1
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Kleiner VA, Fearns R. How does the polymerase of non-segmented negative strand RNA viruses commit to transcription or genome replication? J Virol 2024:e0033224. [PMID: 39078194 DOI: 10.1128/jvi.00332-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024] Open
Abstract
The Mononegavirales, or non-segmented negative-sense RNA viruses (nsNSVs), includes significant human pathogens, such as respiratory syncytial virus, parainfluenza virus, measles virus, Ebola virus, and rabies virus. Although these viruses differ widely in their pathogenic properties, they are united by each having a genome consisting of a single strand of negative-sense RNA. Consistent with their shared genome structure, the nsNSVs have evolved similar ways to transcribe their genome into mRNAs and replicate it to produce new genomes. Importantly, both mRNA transcription and genome replication are performed by a single virus-encoded polymerase. A fundamental and intriguing question is: how does the nsNSV polymerase commit to being either an mRNA transcriptase or a replicase? The polymerase must become committed to one process or the other either before it interacts with the genome template or in its initial interactions with the promoter sequence at the 3´ end of the genomic RNA. This review examines the biochemical, molecular biology, and structural biology data regarding the first steps of transcription and RNA replication that have been gathered over several decades for different families of nsNSVs. These findings are discussed in relation to possible models that could explain how an nsNSV polymerase initiates and commits to either transcription or genome replication.
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Affiliation(s)
- Victoria A Kleiner
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
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2
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Mili M, Bachu V, Kuri PR, Singh NK, Goswami P. Improving synthesis and binding affinities of nucleic acid aptamers and their therapeutics and diagnostic applications. Biophys Chem 2024; 309:107218. [PMID: 38547671 DOI: 10.1016/j.bpc.2024.107218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/21/2024] [Accepted: 03/17/2024] [Indexed: 04/22/2024]
Abstract
Nucleic acid aptamers have captivated the attention of analytical and medicinal scientists globally due to their several advantages as recognition molecules over conventional antibodies because of their small size, simple and inexpensive synthesis, broad target range, and high stability in varied environmental conditions. These recognition molecules can be chemically modified to make them resistant to nuclease action in blood serum, reduce rapid renel clearance, improve the target affinity and selectivity, and make them amenable to chemically conjugate with a support system that facilitates their selective applications. This review focuses on the development of efficient aptamer candidates and their application in clinical diagnosis and therapeutic applications. Significant advances have been made in aptamer-based diagnosis of infectious and non-infectious diseases. Collaterally, the progress made in therapeutic applications of aptamers is encouraging, as evident from their use in diagnosing cancer, neurodegenerative diseases, microbial infection, and in imaging. This review also updates the progress on clinical trials of many aptamer-based products of commercial interests. The key development and critical issues on the subject have been summarized in the concluding remarks.
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Affiliation(s)
- Malaya Mili
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Vinay Bachu
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | - Pooja Rani Kuri
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India
| | | | - Pranab Goswami
- Department of Biosciences and Bioengineering, IIT Guwahati, 781039, Assam, India.
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3
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Wu C, Wagner ND, Moyle AB, Feng A, Sharma N, Stubbs SH, Donahue C, Davey RA, Gross ML, Leung DW, Amarasinghe GK. Disruption of Ebola NP 0VP35 Inclusion Body-like Structures reduce Viral Infection. J Mol Biol 2023; 435:168241. [PMID: 37598728 DOI: 10.1016/j.jmb.2023.168241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023]
Abstract
Viral inclusion bodies (IBs) are potential sites of viral replication and assembly. How viral IBs form remains poorly defined. Here we describe a combined biophysical and cellular approach to identify the components necessary for IB formation during Ebola virus (EBOV) infection. We find that the eNP0VP35 complex containing Ebola nucleoprotein (eNP) and viral protein 35 (eVP35), the functional equivalents of nucleoprotein (N) and phosphoprotein (P) in non-segmented negative strand viruses (NNSVs), phase separates to form inclusion bodies. Phase separation of eNP0VP35 is reversible and modulated by ionic strength. The multivalency of eVP35, and not eNP, is also critical for phase separation. Furthermore, overexpression of an eVP35 peptide disrupts eNP0VP35 complex formation, leading to reduced frequency of IB formation and limited viral infection. Together, our results show that upon EBOV infection, the eNP0VP35 complex forms the minimum unit to drive IB formation and viral replication.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Annie Feng
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Nitin Sharma
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sarah H Stubbs
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Callie Donahue
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
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4
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Fang J, Castillon G, Phan S, McArdle S, Hariharan C, Adams A, Ellisman MH, Deniz AA, Saphire EO. Spatial and functional arrangement of Ebola virus polymerase inside phase-separated viral factories. Nat Commun 2023; 14:4159. [PMID: 37443171 PMCID: PMC10345124 DOI: 10.1038/s41467-023-39821-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Ebola virus (EBOV) infection induces the formation of membrane-less, cytoplasmic compartments termed viral factories, in which multiple viral proteins gather and coordinate viral transcription, replication, and assembly. Key to viral factory function is the recruitment of EBOV polymerase, a multifunctional machine that mediates transcription and replication of the viral RNA genome. We show that intracellularly reconstituted EBOV viral factories are biomolecular condensates, with composition-dependent internal exchange dynamics that likely facilitates viral replication. Within the viral factory, we found the EBOV polymerase clusters into foci. The distance between these foci increases when viral replication is enabled. In addition to the typical droplet-like viral factories, we report the formation of network-like viral factories during EBOV infection. Unlike droplet-like viral factories, network-like factories are inactive for EBOV nucleocapsid assembly. This unique view of EBOV propagation suggests a form-to-function relationship that describes how physical properties and internal structures of biomolecular condensates influence viral biogenesis.
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Affiliation(s)
- Jingru Fang
- La Jolla Institute for Immunology, La Jolla, CA, USA
- Scripps Research, La Jolla, CA, USA
| | - Guillaume Castillon
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, CA, USA
| | - Sara McArdle
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Aiyana Adams
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, CA, USA
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5
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Zinzula L, Mereu AM, Orsini M, Seeleitner C, Bracher A, Nagy I, Baumeister W. Ebola and Marburg virus VP35 coiled-coil validated as antiviral target by tripartite split-GFP complementation. iScience 2022; 25:105354. [PMID: 36325051 PMCID: PMC9619376 DOI: 10.1016/j.isci.2022.105354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 11/30/2022] Open
Abstract
Ebola virus (EBOV) and Marburg virus (MARV) are highly pathogenic viruses in humans, against which approved antivirals are lacking. During EBOV and MARV infection, coiled-coil mediated oligomerization is essential for the virion protein 35 (VP35) polymerase co-factor function and type I interferon antagonism, making VP35 coiled-coil an elective drug target. We established a tripartite split-green fluorescent protein (GFP) fluorescence complementation (FC) system based on recombinant GFP-tagged EBOV and MARV VP35, which probes VP35 coiled-coil assembly by monitoring fluorescence on E. coli colonies, or in vitro in 96/384-multiwell. Oligomerization-defective VP35 mutants showed that correct coiled-coil knobs-into-holes pairing within VP35 oligomer is pre-requisite for GFP tags and GFP detector to reconstitute fluorescing full-length GFP. The method was validated by screening a small compound library, which identified Myricetin and 4,5,6,7-Tetrabromobenzotriazole as inhibitors of EBOV and MARV VP35 oligomerization-dependent FC with low-micromolar IC50 values. These findings substantiate the VP35 coiled-coil value as antiviral target. Ebola and Marburg virus VP35 oligomerize via trimeric and tetrameric coiled-coil VP35 coiled-coil assembly triggers fluorescence of a tripartite split-GFP system Mutations perturbing VP35 coiled-coil hamper split-GFP complementation Myricetin and TBBT inhibit split-GFP complementation mediated by VP35 coiled-coil
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Affiliation(s)
- Luca Zinzula
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
- Corresponding author
| | - Angela Maria Mereu
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Massimiliano Orsini
- Istituto Zooprofilattico Sperimentale delle Venezie, Department of Risk Analysis and Public Health Surveillance, Viale dell’Università 10, 35020 Legnaro, Italy
| | - Christine Seeleitner
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andreas Bracher
- The Max-Planck Institute of Biochemistry, Department of Cellular Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - István Nagy
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
- Corresponding author
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6
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Wu C, Holehouse AS, Leung DW, Amarasinghe GK, Dutch RE. Liquid Phase Partitioning in Virus Replication: Observations and Opportunities. Annu Rev Virol 2022; 9:285-306. [PMID: 35709511 DOI: 10.1146/annurev-virology-093020-013659] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses frequently carry out replication in specialized compartments within cells. The effect of these structures on virus replication is poorly understood. Recent research supports phase separation as a foundational principle for organization of cellular components with the potential to influence viral replication. In this review, phase separation is described in the context of formation of viral replication centers, with an emphasis on the nonsegmented negative-strand RNA viruses. Consideration is given to the interplay between phase separation and the critical processes of viral transcription and genome replication, and the role of these regions in pathogen-host interactions is discussed. Finally, critical questions that must be addressed to fully understand how phase separation influences viral replication and the viral life cycle are presented, along with information about new approaches that could be used to make important breakthroughs in this emerging field.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Science and Engineering Living Systems, Washington University, St. Louis, Missouri, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca Ellis Dutch
- Department of Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, Lexington, Kentucky, USA;
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7
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Simanjuntak Y, Schamoni-Kast K, Grün A, Uetrecht C, Scaturro P. Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology. Viruses 2021; 13:668. [PMID: 33924391 PMCID: PMC8070632 DOI: 10.3390/v13040668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/01/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023] Open
Abstract
RNA viruses cause a wide range of human diseases that are associated with high mortality and morbidity. In the past decades, the rise of genetic-based screening methods and high-throughput sequencing approaches allowed the uncovering of unique and elusive aspects of RNA virus replication and pathogenesis at an unprecedented scale. However, viruses often hijack critical host functions or trigger pathological dysfunctions, perturbing cellular proteostasis, macromolecular complex organization or stoichiometry, and post-translational modifications. Such effects require the monitoring of proteins and proteoforms both on a global scale and at the structural level. Mass spectrometry (MS) has recently emerged as an important component of the RNA virus biology toolbox, with its potential to shed light on critical aspects of virus-host perturbations and streamline the identification of antiviral targets. Moreover, multiple novel MS tools are available to study the structure of large protein complexes, providing detailed information on the exact stoichiometry of cellular and viral protein complexes and critical mechanistic insights into their functions. Here, we review top-down and bottom-up mass spectrometry-based approaches in RNA virus biology with a special focus on the most recent developments in characterizing host responses, and their translational implications to identify novel tractable antiviral targets.
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Affiliation(s)
- Yogy Simanjuntak
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Kira Schamoni-Kast
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Alice Grün
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Pietro Scaturro
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
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8
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Crystal structure of human LC8 bound to a peptide from Ebola virus VP35. J Microbiol 2021; 59:410-416. [PMID: 33630249 DOI: 10.1007/s12275-021-0641-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
Zaire ebolavirus, commonly called Ebola virus (EBOV), is an RNA virus that causes severe hemorrhagic fever with high mortality. Viral protein 35 (VP35) is a virulence factor encoded in the EBOV genome. VP35 inhibits host innate immune responses and functions as a critical cofactor for viral RNA replication. EBOV VP35 contains a short conserved motif that interacts with dynein light chain 8 (LC8), which serves as a regulatory hub protein by associating with various LC8-binding proteins. Herein, we present the crystal structure of human LC8 bound to the peptide comprising residues 67-76 of EBOV VP35. Two VP35 peptides were found to interact with homodimeric LC8 by extending the central β-sheets, constituting a 2:2 complex. Structural analysis demonstrated that the intermolecular binding between LC8 and VP35 is mainly sustained by a network of hydrogen bonds and supported by hydrophobic interactions in which Thr73 and Thr75 of VP35 are involved. These findings were verified by binding measurements using isothermal titration calorimetry. Biochemical analyses also verified that residues 67-76 of EBOV VP35 constitute a core region for interaction with LC8. In addition, corresponding motifs from other members of the genus Ebolavirus commonly bound to LC8 but with different binding affinities. Particularly, VP35 peptides originating from pathogenic species interacted with LC8 with higher affinity than those from noninfectious species, suggesting that the binding of VP35 to LC8 is associated with the pathogenicity of the Ebolavirus species.
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9
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Shu T, Gan T, Bai P, Wang X, Qian Q, Zhou H, Cheng Q, Qiu Y, Yin L, Zhong J, Zhou X. Ebola virus VP35 has novel NTPase and helicase-like activities. Nucleic Acids Res 2019; 47:5837-5851. [PMID: 31066445 PMCID: PMC6582406 DOI: 10.1093/nar/gkz340] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/21/2019] [Accepted: 04/25/2019] [Indexed: 12/13/2022] Open
Abstract
Ebola virus (EBOV) is a non-segmented, negative-sense RNA virus (NNSV) in the family Filoviridae, and is recognized as one of the most lethal pathogens in the planet. For RNA viruses, cellular or virus-encoded RNA helicases play pivotal roles in viral life cycles by remodelling viral RNA structures and/or unwinding viral dsRNA produced during replication. However, no helicase or helicase-like activity has ever been found to associate with any NNSV-encoded proteins, and it is unknown whether the replication of NNSVs requires the participation of any viral or cellular helicase. Here, we show that despite of containing no conserved NTPase/helicase motifs, EBOV VP35 possesses the NTPase and helicase-like activities that can hydrolyse all types of NTPs and unwind RNA helices in an NTP-dependent manner, respectively. Moreover, guanidine hydrochloride, an FDA-approved compound and inhibitor of certain viral helicases, inhibited the NTPase and helicase-like activities of VP35 as well as the replication/transcription of an EBOV minigenome replicon in cells, highlighting the importance of VP35 helicase-like activity during EBOV life cycle. Together, our findings provide the first demonstration of the NTPase/helicase-like activity encoded by EBOV, and would foster our understanding of EBOV and NNSVs.
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Affiliation(s)
- Ting Shu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Tianyu Gan
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, CAS, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Bai
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiaotong Wang
- University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, Hubei 430071, China.,Wuhan National Biosafety Laboratory, Mega-Science Center for Bio-Safety Research, CAS, Wuhan, Hubei 430071, China
| | - Qi Qian
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.,State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, Hubei 430071, China.,Wuhan National Biosafety Laboratory, Mega-Science Center for Bio-Safety Research, CAS, Wuhan, Hubei 430071, China
| | - Hui Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.,State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, Hubei 430071, China.,Wuhan National Biosafety Laboratory, Mega-Science Center for Bio-Safety Research, CAS, Wuhan, Hubei 430071, China
| | - Qi Cheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yang Qiu
- University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, Hubei 430071, China.,Wuhan National Biosafety Laboratory, Mega-Science Center for Bio-Safety Research, CAS, Wuhan, Hubei 430071, China
| | - Lei Yin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Jin Zhong
- Unit of Viral Hepatitis, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, CAS, Shanghai 200031, China.,Wuhan National Biosafety Laboratory, Mega-Science Center for Bio-Safety Research, CAS, Wuhan, Hubei 430071, China
| | - Xi Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, Hubei 430071, China.,Wuhan National Biosafety Laboratory, Mega-Science Center for Bio-Safety Research, CAS, Wuhan, Hubei 430071, China
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10
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Mechanisms of Non-segmented Negative Sense RNA Viral Antagonism of Host RIG-I-Like Receptors. J Mol Biol 2019; 431:4281-4289. [PMID: 31202887 DOI: 10.1016/j.jmb.2019.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/29/2019] [Accepted: 06/05/2019] [Indexed: 12/25/2022]
Abstract
The pattern recognition receptors RIG-I-like receptors (RLRs) are critical molecules for cytosolic viral recognition and for subsequent activation of type I interferon production. The interferon signaling pathway plays a key role in viral detection and generating antiviral responses. Among the many pathogens, the non-segmented negative sense RNA viruses target the RLR pathway using a variety of mechanisms. Here, I review the current state of knowledge on the molecular mechanisms that allow non-segmented negative sense RNA virus recognition and antagonism of RLRs.
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11
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Martell HJ, Masterson SG, McGreig JE, Michaelis M, Wass MN. Is the Bombali virus pathogenic in humans? Bioinformatics 2019; 35:3553-3558. [DOI: 10.1093/bioinformatics/btz267] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/14/2019] [Accepted: 04/15/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Motivation
The potential of the Bombali virus, a novel Ebolavirus, to cause disease in humans remains unknown. We have previously identified potential determinants of Ebolavirus pathogenicity in humans by analysing the amino acid positions that are differentially conserved (specificity determining positions; SDPs) between human pathogenic Ebolaviruses and the non-pathogenic Reston virus. Here, we include the many Ebolavirus genome sequences that have since become available into our analysis and investigate the amino acid sequence of the Bombali virus proteins at the SDPs that discriminate between human pathogenic and non-human pathogenic Ebolaviruses.
Results
The use of 1408 Ebolavirus genomes (196 in the original analysis) resulted in a set of 166 SDPs (reduced from 180), 146 (88%) of which were retained from the original analysis. This indicates the robustness of our approach and refines the set of SDPs that distinguish human pathogenic Ebolaviruses from Reston virus. At SDPs, Bombali virus shared the majority of amino acids with the human pathogenic Ebolaviruses (63.25%). However, for two SDPs in VP24 (M136L, R139S) that have been proposed to be critical for the lack of Reston virus human pathogenicity because they alter the VP24-karyopherin interaction, the Bombali virus amino acids match those of Reston virus. Thus, Bombali virus may not be pathogenic in humans. Supporting this, no Bombali virus-associated disease outbreaks have been reported, although Bombali virus was isolated from fruit bats cohabitating in close contact with humans, and anti-Ebolavirus antibodies that may indicate contact with Bombali virus have been detected in humans.
Availability and implementation
Data files are available from https://github.com/wasslab/EbolavirusSDPsBioinformatics2019.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Henry J Martell
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Stuart G Masterson
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Jake E McGreig
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Martin Michaelis
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Mark N Wass
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, UK
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12
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Di Palma F, Daino GL, Ramaswamy VK, Corona A, Frau A, Fanunza E, Vargiu AV, Tramontano E, Ruggerone P. Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition. Antivir Chem Chemother 2019; 27:2040206619889220. [PMID: 31744306 PMCID: PMC6883671 DOI: 10.1177/2040206619889220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 01/10/2023] Open
Abstract
Ebola virus high lethality relies on its ability to efficiently bypass the host innate antiviral response, which senses the viral dsRNA through the RIG-I receptor and induces type I interferon α/β production. In the bypassing action, the Ebola virus protein VP35 plays a pivotal role at multiple levels of the RIG-I cascade, masking the viral 5′-triphosphorylated dsRNA from RIG-I, and interacting with other cascade components. The VP35 type I interferon inhibition is exerted by the C-terminal domain, while the N-terminal domain, containing a coiled-coil region, is primarily required for oligomerization. However, mutations at key VP35 residues L90/93/107A (VP35-3m) in the coiled-coil region were reported to affect oligomerization and reduce type I interferon antagonism, indicating a possible but unclear role of homo-oligomerization on VP35 interaction with the RIG-I pathway components. In this work, we investigated the VP35 dimerization thermodynamics and its contribution to type I interferon antagonism by computational and biological methods. Focusing on the coiled-coil region, we combined coarse-grained and all-atom simulations on wild type VP35 and VP35-3m homo-dimerization. According to our results, wild type VP35 coiled-coil is able to self-assemble into dimers, while VP35-3m coiled-coil shows poor propensity to even dimerize. Free-energy calculations confirmed the key role of L90, L93 and L107 in stabilizing the coiled-coil homo-dimeric structure. In vitro type I interferon antagonism studies, using full-length wild type VP35 and VP35-3m, revealed that VP35 homo-dimerization is an essential preliminary step for dsRNA binding, which appears to be the main factor of the VP35 RIG-I cascade inhibition, while it is not essential to block the other steps.
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Affiliation(s)
- Francesco Di Palma
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
| | - Gian Luca Daino
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | | | - Angela Corona
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Aldo Frau
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Elisa Fanunza
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale
delle Ricerche (CNR), Monserrato, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
- Istituto Officina dei Materiali (CNR-IOM), UOS Cagliari SLACS,
Monserrato, Italy
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