title: Temporal SILAC-based quantitative proteomics identifies host factors involved in chikungunya virus replication.
abstract: Chikungunya virus (CHIKV) is an arthropod-borne reemerging human pathogen that generally causes a severe persisting arthritis. Since 2005, the virus has infected millions of people during outbreaks in Africa, Indian Ocean Islands, Asia, and South/Central America. Many steps of the replication and expression of CHIKV's 12-kb RNA genome are highly dependent on cellular factors, which thus constitute potential therapeutic targets. SILAC and LC-MS/MS were used to define the temporal dynamics of the cellular response to infection. Using samples harvested at 8, 10, and 12 h postinfection, over 4700 proteins were identified and per time point 2800-3500 proteins could be quantified in both biological replicates. At 8, 10, and 12 h postinfection, 13, 38, and 106 proteins, respectively, were differentially expressed. The majority of these proteins showed decreased abundance. Most subunits of the RNA polymerase II complex were progressively degraded, which likely contributes to the transcriptional host shut-off observed during CHIKV infection. Overexpression of four proteins that were significantly downregulated (Rho family GTPase 3 (Rnd3), DEAD box helicase 56 (DDX56), polo-like kinase 1 (Plk1), and ubiquitin-conjugating enzyme E2C (UbcH10) reduced susceptibility of cells to CHIKV infection, suggesting that infection-induced downregulation of these proteins is beneficial for CHIKV replication. All MS data have been deposited in the ProteomeXchange with identifier PXD001330 (http://proteomecentral.proteomexchange.org/dataset/PXD001330).
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, The Netherlands.|Department of Immunohematology and Blood transfusion, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Emmely E
authors.initials: EE
authors.lastname: Treffers
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Ali
authors.initials: A
authors.lastname: Tas
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Florine E M
authors.initials: FE
authors.lastname: Scholte
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Myrthe N
authors.initials: MN
authors.lastname: Van
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Matthias T
authors.initials: MT
authors.lastname: Heemskerk
authors.affiliation: Department of Immunohematology and Blood transfusion, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Arnoud H
authors.initials: AH
authors.lastname: de Ru
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Snijder
authors.affiliation: Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Martijn J
authors.initials: MJ
authors.lastname: van Hemert
authors.affiliation: Department of Immunohematology and Blood transfusion, Leiden University Medical Center, ZA, Leiden, The Netherlands.
authors.forename: Peter A
authors.initials: PA
authors.lastname: van Veelen
mesh_terms: D002460:Cell Line; D002646:Chikungunya virus / Q000235:genetics / Q000502:physiology*; D006801:Humans; D008856:Microscopy, Fluorescence; D040901:Proteomics; D014764:Viral Proteins / Q000378:metabolism; D014779:Virus Replication / Q000235:genetics*
chemical_list: D014764:Viral Proteins
keywords: Alphavirus; Chikungunya virus; Microbiology; SILAC; Temporal proteomics; Virus-host interactions