Early and late pre-mRNA processing of budgerigar fledgling disease virus 1: identification of viral RNA 5' and 3' ends and internal splice junctions.

Budgerigar fledgling disease virus 1 (BFDV-1) is the first avian polyomavirus to be identified, and it possesses uncommon structural and biological properties. Here we present an analysis of the processed viral RNAs in infected chicken embryo fibroblast cells. Two early and 18 late BFDV-1 mRNAs were defined according to their 5' ends and internal splice patterns. In the early region of the genome an incomplete splice reaction covering 195 nt is responsible for creating two mRNAs that could encode small t and large T antigens, which would be initiated from a hypothetical early promoter, PE. The late mRNA 5' ends define two putative promoter regions (PL1 and PL2), 111 nt apart in the BFDV-1 genome non-coding region. The overall splicing pattern of the late mRNAs is further complicated by an alternative splice reaction of intron 2 (deletion of either 64 nt in intron 2a or of 256 nt in intron 2b) and a splice removing intron 3 (870 nt), resulting in deletion of most of the VP2-VP3 coding region. The positions of the late mRNA 5' ends and the splicing pattern indicate the existence of two open reading frames, putatively encoding two pairs of agnoproteins, in the 5' region of several late mRNAs. These mRNAs appear to be bicistronic and to encode one of the agnoproteins together with one of the viral coat proteins.