RNA structural constraints in the evolution of the influenza A virus genome NP segment

A Gultyaev, A Tsyganov-Bodounov, Monique Spronken, Stephanie Kooij, Ron Fouchier, RCL Olsthoorn

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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.
Original languageUndefined/Unknown
Pages (from-to)942-952
Number of pages11
JournalRNA Biology
Volume11
Issue number7
DOIs
Publication statusPublished - 2014

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