Influenza virus pseudoknot explained

Influenza pseudoknot
Width:	226px
Symbol:	PK-IAV
Rfam:	RF01099
Rna Type:	Cis-reg
Tax Domain:	Orthomyxoviridae

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]}

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

• Non-coding RNA

Notes and References

1. Gultyaev AP, Olsthoorn RC . A family of non-classical pseudoknots in influenza A and B viruses . RNA Biol . 7 . 2 . 125–129 . March 2010 . 20200490 . 10.4161/rna.7.2.11287. 2010-07-13. 1887/3631581 . free .
2. Brierley I, Pennell S, Gilbert RJ . Viral RNA pseudoknots: versatile motifs in gene expression and replication . Nat. Rev. Microbiol. . 5 . 8 . 598–610 . August 2007 . 17632571 . 10.1038/nrmicro1704 . 7096944 .
3. Pleij CW . Pseudoknots: a new motif in the RNA game . Trends Biochem. Sci. . 15 . 4 . 143–147 . April 1990 . 1692647 . 10.1016/0968-0004(90)90214-v.
4. 10.1016/S0959-440X(94)90101-5 . RNA pseudoknots . 1994 . Pleij . C. . Current Opinion in Structural Biology . 4 . 3 . 337–344. 7133496 .
5. Gultyaev AP, Heus HA, Olsthoorn RC . An RNA conformational shift in recent H5N1 influenza A viruses . Bioinformatics . 23 . 3 . 272–276 . February 2007 . 17090581 . 10.1093/bioinformatics/btl559 . free . 1887/3631595 . free .
6. Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH . 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 . March 2012 . 22685560. 10.1371/journal.pone.0038323. Lewin . Alfred. 3369869. 2012PLoSO...738323M . free .
7. Moss WN, Dela-Moss LI, Priore SF, Turner DH . The influenza A segment 7 mRNA 3' splice site pseudoknot/hairpin family. . RNA Biology . 9 . 11 . 1305–1310 . October 2012 . 23064116 . 10.4161/rna.22343 . https://archive.today/20131013155233/https://www.landesbioscience.com/journals/rnabiology/article/22343/?nocache=332531166 . dead . 2013-10-13 . 3597570 .