Abstract
BackgroundThe ARABIDOPSIS SKP1-LIKE1 (ASK1) protein functions as a subunit of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligases. Previous genetic studies showed that ASK1 plays important roles in Arabidopsis flower development and male meiosis. However, the molecular impact of ASK1-containing SCF E3 ubiquitin ligases (ASK1-E3s) on the floral proteome and transcriptome is unknown.ResultsHere we identified proteins that are potentially regulated by ASK1-E3s by comparing floral bud proteomes of wild-type and the ask1 mutant plants. More than 200 proteins were detected in the ask1 mutant but not in wild-type and >300 were detected at higher levels in the ask1 mutant than in wild-type, but their RNA levels were not significantly different between wild-type and ask1 floral buds as shown by transcriptomics analysis, suggesting that they are likely regulated at the protein level by ASK1-E3s. Integrated analyses of floral proteomics and transcriptomics of ask1 and wild-type uncovered several potential aspects of ASK1-E3 functions, including regulation of transcription regulators, kinases, peptidases, and ribosomal proteins, with implications on possible mechanisms of ASK1-E3 functions in floral development.ConclusionsOur results suggested that ASK1-E3s play important roles in Arabidopsis protein degradation during flower development. This study opens up new possibilities for further functional studies of these candidate E3 substrates.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0571-9) contains supplementary material, which is available to authorized users.
Highlights
The ARABIDOPSIS SKP1-LIKE1 (ASK1) protein functions as a subunit of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligases
Transcriptomic analysis of Landsberg erecta (Ler) and ask1 floral buds To determine the effect of the ask1 mutation on the floral transcriptome, WT (Ler) and ask1 floral bud transcriptomes were analyzed using GeneChip Arabidopsis ATH1 Genome Array
We found that 74 and 42 genes were upregulated and down-regulated, respectively, in ask1 transcriptome compared with Ler (Additional files 1 and 2)
Summary
The ARABIDOPSIS SKP1-LIKE1 (ASK1) protein functions as a subunit of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligases. The ubiquitin-proteasome system (UPS) plays important roles in targeted protein degradation, thereby regulating a variety of cellular processes [1,2,3]. The UPS regulates many processes in plants, including development and biotic/abiotic stress responses [1, 3,4,5]. This broad spectrum of functions is made possible by the large number of genes encoding components in the UPS. The modular design of multimeric E3 ubiquitin ligases including the SKP1-CUL1-F-box (SCF) complexes greatly expands the likely number of proteins that can be ubiquitinated. The combination of these components can form various SCF complexes to ubiquitinate numerous substrate proteins
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