Origin and evolution of the main starch biosynthetic enzymes

Starch, a semi-crystalline energy storage form primarily found in plant plastids plays a crucial role in various food or no-food applications. Despite the starch biosynthetic pathway's main enzymes have been characterized, their origin and evolution remained a subject of debate. In this study, we conducted the comprehensive phylogenetic and structural analysis of three types of starch biosynthetic enzymes: starch synthase (SS), starch branching enzyme (SBE) and isoamylase-type debranching enzyme (ISA) from 51,151 annotated genomes. Our findings provide valuable insights into the possible scenario for the origin and evolution of the starch biosynthetic pathway. Initially, the ancestor of SBE can be traced back to an unidentified bacterium that existed before the formation of the last eukaryotic common ancestor (LECA) via horizontal gene transfer (HGT). This transfer event likely provided the eukaryote ancestor with the ability to synthesize glycogen. Furthermore, during the emergence of Archaeplastida, one clade of SS was transferred from Deltaproteobacteria by HGT, while ISA and the other clade of SS originated from Chlamydiae through endosymbiosis gene transfer (EGT). Both these transfer events collectively contributed to the establishment of the original starch biosynthetic pathway. Subsequently, after the divergence of Viridiplantae from Rhodophyta, all three enzymes underwent multiple duplications and N-terminus extension domain modifications, resulting in the formation of functionally specialized isoforms and ultimately leading to the complete starch biosynthetic pathway. By shedding light on the evolutionary origins of key enzymes involved in the starch biosynthetic pathway, this study provides important insights into the evolutionary events of plants.

Hierarchical structural modification of starch via non-thermal plasma: A state-of-the-art review

The hierarchical architecture of natural and processed starches with different surface and internal structures determines their final physicochemical properties. However, the oriented control of starch structure presents a significant challenge, and non-thermal plasma (cold plasma, CP) has gradually been used to design and tailor starch macromolecules, though without clear illustration. In this review, the multi-scale structure (i.e., chain-length distribution, crystal structure, lamellar structure, and particle surface) of starch is summarized by CP treatment. The plasma type, mode, medium gas and mechanism are also illustrated, as well as their sustainable food applications, such as in food taste, safety, and packaging. The effects of CP on the chain-length distribution, lamellar structure, amorphous zone, and particle surface/core of starch includes irregularity due to the complex of CP types, action modes, and reactive conditions. CP-induced chain breaks lead to short-chain distributions in starch, but this rule is no longer useful when CP is combined with other physical treatments. The degree but not type of starch crystals is indirectly influenced by CP through attacking the amorphous region. Furthermore, the CP-induced surface corrosion and channel disintegration of starch cause changes in functional properties for starch-related applications.

A comparative evaluation of chemical composition and nutritional value of bamboo rice and major cereals reveals the potential utility of bamboo rice as functional food

Bamboo rice refers to the edible seeds collected from bamboo plants, but the nutritional and chemical compositions of bamboo rice are unknown. Here, we evaluated the nutritional value of two types of bamboo seeds by comparing them to rice and wheat. The fiber, protein, and microelement contents were much higher in bamboo seeds than in rice and wheat seeds. The flavonoids content was 5- and 10-folds higher in Moso bamboo seeds than in rice and wheat seeds, respectively. Amino acid profiles exhibited that most of amino acids were abundant in bamboo seeds compared to rice and wheat seeds. While water-soluble B vitamins and fatty acids in bamboo seeds were similar to those in rice and wheat seeds. Accordingly, rice and wheat may thus be substituted by bamboo rice which is a potentially functional food. Its high flavonoid content may be further exploited by the food industry.

Starch fine molecular structures: The basis for designer rice with slower digestibility and desirable texture properties

Development of whole rice with low glycaemic index has been achieved, however, these rices are frequently associated with a poor texture property. Recent advances in terms of understanding the importance of starch fine molecular structures on the starch digestibility/texture of cooked whole rice have shed new insights on mechanisms of starch digestibility and texture from molecular levels. With an extensive discussion on the correlative and causal relationships among starch molecular structure, texture and starch digestibility of cooked whole rice, this review identified desirable starch fine molecular structures contributing to both slow starch digestibility and preferable textures. For instance, the selection of rice variety having more amylopectin intermediate chains while less amylopectin long chains might help develop cooked whole rice with both slower starch digestibility and softer texture. The information could help rice industry transform cooked whole rice into a healthier food product with slow starch digestibility and desirable texture.

Influence of Resistant Starch in Whole Rice on Human Gut Microbiota─From Correlation Implications to Possible Causal Mechanisms

Rice is the main staple food for a large population around the world, while it generally has a high glycemic index and low resistant starch (RS) content. Although many strategies have been applied to develop healthier rice products with increased RS contents, their actual effects on gut microbiota and human health remain elusive. In this review, currently available production methods of rice RS are briefly summarized, followed by a critical discussion on their interactions with gut microbiota and subsequent effects on human health, from correlation implications to causal mechanisms. Different contents, types, and structures of RS have been produced by strategies such as genetic manipulation and controlling cooking conditions. The difference can largely determine effects of rice RS on gut microbiota composition and metabolites by specific RS-gut microbiota interactions. This review can thus help the rice industry develop rice products with desirable RS contents and structures to generally improve human health.

Combined effects of starch fine molecular structures and storage temperatures on long-term rice amylopectin retrogradation property

Though the retrogradation property as affected by starch fine molecular structures has been widely investigated, it remains largely unexplored how concurrent starch structures and storage conditions e.g. temperature tailor the starch retrogradation property. The amylopectin long-term retrogradation for 8 different rice starches with a broad range of amylose content was thus investigated under different storage temperatures. Results showed that gelatinized starch stored at -20 °C generally had a narrower melting temperature range from differential scanning calorimetry, while larger cells and thicker cell walls in the gel matrix than that stored at 4 °C. Different linear correlations were found between starch fine molecular structures and amylopectin retrogradation parameters when starch was stored under different temperatures. For example, the melting enthalpy of retrograded starch double helices was negatively correlated with the amount of amylose intermediate chains at 4 °C, while positively correlated with the relative length of amylopectin short chains at -20 °C. Under both temperatures, rice starch R250 had the highest retrogradation enthalpy. These results could help the rice industry improve both the nutritional and textural attributes of cooked rice by selecting starch with desirable molecular structures and optimizing the storage conditions for rice after cooking.

Consecutive reaction kinetics model reveals the nature of long-term rice amylopectin retrogradation characteristics

Starch retrogradation involves nucleation and crystal growth steps, while their relative contribution to the overall retrogradation kinetics and relations with starch fine molecular structures have not been elucidated. In this study, a consecutive reaction kinetics model (CRK) was developed to fit long-term retrogradation kinetics curves for 10 rice starches with distinct molecular structures. Starch chain-length distributions (CLDs) and melting enthalpy kinetics curves for these starches were obtained from our published data. It was shown that these melting enthalpy kinetics curves can be satisfactorily deconvoluted by the CRK model into a combination of nucleation and crystal growth curves. Correlation analysis between CRK model-fitted parameters with starch CLDs showed that starch retrogradation nucleation and crystal growth steps were controlled by distinct starch fine molecular structures. These results have practical applications, as it enables a separate regulation of nucleation and crystal growth steps during retrogradation process of starch-based foods for desirable nutritional properties.

Molecular brewing: The molecular structural effects of starch adjuncts on barley malt brewing performances

In this study, the effects of starch adjuncts with different fine molecular structures obtained by size-exclusion chromatography on the mashing and fermentation efficiencies of barley malts were investigated. Following fermentation, violate compounds of freshly-fermented beer samples were determined by headspace-solid-phase microextraction coupled with gas chromatography-mass spectrometry analysis (HS-SMPE-GC-MS). High performance liquid chromatography results showed that depending on their molecular structures, starch adjuncts addition significantly increased wort maltose and maltotriose content, whereas reducing the glucose content and thus both the ratios of glucose and maltotriose to that of the maltose. The whole fermentation by dry beer yeast was finished within the first 48 h and reached to equilibrium for the rest 72 h, represented by the stable soluble protein content. Results also showed that the addition of starch adjuncts resulted into increased alcohol content, which was mainly attributed to the altered glucose/maltose ratio. The HS-SPME-GC-MS results showed that whether or not with starch adjuncts addition, the composition of violate compounds were not significantly influenced, their content, on the contrary, were altered, represented by different peak heights. This study provides important information concerning the molecular effects of starch adjuncts on brewing performances of barley malts, and also provides a new pathway for choosing suitable types of adjuncts for making beer with better quality.

Align resistant starch structures from plant-based foods with human gut microbiome for personalized health promotion

Resistant starch (RS) is beneficial for human health through its interactions with gut microbiota. However, the alignment between RS structures with gut microbiota profile and consequentially health benefits remain elusive. This review summarizes current understanding of RS complex structures and their interactions with the gut microbiota, aiming to highlight the possibility of manipulating RS structures for a targeted and predictable gut microbiota shift for human health in a personalized way. Current definition of RS types is strongly associated with starch digestion behaviors in small intestine, which does not precisely reflect their interactions with human gut microbiota. Distinct alterations of gut microbiota could be associated with the same RS type. The principles to describe the specificity of different RS structural characteristics in terms of aligning with human gut microbiota shift was proposed in this review, which could result in new definitions of RS types from the microbial perspectives. To consider the highly variable personal features, a machine-learning algorithm to integrate different personalized factors and better understand the complex interaction between RS and gut microbiota and its effects on individual health was explained. This review contains important information to bring interactions between RS and gut microbiota to translational practice.

A kinetics-based decomposition approach to reveal the nature of starch asymmetric gelatinization thermograms at non-isothermal conditions

Starch gelatinization under non-isothermal conditions with limited moisture content is a common industrial process involved in the processing of many starchy foods, while the nature of its asymmetric differential scanning calorimetry thermograms is still undefinable. This study for the first time developed a kinetics-based mathematical model, which could yield a parameterization of gelatinization thermograms that are essentially the same as experimental ones. Even more, the model is capable of decomposing gelatinization thermograms into kinetics-based sub-patterns, and revealing hidden features. By applying this newly developed methodology to nine starches with different plant origins and correlated with their lamellar structures, the results indicated that distinctly arranged groups (sub-components) of semi-crystalline lamellae with different thermal stabilities are existed in the native starch granules. This gives ways to better understand starch structure-property relations, and suggests useful directions for food manufactures to produce functional foods by understanding and differentially controlling the starch gelatinization sub-components.

Expression Pattern of Starch Biosynthesis Genes in Relation to the Starch Molecular Structure in High-Amylose Maize

The molecular structure and the expression levels of starch biosynthesis-related genes of three types of high-amylose maize (HAM) genotypes and one normal maize (NM) genotype at 5-35 days after pollination (DAP) were studied. Size exclusion chromatography (SEC) analysis showed that the molecular size of amylopectin molecules in NM increased from 5 to 35 DAP and the amylose content in HAM genotypes increased from 15 to 35 DAP. Correlation analysis for both NM and HAMs combined showed that SBEIIb and ISAII were negatively correlated with the contents of amylose and long amylopectin chains (DP > 30) and positively correlated with the content of short amylopectin chains (DP ≤ 31) and the molecular size of amylopectin molecules. Correlation analysis for only the HAMs showed that amylose content was negatively correlated with SBEI and SSIIa. In both correlation analyses, SSIIa showed a negative correlation with the average chain lengths of amylose chains.

Relations between rice starch fine molecular and lamellar/crystalline structures

Starch lamellar and crystalline structures are important controller of its physicochemical and digestion properties. Here, starch lamellar/crystalline structures of 16 different rice starches were investigated and correlated with their chain-length distributions (CLDs) and molecular size distributions. Results showed that the thickness of amorphous lamellae was mainly correlated with the amount of amylose short and medium chains. Thickness of both amorphous and crystalline lamellae was negatively correlated with the amount of amylopectin medium chains and relative length of amylopectin short chains. The degree of crystallinity was negatively correlated with the amount of amylose short and long chains. The lamellar ordering, fractal nature and thickness polydispersity were also related to the starch CLDs. Whereas, starch molecular size distributions were shown to be lack of correlations with the starch lamellar/crystalline structures. This study helps a better understanding of the molecular nature of starch semi-crystalline lamellae.

Causal relations among starch fine molecular structure, lamellar/crystalline structure and in vitro digestion kinetics of native rice starch

Causal relations among starch fine molecular structures, lamellar/crystalline structures, and the in vitro digestion kinetics of native rice starches.

A combined action of amylose and amylopectin fine molecular structures in determining the starch pasting and retrogradation property

Starch fine molecular structures are of essentially important in determining its pasting and retrogradation properties. In this study, 10 different starches from various botanical sources were selected to investigate the combined action of amylose and amylopectin molecules in determining the starch physicochemical properties. Correlation between starch structural parameters with the pasting and retrogradation properties showed that amylose and amylopectin CLDs do not affect these properties in isolation. Such as, the amount of amylose long chains and amylopectin short chains are both positively correlated with the melting temperatures and enthalpy of retrograded starches. Furthermore, relatively longer amylose short to medium chains can result in higher trough and breakdown viscosity, while higher amount of amylopectin medium to long chains result in higher peak viscosity. The results help a better understanding of the importance of amylose and amylopectin fine molecular structures in determining starch functional properties.

Parameterizing starch chain-length distributions for structure-property relations

Understanding starch structure-property relationship is important for the development of new generation of starch-based foods with desirable functions. Recent developments of methodologies on the characterisation of starch molecular structures, especially how to parameterize the starch chain-length distribution (CLD) by few biologically meaningful parameters have brought new insights to explain starch physicochemical properties from molecular levels. Especially, it has shown that gelatinization temperatures are largely controlled by amylopectin short chains, while the retrogradation rate of starch molecules is controlled by amylose content, amylose short to medium chains, amylopectin external and internal chain length. Starch pasting and digestion properties are also controlled to a significant extent by its CLD. With extensive discussion of correlative and casual relations between starch CLD with its physicochemical properties, this review aims to establish a holistic starch structure-property relationship. It enables food producers to develop functional foods based on a precise understanding of starch structure-property relations.

Effects of Nonstarch Genetic Modifications on Starch Structure and Properties

This paper examines if, in maize, starch structure and starch-dependent properties might be altered by pleiotropic effects arising from genetic modifications that are not directly related to starch synthesis. The molecular structure, specifically the starch chain-length distributions (CLDs), of two maize lines transformed with Bar (bialaphos resistance) and Cry1c genes (an artificial gene, encoding proteinaceous insecticidal δ-endotoxins) were compared to those of their control lines. The two transgenes are responsible for herbicidal resistance and insect tolerance, respectively. The starch CLDs were measured by enzymatic debranching and measuring the molecular weight distributions of the resulting linear chains. It was found that although all the lines had similar amylose contents, the CLDs of both amylopectin and amylose for Cry1c were noticeably different from the others, having more short amylopectin and long amylose chains. These CLDs are known to affect functional properties, and indeed it was found that the Cry1c transgenic lines showed a lower gelatinization temperature and faster digestion rate than the control or Bar lines. However, a slower digestion rate is nutritionally desirable. Thus, pleiotropic effects from genetic modifications can indirectly but significantly affect the starch synthesis pathway and thus change functional properties of significance for human health.

Accurate and sensitive quantitation of glucose and glucose phosphates derived from storage carbohydrates by mass spectrometry

The addition of phosphate groups into glycogen modulates its branching pattern and solubility which all impact its accessibility to glycogen interacting enzymes. As glycogen architecture modulates its metabolism, it is essential to accurately evaluate and quantify its phosphate content. Simultaneous direct quantitation of glucose and its phosphate esters requires an assay with high sensitivity and a robust dynamic range. Herein, we describe a highly-sensitive method for the accurate detection of both glycogen-derived glucose and glucose-phosphate esters utilizing gas-chromatography coupled mass spectrometry. Using this method, we observed higher glycogen levels in the liver compared to skeletal muscle, but skeletal muscle contained many more phosphate esters. Importantly, this method can detect femtomole levels of glucose and glucose phosphate esters within an extremely robust dynamic range with excellent accuracy and reproducibility. The method can also be easily adapted for the quantification of plant starch, amylopectin or other biopolymers.

Competition between Granule Bound Starch Synthase and Starch Branching Enzyme in Starch Biosynthesis

BACKGROUND

Starch branching enzymes (SBE) and granule-bound starch synthase (GBSS) are two important enzymes for starch biosynthesis. SBE mainly contributes to the formation of side branches, and GBSS mainly contributes for the synthesis of amylose molecules. However, there are still gaps in the understanding of possible interactions between SBE and GBSS.

RESULTS

Nineteen natural rice varieties with amylose contents up to 28% were used. The molecular structure, in the form of the chain-length distribution (CLDs, the distribution of the number of monomer units in each branch) was measured after enzymatic debranching, using fluorophore-assisted carbohydrate electrophoresis for amylopectin and size- exclusion chromatography for amylose. The resulting distributions were fitted to two mathematical models based on the underlying biosynthetic processes, which express the CLDs in terms of parameters reflecting relevant enzyme activities.

CONCLUSIONS

Finding statistically valid correlations between the values of these parameters showed that GBSSI and SBEI compete for substrates during rice starch biosynthesis, and synthesis of amylose short chains involves several enzymes including GBSSI, SBE and SSS (soluble starch synthase). Since the amylose CLD is important for a number of functional properties such as digestion rate, this knowledge is potentially useful for developing varieties with improved functional properties.

CRISPR/Cas9 mutations in the rice Waxy/GBSSI gene induce allele-specific and zygosity-dependent feedback effects on endosperm starch biosynthesis

Induced mutations in the waxy locus in rice endosperm did not abolish GBSS activity completely. Compensatory mechanisms in endosperm and leaves caused a major reprogramming of the starch biosynthetic machinery. The mutation of genes in the starch biosynthesis pathway has a profound effect on starch quality and quantity and is an important target for plant breeders. Mutations in endosperm starch biosynthetic genes may impact starch metabolism in vegetative tissues such as leaves in unexpected ways due to the complex feedback mechanisms regulating the pathway. Surprisingly this aspect of global starch metabolism has received little attention. We used CRISPR/Cas9 to introduce mutations affecting the Waxy (Wx) locus encoding granule-bound starch synthase I (GBSSI) in rice endosperm. Our specific objective was to develop a mechanistic understanding of how the endogenous starch biosynthetic machinery might be affected at the transcriptional level following the targeted knock out of GBSSI in the endosperm. We found that the mutations reduced but did not abolish GBSS activity in seeds due to partial compensation caused by the upregulation of GBSSII. The GBSS activity in the mutants was 61-71% of wild-type levels, similarly to two irradiation mutants, but the amylose content declined to 8-12% in heterozygous seeds and to as low as 5% in homozygous seeds, accompanied by abnormal cellular organization in the aleurone layer and amorphous starch grain structures. Expression of many other starch biosynthetic genes was modulated in seeds and leaves. This modulation of gene expression resulted in changes in AGPase and sucrose synthase activity that explained the corresponding levels of starch and soluble sugars.

Functional Roles of Starch Binding Domains and Surface Binding Sites in Enzymes Involved in Starch Biosynthesis

Biosynthesis of starch is catalyzed by a cascade of enzymes. The activity of a large number of these enzymes depends on interaction with polymeric substrates via carbohydrate binding sites, which are situated outside of the catalytic site and its immediate surroundings including the substrate-binding crevice. Such secondary binding sites can belong to distinct starch binding domains (SBDs), classified as carbohydrate binding modules (CBMs), or be surface binding sites (SBSs) exposed on the surface of catalytic domains. Currently in the Carbohydrate-Active enZYmes (CAZy) database SBDs are found in 13 CBM families. Four of these families; CBM20, CBM45, CBM48, and CBM53 are represented in enzymes involved in starch biosynthesis, namely starch synthases, branching enzymes, isoamylases, glucan, water dikinases, and α-glucan phosphatases. A critical role of the SBD in activity has not been demonstrated for any of these enzymes. Among the well-characterized SBDs important for starch biosynthesis are three CBM53s of Arabidopsis thaliana starch synthase III, which have modest affinity. SBSs, which are overall less widespread than SBDs, have been reported in some branching enzymes, isoamylases, synthases, phosphatases, and phosphorylases active in starch biosynthesis. SBSs appear to exert roles similar to CBMs. SBSs, however, have also been shown to modulate specificity for example by discriminating the length of chains transferred by branching enzymes. Notably, the difference in rate of occurrence between SBDs and SBSs may be due to lack of awareness of SBSs. Thus, SBSs as opposed to CBMs are not recognized at the protein sequence level, which hampers their identification. Moreover, only a few SBSs in enzymes involved in starch biosynthesis have been functionally characterized, typically by structure-guided site-directed mutagenesis. The glucan phosphatase Like SEX4 2 from A. thaliana has two SBSs with weak affinity for β-cyclodextrin, amylose and amylopectin, which were indicated by mutational analysis to be more important than the active site for initial substrate recognition. The present review provides an update on occurrence of functional SBDs and SBSs in enzymes involved in starch biosynthesis.