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Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain.

Prusa J, Missak J, Kittrell J, Evans JJ, Tapprich WE - Nucleic Acids Res. (2014)

Bottom Line: Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation.Neither the parent SLII nor the remaining domains of the background 5'UTR were structurally altered by the exchange, supporting an independent mechanism of folding and function.We show that the attenuated 5'UTR lacks structure in the SLII cardiovirulence determinant.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, University of Nebraska at Omaha, Omaha, NE 68182, USA.

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Related in: MedlinePlus

Chemical probing results for CV-B3/28 and CV-B3/GA domains I and V. For all sequencing gels, arrows indicate modified positions and vertical lines between two nucleotide positions indicate that all positions between and including the positions shown are modified. Sequencing tracks indicating the nucleotide positions are labelled A, C, G and U. Tracks with chemically modified RNA are labelled (+) and tracks with unmodified RNA are labelled (−). (A) 12% sequencing gel showing CV-B3/28 domain I. (B) 12% sequencing gel showing CV-B3/GA domain I. (C) Predicted secondary structure model of CV-B3/28 domain I. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. (D) Predicted secondary structure model of CV-B3/GA. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. Enlarged nucleotide positions are substituted or inserted in CV-B3/GA. The position with the slash is deleted in CV-B3/GA. (E) 12% sequencing gel showing CV-B3/28 domain V. (F) 12% sequencing gel showing CV-B3/GA domain V. (G) Predicted secondary structure model of CV-B3/28 domain V. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. (H) Predicted secondary structure model of CV-B3/GA domain V. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. Enlarged nucleotide positions are substituted in CV-B3/GA.
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Figure 5: Chemical probing results for CV-B3/28 and CV-B3/GA domains I and V. For all sequencing gels, arrows indicate modified positions and vertical lines between two nucleotide positions indicate that all positions between and including the positions shown are modified. Sequencing tracks indicating the nucleotide positions are labelled A, C, G and U. Tracks with chemically modified RNA are labelled (+) and tracks with unmodified RNA are labelled (−). (A) 12% sequencing gel showing CV-B3/28 domain I. (B) 12% sequencing gel showing CV-B3/GA domain I. (C) Predicted secondary structure model of CV-B3/28 domain I. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. (D) Predicted secondary structure model of CV-B3/GA. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. Enlarged nucleotide positions are substituted or inserted in CV-B3/GA. The position with the slash is deleted in CV-B3/GA. (E) 12% sequencing gel showing CV-B3/28 domain V. (F) 12% sequencing gel showing CV-B3/GA domain V. (G) Predicted secondary structure model of CV-B3/28 domain V. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. (H) Predicted secondary structure model of CV-B3/GA domain V. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. Enlarged nucleotide positions are substituted in CV-B3/GA.

Mentions: The structure of domains I, II, III, IV, V and VI for both CV-B3/28 and CV-B3/GA were determined with chemical probing analysis. The chemical probing results for domain I (Figure 5A–D) and domain V (Figure 5E–H) are shown in Figure 5 as representatives of the overall comparison. No major structure differences between CV-B3/GA and CV-B3/28 were observed in domains I, III, IV, V or VI. Minor alterations were observed in the structural domains outside of SLII, however these changes were highly localized when compared to the clear differences observed in SLII.


Major alteration in coxsackievirus B3 genomic RNA structure distinguishes a virulent strain from an avirulent strain.

Prusa J, Missak J, Kittrell J, Evans JJ, Tapprich WE - Nucleic Acids Res. (2014)

Chemical probing results for CV-B3/28 and CV-B3/GA domains I and V. For all sequencing gels, arrows indicate modified positions and vertical lines between two nucleotide positions indicate that all positions between and including the positions shown are modified. Sequencing tracks indicating the nucleotide positions are labelled A, C, G and U. Tracks with chemically modified RNA are labelled (+) and tracks with unmodified RNA are labelled (−). (A) 12% sequencing gel showing CV-B3/28 domain I. (B) 12% sequencing gel showing CV-B3/GA domain I. (C) Predicted secondary structure model of CV-B3/28 domain I. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. (D) Predicted secondary structure model of CV-B3/GA. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. Enlarged nucleotide positions are substituted or inserted in CV-B3/GA. The position with the slash is deleted in CV-B3/GA. (E) 12% sequencing gel showing CV-B3/28 domain V. (F) 12% sequencing gel showing CV-B3/GA domain V. (G) Predicted secondary structure model of CV-B3/28 domain V. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. (H) Predicted secondary structure model of CV-B3/GA domain V. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. Enlarged nucleotide positions are substituted in CV-B3/GA.
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Figure 5: Chemical probing results for CV-B3/28 and CV-B3/GA domains I and V. For all sequencing gels, arrows indicate modified positions and vertical lines between two nucleotide positions indicate that all positions between and including the positions shown are modified. Sequencing tracks indicating the nucleotide positions are labelled A, C, G and U. Tracks with chemically modified RNA are labelled (+) and tracks with unmodified RNA are labelled (−). (A) 12% sequencing gel showing CV-B3/28 domain I. (B) 12% sequencing gel showing CV-B3/GA domain I. (C) Predicted secondary structure model of CV-B3/28 domain I. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. (D) Predicted secondary structure model of CV-B3/GA. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. Enlarged nucleotide positions are substituted or inserted in CV-B3/GA. The position with the slash is deleted in CV-B3/GA. (E) 12% sequencing gel showing CV-B3/28 domain V. (F) 12% sequencing gel showing CV-B3/GA domain V. (G) Predicted secondary structure model of CV-B3/28 domain V. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. (H) Predicted secondary structure model of CV-B3/GA domain V. Modified positions are indicated with a circle. Closed circles indicate heavily modified positions and open circles indicate moderately modified positions. Enlarged nucleotide positions are substituted in CV-B3/GA.
Mentions: The structure of domains I, II, III, IV, V and VI for both CV-B3/28 and CV-B3/GA were determined with chemical probing analysis. The chemical probing results for domain I (Figure 5A–D) and domain V (Figure 5E–H) are shown in Figure 5 as representatives of the overall comparison. No major structure differences between CV-B3/GA and CV-B3/28 were observed in domains I, III, IV, V or VI. Minor alterations were observed in the structural domains outside of SLII, however these changes were highly localized when compared to the clear differences observed in SLII.

Bottom Line: Comparative sequence analysis of 170 closely related enteroviruses revealed that the SLII region lacks conservation.Neither the parent SLII nor the remaining domains of the background 5'UTR were structurally altered by the exchange, supporting an independent mechanism of folding and function.We show that the attenuated 5'UTR lacks structure in the SLII cardiovirulence determinant.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, University of Nebraska at Omaha, Omaha, NE 68182, USA.

Show MeSH
Related in: MedlinePlus