Secondary structure model of the naked segment 7 influenza A virus genomic RNA.
The influenza A virus (IAV) genome comprises eight negative-sense viral (v)RNA segments. The seventh segment of the genome encodes two essential viral proteins and is specifically packaged alongside the other seven vRNAs. To gain insights into the possible roles of RNA structure both within and without virions, a secondary structure model of a naked (protein-free) segment 7 vRNA (vRNA7) has been determined using chemical mapping and thermodynamic energy minimization. The proposed structure model was validated using microarray mapping, RNase H cleavage and comparative sequence analysis. Additionally, the detailed structures of three vRNA7 fragment constructs - comprising independently folded subdomains - were determined. Much of the proposed vRNA7 structure is preserved between IAV strains, suggesting their importance in the influenza replication cycle. Possible structure rearrangements, which allow or preclude long-range RNA interactions, are also proposed.
Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Agnieszka
A
Ruszkowska
Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Elzbieta
E
Lenartowicz
Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
Walter N
WN
Moss
Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Ryszard
R
Kierzek
Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
Elzbieta
E
Kierzek
D016679:Genome, Viral / Q000235:genetics; D009980:Influenza A virus / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism*; D016914:Ribonuclease H / Q000378:metabolism; D013816:Thermodynamics
D012367:RNA, Viral; D016914:Ribonuclease H
RNA segmented genome; RNA structure; chemical probing; influenza A virus; microarray mapping