Dataset Information

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling.

ABSTRACT: Modern rice cultivars have large panicle but their yield potential is often not fully achieved due to poor grain-filling of late-flowering inferior spikelets (IS). Our earlier work suggested a broad transcriptional reprogramming during grain filling and showed a difference in gene expression between IS and earlier-flowering superior spikelets (SS). However, the links between the abundances of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied to investigate SS and IS proteomes. A total of 304 proteins of widely differing functionality were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundances of most of the differentially expressed proteins are not correlated to the respective transcript levels, indicating that an extra layer of gene regulation which may exist during rice grain filling. Our findings raised an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.

SUBMITTER: Zhu FY

PROVIDER: S-EPMC5169098 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling.

Zhu Fu-Yuan FY Chen Mo-Xian MX Su Yu-Wen YW Xu Xuezhong X Ye Neng-Hui NH Cao Yun-Ying YY Lin Sheng S Liu Tie-Yuan TY Li Hao-Xuan HX Wang Guan-Qun GQ Jin Yu Y Gu Yong-Hai YH Chan Wai-Lung WL Lo Clive C Peng Xinxiang X Zhu Guohui G Zhang Jianhua J

Frontiers in plant science 20161220

Modern rice cultivars have large panicle but their yield potential is often not fully achieved due to poor grain-filling of late-flowering inferior spikelets (IS). Our earlier work suggested a broad transcriptional reprogramming during grain filling and showed a difference in gene expression between IS and earlier-flowering superior spikelets (SS). However, the links between the abundances of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window a ...[more]

PMID: 28066479

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Project description:BackgroundThe asynchronous filling between superior spikelets (SS) and inferior spikelets (IS) in rice has become a research hotspot. The stagnant development and poor grain filling of IS limit yields and the formation of good quality rice. A large number of studies on this phenomenon have been carried out from the genome, transcriptome and proteome level, indicating that asynchronous filling of SS and IS filling is a complex, but orderly physiological and biochemical process involving changes of a large number of genes, protein expression and modification. However, the analysis of metabolomics differences between SS and IS is rarely reported currently.ResultsThis study utilized untargeted metabolomics and identified 162 metabolites in rice spikelets. Among them, 17 differential metabolites associated with unsynchronized grain filling between SS and IS, 27 metabolites were related to the stagnant development of IS and 35 metabolites related to the lower maximum grain-filling rate of IS compared with the SS. We found that soluble sugars were an important metabolite during grain filling for SS and IS. Absolute quantification was used to further analyze the dynamic changes of 4 types of soluble sugars (sucrose, fructose, glucose, and trehalose) between SS and IS. The results showed that sucrose and trehalose were closely associated with the dynamic characteristics of grain filling between SS and IS. The application of exogenous sugar showed that trehalose functioned as a key sugar signal during grain filling of IS. Trehalose regulated the expression of genes related to sucrose conversion and starch synthesis, thereby promoting the conversion of sucrose to starch. The difference in the spatiotemporal expression of TPS-2 and TPP-1 between SS and IS was an important reason that led to the asynchronous change in the trehalose content between SS and IS.ConclusionsThe results from this study are helpful for understanding the difference in grain filling between SS and IS at the metabolite level. In addition, the present results can also provide a theoretical basis for the next step of using metabolites to regulate the filling of IS.

Project description:BackgroundLarge-panicle rice varieties often fail to achieve their yield potential due to poor grain filling of late-flowering inferior spikelets (IS). The physiological and molecular mechanisms of poor IS grain filling, and whether an increase in assimilate supply could regulate protein abundance and consequently improve IS grain filling for japonica rice with large panicles is still partially understood.ResultsA field experiment was performed with two spikelet removal treatments at anthesis in the large-panicle japonica rice line W1844, including removal of the top 1/3 of spikelets (T1) and removal of the top 2/3 of spikelets (T2), with no spikelet removal as a control (T0). The size, weight, setting rate, and grain filling rate of IS were significantly increased after spikelet removing. The biological functions of the differentially expressed proteins (DEPs) between superior and inferior spikelets as well as the response of IS to the removal of superior spikelets (SS) were investigated by using iTRAQ at 10 days post anthesis. A total of 159, 87, and 28 DEPs were identified from group A (T0-SS/T0-IS), group B (T0-SS/T2-IS), and group C (T2-IS/T0-IS), respectively. Among these, 104, 63, and 22 proteins were up-regulated, and 55, 24, and 6 proteins were down-regulated, respectively. Approximately half of these DEPs were involved in carbohydrate metabolism (sucrose-to-starch metabolism and energy metabolism) and protein metabolism (protein synthesis, folding, degradation, and storage).ConclusionsReduced endosperm cell division and decreased activities of key enzymes associated with sucrose-starch metabolism and nitrogen metabolism are mainly attributed to the poor sink strength of IS. In addition, due to weakened photosynthesis and respiration, IS are unable to obtain a timely supply of materials and energy after fertilization, which might be resulted in the stagnation of IS development. Finally, an increased abundance of 14-3-3 protein in IS could be involved in the inhibition of starch synthesis. The removal of SS contributed to transfer of assimilates to IS and enhanced enzymatic activities of carbon metabolism (sucrose synthase, starch branching enzyme, soluble starch synthase, and pullulanase) and nitrogen metabolism (aspartate amino transferase and alanine amino transferase), promoting starch and protein synthesis in IS. In addition, improvements in energy metabolism (greater abundance of pyrophosphate-fructose 6-phosphate 1-phosphotransferase) might be played a vital role in inducing the initiation of grain filling. These results collectively demonstrate that carbohydrate supply is the main cause of poor IS grain filling.

Project description:Breeding programs for increasing spikelet number in rice have resulted in compactness of the panicle, accompanied by poor grain filling in inferior spikelets. Although the inefficient utilization of assimilate has been indicated as responsible for this poor grain filling, the underlying cause remains elusive. The current study utilized the suppression subtractive hybridization technique to identify 57 and 79 genes that overexpressed in the superior and inferior spikelets (with respect to each other), respectively, of the compact-panicle rice cultivar Mahalaxmi. Functional categorization of these differentially expressed genes revealed a marked metabolic difference between the spikelets according to their spatial location on the panicle. The expression of genes encoding seed storage proteins was dominant in inferior spikelets, whereas genes encoding regulatory proteins, such as serine-threonine kinase, zinc finger protein and E3 ligase, were highly expressed in superior spikelets. The expression patterns of these genes in the inferior and superior spikelets of Mahalaxmi were similar to those observed in another compact-panicle cultivar, OR-1918, but differed from those obtained in two lax-panicle cultivars, Upahar and Lalat. The results first suggest that the regulatory proteins abundantly expressed in the superior spikelets of compact-panicle cultivars and in both the superior and inferior spikelets of lax-panicle cultivars but poorly expressed in the inferior spikelets of compact-panicle cultivars promote grain filling. Second, the high expression of seed-storage proteins observed in the inferior spikelets of compact-panicle cultivars appears to inhibit the grain filling process. Third, the low expression of enzymes of the Krebs cycle in inferior spikelets compared with superior spikelets of compact-panicle cultivars is bound to lead to poor ATP generation in the former and consequently limit starch biosynthesis, an ATP-consuming process, resulting in poor grain filling.

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SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling.

Publications

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling.

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