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Influenza virus pseudoknot

FieldValue
NameInfluenza pseudoknot
imageConsensus secondary structure of the Influenza Pseudoknot family of RNA motifs.png
width226px
captionThe consensus secondary structure of the Influenza pseudoknot family of RNA motifs
SymbolPK-IAV
RfamRF01099
RNA_typeCis-reg
Tax_domainOrthomyxoviridae;

The Influenza virus pseudoknot is an RNA pseudoknot structure formed in one of the non-structural coding segments (NS) of influenza virus genome. Pseudoknots are commonly found in viral genomes, especially RNA viruses, where they incorporate an RNA splice site and can have a wide range of functions. The orientation of the coaxially stacked stems in the influenza pseudoknot, however, differs from the most common topology in "classical" RNA pseudoknots.

The pseudoknot structure is very similar in influenzavirus A and influenzavirus B. A unique point mutation occurring in the strains of influenza A virus subtype H5N1 after 2001 has been suggested to result in RNA conformational shift, favouring an alternative hairpin structure instead of the pseudoknot.

Another pseudoknot occurs at the Influenza A Segment 7 Splice Site, which is used to produce the important viral M2 ion channel protein. Both pseudoknots have the possibility of alternating between hairpin loop and pseudoknot conformations, which place splicing regulatory motifs in different structural contexts.

References

References

  1. (March 2010). "A family of non-classical pseudoknots in influenza A and B viruses". RNA Biol.
  2. (August 2007). "Viral RNA pseudoknots: versatile motifs in gene expression and replication". Nat. Rev. Microbiol..
  3. Pleij CW. (April 1990). "Pseudoknots: a new motif in the RNA game". Trends Biochem. Sci..
  4. (1994). "RNA pseudoknots". Current Opinion in Structural Biology.
  5. (February 2007). "An RNA conformational shift in recent H5N1 influenza A viruses". Bioinformatics.
  6. (March 2012). "The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin.". PLOS ONE.
  7. (October 2012). "The influenza A segment 7 mRNA 3' splice site pseudoknot/hairpin family.". RNA Biology.
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non-coding-rna cis-regulatory-rna-elements
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