PIF4 promotes stomatal movement during fluctuating light coincidant with drought stress via the SAL1-PAP signaling pathway (ChIP-Seq)
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ABSTRACT:
PROVIDER: PRJNA1203218 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31836050_1.fastq.gz | Fastqsanger.gz | |||
| SRR31836050_2.fastq.gz | Fastqsanger.gz | |||
| SRR31836051_1.fastq.gz | Fastqsanger.gz | |||
| SRR31836051_2.fastq.gz | Fastqsanger.gz | |||
| SRR31836052_1.fastq.gz | Fastqsanger.gz |
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Project description:Fluctuating light (FL) usually occur concomitantly with drought stress (DS); this combined (FL-DS) condition influences intrinsic water use efficiency (iWUE) pattern during FL and DS response. However, the molecular mechanisms governing iWUE during FL-DS combined events in rice remain unexplored. In this study, we quantified iWUE kinetics in 200 rice accessions exposed to a 20-day FL-DS. Using genome-wide association studies (GWAS), we identified a significant gene variation in the phytochrome-interacting factor (OsPIF4) gene which significantly associated with a novel trait, iWUEFL. This gene variation was highly expressed in the high iWUEFL subgroup. Two haplotypes containing nine SNPs of OsPIF4 were classified, where the mutation of v3 SNP at its promoter shows substantially reduced activities of promoter and greatest sensitivity to FL among mutation of other SNPs via protoplast transient transformation approach. Mutation at v3 SNP (PIF4v3m) and overexpression of OsPIF4 resulted in at least 20% reduction and 25% increase in iWUEFL under FL-DS, compared it to WT, respectively. Two genes (OsSAL1 and OsNHX1) were identified with the most significant differences in expression between PIF4v3m and WT based on transcriptome analysis. PIF4v3m displayed an 85% reduction in adenosine 3', 5'-diphosphate (PAP) levels and a 73% increase in OsSAL1 gene expression compared to WT. Moreover, our results revealed that OsPIF4 has a dual role in repressing OsSAL1 transcriptionally and activating OsNHX1 by binding to their G-box motifs. This regulatory mechanism increased by 16% (sal1) and 10% (OsNHX1-OE) in iWUEFL compared to WT under FL-DS. OsPIF4 haplotypic distribution is strongly associated with the local light regime where accessions originated. This study highlights the key role of OsPIF4 in enhancing iWUEFL during FL-DS by regulating chloroplast retrograde signaling pathways and vacuolar ion exchanges.
2024-12-27 | GSE285356 | GEO
Project description:Environmental factors shape the phenotypes of multicellular organisms. The production of stomata—the epidermal pores required for gas exchange in plants—is highly plastic, and provides a powerful platform to address environmental influence on cell differentiation [1-3]. Rising temperatures are already impacting plant growth, a trend expected to worsen in the near future [4]. High temperature inhibits stomatal production but the underlying mechanism is not known [5]. Here, we show that elevated temperature suppresses the expression of SPEECHLESS (SPCH), the bHLH transcription factor that serves as the master regulator of stomatal lineage initiation [6,7]. Our genetic and expression analyses indicate that the suppression of SPCH and stomatal production is mediated by the bHLH transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a core component of high temperature signaling [8]. Importantly, we demonstrate that upon exposure to high temperature, PIF4 accumulates in the stomatal precursors and binds to the promoter of SPCH. In addition, we find SPCH feeds back negatively to the PIF4 gene. We propose a model where the high temperature-activated PIF4 binds and represses SPCH expression to restrict stomatal production at high temperature. Our work identifies a molecular link connecting high temperature signaling and stomatal development, and reveals a direct mechanism by which production of a specific cell lineage can be controlled by a broadly-expressed environmental signaling factor.
2018-04-05 | GSE110302 | GEO
Project description:Drought and salt stress severely inhibit plant growth and development. However, the regulatory mechanisms of plants in response to these stresses are not fully understood. Here we find that the expression of a WRKY transcription factor WRKY46 is rapidly induced by drought, salt and oxidative stresses. Mutations of WRKY46 by T-DNA insertion lead to more sensitive to drought and salt stress, whereas, overexpression of WRKY46 exhibits hypersensitive in soil culture with higher water loss rate, but increased tolerance on the agar plates. ABA induced stomatal closing is impaired in the WRKY46 overexpressing line (OV46), which is potentially due to the lower ROS accumulation in the guard cells. Real-time qPCR and GUS activity assay further demonstrate that WRKY46 is expressed in guard cells, but its expression is not affected by dehydration treatment, suggesting different regulatory mechanisms for WRKY46 between guard cells and other WRKY46 expressed tissues. The stomatal movement and conductance assay indicate that WRKY46 is involved in light-dependent stomatal opening. Further microarray analysis reveals that WRKY46 regulates a set of genes involved in cellular osmoprotection and redox homeostasis under dehydration stress. Determinations of ROS and MDA content confirm its role in oxidative detoxification under stress. Furthermore, we find that WRKY46 modulates light-dependent starch metabolism in guard cells via regulating QQS gene expression. Taken together, we demonstrate that WRKY46 plays a role in modulating cellular osmoprotection and redox homeostasis under drought and salt stress, and functions independently in stomatal movement via regulating light-dependent starch metabolism and ROS levels in guard cells. We used microarrays to identify the certain downstream genes regulated by WRKY46 under normal and dehydration conditions.
2015-02-01 | GSE49418 | GEO
Project description:Drought and salt stress severely inhibit plant growth and development. However, the regulatory mechanisms of plants in response to these stresses are not fully understood. Here we find that the expression of a WRKY transcription factor WRKY46 is rapidly induced by drought, salt and oxidative stresses. Mutations of WRKY46 by T-DNA insertion lead to more sensitive to drought and salt stress, whereas, overexpression of WRKY46 exhibits hypersensitive in soil culture with higher water loss rate, but increased tolerance on the agar plates. ABA induced stomatal closing is impaired in the WRKY46 overexpressing line (OV46), which is potentially due to the lower ROS accumulation in the guard cells. Real-time qPCR and GUS activity assay further demonstrate that WRKY46 is expressed in guard cells, but its expression is not affected by dehydration treatment, suggesting different regulatory mechanisms for WRKY46 between guard cells and other WRKY46 expressed tissues. The stomatal movement and conductance assay indicate that WRKY46 is involved in light-dependent stomatal opening. Further microarray analysis reveals that WRKY46 regulates a set of genes involved in cellular osmoprotection and redox homeostasis under dehydration stress. Determinations of ROS and MDA content confirm its role in oxidative detoxification under stress. Furthermore, we find that WRKY46 modulates light-dependent starch metabolism in guard cells via regulating QQS gene expression. Taken together, we demonstrate that WRKY46 plays a role in modulating cellular osmoprotection and redox homeostasis under drought and salt stress, and functions independently in stomatal movement via regulating light-dependent starch metabolism and ROS levels in guard cells. We used microarrays to identify the certain downstream genes regulated by WRKY46 under normal and dehydration conditions. One-week-old Arabidopsis seedlings of wild-type Col-0 (WT) and WRKY46 overexpressing line (46T) with or without dehydration treatment for 1 h were harvested and used for RNA extraction and hybridization to Affymetrix Arabidopsis ATH1 microarrays. The experiment includes 3 biological replicates.
2015-02-01 | E-GEOD-49418 | biostudies-arrayexpress
Project description:Chloroplast-nuclear retrograde signaling is viewed as a mechanism for inter-organelle communication. Here we show the SAL1-PAP (3′-phosphoadenosine 5′- phosphate) retrograde pathway functions more broadly in guard cells, interacting with abscisic acid (ABA) signaling at least in part via exoribonucleases. Unexpectedly, PAP bypasses the canonical signaling components ABA Insensitive 1 (ABI1) and Open Stomata 1 (OST1) by priming an alternative pathway that restores ABA-responsive gene expression, ROS bursts, ion channel function and stomatal closure in ost1-2. This alternative pathway up-regulates lowly expressed Calcium Dependent Protein Kinases (CDPKs) which have the capacity to activate the key slow anion channel SLAC1 in response to ABA-mediated and ost1-2 independent calcium release. The role of PAP in priming an alternative pathway to bypass components previously considered essential for stomatal closure demonstrates how a chloroplast signal can have broader roles as a secondary messenger to directly intersect with and tune hormone signaling.
2017-03-21 | GSE84997 | GEO
Project description:We intend to identify transporters and their regulators involved in barley stomatal movement as well as components of the ABA signaling pathway. We isolated epidermal peels where only stomatal guard cells and their subsidiary cells survived, while other epidermal cell were mechanically disrupted and sequenced the resulting RNAs. Thus we analyzed transcripts differentially expressed between the barley stomatal complex and total leaves. These data served as the first overview of genes expressed in the stomatal complex and for cloning of relevant transporters.
2018-02-21 | E-MTAB-5877 | biostudies-arrayexpress
Project description:Direct control of SPEECHLESS by PIF4 in the high temperature response of stomatal development
| PRJNA433404 | ENA
Project description:Stomata in the plant epidermis play a vital role in growth and survival by controlling gas exchange and immunity to pathogens. A genetic frame of key transcriptional factors and cellular communication has been established, by which plants modulate stomatal cell fate and patterning. miRNAs contribute to functional and developmental plasticity in multicellular organisms. However, it remains very elusive as to whether miRNAs pitch in stomatal development. Here, we reveal dynamic miRNA expression profiles from stomatal lineage cells in a development stage-specific manner and show that stomatal lineage miRNAs positively and negatively regulate stomatal formation and pattern to avoid clustered and paired stomata. Target prediction of stomatal lineage miRNAs suggests potential cellular processes involved in stomatal development. Furthermore, dysregulation of stomatal lineage miRNAs and their target mRNAs disclose unexpected genetic pathways modulating stomatal development. Our study demonstrates that miRNAs constitute an additional layer in the complex regulatory mechanism of stomatal development.
2020-02-03 | GSE140918 | GEO
Project description:Regulation of Stomatal Development by Stomatal Lineage miRNAs
| PRJNA591466 | ENA
Project description:To investigate the effect of the interaction between the MRG1/2 and PIF4, here we analysed differentially expressed genes compared to the mutant and wild-type by RNA-seq under different temperature. We performed gene expression profiling analysis using data obtained from RNA-seq of WT, mrg1 mrg2, pif4, and mrg1 mrg2 pif4 plants at 22degC and 28degC.
2024-01-04 | GSE213025 | GEO