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. 2015 Jul 31;10(7):e0133696.
doi: 10.1371/journal.pone.0133696. eCollection 2015.

Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.)

Shuzhen Wang  1 , Wenyue Chen  2 , Wenfei Xiao  2 , Changdeng Yang  3 , Ya Xin  2 , Jieren Qiu  2 , Weimin Hu  4 , Wu Ying  2 , Yaping Fu  3 , Jianxin Tong  2 , Guocheng Hu  3 , Zhongzhong Chen  2 , Xianping Fang  2 , Hong Yu  2 , Wenguo Lai  2 , Songlin Ruan  2 , Huasheng Ma  2
Affiliations

Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.)

Shuzhen Wang et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Phenotype of rice hull in three growth stages.
A, awn; AN, anther; L, lemma; P, palea; PK1, booting stage; PK2, flowering stage; PK3, milk-ripe stage.
Fig 2
Fig 2. Quantitative comparison of protein expression in the three developmental stages.
(A) Hierarchical clustering analysis of protein expression in three growth stages of rice hull. (B) Protein expression correlations in three growth stages of rice hull. PK1, booting stage; PK2, flowering stage; PK3, milk-ripe stage.
Fig 3
Fig 3. Gene ontology analysis of differentially expressed proteins in three growth stages of rice hull.
PK1, booting stage; PK2, flowering stage; PK3, milk-ripe stage.
Fig 4
Fig 4. Molecular function analysis of differentially expressed proteins in three growth stages of rice hull.
P1, booting stage; P2, flowering stage; P3, milk-ripe stage.
Fig 5
Fig 5. Validation of differentially expressed proteins in chlorophyll biosynthesis pathways.
P1, booting stage; P2, flowering stage; P3, milk-ripe stage.
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