Figures (10)  Tables (1)
    • Figure 1. 

      Characteristics of the ubiquitinated proteome of rice endosperm and QC validation of MS data. (a) Mass error distribution of all identified ubiquitinated peptides. (b) Peptide length distribution. (c) Frequency distribution of ubiquitinated proteins according to the number of ubiquitination sites identified.

    • Figure 2. 

      Analysis of ubiquitinated proteins and motifs. (a) Gene ontology (GO) functional characterization of ubiquitinated proteins. (b) Subcellular localization of ubiquitinated proteins. From the inside out, the ring represents 9311-C, 9311-H, GLA4-C and GLA4-H, respectively. (c) Motif enrichment analysis of ubiquitinated proteins.

    • Figure 3. 

      A temperature regulated rice endosperm ubiquitome. (a) The number of ubiquitinated proteins, peptides and sites detected in four group samples. (b) Venn diagram of ubiquitination sites (proteins) detected in four group samples. (c) PCA based on ubiquitination intensity across all four sample groups with three biological repetitions. (d) Differentially expression profiles of ubiquitination sites (proteins) in 9311 and GLA4 under high-temperature stress. The expression profiles of selected ubiquitination sites (p < 0.05, log2(fold-change) >1) were normalized using the Z-score and presented in a heatmap.

    • Figure 4. 

      Comparison of differentially ubiquitinated sites and proteins in 9311 and GLA4 under high-temperature stress.

    • Figure 5. 

      Enrichment analysis of differentially expressed ubiquitinated proteins based on Gene Ontology (GO) terms.

    • Figure 6. 

      KEGG classification and enrichment analysis of differentially ubiquitinated proteins. (a) Number of differentially ubiquitinated proteins based on KEGG classification in 9311 and GLA4. (b) KEGG enrichment analysis of differentially ubiquitinated proteins in 9311.

    • Figure 7. 

      Sucrose and starch pathway at the ubiquitination levels in rice endosperm under high-temperature stress.

    • Figure 8. 

      Structure of GBSSI. (a) Domain structure of GBSSI and ubiquitination sites with significant differences in response to high-temperature stress. (b) 3D model of GBSSI and the relationship between ubiquitination sites K462 and ADP, SO4 (salt bridge or hydrogen bond).

    • Figure 9. 

      Domain structure of (a) BEs, (b) PUL and (c) Pho1 as well as their ubiquitination sites with significant differences in response to heat stress. Residues in red indicate the ubiquitination site. Non-ubiquitinated residues are shown in dark grey.

    • Figure 10. 

      Ribosome system at the ubiquitination levels in rice endosperm under high-temperature stress. Grey shadings represent ubiquitinated proteins with no significant differences under heat stress. Red and blue shadings indicate up-regulated and down-regulated ubiquitinated proteins, respectively. Orange shading displays a combination of up- and down-regulated ubiquitinated sites in the same ubiquitinated protein.

    • Gene nameAnnotationProtein entryModification site(s)
      SUS1Sucrose synthase 1BGIOSGA010570K172, K177
      SUS2Sucrose synthase 2BGIOSGA021739K160, K165, K176, K804
      SUS3Sucrose synthase 3BGIOSGA026140K172, K177, K541, K544, K588
      FKFructokinaseBGIOSGA027875K143
      UGPaseUDP-glucose pyrophosphorylaseBGIOSGA031231K27, K150, K303, K306
      AGPS1ADP-glucose pyrophosphorylase small subunit 1BGIOSGA030039K94, K464, K484
      AGPS2ADP-glucose pyrophosphorylase small subunit 2BGIOSGA027135K106, K132, K385, K403, K406, K476, K496
      AGPL2ADP-glucose pyrophosphorylase large subunit 2BGIOSGA004052K41, K78, K134, K191, K227, K254, K316, K338, K394, K396, K463, K508, K513
      AGPL3ADP-glucose pyrophosphorylase large subunit 3BGIOSGA017490K509
      GBSSIGranule bound starch synthase IBGIOSGA022241K130, K173, K177, K181, K192, K258, K371, K381, K385, K399, K462, K517, K530, K549, K571, K575
      BEIStarch branching enzyme IBGIOSGA020506K103, K108, K122
      BEIIbStarch branching enzyme IIbBGIOSGA006344K134
      PULStarch debranching enzyme:PullulanaseBGIOSGA015875K230, K330, K431, K736, K884
      PHO1Plastidial phosphorylaseBGIOSGA009780K277, K445, K941

      Table 1. 

      Ubiquitination sites related to sucrose and starch metabolism in rice endosperm.