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The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin.

Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH - PLoS ONE (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America.

ABSTRACT
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.

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Consensus sequence and structure.(A) PK and (B) HP. Canonical pairs are indicated with solid bars and putative non-canonical pairs with dashed lines. Stem mutations that preserve base pairing are colored green for single (consistent) point mutations and blue for double (compensatory) point mutations when they occur in five or more sequences. Mutations with implications for non-canonical pairs are indicated in grey. Potential base triples are indicated with orange dashed lines. The exact interaction between the base pair and loop residue, however, cannot be inferred from available data. Putative helical stacking is indicated with a blue dashed line.
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pone-0038323-g005: Consensus sequence and structure.(A) PK and (B) HP. Canonical pairs are indicated with solid bars and putative non-canonical pairs with dashed lines. Stem mutations that preserve base pairing are colored green for single (consistent) point mutations and blue for double (compensatory) point mutations when they occur in five or more sequences. Mutations with implications for non-canonical pairs are indicated in grey. Potential base triples are indicated with orange dashed lines. The exact interaction between the base pair and loop residue, however, cannot be inferred from available data. Putative helical stacking is indicated with a blue dashed line.

Mentions: Both conformations of the 3′ splice site are well conserved throughout the alignment of all unique Influenza A sequences. All helices are greater than 92% conserved and canonical pairing, on average, is 95% conserved (Table S2). Every helix has at least one consistent or compensatory mutation (Fig. 5). When mutations led to non-canonical pairs, they were most often CA (2.9%) or GA pairs (1.3%). These CA and GA pairs occur mainly in the middle of helices: e.g. pair 691–700 in P1, 711–739 in P2, and 720–729 in P3 (Fig. 5, Table S2). Other types of non-canonical pairs were rarely observed (Table S2).


The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin.

Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH - PLoS ONE (2012)

Consensus sequence and structure.(A) PK and (B) HP. Canonical pairs are indicated with solid bars and putative non-canonical pairs with dashed lines. Stem mutations that preserve base pairing are colored green for single (consistent) point mutations and blue for double (compensatory) point mutations when they occur in five or more sequences. Mutations with implications for non-canonical pairs are indicated in grey. Potential base triples are indicated with orange dashed lines. The exact interaction between the base pair and loop residue, however, cannot be inferred from available data. Putative helical stacking is indicated with a blue dashed line.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3369869&req=5

pone-0038323-g005: Consensus sequence and structure.(A) PK and (B) HP. Canonical pairs are indicated with solid bars and putative non-canonical pairs with dashed lines. Stem mutations that preserve base pairing are colored green for single (consistent) point mutations and blue for double (compensatory) point mutations when they occur in five or more sequences. Mutations with implications for non-canonical pairs are indicated in grey. Potential base triples are indicated with orange dashed lines. The exact interaction between the base pair and loop residue, however, cannot be inferred from available data. Putative helical stacking is indicated with a blue dashed line.
Mentions: Both conformations of the 3′ splice site are well conserved throughout the alignment of all unique Influenza A sequences. All helices are greater than 92% conserved and canonical pairing, on average, is 95% conserved (Table S2). Every helix has at least one consistent or compensatory mutation (Fig. 5). When mutations led to non-canonical pairs, they were most often CA (2.9%) or GA pairs (1.3%). These CA and GA pairs occur mainly in the middle of helices: e.g. pair 691–700 in P1, 711–739 in P2, and 720–729 in P3 (Fig. 5, Table S2). Other types of non-canonical pairs were rarely observed (Table S2).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus