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Key Message: Sixty-three proteins were identified to be differentially accumulated due to iron deficiency in shoot and root. The importance of these proteins alterations on shoot physiology is discussed. Iron (Fe) is an essential micronutrient for plant growth and its accumulation affects the quality of edible plant organs. To investigate the adaptive mechanism of a Chinese rice variety grown under iron deficiency, proteins differentially accumulated in leaves and roots of Yangdao 6, an indica cultivar, under Fe deficiency growth condition, were profiled using a two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS). The accumulations of seventy-three proteins were detected to be increased or decreased upon iron deficiency, and sixty-three of them were successfully identified. Among the sixty-three proteins, a total of forty proteins were identified in rice leaves, and twenty-three proteins were in roots. Most of these proteins are involved in photosynthesis, C metabolism, oxidative stress, Adenosine triphosphate synthesis, cell growth or signal transduction. The results provide a comprehensive way to understand, at the level of proteins, the adaptive mechanism used by rice shoots and roots under iron deficiency.

Background: Grain chalkiness is a complex trait adversely affecting appearance and milling quality, and therefore has been one of principal targets for rice improvement. Eliminating chalkiness from rice has been a daunting task due to the complex interaction between genotype and environment and the lack of molecular markers. In addition, the molecular mechanisms underlying grain chalkiness formation are still imperfectly understood., Results: We identified a notched-belly mutant (DY1102) with high percentage of white-belly, which only occurs in the bottom part proximal to the embryo. Using this mutant, a novel comparison system that can minimize the effect of genetic background and growing environment was developed. An iTRAQ-based comparative display of the proteins between the bottom chalky part and the upper translucent part of grains of DY1102 was performed. A total of 113 proteins responsible for chalkiness formation was identified. Among them, 70 proteins are up-regulated and 43 down-regulated. Approximately half of these differentially expressed proteins involved in central metabolic or regulatory pathways including carbohydrate metabolism (especially cell wall synthesis) and protein synthesis, folding and degradation, providing proteomic confirmation of the notion that chalkiness formation involves diverse but delicately regulated pathways. Protein metabolism was the most abundant category, accounting for 27.4% of the total differentially expressed proteins. In addition, down regulation of PDIL 2-3 and BiP was detected in the chalky tissue, indicating the important role of protein metabolism in grain chalkiness formation., Conclusions: Using this novel comparison system, our comprehensive survey of endosperm proteomics in the notched-belly mutant provides a valuable proteomic resource for the characterization of pathways contributing to chalkiness formation at molecular and biochemical levels.

Nitrogen plays a central role in rice growth and development because it modulates a wide variety of processes, including cytokinin (CK) metabolism. CK-mediated signaling is also related to nitrogen metabolism. The functional relation between nitrogen and CK are extremely complex and unclear. In this study, a comparative proteomic analysis was carried out to analyze proteins regulated by nitrogen and CK in rice roots. Proteins extracted from rice roots are separated by two-dimensional polyacrylamide gel electrophoresis. Thirty-two protein spots that expressed similarly by nitrogen and CK treatments are selected for identification by mass spectrometry. Of these spots, 28 are successfully identified. These proteins were categorized into classes related to energy, metabolism, disease/defense, protein degradation, signal transduction, transposons, and unclear classification. Energy gives the largest functional category, suggesting that the glycolysis (two enzymes detected) and tricarboxylic acid cycle (six enzymes detected) are accurately regulated by nitrogen and CK, thus promoting the synthesis of amino acid. The identification of novel proteins provides new insights into the coordination of nitrogen and CK in rice. The possible role of these proteins is discussed.

With the intensification of global warming, rice production is facing new challenges. Field evidence indicates that elevated temperature during rice grain-filling leads to the further deterioration of grain quality. In order to clarify the potential regulatory mechanism of elevated temperature on the formation of rice quality, the DIA mass spectrometry method under the background of field warming was conducted to investigate the regulatory effects of high temperature on grain development and material accumulation pathways. The results showed that a total of 840 differentially expressed proteins were identified during the grain-filling process under elevated temperature. These differentially expressed proteins participated in carbon metabolism, amino acid biosynthesis, signal transduction, protein synthesis, and alternately affected the material accumulation of rice grains. The significant up-regulation of PPROL 14E, PSB28, granule-bound starch synthase I, and the significant down-regulation of 26.7 kDa heat shock protein would lead to the component difference in grain starch and storage proteins, and that could be responsible for the degradation of rice quality under elevated temperature. Results suggested that proteins specifically expressed under elevated temperature could be the key candidates for elucidating the potential regulatory mechanism of warming on rice development and quality formation. In-depth study on the metabolism of storage compounds would be contributed in further proposing high-quality cultivation control measures suitable for climate warming. [ABSTRACT FROM AUTHOR]

The size of rice leaves is tightly controlled by environmental and genetic factors. Several functional genes control leaf growth and development by regulating cell expansion and cell cycle activity. The regulation of leaf growth, particularly the effects of environmental conditions on leaf size, is still poorly understood. We examined the environmental control of leaf size in rice (Oryza sativa) by performing a comparative proteomic analysis, which showed that exposure to high-nitrogen levels produced enlarged leaves. The enhanced leaf growth occurred mainly as a result of an increased number of cell cycles. Two proteins related to cell division, FtsZ and ERBB3 binding protein, were increased by nitrogen treatment in the developing leaves. The expression of a type-A response regulator, OsRR2, was also elevated in developing leaves. OsRR2 acts as a negative regulator of cytokinin signaling and may reduce the cytokinin content in developing leaves; a low cytokinin level is necessary for leaf development. By analyzing the proteome response to nitrogen in both developing and mature leaves, we provide deeper insight into the mechanism by which nitrogen treatment affects the phenotype. [ABSTRACT FROM AUTHOR]

Apical dominance refers to the inhibition of shoot branching by the dominant shoot apex. The underlying mechanisms of apical dominance, especially in rice ( Oryza sativa), remain a subject of debate. Here, we studied apical dominance in the indica rice variety 'Yangdao 6' and carried out a comparative proteomic analysis to analyze the different levels of expression of proteins after decapitation. A total of 38 differentially expressed proteins in nodes and buds were successfully identified by MALDI-TOF/TOF and these proteins comprised ten functional categories. Among them, several proteins in this study involved in signal transduction, transporters, and cytokinin biosynthesis may play an important role in the mechanism of apical dominance. In addition, qRT-PCR was used to quantitate the expression levels of several genes in rice nodes and buds. The results showed that after decapitation, the expression level of a CK synthesis gene, OsLOG7, was reduced in buds, however, expression levels of several CK synthesis genes, OsIPTs, were markedly increased in nodes, indicating that after panicle removal, cytokinins were synthesized in nodes and subsequently delivered to buds, which will trigger release from dormancy in buds. Expression levels of several strigolactone-related genes were reduced in nodes after decapitation, which may become a factor facilitating auxin transport out of buds to stems. [ABSTRACT FROM AUTHOR]

In recent years, the application of proteomic approaches as a tool for global expression analysis and protein identification has been highly efficient in the field of plant research. A solution culture experiment involving two nitrogen treatments, 0.14 mM NHNO (low nitrogen (N)) and 1.07 mM NHNO (control), was conducted to investigate the response of rice root to low N stress. Root system architecture changed markedly under low N stress, with more lateral roots occurring on the lower part of adventitious roots and longer lateral roots on the upper part, compared to the control. A proteomic approach was employed to further study the rice responses to low N stress. Proteins extracted from roots were profiled by two-dimensional gel electrophoresis, and differentially expressed proteins were analyzed by mass spectrometry. Twelve protein spots were successfully identified by mass spectrometry, 11 of which had known functions. Of these, four were involved with the tricarboxylic acid cycle, two with adenylate metabolism, two with phenylpropanoid metabolism, and two with protein degradation. These differentially expressed proteins play an important role in the responsive mechanisms of rice root to low N stress, and uncovering how the rice proteins respond to low N stress could contribute to improving the nitrogen use efficiency. [ABSTRACT FROM AUTHOR]