Dataset Information

Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus.

ABSTRACT: 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.

SUBMITTER: Salem NM

PROVIDER: S-EPMC4324725 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus.

Salem Nida' M NM Miller W Allen WA Rowhani Adib A Golino Deborah A DA Moyne Anne-Laure AL Falk Bryce W BW

Virology 20080307 2

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 f ...[more]

PMID: 18329064

Similar Datasets

Project description:Wheat (Tritium aestivum L.) production is essential for global food security. Infection of barley yellow dwarf virus-GAV (BYDV-GAV) results in wheat showing leaf yellowing and plant dwarfism symptom. To explore the molecular and ultrastructural mechanisms underlying yellow dwarf symptom formation in BYDV-GAV-infected wheat, we investigated the chloroplast ultrastructure via transmission electron microscopy (TEM), examined the contents of the virus, H?O?, and chlorophyll in Zhong8601, and studied the comparative transcriptome through microarray analyses in the susceptible wheat line Zhong8601 after virus infection. TEM images indicated that chloroplasts in BYDV-GAV-infected Zhong8601 leaf cells were fragmentized. Where thylakoids were not well developed, starch granules and plastoglobules were rare. Compared with mock-inoculated Zhong8601, chlorophyll content was markedly reduced, but the virus and H?O? contents were significantly higher in BYDV-GAV-infected Zhong8601. The transcriptomic analyses revealed that chlorophyll biosynthesis and chloroplast related transcripts, encoding chlorophyll a/b binding protein, glucose-6-phosphate/phosphate translocator 2, and glutamyl-tRNA reductase 1, were down-regulated in BYDV-GAV-infected Zhong8601. Some phytohormone signaling-related transcripts, including abscisic acid (ABA) signaling factors (phospholipase D alpha 1 and calcineurin B-like protein 9) and nine ethylene response factors, were up-regulated. Additionally, reactive oxygen species (ROS)-related genes were transcriptionally regulated in BYDV-GAV infected Zhong8601, including three up-regulated transcripts encoding germin-like proteins (promoting ROS accumulation) and four down-regulated transcripts encoding peroxides (scavenging ROS). These results clearly suggest that the yellow dwarf symptom formation is mainly attributed to reduced chlorophyll content and fragmentized chloroplasts caused by down-regulation of the chlorophyll and chloroplast biosynthesis related genes, ROS excessive accumulation, and precisely transcriptional regulation of the above-mentioned ABA and ethylene signaling- and ROS-related genes in susceptible wheat infected by BYDV-GAV.

Project description:Barley yellow dwarf viruses (BYDVs) are one of the most widespread and economically important plant viruses affecting many cereal crops. Growing resistant varieties remains the most promising approach to reduce the impact of BYDVs. A Recent RNA sequencing analysis has revealed potential genes that respond to BYDV infection in resistant barley genotypes. Together with a comprehensive review of the current knowledge on disease resistance in plants, we selected nine putative barley and wheat genes to investigate their involvement in resistance to BYDV-PAV infection. The target classes of genes were (i) nucleotide binding site (NBS) leucine-rich repeat (LRR), (ii) coiled-coil nucleotide-binding leucine-rich repeat (CC-NB-LRR), (iii) LRR receptor-like kinase (RLK), (iv) casein kinase, (v) protein kinase, (vi) protein phosphatase subunits and the transcription factors (TF) (vii) MYB TF, (viii) GRAS (gibberellic acid-insensitive (GAI), repressor of GAI (RGA) and scarecrow (SCR)), and (ix) the MADS-box TF family. Expression of genes was analysed for six genotypes with different levels of resistance. As in previous reports, the highest BYDV-PAV titre was found in the susceptible genotypes Graciosa in barley and Semper and SGS 27-02 in wheat, which contrast with the resistant genotypes PRS-3628 and Wysor of wheat and barley, respectively. Statistically significant changes in wheat show up-regulation of NBS-LRR, CC-NBS-LRR and RLK in the susceptible genotypes and down-regulation in the resistant genotypes in response to BYDV-PAV. Similar up-regulation of NBS-LRR, CC-NBS-LRR, RLK and MYB TF in response to BYDV-PAV was also observed in the susceptible barley genotypes. However, no significant changes in the expression of these genes were generally observed in the resistant barley genotypes, except for the down-regulation of RLK. Casein kinase and Protein phosphatase were up-regulated early, 10 days after inoculation (dai) in the susceptible wheat genotypes, while the latter was down-regulated at 30 dai in resistant genotypes. Protein kinase was down-regulated both earlier (10 dai) and later (30 dai) in the susceptible wheat genotypes, but only in the later dai in the resistant genotypes. In contrast, GRAS TF and MYB TF were up-regulated in the susceptible wheat genotypes while no significant differences in MADS TF expression was observed. Protein kinase, Casein kinase (30 dai), MYB TF and GRAS TF (10 dai) were all up-regulated in the susceptible barley genotypes. However, no significant differences were found between the resistant and susceptible barley genotypes for the Protein phosphatase and MADS FT genes. Overall, our results showed a clear differentiation of gene expression patterns in both resistant and susceptible genotypes of wheat and barley. Therefore, further research on RLK, NBS-LRR, CC-NBS-LRR, GRAS TF and MYB TF can lead to BYDV-PAV resistance in cereals.

Dataset Information

Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus.

Publications

Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets