title: Proteomic Analysis of Phosphoproteins in the Rice Nucleus During the Early Stage of Seed Germination.
abstract: The early stage of seed germination is the first step in the plant life cycle without visible morphological change. To investigate the mechanism controlling the early stage of rice seed germination, we performed gel-and label-free nuclear phosphoproteomics. A total of 3467 phosphopeptides belonging to 102 nuclear phosphoproteins from rice embryos were identified. Protein-synthesis-related proteins were mainly phosphorylated. During the first 24 h following imbibition, 115 nuclear phosphoproteins were identified, and significant changes in the phosphorylation level over time were observed in 29 phosphoproteins. Cluster analysis indicated that nucleotide-binding proteins and zinc finger CCCH- and BED-type proteins increased in abundance during the first 12 h of imbibition and then decreased. The in silico protein-protein interactions for 29 nuclear phosphoproteins indicated that the Sas10/Utp3 protein, which functions in snoRNA binding and gene silencing, was the center of the phosphoprotein network in nuclei. The germination rate of seeds was significantly slowed with phosphatase inhibitor treatment. The mRNA expression of the zinc finger CCCH-type protein did not change, and the zinc finger BED-type protein was upregulated in rice embryos during the early stage of germination with phosphatase inhibitor treatment. These results suggest that the phosphorylation and dephosphorylation of nuclear proteins are involved in rice seed germination. Furthermore, transcription factors such as zinc finger CCCH- and BED-type proteins might play a key role through nuclear phosphoproteins, and Sas10/Utp3 protein might interact with nuclear phosphoproteins in rice embryos to mediate the early stage of seed germination.
authors.affiliation: †Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.|‡National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.affiliation: ‡National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
authors.forename: Xiaojian
authors.initials: X
authors.lastname: Yin
authors.affiliation: §Department of Life Science and Informatics, Maebashi Institute of Technology, Maebashi 371-0816, Japan.
authors.forename: Katsumi
authors.initials: K
authors.lastname: Sakata
authors.affiliation: †Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
authors.forename: Pingfang
authors.initials: P
authors.lastname: Yang
authors.affiliation: ‡National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
authors.forename: Setsuko
authors.initials: S
authors.lastname: Komatsu
mesh_terms: D018525:Germination; D013058:Mass Spectrometry; D009687:Nuclear Proteins / Q000032:analysis*; D012275:Oryza / Q000737:chemistry* / Q000196:embryology / Q000502:physiology; D010750:Phosphoproteins / Q000032:analysis*; D010940:Plant Proteins / Q000032:analysis*; D020543:Proteome; D012639:Seeds / Q000502:physiology*
chemical_list: D009687:Nuclear Proteins; D010750:Phosphoproteins; D010940:Plant Proteins; D020543:Proteome
keywords: germination; nucleus; phosphonetwork; phosphoproteomics; rice