title: Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.).
abstract: Rice hull, the outer cover of the rice grain, determines grain shape and size. Changes in the rice hull proteome in different growth stages may reflect the underlying mechanisms involved in grain development. To better understand these changes, isobaric tags for relative and absolute quantitative (iTRAQ) MS/MS was used to detect statistically significant changes in the rice hull proteome in the booting, flowering, and milk-ripe growth stages. Differentially expressed proteins were analyzed to predict their potential functions during development. Gene ontology (GO) terms and pathways were used to evaluate the biological mechanisms involved in rice hull at the three growth stages. In total, 5,268 proteins were detected and characterized, of which 563 were differentially expressed across the development stages. The results showed that the flowering and milk-ripe stage proteomes were more similar to each other (r=0.61) than either was to the booting stage proteome. A GO enrichment analysis of the differentially expressed proteins was used to predict their roles during rice hull development. The potential functions of 25 significantly differentially expressed proteins were used to evaluate their possible roles at various growth stages. Among these proteins, an unannotated protein (Q7X8A1) was found to be overexpressed especially in the flowering stage, while a putative uncharacterized protein (B8BF94) and an aldehyde dehydrogenase (Q9FPK6) were overexpressed only in the milk-ripe stage. Pathways regulated by differentially expressed proteins were also analyzed. Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), and two magnesium-chelatase subunits, ChlD (Q6ATS0), and ChlI (Q53RM0), were associated with chlorophyll biosynthesis at different developmental stages. The expression of Q9SDJ2 in the flowering and milk-ripe stages was validated by qRT-PCR. The 25 candidate proteins may be pivotal markers for controlling rice hull development at various growth stages and chlorophyll biosynthesis pathway related proteins, especially magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), may provide new insights into the molecular mechanisms of rice hull development and chlorophyll associated regulation.
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310012, China.
authors.forename: Shuzhen
authors.initials: S
authors.lastname: Wang
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Wenyue
authors.initials: W
authors.lastname: Chen
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Wenfei
authors.initials: W
authors.lastname: Xiao
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Changdeng
authors.initials: C
authors.lastname: Yang
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Ya
authors.initials: Y
authors.lastname: Xin
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Jieren
authors.initials: J
authors.lastname: Qiu
authors.affiliation: Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310012, China.
authors.forename: Weimin
authors.initials: W
authors.lastname: Hu
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Wu
authors.initials: W
authors.lastname: Ying
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Fu
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Tong
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
authors.forename: Guocheng
authors.initials: G
authors.lastname: Hu
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Zhongzhong
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Xianping
authors.initials: X
authors.lastname: Fang
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Yu
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Wenguo
authors.initials: W
authors.lastname: Lai
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Songlin
authors.initials: S
authors.lastname: Ruan
authors.affiliation: Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
authors.forename: Huasheng
authors.initials: H
authors.lastname: Ma
mesh_terms: D002853:Chromatography, Liquid; D063990:Gene Ontology; D017343:Genes, Plant; D012275:Oryza / Q000737:chemistry* / Q000235:genetics / Q000254:growth & development; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D040901:Proteomics; D060888:Real-Time Polymerase Chain Reaction; D053719:Tandem Mass Spectrometry
chemical_list: D010940:Plant Proteins