title: Identification of a Conserved RNA-dependent RNA Polymerase (RdRp)-RNA Interface Required for Flaviviral Replication.
abstract: Dengue virus, an ∼10.7-kb positive-sense RNA virus, is the most common arthropod-communicated pathogen in the world. Despite dengue's clear epidemiological importance, mechanisms for its replication remain elusive. Here, we probed the entire dengue genome for interactions with viral RNA-dependent RNA polymerase (RdRp), and we identified the dominant interaction as a loop-forming ACAG motif in the 3' positive-stranded terminus, complicating the prevailing model of replication. A subset of interactions coincides with known flaviviral recombination sites inside the viral protein-coding region. Specific recognition of the RNA element occurs via an arginine patch in the C-terminal thumb domain of RdRp. We also show that the highly conserved nature of the consensus RNA motif may relate to its tolerance to various mutations in the interacting region of RdRp. Disruption of the interaction resulted in loss of viral replication ability in cells. This unique RdRp-RNA interface is found throughout flaviviruses, implying possibilities for broad disease interventions.
authors.affiliation: From the Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170 and.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Hodge
authors.affiliation: From the Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170 and.
authors.forename: Chairat
authors.initials: C
authors.lastname: Tunghirun
authors.affiliation: From the Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170 and.
authors.forename: Maliwan
authors.initials: M
authors.lastname: Kamkaew
authors.affiliation: the Department of Anatomy and.
authors.forename: Thawornchai
authors.initials: T
authors.lastname: Limjindaporn
authors.affiliation: Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
authors.forename: Pa-Thai
authors.initials: PT
authors.lastname: Yenchitsomanus
authors.affiliation: From the Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170 and sarin.chi@mahidol.ac.th.
authors.forename: Sarin
authors.initials: S
authors.lastname: Chimnaronk
mesh_terms: D003716:Dengue Virus / Q000502:physiology*; D059372:Nucleotide Motifs; D000072417:Protein Domains; D012367:RNA, Viral / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014779:Virus Replication / Q000502:physiology*
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase
keywords: RNA-dependent RNA polymerase (RdRp); dengue virus (DENV); untranslated region (UTR); viral non-structural protein (NS) 5; viral polymerase; viral protein; viral replication; virology; yeast three-hybrid (Y3H)