Completion of the mapping of transcription start sites for the five-gene block subgenomic RNAs of Beet yellows Closterovirus and identification of putative subgenomic promoters

In the positive-senseRNAgenome of Beet yellows Closterovirus (BYV), the 3-terminal open reading frames (ORFs) 2–8 are expressed as a nested set of subgenomic (sg) RNAs. ORFs 2–6, coding for the structural and movement proteins, form a ‘five-gene block’ conserved in closteroviruses. We mapped the 5-end of the ORF 4 sgRNA, which encodes the p64 protein, at adenosine-11169 in the BYV genome. This completes the mapping of the transcription start sites for the five-gene block sgRNAs of BYV. Computer-assisted analysis of the sequences upstream of BYV ORFs 2, 3, 4, 5, and 6 revealed two conserved motifs, which might constitute the subgenomic promoter elements. These motifs are conserved in the equivalent positions upstream of three orthologous genes of Citrus tristeza Closterovirus and two orthologous genes of Beet yellow stunt Closterovirus.