Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.)

Abstract

Rice (Oryza sativa L.) seed serves as a major food source for over half of the global population. Though it has been long recognized that phosphorylation plays an essential role in rice seed development, the phosphorylation events and dynamics in this process remain largely unknown so far. Here, we report the first large scale identification of rice seed phosphoproteins and phosphosites by using a quantitative phosphoproteomic approach. Thorough proteomic studies in pistils and seeds at 3, 7 days after pollination resulted in the successful identification of 3885, 4313 and 4135 phosphopeptides respectively. A total of 2487 proteins were differentially phosphorylated among the three stages, including Kip related protein 1, Rice basic leucine zipper factor 1, Rice prolamin box binding factor and numerous other master regulators of rice seed development. Moreover, differentially phosphorylated proteins may be extensively involved in the biosynthesis and signaling pathways of phytohormones such as auxin, gibberellin, abscisic acid and brassinosteroid. Our results strongly indicated that protein phosphorylation is a key mechanism regulating cell proliferation and enlargement, phytohormone biosynthesis and signaling, grain filling and grain quality during rice seed development. Overall, the current study enhanced our understanding of the rice phosphoproteome and shed novel insight into the regulatory mechanism of rice seed development.

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 ).…”

“…[sF] was annotated to be a low frequency motif in plants by a previous meta-analysis (van Wijk et al, 2014). However, it seemed to be not the case, at least in rice, because two recent studies both found that [sF] was over-represented in rice leaves and developing seeds (Hou et al, 2015; Qiu et al, 2016). In the current study, we detected 252 hits of [sF] in rice young seedlings, which again supported that [sF] is a highly conserved motif for phosphorylation.…”

NF‐YB1‐YC12‐bHLH144 complex directly activates Wx to regulate grain quality in rice (Oryza sativa L.)

“…The RNA of all the tissues except developing seeds was extracted by Trizol (Invitrogen, Carlsbad, CA). The extraction of developing seed RNA was conducted using a modified SDS-Trizol method (Qiu et al, 2016). RNA reverse transcrition and qRT-PCR were performed with technical triplicates as described by .…”

Genome-Wide Identification of lncRNAs During Rice Seed Development

“…Rice seed development starts from the pistils before pollination, further undergoes double fertilization, rapid proliferation and differentiation of the embryo, then the endosperm cells gradually differentiate into aleuronic cells and starch storage cells and finally to mature seeds. Pistils before pollination and seeds at around 3 and 7 DAP represent the three critical time points before fertilization, rapid division and differentiation of rice seed, respectively [19]. The experiment finally yielded 8.03 × 10 7 , 6.59 × 10 7 , 9.06 × 10 7 clean reads in 0, 3, 7 DAP datasets, respectively (Table S2).…”