Expression of proteins in superior and inferior spikelets of rice during grain filling under different irrigation regimes

Abstract

Poor grain filling of later-flowering inferior spikelets is a serious problem in modern rice cultivars, but the reason and regulation remain unclear. This study investigated post-anthesis protein expression in relation with grain filling and the possibility to use irrigation methods to enhance grain filling through regulating protein expression. One japonica rice cultivar was field-grown under three irrigation treatments imposed during the grain filling period: alternate wetting and moderate soil-drying (WMD), alternate wetting and severe soil-drying (WSD), and conventional irrigation. High resolution 2DE, combined with MALDI/TOF, was used to compare differential protein expression between superior and inferior spikelets. Results showed that the expression of proteins that function in photosynthesis, carbohydrate and energy metabolism, amino acids metabolism and defense responses were largely down-regulated in inferior spikelets compared to those in superior spikelets. The WMD treatment enhanced grain filling rate and the expression of these proteins, whereas the WSD treatment decreased them. Similar results were observed for transcript levels of the genes encoding these proteins. These results suggest that down-regulated expression of the proteins associated with grain filling contribute to the poor grain filling of inferior spikelets, and post-anthesis WMD could improve grain filling through regulating protein expression in the spikelets.

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

“…Such findings suggested that those biological processes including protein and major CHO metabolism as well as photosynthesis are likely to be negatively affected during rice grain-filling in IS, while the processes of development and stress responses are highly correlated with the poor graining of IS. More interestingly, in this study, the number of proteins with reduced abundances is 3–4 times more than the number of proteins with increased abundances, similar to a previous gel-based proteomics investigation comparing the grain-filling process between IS and SS (Chen et al, 2016). In addition, we analyzed the identified proteins from SWATH-MS data using a multifaceted bioinformatic approach for the comprehensive elaboration of differentially expressed proteins between IS and SS.…”

“…The overall down-regulation of photosynthesis-related proteins in IS possibly led to an unfavorable environment that in turn affected the activity of enzymes involved in glycolysis and sucrose-to-starch conversion, thus contributing to the poor graining of IS. Moreover, abundances of proteins involved in the photosynthetic photorespiration (Os03g57220 and Os12g22030) and Calvin cycle (e.g., Os03g03720 and Os01g02880) were also shown to be decreased in IS compared to SS, consistent with the photosynthetic proteome changes occurring in previous investigation of proteome changes between IS and SS (Zhang et al, 2014; Chen et al, 2016). However, the number of photosynthesis-related proteins identified in this study were three–fourfold more in comparison to the proteomics data of previous 2D gel-based studies between IS and SS (Zhang et al, 2014, 2015), indicating a high throughput and accuracy advantage of SWATH-based technology used in this study and also enrich the understanding of photosynthesis proteins involve the grain-filling process.…”

“…Proteome changes in protein metabolism category included protein biosynthesis, folding and activation as well as degradation. A total of 51 proteins involved in protein synthesis were identified by SWATH-MS analysis in this study, which were substantially higher in terms of number of the translation-related proteins reported previously for the proteomes comparison between IS and SS (Zhang et al, 2015; Chen et al, 2016). Among them, there were 41 ribosomal proteins, which have been linked with cell structure and plant development (Yao et al, 2008), six proteins involved in translation initiation and four proteins involved in elongation showed reduced abundance in IS during the grain-filling ( Supplementary Table S1 ), suggesting an suppression of translational activities in the IS development.…”

“…Few proteomic investigations on differential grain-filling between rice IS and SS were carried out previously using 2D gel-based approaches (Zhang et al, 2014; Chen et al, 2016). However, this approach does not provide accurate quantification and large-scale identification of differentially expressed proteins (Zhang et al, 2014; Chen et al, 2016).…”

“…However, this approach does not provide accurate quantification and large-scale identification of differentially expressed proteins (Zhang et al, 2014; Chen et al, 2016). In this study, the changes in the proteome profile between rice IS and SS during the grain-filling process were examined using the recently developed SWATH-MS (Sequential Window Acquisition of All Theoretical Mass Spectra -Mass Spectrometry)-based quantitative proteomics approach in combination with bioinformatic analysis.…”