A novel viral RNA species in Sindbis virus-infected cells
Journal of Virology
Sindbis virus (SIN), the type alphavirus, has been studied extensively to identify the viral cis-acting sequences and proteins involved in RNA transcription and replication. However, very little is known about how these processes are coordinated. For example, synthesis of the genomic RNA and the subgenomic mRNA depends on the minus strand. Do these activities occur independently on different templates, or can replication and transcription take place simultaneously on the same template? We
... template? We describe the appearance of a SINspecific, plus-sense RNA that is intermediate in size between the genomic and subgenomic RNA species. This RNA, designated RNA II, is observed in a number of different cell lines, both early and late in infection. The number of RNA II species, their sizes, and their abundances are influenced by the subgenomic promoter. We have mapped the 3 end of RNA II to a site within the subgenomic promoter, four nucleotides before the initiation site of the subgenomic mRNA. Our results indicate that the appearance of RNA II is correlated with subgenomic mRNA transcription, such that strong or active promoters tend to increase the abundance of RNA II, relative to weak or less active promoters. RNA II is most abundantly detected with the full promoter and is at much lower abundance with the minimal promoter. The possible origins of RNA II are discussed. on May 9, 2020 by guest http://jvi.asm.org/ Downloaded from a The in vivo incorporated label of each RNA species (relative to the genomic RNA of the virus) was quantitated on a Bio-Rad PhosphorImager and used to calculate the relative molar ratios shown. G refers to the genomic RNA, STR and CAT refer to the STR and CAT subgenomic RNAs, and Sm and Lg refer to the small and large RNA II species, respectively. SD, standard deviation of each RNA ratio, from n experiments. b n, number of independent experiments performed.