Quantitative analysis of the grain amyloplast proteome reveals differences in metabolism between two wheat cultivars at two stages of grain development

Abstract

Background: Wheat (Triticum aestivum L.) is one of the world's most important grain crops. The amyloplast, a specialized organelle, is the major site for starch synthesis and storage in wheat grain. Understanding the metabolism in amyloplast during grain development in wheat cultivars with different quality traits will provide useful information for potential yield and quality improvement.

Results: Two wheat cultivars, ZM366 and YM49-198 that differ in kernel hardness and starch characteristics, were used to examine the metabolic changes in amyloplasts at 10 and 15 days after anthesis (DAA) using label-free-based proteome analysis. We identified 523 differentially expressed proteins (DEPs) between 10 DAA and 15 DAA, and 229 DEPs between ZM366 and YM49-198. These DEPs mainly participate in eight biochemical processes: carbohydrate metabolism, nitrogen metabolism, stress/defense, transport, energetics-related, signal transduction, protein synthesis/assembly/degradation, and nucleic acid-related processes. Among these proteins, the DEPs showing higher expression levels at 10 DAA are mainly involved in carbohydrate metabolism, stress/defense, and nucleic acid related processes, whereas DEPs with higher expression levels at 15 DAA are mainly carbohydrate metabolism, energetics-related, and transport-related proteins. Among the DEPs between the two cultivars, ZM366 had more up-regulated proteins than YM49-198, and these are mainly involved in carbohydrate metabolism, nucleic acid-related processes, and transport.

Conclusions: The results of our study indicate that wheat grain amyloplast has the broad metabolic capability. The DEPs involved in carbohydrate metabolism, nucleic acids, stress/defense, and transport processes, with grain development and cultivar differences, are possibly responsible for different grain characteristics, especially with respect to yield and quality-related traits.

Keywords: Amyloplast; Grain development; Proteome; Starch characteristics; Wheat.

Fig. 1

Starch granule size distribution of two wheat cultivars at 10 DAA and 15 DAA

Fig. 2

Function classifications of DEPs identified in wheat grain of cultivar ZM366 (A1, A2), and YM49–198 (B1, B2) at two grain developmental stages. A1, Up-regulation DEPs of wheat cultivar ZM366 from 10DAA to 15DAA; A2, Down-regulation DEPs of wheat cultivar ZM366 from 10DAA to 15DAA; B1, Up-regulation DEPs of wheat cultivar YM49–198 from 10DAA to 15DAA; B2, Down-regulation DEPs of wheat cultivar YM49–198 from 10DAA to 15DAA

Fig. 3

Hierarchical clustering analysis of DEPs identified in grain amyloplast during grain development. A1, A2: DEPs of ZM366 (A1) and YM49–198 (A2) involved in carbohydrate metabolism related proteins, including starch metabolism (A1-I, A2-I), photosynthesis (A1-II, A2-II), glycolysis (A1-III, A2-III), and other carbohydrate metabolism (A1-IV, A2-IV). B1, B2: DEPs of ZM366 (B1) and YM49–198 (B2) involved in nucleic acid-related proteins, including histone (B1-I, B2-I), RNA binding (B1-II, B2-II), 40S/60S ribosomal protein (B1-III, B2-III), translation initiation/elongation factor (B1-IV, B2-IV), and other nucleic acid-related proteins (B1-V, B2-V). C1, C2: DEPs of ZM366 (C1) and YM49–198 (C2) involved in stress/defense proteins, including serpin (C1-I, C2-I), serine-type endospeptidase/alpha-amylase/trypsin inhibitor (C1-II, C2-II), chaperone/heat shock protein (C1-III, C2-III), antioxidant system (C1-IV, C2-IV), and other stress/defense related proteins (C1-V, C2-V). D1, D2: DEPs of ZM366 (D1) and YM49–198 (D2) involved in transport, including ADPG brittle (D1-I, D2-I), protein transporter (D1-II, D2-II), ADP, ATP carrier (D1-III, D2-III), and others transport proteins (D1-IV, D2-IV). E1, E2: DEPs of ZM366 (E1) and YM49–198 (E2) involved in protein synthesis/assembly/degradation. F1, F2: DEPs of ZM366 (F1) and YM49–198 (F2) involved in signal transduction. Red color, the higher abundance of protein expression; Green color, the lower abundance of protein expression

Fig. 4

The number of cultivar-specific expressed proteins and differentially expressed proteins of wheat cultivar ZM366 and YM49–198 at 10 DAA and 15 DAA, respectively. a, Number of cultivar-specific expressed proteins of ZM366 and YM49–198 at 10 DAA and 15 DAA. b, Number of differentially expressed proteins of ZM366 and YM49–198 at 10 DAA and 15 DAA

Fig. 5

Function classification of cultivar-specific expressed proteins identified in wheat grain amyloplast at 10 DAA and 15 DAA. (A10, A15), Function classification of cultivar-specific expressed proteins identified in wheat cultivar ZM366 at 10 DAA and 15 DAA, respectively. (B10, B15), Function classification of cultivar-specific expressed proteins identified in wheat cultivar YM49–198 at 10 DAA and 15 DAA, respectively

Fig. 6

Function classifications of DEPs identified in grain amyloplast between wheat cultivar ZM366 and YM49–198. A1, DEPs identified in wheat grain at 10 DAA; A2, DEPs identified in wheat grain at 15 DAA

Fig. 7

Comparison of protein and mRNA expression patterns of 7 representative DEPs at 10 DAA and 15 DAA. Pro-ZM and Pro-YM represent protein expression pattern of cultivar ZM366 and YM49–198, respectively. mRNA-ZM and mRNA-YM represent mRNA expression pattern of cultivar ZM366 and YM49–198, respectively. P1, P2, P3, P4, P5, P6, P7 represent protein A0A1D6D1Q3, A0A1D5YUK3, P12782, M7ZFX1, A0A1D5VEF1, and M8A7K2, respectively