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...

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Bibliographic Details
Published in:PloS one 2012-06, Vol.7 (6), p.e38323
Main Authors: Moss, Walter N, Dela-Moss, Lumbini I, Kierzek, Elzbieta, Kierzek, Ryszard, Priore, Salvatore F, Turner, Douglas H
Format: Article
Language:English
Subjects:
Acids
Analysis
Animals
Bacillus subtilis
Base Sequence
Binding sites
Binding Sites - genetics
Biochemistry
Biology
Birds
Cations
Chemistry
Cobalt
Cobalt - pharmacology
Equilibrium
Genomes
Influenza
Influenza A
Influenza A virus - genetics
Influenza in Birds - virology
Medicine
Messenger RNA
Molecular Sequence Data
mRNA
Mutation
Nuclear Proteins - metabolism
Nucleic Acid Conformation - drug effects
Oligonucleotides
Proteins
RNA Precursors - chemistry
RNA Precursors - genetics
RNA Splice Sites - genetics
RNA Splicing
RNA, Messenger - chemistry
RNA, Messenger - genetics
RNA, Viral - chemistry
RNA, Viral - genetics
RNA-Binding Proteins - metabolism
Splicing factors
Viral Matrix Proteins - genetics
Virions
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0038323