Protonatable Hairpins Are Conserved in the 5'-Untranslated Region of Tymovirus RNAs

Abstract

The secondary structures of the 5'-untranslated region (5'-UTR) of five different tymoviruses have been determined by structure probing, computer prediction and sequence comparison. Despite large sequence differences, there are remarkable similarities in the secondary structure. In all viruses two or four hairpins are found, most of which contain a symmetrical internal loop consisting of adjacent C-C or C-A mismatches. Since it is known that such mismatches can be protonated and protonated cytosines play an important role in RNA-protein interactions in tymoviral virions, the influence of pH on the conformation of the internal loop was studied. UV melting experiments and 1-dimensional proton NMR at varying pH values and salt concentrations confirm that the hairpins can be protonated under relatively mild conditions. The hairpin found in the 5'-UTR of erysimum latent virus, which has an asymmetrical internal loop consisting of cytosines and uridines, shows comparable behaviour. It is concluded that all tymoviral RNAs contain protonatable hairpins in the 5'-UTR. Binding experiments with empty viral capsids, however, do not yet establish a role in capsid protein binding.

Genomic and biological characterization of chiltepín yellow mosaic virus, a new tymovirus infecting Capsicum annuum var. aviculare in Mexico

“…The 5'-UTR of all the previously described species can be folded in a series of hairpins, three in most species, with protonable internal loops consisting in C-C and C-U mismatches [29,44]. Important functional roles in encapsidation, translation and viral accumulation have been assigned to these hairpins [45].…”

Characterization of a Replication Element in the Coat Protein ORF of Turnip Yellow Mosaic Virus

“…5'-UTR of TYMV gRNA has two hairpin structures, which had been implicated both in replication and encapsidation of viral RNA. Two hairpins present in TYMV 5'-UTR contain a symmetrical internal loop consisting of C-C or C-A mismatches (9).…”

Role of 5'-UTR hairpins of the Turnip yellow mosaic virus RNA in replication and systemic movement

“…Despite large sequence differences, Hellendoorn et al (4) observed remarkable similarity among tymoviruses in the secondary structures of their 5' untranslated regions (5'-UTR), which contain a symmetrical internal loop consisting of C-C or C-A mismatches. Hairpin structures containing the mismatches were reported to become more stable at low pH by C-C and C-A base pairing due to protonated C residues (4,5).…”

“…Hairpin structures containing the mismatches were reported to become more stable at low pH by C-C and C-A base pairing due to protonated C residues (4,5). TYMV gRNA has two such hairpin structures in its 5'-UTR, which were reported to be essential for replication and long-distance systemic movement; lack of the 5'-UTR hairpins resulted in significantly reduced disease symptoms and deficient viral spread (6).…”