Abstract
BACKGROUND: Protein phosphorylation regulated by plant hormone is involved in the coordination of fundamental plant development. Brassinosteroids (BRs), a group of phytohormones, regulated phosphorylation dynamics remains to be delineated in plants. In this study, we performed a mass spectrometry (MS)-based phosphoproteomics to conduct a global and dynamic phosphoproteome profiling across five time points of BR treatment in the period between 5 min and 12 h. MS coupling with phosphopeptide enrichment techniques has become the powerful tool for profiling protein phosphorylation. However, MS-based methods tend to have data consistency and coverage issues. To address these issues, bioinformatics approaches were used to complement the non-detected proteins and recover the dynamics of phosphorylation events. RESULTS: A total of 1104 unique phosphorylated peptides from 739 unique phosphoproteins were identified. The time-dependent gene ontology (GO) analysis shows the transition of biological processes from signaling transduction to morphogenesis and stress response. The protein-protein interaction analysis found that most of identified phosphoproteins have strongly connections with known BR signaling components. The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families. To uncover the dynamic activities of kinases, the enriched motifs were combined with phosphorylation profiles and revealed that the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively. The time-dependent kinase-substrate interaction networks were constructed and showed many substrates are the downstream of other signals, such as auxin and ABA signaling. While comparing BR responsive phosphoproteome and gene expression data, we found most of phosphorylation changes were not led by gene expression changes. Our results suggested many downstream proteins of BR signaling are induced by phosphorylation via various kinases, not through transcriptional regulation. CONCLUSIONS: Through a large-scale dynamic profile of phosphoproteome coupled with bioinformatics, a complicated kinase-centered network related to BR-regulated growth was deciphered. The phosphoproteins and phosphosites identified in our study provide a useful dataset for revealing signaling networks of BR regulation, and also expanded our knowledge of protein phosphorylation modification in plants as well as further deal to solve the plant growth problems.
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Claims 13
Claim · model-written summary
The phosphoproteome analysis identified 1104 phosphorylated peptides from 739 phosphoproteins.
- Taxon
- Arabidopsis
Arabidopsist0 - Outcome
- unique phosphorylated peptidese0
- Value
- 1104 unique phosphorylated peptidese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A total of 1104 unique phosphorylated peptides from 739 unique phosphoproteins were identified.”
t0“Arabidopsis”
Claim · model-written summary
The same analysis identified 739 unique phosphoproteins.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- unique phosphoproteinse0
- Value
- 739 unique phosphoproteinse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A total of 1104 unique phosphorylated peptides from 739 unique phosphoproteins were identified.”
t0“Arabidopsis”
Claim · model-written summary
Time-dependent GO analysis showed a shift from signaling transduction to morphogenesis and stress response.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- transition of biological processes from signaling transduction to morphogenesis and stress responsee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The time-dependent gene ontology (GO) analysis shows the transition of biological processes from signaling transduction to morphogenesis and stress response.”
t0“Arabidopsis”
Claim · model-written summary
Most identified phosphoproteins were strongly connected to known BR signaling components.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- identified phosphoproteinse0
- Outcome
- strongly connections with known BR signaling componentse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The protein-protein interaction analysis found that most of identified phosphoproteins have strongly connections with known BR signaling components.”
t0“Arabidopsis”
Claim · model-written summary
Motif-X identified 15 enriched motifs.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- enriched motifse0
- Value
- 15 enriched motifse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families.”
t0“Arabidopsis”
Claim · model-written summary
Eleven enriched motifs corresponded to six known kinase families.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- motifs, 11 of which correspond to 6 known kinase familiese0
- Value
- 11 of which correspond to 6 known kinase familiese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The analysis by using Motif-X was performed to identify 15 enriched motifs, 11 of which correspond to 6 known kinase families.”
t0“Arabidopsis”
Claim · model-written summary
Casein kinase 2 substrates were significantly phosphorylated at the start of BR treatment.
- Taxon
- ArabidopsisArabidopsist0
- Treatment
- BR treatmente0
- Gene
- casein kinase 2e0
- Outcome
- substrates of casein kinase 2e0
- Direction
- phosphorylatede0
- Qualifier
- initial timee0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively.”
t0“Arabidopsis”
Claim · model-written summary
Mitogen-activated protein kinase substrates were significantly dephosphorylated at the start of BR treatment.
- Taxon
- ArabidopsisArabidopsist0
- Treatment
- BR treatmente0
- Gene
- mitogen-activated protein kinasee0
- Outcome
- substrates of casein kinase 2 and mitogen-activated protein kinasee0
- Direction
- dephosphorylatede0
- Qualifier
- initial timee0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the substrates of casein kinase 2 and mitogen-activated protein kinase were significantly phosphorylated and dephosphorylated at initial time of BR treatment, respectively.”
t0“Arabidopsis”
Claim · model-written summary
Time-dependent kinase-substrate networks indicated many substrates downstream of auxin and ABA signals.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- many substrates are the downstream of other signals, such as auxin and ABA signalinge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The time-dependent kinase-substrate interaction networks were constructed and showed many substrates are the downstream of other signals, such as auxin and ABA signaling.”
t0“Arabidopsis”
Claim · model-written summary
Most BR-responsive phosphorylation changes were not driven by gene expression changes.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- gene expression changese0
- Outcome
- phosphorylation changese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we found most of phosphorylation changes were not led by gene expression changes.”
t0“Arabidopsis”
Claim · model-written summary
The authors interpret downstream BR signaling proteins as being induced by kinase phosphorylation rather than transcriptional regulation.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- various kinasese0
- Outcome
- downstream proteins of BR signalinge0
- Qualifier
- not through transcriptional regulatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“many downstream proteins of BR signaling are induced by phosphorylation via various kinases, not through transcriptional regulation.”
t0“Arabidopsis”
Claim · model-written summary
The study deciphered a kinase-centered network related to BR-regulated growth.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- kinase-centered network related to BR-regulated growthe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a complicated kinase-centered network related to BR-regulated growth was deciphered.”
t0“Arabidopsis”
Claim · model-written summary
The identified phosphoproteins and phosphosites provide a dataset for BR signaling studies.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- useful dataset for revealing signaling networks of BR regulatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The phosphoproteins and phosphosites identified in our study provide a useful dataset for revealing signaling networks of BR regulation”
t0“Arabidopsis”