Evidence supporting a premature termination mechanism for subgenomic RNA transcription in Pelargonium line pattern virus: identification of a critical long-range RNA-RNA interaction and functional variants through mutagenesis

Pelargonium line pattern virus (PLPV) is a plus-strand RNA virus that has been proposed as type species of a tentative new genus, Pelarspovirus, in the family Tombusviridae. One of the singular traits of members of this prospective genus is the production of a unique subgenomic (sg) mRNA that is structurally and functionally tricistronic. Here, we have aimed to get insights into the mechanism that governs PLPV sg mRNA transcription. A long-range RNA-RNA interaction that is critical for the process has been identified through RNA folding predictions and mutational analysis of the viral genome. Such interaction seems to occur in the plus-strand, likely acts in cis, and specifically mediates the synthesis of sg RNA-sized minus-strand. The accumulation of this RNA species is easily detectable in plants and its generation can be uncoupled from that of the plus-strand sg mRNA. All these data together with the observation that 5' ends of PLPV genomic and sg mRNAs have sequence resemblances (as expected if both act as promoters in the corresponding minus-strand), support that premature termination is the mechanism underlying PLPV sg mRNA formation.We thank K. Andrew White for his kind advice on this study. This work was supported by the Ministerio de Investigacion, Ciencia e Innovacion (MICINN, Spain) and the Ministerio de Economia y Competitividad (MINECO, Spain) through grants BFU2009-11699 and BFU2012-36095, respectively, and by the Generalitat Valenciana through grant ACOMP/2012/100 (to C. H.). M. B.-P. was the recipient of predoctoral contracts from MICINN and MINECO.Blanco Pérez, M.; Hernandez Fort, C. (2016). Evidence supporting a premature termination mechanism for subgenomic RNA transcription in Pelargonium line pattern virus: identification of a critical long-range RNA-RNA interaction and functional variants through mutagenesis. Journal of General Virology. 97:1469-1480. https://doi.org/10.1099/jgv.0.000459146914809