Publication Type:Journal Article
Source:Virology, Volume 375, Number 2, p.354-60 (2008)
ISBN:0042-6822 (Print)<br/>0042-6822 (Linking)
Keywords:3' Untranslated Regions/genetics, 5' Untranslated Regions/genetics, Base Sequence, Gene Expression, Genome, Viral, Luteovirus/ genetics, Molecular Sequence Data, Nucleic Acid Conformation, Open Reading Frames/genetics, Phylogeny, Plant Bark/virology, Plant Diseases/virology, RNA Replicase/genetics/metabolism, RNA, Viral/ genetics, Rosa/virology, Satellite Viruses/ genetics, Sequence Analysis, RNA
We determined the complete nucleotide sequence of the Rose spring dwarf-associated virus (RSDaV) genomic RNA (GenBank accession no. EU024678) and compared its predicted RNA structural characteristics affecting gene expression. A cDNA library was derived from RSDaV double-stranded RNAs (dsRNAs) purified from infected tissue. Nucleotide sequence analysis of the cloned cDNAs, plus for clones generated by 5'- and 3'-RACE showed the RSDaV genomic RNA to be 5808 nucleotides. The genomic RNA contains five major open reading frames (ORFs), and three small ORFs in the 3'-terminal 800 nucleotides, typical for viruses of genus Luteovirus in the family Luteoviridae. Northern blot hybridization analysis revealed the genomic RNA and two prominent subgenomic RNAs of approximately 3 kb and 1 kb. Putative 5' ends of the sgRNAs were predicted by identification of conserved sequences and secondary structures which resembled the Barley yellow dwarf virus (BYDV) genomic RNA 5' end and subgenomic RNA promoter sequences. Secondary structures of the BYDV-like ribosomal frameshift elements and cap-independent translation elements, including long-distance base pairing spanning four kb were identified. These contain similarities but also informative differences with the BYDV structures, including a strikingly different structure predicted for the 3' cap-independent translation element. These analyses of the RSDaV genomic RNA show more complexity for the RNA structural elements for members of the Luteoviridae.
Salem, Nida' M<br/>Miller, W Allen<br/>Rowhani, Adib<br/>Golino, Deborah A<br/>Moyne, Anne-Laure<br/>Falk, Bryce W<br/>GM 067104/GM/NIGMS NIH HHS/United States<br/>R01 GM067104/GM/NIGMS NIH HHS/United States<br/>R56 GM067104/GM/NIGMS NIH HHS/United States<br/>R56 GM067104-05/GM/NIGMS NIH HHS/United States<br/>Research Support, N.I.H., Extramural<br/>Research Support, Non-U.S. Gov't<br/>Research Support, U.S. Gov't, Non-P.H.S.<br/>United States<br/>Virology. 2008 Jun 5;375(2):354-60. doi: 10.1016/j.virol.2008.01.035. Epub 2008 Mar 7.