title: Influenza B virus has global ordered RNA structure in (+) and (-) strands but relatively less stable predicted RNA folding free energy than allowed by the encoded protein sequence.
abstract: BACKGROUND
  Influenza A virus contributes to seasonal epidemics and pandemics and contains Global Ordered RNA structure (GORS) in the nucleoprotein (NP), non-structural (NS), PB2, and M segments. A related virus, influenza B, is also a major annual public health threat, but unlike influenza A is very selective to human hosts. This study extends the search for GORS to influenza B.
  
  
  RESULTS
  A survey of all available influenza B sequences reveals GORS in the (+) and (-)RNAs of the NP, NS, PB2, and PB1 gene segments. The results are similar to influenza A, except GORS is observed for the M1 segment of influenza A but not for PB1. In general, the folding free energies of human-specific influenza B RNA segments are less stable than allowable by the encoded amino acid sequence. This is consistent with findings in influenza A, where human-specific influenza RNA folds are less stable than avian and swine strains.
  
  
  CONCLUSIONS
  These results reveal fundamental molecular similarities and differences between Influenza A and B and suggest a rational basis for choosing segments to target with therapeutics and for viral attenuation for live vaccines by altering RNA folding stability.
authors: Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY 14627-0216, USA. turner@chem.rochester.edu.
authors: Salvatore F
authors: SF
authors: Priore
authors: Walter N
authors: WN
authors: Moss
authors: Douglas H
authors: DH
authors: Turner
mesh_terms: D001482:Base Composition; D009980:Influenza A virus / Q000737:chemistry / Q000235:genetics; D009981:Influenza B virus / Q000737:chemistry* / Q000235:genetics; D009690:Nucleic Acid Conformation; D009698:Nucleoproteins / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding; D013816:Thermodynamics; D014763:Viral Matrix Proteins / Q000737:chemistry* / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000737:chemistry* / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: C545845:M1 matrix protein, influenza B virus; D009698:Nucleoproteins; C502893:PB2 protein, influenza virus; D014763:Viral Matrix Proteins; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins
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