Co-evolving pairs of complementary nucleotide sequence regions as candidates for bundling signals in viruses with segmented genomes

Publication date: June 2018Source: Meta Gene, Volume 16Author(s): Yoshiyuki SuzukiAbstractSome of RNA viruses with segmented genomes are believed to undergo selective packaging, in which one copy of each genomic segment is incorporated into a virion. The selective packaging is thought to be mediated by supra-molecular complex formation of genomic RNA segments through inter-segmental base pairing of complementary nucleotide sequence regions termed the bundling signal. Here the nucleotide sequences of 10 genomic segments (large: L1, L2, and L3; medium: M1, M2, and M3; and small: S1, S2, S3, and S4) for 29 avian (ARV) and 8 pteropine (PRV) orthoreovirus isolates were analyzed to identify co-evolving pairs of complementary nucleotide sequence regions within and between genomic segments. The co-evolving pairs within and between genomic segments were predicted to be involved in intra-segmental and inter-segmental interactions, respectively. One co-evolving pair each was identified within M1 and S3, and both pairs indeed tended to constitute stems in the intra-segmental RNA secondary structures. In addition, one co-evolving pair each was identified between S3 and S4, L2 and S4, and L3 and M1, and the co-evolving pair between S3 and S4 tended to constitute loops in the intra-segmental RNA secondary structures. The co-evolving pair identified between S3 and S4 was considered as a candidate for the bundling signal in ARV and PRV.
Source: Meta Gene - Category: Genetics & Stem Cells Source Type: research
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