Publication Information
Lin et al., 2015
Abstract
BMC Genomics. 2015 Jul 18;16(1):533. doi: 10.1186/s12864-015-1753-4.
Integrating Phosphoproteomics and Bioinformatics to Study
Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis.
Lin LL(1), Hsu CL(2), Hu CW(3), Ko SY(4), Hsieh HL(5), Huang HC(6), Juan
HF(7)(8)(9).
Author information:
(1)Department of Life Science, National Taiwan University, No. 1, Sec. 4,
Roosevelt Road, Taipei, 106, Taiwan. f94b43019@ntu.edu.tw.
(2)Department of Life Science, National Taiwan University, No. 1, Sec. 4,
Roosevelt Road, Taipei, 106, Taiwan. chialanghsu@ntu.edu.tw.
(3)Institute of Molecular and Cellular Biology, National Taiwan University, No.
1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. hkmq8195@yahoo.com.tw.
(4)Institute of Molecular and Cellular Biology, National Taiwan University, No.
1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. kirhun76@gmail.com.
(5)Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4,
Roosevelt Road, Taipei, 106, Taiwan. hlhsieh@ntu.edu.tw.
(6)Institute of Biomedical Informatics, Center for Systems and Synthetic
Biology, National Yang-Ming University, No.155, Sec.2, Linong Street, Taipei,
112, Taiwan. hsuancheng@ym.edu.tw.
(7)Department of Life Science, National Taiwan University, No. 1, Sec. 4,
Roosevelt Road, Taipei, 106, Taiwan. yukijuan@ntu.edu.tw.
(8)Institute of Molecular and Cellular Biology, National Taiwan University, No.
1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. yukijuan@ntu.edu.tw.
(9)Graduate Institute of Biomedical Electronic and Bioinformatics, National
Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan.
yukijuan@ntu.edu.tw.
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.
DOI: 10.1186/s12864-015-1753-4
PMCID: PMC4506601
PMID: 26187819 [Indexed for MEDLINE]
