Comparative phosphoproteomic analysis of raf22raf36 in Arabidopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)
SUBMITTER: Taishi Umezawa
PROVIDER: PXD021372 | JPOST Repository | Sat May 15 00:00:00 BST 2021
REPOSITORIES: jPOST
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 1_1.wiff.scan | Wiff | |||
| 1_2.wiff.scan | Wiff | |||
| 1_3.wiff.scan | Wiff | |||
| 24_2.wiff.scan | Wiff | |||
| 24_3.wiff.scan | Wiff |
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Project description:A phythormone abscisic acid (ABA) has a major role in abiotic stress responses in plants, and subclass III SNF1-related protein kinase 2 (SnRK2) mediates ABA signaling. In this study, we identified Raf36, a group C Raf-like protein kinase in Arabidopsis, as an interacting protein with SnRK2. A series of reverse genetic and biochemical analyses revealed that Raf36 negatively regulates ABA responses and is directly phosphorylated by SnRK2s. In addition, we found that Raf22, another C-type Raf-like kinase, functions partially redundantly with Raf36 to regulate ABA responses. Comparative phosphoproteomic analysis using Arabidopsis wild-type and raf22raf36-1 plants indicate proteins that are phosphorylated downstream of Raf36 and Raf22 in planta. Together, these results reveal a novel subsection of ABA-responsive phosphosignaling pathways branching from SnRK2.
2020-12-22 | PXD016894 | JPOST Repository
Project description:Plants physiological mechanisms are affected by Abscisic acid (ABA) via changing gene expression and empowers plants to adapt in numerous environments. Plants have evolved their protection mechanisms for seed germination and abiotic environments to deal with critical harsh conditions. Here, we have explored those changes in Arabidopsis thaliana plants subjected to multiple abiotic stresses. AtBro1 transcripts showed up-regulation in the presence of salt, ABA and mannitol stress conditions. AtBRO1 over-expression lines exhibited robust tolerance to drought and salt stress. Further, ABA elicits resistance responses in loss-of-function bro1-1 mutant plants and AtBro1 positively regulates drought resistance in Arabidopsis. Promoter of AtBro1 fused with GUS showed GUS expression mainly in the rosette leaves and floral clusters, especially in anthers. AtBro1 protein was found to be localized in the plasma membrane of Arabidopsis at the subcellular level by using AtBro1::GFP fusion. Using a broad RNA-sequencing analysis, we observed that early transcriptional responses prompted by ABA induction exhibit specific quantitative differences at different time points, suggesting that ABA stimulates resistance responses in bro1-1 mutant plants. Additionally, transcripts levels of MOP9.5, MRD1, HEI10, and MIOX4 were altered in loss-of-function mutant plants which are involved in different stress conditions. Collectively, our results have shown that AtBro1 is involved in a significant role by regulating plant transcriptional response to ABA and induction of resistance response against abiotic stress.
2023-04-18 | GSE225062 | GEO
Project description:FERONIA (FER) receptor kinase has a versatile role in plant growth and development, biotic and abiotic stress responses, and reproduction. To gain new insights into the molecular interplay of these processes and to identify new functions of FER, we carried out quantitative transcriptome, proteome, and phosphoproteome profiling of wild type (WT) and a loss-of-function fer mutant in Arabidopsis plants. Gene Ontology terms for hormone signaling, abiotic stress, and biotic stress were significantly enriched among mis-expressed transcripts, proteins, and/or mis-phosphorylated proteins, in agreement with FER’s known roles in these processes. Analysis of multi-omics data and subsequent experimental evidence identified previously unknown functions of FER in ER (Endoplasmic Reticulum) body formation, glucosinolate biosynthesis. FER functions through transcription factor NAI1 to mediate ER body. FER also negatively regulates indole glucosinolates biosynthesis, partially through NAI1. Furthermore, we found that a group of abscisic acid (ABA)-induced transcription factors are hypo-phosphorylated in the fer mutant and demonstrated that FER acts through ABI5 to negatively regulate the ABA response during germination. Our integrated-omics study therefore reveals novel functions of FER and provides new insights into the underlying mechanisms of FER function.
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2019-11-13 | PXD014298 | Pride
Project description:Abscisic acid (ABA) plays essential roles in plant development and responses to environmental stress. ABA induces subcellular translocation and degradation of the guanine nucleotide exchange factor RopGEF1 thus facilitating ABA core signal transduction. However, the underlying mechanisms for ABA-triggered RopGEF1 trafficking/degradation remain unknown. Studies have revealed that RopGEFs associate with receptor-like kinases to convey developmental signals to small ROP GTPases. However, how the activities of RopGEFs are modulated is not well understood. Type 2C protein phosphatases stabilize the RopGEF1 protein, indicating that phosphorylation may trigger RopGEF1 trafficking and degradation. We have screened inhibitors followed by several protein kinase mutants and find that quadruple mutant plants in the Arabidopsis calcium-dependent protein kinases (CPKs) cpk3/4/6/11 disrupt ABA-induced trafficking and degradation of RopGEF1. Moreover, cpk3/4/6/11 partially impairs ABA inhibition of germination. Several CPKs interact with RopGEF1. CPK4 binds to and phosphorylates RopGEF1 and promotes the degradation of RopGEF1. CPK-mediated phosphorylation of RopGEF1 at specific N-terminal serine residues causes the degradation of RopGEF1 and mutation of these sites also compromises the RopGEF1 over-expression phenotype in root hair development in Arabidopsis. Our findings establish the physiological and molecular functions and relevance of calcium-dependent protein kinases in regulation of RopGEF1 and illuminate physiological roles of a CPK-GEF-ROP module in abscisic acid signaling and plant development. We further discuss that CPK-dependent RopGEF degradation during abiotic stress could provide a mechanism for down-regulation of RopGEF-dependent growth responses.
2019-11-12 | PXD009422 | Pride
Project description:Abscisic acid (ABA) plays essential roles in plant development and responses to environmental stress. ABA induces subcellular translocation and degradation of the guanine nucleotide exchange factor RopGEF1 thus facilitating ABA core signal transduction. However, the underlying mechanisms for ABA-triggered RopGEF1 trafficking/degradation remain unknown. Studies have revealed that RopGEFs associate with receptor-like kinases to convey developmental signals to small ROP GTPases. However, how the activities of RopGEFs are modulated is not well understood. Type 2C protein phosphatases stabilize the RopGEF1 protein, indicating that phosphorylation may trigger RopGEF1 trafficking and degradation. We have screened inhibitors followed by several protein kinase mutants and find that quadruple mutant plants in the Arabidopsis calcium-dependent protein kinases (CPKs) cpk3/4/6/11 disrupt ABA-induced trafficking and degradation of RopGEF1. Moreover, cpk3/4/6/11 partially impairs ABA inhibition of germination. Several CPKs interact with RopGEF1. CPK4 binds to and phosphorylates RopGEF1 and promotes the degradation of RopGEF1. CPK-mediated phosphorylation of RopGEF1 at specific N-terminal serine residues causes the degradation of RopGEF1 and mutation of these sites also compromises the RopGEF1 over-expression phenotype in root hair development in Arabidopsis. Our findings establish the physiological and molecular functions and relevance of calcium-dependent protein kinases in regulation of RopGEF1 and illuminate physiological roles of a CPK-GEF-ROP module in abscisic acid signaling and plant development. We further discuss that CPK-dependent RopGEF degradation during abiotic stress could provide a mechanism for down-regulation of RopGEF-dependent growth responses.
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Project description:High salinity is one of the major environmental factors, which hampers plant growth, development and productivity. To better understand the regulatory mechanisms by which plants cope with salt stress, we used genetic approaches to identify salt hypersensitive mutant 9 (sahy9), a new allele of apum23, in Arabidopsis thaliana. The sahy9/apum23 mutant seedlings display postgemination developmental arrest and later become bleached under agar plates supplemented with various salt stressors. Transcriptomic and proteomic analyses of the salt-treated sahy9/apum23 and wild-type seedlings revealed differential expression of genes with similar functional categories, primarily including cellular and metabolic processes, and abiotic and biotic stress responses. However, the consistency of gene expression at both transcript and protein levels is low (), suggesting the involvement of posttranscriptional processing in salt response. Furthermore, the altered gene/protein expression mediated by SAHY9/APUM23 in salt sensitivity is involved in several functional groups, particularly in ABA biosynthesis and signaling, abiotic stress response, LEA proteins, and ribosome biogenesis-related genes. Importantly, NCED3, a key gene involved in ABA biosynthesis, and major ABA responsive marker genes, such as RD20 and RD29B, are down-regulated at both transcript and protein levels in sahy9/apum23 under salt stress. Consistently, lower contents of ABA and proline, and expression changes of a subset of LEA proteins also support the nature of sahy9/apum23 showing salt hypersensitivity. Collectively, these data suggest that SAHY9/APUM23-mediated salt response is associated with ABA signaling pathway and its downstream stress responsive or tolerant genes.
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Project description:Pathak2013 - MAPK activation in response to various abiotic stresses
MAPK activation mechanism in response to various abiotic stress conditions, such as cold, salt, drought, H2O2, heavy metal and ethylene, in plants
This model is described in the article:
Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach.
Pathak RK, Taj G, Pandey D, Arora S, Kumar A.
Bioinformation 2013; 9(9): 443-449
Abstract:
Mitogen-Activated Protein Kinases (MAPKs) cascade plays an important role in regulating plant growth and development, generating cellular responses to the extracellular stimuli. MAPKs cascade mainly consist of three sub-families i.e. mitogen-activated protein kinase kinase kinase (MAPKKK), mitogen-activated protein kinase kinase (MAPKK) and mitogen activated protein kinase (MAPK), several cascades of which are activated by various abiotic and biotic stresses. In this work we have modeled the holistic molecular mechanisms essential to MAPKs activation in response to several abiotic and biotic stresses through a system biology approach and performed its simulation studies. As extent of abiotic and biotic stresses goes on increasing, the process of cell division, cell growth and cell differentiation slow down in time dependent manner. The models developed depict the combinatorial and multicomponent signaling triggered in response to several abiotic and biotic factors. These models can be used to predict behavior of cells in event of various stresses depending on their time and exposure through activation of complex signaling cascades.
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2024-09-02 | BIOMD0000000491 | BioModels