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

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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.

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Abbreviations

DAP:

Days after pollination

DP:

Differentially phosphorylated

FDR:

False discovery rate

MASS:

Mass spectrum

MAPK:

Mitogen-activated protein kinase

MLPK:

M-locus protein kinase

PTM:

Post-translational modification

SI:

Self-incompatibility

SRK:

S-locus receptor kinase

BR:

Brassinosteroid

IAA:

Indole-3-acetic acid

TCA:

Trichloroacetic acid

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Acknowledgments

We thank Dr. Zhiguo Er of China National Rice Research Institute for assistance in the bioinformatics analysis, Dr. Hana Mujahid of Mississippi State University, USA for critical review of the manuscript. This work was supported by Agricultural Sciences and Technologies Innovation Program of Chinese Academy of Agricultural Sciences (CAAS) to Rice Reproductive Developmental Biology Group, “Elite Youth” Program (CAAS) to Jian Zhang, and National Natural Science Foundation of China (Grant Number: 31401366).

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    Authors and Affiliations

    1. State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, People’s Republic of China

      Jiehua Qiu, Yuxuan Hou, Xiaohong Tong, Yifeng Wang, Haiyan Lin, Qing Liu, Wen Zhang, Zhiyong Li & Jian Zhang

    2. Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA

      Babi R. Nallamilli

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    Corresponding author

    Correspondence to Jian Zhang.

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    Additional information

    Jiehua Qiu and Yuxuan Hou have contributed equally to this paper.

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    Supplementary Table 1

    The DP proteins identified in this study (XLSX 4625 kb)

    Supplementary Fig. 1

    Subcellular localization of KRP1–GFP fusion protein in rice protoplast cells. A nuclear marker protein, D53, fused with mKate, was used as a positive control. Scale bars = 5 mm. (a) 35S:KRP1-GFP; (b) 35S:D5-mKate; (c) bright field; (d) merged (EPS 2436 kb)

    Supplementary Fig. 2

    Enriched KEGG pathways of DP proteins. (a) Spliceosome; (b) basal transcription factors; (c) snare interactions in vascular transport; (d) endocytosis. Red asterisks indicate the DP proteins detected in this study (EPS 9567 kb)

    Supplementary Fig. 3

    Mass spectrum maps of the four identified phosphopeptides from rice TRAB1 (LOC_Os08g36790) (EPS 19911 kb)

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    Qiu, J., Hou, Y., Tong, X. et al. Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.). Plant Mol Biol 90, 249–265 (2016). https://doi.org/10.1007/s11103-015-0410-2

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    • DOI: https://doi.org/10.1007/s11103-015-0410-2

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