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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 28 SLII GA and GA SLII 28 chimeras. Positions 104–180 were exchanged between CV-B3/28 and CV-B3/GA. 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 28 SLII GA (CV-B3/28 5′UTR with CV-B3/GA SLII). (B) 12% sequencing gel showing GA SLII 28 (CV-B3/GA 5′UTR with CV-B3/28 SLII). (C) 12% sequencing gel showing 28 SLII GA. (D) 12% sequencing gel showing GA SLII 28.
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Figure 4: Chemical probing results for 28 SLII GA and GA SLII 28 chimeras. Positions 104–180 were exchanged between CV-B3/28 and CV-B3/GA. 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 28 SLII GA (CV-B3/28 5′UTR with CV-B3/GA SLII). (B) 12% sequencing gel showing GA SLII 28 (CV-B3/GA 5′UTR with CV-B3/28 SLII). (C) 12% sequencing gel showing 28 SLII GA. (D) 12% sequencing gel showing GA SLII 28.

Mentions: To further explore the 5′UTR RNA structure of virulent and avirulent isolates, SLII (104–184) was exchanged between CV-B3/28 and CV-B3/GA to generate the chimeric constructs 28 SLII GA (CV-B3/28 5′UTR with CV-B3/GA SLII) and GA SLII 28 (CV-B3/GA 5′UTR with CV-B3/28 SLII). As found in the parent molecules, 28 SLII GA was heavily modified in the SLII region (Figure 4A and C) and GA SLII 28 was protected (Figure 4B and D). Thus, probing results for 28 SLII GA matched that of the non-chimeric CV-B3/GA SLII and probing results for GA SLII 28 matched that of the non-chimeric CV-B3/28. The other five 5′UTR structural domains in 28 SLII GA and GA SLII 28 were also analysed with chemical probing analysis and no changes occurred in the structural domains outside of SLII in either chimera (data not shown).


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 28 SLII GA and GA SLII 28 chimeras. Positions 104–180 were exchanged between CV-B3/28 and CV-B3/GA. 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 28 SLII GA (CV-B3/28 5′UTR with CV-B3/GA SLII). (B) 12% sequencing gel showing GA SLII 28 (CV-B3/GA 5′UTR with CV-B3/28 SLII). (C) 12% sequencing gel showing 28 SLII GA. (D) 12% sequencing gel showing GA SLII 28.
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Figure 4: Chemical probing results for 28 SLII GA and GA SLII 28 chimeras. Positions 104–180 were exchanged between CV-B3/28 and CV-B3/GA. 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 28 SLII GA (CV-B3/28 5′UTR with CV-B3/GA SLII). (B) 12% sequencing gel showing GA SLII 28 (CV-B3/GA 5′UTR with CV-B3/28 SLII). (C) 12% sequencing gel showing 28 SLII GA. (D) 12% sequencing gel showing GA SLII 28.
Mentions: To further explore the 5′UTR RNA structure of virulent and avirulent isolates, SLII (104–184) was exchanged between CV-B3/28 and CV-B3/GA to generate the chimeric constructs 28 SLII GA (CV-B3/28 5′UTR with CV-B3/GA SLII) and GA SLII 28 (CV-B3/GA 5′UTR with CV-B3/28 SLII). As found in the parent molecules, 28 SLII GA was heavily modified in the SLII region (Figure 4A and C) and GA SLII 28 was protected (Figure 4B and D). Thus, probing results for 28 SLII GA matched that of the non-chimeric CV-B3/GA SLII and probing results for GA SLII 28 matched that of the non-chimeric CV-B3/28. The other five 5′UTR structural domains in 28 SLII GA and GA SLII 28 were also analysed with chemical probing analysis and no changes occurred in the structural domains outside of SLII in either chimera (data not shown).

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