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. 2010 Oct;41(2):181-91.
doi: 10.1007/s11262-010-0512-5. Epub 2010 Jul 17.

Correlation between recombination junctions and RNA secondary structure elements in poliovirus Sabin strains

Evaggelos Dedepsidis  1 , Zaharoula Kyriakopoulou, Vaia Pliaka, Panayotis Markoulatos
Affiliations

Correlation between recombination junctions and RNA secondary structure elements in poliovirus Sabin strains

Evaggelos Dedepsidis et al. Virus Genes. 2010 Oct.

Abstract

In order to test the hypothesis that RNA structural elements promote the distribution of certain types of recombination junctions in each one of the 2C and 3D poliovirus genomic regions (Sabin 3/Sabin 2 or Sabin 1 in 2C and Sabin 2/Sabin 1 or Sabin 3 in 3D), we searched in 2C and 3D regions of reference Sabin strains for high probability RNA structural elements that could promote recombination. Recombination junctions that were identified in clinical strains of this study, as well as in clinical strains of previous studies, were superimposed on RNA secondary structure models of 2C and 3D genomic regions. Furthermore, we created an in vitro model, based on double infection of cell-culture with two poliovirus strains, for the production and identification of recombinant Sabin strains in 2C and 3D regions. Our intention was to compare the results that refer to the correlation of recombination junctions and RNA secondary structures in 2C and 3D regions of clinical strains, with the respective results of the in vitro model. Most of the recombination junctions of the clinical strains were correlated with RNA secondary structure elements, which were identical between recombining Sabin strains, and also presented high predictive value. In consensus were, the respective results originated from the in vitro model. We propose that the distribution of specific types of recombination junctions in certain regions of Sabin strains is not fortuitous and is correlated with RNA secondary structure elements identical to both recombination partners. Furthermore, results of this study highlight an important role for the stem region of the RNA structure elements in promoting recombination.

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Figures

Fig. 1
Fig. 1
a Schematic representation of the recombinant genomes of C6, C7, and C9 clinical isolates of this study. Accession numbers EU598486, EU598488, and EU598487, respectively. b Schematic representation of the recombinant genomes of V1, V2, V3, V4, V5, and V6 isolates, generated from the cell-culture in vitro model used in this study
Fig. 2
Fig. 2
Representation of recombination junctions of isolates D6, EPA, EPB, EPC, C9, and D5 in RNA secondary structure elements of 2C genomic region of Sabin 2 and Sabin 3 reference strains
Fig. 3
Fig. 3
Representation of recombination junctions of isolates IM, D18, and C6 in RNA secondary structure elements of 3D genomic region of Sabin 1 and Sabin 2 reference strains
Fig. 4
Fig. 4
Representation of the proposed modified model for the mechanism of RNA recombination in poliovirus. a High probability RNA secondary structure elements identical between the recombining molecules. b Formation of the heteroduplex in regions which have the potential to form high probability RNA secondary structure elements identical between the two recombining partners. c Detachment of the negative nascent strand from the template genome. d Attachment of the negative nascent strand to another template genome
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