Tospovirus ambisense genomic RNA segments use almost complete repertoire of stable tetraloops in the intergenic region

Abstract

Summary: The intergenic regions of the ambisense RNA segments of viruses from the Tospovirus genus form large extended RNA structures that regulate virus replication. Using comparative structure analysis, we show the presence of conserved alternative conformations at the apical parts of these structures. In one conformation, a branched Y-shape, the 5 0 -proximal hairpin arms are mostly capped by exceptionally stable tetraloop motifs. The tetraloop hairpins are folded in both virus and virus-complementary sense RNAs, and different tetraloops can functionally replace each other. Folding simulations show that the branched Y-shape structures can undergo a conformational transition to alternative extended rod-like conformations. Functional importance of both alternatives is supported by nucleotide covariations. The balanced equilibrium between alternative structures is evidenced by native gel electrophoresis of mutant RNA transcripts with shifted equilibria. The tetraloops play a role in the stability and dynamics of structures but may also be recognized by proteins involved in translation and/or replication.

Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops

“…As noted above, the Z-turn GAAA loop capping helix 35a in the 50S of Haloarcula marismortui could exchange with YNMG sequences. Further, convincing evidence of sequence exchange that leads to similar folds has been reported in studies of viral RNA hairpins (Melchers et al 2006;Liu et al 2009;Zoll et al 2011;Clabbers et al 2014;Prostova et al 2015).…”

Iris yellow spot virus (Tospovirus: Bunyaviridae): from obscurity to research priority

“…Both coding ORFs of S and M RNA are separated by intergenic regions rich in A and U residues with potential for internal pairing, and are probably involved in transcription termination of the subgenomic RNAs (http://onlinelibrary.wiley.com/doi/10.1111/mpp.12177/suppinfo) (Adkins, ; Nichol et al ., ). The tetraloop motif is speculated to determine the binding of translation factors or other proteins (Clabbers et al ., ).…”

“…S3B) (Adkins, 2000;Nichol et al, 2005). The tetraloop motif is speculated to determine the binding of translation factors or other proteins (Clabbers et al, 2014).…”

Sequence analysis of Indian iris yellow spot virus ambisense genome segments: evidence of interspecies RNA recombination

“…The IGRs of IYSV and other tospoviruses likely contain extensive secondary structure [5], and it is possible that these structures predispose these genome regions to recombination [24]. Alternatively, it is also possible that natural selection specifically favors recombination events that fall either outside of, or on the periphery of, coding region sequences.…”

“…The genome of IYSV is tripartite, composed of three RNA segments: the small RNA (S-RNA), medium RNA (M-RNA) and large RNA (L-RNA). The L-RNA segment has a negative-sense orientation, while the M-and S-RNAs both have an ambisense orientation [5]. L-RNA encodes an RNA-dependent RNA polymerase (RdRp) [1].…”