Ontology highlight
ABSTRACT:
PROVIDER: PRJNA486675 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7718950.fastq.gz | Fastqsanger.gz | |||
| SRR7718960.fastq.gz | Fastqsanger.gz | |||
| SRR7718951.fastq.gz | Fastqsanger.gz | |||
| SRR7718961.fastq.gz | Fastqsanger.gz | |||
| SRR7718952.fastq.gz | Fastqsanger.gz |
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Project description:Using a crucifer-infecting strain of Tobacco Mosaic Virus (TMV-Cg) and Arabidopsis thaliana as a model system, we analyzed the viral small RNA profile in wild-type plants as well as rdr mutants by applying small RNA deep sequencing technology. Over 100,000 TMV-Cg-specific small RNA reads, mostly of 21- (78.4%) and 22-nucleotide (12.9%) in size and originating predominately (79.9%) from the genomic sense RNA strand, were captured at an early infection stage, yielding the first high-resolution small RNA map for a plant virus. The TMV-Cg genome harbored multiple, highly reproducible small RNA-generating hot spots that corresponded to regions with no apparent local hairpin-forming capacity. Significantly, both the rdr1 and rdr6 mutants exhibited globally reduced levels of viral small RNA production as well as reduced strand bias in viral small RNA population, revealing an important role for these host RDRs in viral siRNA biogenesis. In addition, an informatics analysis showed that a large set of host genes could be potentially targeted by TMV-Cg-derived siRNAs for posttranscriptional silencing, raising the interesting possibility for a hidden layer of widespread virus-host interactions that may contribute to viral pathogenicity and host specificity.
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Project description:Phosphorylation and O-GlcNAcylation are widespread post-translational modifications (PTMs) often sharing protein targets. Numerous studies have reported phosphorylation of plant virus proteins. In plants, research on O-GlcNAcylation lags behind regarding other eukaryotes and information about O-GlcNAcylated plant viral proteins is extremely scarce. The potyvirus Plum pox virus (PPV) causes sharka disease in Prunus trees, and also infects a wide range of experimental hosts. Capsid protein (CP) from virions of the PPV-R isolate purified from herbaceous plants can be extensively modified by O-GlcNAcylation and phosphorylation. In this study, a combination of proteomics and biochemical approaches has been employed to broaden knowledge of PPV CP PTMs. CP proved to be modified regardless it is assembled or not in mature particles. PTMs of CP occur in the natural host Prunus persica, similar to what happens in herbaceous plants. Additionally, we observe O-GlcNAcylation and phosphorylation are general features of different PPV strains, suggesting that roles of these modifications are part of overall strategies deployed during plant-virus interactions. Interestingly, phosphorylation at a casein kinase II motif conserved among potyviral CPs exhibits strain specificity in PPV; however, it does not display the critical role attributed to same modification in the CP of another potyvirus, Potato virus A.
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Project description:Small RNAs comprise a group of non coding RNAs which play significant role in the genetic regulation of growth and development in plants. The most important members of this family are the small inhibiting RNAs (siRNAs) and microRNAs (miRNAs). They are processed by the DICER like proteins in plants and incorporated into the RNA induced silencing complex to silence the cognate mRNAs by sequence specific cleavage. High throughput sequencing strategies have enabled the identification of complete gamut of small RNA sequences present in a plant tissue at a particular point of time enabling the study of their biological significance in different plant tissues. The small RNA profile of each plant shows few plant conserved sequences, few species specific sequences and few novel RNA sequences characteristic of each cultivar. Here we have performed high throughput sequencing of small RNA population derived from leaves of an elite edible Indian cultivar of banana cv. Rasthali (‘Silk’ subgroup with AAB genotype) to identify the microRNAs and other important small RNAs being expressed in the leaves of banana cv Rasthali.
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