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Comparison col0 vs 003d-Study of the function of SCF complexes in Arabidopsis.

ABSTRACT: af01_cul3a2_cul3b - comparison col0 vs 003d - Cullin proteins belong to a multigene family that includes at least three members in budding yeast, six in human, five in C. elegans and five in Arabidopsis thaliana. All cullins analyzed so far directly interact with RBX1/HRT1/ROC1, a RING finger protein, thereby forming the core module of different ubiquitin ligase complexes, which specifically recruit substrate proteins for ubiquitylation and subsequent degradation by the proteasome. CULLIN1, the only cullin protein studied so far in plants, has been shown to be essential for plant development and to play a role in multiple signalling cascades. Here, we report on the first molecular and genetic characterisation of a plant Cullin 3. In contrast to fungi and animals, the genome of the model plant Arabidopsis thaliana contains two related CULLIN 3 genes, called CUL3A and CUL3B. We found that CUL3A is ubiquitously expressed in plants and that the CUL3A protein is also able to interact with RBX1 and certain Arabidopsis BTB-domain proteins. In order to determine the role of CUL3A in plant development, we used a reverse genetic approach and identified T-DNA insertion mutants. cul3a null mutants flower slightly latter than the control plants and their hypocotyls exhibit a reduced sensitivity to far red light. The viability of the cul3a mutant plants suggests functional redundancy between both CUL3 genes in plants. - Comparaison of AtCul3b (mutant of Gabi collection) and Col0. Keywords: wt vs mutant comparison

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE7972 | GEO | 2007/06/20

SECONDARY ACCESSION(S): PRJNA100731

REPOSITORIES: GEO

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Project description:Purpose: Overexpression of VDE, ZEP and PsbS (VPZ) in plants confers enhanced dynamics of non-photochemical quenching of NPQ under FL light. VPZ overexpression in tobacco has been reported to increase plant biomass under fluctuating light. However, our work demonstrates that such strategy had no advantageous effect when asssayed in Arabidopsis thaliana. To investigate whether this observation is due to impairements in signaling pathways due to the expression of VPZ in Arabidopsis thaliana, transcriptome profiles of VPZ plants exposed to fluctuating light or high light were conducted. Methods: mRNA-Seq libraries were prepared from 21-d-old Col0 plants and VPZ lines #2 and #4 cultivated under standard control conditions and then exposed to fluctuating light or high light for 6h and 30 h. Standard Illumina protocols were used for mRNA-Seq sequencing. Triplicates for 3 independent plants were used. Adaptor sequences were removed with Trimmomatic and resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. Normalised counts reads were quantified with featureCounts to provide processed data files and differential expression analysis were conducted with the DEseq2 pipeline. Results: mRNA-Seq libraries contained app. 9 milion reads each. Transcript analysis for differential gene expression was conducted according to the Tophat/featureCounts/DESeq2 pipeline. To declare significant differences, a cut-off for absolute log2(FC) ≥ 1 compared to the initial timepoint (0h) and FDR ≤ 0.05 was applied. Significant transcripts exclusively found for Col0 and both VPZ lines in each time-point were considered for subsequent analysis. Accordingly, 528 and 415 transcripts (6h and 30h) were found for Col0, and 326 and 896 (6h and 30h) for the VPZ under control conditions. For FL, 490 and 591 transcripts qualified as specific (6h and 30h) for Col0 and 938 and 401 (6h and 30h) for VPZ. Strikingly, the amount of transcripts raised to 2847 and 2902 DEGs (6h and 30h) for Col0, whereas only 546 and 304 (6h and 30h) were detected for VPZ under HL. transcripts). Conclusions: the overexpression of VPZ in Arabidopsis leads to particular transcriptome response under fluctuating light related to changes in photosynthesis and response to abscisic acid, among all. However, Col0 displayed wider transcriptome responses than VPZ after exposure to high light .

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Comparison col0 vs 003d-Study of the function of SCF complexes in Arabidopsis.

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