3′-coterminal subgenomic RNAs and putative cis-acting elements of Grapevine leafroll-associated virus 3 reveals ‘unique’ features of gene expression strategy in the genus Ampelovirus | Jarugula et al. Virology Journal 2010 7 180 http content 7 1 180 VIROLOGY JOURNAL RESEARCH Open Access 3 -coterminal subgenomic RNAs and putative cis-acting elements of Grapevine leafroll-associated virus 3 reveals unique features of gene expression strategy in the genus Ampelovirus Sridhar Jarugula1 Siddarame Gowda2 William O Dawson2 Rayapati A Naidu1 Abstract Background The family Closteroviridae comprises genera with monopartite genomes Closterovirus and Ampelovirus and with bipartite and tripartite genomes Crinivirus. By contrast to closteroviruses in the genera Closterovirus and Crinivirus much less is known about the molecular biology of viruses in the genus Ampelovirus although they cause serious diseases in agriculturally important perennial crops like grapevines pineapple cherries and plums. Results The gene expression and cis-acting elements of Grapevine leafroll-associated virus 3 GLRaV-3 genus Ampelovirus was examined and compared to that of other members of the family Closteroviridae. Six putative 3 -coterminal subgenomic sg RNAs were abundantly present in grapevine Vitis vinifera infected with GLRaV-3. The sgRNAs for coat protein CP p21 p20A and p20B were confirmed using gene-specific riboprobes in Northern blot analysis. The 5 -termini of sgRNAs specific to CP p21 p20A and p20B were mapped in the 18 498 nucleotide nt virus genome and their leader sequences determined to be 48 23 95 and 125 nt respectively. No conserved motifs were found around the transcription start site or in the leader sequence of these sgRNAs. The predicted secondary structure analysis of sequences around the start site failed to reveal any conserved motifs among the four sgRNAs. The GLRaV-3 isolate from Washington had a 737 nt long 5 nontranslated region NTR with a tandem repeat of 65 nt sequence and differed in sequence and predicted secondary structure with a South Africa isolate. Comparison of the dissimilar sequences of the 5 NTRs did not reveal any common
