Identification of Structure-Controlling Rice Biosynthesis Enzymes

Starch molecular structure and diabetes

Starch is a primary source of food energy for human beings. Its chain-length distribution (CLD) is a major structural feature influencing physiologically-important properties, such as digestibility and palatability, of starch-containing foods. Diabetes, which is of epidemic proportions in many countries, is related to the rate of starch digestion in foods. Isoforms of three biosynthesis enzymes, starch synthase, starch branching enzymes and debranching enzymes, control the CLDs of starch, which can be measured by methods such as size-exclusion chromatography and fluorophore-assisted carbohydrate electrophoresis. Fitting observed CLDs to biosynthesis-based models based on the ratios of the activities of those isoforms yields biosynthesis-related parameters describing CLD features. This review examines CLD measurement, fitting CLDs to models, relations between CLDs, the occurrence and management of diabetes, and how plant breeders can develop varieties to optimize digestibility and palatability together, to develop starch-based foods with both a lower risk of diabetes and acceptable taste.

The effects of chain-length distributions on starch-related properties in waxy rices

Normal rice starch consists of amylopectin and amylose, whose relative amounts and chain-length distributions (CLDs) are major determinants of the digestibility and rheology of cooked rice, and are related to metabolic health and consumer preference. Here, the mechanism of how molecular structural features of pure amylopectin (waxy) starches affect starch properties was explored. Following debranching, chain-length distributions of seven waxy varieties were measured using size-exclusion chromatography, and parameterized using biosynthesis-based models, which involve breaking up the chain-length distribution into contributions from five enzyme sets covering overlapping ranges of chain length; structure-property correlations involving the fifth set were found to be statistically significant. Digestibility was measured in vitro, and parameters for the slower and longer digestion phase quantified using non-linear least-squares fitting. The coefficient for the significant correlation involving amylopectin fine structure for the fifth set was -0.903, while the amounts of amylopectin short and long chains were found to dominate breakdown viscosity (correlation coefficients 0.801 and - 0.911, respectively). This provides a methodology for finding or developing healthier starch in terms of lower digestion rate, while also having acceptable palatability. As rice breeders can to some extent control CLDs, this can help the development of waxy rices with improved properties.

Rheological properties of indica rice determined by starch structure related enzymatic activities during after-ripening

The processing quality of indica rice must undergo ripening after harvest to achieve stability and improvement. However, the mechanism underlying this process remains incompletely elucidated. Starch, the predominant component in indica rice, plays a crucial role in determining its properties. This study focused on analyzing the rheological properties and starch fine structure, as well as the related biosynthetic enzymes of indica rice during the after-ripening process. The results showed that after-ripened rice exhibited increased elastic modulus (G') and viscous modulus (G″), accompanied by a decrease in the loss tangent (Tan δ), indicating an enhancement in viscoelasticity and the gel network structure. Moreover, the proportions of amylopectin super long chains (DP 37-60) decreased, while those of medium chains (DP 13-24 and DP 25-36) or short chains (DP 6-12) of amylopectin increased. Additionally, the activities of starch branching enzyme (SBE) and starch debranching enzyme (DBE) declined over the after-ripening period. Pearson correlation analysis revealed that the rheological properties of after-ripened rice were correlated with the chain length distribution (CLD) of starch, which, in turn, was associated with its related endogenous enzymes. These findings provied new insights into understanding the quality changes of after-ripened indica rice.

Development of a model for granule-bound starch synthase I activity using free-energy calculations

Starch is a branched polymer of glucose with two components, both of which have (1 → 4)-α linear links and (1 → 6)-α branch points: amylopectin, of high molecular weight with many short branches, and amylose, of lower molecular weight and only a few long-chain branches. Granule-bound starch synthase I (GBSSI) is one of the main enzymes controlling amylose synthesis and chain-length distribution. As production of different GBSSI mutants is time-consuming and laborious, molecular dynamics (MD) simulations are used here to predict the binding of different GBSSI mutants to a representative amylose fragment. The simulations were atomistic, with explicit solvent and docking, a method successfully used to understand the binding of wild-type GBSSI to amylose fragments. The binding of GBSSI to G5 (a pentasaccharide amylose fragment) is combined with free-energy calculations employing a thermodynamic integration method to predict the effects of mutations on enzyme activity. Ten GBSSI mutants with different enzyme activities were analyzed to find the structural and energy changes among different single amino-acid mutants and their possible relationship to starch characteristics. Comparing the structural changes and the relative binding free energy of G5 to the wild type GBSSI and GBSSI mutants, it was found that mutants with negative binding energy (lower than -2.0 kcal/mol) are more likely to have higher enzyme activity and amylose content compared to the wild type. This theoretical paper used simulations and robust free energy calculations to interpret in planta data with potential predictions as to what mutants might be generated to give desired properties. This study can be used to help develop grains with improved functional properties.

Effects of the Molecular Structure of Starch in Foods on Human Health

Starch provides approximately half of humans' food energy, and its structural features influence human health. The most important structural feature is the chain length distribution (CLD), which affects properties such as the digestibility of starch-containing foods. The rate of digestion of such foods has a strong correlation with the prevalence and treatment of diseases such as diabetes, cardiovascular disease and obesity. Starch CLDs can be divided into multiple regions of degrees of polymerization, wherein the CLD in a given region is predominantly, but not exclusively, formed by a particular set of starch biosynthesis enzymes: starch synthases, starch branching enzymes and debranching enzymes. Biosynthesis-based models have been developed relating the ratios of the various enzyme activities in each set to the CLD component produced by that set. Fitting the observed CLDs to these models yields a small number of biosynthesis-related parameters, which, taken together, describe the entire CLD. This review highlights how CLDs can be measured and how the model-based parameters obtained from fitting these distributions are related to the properties of starch-based foods significant for health, and it considers how this knowledge could be used to develop plant varieties to provide foods with improved properties.

Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century

The eating and cooking quality (ECQ) of rice is critical for determining its economic value in the marketplace and promoting consumer acceptance. It has therefore been of paramount importance in rice breeding programs. Here, we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in rice. Innovations in gene- and genome-editing techniques have enabled improvements in rice ECQ. Significant genes and quantitative trait loci (QTLs) have been shown to regulate starch composition, thereby affecting amylose content and thermal and pasting properties. A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and aroma. Marker-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ properties. The post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.

Functional Interactions between Enzymes Involved in Amylose and Amylopectin Biosynthesis in Rice Based on Mathematical Models

Starch biosynthesis is controlled by multiple enzymes, including granule-bound starch synthase I (GBSSI), soluble starch synthases (SSs), branching enzymes (BEs), and debranching enzymes (DBEs). Although the role of individual isoforms has been primarily elucidated, the precise information about how they work together in the synthesis of specific amylose and amylopectin chains is still unclear. In this study, starch molecular chain-length distributions (CLDs) of five rice varieties with different amylose contents were measured by fluorophore-assisted carbohydrate electrophoresis and size-exclusion chromatography and fitted with two mathematical models, and the protein abundance of 11 starch synthesis-related enzymes was measured by western blotting. The correlation between model fitting parameters of amylose and amylopectin CLDs demonstrated that amylose and amylopectin syntheses are closely dependent. GBSSI could interact with BEI, BEIIb, SSIIa, SSIVb, ISA1, PUL, and PHO1 to synthesize the amylopectin intermediate and long chains as well as amylose chains. In addition, the interaction among SSIVb and SSI, SSIIa, BEI, BEIIb, ISA1, and PUL possibly suggests that SSIVb assists them to synthesize the amylopectin chains. The results can help understand the mechanisms about the functional interaction of different enzyme isoforms in starch biosynthesis.

Understanding the Binding of Starch Fragments to Granule-Bound Starch Synthase

Granule-bound starch synthase (GBSS) plays a major role, that of chain elongation, in the biosynthesis of amylose, a starch component with mostly (1 → 4)-α connected long chains of glucose with a few (1 → 6)-α branch points. Chain-length distributions (CLDs) of amylose affect functional properties, which can be controlled by changing appropriate residues on granule-bound starch synthase (GBSS). Knowing the binding of GBSS and amylose at a molecular level can help better determine the key amino acids on GBSS that affect CLDs of amylose for subsequent use in molecular engineering. Atomistic molecular dynamics simulations with explicit solvent and docking approaches were used in this study to build a model of the binding between rice GBSS and amylose. Amylose fragments containing 3-12 linearly linked glucose units were built to represent the starch fragments. The stability of the complexes, interactions between GBSS and sugars, and difference in structure/conformation of bound and free starch fragments were analyzed. The study found that starch/amylose fragments with 5 or 6 glucose units were suitable for modeling starch binding to GBSS. The removal of an interdomain disulfide on GBSS was found to affect both GBSS and starch stability. Key residues that could affect the binding ability were also indicated. This model can help rationalize the design of mutants and suggest ways to make single-point mutations, which could be used to develop plants producing starches with improved functional properties.