Comparative Phosphoproteomic Analysis of the Developing Seeds in Two Indica Rice (Oryza sativa L.) Cultivars with Different Starch Quality

Abstract

Protein phosphorylation plays important roles in regulation of various molecular events such as plant growth and seed development. However, its involvement in starch biosynthesis is less understood. Here, a comparative phosphoproteomic analysis of two indica rice cultivars during grain development was performed. A total of 2079 and 2434 phosphopeptides from 1273 and 1442 phosphoproteins were identified, covering 2441 and 2808 phosphosites in indica rice 9311 and Guangluai4 (GLA4), respectively. Comparative analysis identified 303 differentially phosphorylated peptides, and 120 and 258 specifically phosphorylated peptides in 9311 and GLA4, respectively. Phosphopeptides in starch biosynthesis related enzymes such as AGPase, SSIIa, SSIIIa, BEI, BEIIb, PUL, and Pho1were identified. GLA4 and 9311 had different amylose content, pasting viscosities, and gelatinization temperature, suggesting subtle difference in starch biosynthesis and regulation between GLA4 and 9311. Our study will give added impetus to further understanding the regulatory mechanism of starch biosynthesis at the phosphorylation level.

Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice

“…Recently, the phosphoproteins involved in starch biosynthesis of indica rice cultivars (9311 and Guangluai4) including AGPase (three sites) AGPS2 (five sites), SSIIa (one site), SSIIIa (one site), BEI (four sites), BEIIb (two sites), PUL (three sites) and Pho1 (two sites) were reported by Pang et al [ 28 ] ( Table 4 ).…”

“…In eukaryotes, the most common class of phosphorylation is found on serine (S), threonine (T), and tyrosine (Y) residues [ 96 , 97 ] in which the γ-phosphate group covalently reacts with the hydroxyl group of amino acid side chains by potein kinases [ 98 ]. A large scale of phosphosites and phosphoproteins has been identified using phosphoproteomic technologies in many cereals such as rice [ 27 , 28 , 31 , 99 , 100 , 101 , 102 , 103 ], wheat [ 104 , 105 , 106 , 107 , 108 ], barley [ 109 , 110 ], and maize [ 111 , 112 , 113 , 114 , 115 ]. Phosphoserine (>90%) is a major phosphorylation type of rice endosperm, followed by phosphothreonine (6–9%) and phosphotyrosine (0.1–0.4%) [ 28 , 31 ].…”

“…Using two-dimensional gel electrophoresis (2-DE)-based protein identification method equipped with mass spectrometric techniques, the profile of entire protein expression can be rapidly generated with highly reproducible [ 17 , 20 ], allowing for selection of the reasonable gene(s), which is possibly involved in regulatory mechanisms underlying starch biosynthesis [ 13 , 21 , 22 ]. In the last two decades, proteomic analyses of rice endosperm have been applied to a broad range of processes including differentially expressed proteins from the specific issues of plant tissues/organs [ 23 ], developmental stages [ 13 , 21 , 22 , 24 , 25 , 26 ], chalky and translucent parts [ 19 ], as well as under high temperature (HT) condition [ 13 , 27 , 28 ] in which the starch biosynthesis-related proteins were affected and reported.…”

“…Recently, a number of PTMs have been identified and verified by many highly effective techniques, coupled with database and bioinformatics tools. In rice endosperm, PTMs targeted starch biosynthesis proteins have been identified including phosphorylation [ 27 , 28 , 31 ], acetylation [ 30 , 32 , 33 , 34 ], succinylation [ 34 ], malonylation [ 35 ], and lysine 2-hydroxyisobutyrylation [ 36 ].…”

“…As the global population grows, it is expected that, by 2035, additional demand of approximately 112 million metric tons of rice needs to be produced to keep food security [ 37 ]. Understanding the function of proteomics and PTMs in rice seeds will contribute to our understanding of the mechanism and regulation of starch biosynthesis, which is one of the most important topics for high-yield and high-quality rice production [ 8 , 28 , 38 , 39 ]. This review summarizes the current knowledge in starch biosynthesis proteins through the studies of proteomics and PTMs, delving into the contribution of starch biosynthesis proteins to starch properties and functionality.…”