title: Integrating Phosphoproteomics and Bioinformatics to Study Brassinosteroid-Regulated Phosphorylation Dynamics in Arabidopsis.
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.
authors.affiliation: Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. f94b43019@ntu.edu.tw.
authors.forename: Li-Ling
authors.initials: LL
authors.lastname: Lin
authors.affiliation: Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. chialanghsu@ntu.edu.tw.
authors.forename: Chia-Lang
authors.initials: CL
authors.lastname: Hsu
authors.affiliation: Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. hkmq8195@yahoo.com.tw.
authors.forename: Chia-Wei
authors.initials: CW
authors.lastname: Hu
authors.affiliation: Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. kirhun76@gmail.com.
authors.forename: Shiao-Yun
authors.initials: SY
authors.lastname: Ko
authors.affiliation: Institute of Plant Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. hlhsieh@ntu.edu.tw.
authors.forename: Hsu-Liang
authors.initials: HL
authors.lastname: Hsieh
authors.affiliation: 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.
authors.forename: Hsuan-Cheng
authors.initials: HC
authors.lastname: Huang
authors.affiliation: Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. yukijuan@ntu.edu.tw.|Institute of Molecular and Cellular Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. yukijuan@ntu.edu.tw.|Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 106, Taiwan. yukijuan@ntu.edu.tw.
authors.forename: Hsueh-Fen
authors.initials: HF
authors.lastname: Juan
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D060406:Brassinosteroids / Q000378:metabolism*; D019295:Computational Biology; D010750:Phosphoproteins / Q000096:biosynthesis* / Q000235:genetics; D010766:Phosphorylation / Q000235:genetics*; D040901:Proteomics
chemical_list: D060406:Brassinosteroids; D010750:Phosphoproteins