3
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Ivanov A, Ramanathan P, Parry C, Ilinykh PA, Lin X, Petukhov M, Obukhov Y, Ammosova T, Amarasinghe GK, Bukreyev A, Nekhai S. Global phosphoproteomic analysis of Ebola virions reveals a novel role for VP35 phosphorylation-dependent regulation of genome transcription. Cell Mol Life Sci 2020; 77:2579-2603. [PMID: 31562565 PMCID: PMC7101265 DOI: 10.1007/s00018-019-03303-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/26/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022]
Abstract
Ebola virus (EBOV) causes severe human disease with a high case fatality rate. The balance of evidence implies that the virus circulates in bats. The molecular basis for host-viral interactions, including the role for phosphorylation during infections, is largely undescribed. To address this, and to better understand the biology of EBOV, the phosphorylation of EBOV proteins was analyzed in virions purified from infected monkey Vero-E6 cells and bat EpoNi/22.1 cells using high-resolution mass spectrometry. All EBOV structural proteins were detected with high coverage, along with phosphopeptides. Phosphorylation sites were identified in all viral structural proteins. Comparison of EBOV protein phosphorylation in monkey and bat cells showed only partial overlap of phosphorylation sites, with shared sites found in NP, VP35, and VP24 proteins, and no common sites in the other proteins. Three-dimensional structural models were built for NP, VP35, VP40, GP, VP30 and VP24 proteins using available crystal structures or by de novo structure prediction to elucidate the potential role of the phosphorylation sites. Phosphorylation of one of the identified sites in VP35, Thr-210, was demonstrated to govern the transcriptional activity of the EBOV polymerase complex. Thr-210 phosphorylation was also shown to be important for VP35 interaction with NP. This is the first study to compare phosphorylation of all EBOV virion proteins produced in primate versus bat cells, and to demonstrate the role of VP35 phosphorylation in the viral life cycle. The results uncover a novel mechanism of EBOV transcription and identify novel targets for antiviral drug development.
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Affiliation(s)
- Andrey Ivanov
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
| | - Palaniappan Ramanathan
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA
| | - Christian Parry
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- Department of Microbiology, Howard University, Washington, D.C., 20059, USA
| | - Philipp A Ilinykh
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA
| | - Xionghao Lin
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- College of Dentistry, Howard University, Washington, D.C., 20059, USA
| | - Michael Petukhov
- Division of Molecular and Radiation Biophysics, Russian Nuclear Physics Institute Named After B. P. Konstantinov, National Research Center "Kurchatov Institute", Gatchina, 188300, Russia
- Russian Scientific Center of Radiology and Surgical Technologies Named After A. M. Granov, St. Petersburg, 197758, Russia
| | - Yuri Obukhov
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
| | - Tatiana Ammosova
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA
- Department of Medicine, Howard University, Washington, D.C., 20059, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
- Department of Microbiology and Immunology, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
- Galveston National Laboratory, University of Texas, Medical Branch at Galveston, 301 University Boulevard, Galveston, TX, 77574-0609, USA.
| | - Sergei Nekhai
- Center for Sickle Cell Disease, Howard University, 2201 Georgia Ave., N.W., Suite 321D, Washington, D.C., 20059, USA.
- Department of Microbiology, Howard University, Washington, D.C., 20059, USA.
- Department of Medicine, Howard University, Washington, D.C., 20059, USA.
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10
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Kuhn JH, Andersen KG, Bào Y, Bavari S, Becker S, Bennett RS, Bergman NH, Blinkova O, Bradfute S, Brister JR, Bukreyev A, Chandran K, Chepurnov AA, Davey RA, Dietzgen RG, Doggett NA, Dolnik O, Dye JM, Enterlein S, Fenimore PW, Formenty P, Freiberg AN, Garry RF, Garza NL, Gire SK, Gonzalez JP, Griffiths A, Happi CT, Hensley LE, Herbert AS, Hevey MC, Hoenen T, Honko AN, Ignatyev GM, Jahrling PB, Johnson JC, Johnson KM, Kindrachuk J, Klenk HD, Kobinger G, Kochel TJ, Lackemeyer MG, Lackner DF, Leroy EM, Lever MS, Mühlberger E, Netesov SV, Olinger GG, Omilabu SA, Palacios G, Panchal RG, Park DJ, Patterson JL, Paweska JT, Peters CJ, Pettitt J, Pitt L, Radoshitzky SR, Ryabchikova EI, Saphire EO, Sabeti PC, Sealfon R, Shestopalov AM, Smither SJ, Sullivan NJ, Swanepoel R, Takada A, Towner JS, van der Groen G, Volchkov VE, Volchkova VA, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST. Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names. Viruses 2014; 6:3663-82. [PMID: 25256396 PMCID: PMC4189044 DOI: 10.3390/v6093663] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022] Open
Abstract
Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information's (NCBI's) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Kristian G Andersen
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany.
| | - Richard S Bennett
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA.
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA.
| | - Olga Blinkova
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | | | - J Rodney Brister
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Alexander Bukreyev
- Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Alexander A Chepurnov
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Robert A Davey
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Ralf G Dietzgen
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Norman A Doggett
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Olga Dolnik
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany.
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Sven Enterlein
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Paul W Fenimore
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Pierre Formenty
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Alexander N Freiberg
- Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Robert F Garry
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Nicole L Garza
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Stephen K Gire
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Jean-Paul Gonzalez
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. :
| | - Anthony Griffiths
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Christian T Happi
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Andrew S Herbert
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Michael C Hevey
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA.
| | - Thomas Hoenen
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Anna N Honko
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Georgy M Ignatyev
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Peter B Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Joshua C Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Karl M Johnson
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Jason Kindrachuk
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Hans-Dieter Klenk
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany.
| | - Gary Kobinger
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Tadeusz J Kochel
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA.
| | - Matthew G Lackemeyer
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Daniel F Lackner
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA.
| | - Eric M Leroy
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Mark S Lever
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Elke Mühlberger
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Sergey V Netesov
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Gene G Olinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Sunday A Omilabu
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Rekha G Panchal
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Daniel J Park
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Jean L Patterson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Janusz T Paweska
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Clarence J Peters
- Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - James Pettitt
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Louise Pitt
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Elena I Ryabchikova
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Erica Ollmann Saphire
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Rachel Sealfon
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | | | - Sophie J Smither
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Nancy J Sullivan
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Robert Swanepoel
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Ayato Takada
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Jonathan S Towner
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Guido van der Groen
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Viktor E Volchkov
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Valentina A Volchkova
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Victoria Wahl-Jensen
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA.
| | - Travis K Warren
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Kelly L Warfield
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Manfred Weidmann
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Stuart T Nichol
- IViral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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