The Arabidopsis Zinc Finger Protein 3 integrates ABA and light signaling in seed germination and plant development
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE48661 | GEO | 2014/01/01
SECONDARY ACCESSION(S): PRJNA210964
REPOSITORIES: GEO
Similar Datasets
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: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 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:In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. Three biological replicates for 4-d-old seedlings grown under dark or red-light and long-day (0.5 ?mole m-2 sec-1) contitions.
2013-07-22 | E-GEOD-30910 | biostudies-arrayexpress
Project description:It has been known that ABA INSENSITIVE 5 (ABI5) plays a vital role in regulating seed germination. In the present experiment, we showed that 3-amino-1,2,4-triazole (3-AT) inhibits seed germination of the loss-of-function mutant abi5-1, but promotes seed germination of the ABI5-overexpression transgenic line, and that ABI5 affects reactive oxygen species (ROS) homeostasis. RNA-sequencing analysis indicates that the transcription of the genes involved in ROS metabolic process or genes responsive to ROS stress is impaired in abi5-1 seeds. Together, all the findings suggest that ABI5 regulates seed germination at least partly by affecting ROS homeostasis.
2017-07-11 | GSE90004 | GEO
Project description:In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development.
2013-07-22 | GSE30910 | GEO
Project description:Light inhibits the seed germination in the Cypriot accession (CYP) of Aethionema arabicum. Extended light illumination also induces a secondary seed dormancy that inhibits the germination even if the seeds were transferred back to darkness. A forward genetic screen identified rgl2 mutant, that show light inhibited germination, but fails to re-enter the secondary dormancy. This analysis aims to compare the seed transcriptome before or after the dormancy was established by light illumination (100 µmol/m2s; white light). One day light treatment (1dL) inhibits the germination but the seeds are not yet dormant. Seven day (7dL) long light treatment induces dormancy in the WT but not in the rgl2 mutant.
2023-09-01 | GSE237220 | GEO
Project description:Seed germination is the initial step of the whole life cycle for an individual plant, and thus it needs to be tightly controlled to avoid the growth of plants under unfavorable conditions, such as high salinity and drought stress. It has been well known that ABA signaling pathway plays a key role in the regulation of seed germination. In this study, we found that FER, a receptor-like kinase that belongs to CrRLK1L subfamily, regulates seed germination under ABA or stress conditions via the modulation of ABI5 protein stability. Biochemical data indicate that FER interacts with and phosphorylates CARK1 protein, a receptor-like cytoplasmic kinase (RLCK) that is classified into the RLCK VIII subfamily. FER phosphorylates the Ser233 and Thr234 residues of CARK1, and these two residues are located in the activation loop and are required for the activation of CARK1. The CARK1 protein with the substitutions of these two amino acids to Ala exhibits reduced kinase activity and is not able to rescue the faster seed germination phenotype of cark1 mutant under ABA conditions. In both fer-4 and cark1 mutant, the ABA-triggered activation of SnRK2.6 and ABI5 protein accumulation were attenuated compared with the wild-type. Taken together, our study not only reveals a RLCK protein that functions directly downstream of FER to transduce external signals, but also provides a novel mechanistic insight into the understanding of seed germination regulation via ABA-mediated signaling pathways.
2024-09-14 | PXD047594 | Pride
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:Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment. Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses
2005-09-04 | GSE3038 | GEO