The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin.
The 3' splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions. Native gel analysis, enzymatic/chemical structure probing, and oligonucleotide binding studies of a 63 nt fragment, containing the 3' splice site, key residues of an SF2/ASF splicing factor binding site, and a polypyrimidine tract, provide evidence for an equilibrium between pseudoknot and hairpin structures. This equilibrium is sensitive to multivalent cations, and can be forced towards the pseudoknot by addition of 5 mM cobalt hexammine. In the two conformations, the splice site and other functional elements exist in very different structural environments. In particular, the splice site is sequestered in the middle of a double helix in the pseudoknot conformation, while in the hairpin it resides in a two-by-two nucleotide internal loop. The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site.
Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America.
Walter N
WN
Moss
Lumbini I
LI
Dela-Moss
Elzbieta
E
Kierzek
Ryszard
R
Kierzek
Salvatore F
SF
Priore
Douglas H
DH
Turner
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D001717:Birds; D003035:Cobalt / Q000494:pharmacology; D009980:Influenza A virus / Q000235:genetics*; D005585:Influenza in Birds / Q000821:virology; D008969:Molecular Sequence Data; D009154:Mutation; D009687:Nuclear Proteins / Q000378:metabolism; D009690:Nucleic Acid Conformation / Q000187:drug effects; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics*; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000378:metabolism; D014763:Viral Matrix Proteins / Q000235:genetics; D000086082:Viroporin Proteins
D003035:Cobalt; D009687:Nuclear Proteins; D012322:RNA Precursors; D022821:RNA Splice Sites; D012333:RNA, Messenger; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D014763:Viral Matrix Proteins; C488937:M2 protein, Influenza A virus; D000086082:Viroporin Proteins; C032300:hexaamminecobalt(II)