title: RNA sequences and structures required for the recruitment and activity of the dengue virus polymerase.
abstract: Dengue virus RNA-dependent RNA polymerase specifically binds to the viral genome by interacting with a promoter element known as stem-loop A (SLA). Although a great deal has been learned in recent years about the function of this promoter in dengue virus-infected cells, the molecular details that explain how the SLA interacts with the polymerase to promote viral RNA synthesis remain poorly understood. Using RNA binding and polymerase activity assays, we defined two elements of the SLA that are involved in polymerase interaction and RNA synthesis. Mutations at the top of the SLA resulted in RNAs that retained the ability to bind the polymerase but impaired promoter-dependent RNA synthesis. These results indicate that protein binding to the SLA is not sufficient to induce polymerase activity and that specific nucleotides of the SLA are necessary to render an active polymerase-promoter complex for RNA synthesis. We also report that protein binding to the viral RNA induces conformational changes downstream of the promoter element. Furthermore, we found that structured RNA elements at the 3' end of the template repress dengue virus polymerase activity in the context of a fully active SLA promoter. Using assays to evaluate initiation of RNA synthesis at the viral 3'-UTR, we found that the RNA-RNA interaction mediated by 5'-3'-hybridization was able to release the silencing effect of the 3'-stem-loop structure. We propose that the long range RNA-RNA interactions in the viral genome play multiple roles during RNA synthesis. Together, we provide new molecular details about the promoter-dependent dengue virus RNA polymerase activity.
authors.affiliation: Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires 1405, Argentina.
authors.forename: Claudia V
authors.initials: CV
authors.lastname: Filomatori
authors.forename: Nestor G
authors.initials: NG
authors.lastname: Iglesias
authors.forename: Sergio M
authors.initials: SM
authors.lastname: Villordo
authors.forename: Diego E
authors.initials: DE
authors.lastname: Alvarez
authors.forename: Andrea V
authors.initials: AV
authors.lastname: Gamarnik
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D003716:Dengue Virus / Q000235:genetics*; D008780:Methyltransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016296:Mutagenesis / Q000502:physiology; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017434:Protein Structure, Tertiary; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: C096041:NS5 protein, flavivirus; D012367:RNA, Viral; D011994:Recombinant Proteins; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins; D008780:Methyltransferases; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases