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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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Related in: MedlinePlus

Histogram of all unique influenza A sequences grouped by expected stability of pseudoknot mutations.The stability metric is calculated as the fraction of nucleotides that are canonically paired, multiplied by the fraction of GC pairs. Above each bar is a pie chart that gives the percentage of sequences that infect a given host. Other/Mixed strains are those where the majority of sequences infected an animal from other than human, swine, or avian species; or where they could infect more than one type of host species.
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pone-0038323-g006: Histogram of all unique influenza A sequences grouped by expected stability of pseudoknot mutations.The stability metric is calculated as the fraction of nucleotides that are canonically paired, multiplied by the fraction of GC pairs. Above each bar is a pie chart that gives the percentage of sequences that infect a given host. Other/Mixed strains are those where the majority of sequences infected an animal from other than human, swine, or avian species; or where they could infect more than one type of host species.

Mentions: On average, the pseudoknot structures expected to be most stable have 18 canonical base pairs, 50% of which are GC pairs (Table S3). The structures expected to be least stable have, on average, 16 canonical base pairs and only 31% of them are GC pairs. When clustered by the fraction of GC pairs and canonical pairs, five groups are apparent (Fig. 6). The number of unique sequences that fall within each cluster follows a bell-shaped distribution (Fig. 6). The stable clusters have sequences that allow for a greater number of canonical pairs and, in particular, GC pairs. For example, across all unique sequences, positions 684 and 715 are most often UG pairs, but in the stable clusters they are primarily CG pairs. Conversely, the less stable clusters are comprised of sequences that do not allow for as many canonical and GC pairs. Positions 711 and 739, for example, most often form a GC pair; in the less stable strains, however, these positions are mostly AC pairs (Table S2). The hairpin structure metrics globally follow that of the pseudoknot (Table S3).


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)

Histogram of all unique influenza A sequences grouped by expected stability of pseudoknot mutations.The stability metric is calculated as the fraction of nucleotides that are canonically paired, multiplied by the fraction of GC pairs. Above each bar is a pie chart that gives the percentage of sequences that infect a given host. Other/Mixed strains are those where the majority of sequences infected an animal from other than human, swine, or avian species; or where they could infect more than one type of host species.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369869&req=5

pone-0038323-g006: Histogram of all unique influenza A sequences grouped by expected stability of pseudoknot mutations.The stability metric is calculated as the fraction of nucleotides that are canonically paired, multiplied by the fraction of GC pairs. Above each bar is a pie chart that gives the percentage of sequences that infect a given host. Other/Mixed strains are those where the majority of sequences infected an animal from other than human, swine, or avian species; or where they could infect more than one type of host species.
Mentions: On average, the pseudoknot structures expected to be most stable have 18 canonical base pairs, 50% of which are GC pairs (Table S3). The structures expected to be least stable have, on average, 16 canonical base pairs and only 31% of them are GC pairs. When clustered by the fraction of GC pairs and canonical pairs, five groups are apparent (Fig. 6). The number of unique sequences that fall within each cluster follows a bell-shaped distribution (Fig. 6). The stable clusters have sequences that allow for a greater number of canonical pairs and, in particular, GC pairs. For example, across all unique sequences, positions 684 and 715 are most often UG pairs, but in the stable clusters they are primarily CG pairs. Conversely, the less stable clusters are comprised of sequences that do not allow for as many canonical and GC pairs. Positions 711 and 739, for example, most often form a GC pair; in the less stable strains, however, these positions are mostly AC pairs (Table S2). The hairpin structure metrics globally follow that of the pseudoknot (Table S3).

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