Influenza virus pseudoknot

The Influenza virus pseudoknot is an RNA pseudoknot structure formed in one of the non-structural coding segments (NS) of influenza virus genome.[1] 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.[2] The orientation of the coaxially stacked stems in the influenza pseudoknot, however, differs from the most common topology in "classical" RNA pseudoknots.[3][4]

Influenza pseudoknot
The consensus secondary structure of the Influenza pseudoknot family of RNA motifs
Identifiers
SymbolPK-IAV
RfamRF01099
Other data
RNA typeCis-reg
Domain(s)Orthomyxoviridae;
PDB structuresPDBe

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,[5] favouring an alternative hairpin structure instead of the pseudoknot.[1]

Another pseudoknot occurs at the Influenza A Segment 7 Splice Site, which is used to produce the important viral M2 ion channel protein.[6][7] Both pseudoknots have the possibility of alternating between hairpin loop and pseudoknot conformations, which place splicing regulatory motifs in different structural contexts.

See also

References
  1. Gultyaev AP, Olsthoorn RC (March 2010). "A family of non-classical pseudoknots in influenza A and B viruses". RNA Biol. 7 (2): 125–129. doi:10.4161/rna.7.2.11287. PMID 20200490. Retrieved 2010-07-13.
  2. Brierley I, Pennell S, Gilbert RJ (August 2007). "Viral RNA pseudoknots: versatile motifs in gene expression and replication". Nat. Rev. Microbiol. 5 (8): 598–610. doi:10.1038/nrmicro1704. PMC 7096944. PMID 17632571.
  3. Pleij CW (April 1990). "Pseudoknots: a new motif in the RNA game". Trends Biochem. Sci. 15 (4): 143–147. doi:10.1016/0968-0004(90)90214-v. PMID 1692647.
  4. Pleij, C. (1994). "RNA pseudoknots". Current Opinion in Structural Biology. 4 (3): 337–344. doi:10.1016/S0959-440X(94)90101-5. PMC 7133496.
  5. Gultyaev AP, Heus HA, Olsthoorn RC (February 2007). "An RNA conformational shift in recent H5N1 influenza A viruses". Bioinformatics. 23 (3): 272–276. doi:10.1093/bioinformatics/btl559. PMID 17090581.
  6. Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH (March 2012). Lewin A (ed.). "The 3′ Splice Site of Influenza A Segment 7 mRNA Can Exist in Two Conformations: A Pseudoknot and a Hairpin". PLOS ONE. 7 (6): e38323. Bibcode:2012PLoSO...738323M. doi:10.1371/journal.pone.0038323. PMC 3369869. PMID 22685560.
  7. Moss WN, Dela-Moss LI, Priore SF, Turner DH (October 2012). "The influenza A segment 7 mRNA 3' splice site pseudoknot/hairpin family". RNA Biology. 9 (11): 1305–1310. doi:10.4161/rna.22343. PMC 3597570. PMID 23064116. Archived from the original on 2013-10-13.
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