Abstract
Ambisense viruses are negative-sense single-stranded RNA viruses that use a unique expression strategy. Their genome contains at least one ambisense RNA segment that carries two oppositely oriented reading frames separated by an intergenic region. It is believed that a structural RNA element within the intergenic region is involved in transcription termination. However, a general overview over the structural repertoire of ambisense intergenic regions is currently lacking. In this study we investigated the structural potential of the intergenic regions of all known ambisense viruses and compared their structural repertoire by structure-guided clustering. Intergenic regions of most ambisense viruses possess a high potential to build stable secondary structures and many viruses share common structural motifs in the intergenic regions of their ambisense segments. We demonstrate that (i) within the phylogenetic virus groups sets of conserved functional structures are present, but that (ii) between the groups conservation is low to non-existent. These results reflect a high degree of freedom to regulate ambisense transcription termination and also imply that the genetic strategy of having an ambisense RNA genome has evolved several times independently.
Highlights
Ambisense viruses comprise a subsection of the segmented negative-sense single-stranded RNA viruses
We demonstrate that the intergenic region (IGR) of most ambisense viruses have a high potential to build stable secondary structures, many of which are conserved within the phylogenetic groups, but not between them
The CDSs of PV appear to contain potentially structured regions, while their IGRs can be subdivided into three groups: i) those with no structural potential within IGRs at all (24% and 43% for v and vc, respectively), ii) those containing local optimal segments, whose maximum squared z-score (MZ) peak is lower than that of the CDSs (25% and 45% for v and vc, respectively), and iii) those containing the highest MZ peak in the entire sequence, including CDSs (51% and 12% for v and vc, respectively)
Summary
Ambisense viruses comprise a subsection of the segmented negative-sense single-stranded RNA viruses. In contrast to the genome of the purely negative-sense RNA viruses, the ambisense genome contains at least one segment with an additional positive-sense reading frame[1]. Arenaviruses and Phleboviruses infect animals and humans, while Tospoviruses and Tenuiviruses infect plants. It has been shown for some of the ambisense viruses, e.g. Arenavirus or Phleboviruses that transcription termination takes place within the IGR3–8 and it is suspected that a secondary structure element is involved in the termination process. A general overview of the structural repertoire of ambisense IGRs is lacking. Our findings imply that such structures are functional and that the ambisense coding strategy may have arisen several times independently during the evolution of segmented negative-strand RNA viruses
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