Proteomic analysis of proteins related to rice grain chalkiness using iTRAQ and a novel comparison system based on a notched-belly mutant with white-belly

Abstract

BackgroundGrain chalkiness is a complex trait adversely affecting appearance and milling quality, and therefore has been one of principal targets for rice improvement. Eliminating chalkiness from rice has been a daunting task due to the complex interaction between genotype and environment and the lack of molecular markers. In addition, the molecular mechanisms underlying grain chalkiness formation are still imperfectly understood.ResultsWe identified a notched-belly mutant (DY1102) with high percentage of white-belly, which only occurs in the bottom part proximal to the embryo. Using this mutant, a novel comparison system that can minimize the effect of genetic background and growing environment was developed. An iTRAQ-based comparative display of the proteins between the bottom chalky part and the upper translucent part of grains of DY1102 was performed. A total of 113 proteins responsible for chalkiness formation was identified. Among them, 70 proteins are up-regulated and 43 down-regulated. Approximately half of these differentially expressed proteins involved in central metabolic or regulatory pathways including carbohydrate metabolism (especially cell wall synthesis) and protein synthesis, folding and degradation, providing proteomic confirmation of the notion that chalkiness formation involves diverse but delicately regulated pathways. Protein metabolism was the most abundant category, accounting for 27.4% of the total differentially expressed proteins. In addition, down regulation of PDIL 2–3 and BiP was detected in the chalky tissue, indicating the important role of protein metabolism in grain chalkiness formation.ConclusionsUsing this novel comparison system, our comprehensive survey of endosperm proteomics in the notched-belly mutant provides a valuable proteomic resource for the characterization of pathways contributing to chalkiness formation at molecular and biochemical levels.

Chalky part differs in chemical composition from translucent part of japonica rice grains as revealed by a notched‐belly mutant with white‐belly

“…Substantial advances in elucidating the mechanisms governing chalkiness formation have been made, as evidenced by the cloning of controlling genes like Chalk5 , and the comprehensive analysis of related enzymes and their regulatory pathways by the tools of proteomics and transcriptomics . However, the molecular and biochemical mechanisms underlying chalkiness formation are still imperfectly understood, owing to the complex interaction between genotype and environment.…”

“…A notched‐belly mutant (DY1102) with high occurrence of white‐belly grains was used in this study. Identification and characterization of the mutant were presented in detail in our previous report . Briefly, the mutant has a high percentage of notched‐belly grain (83%), of which 85% had white‐belly that occurs only in the bottom part proximal to the embryo (Fig.…”

“…Examined by scanning electron microscopy (SEM), disorganized starch granules was noted as a common feature of the opaque tissues, indicative of the incomplete development of amyloplast . Chemical analysis further showed that chalky grains differ from translucent kernels with respect to amylose content and amylopectin fine structure . Generally, chalky grains contained lower amylose content and showed a higher ratio of short branch‐chain of amylopectin in comparison with translucent grains, indicating that starch synthesis in chalky grains may slightly favor glucan chain branching over chain elongation.…”

Rice endosperm produces an underglycosylated and potent form of the HIV‐neutralizing monoclonal antibody 2G12

“…This hypothesis was supported by the greater abundance of PRO7, a seed storage protein and GRXC8 (glutaredoxin‐C8), an enzyme that scavenges reactive oxygen species (Lin et al ., ). In rice, prolamins accumulate in the PB‐I compartments which bud directly from the ER.…”

Effective Strategies for Enhancing Tolerance to High-Temperature Stress in Rice during the Reproductive and Ripening Stages

“…Meanwhile, accumulations of prolamin and globulin, but not of glutelin and albumin, are reduced under high temperatures (Yamakawa et al 2007;Lin et al 2010). Enhanced expression of small heat shock proteins or redox homeostasis-related genes under high temperatures is strongly correlated with the occurrence of chalky grains, as demonstrated in studies of various conventional cultivars and transgenic lines of rice (Lin et al 2005(Lin et al , 2014Liu et al 2010Liu et al , 2011. Metabolomic analysis of the developing caryopsis has indicated that high temperatures decrease the levels of glucose, fructose, most sugar phosphates, and organic acids involved in glycolysis/gluconeogenesis and the TCA cycle while increasing the amounts of sucrose, UDP-glucose, and ADP-glucose (Yamakawa and Hakata 2010).…”