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Comparative mRNA and sRNA transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE85070 | GEO | 2017/01/11

SECONDARY ACCESSION(S): PRJNA336052

REPOSITORIES: GEO

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Comparative sRNA-Seq analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

Project description:Belonging to the Carmovirus family, Turnip crinkle virus (TCV) is a positive-strand RNA virus that can infect Arabidopsis. Most Arabidopsis ecotypes are highly susceptible to TCV, except for the TCV resistant line Di-17 derived from ecotype Dijon. Previous studies showed that many of the stress related genes have changed significantly after TCV infection. Besides the virus-triggered genes, small RNAs also play critical roles in plant defense by triggering either transcriptional and/or post-transcriptional gene silencing. In this study, TCV-infected wildtype Arabidopsis thaliana and dcl1-9 mutant plants were subjected to transcriptome and small RNA analysis to investigate the role of DCL1 in virus defense network.

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Comparative transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

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Comparative mRNA and sRNA transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

Project description:Comparative mRNA and sRNA transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

| PRJNA336052 | ENA

Analyses of RNA-Seq and sRNA-Seq data reveal a complex network of anti-viral defense in TCV-infected Arabidopsis thaliana.

Project description:In order to identify specific plant anti-viral genes related to the miRNA regulatory pathway, RNA-Seq and sRNA-Seq were performed using Arabidopsis WT and dcl1-9 mutant line. A total of 5,204 DEGs were identified in TCV-infected WT plants. In contrast, only 595 DEGs were obtained in the infected dcl1-9 mutant plants. GO enrichment analysis of the shared DEGs and dcl1-9 unique DEGs showed that a wide range of biological processes were affected in the infected WT plants. In addition, miRNAs displayed different patterns between mock and infected WT plants. This is the first global view of dcl1-9 transcriptome which provides TCV responsive miRNAs data. In conclusion, our results indicated the significance of DCL1 and suggested that PPR genes may play an important role in plant anti-viral defense.

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Induced folding in RNA recognition by Arabidopsis thaliana DCL1.

Project description:DCL1 is the ribonuclease that carries out miRNA biogenesis in plants. The enzyme has two tandem double stranded RNA binding domains (dsRBDs) in its C-terminus. Here we show that the first of these domains binds precursor RNA fragments when isolated and cooperates with the second domain in the recognition of substrate RNA. Remarkably, despite showing RNA binding activity, this domain is intrinsically disordered. We found that it acquires a folded conformation when bound to its substrate, being the first report of a complete dsRBD folding upon binding. The free unfolded form shows tendency to adopt folded conformations, and goes through an unfolded bound state prior to the folding event. The significance of these results is discussed by comparison with the behavior of other dsRBDs.

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Crystal structure of Arabidopsis thaliana peroxiredoxin A C119S mutant.

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