/21/2022] [Indexed: 12/31/2022] Open
Abstract
The histopathological investigations of oral lesions are a basic approach for diagnosing ongoing cancer or pre-cancer associated pathological attributes in the dissected biopsy. The early detection and management of potentially malignant disorders of the lip and oral cavity that require intervention may reduce malignant transformations, or in case any malignancy is detected during surveillance, the appropriate treatment may improve survival rates. This would guide the clinicians to decide the appropriate treatment modality or lesion to achieve a more favorable prognosis. MCM2 protein is involved in DNA replication providing additional information about the prognosis of neoplasms. Some authors have pointed out that MCM proteins have been inversely correlated with salivary tumour differentiation and therefore could be an indicator of proliferation potential. Therefore, it is essential to find the expression of the MCM2 gene in oral leukoplakia and oral squamous cell carcinoma. Electronic databases like Ebscohost, Livivo, Google Scholar and PubMed were searched. Based on the inclusion and exclusion criteria, 2 reviewers (MS and SN) independently selected the relevant articles. Any disagreement was discussed until a consensus was reached. We used the QUADAS-2 tool to assess the quality of the included studies over four key domains: patient selection, index test, reference standard and flow and timing of participants through the study. 10 out of 57 titles were found to meet the eligibility criteria. Biopsied tissue with immunohistochemical staining or advanced diagnostic studies were included. A total of 901 samples were included in the study and different groups were normal oral mucosa (NOM), oral epithelial dysplasia (OED) and oral squamous cell carcinoma (OSCC). MCM2 proteins are useful diagnostic markers for distinguishing malignant from benign epithelial dysplasia and for early detection and diagnosis of OSCC as an adjunct to clinicopathological parameters. Supplementary Information The online version contains supplementary material available at 10.1007/s12070-022-03296-7.
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Affiliation(s)
- Manisha S. Ahire
- Department of Oral Pathology & Microbiology, Government Dental College & Hospital, PD’Mello Road, St.George Hospital Campus, Near Chatrapati Shivaji Terminus, Mumbai, Maharashtra 400001 India
| | - Saurabh R. Nagar
- Department of Pathology, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Mumbai, India
- Homi Bhabha National Institute, Mumbai, 400012 India
| | - Zaneta Ivy D’souza
- Department of Oral Pathology & Microbiology, Nair Hospital Dental College, Dr. A.L.Nair Road, Mumbai Central, Mumbai, 400008 India
| | - J. V. Tupkari
- Department of Oral Pathology & Microbiology, Government Dental College & Hospital, PD’Mello Road, St.George Hospital Campus, Near Chatrapati Shivaji Terminus, Mumbai, Maharashtra 400001 India
| | - Shubhangi M. Dalvi
- Department of Biochemistry, Grant Government Dental College & Hospital, JJ Marg, Nagpada, Byculla, Mumbai, Maharashtra 400008 India
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20
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Kejriwal R, Evans T, Calabrese J, Swistak L, Alexandrescu L, Cohen M, Rahman N, Henriksen N, Charan Dash R, Hadden MK, Stonehouse NJ, Rowlands DJ, Kingston NJ, Hartnoll M, Dobson SJ, White SJ. Development of Enterovirus Antiviral Agents That Target the Viral 2C Protein. ChemMedChem 2023; 18:e202200541. [PMID: 36792530 DOI: 10.1002/cmdc.202200541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
The Enterovirus (EV) genus includes several important human and animal pathogens. EV-A71, EV-D68, poliovirus (PV), and coxsackievirus (CV) outbreaks have affected millions worldwide, causing a range of upper respiratory, skin, and neuromuscular diseases, including acute flaccid myelitis, and hand-foot-and-mouth disease. There are no FDA-approved antiviral therapeutics for these enteroviruses. This study describes novel antiviral compounds targeting the conserved non-structural viral protein 2C with low micromolar to nanomolar IC50 values. The selection of resistant mutants resulted in amino acid substitutions in the viral capsid protein, implying these compounds may play a role in inhibiting the interaction of 2C and the capsid protein. The assembly and encapsidation stages of the viral life cycle still need to be fully understood, and the inhibitors reported here could be useful probes in understanding these processes.
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Affiliation(s)
- Rishabh Kejriwal
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Tristan Evans
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Joshua Calabrese
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Lea Swistak
- Institut Pasteur, Université Paris Cité Dynamics of Host-Pathogen Interactions Unit, 75015, Paris, France
| | - Lauren Alexandrescu
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Michelle Cohen
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Nahian Rahman
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
| | - Niel Henriksen
- Atomwise Inc., 717 Market St #800, San Francisco, CA 94103, USA
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, CT 06029-3092, USA
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, CT 06029-3092, USA
| | - Nicola J Stonehouse
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Rowlands
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Natalie J Kingston
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Madeline Hartnoll
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Samuel J Dobson
- School of Molecular and Cellular Biology Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Simon J White
- Biology/Physics Building Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit-3125, Storrs, CT 06269-3125, USA
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21
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Gillich N, Zhang Z, Binder M, Urban S, Bartenschlager R. Effect of variants in LGP2 on MDA5-mediated activation of interferon response and suppression of hepatitis D virus replication. J Hepatol 2023; 78:78-89. [PMID: 36152765 DOI: 10.1016/j.jhep.2022.08.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/11/2022] [Accepted: 08/30/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND & AIMS Retinoic acid inducible gene I (RIG-I)-like receptors (RLRs), including RIG-I, melanoma differentiation-associated protein 5 (MDA5), and laboratory of genetics and physiology 2 (LGP2), sense viral RNA to induce the antiviral interferon (IFN) response. LGP2, unable to activate the IFN response itself, modulates RIG-I and MDA5 signalling. HDV, a small RNA virus causing the most severe form of viral hepatitis, is sensed by MDA5. The mechanism underlying IFN induction and its effect on HDV replication is unclear. Here, we aimed to unveil the role of LGP2 and clinically relevant variants thereof in these processes. METHODS RLRs were depleted in HDV susceptible HepaRGNTCP cells and primary human hepatocytes. Cells were reconstituted to express different LGP2 versions. HDV and IFN markers were quantified in a time-resolved manner. Interaction studies among LGP2, MDA5, and RNA were performed by pull-down assays. RESULTS LGP2 is essential for the MDA5-mediated IFN response induced upon HDV infection. This induction requires both RNA binding and ATPase activities of LGP2. The IFN response only moderately reduced HDV replication in resting cells but profoundly suppressed cell division-mediated HDV spread. An LGP2 variant (Q425R), predominating in Africans who develop less severe chronic hepatitis D, mediated detectably higher basal and faster HDV-induced IFN response as well as stronger HDV suppression. Mechanistically, LGP2 RNA binding was a prerequisite for the formation of stable MDA5-RNA complexes. MDA5 binding to RNA was enhanced by the Q425R LGP2 variant. CONCLUSIONS LGP2 is essential to mount an antiviral IFN response induced by HDV and stabilises MDA5-RNA interaction required for downstream signalling. The natural Q425R LGP2 is a gain-of-function variant and might contribute to an attenuated course of hepatitis D. IMPACT AND IMPLICATIONS HDV is the causative pathogen of chronic hepatitis D, a severe form of viral hepatitis that can lead to cirrhosis and hepatocellular carcinoma. Upon infection, the human immune system senses HDV and mounts an antiviral interferon (IFN) response. Here, we demonstrate that the immune sensor LGP2 cooperates with MDA5 to mount an IFN response that represses HDV replication. We mapped LGP2 determinants required for IFN system activation and characterised several natural genetic variants of LGP2. One of them reported to predominate in sub-Saharan Africans can accelerate HDV-induced IFN responses, arguing that genetic determinants, possibly including LGP2, might contribute to slower disease progression in this population. Our results will hopefully prompt further studies on genetic variations in LGP2 and other components of the innate immune sensing system, including assessments of their possible impact on the course of viral infection.
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Affiliation(s)
- Nadine Gillich
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zhenfeng Zhang
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response," Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Center for Infection Research (DZIF) - Heidelberg Partner Site, Heidelberg, Germany.
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany; German Center for Infection Research (DZIF) - Heidelberg Partner Site, Heidelberg, Germany.
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22
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Dai L, Lu L, Zhang X, Wu J, Li J, Lin Z. Identification of small-molecule inhibitors of the DNA repair proteins RuvAB from Pseudomonas aeruginosa. Bioorg Med Chem 2022; 73:117022. [PMID: 36155320 DOI: 10.1016/j.bmc.2022.117022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022]
Abstract
The Holliday junction (HJ) branch migrator RuvAB complex plays a fundamental role during homologous recombination and DNA damage repair, and therefore, is an attractive target for the treatment of bacterial pathogens. Pseudomonas aeruginosa (P. aeruginosa, Pa) is one of the most common clinical opportunistic bacterial pathogens, which can cause a series of life-threatening acute or chronic infections. Here, we performed a high throughput small-molecule screening targeting PaRuvAB using the FRET-based HJ branch migration assay. We identified that corilagin, bardoxolone methyl (BM) and 10-(6'-plastoquinonyl) decyltriphenylphosphonium (SKQ1) could efficiently inhibit the branch migration activity of PaRuvAB, with IC50 values of 0.40 ± 0.04 μM, 0.38 ± 0.05 μM and 4.64 ± 0.27 μM, respectively. Further biochemical and molecular docking analyses demonstrated that corilagin directly bound to PaRuvB at the ATPase domain, and thus prevented ATP hydrolysis. In contrast, BM and SKQ1 acted through blocking the interactions between PaRuvA and HJ DNA. Finally, these compounds were shown to increase the susceptibility of P. aeruginosa to UV-C irradiation. Our work, for the first time, reports the small-molecule inhibitors of RuvA and RuvB from any species, providing valuable chemical tools to dissect the functional role of each individual protein in vivo.
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Affiliation(s)
- Lin Dai
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Lian Lu
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Xu Zhang
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Juhong Wu
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou 350108, China.
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23
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Zandi M, Behboudi E, Shojaei MR, Soltani S, Karami H. Letter to the Editor Regarding "An Overview on Serology and Molecular Tests for COVID-19: An Important Challenge of the Current Century (doi: 10.22034/iji.2021.88660.1894.)". Iran J Immunol 2022; 19:337. [PMID: 36190387 DOI: 10.22034/iji.2022.91791.2107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently in a review article by Mansourabadi et al. published in the Iranian Journal of Immunology, the authors described the serological and molecular tests for COVID-19 (1). The mentioned review considered helicase (Hel) as a structural protein of SARS-CoV-2 (1). However, based on evidence, the genome of novel coronavirus is approximately 30kb in length and encodes only four structural proteins, including spike (S), envelope (E), membrane (M), and nucleoprotein (N) (2, 3), although helicase (NSP13) as a nonstructural protein such as RNA-dependent RNA polymerases (NSP12) encoded by the ORF region and is involved in the replication of the virus (3).In addition, authors reported that hemagglutinin esterase could be used as a favorite target for SARS-CoV-2 Real-time PCR (1); however, scientific evidence shows that SARS-CoV-2 as a betacoronavirus lineage B like SARS-CoV lacks hemagglutinin esterase (4-6); thus this protein cannot be a target for detection of SARS-CoV-2.
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Affiliation(s)
- Milad Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Emad Behboudi
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammad Reza Shojaei
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Karami
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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24
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Lu L, Peng Y, Yao H, Wang Y, Li J, Yang Y, Lin Z. Punicalagin as an allosteric NSP13 helicase inhibitor potently suppresses SARS-CoV-2 replication in vitro. Antiviral Res 2022; 206:105389. [PMID: 35985407 PMCID: PMC9381947 DOI: 10.1016/j.antiviral.2022.105389] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/20/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) helicase NSP13 plays a conserved role in the replication of coronaviruses and has been identified as an ideal target for the development of antiviral drugs against SARS-CoV-2. Here, we identify a novel NSP13 helicase inhibitor punicalagin (PUG) through high-throughput screening. Surface plasmon resonance (SPR)-based analysis and molecular docking calculation reveal that PUG directly binds NSP13 on the interface of domains 1A and 2A, with a KD value of 21.6 nM. Further biochemical and structural analyses suggest that PUG inhibits NSP13 on ATP hydrolysis and prevents it binding to DNA substrates. Finally, the antiviral studies show that PUG effectively suppresses the SARS-CoV-2 replication in A549-ACE2 and Vero cells, with EC50 values of 347 nM and 196 nM, respectively. Our work demonstrates the potential application of PUG in the treatment of coronavirus disease 2019 (COVID-19) and identifies an allosteric inhibition mechanism for future drug design targeting the viral helicases.
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Affiliation(s)
- Lian Lu
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Huiqiao Yao
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China.
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
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25
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Vanson S, Li Y, Wood RD, Doublié S. Probing the structure and function of polymerase θ helicase-like domain. DNA Repair (Amst) 2022; 116:103358. [PMID: 35753097 PMCID: PMC10329254 DOI: 10.1016/j.dnarep.2022.103358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/19/2022]
Abstract
DNA Polymerase θ is the key actuator of the recently identified double-strand break repair pathway, theta-mediated end joining (TMEJ). It is the only known polymerase to have a 3-domain architecture containing an independently functional family A DNA polymerase tethered by a long central region to an N-terminal helicase-like domain (HLD). Full-length polymerase θ and the isolated HLD hydrolyze ATP in the presence of DNA, but no processive DNA duplex unwinding has been observed. Based on sequence and structure conservation, the HLD is classified as a member of helicase superfamily II and, more specifically, the Ski2-like family. The specific subdomain composition and organization most closely resemble that of archaeal DNA repair helicases Hel308 and Hjm. The underlying structural basis as to why the HLD is not able to processively unwind duplex DNA, despite its similarity to bona fide helicases, remains elusive. Activities of the HLD include ATP hydrolysis, protein displacement, and annealing of complementary DNA. These observations have led to speculation about the role of the HLD within the context of double-strand break repair via TMEJ, such as removal of single-stranded DNA binding proteins like RPA and RAD51 and microhomology alignment. This review summarizes the structural classification and organization of the polymerase θ HLD and its homologs and explores emerging data on its biochemical activities. We conclude with a simple, speculative model for the HLD's role in TMEJ.
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Affiliation(s)
- Scott Vanson
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA
| | - Yuzhen Li
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, TX 77230, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, TX 77230, USA.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA.
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26
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Ozaslan D, Byrd AK, Belachew B, Raney KD. Alignment of helicases on single-stranded DNA increases activity. Methods Enzymol 2022; 672:29-54. [PMID: 35934480 PMCID: PMC9421817 DOI: 10.1016/bs.mie.2022.03.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helicases function in most biological processes that utilize RNA or DNA nucleic acids including replication, recombination, repair, transcription, splicing, and translation. They are motor proteins that bind ATP and then catalyze hydrolysis to release energy which is transduced for conformational changes. Different conformations correspond to different steps in a process that results in movement of the enzyme along the nucleic acid track in a unidirectional manner. Some helicases such as DEAD-box helicases do not translocate, but these enzymes transduce chemical energy from ATP hydrolysis to unwind secondary structure in DNA or RNA. Some helicases function as monomers while others assemble into defined structures, either dimers or higher order oligomers. Dda helicase from bacteriophage T4 and NS3 helicase domain from the hepatitis C virus are examples of monomeric helicases. These helicases can bind to single-stranded DNA in a manner that appears like train engines on a track. When monomeric helicases align on DNA, the activity of the enzymes increases. Helicase activity can include the rate of duplex unwinding and the total number of base pairs melted during a single binding event or processivity. Dda and NS3h are considered as having low processivity, unwinding fewer than 50 base pairs per binding event. Here, we report fusing two molecules of NS3h molecules together through genetically linking the C-terminus of one molecule to the N-terminus of a second NS3h molecule. We observed increased processivity relative to NS3h possibly arising from the increased probability that at least one of the helicases will completely unwind the DNA prior to dissociation. The dimeric enzyme also binds DNA more like the full-length NS3 helicase. Finally, the dimer can displace streptavidin from biotin-labeled oligonucleotide, whereas monomeric NS3h cannot.
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Affiliation(s)
- Deniz Ozaslan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
| | - Binyam Belachew
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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27
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Fung SY, Siu KL, Lin H, Chan CP, Yeung ML, Jin DY. SARS-CoV-2 NSP13 helicase suppresses interferon signaling by perturbing JAK1 phosphorylation of STAT1. Cell Biosci 2022; 12:36. [PMID: 35317858 PMCID: PMC8939493 DOI: 10.1186/s13578-022-00770-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/02/2022] [Indexed: 12/15/2022] Open
Abstract
Background SARS-CoV-2 is the causative agent of COVID-19. Overproduction and release of proinflammatory cytokines are the underlying cause of severe COVID-19. Treatment of this condition with JAK inhibitors is a double-edged sword, which might result in the suppression of proinflammatory cytokine storm and the concurrent enhancement of viral infection, since JAK signaling is essential for host antiviral response. Improving the current JAK inhibitor therapy requires a detailed molecular analysis on how SARS-CoV-2 modulates interferon (IFN)-induced activation of JAK-STAT signaling. Results In this study, we focused on the molecular mechanism by which SARS-CoV-2 NSP13 helicase suppresses IFN signaling. Expression of SARS-CoV-2 NSP13 alleviated transcriptional activity driven by type I and type II IFN-responsive enhancer elements. It also prevented nuclear translocation of STAT1 and STAT2. The suppression of NSP13 on IFN signaling occurred at the step of STAT1 phosphorylation. Nucleic acid binding-defective mutant K345A K347A and NTPase-deficient mutant E375A of NSP13 were found to have largely lost the ability to suppress IFN-β-induced STAT1 phosphorylation and transcriptional activation, indicating the requirement of the helicase activity for NSP13-mediated inhibition of STAT1 phosphorylation. NSP13 did not interact with JAK1 nor prevent STAT1-JAK1 complex formation. Mechanistically, NSP13 interacted with STAT1 to prevent JAK1 kinase from phosphorylating STAT1. Conclusion SARS-CoV-2 NSP13 helicase broadly suppresses IFN signaling by targeting JAK1 phosphorylation of STAT1.
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Affiliation(s)
- Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Huayue Lin
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Ching-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China
| | - Man Lung Yeung
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China.,Department of Microbiology, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China. .,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, China.
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28
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Yue K, Yao B, Shi Y, Yang Y, Qian Z, Ci Y, Shi L. The stalk domain of SARS-CoV-2 NSP13 is essential for its helicase activity. Biochem Biophys Res Commun 2022; 601:129-136. [PMID: 35245742 PMCID: PMC8864812 DOI: 10.1016/j.bbrc.2022.02.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/11/2022]
Abstract
COVID-19, caused by SARS-CoV-2, has been spreading worldwide for more than two years and has led to immense challenges to human health. Despite the great efforts that have been made, our understanding of SARS-CoV-2 is still limited. The viral helicase, NSP13 is an important enzyme involved in SARS-CoV-2 replication and transcription. Here we highlight the important role of the stalk domain in the enzymatic activity of NSP13. Without the stalk domain, NSP13 loses its dsRNA unwinding ability due to the lack of ATPase activity. The stalk domain of NSP13 also provides a rigid connection between the ZBD and helicase domain. We found that the tight connection between the stalk and helicase is necessary for NSP13-mediated dsRNA unwinding. When a short flexible linker was inserted between the stalk and helicase domains, the helicase activity of NSP13 was impaired, although its ATPase activity remained intact. Further study demonstrated that linker insertion between the stalk and helicase domains attenuated the RNA binding ability and affected the thermal stability of NSP13. In summary, our results suggest the crucial role of the stalk domain in NSP13 enzymatic activity and provide mechanistic insight into dsRNA unwinding by SARS-CoV-2 NSP13.
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Affiliation(s)
- Kun Yue
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Bin Yao
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Yingchao Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Yang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhaohui Qian
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, 100176, China
| | - Yali Ci
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Lei Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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29
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Bi L, Qin Z, Hou XM, Modesti M, Sun B. Simultaneous Mechanical and Fluorescence Detection of Helicase-Catalyzed DNA Unwinding. Methods Mol Biol 2022; 2478:329-347. [PMID: 36063326 DOI: 10.1007/978-1-0716-2229-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Helicases are ubiquitous molecular motor proteins that utilize the energy derived from the hydrolysis of nucleoside triphosphates (NTPs) to transiently convert the duplex form of nucleic acids to single-stranded intermediates for many biological processes. These enzymes play vital roles in nearly all aspects of nucleic acid metabolism, such as DNA repair and RNA splicing. Understanding helicase's functional roles requires methods to dissect the mechanisms of motor proteins at the molecular level. In the past three decades, there has been a large increase in the application of single-molecule approaches to investigate helicases. These techniques, such as optical tweezers and single-molecule fluorescence, offer capabilities to monitor helicase motions with unprecedented spatiotemporal resolution, to apply quantitative forces to probe the chemo-mechanical activities of these motors and to resolve helicase heterogeneity at the single-molecule level. In this chapter, we describe a single-molecule method that combines optical tweezers with confocal fluorescence microscopy to study helicase-catalyzed DNA unwinding. Using Bloom syndrome protein (BLM), a multifunctional helicase that maintains genome stability, as an example, we show that this method allows for the simultaneous detection of displacement, force and fluorescence signals of a single DNA molecule during unwinding in real time, leading to the discovery of a distinct bidirectional unwinding mode of BLM that is activated by a single-stranded DNA binding protein called replication protein A (RPA). We provide detailed instructions on how to prepare two DNA templates to be used in the assays, purify the BLM and RPA proteins, perform single-molecule experiments, and acquire and analyse the data.
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Affiliation(s)
- Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhenheng Qin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Mauro Modesti
- Cancer Research Center of Marseille, Marseille, France
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Taylor AMK, Okoniewski SR, Uyetake L, Perkins TT. Force-Activated DNA Substrates for In Situ Generation of ssDNA and Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay. Methods Mol Biol 2022; 2478:273-312. [PMID: 36063324 DOI: 10.1007/978-1-0716-2229-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-molecule force spectroscopy can precisely probe the biomechanical interactions of proteins that unwind duplex DNA and bind to and wrap around single-stranded (ss)DNA. Yet assembly of the required substrates, which often contain a ssDNA segment embedded within a larger double-stranded (ds)DNA construct, can be time-consuming and inefficient, particularly when using a standard three-way hybridization protocol. In this chapter, we detail how to construct a variety of force-activated DNA substrates more efficiently. To do so, we engineered a dsDNA molecule with a designed sequence of specified GC content positioned between two enzymatically induced, site-specific nicks. Partially pulling this substrate into the overstretching transition of DNA (~65 pN) using an optical trap led to controlled dissociation of the ssDNA segment delineated by the two nicks. Here, we describe protocols for generating ssDNA of up to 1000 nucleotides as well as more complex structures, such as a 120-base-pair DNA hairpin positioned next to a 33-nucleotide ssDNA segment. The utility of the hairpin substrate was demonstrated by measuring the motion of E. coli. RecQ, a 3'-to-5' DNA helicase.
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Affiliation(s)
- Arnulf M K Taylor
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Stephen R Okoniewski
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA.
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Thompson MD, Malone EG, Byrd AK. Monitoring helicase-catalyzed unwinding of multiple duplexes simultaneously. Methods Enzymol 2022; 672:1-27. [PMID: 35934470 PMCID: PMC9397138 DOI: 10.1016/bs.mie.2022.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Helicases catalyze the unwinding of duplex nucleic acids to aid a variety of cellular processes. Although helicases unwind duplex DNA in the same direction that they translocate on single-stranded DNA, forked duplexes provide opportunities to monitor unwinding by helicase monomers bound to each arm of the fork. The activity of the helicase bound to the displaced strand can be discerned alongside the helicase bound to the translocase strand using a forked substrate with accessible duplexes on both strands labeled with different fluorophores. In order to quantify the effect of protein-protein interactions on the activity of multiple monomers of the Bacteroides fragilis Pif1 helicase bound to separate strands of a forked DNA junction, an ensemble gel-based assay for monitoring simultaneous duplex unwinding was developed (Su et al., 2019). Here, the use of that assay is described for measuring the total product formation and rate constants of product formation of multiple duplexes on a single nucleic acid substrate. Use of this assay may aid characterization of protein-protein interactions between multiple helicase monomers at forked nucleic acid junctions and can assist with the characterization of helicase action on the displaced strand of forked duplexes.
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Affiliation(s)
- Matthew D Thompson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Emory G Malone
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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Grabarczyk DB. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Subcell Biochem 2022; 99:83-107. [PMID: 36151374 DOI: 10.1007/978-3-031-00793-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
As well as accurately duplicating DNA, the eukaryotic replisome performs a variety of other crucial tasks to maintain genomic stability. For example, organizational elements, like cohesin, must be transferred from the front of the fork to the new strands, and when there is replication stress, forks need to be protected and checkpoint signalling activated. The Tof1-Csm3 (or Timeless-Tipin in humans) Fork Protection Complex (FPC) ensures efficient replisome progression and is required for a range of replication-associated activities. Recent studies have begun to reveal the structure of this complex, and how it functions within the replisome to perform its diverse roles. The core of the FPC acts as a DNA grip on the front of the replisome to regulate fork progression. Other flexibly linked domains and motifs mediate interactions with proteins and specific DNA structures, enabling the FPC to act as a hub at the head of the replication fork.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
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Akinnusi PA, Olubode SO, Salaudeen WA. Molecular binding studies of anthocyanins with multiple antiviral activities against SARS-CoV-2. Bull Natl Res Cent 2022; 46:102. [PMID: 35431537 PMCID: PMC9006501 DOI: 10.1186/s42269-022-00786-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/30/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND The search for ideal drugs with absolute antiviral activity against SARS-CoV-2 is still in place, and attention has been recently drawn to natural products. Several molecular targets have been identified as points of therapeutic intervention. The targets used in this study include SARS-CoV-2 helicase, spike protein, RNA-dependent RNA polymerase, main protease, and human ACE-2. An integrative computer-aided approach, which includes molecular docking, pharmacophore modeling, and pharmacokinetic profiling, was employed to identify anthocyanins with robust multiple antiviral activities against these SARS-CoV-2 targets. RESULT Four anthocyanins (Delphinidin 3-O-glucosyl-glucoside, Cyanidin 3-O-glucosyl-rutinoside, Cyanidin 3-(p-coumaroyl)-diglucoside-5-glucoside), and Nasunin) with robust multiple inhibitory interactions were identified from a library of 118 anthocyanins using computer-aided techniques. These compounds exhibited very good binding affinity to the protein targets and moderate pharmacokinetic profiles. However, Cyanidin 3-O-glucosyl-rutinoside is reported to be the most suitable drug candidate with multiple antiviral effects against SARS-CoV-2 due to its good binding affinity to all five protein targets engaged in the study. CONCLUSIONS The anthocyanins reported in this study exhibit robust binding affinities and strong inhibitory molecular interactions with the target proteins and could be well exploited as potential drug candidates with potent multiple antiviral effects against COVID-19.
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Abstract
RNA viruses cause many routine illnesses, such as the common cold and the flu. Recently, more deadly diseases have emerged from this family of viruses. The hepatitis C virus has had a devastating impact worldwide. Despite the cures developed in the U.S. and Europe, economically disadvantaged countries remain afflicted by HCV infection due to the high cost of these medications. More recently, COVID-19 has swept across the world, killing millions and disrupting economies and lifestyles; the virus responsible for this pandemic is a coronavirus. Our understanding of HCV and SARS CoV-2 replication is still in its infancy. Helicases play a critical role in the replication, transcription and translation of viruses. These key enzymes need extensive study not only as an essential player in the viral lifecycle, but also as targets for antiviral therapeutics. In this review, we highlight the current knowledge for RNA helicases of high importance to human health.
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Affiliation(s)
- John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Binyam Belachew
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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Abstract
Ring-shaped hexameric helicases are essential motor proteins that separate duplex nucleic acid strands for DNA replication, recombination, and transcriptional regulation. Two evolutionarily distinct lineages of these enzymes, predicated on RecA and AAA+ ATPase folds, have been identified and characterized to date. Hexameric helicases couple NTP hydrolysis with conformational changes that move nucleic acid substrates through a central pore in the enzyme. How hexameric helicases productively engage client DNA or RNA segments and use successive rounds of NTPase activity to power translocation and unwinding have been longstanding questions in the field. Recent structural and biophysical findings are beginning to reveal commonalities in NTP hydrolysis and substrate translocation by diverse hexameric helicase families. Here, we review these molecular mechanisms and highlight aspects of their function that are yet to be understood.
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Taheri F, Ownagh A, Mardani K. Phylogenetic and molecular analysis based on genes 16S-rRNA, OMPA and POMP to identify Chlamydia abortus infection occurrence at the milk samples of goats and sheep in west Azerbaijan of Iran. Iran J Microbiol 2021; 13:480-487. [PMID: 34557276 PMCID: PMC8421589 DOI: 10.18502/ijm.v13i4.6972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background and Objectives: Enzootic abortion in sheep and goats, also called ovine enzootic abortion (OEA) or enzootic abortion of ewes (EAE), is caused by Chlamydia abortus. The disease has a major economic impact as it represents the most important cause of lamb loss in sheep in parts of Europe, North America and Africa. This serious and potentially life-threatening zoonosis can also affect pregnant women after contact with lambing ewes, leading to severe febrile illness in pregnancy and loss of the foetus. Materials and Methods: The present study was conducted to the Phylogenetic and Molecular Analysis based on Genes 16S-rRNA, OmpA and POMP of C. abortus in milk samples collected from sheep and goats in West Azerbaijan province, Iran. During 2018, a total number of 360 milk samples were collected from sheep (n = 180) and goats (n = 180) of different regions of the province. All milk samples were subjected to DNA extraction and examined by PCR. Results: Among 360 milk samples collected from sheep and goats, 31 (8.611%; 95% CI=6.13–11.96) were positive for Chlamydia spp. The helicase, 16S-rRNA and ompA genes were examined and resulted in 8, 31, 31 of positive samples respectively. The accession numbers have been deposited in GenBank (NCBI) (MT367602 and MT367603). Conclusion: Phylogenetic analysis based on the gene of helicase showed that most of the isolates shared similarity > 99.97%.
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Affiliation(s)
- Fariba Taheri
- Department of Microbiology, School of Veterinary Medicine, Urmia University, Urmia, West Azerbaijan, Iran
| | - Abdulghaffar Ownagh
- Department of Microbiology, School of Veterinary Medicine, Urmia University, Urmia, West Azerbaijan, Iran
| | - Karim Mardani
- Department of Food Hygiene and Quality Control, School of Veterinary Medicine, Urmia University, Urmia, West Azerbaijan, Iran
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Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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Datta A, Pollock KJ, Kormuth KA, Brosh RM. G-Quadruplex Assembly by Ribosomal DNA: Emerging Roles in Disease Pathogenesis and Cancer Biology. Cytogenet Genome Res 2021; 161:285-296. [PMID: 34469893 DOI: 10.1159/000516394] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/03/2021] [Indexed: 12/15/2022] Open
Abstract
Unique repetitive elements of the eukaryotic genome can be problematic for cellular DNA replication and transcription and pose a source of genomic instability. Human ribosomal DNA (rDNA) exists as repeating units clustered together on several chromosomes. Understanding the molecular mechanisms whereby rDNA interferes with normal genome homeostasis is the subject of this review. We discuss the instability of rDNA as a driver of senescence and the important roles of helicases to suppress its deleterious effects. The propensity of rDNA that is rich in guanine bases to form G-quadruplexes (G4) is discussed and evaluated in disease pathogenesis. Targeting G4 in the ribosomes and other chromosomal loci may represent a useful synthetic lethal approach to combating cancer.
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Affiliation(s)
- Arindam Datta
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Kevin J Pollock
- Department of Biology, Bethany College, Bethany, West Virginia, USA
| | - Karen A Kormuth
- Department of Biology, Bethany College, Bethany, West Virginia, USA
| | - Robert M Brosh
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
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Wang J, Zhao D, Li J, Hu M, Xin X, Price MA, Li Q, Liu L, Li S, Rosser SJ, Zhang C, Bi C, Zhang X. Helicase-AID: A novel molecular device for base editing at random genomic loci. Metab Eng 2021; 67:396-402. [PMID: 34411701 DOI: 10.1016/j.ymben.2021.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/06/2021] [Accepted: 08/14/2021] [Indexed: 01/09/2023]
Abstract
CRISPR-enabled deaminase base editing has become a powerful tool for precisely editing nucleotides on the chromosome. In this study DNA helicases, such as Escherichia coli DnaB, were fused to activation-induced cytidine deaminase (AID) to form enzyme complexes which randomly introduces edited bases throughout the chromosome. DnaB-AID was found to increase 2.5 × 103 fold relative to the mutagenesis frequency of wildtype. 97.9% of these edits were observed on the leading strand during DNA replication suggesting deamination to be highly coordinated with DNA replication. Using DnaB-AID, a 371.4% increase in β-carotene production was obtained following four rounds of editing. In Saccharomyces cerevisiae Helicase-AID was constructed by fusing AID to one of the subunits of eukaryotic helicase Mcm2-7 complex, MCM5. Using MCM5-AID, the average editing efficiency of five strains was 2.1 ± 0.4 × 103 fold higher than the native genomic mutation rate. MCM5-AID was able to improve β-carotene production of S. cerevisiae 4742crt by 75.4% following eight rounds of editing. The S. cerevisiae MCM5-AID technique is the first biological tool for generating and accumulating single base mutations in eukaryotic chromosomes. Since the helicase complex is highly conservative in all eukaryotes, Helicase-AID could be adapted for various applications and research in all eukaryotic cells.
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Affiliation(s)
- Jie Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Muzi Hu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiuqing Xin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Marcus A Price
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Qingyan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Li Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Susan J Rosser
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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Abstract
Flaviviruses such as dengue, Japanese encephalitis, West Nile, Yellow Fever and Zika virus, cause viral hemorrhagic fever and encephalitis in humans. However, antiviral therapeutics to treat or prevent flavivirus infections are not yet available. Thus, there is pressing need to develop therapeutics and vaccines that target flavivirus infections. All flaviviruses carry a positive-sense single-stranded RNA genome, which encodes ten proteins; three structural proteins form the virus shell, and seven nonstructural (NS) proteins are involved in replication of the viral genome. While all NS proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) are part of a functional membrane-bound replication complex, enzymatic activities required for flaviviral replication reside in only two NS proteins, NS3 and NS5. NS3 functions as a protease, helicase, and triphosphatase, and NS5 as a capping enzyme, methyltransferase, and RNA-dependent RNA polymerase. In this chapter, we provide an overview of viral replication focusing on the structure and function of NS3 and NS5 replicases. We further describe strategies and examples of current efforts to identify potential flavivirus inhibitors against NS3 and NS5 enzymatic activities that can be developed as therapeutic agents to combat flavivirus infections.
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Affiliation(s)
- Ekaterina Knyazhanskaya
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Marc C Morais
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX, United States.
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Teng FY, Jiang ZZ, Guo M, Tan XZ, Chen F, Xi XG, Xu Y. G-quadruplex DNA: a novel target for drug design. Cell Mol Life Sci 2021; 78:6557-83. [PMID: 34459951 DOI: 10.1007/s00018-021-03921-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
G-quadruplex (G4) DNA is a type of quadruple helix structure formed by a continuous guanine-rich DNA sequence. Emerging evidence in recent years authenticated that G4 DNA structures exist both in cell-free and cellular systems, and function in different diseases, especially in various cancers, aging, neurological diseases, and have been considered novel promising targets for drug design. In this review, we summarize the detection method and the structure of G4, highlighting some non-canonical G4 DNA structures, such as G4 with a bulge, a vacancy, or a hairpin. Subsequently, the functions of G4 DNA in physiological processes are discussed, especially their regulation of DNA replication, transcription of disease-related genes (c-MYC, BCL-2, KRAS, c-KIT et al.), telomere maintenance, and epigenetic regulation. Typical G4 ligands that target promoters and telomeres for drug design are also reviewed, including ellipticine derivatives, quinoxaline analogs, telomestatin analogs, berberine derivatives, and CX-5461, which is currently in advanced phase I/II clinical trials for patients with hematologic cancer and BRCA1/2-deficient tumors. Furthermore, since the long-term stable existence of G4 DNA structures could result in genomic instability, we summarized the G4 unfolding mechanisms emerged recently by multiple G4-specific DNA helicases, such as Pif1, RecQ family helicases, FANCJ, and DHX36. This review aims to present a general overview of the field of G-quadruplex DNA that has progressed in recent years and provides potential strategies for drug design and disease treatment.
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Jarillo J, Ibarra B, Cao-García FJ. DNA replication: In vitro single-molecule manipulation data analysis and models. Comput Struct Biotechnol J 2021; 19:3765-3778. [PMID: 34285777 PMCID: PMC8267548 DOI: 10.1016/j.csbj.2021.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/05/2022] Open
Abstract
Data analysis allows to extract information from the noisy single-molecule data. Models provide insight in the underlying biochemical processes. Ligands can activate or inhibit DNA replication and DNA unwinding.
DNA replication is a key biochemical process of the cell cycle. In the last years, analysis of in vitro single-molecule DNA replication events has provided new information that cannot be obtained with ensembles studies. Here, we introduce crucial techniques for the proper analysis and modelling of DNA replication in vitro single-molecule manipulation data. Specifically, we review some of the main methods to analyze and model the real-time kinetics of the two main molecular motors of the replisome: DNA polymerase and DNA helicase. Our goal is to facilitate access to and understanding of these techniques to promotetheir use in the study of DNA replication at the single-molecule level. A proper analysis of single-molecule data is crucial to obtain a detailed picture of, among others, the kinetics rates, equilibrium contants and conformational changes of the system under study. The techniques presented here have been used or can be adapted to study the operation of other proteins involved in nucleic acids metabolism.
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Affiliation(s)
- Javier Jarillo
- University of Namur, Institute of Life-Earth-Environment, Namur Center for Complex Systems, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/ Faraday 9, 28049 Madrid, Spain
| | - Francisco Javier Cao-García
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/ Faraday 9, 28049 Madrid, Spain.,Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
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43
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Spratt AN, Gallazzi F, Quinn TP, Lorson CL, Sönnerborg A, Singh K. Coronavirus helicases: attractive and unique targets of antiviral drug-development and therapeutic patents. Expert Opin Ther Pat 2021; 31:339-350. [PMID: 33593200 PMCID: PMC8074651 DOI: 10.1080/13543776.2021.1884224] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction: Coronaviruses encode a helicase that is essential for viral replication and represents an excellent antiviral target. However, only a few coronavirus helicase inhibitors have been patented. These patents include drug-like compound SSYA10-001, aryl diketo acids (ADK), and dihydroxychromones. Additionally, adamantane-derived bananins, natural flavonoids, one acrylamide derivative [(E)-3-(furan-2-yl)-N-(4-sulfamoylphenyl)acrylamide], a purine derivative (7-ethyl-8-mercapto-3-methyl-3,7-dihydro-1 H-purine-2,6-dione), and a few bismuth complexes. The IC50 of patented inhibitors ranges between 0.82 μM and 8.95 μM, depending upon the assays used. Considering the urgency of clinical interventions against Coronavirus Disease-19 (COVID-19), it is important to consider developing antiviral portfolios consisting of small molecules. Areas covered: This review examines coronavirus helicases as antiviral targets, and the potential of previously patented and experimental compounds to inhibit the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) helicase. Expert opinion: Small molecule coronavirus helicase inhibitors represent attractive pharmacological modalities for the treatment of coronaviruses such as SARS-CoV and SARS-CoV-2. Rightfully so, the current emphasis is focused upon the development of vaccines. However, vaccines may not work for everyone and broad-based adoption of vaccinations is an increasingly challenging societal endeavor. Therefore, it is important to develop additional pharmacological antivirals against the highly conserved coronavirus helicases to broadly protect against this and subsequent coronavirus epidemics.
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Affiliation(s)
- Austin N Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Fabio Gallazzi
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Thomas P Quinn
- cDepartment of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,dDepartment of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- eDivision of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,fDepartment of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,gSanctum Therapeutics Corporation, Sunnyvale, CA, USA
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Sourabh S, Chauhan M, Yasmin R, Shehzad S, Gupta D, Tuteja R. Plasmodium falciparum DDX17 is an RNA helicase crucial for parasite development. Biochem Biophys Rep 2021; 26:101000. [PMID: 33981864 PMCID: PMC8081931 DOI: 10.1016/j.bbrep.2021.101000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/09/2021] [Accepted: 04/07/2021] [Indexed: 11/05/2022] Open
Abstract
Malaria is one of the major global health concerns still prevailing in this 21st century. Even the effect of artemisinin combination therapies (ACT) have declined and causing more mortality across the globe. Therefore, it is important to understand the basic biology of malaria parasite in order to find novel drug targets. Helicases play important role in nucleic acid metabolism and are components of cellular machinery in various organisms. In this manuscript we have performed the biochemical characterization of homologue of DDX17 from Plasmodium falciparum (PfDDX17). Our results show that PfDDX17 is an active RNA helicase and uses mostly ATP for its function. The qRT-PCR experiment results suggest that PfDDX17 is highly expressed in the trophozoite stage and it is localised mainly in the cytoplasm and in infected RBC (iRBC) membrane mostly in the trophozoite stage. The dsRNA knockdown study suggests that PfDDX17 is important for cell cycle progression. These studies report the biochemical functions of PfDDX17 helicase and further augment the fundamental knowledge about helicase families of P. falciparum. Biochemical characterization of homologue of DDX17 from Plasmodium falciparum (PfDDX17) is presented. Results show that PfDDX17 is an active RNA helicase and uses mostly ATP for its function. Results also suggest that PfDDX17 is highly expressed in the trophozoite stage. dsRNA knockdown study revealed that PfDDX17 is important for cell cycle progression.
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Affiliation(s)
- Suman Sourabh
- Parasite Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manish Chauhan
- Parasite Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rahena Yasmin
- Parasite Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sadaf Shehzad
- Translational Bioinformatics Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Renu Tuteja
- Parasite Biology Group, ICGEB, P. O. Box 10504, Aruna Asaf Ali Marg, New Delhi, 110067, India
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McRae EKS, Dupas SJ, Atefi N, McKenna SA. Monitoring Enzymatic RNA G-Quadruplex Unwinding Activities by Nuclease Sensitivity and Reverse Transcription Stop Assays. Methods Mol Biol 2021; 2209:163-173. [PMID: 33201469 DOI: 10.1007/978-1-0716-0935-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Multiple different methods have been employed to investigate the unwinding of RNA G-quadruplexes by various helicase proteins. Each has their own pitfalls, namely, looking at non-native or chemically modified RNA sequences, biasing the unwinding process with competing trap nucleotides, and a lack of context sequence to the 5' and 3' of the RNA G-quadruplex structure. Herein we present two straightforward methods that allow for quadruplex unwinding to be monitored on native RNA sequences without the use of fluorescent modifications, specialized equipment, or trap nucleotides to be employed.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Steven J Dupas
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Negar Atefi
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada. .,Manitoba Institute for Materials, University of Manitoba, Winnipeg, MB, Canada.
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Halgasova N, Krajcikova D, Kraus D, Bukovska G. The helicase core accessory regions of the phage BFK20 DnaB-like helicase gp43 significantly affect its activity, oligomeric state and DNA binding properties. Virology 2021; 558:96-109. [PMID: 33744744 DOI: 10.1016/j.virol.2021.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/23/2021] [Accepted: 02/28/2021] [Indexed: 11/23/2022]
Abstract
The multifunctional phage replication protein gp43 is composed of an N-terminal prim-pol domain and a C-terminal domain similar to the SF4-type replicative helicases. We prepared four mutants all missing the prim-pol domain with the helicase core flanked by accessory N- and C-terminal regions truncated to varying extents. The shortest fragment still possessing strong ssDNA-dependent ATPase activity and helicase activity was gp43HEL519-983. The other proteins tested were gp43HEL557-983, gp43HEL519-855 and gp43HEL519-896. Removal of the 38 N-terminal residues in gp43HEL557-983, or the 128 and 87 C-terminal residues in gp43HEL519-855 and gp43HEL519-896, resulted in a significant decrease in the ATPase activities. The 38-amino acid N-terminal region has probably a function in modulating DNA binding and protein oligomerization. Deletion of the 87 C-terminal residues resulted in a twofold increase in the unwinding rate. This region is likely indispensable for binding to DNA substrates.
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Lv X, Wang W, Zhao Q, Qiao X, Wang L, Yan Y, Han S, Liu Z, Wang L, Song L. A truncated intracellular Dicer-like molecule involves in antiviral immune recognition of oyster Crassostrea gigas. Dev Comp Immunol 2021; 116:103931. [PMID: 33220355 DOI: 10.1016/j.dci.2020.103931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
The enzyme Dicer is best known for its role as an endoribonuclease in the small RNA pathway, playing a crucial role in recognizing viral double-stranded RNA (dsRNA) and inducing down-stream cascades to mediate anti-virus immunity. In the present study, a truncated Dicer-like gene was identified from oyster Crassostrea gigas, and its open reading frame (ORF) encoded a polypeptide (designed as CgDCL) of 530 amino acids. The CgDCL contained one N-terminal DEAD domain and a C-terminal helicase domain, but lack the conserved PAZ domain, ribonuclease domain (RIBOc) and dsRNA binding domain. The mRNA transcripts of CgDCL were detected in all the examined tissues with high expression levels in lip, gills and haemocytes, which were 62.06-fold, 48.91-fold and 47.13-fold (p < 0.05) of that in mantle, respectively. In the primarily cultured oyster haemocytes, the mRNA transcripts of CgDCL were significantly induced at 12 h after poly(I:C) stimulation, which were 4.04-fold (p < 0.05) of that in control group. The expression level of CgDCL mRNA in haemocytes was up-regulated significantly after dsRNA and recombinant interferon-like protein (rCgIFNLP) injection, which was 12.87-fold (p < 0.01) and 3.22-fold (p < 0.05) of that in control group, respectively. CgDCL proteins were mainly distributed in the cytoplasm of haemocytes. The recombinant CgDCL protein displayed binding activity to dsRNA and poly(I:C), but no obvious dsRNA cleavage activity. These results collectively suggest that truncated CgDCL from C. gigas was able to be activated by poly(I:C), dsRNA and CgIFNLP, and functioned as an intracellular recognition molecule to bind nucleic acid of virus, indicating a potential mutual cooperation between RNAi and IFN-like system in anti-virus immunity of oysters.
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Affiliation(s)
- Xiaojing Lv
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Qi Zhao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Xue Qiao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Liyan Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Yunchen Yan
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Shuo Han
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering (Guangdong,Zhuhai), Zhuhai, 519000, China; Laboratory of Marine Fisheries Science and Food Production Process, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
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Chen X, Ali YI, Fisher CEL, Arribas-Bosacoma R, Rajasekaran MB, Williams G, Walker S, Booth JR, Hudson JJR, Roe SM, Pearl LH, Ward SE, Pearl FMG, Oliver AW. Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein. eLife 2021; 10:e65339. [PMID: 33647232 PMCID: PMC7924943 DOI: 10.7554/elife.65339] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/16/2021] [Indexed: 12/28/2022] Open
Abstract
BLM (Bloom syndrome protein) is a RECQ-family helicase involved in the dissolution of complex DNA structures and repair intermediates. Synthetic lethality analysis implicates BLM as a promising target in a range of cancers with defects in the DNA damage response; however, selective small molecule inhibitors of defined mechanism are currently lacking. Here, we identify and characterise a specific inhibitor of BLM's ATPase-coupled DNA helicase activity, by allosteric trapping of a DNA-bound translocation intermediate. Crystallographic structures of BLM-DNA-ADP-inhibitor complexes identify a hitherto unknown interdomain interface, whose opening and closing are integral to translocation of ssDNA, and which provides a highly selective pocket for drug discovery. Comparison with structures of other RECQ helicases provides a model for branch migration of Holliday junctions by BLM.
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Affiliation(s)
- Xiangrong Chen
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
- Bioinformatics Lab, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Yusuf I Ali
- Bioinformatics Lab, School of Life Sciences, University of SussexFalmerUnited Kingdom
- Sussex Drug Discovery Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Charlotte EL Fisher
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Raquel Arribas-Bosacoma
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Mohan B Rajasekaran
- Sussex Drug Discovery Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Gareth Williams
- Sussex Drug Discovery Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Sarah Walker
- Sussex Drug Discovery Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Jessica R Booth
- Sussex Drug Discovery Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Jessica JR Hudson
- Sussex Drug Discovery Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - S Mark Roe
- School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Simon E Ward
- Sussex Drug Discovery Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
- Medicines Discovery Institute, Park Place, Cardiff UniversityCardiffUnited Kingdom
| | - Frances MG Pearl
- Bioinformatics Lab, School of Life Sciences, University of SussexFalmerUnited Kingdom
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of SussexFalmerUnited Kingdom
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Ahamad N, Khan S, Mahdi ATA, Xu YJ. Checkpoint functions of RecQ helicases at perturbed DNA replication fork. Curr Genet 2021; 67:369-82. [PMID: 33427950 DOI: 10.1007/s00294-020-01147-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 01/17/2023]
Abstract
DNA replication checkpoint is a cell signaling pathway that is activated in response to perturbed replication. Although it is crucial for maintaining genomic integrity and cell survival, the exact mechanism of the checkpoint signaling remains to be understood. Emerging evidence has shown that RecQ helicases, a large family of helicases that are conserved from bacteria to yeasts and humans, contribute to the replication checkpoint as sensors, adaptors, or regulation targets. Here, we highlight the multiple functions of RecQ helicases in the replication checkpoint in four model organisms and present additional evidence that fission yeast RecQ helicase Rqh1 may participate in the replication checkpoint as a sensor.
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50
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Abstract
In all cell types, a multi-protein machinery is required to accurately duplicate the large duplex DNA genome. This central life process requires five core replisome factors in all cellular life forms studied thus far. Unexpectedly, three of the five core replisome factors have no common ancestor between bacteria and eukaryotes. Accordingly, the replisome machines of bacteria and eukaryotes have important distinctions in the way that they are organized and function. This chapter outlines the major replication proteins that perform DNA duplication at replication forks, with particular attention to differences and similarities in the strategies used by eukaryotes and bacteria.
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Affiliation(s)
- Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, USA, 10065. .,Howard Hughes Medical Institute, The Rockefeller University, New York, USA, 10065.
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