The COP9 Signalosome regulates seed germination by facilitating protein degradation of RGL2 and ABI5
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA415950 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6223120.fastq.gz | Fastqsanger.gz | |||
| SRR6223130.fastq.gz | Fastqsanger.gz | |||
| SRR6223121.fastq.gz | Fastqsanger.gz | |||
| SRR6223131.fastq.gz | Fastqsanger.gz | |||
| SRR6223112.fastq.gz | Fastqsanger.gz |
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Project description:The control of seed germination and seed dormancy are critical for the successful propagation of plant species, and are important agricultural traits. Seed germination is tightly controlled by the balance of gibberellin (GA) and abscisic acid (ABA), and is influenced by environmental factors. The COP9 Signalosome (CSN) is a conserved multi-subunit protein complex that is best known as a regulator of the Cullin-RING family of ubiquitin E3 ligases (CRLs). Multiple viable mutants of the CSN showed poor germination, except for csn5b-1. Detailed analyses showed that csn1-10 has a stronger seed dormancy, while csn5a-1 mutants exhibit retarded seed germination in addition to hyperdormancy. Both csn5a-1 and csn1-10 plants show defects in the timely removal of the germination inhibitors: RGL2, a repressor of GA signaling, and ABI5, an effector of ABA responses. We provide genetic evidence to demonstrate that the germination phenotype of csn1-10 is caused by over-accumulation of RGL2, a substrate of the SCF (CRL1) ubiquitin E3 ligase, while the csn5a-1 phenotype is caused by over-accumulation of RGL2 as well as ABI5. The genetic data are consistent with the hypothesis that CSN5A regulates ABI5 by a mechanism that may not involve CSN1. Transcriptome analyses suggest that CSN1 has a more prominent role than CSN5A during seed maturation, but CSN5A plays a more important role than CSN1 during seed germination, further supporting the functional distinction of these two CSN genes. Our study delineates the molecular targets of the CSN complex in seed germination, and reveals that CSN5 has additional functions in regulating ABI5, thus the ABA signaling pathway.
2018-02-08 | GSE106223 | GEO
Project description:ZFP3, a nuclear C2H2 zinc finger protein acts as a negative regulator of ABA- suppressed germination. Regulated over-expression of ZFP3 and closely related ZFP1, ZFP4, ZFP6 and ZFP7 confers ABA insensitivity to seed germination while the zfp3,zfp4 double mutant displays enhanced ABA susceptibility. Reduced expression of a large set of ABA-induced genes such as RAB18 and transcription factors ABI3, ABI4, ABI5 and RGL2 in ZFP3ox seedling suggests that ZFP3 indeed negatively regulates ABA signaling. Analysis of ZFP3ox plants revealed multiple phenotypic alterations such as semidwarf growth habit, defects in fertility and enhanced sensitivity of hypocotyl elongation to red but not to far-red or blue light. Analysis of genetic interactions with phytochrome and abi mutants suggested that ZFP3 amplifies red light signals perceived by photoreceptors other than phyB, and controlled by ABI5 downstream of ZFP3.
2014-01-01 | GSE48661 | GEO
Project description:ZFP3, a nuclear C2H2 zinc finger protein acts as a negative regulator of ABA- suppressed germination. Regulated over-expression of ZFP3 and closely related ZFP1, ZFP4, ZFP6 and ZFP7 confers ABA insensitivity to seed germination while the zfp3,zfp4 double mutant displays enhanced ABA susceptibility. Reduced expression of a large set of ABA-induced genes such as RAB18 and transcription factors ABI3, ABI4, ABI5 and RGL2 in ZFP3ox seedling suggests that ZFP3 indeed negatively regulates ABA signaling. Analysis of ZFP3ox plants revealed multiple phenotypic alterations such as semidwarf growth habit, defects in fertility and enhanced sensitivity of hypocotyl elongation to red but not to far-red or blue light. Analysis of genetic interactions with phytochrome and abi mutants suggested that ZFP3 amplifies red light signals perceived by photoreceptors other than phyB, and controlled by ABI5 downstream of ZFP3. Comparison of ZFP3 overexpressing and wild type Arabidopsis seedlings
2014-01-01 | E-GEOD-48661 | biostudies-arrayexpress
Project description:The COP9 signalosome protein complex has a central role in the regulation of development of multi-cellular organisms. While the function of this complex in ubiquitin-mediated protein degradation is well established, results over the past few years have hinted that the COP9 signalosome may function more broadly in the regulation of gene expression. Here, using DamID technology, we show that COP9 signalosome subunit 7 functionally associates with a large number of genomic loci in the Drosophila genome, and show that the expression of many genes within these loci is COP9 signalosome-dependent. This association is likely direct as we show CSN7 binds DNA in vitro. The genes targeted by CSN7 are preferentially enriched for transcriptionally active regions of the genome, and are involved in the regulation of distinct gene ontology groupings including imaginal disc development and cell-cycle control.
2014-09-22 | GSE61605 | GEO
Project description:NUCLEOPORIN 1 (NUP1), a member of the Nuclear Pore Complex (NPC), is located on the inner side of the nuclear membrane. It is highly expressed in seeds; however, its role in seeds including germination has not been explored yet. Here, we identified an ABA hypersensitive phenotype of nup1 during germination. ABA treatment drastically changes the expression pattern of thousands of genes in nup1, including the major transcription factors (TFs) involved in germination, ABI3, ABI4, and ABI5. Double mutant analysis of NUP1 and these ABA-related genes showed that mutations in ABI5 can rescue the phenotype of nup1, suggesting that NUP1 acts upstream of ABI5 to regulate seed germination. ABI5, a negative regulator of germination was previously reported to be predominantly expressed in nucleus. Our subnuclear localization study indicates ABI5 is mostly localized in nucleoplasm. It is abundant in dry seeds and rapidly degraded during germination, but the details of its degradation site is unclear. Here, we found that NUP1 is physically associated with ABI5 and the 19S regulatory particle (RP) of the 26S proteasome near NPC. Mutation in NUP1 delayed the ABI5 degradation through its post-translation retention in nucleolus after abiotic stress treatment. Taken together, we propose, NUP1 anchors the proteasome to NPC and modulates Arabidopsis seed germination through proteasome-mediated degradation of ABI5 in the vicinity of NPC in nucleoplasm.
2023-08-14 | GSE189513 | GEO
Project description:The COP9 signalosome protein complex has a central role in the regulation of development of multi-cellular organisms. While the function of this complex in ubiquitin-mediated protein degradation is well established, results over the past few years have hinted that the COP9 signalosome may function more broadly in the regulation of gene expression. Here, using DamID technology, we show that COP9 signalosome subunit 7 functionally associates with a large number of genomic loci in the Drosophila genome, and show that the expression of many genes within these loci is COP9 signalosome-dependent. This association is likely direct as we show CSN7 binds DNA in vitro. The genes targeted by CSN7 are preferentially enriched for transcriptionally active regions of the genome, and are involved in the regulation of distinct gene ontology groupings including imaginal disc development and cell-cycle control. DamID experiments were done in Drosophila Kc167 cells. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. The experiment contains 4 samples, three biological replicates and one reverse dye orientation. For each sample Dam-fusion material was hybridized over Dam-only material.
2014-09-22 | E-GEOD-61605 | biostudies-arrayexpress
Project description:To shed light on the genetic events downstream of DELLA proteins, we have employed a microarray expression profiling of Arabidopsis thaliana seeds to identify target genes of the DELLA protein RGL2. Seeds of the germinating ga1-3 rga-t2 rgl2-1 and the non-germinating ga1-3 rga-t2 mutant were stratified, and RNA was extracted after five days. Transcript profiles of the non-germinating seeds closely resemble profiles of dormant seeds, and several transcription factors involved in light- and phytohormone-regulated signalling pathways appear to be up-regulated, suggesting that RGL2 controls various physiological aspects to inhibit seed germination.
2012-08-31 | GSE40485 | GEO
Project description:To shed light on the genetic events downstream of DELLA proteins, we have employed a microarray expression profiling of Arabidopsis thaliana seeds to identify target genes of the DELLA protein RGL2. Seeds of the germinating ga1-3 rga-t2 rgl2-1 and the non-germinating ga1-3 rga-t2 mutant were stratified, and RNA was extracted after five days. Transcript profiles of the non-germinating seeds closely resemble profiles of dormant seeds, and several transcription factors involved in light- and phytohormone-regulated signalling pathways appear to be up-regulated, suggesting that RGL2 controls various physiological aspects to inhibit seed germination. Gene expression five days after stratification was measured in ga1-3 rga-t2 seeds, using seeds of the ga1-3 rga-t2 rgl2-1 mutant as reference. Two biological replicates were performed for each sample.
2012-08-31 | E-GEOD-40485 | biostudies-arrayexpress
Project description:The control of seed germination and seed dormancy are critical for the successful propagation of plant species, and are important agricultural traits. Seed germination is tightly controlled by the balance of gibberellin (GA) and abscisic acid (ABA), and is influenced by environmental factors. The COP9 Signalosome (CSN) is a conserved multi-subunit protein complex that is best known as a regulator of the Cullin-RING family of ubiquitin E3 ligases (CRLs). Multiple viable mutants of the CSN showed poor germination, except for csn5b-1. Detailed analyses showed that csn1-10 has a stronger seed dormancy, while csn5a-1 mutants exhibit retarded seed germination in addition to hyperdormancy. Both csn5a-1 and csn1-10 plants show defects in the timely removal of the germination inhibitors: RGL2, a repressor of GA signaling, and ABI5, an effector of ABA responses. We provide genetic evidence to demonstrate that the germination phenotype of csn1-10 is caused by over-accumulation of RGL2, a substrate of the SCF (CRL1) ubiquitin E3 ligase, while the csn5a-1 phenotype is caused by over-accumulation of RGL2 as well as ABI5. The genetic data are consistent with the hypothesis that CSN5A regulates ABI5 by a mechanism that may not involve CSN1. Transcriptome analyses suggest that CSN1 has a more prominent role than CSN5A during seed maturation, but CSN5A plays a more important role than CSN1 during seed germination, further supporting the functional distinction of these two CSN genes. Our study delineates the molecular targets of the CSN complex in seed germination, and reveals that CSN5 has additional functions in regulating ABI5, thus the ABA signaling pathway.
| S-EPMC5834205 | biostudies-literature
Project description:The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 Signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 Signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. Results: We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function mutants of the COP9 Signalosome. Our results indicate that the COP9 Signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. In addition, our analyses suggest that COP9 Signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 Signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 Signalosome conservation among eukaryotes may also suggest that COP9 Signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. We report the application of Bisulfite-sequencing to compare methylation of two CSN mutants with their corresponding wild types: a non-lethal csn5a-1 mutant, vs. columbia ecotype, and a lethal, csn8 mutant, vs. Wassilewskija ecotype
2020-07-28 | GSE119259 | GEO