A NOVEL VIRAL-RNA SPECIES IN SINDBIS VIRUS-INFECTED CELLS

Sindbis virus (SIN), the type alphavirus, has been studied extensively to identify the viral cis-acting sequences and proteins involved in R NA transcription and replication. However, very little is known about how these processes are coordinated. For example, synthesis of the gen omic RNA and the subgenomic mRNA depends on the minus strand. Do these activities occur independently on different templates, or can replica tion and transcription take place simultaneously on the same template? We describe the appearance of a SIN-specific, plus-sense RNA that is intermediate in size between the genomic and subgenomic RNA species. T his 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 pr omoter. We have mapped the 3' end of RNA II to a site within the subge nomic promoter, four nucleotides before the initiation site of the sub genomic mRNA. Our results indicate that the appearance of RNA II is co rrelated with subgenomic mRNA transcription, such that strong or activ e 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 promote r. The possible origins of RNA II are discussed.