Generation of a fertile ask1 mutant uncovers a comprehensive set of SCF‐mediated intracellular functions
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ABSTRACT:
PROVIDER: PRJNA549259 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9310690_1.fastq.gz | Fastqsanger.gz | |||
| SRR9310690_2.fastq.gz | Fastqsanger.gz | |||
| SRR9310691_1.fastq.gz | Fastqsanger.gz | |||
| SRR9310691_2.fastq.gz | Fastqsanger.gz | |||
| SRR9310692_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Ubiquitin-mediated proteolysis by the 26S proteasome is a critical regulatory mechanism controlling many biological processes. The multi-subunit Skp1-Cullin1-F-box (SCF) complexes are designed to select substrates for ubiquitylation in all eukaryotes. Within these complexes, the Skp1 protein is defined as the bridge between the F-box and the Cullin1 proteins. In Arabidopsis thaliana, there are 19 Arabidopsis Skp1-Like (ASK) genes that encode Skp1 proteins. Our previous genomics and evolutionary studies suggest that ASK1 plays a predominant role in the ASK family. To demonstrate this hypothesis, we genetically introduced the same Ds insertion allele of ask1-1 in Ler into the Arabidopsis Col-0 reference genome. The ask1-1 allele was initially obtained from an ask1-1(+/-)ask2-1(+/-)/LerWs double heterozygous mutant (Liu et al., 2004). To identify the breadth and depth of SCF functions, we applied RNA-Seq sequencing to systematically analyze the perturbation of transcriptomes in both floral bud and open flower tissues in this novel ask1 mutant. Method: Two replicates of total RNA were extracted from 10-50 mg of floral buds or open flowers from Col-0, ask1, and ASK1 (WT allele) primary inflorescences five hours after dawn grown under a long-day photoperiod condition. The NucleoSpin® RNA kit (Macherey-Nagel) was used for RNA extraction following the manufacturer’s instructions. 1 μg each from the 12 RNA samples was used for pair end 150-mer deep sequencing using a NovaSeq 6000 platform (Novogene). Adapter and low-quality sequences in the raw FASTQ sequencing data were removed to produce valid sequences using Trimmomatic (phred=33, minimum length=36; (Bolger et al., 2014)), which were further aligned to the A. thaliana Col-0 reference genome (TAIR10; www.arabidopsis.org) via TOPHAT2 (Kim et al., 2013a) to identify accepted hits of each locus. HTSeq was then used to calculate an absolute expression level (counts) of each locus based on the accepted hits (Anders et al., 2015). The resulting counts per locus were normalized to counts per million reads (CPM) among all 12 libraries and used to identify groups of SDEGs in bud and open flower tissues in ask1 and ASK1 through comparing to the WT bud and open flower tissues, respectively, by edgeR (Log2FC ≥ 1; FDR < 0.01%; (Robinson et al., 2010)). Results: In total, 52 and 54 SDEGs were identified to be up-regulated and down-regulated, respectively, in ASK1 BC10F4 bud tissues; and 13 and 3 SDEGs were identified to be up-regulated and down-regulated, respectively, in ASK1 BC10F4 open flower tissues (2-fold change (FC) with a false discovery rate (FDR) < 0.01). However, 306 and 941 SDEGs (in total 1,247) in ask1 bud tissues and 392 and 1,137 SDEGs (in total 1,529) in ask1 open flower tissues were identified to be up-regulated and down-regulated, respectively (2-FC and FDR < 0.01). Conclusions: Compared to Col-0, 527 and 640 SDEGs were identified in Ler and Ws, respectively, which were greatly higher than the number of SDEGs identified in ASK1 floral bud (Fisher’s exact test, p = 6.0e-82 and 7.5e-112, respectively) and open flower tissues (Fisher’s exact test, p = 7.4e-150 and 1.2e-186, respectively). Therefore, we concluded that the genetic background of ASK1 and ask1 are isogenic to Col-0. The large array of SDEGs identified in both floral buds and open flower tissues in ask1 demonstrated a wide range of roles of ASK1-containing SCF complexes.
2020-08-20 | GSE132841 | GEO
Project description:we used proximity labeling of ASK1, a core SCF adaptor, to profile dynamic changes in SCF-associated networks during Pseudomonas syringae infection. This analysis revealed widespread remodeling of F-box proteins and immune-related regulators, including several previously uncharacterized components.
2026-03-05 | PXD063820 | Pride
Project description:To elucidate the potential function of ASK1 in adipose tissues, microarray analysis was performed using iBAT and eWAT. Tissue samples were collected from 10-week-old male mice, and RNA samples derived from three individuals were pooled to analyze. These data provide novel insights into the physiological functions of ASK1. To elucidate the potential function of ASK1 in adipose tissues, microarray analysis was performed using iBAT and eWAT.
2016-01-08 | E-GEOD-76660 | biostudies-arrayexpress
Project description:ARABIDOPSIS SKP1-LIKE1 (ASK1) protein is involved in regulating flower development. We have compared ask1 mutant floral transcriptome with wild-type Ler to identify the role of ASK1-containing E3 ubiquitin ligases in regulating flower transcriptome. In this dataset, we include the expression data obtained from Arabidopsis thaliana Ler and ask1 mutant flower buds. We identified 42 genes and 74 genes that are down-regulated and up-regulated, respectively. Totally 5 samples were analyzed: 3 samples of ask1 and 2 samples of Ler. The average values were compared between ask1 and Ler.
2013-02-01 | E-GEOD-42841 | biostudies-arrayexpress
Project description:To explore the roles of macrophage NFATc3 and ASK1 in metabolic dysfunction-associated steatohepatitis, we generated macrophage-specific Nfatc3 knockout mice (Nfatc3-MKO), macrophage-specific Ask1 knockout mice (Ask1-MKO),macrophage-specific double knockout (MDKO) mice, macrophage-specific Nfatc3 knockin mice (Nfatc3-MKI), and macrophage-specific Ask1 knockin mice (Ask1-MKI). Lyz2-Cre mice were used as control. Eight-week-old male Lyz2-Cre, Nfatc3-MKO, Ask1-MKO, and MDKO mice were treated with methionine- and choline-deficient (MCD) diet for 4 weeks. Subsequently, mouse liver tissues were isolated and subjected to RNA sequencing analysis. In addition, mouse bone marrow-derived macrophages (BMDMs) were isolated from Lyz2-Cre, Nfatc3-MKI, and Ask1-MKI mice and were also subjected to RNA sequencing analysis.
2026-01-20 | GSE314637 | GEO
Project description:To elucidate the potential function of ASK1 in adipose tissues, microarray analysis was performed using iBAT and eWAT. Tissue samples were collected from 10-week-old male mice, and RNA samples derived from three individuals were pooled to analyze. These data provide novel insights into the physiological functions of ASK1.
2016-01-08 | GSE76660 | GEO
Project description:Deubiquitinating enzymes have gained more and more attention in the field of pathological cardiac hypertrophy. In this study, we explored the role of a deubiquitinase, OTUD1, in the transverse aortic constriction (TAC) induced cardiac hypertrophy. We found the upregulation of OTUD1 in heart tissues of TAC mice. OTUD1 overexpression promoted cardiac hypertrophy, cardiac fibrosis and apoptosis. Conversely, OTUD1 depletion alleviated these pathological changes both in vivo and in vitro. Mechanistically, ASK1 was identified as one substrate of OTUD1 using co-immunoprecipitation followed with LC-MS/MS. Interestingly, OTUD1 didn’t deubiquitinate ASK1, but increased the phosphorylation level of ASK1 during the process of cardiac hypertrophy. We found that PGAM5, the upper stream regulator of ASK1, was stabilized by OTUD1 in a K63 ubiquitin chain dependent way, which reminded us OTUD1 increased the phosphorylation level of ASK1 by deubiquitinating PGAM5. This study identified the OTUD1-ASK1 axis as a potential therapeutic target for pathological cardiac hypertrophy.
2023-09-05 | GSE241809 | GEO
Project description:E3 ubiquitin ligases mediate the last step of the ubiquitination pathwayin the ubiquitin-proteasome system (UPS). By targeting transcriptional regulators for their turnover, E3s play a crucial role in every aspect of plant biology. In plants, SKP1/CULLIN1/F-BOX PROTEIN (SCF)-type E3 ubiquitin ligases are essential for the perception and signaling of several key hormones including auxins and jasmonates (JAs). F-box proteins, TRANSPORT INHIBITOR RESPONSE 1 (TIR1) and CORONATINE INSENSITIVE 1 (COI1) bind directly transcriptional repressors AUX/IAAs and JAZs in an auxin- and JAs-depending manner, respectively, which permits the perception of the hormones and transcriptional activation of signaling pathways. Redox modification of proteins mainly by S-nitrosation of cysteines via nitric oxide (NO) has emerged as a valued regulatory mechanism in physiological processes requiring its rapid and versatile integration. Previously, we demonstrated that TIR1 and ASK1 (Arabidopsis thaliana SKP1) are targets of S-nitrosation, and these (NO)-dependent post-translational modifications enhance protein-protein interactions, and positively regulate SCFTIR1 complex assembly and expression of auxin response genes. In this work, we provide evidence on the modulation of SCFCOI1 complex by different S-nitrosation events. We demonstrated that S-nitrosation of ASK1 Cys118 enhanced ASK1-COI1 protein-protein interaction. Overexpression of non-nitrosable ask1 mutant protein impaired the activation of JA-responsive genes mediated by SCFCOI1 illustrating the functional relevance of this redox-mediated regulation in planta. Additionally, in silico analysis positioned COI1 as a promising S-nitrosation target. The regulation of SCF components involved in hormonal perception by S- nitrosation may represent a key strategy to determine the precise time and site-dependent activation of each hormonal signaling pathway, and highlights NO as a pivotal molecular player in these scenarios.
2022-04-04 | PXD030054 | Pride
Project description:ARABIDOPSIS SKP1-LIKE1 (ASK1) protein is involved in regulating flower development. We have compared ask1 mutant floral transcriptome with wild-type Ler to identify the role of ASK1-containing E3 ubiquitin ligases in regulating flower transcriptome. In this dataset, we include the expression data obtained from Arabidopsis thaliana Ler and ask1 mutant flower buds. We identified 42 genes and 74 genes that are down-regulated and up-regulated, respectively.
2013-02-01 | GSE42841 | GEO