Analysis of phosphoproteome in rice pistil

Abstract

As the female reproductive part of a flower, the pistil consists of the ovary, style, and stigma, and is a critical organ for the process from pollen recognition to fertilization and seed formation. Previous studies on pollen–pistil interaction mainly focused on gene expression changes with comparative transcriptomics or proteomics method. However, studies on protein PTMs are still lacking. Here we report a phosphoproteomic study on mature pistil of rice. Using IMAC enrichment, hydrophilic interaction chromatography fraction and high‐accuracy MS instrument (TripleTOF 5600), 2347 of high‐confidence (Ascore ≥ 19, p ≤ 0.01), phosphorylation sites corresponding to 1588 phosphoproteins were identified. Among them, 1369 phosphorylation sites within 654 phosphoproteins were newly identified; 41 serine phosphorylation motifs, which belong to three groups: proline‐directed, basophilic, and acidic motifs were identified after analysis by motif‐X. Two hundred and one genes whose phosphopeptides were identified here showed tissue‐specific expression in pistil based on information mining of previous microarray data. All MS data have been deposited in the ProteomeXchange with identifier PXD000923 (http://proteomecentral.proteomexchange.org/dataset/PXD000923). This study will help us to understand pistil development and pollination on the posttranslational level.

A Quantitative Proteomic Analysis of Brassinosteroid-induced Protein Phosphorylation in Rice (Oryza sativa L.)

“…Of the phosphosites detected at 0 h, 89.7% were phosphoserine, 9.9% were phosphothreonine, and 0.4% were phosphotyrosines ( Figure 1B ), and the proportions were similar at the other two sampling times. Emerging evidences have shown that the distribution ratios of phosphorylation amino acids are much conserved in plants, despite the great variety of species, tissue and treatment applied (Han et al, 2014; Lv et al, 2014; Wang K. et al, 2014; Zhang M. et al, 2014; Hou et al, 2015; Qiu et al, 2016). In the three samples, 92.9–93.3% of the peptides carried only one phosphorylation group, 6.5–6.8% of the peptides carried two phosphorylation modifications, whereas only less than 0.3% of peptides had more than two phosphorylation modifications ( Figure 1C ).…”

Assessment of Hepatocellular Carcinoma Metastasis Glycobiomarkers Using Advanced Quantitative N-glycoproteome Analysis

“…Motif extractor (Motif-X, http://motif-x.med.harvard.edu) was used to identify overrepresented glycosylation motifs. Proteins annotated in International Protein Index (IPI) human proteome database were used as background and the significance value was set as 0.000001 (Schwartz and Gygi, 2005; Chou and Schwartz, 2011; Wang et al, 2014; Zhang et al, 2015). …”

Abundant protein phosphorylation potentially regulates Arabidopsis anther development

“…Another phosphoproteomic study identified 139 phosphoproteins from mature pollen grains and germinating pollen in tobacco (Fila et al , 2012). Also, Wang et al (2014) performed a large scale phosphoproteomic analysis using rice pistil tissue and identified 2347 phosphorylation sites from 1588 phosphoproteins.…”