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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

Sequence logo showing conservation between positions 110–136 in 170 aligned 5′UTR sequences. The numbers on the x-axis correspond to nucleotide positions found in the CV-B3/28 5′UTR. Positions where the alignment shows insertions in the CV-B3/28 sequence are labelled with *. The level of conservation at each position is measured in bits on the y-axis where two bits indicate the highest level of conservation at each position.
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Figure 3: Sequence logo showing conservation between positions 110–136 in 170 aligned 5′UTR sequences. The numbers on the x-axis correspond to nucleotide positions found in the CV-B3/28 5′UTR. Positions where the alignment shows insertions in the CV-B3/28 sequence are labelled with *. The level of conservation at each position is measured in bits on the y-axis where two bits indicate the highest level of conservation at each position.

Mentions: The lack of conservation and the structural differences between CV-B3/28 and CV-B3/GA in the SLII region raised questions about this region's sequence conservation among other enteroviruses. We compared the sequence of this region in 170 diverse enteroviruses including coxsackieviruses, polioviruses and numbered enteroviruses. Representatives of Enterovirus A, Enterovirus B and Enterovirus C were included in the analysis. Only full-length genomes were included in the alignment. The genomes were aligned and the region spanning 117–127 was not conserved. This is illustrated in a sequence logo (Figure 3), where the short letters correspond to poorly conserved regions and tall letters correspond to highly conserved regions. The CV-B3/28 nucleotide position numbering is shown in the sequence logo x-axis. Interestingly, the largest single stretch of poor SLII sequence conservation corresponds to the region with the most sequence differences between CV-B3/28 and CV-B3/GA and also corresponds with the region where we detect major structural differences in the 5′UTRs.


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)

Sequence logo showing conservation between positions 110–136 in 170 aligned 5′UTR sequences. The numbers on the x-axis correspond to nucleotide positions found in the CV-B3/28 5′UTR. Positions where the alignment shows insertions in the CV-B3/28 sequence are labelled with *. The level of conservation at each position is measured in bits on the y-axis where two bits indicate the highest level of conservation at each position.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150801&req=5

Figure 3: Sequence logo showing conservation between positions 110–136 in 170 aligned 5′UTR sequences. The numbers on the x-axis correspond to nucleotide positions found in the CV-B3/28 5′UTR. Positions where the alignment shows insertions in the CV-B3/28 sequence are labelled with *. The level of conservation at each position is measured in bits on the y-axis where two bits indicate the highest level of conservation at each position.
Mentions: The lack of conservation and the structural differences between CV-B3/28 and CV-B3/GA in the SLII region raised questions about this region's sequence conservation among other enteroviruses. We compared the sequence of this region in 170 diverse enteroviruses including coxsackieviruses, polioviruses and numbered enteroviruses. Representatives of Enterovirus A, Enterovirus B and Enterovirus C were included in the analysis. Only full-length genomes were included in the alignment. The genomes were aligned and the region spanning 117–127 was not conserved. This is illustrated in a sequence logo (Figure 3), where the short letters correspond to poorly conserved regions and tall letters correspond to highly conserved regions. The CV-B3/28 nucleotide position numbering is shown in the sequence logo x-axis. Interestingly, the largest single stretch of poor SLII sequence conservation corresponds to the region with the most sequence differences between CV-B3/28 and CV-B3/GA and also corresponds with the region where we detect major structural differences in the 5′UTRs.

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