Regulatory activity of distal and core RNA elements in tombusvirus subgenomic mRNA2 transcription

Positive-strand RNA viruses that encode multiple cistrons often mediate exp ression of T-encoded open reading frames via RNA-templated transcription of subgenomic (sg) mRNAs. Tomato bushy stunt virus (TBSV) is a positive-stran d RNA virus that transcribes two such sg mRNAs during infections. We have p reviously identified a distal element (DE), located similar to 1100 nucleot ides upstream from the initiation site of sg mRNA2 transcription, part of w hich must base pair with a portion of a core element (CE), located just 5' to the initiation site, for efficient transcription to occur (Zhang, G., Sl owinski, V., and White, K. A (1999) RNA 5, 550-561). Here we have analyzed further this long distance RNA-RNA interaction and have investigated the re gulatory roles of other subelements within the DE and CE. Our results indic ate that M the functional base-pairing interaction between these elements o ccurs in the positive strand and that the interaction likely acts to proper ly position other subelements, (ii) two previously undefined subelements wi thin the DE and CE are important and essential, respectively, for efficient sg mRNA2 accumulation, and (iii) the production of (-)-strand sg mRNA2 can be uncoupled from the synthesis of its (+)-strand complement. These data p rovide important insight into the mechanism of sg mRNA2 transcription.