title: RNA structural constraints in the evolution of the influenza A virus genome NP segment.
abstract: Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed.
authors.affiliation: Department of Viroscience, Erasmus Medical Center, The Netherlands; Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, The Netherlands;
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Gultyaev
authors.affiliation: Leiden Institute of Chemistry, Leiden University, P.O.Box 9502, 2300 RA Leiden, The Netherlands;; Current address: Illumina UK Ltd., Chesterford Research Park, Little Chesterford, Essex, UK;
authors.forename: Anton
authors.initials: A
authors.lastname: Tsyganov-Bodounov
authors.affiliation: Department of Viroscience, Erasmus Medical Center, The Netherlands.
authors.forename: Monique I J
authors.initials: MI
authors.lastname: Spronken
authors.affiliation: Department of Viroscience, Erasmus Medical Center, The Netherlands; Current address: BaseClear B.V., Einsteinweg, The Netherlands.
authors.forename: Sander
authors.initials: S
authors.lastname: van der Kooij
authors.affiliation: Department of Viroscience, Erasmus Medical Center, The Netherlands.
authors.forename: Ron A M
authors.initials: RA
authors.lastname: Fouchier
authors.affiliation: Leiden Institute of Chemistry, Leiden University, P.O.Box 9502, 2300 RA Leiden, The Netherlands;
authors.forename: René C L
authors.initials: RC
authors.lastname: Olsthoorn
mesh_terms: D000818:Animals; D004285:Dogs; D019143:Evolution, Molecular; D057809:HEK293 Cells; D006801:Humans; D009980:Influenza A virus / Q000737:chemistry / Q000235:genetics / Q000502:physiology*; D061985:Madin Darby Canine Kidney Cells; D008958:Models, Molecular; D009154:Mutation; D019590:Nucleocapsid Proteins; D059370:RNA Folding; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics*; D014758:Viral Core Proteins / Q000737:chemistry* / Q000235:genetics*; D019065:Virus Assembly
chemical_list: C048842:NP protein, Influenza A virus; D019590:Nucleocapsid Proteins; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D014758:Viral Core Proteins
keywords: RNA pseudoknot; RNA structure; influenza A virus; mutual information; negative-sense RNA viruses