Mutations in the gene encoding starch synthase II profoundly alter amylopectin structure in pea embryos

Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities

The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

Critical examination of the characterization techniques, and the evidence, for the existence of extra-long amylopectin chains

It has been suggested that amylopectin can contain small but significant amounts of extra-long chains (ELCs), which could affect functional properties, and also would have implications for the mechanism of starch biosynthesis. However, current evidence for the existence of ELCs is ambiguous. The amylose/amylopectin separation and the characterization techniques used for the investigation of ELCs are reviewed, problems in those techniques are examined, and studies of ELCs of amylopectin are discussed. A model for the biosynthesis of amylopectin chains in terms of conventional biosynthesis enzymes, which provides an excellent fit to a large amount of experimental data, is used to provide a rigorous definition of ELCs. In addition, current investigations of ELCs, involving separation, is hindered by the lack of a method to quantitatively separate all the amylopectin from starch without any traces of residual amylose (which would have long chains). Unambiguous evidence for the existence of ELCs can be obtained using two-dimensional (2D) characterization, these dimensions being the degree of polymerization of a chain and the size of the whole molecule. Available 2D data indicate that there are no ELCs present in currently detectable quantities in native rice starches. However, concluding this more rigorously requires improvements in the resolution of current 2D methods.

Main Characteristics of Processed Grain Starch Products and Physicochemical Features of the Starches from Maize (Zea mays L.) with Different Genotypes

To understand the relationship between the genotype of maize plants and differences in their origin and the ploidy of the genome, which carry gene alleles programming the biosynthesis of various starch modifications, the thermodynamic and morphological features of starches from the grains of these plants have been studied. This study investigated the peculiarities of starch extracted from subspecies of maize (the dry matter mass (DM) fraction, starch content in grain DM, ash content in grain DM, and amylose content in starch) belonging to different genotypes within the framework of the program for the investigation of polymorphism of the world collection of plant genetic resources VIR. Among the starch genotypes of maize studied, four groups comprised the waxy (wx), conditionally high amylose ("ae"), sugar (su), and wild (WT) genotypes. Starches with an amylose content of over 30% conditionally belonged to the "ae" genotype. The starches of the su genotype had fewer starch granules than other investigated genotypes. An increase in amylose content in the investigated starches, accompanied by a decrease in their thermodynamic melting parameters, induced the accumulation of defective structures in the starches under study. The thermodynamic parameters evaluated for dissociation of the amylose-lipid complex were temperature (T_aml) and enthalpy (H_aml); for the su genotype, temperature and enthalpy values of dissociation of the amylose-lipid complex were higher than in the starches from the "ae" and WT genotypes. This study has shown that the amylose content in starch and the individual features of the maize genotype determine the thermodynamic melting parameters of the starches under study.

Structure and genetic regulation of starch formation in sorghum (Sorghum bicolor (L.) Moench) endosperm: A review

This review focuses on the structure and genetic regulation of starch formation in sorghum (Sorghum bicolor (L.) Moench) endosperm. Sorghum is an important cereal crop that is well suited to grow in regions with high temperatures and limited water resources due to its C4 metabolism. The endosperm of sorghum kernels is a rich source of starch, which is composed of two main components: amylose and amylopectin. The synthesis of starch in sorghum endosperm involves multiple enzymatic reactions, which are regulated by complex genetic and environmental factors. Recent research has identified several genes involved in the regulation of starch synthesis in sorghum endosperm. In addition, the structure and properties of sorghum starch can also be influenced by environmental factors such as temperature, water availability, and soil nutrients. A better understanding of the structure and genetic regulation of starch formation in sorghum endosperm can have important implications for the development of sorghum-based products with improved quality and nutritional value. This review provides a comprehensive summary of the current knowledge on the structure and genetic regulation of starch formation in sorghum endosperm and highlights the potential for future research to further improve our understanding of this important process.

An allelic series of starch-branching enzyme mutants in pea (Pisum sativum L.) reveals complex relationships with seed starch phenotypes

A set of mutant pea lines carrying induced mutations within the major seed-expressed starch-branching enzyme gene has been characterised at the molecular, chemical and agronomic levels. Eight of the induced mutations, three of which predicted a premature stop codon, were compared with the naturally occurring starch-branching enzyme mutation within the same genetic background. Starch, amylose and sugar measurements, coupled with analysis by ultra-high performance liquid chromatography-size exclusion chromatography of starches, identified a range of phenotypes which were grouped according to the nature of the mutation. Homology modelling of proteins supported the differences in phenotypes observed. Differences in field performance were evident for selected mutants, particularly in seed yield and mean seed weight traits for early compared with late spring sowings. The data show the potential of an allelic series of mutants at this locus for nutritional studies. CHEMICAL COMPOUNDS: starch, amylose, amylopectin, raffinose, stachyose, verbascose.

Starch synthase II plays a crucial role in starch biosynthesis and the formation of multienzyme complexes in cassava storage roots

Starch is a glucose polymer synthesized by green plants for energy storage and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis and the formation of protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII, and MeISAII. MeSSII-RNAi cassava lines showed increased amylose content and reduced biosynthesis of the intermediate chain of amylopectin (B1 type) in their storage roots, leading to altered starch physicochemical properties. Furthermore, gel permeation chromatography analysis of starch biosynthetic enzymes between wild type and MeSSII-RNAi lines confirmed the key role of MeSSII in the organization of heteromeric starch synthetic protein complexes. The lack of MeSSII in cassava also reduced the capacity of MeSSI, MeSBEII, MeISAI, and MeISAII to bind to starch granules. These findings shed light on the key components of the starch biosynthesis machinery in root crops.

High-amylose starch: Structure, functionality and applications

Starch with a high amylose (AM) content (high AM starch, HAS) has attracted increasing research attention due to its industrial application potential, such as functional foods and biodegradable packaging. In the past two decades, HAS structure, functionality, and applications have been the research hotspots. However, a review that comprehensively summarizes these areas is lacking, making it difficult for interested readers to keep track of past and recent advances. In this review, we highlight studies that benefited from rapidly developing techniques, and systematically review the structure, functionality, and applications of HAS. We particularly emphasize the relationships between HAS molecular structure and physicochemical properties.

Integrated Transcriptomic and Bioinformatics Analyses Reveal the Molecular Mechanisms for the Differences in Seed Oil and Starch Content Between Glycine max and Cicer arietinum

The seed oil and starch content of soybean are significantly different from that of chickpea. However, there are limited studies on its molecular mechanisms. To address this issue, we conducted integrated transcriptomic and bioinformatics analyses for species-specific genes and acyl-lipid-, starch-, and carbon metabolism-related genes. Among seven expressional patterns of soybean-specific genes, four were highly expressed at the middle- and late oil accumulation stages; these genes significantly enriched fatty acid synthesis and carbon metabolism, and along with common acetyl CoA carboxylase (ACCase) highly expressed at soybean middle seed development stage, common starch-degrading enzyme beta-amylase-5 (BAM5) was highly expressed at soybean early seed development stage and oil synthesis-related genes ACCase, KAS, KAR, ACP, and long-chain acyl-CoA synthetase (LACS) were co-expressed with WRI1, which may result in high seed oil content and low seed starch content in soybean. The common ADP-glucose pyrophosphorylase (AGPase) was highly expressed at chickpea middle seed development stage, along with more starch biosynthesis genes co-expressed with four-transcription-factor homologous genes in chickpea than in soybean, and the common WRI1 was not co-expressed with oil synthesis genes in chickpea, which may result in high seed starch content and low seed oil content in chickpea. The above results may be used to improve chickpea seed oil content in two ways. One is to edit CaWRI1 to co-express with oil synthesis-related genes, which may increase carbon metabolites flowing to oil synthesis, and another is to increase the expression levels of miRNA159 and miRNA319 to inhibit the expression of MYB33, which may downregulate starch synthesis-related genes, making more carbon metabolites flow into oil synthesis. Our study will provide a basis for future breeding efforts to increase the oil content of chickpea seeds.

Understanding Starch Metabolism in Pea Seeds towards Tailoring Functionality for Value-Added Utilization

Starch is the most abundant storage carbohydrate and a major component in pea seeds, accounting for about 50% of dry seed weight. As a by-product of pea protein processing, current uses for pea starch are limited to low-value, commodity markets. The globally growing demand for pea protein poses a great challenge for the pea fractionation industry to develop new markets for starch valorization. However, there exist gaps in our understanding of the genetic mechanism underlying starch metabolism, and its relationship with physicochemical and functional properties, which is a prerequisite for targeted tailoring functionality and innovative applications of starch. This review outlines the understanding of starch metabolism with a particular focus on peas and highlights the knowledge of pea starch granule structure and its relationship with functional properties, and industrial applications. Using the currently available pea genetics and genomics knowledge and breakthroughs in omics technologies, we discuss the perspectives and possible avenues to advance our understanding of starch metabolism in peas at an unprecedented level, to ultimately enable the molecular design of multi-functional native pea starch and to create value-added utilization.

Perspectives on the genetic improvement of health- and nutrition-related traits in pea

Pea (Pisum sativum L.) is a widely grown pulse crop that is a source of protein, starch and micronutrients in both human diets and livestock feeds. There is currently a strong global focus on making agriculture and food production systems more sustainable, and pea has one of the smallest carbon footprints of all crops. Multiple genetic loci have been identified that influence pea seed protein content, but protein composition is also important nutritionally. Studies have previously identified gene families encoding individual seed protein classes, now documented in a reference pea genome assembly. Much is also known about loci affecting starch metabolism in pea, with research especially focusing on improving concentrations of resistant starch, which has a positive effect on maintaining blood glucose homeostasis. Diversity in natural germplasm for micronutrient concentrations and mineral hyperaccumulation mutants have been discovered, with quantitative trait loci on multiple linkage groups identified for seed micronutrient concentrations. Antinutrients, which affect nutrient bioavailability, must also be considered; mutants in which the concentrations of important antinutrients including phytate and trypsin inhibitors are reduced have already been discovered. Current knowledge on the genetics of nutritional traits in pea will greatly assist with crop improvement for specific end uses, and further identification of genes involved will help advance our knowledge of the control of the synthesis of seed compounds.

Intra-Sample Heterogeneity of Potato Starch Reveals Fluctuation of Starch-Binding Proteins According to Granule Morphology

Starch granule morphology is highly variable depending on the botanical origin. Moreover, all investigated plant species display intra-tissular variability of granule size. In potato tubers, the size distribution of starch granules follows a unimodal pattern with diameters ranging from 5 to 100 µm. Several evidences indicate that granule morphology in plants is related to the complex starch metabolic pathway. However, the intra-sample variability of starch-binding metabolic proteins remains unknown. Here, we report on the molecular characterization of size-fractionated potato starch granules with average diameters of 14.2 ± 3.7 µm, 24.5 ± 6.5 µm, 47.7 ± 12.8 µm, and 61.8 ± 17.4 µm. In addition to changes in the phosphate contents as well as small differences in the amylopectin structure, we found that the starch-binding protein stoichiometry varies significantly according to granule size. Label-free quantitative proteomics of each granule fraction revealed that individual proteins can be grouped according to four distinct abundance patterns. This study corroborates that the starch proteome may influence starch granule growth and architecture and opens up new perspectives in understanding the dynamics of starch biosynthesis.

MIGS as a Simple and Efficient Method for Gene Silencing in Rice

MiRNA-induced gene silencing (MIGS) technology is a special kind of RNA interference technology that uses miR173 to mediate the production of trans-acting siRNA (ta-siRNA) to achieve target gene silencing. This technique has successfully mediated the silencing of interested genes in plants such as Arabidopsis, tobacco, petunia, etc. In order to establish the MIGS technology system in monocots such as rice, we constructed the MIGS backbone vectors pZHY930, pZHY931, pZHY932, and pZHY933 with different with promoters to regulate the expression of miR173 and miR173_ts. The rice OsPDS reporter gene was selected to compare the efficiency of four MIGS backbone vectors by the ratio of albino plants. The results showed that all the four backbone vectors could effectively mediate the target gene silencing, and pZHY932 showed highest efficiency up to 90%. Through MIGS silencing of endogenous OsROC5 and OsLZAY1 in rice, we successfully obtained rice mutant plants with rice leaf roll and tillering angles increasing, and further confirmed that MIGS backbone vector can efficiently mediate target gene silencing in rice. On the other hand, in order to verify the efficiency of MIGS-mediated multi-gene silencing in rice, we constructed two double-gene silencing vectors OsPDS and OsROC5, OsPDS and OsLZAY1, based on pZHY932 backbone vector. Double mutant rice plants with increased leaf and albino tiller angles. And we successfully obtained bladed leaf albino seedling and increased tillering angle albino seedling double-silencing mutations. We further constructed a MIGS-OsGBSS gene silencing vector and obtained rice materials with significantly reduced amylose content. This result indicated that MIGS could be an efficient method in monocots gene silencing and gene function analysis.

Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes

BACKGROUND

Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea.

RESULTS

To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways.

CONCLUSIONS

The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

Genetic Variation Controlling Wrinkled Seed Phenotypes in Pisum: How Lucky Was Mendel?

One of the traits studied by Mendel in pea (Pisum sativum L.) was the wrinkled-seeded phenotype, and the molecular basis for a mutation underlying this phenotype was discovered in the 1990s. Although the starch-branching enzyme gene mutation identified at the genetic locus r is most likely to be that in seeds available to Mendel in the mid-1800s, it has remained an open question as to whether or not additional natural mutations in this gene exist within Pisum germplasm collections. Here, we explore this question and show that all but two wrinkled-seeded variants in one such collection correspond to either the mutant allele described previously for the r locus or a mutation at a second genetic locus, rb, affecting the gene encoding the large subunit of Adenosine diphosphoglucose (ADP-glucose) pyrophosphorylase; the molecular basis for the rb mutation is described here. The genetic basis for the phenotype of one (JI 2110) of the two lines which are neither r nor rb has been studied in crosses with a round-seeded variant (JI 281); for which extensive genetic marker data were expected. In marked contrast to the trait studied by Mendel and the rb phenotype; the data suggest that the wrinkled-seeded phenotype in JI 2110 is maternally determined, controlled by two genetic loci, and the extent to which it is manifested is very sensitive to the environment. Metabolite analysis of the cotyledons of JI 2110 revealed a profile for sucrose and sucrose-derived compounds that was more similar to that of wild-type round-seeded, than that of wrinkled-seeded r, pea lines. However, the metabolite profile of the seed coat (testa) of JI 2110 was distinct from that of other round-seeded genotypes tested which, together with analysis of recombinant inbred progeny lines, suggests an explanation for the seed phenotype.

A soluble starch synthase I gene, IbSSI, alters the content, composition, granule size and structure of starch in transgenic sweet potato

Soluble starch synthase I (SSI) is a key enzyme in the biosynthesis of plant amylopectin. In this study, the gene named IbSSI, was cloned from sweet potato, an important starch crop. A high expression level of IbSSI was detected in the leaves and storage roots of the sweet potato. Its overexpression significantly increased the content and granule size of starch and the proportion of amylopectin by up-regulating starch biosynthetic genes in the transgenic plants compared with wild-type plants (WT) and RNA interference plants. The frequency of chains with degree of polymerization (DP) 5-8 decreased in the amylopectin fraction of starch, whereas the proportion of chains with DP 9-25 increased in the IbSSI-overexpressing plants compared with WT plants. Further analysis demonstrated that IbSSI was responsible for the synthesis of chains with DP ranging from 9 to 17, which represents a different chain length spectrum in vivo from its counterparts in rice and wheat. These findings suggest that the IbSSI gene plays important roles in determining the content, composition, granule size and structure of starch in sweet potato. This gene may be utilized to improve the content and quality of starch in sweet potato and other plants.

Potato starch synthases: Functions and relationships

Starch, a very compact form of glucose units, is the most abundant form of storage polyglucan in nature. The starch synthesis pathway is among the central biochemical pathways, however, our understanding of this important pathway regarding genetic elements controlling this pathway, is still insufficient. Starch biosynthesis requires the action of several enzymes. Soluble starch synthases (SSs) are a group of key players in starch biosynthesis which have proven their impact on different aspects of the starch biosynthesis and functionalities. These enzymes have been studied in different plant species and organs in detail, however, there seem to be key differences among species regarding their contributions to the starch synthesis. In this review, we consider an update on various SSs with an emphasis on potato SSs as a model for storage organs. The genetics and regulatory mechanisms of potato starch synthases will be highlighted. Different aspects of various isoforms of SSs are also discussed.

A novel GRAS transcription factor, ZmGRAS20, regulates starch biosynthesis in rice endosperm

Starch occupies the maximal component of cereal grains and is pivotal for maize yield and quality. However, the regulatory mechanism of starch synthesis is still poorly understand. In this study, a GRAS transcription factor, ZmGRAS20, was isolated from maize inbred line B73 based on transcriptome sequencing. Quantitative real-time PCR indicated that ZmGRAS20 is specifically expressed in maize endosperm. Transient expression of ZmGRAS20-green fluorescent protein fusion protein in tobacco cells showed a nucleus and membrane localization of the protein. Transactivation assay of ZmGRAS20 demonstrated that it has no transactivation activity in yeast cells. Overexpression of ZmGRAS20 led to a chalky region of ventral endosperm with decreased starch content and defective agronomic characters in transgenic seeds. Moreover, ZmGRAS20-overexpression plants had fewer fractions of long-branched starch chains. Further scanning electron microscopy observation of ZmGRAS20 transgenic seeds exhibited altered starch granules morphology compared with wide type plants. Taken together, these results suggested that ZmGRAS20 may function as a starch synthesis regulatory factor in rice endosperm.

Recreating the synthesis of starch granules in yeast

Starch, as the major nutritional component of our staple crops and a feedstock for industry, is a vital plant product. It is composed of glucose polymers that form massive semi-crystalline granules. Its precise structure and composition determine its functionality and thus applications; however, there is no versatile model system allowing the relationships between the biosynthetic apparatus, glucan structure and properties to be explored. Here, we expressed the core Arabidopsis starch-biosynthesis pathway in Saccharomyces cerevisiae purged of its endogenous glycogen-metabolic enzymes. Systematic variation of the set of biosynthetic enzymes illustrated how each affects glucan structure and solubility. Expression of the complete set resulted in dense, insoluble granules with a starch-like semi-crystalline organization, demonstrating that this system indeed simulates starch biosynthesis. Thus, the yeast system has the potential to accelerate starch research and help create a holistic understanding of starch granule biosynthesis, providing a basis for the targeted biotechnological improvement of crops.

Starch phosphorylation plays an important role in starch biosynthesis

Starch phosphate esters are crucial in starch metabolism and render valuable functionality to starches for various industrial applications. A potato glucan, water dikinase (GWD1) was introduced in tubers of two different potato genetic backgrounds: an amylose-containing line Kardal and the amylose-free mutant amf. In both backgrounds, this resulted in two contrasting effects, a number of plants showed higher phosphate content compared to the respective control, while others lines exhibited lower phosphate content, thereby generating two series of starches with broad-scale variation in phosphate content. The results of systematic analyses on these two series of starches revealed that starch phosphate content strongly influenced starch granule morphology, amylose content, starch fine structure, gelatinization characteristics and freeze-thaw stability of starch gels. Further analyses on the expression level of genes involved in starch metabolism suggested that starch phosphorylation regulates starch synthesis by controlling the carbon flux into starch while simultaneously modulating starch-synthesizing genes.

Formation of starch in plant cells

Starch-rich crops form the basis of our nutrition, but plants have still to yield all their secrets as to how they make this vital substance. Great progress has been made by studying both crop and model systems, and we approach the point of knowing the enzymatic machinery responsible for creating the massive, insoluble starch granules found in plant tissues. Here, we summarize our current understanding of these biosynthetic enzymes, highlighting recent progress in elucidating their specific functions. Yet, in many ways we have only scratched the surface: much uncertainty remains about how these components function together and are controlled. We flag-up recent observations suggesting a significant degree of flexibility during the synthesis of starch and that previously unsuspected non-enzymatic proteins may have a role. We conclude that starch research is not yet a mature subject and that novel experimental and theoretical approaches will be important to advance the field.

Biocatalytic role of potato starch synthase III for α-glucan biosynthesis in Synechocystis sp. PCC6803 mutants

A potato starch synthase III (PSSIII) was expressed in the Synechocystis mutants deficient in either glycogen synthase I (M1) or II (M2) to replenish α-(1,4) linkage synthesizing activity, resulting in new mutants, PM1 and PM2, respectively. These mutants were applied to study the role of exogenous plant starch synthase for starch/glycogen biosynthesis mechanism established in the cyanobacteria. The remaining glycogen synthase genes in PM1 and PM2 were further disrupted to make the mutants PM12 and PM21 which contained PSSIII as the sole glycogen/starch synthase. Among wild type and mutants, there were no significant differences in the amount of α-glucan produced. All the mutants harboring active PSSIII produced α-glucans with relatively much shorter and less longer α-1,4 chains than wild-type glycogen, which was exactly in accordance with the increase in glycogen branching enzyme activity. In fact, α-glucan structure of PM1 was very similar to those of PM12 and PM21, and PM2 had more intermediate chains than M2. This result suggests PSSIII may have distributive elongation property during α-glucan synthesis. In conclusion, the Synechocystis as an expression model system of plant enzymes can be applied to determine the role of starch synthesizing enzymes and their association during α-glucan synthesis.

Inheritance of low pasting temperature in sweetpotato starch and the dosage effect of wild-type alleles

Sweetpotato (Ipomoea batatas (L.) Lam.), which is an outcrossing hexaploid, is one of the most important starch-producing crops in the world. During the last decade, new sweetpotato cultivars, e.g. 'Quick Sweet', which have approximately 20°C lower pasting temperature, slower retrogradation and higher digestibility of raw starch than ordinary cultivars, have been developed in Japan. Genetic analysis of these variants with low pasting temperature starch was conducted in this study. Using 8 variants and 15 normal clones, 26 families were generated. The results from analyzing these progenies suggested that this trait is a qualitative character controlled by one recessive allele (designated spt), which is inherited in a hexasomic manner. A dosage effect of the wild-type Spt allele was found for starch pasting temperature, although the effect was not linear. These results will aid breeders to develop sweetpotato cultivars with a range of starch pasting temperatures.

The different effects of starch synthase IIa mutations or variation on endosperm amylose content of barley, wheat and rice are determined by the distribution of starch synthase I and starch branching enzyme IIb between the starch granule and amyloplast stroma

The distribution of starch synthase I and starch branching enzyme IIb between the starch granule and amyloplast stroma plays an important role in determining endosperm amylose content of cereal grains. Starch synthase IIa (SSIIa) catalyses the polymerisation of intermediate length glucan chains of amylopectin in the endosperm of cereals. Mutations of SSIIa genes in barley and wheat and inactive SSIIa variant in rice induce similar effects on the starch structure and the amylose content, but the severity of the phenotypes is different. This study compared the levels of transcripts and partitioning of proteins of starch synthase I (SSI) and starch branching enzyme IIb (SBEIIb) inside and outside the starch granules in the developing endosperms of these ssIIa mutants and inactive SSIIa variant. Pleiotropic effects on starch granule-bound proteins suggested that the different effects of SSIIa mutations on endosperm amylose content of barley, wheat and rice are determined by the distribution of SSI and SBEIIb between the starch granule and amyloplast stroma in cereals. Regulation of starch synthesis in ssIIa mutants and inactive SSIIa variant may be at post-translational level or the altered amylopectin structure deprives the affinity of SSI and SBEIIb to amylopectin.

Roles of GBSSI and SSIIa in determining amylose fine structure

This study examines the relationships between genetics (single nucleotide polymorphisms (SNPs) in GBSSI and SSIIa genes), starch structure (amylose and amylopectin fine structures), and starch properties (relating to gelatinization). GBSSI and SSIIa SNPs did not alter the starch content of rice grains. GBSSI SNPs can affect the amylose content, but they are incapable of altering the chain-lengths of amylopectin and amylose. The amounts of both long and short amylose branches changed with the same trend as amylose content, and they appeared to affect starch gelatinization properties. SSIIa synthesizes intermediate single-lamella amylopectin chains (DP 16-21), and consequently impacts the gelatinization temperature. Mathematical modelling suggests that the reduction in SSIIa activity significantly increases the activity of SBEII, resulting in a decreased activity ratio of SS to SBE in the enzyme set governing an appropriate chain-length distribution range. This application of the genetics-structure-property paradigm provides selection strategies to produce rice varieties with improved qualities.

Genetic Evidence That Chain Length and Branch Point Distributions Are Linked Determinants of Starch Granule Formation in Arabidopsis

The major component of starch is the branched glucan amylopectin. Structural features of amylopectin, such as the branching pattern and the chain length distribution, are thought to be key factors that enable it to form semicrystalline starch granules. We varied both structural parameters by creating Arabidopsis (Arabidopsis thaliana) mutants lacking combinations of starch synthases (SSs) SS1, SS2, and SS3 (to vary chain lengths) and the debranching enzyme ISOAMYLASE1-ISOAMYLASE2 (ISA; to alter branching pattern). The isa mutant accumulates primarily phytoglycogen in leaf mesophyll cells, with only small amounts of starch in other cell types (epidermis and bundle sheath cells). This balance can be significantly shifted by mutating different SSs. Mutation of SS1 promoted starch synthesis, restoring granules in mesophyll cell plastids. Mutation of SS2 decreased starch synthesis, abolishing granules in epidermal and bundle sheath cells. Thus, the types of SSs present affect the crystallinity and thus the solubility of the glucans made, compensating for or compounding the effects of an aberrant branching pattern. Interestingly, ss2 mutant plants contained small amounts of phytoglycogen in addition to aberrant starch. Likewise, ss2ss3 plants contained phytoglycogen, but were almost devoid of glucan despite retaining other SS isoforms. Surprisingly, glucan production was restored in the ss2ss3isa triple mutants, indicating that SS activity in ss2ss3 per se is not limiting but that the isoamylase suppresses glucan accumulation. We conclude that loss of only SSs can cause phytoglycogen production. This is readily degraded by isoamylase and other enzymes so it does not accumulate and was previously unnoticed.

Suppression of starch synthase I expression affects the granule morphology and granule size and fine structure of starch in wheat endosperm

Studies in Arabidopsis and rice suggest that manipulation of starch synthase I (SSI) expression in wheat may lead to the production of wheat grains with novel starch structure and properties. This work describes the suppression of SSI expression in wheat grains using RNAi technology, which leads to a low level of enzymatic activity for SSI in the developing endosperm, and a low abundance of SSI protein inside the starch granules of mature grains. The amylopectin fraction of starch from the SSI suppressed lines showed an increased frequency of very short chains (degree of polymerization, dp 6 and 7), a lower proportion of short chains (dp 8-12), and more intermediate chains (dp 13-20) than in the grain from their negative segregant lines. In the most severely affected line, amylose content was significantly increased, the morphology of starch granules was changed, and the proportion of B starch granules was significantly reduced. The change of the fine structure of the starch in the SSI-RNAi suppression lines alters the gelatinization temperature, swelling power, and viscosity of the starch. This work demonstrates that the roles of SSI in the determination of starch structure and properties are similar among different cereals and Arabidopsis.

Glycogen synthase isoforms in Synechocystis sp. PCC6803: identification of different roles to produce glycogen by targeted mutagenesis

Synechocystis sp. PCC6803 belongs to cyanobacteria which carry out photosynthesis and has recently become of interest due to the evolutionary link between bacteria and plant species. Similar to other bacteria, the primary carbohydrate storage source of Synechocystis sp. PCC6803 is glycogen. While most bacteria are not known to have any isoforms of glycogen synthase, analysis of the genomic DNA sequence of Synechocystis sp. PCC6803 predicts that this strain encodes two isoforms of glycogen synthase (GS) for synthesizing glycogen structure. To examine the functions of the putative GS genes, each gene (sll1393 or sll0945) was disrupted by double cross-over homologous recombination. Zymogram analysis of the two GS disruption mutants allowed the identification of a protein band corresponding to each GS isoform. Results showed that two GS isoforms (GSI and GSII) are present in Synechocystis sp. PCC6803, and both are involved in glycogen biosynthesis with different elongation properties: GSI is processive and GSII is distributive. Total GS activities in the mutant strains were not affected and were compensated by the remaining isoform. Analysis of the branch-structure of glycogen revealed that the sll1393⁻ mutant (GSI⁻) produced glycogen containing more intermediate-length chains (DP 8–18) at the expense of shorter and longer chains compared with the wild-type strain. The sll0945⁻ mutant (GSII⁻) produced glycogen similar to the wild-type, with only a slightly higher proportion of short chains (DP 4–11). The current study suggests that GS isoforms in Synechocystis sp. PCC6803 have different elongation specificities in the biosynthesis of glycogen, combined with ADP-glucose pyrophosphorylase and glycogen branching enzyme.

Characterization of the spatial and temporal expression of the OsSSII-3 gene encoding a key soluble starch synthase in rice

BACKGROUND

Starch, the major component of rice grain, consists of amylose and amylopectin. SSIIa, a key soluble starch synthase involved in the biosynthesis of rice amylopectin, is a major factor that controls the gelatinization temperature of rice grain. Extensive work has been done and impressive progress has been made in elaborating the function of the gene encoding SSIIa (OsSSII-3). However, the systematic expression analysis of OsSSII-3 is still rare.

RESULTS

In the present study, we performed a comprehensive expression analysis of OsSSII-3 in both the developing seeds and other tissues of indica rice 9311 by using quantitative real-time PCR. The results showed that the gene was dominantly expressed in the developing seeds. In addition, the promoter sequence of OsSSII-3 was cloned and fused with the GUS reporter gene and its expression was carefully monitored in the transgenic rice. The data from both histochemical and fluorometric analyses showed that the OsSSII-3 promoter was capable of driving the target gene to have an endosperm-specific expression, which may be due to the existing of several endosperm-specific motifs in the promoter, including the -300 elements, AACA motifs and GCN4 motifs. This result was quite consistent with that of the endogenous transcription analysis of OsSSII-3.

CONCLUSION

This study not only advanced our understanding of the spatial and temporal expression characteristics of OsSSII-3, but also provided a valuable promoter for future application in generating elite rice varieties with high nutritional or medicinal value.

Effects of homoeologous wheat starch synthase IIa genes on starch properties

Near-isogenic lines (NILs) of the eight haplotypes of starch synthase IIa (SSIIa) were used to analyze the effects of SSIIa gene dosage on branch chain length, gelatinization, pasting, retrogradation, and enzymatic hydrolysis of starches. Compared to wild-type, the amylopectin of lines missing one or more active SSIIa enzymes had increases in the proportion of short branch chains (DP6-10) and decreases in midlength chains (DP11-24), and the size of these differences depended on the dosage of active SSIIa enzymes. Of the three loci, SSIIa-A1 had the smallest contribution to amylopectin structure and SSIIa-B1 the largest. The different effects of the three SSIIa enzymes on starch properties were also seen in gelatinization, retrogradation, pasting, and enzymatic hydrolysis properties. Such differences in starch properties might be useful in influencing the texture and shelf life of food products.

Glucan affinity of starch synthase IIa determines binding of starch synthase I and starch-branching enzyme IIb to starch granules

The sugary-2 mutation in maize (Zea mays L.) is a result of the loss of catalytic activity of the endosperm-specific SS (starch synthase) IIa isoform causing major alterations to amylopectin architecture. The present study reports a biochemical and molecular analysis of an allelic variant of the sugary-2 mutation expressing a catalytically inactive form of SSIIa and sheds new light on its central role in protein–protein interactions and determination of the starch granule proteome. The mutant SSIIa revealed two amino acid substitutions, one being a highly conserved residue (Gly522→Arg) responsible for the loss of catalytic activity and the inability of the mutant SSIIa to bind to starch. Analysis of protein–protein interactions in sugary-2 amyloplasts revealed the same trimeric assembly of soluble SSI, SSIIa and SBE (starch-branching enzyme) IIb found in wild-type amyloplasts, but with greatly reduced activities of SSI and SBEIIb. Chemical cross-linking studies demonstrated that SSIIa is at the core of the complex, interacting with SSI and SBEIIb, which do not interact directly with each other. The sugary-2 mutant starch granules were devoid of amylopectin-synthesizing enzymes, despite the fact that the respective affinities of SSI and SBEIIb from sugary-2 for amylopectin were the same as observed in wild-type. The data support a model whereby granule-bound proteins involved in amylopectin synthesis are partitioned into the starch granule as a result of their association within protein complexes, and that SSIIa plays a crucial role in trafficking SSI and SBEIIb into the granule matrix.

Elongated phytoglycogen chain length in transgenic rice endosperm expressing active starch synthase IIa affects the altered solubility and crystallinity of the storage α-glucan

The relationship between the solubility, crystallinity, and length of the unit chains of plant storage α-glucan was investigated by manipulating the chain length of α-glucans accumulated in a rice mutant. Transgenic lines were produced by introducing a cDNA for starch synthase IIa (SSIIa) from an indica cultivar (SSIIa (I), coding for active SSIIa) into an isoamylase1 (ISA1)-deficient mutant (isa1) that was derived from a japonica cultivar (bearing inactive SSIIa proteins). The water-soluble fraction accounted for >95% of the total α-glucan in the isa1 mutant, whereas it was only 35-70% in the transgenic SSIIa (I)/isa1 lines. Thus, the α-glucans from the SSIIa (I)/isa1 lines were fractionated into soluble and insoluble fractions prior to the following characterizations. X-ray diffraction analysis revealed a weak B-type crystallinity for the α-glucans of the insoluble fraction, while no crystallinity was confirmed for α-glucans in isa1. Concerning the degree of polymerization (DP) ≤30, the chain lengths of these α-glucans differed significantly in the order of SSIIa (I)/isa1 insoluble > SSIIa (I)/isa1 soluble > α-glucans in isa1. The amount of long chains with DP ≥33 was higher in the insoluble fraction α-glucans than in the other two α-glucans. No difference was observed in the chain length distributions of the β-amylase limit dextrins among these α-glucans. These results suggest that in the SSIIa (I)/isa1 transgenic lines, the unit chains of α-glucans were elongated by SSIIa(I), whereas the expression of SSIIa(I) did not affect the branch positions. Thus, the observed insolubility and crystallinity of the insoluble fraction can be attributed to the elongated length of the outer chains due to SSIIa(I).

Starch metabolism in Arabidopsis

Starch is the major non-structural carbohydrate in plants. It serves as an important store of carbon that fuels plant metabolism and growth when they are unable to photosynthesise. This storage can be in leaves and other green tissues, where it is degraded during the night, or in heterotrophic tissues such as roots, seeds and tubers, where it is stored over longer time periods. Arabidopsis accumulates starch in many of its tissues, but mostly in its leaves during the day. It has proven to be a powerful genetic system for discovering how starch is synthesised and degraded, and new proteins and processes have been discovered. Such work has major significance for our starch crops, whose yield and quality could be improved by the application of this knowledge. Research into Arabidopsis starch metabolism has begun to reveal how its daily turnover is integrated into the rest of metabolism and adapted to the environmental conditions. Furthermore, Arabidopsis mutant lines deficient in starch metabolism have been employed as tools to study other biological processes ranging from sugar sensing to gravitropism and flowering time control. This review gives a detailed account of the use of Arabidopsis to study starch metabolism. It describes the major discoveries made and presents an overview of our understanding today, together with some as-yet unresolved questions.

Starch metabolism in Arabidopsis

Starch is the major non-structural carbohydrate in plants. It serves as an important store of carbon that fuels plant metabolism and growth when they are unable to photosynthesise. This storage can be in leaves and other green tissues, where it is degraded during the night, or in heterotrophic tissues such as roots, seeds and tubers, where it is stored over longer time periods. Arabidopsis accumulates starch in many of its tissues, but mostly in its leaves during the day. It has proven to be a powerful genetic system for discovering how starch is synthesised and degraded, and new proteins and processes have been discovered. Such work has major significance for our starch crops, whose yield and quality could be improved by the application of this knowledge. Research into Arabidopsis starch metabolism has begun to reveal how its daily turnover is integrated into the rest of metabolism and adapted to the environmental conditions. Furthermore, Arabidopsis mutant lines deficient in starch metabolism have been employed as tools to study other biological processes ranging from sugar sensing to gravitropism and flowering time control. This review gives a detailed account of the use of Arabidopsis to study starch metabolism. It describes the major discoveries made and presents an overview of our understanding today, together with some as-yet unresolved questions.

Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing

High-throughput sequencing of pooled DNA was applied to polymorphism discovery in candidate genes involved in starch synthesis. This approach employed semi- to long-range PCR (LR-PCR) followed by next-generation sequencing technology. A total of 17 rice starch synthesis genes encoding seven classes of enzymes, including ADP-glucose pyrophosphorylase (AGPase), granule starch synthase (GBSS), soluble starch synthase (SS), starch branching enzyme (BE), starch debranching enzyme (DBE) and starch phosphorylase (SPHOL) and phosphate translocator (GPT1) from 233 genotypes were PCR amplified using semi- to long-range PCR. The amplification products were equimolarly pooled and sequenced using massively parallel sequencing technology (MPS). By detecting single nucleotide polymorphism (SNP)/Indels in both coding and noncoding areas of the genes, we identified genetic differences and characterized the SNP/Indel variation and distribution patterns among individual starch candidate genes. Approximately, 60.9 million reads were generated, of which 54.8 million (90%) mapped to the reference sequences. The average coverage rate ranged from 12,708 to 38,300 times for SSIIa and SSIIIb, respectively. SNPs and single/multiple-base Indels were analysed in a total assembled length of 116,403 bp. In total, 501 SNPs and 113 Indels were detected across the 17 starch-related loci. The ratio of synonymous to nonsynonymous SNPs (Ka/Ks) test indicated GBSSI and isoamylase 1 (ISA1) as the least diversified (most purified) and conservative genes as the studied populations have been through cycles of selection. This report demonstrates a useful strategy for screening germplasm by MPS to discover variants in a specific target group of genes.

Starch biosynthesis in rice endosperm requires the presence of either starch synthase I or IIIa

Starch synthase (SS) I and IIIa are the first and second largest components of total soluble SS activity, respectively, in developing japonica rice (Oryza sativa L.) endosperm. To elucidate the distinct and overlapping functions of these enzymes, double mutants were created by crossing the ss1 null mutant with the ss3a null mutant. In the F(2) generation, two opaque seed types were found to have either the ss1ss1/SS3ass3a or the SS1ss1/ss3ass3a genotype. Phenotypic analyses revealed lower SS activity in the endosperm of these lines than in those of the parent mutant lines since these seeds had different copies of SSI and SSIIIa genes in a heterozygous state. The endosperm of the two types of opaque seeds contained the unique starch with modified fine structure, round-shaped starch granules, high amylose content, and specific physicochemical properties. The seed weight was ∼90% of that of the wild type. The amount of granule-bound starch synthase I (GBSSI) and the activity of ADP-glucose pyrophosphorylase (AGPase) were higher than in the wild type and parent mutant lines. The double-recessive homozygous mutant prepared from both ss1 and ss3a null mutants was considered sterile, while the mutant produced by the leaky ss1 mutant×ss3a null mutant cross was fertile. This present study strongly suggests that at least SSI or SSIIIa is required for starch biosynthesis in rice endosperm.

Starch-branching enzyme IIa is required for proper diurnal cycling of starch in leaves of maize

Starch-branching enzyme (SBE), a glucosyl transferase, is required for the highly regular pattern of α-1,6 bonds in the amylopectin component of starch. In the absence of SBEIIa, as shown previously in the sbe2a mutant of maize (Zea mays), leaf starch has drastically reduced branching and the leaves exhibit a severe senescence-like phenotype. Detailed characterization of the maize sbe2a mutant revealed that SBEIIa is the primary active branching enzyme in the leaf and that in its absence plant growth is affected. Both seedling and mature sbe2a mutant leaves do not properly degrade starch during the night, resulting in hyperaccumulation. In mature sbe2a leaves, starch hyperaccumulation is greatest in visibly senescing regions but also observed in green tissue and is correlated to a drastic reduction in photosynthesis within the leaf. Starch granules from sbe2a leaves observed via scanning electron microscopy and transmission electron microscopy analyses are larger, irregular, and amorphous as compared with the highly regular, discoid starch granules observed in wild-type leaves. This appears to trigger premature senescence, as shown by an increased expression of genes encoding proteins known to be involved in senescence and programmed cell death processes. Together, these results indicate that SBEIIa is required for the proper diurnal cycling of transitory starch within the leaf and suggest that SBEIIa is necessary in producing an amylopectin structure amenable to degradation by starch metabolism enzymes.

Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch

Soluble starch synthases (SSs) are major enzymes involved in starch biosynthesis in developing rice (Oryza sativa L.) endosperm. Despite extensive studies of SSs in various plant species including rice, the functional modes of action among multiple SS genes are still not clear. Here, we generated transgenic RNA interference (RNAi) repressed lines for seven of the eight members of the rice SS gene family and studied their effects on starch synthesis and grain formation. Consistent with their expression domains, RNAi repression of genes that encode isozymes SSI, SSIIa, and SSIIIa had strong effects on grain development, whereas no obvious phenotypic changes were observed in transgenic plants with the other SS genes being RNAi repressed, indicating functional redundancies among the genes. To study the potential functional interactions of SS genes, we generated SSIIa/SSIIIa double repression lines whose kernels displayed a chalky kernel appearance and had increased amylose levels, increased pasting temperatures, and decreased viscosities. The double mutation also reduced short (degree of polymerization (DP) 5-6) and long (DP 12-23) amylopectin chain contents in the grain and increased the medium long types (DP 7-11). The nonadditive nature of the double mutation line suggests that SSIIa and SSIIIa interact with each other during starch synthesis. Such interaction may be physical via starch phophorylase as indicated by our pair-wise yeast two-hybrid assays on major starch synthesis enzymes. Collectively, the data showed that SSIIa and SSIIIa play distinctive, but partially overlapping, roles during rice grain starch synthesis. The possibility of extensive redundancy or complementarity among SS isozymes is discussed.

Inhibition of the expression of the starch synthase II gene leads to lower pasting temperature in sweetpotato starch

The sweetpotato cultivar Quick Sweet (QS) with a lower pasting temperature of starch is a unique breeding material, but the biochemical background of this property has been unknown. To assess the physiological impact of the reduced isoform II activity of starch synthase (SSII) on the starch properties in sweetpotato storage root, transgenic sweetpotato plants with reduced expressions of the SSII gene were generated and evaluated. All of the starches from transgenic plants showed lower pasting temperatures and breakdown measured by a Rapid Visco Analyzer. The pasting temperatures in transgenic plants were approximately 10-15 degrees C lower than in wild-type plants. Distribution of the amylopectin chain length of the transgenic lines showed marked differences compared to that in wild-type plants: more chains with degree of polymerization (DP) 6-11 and fewer chains with DP 13-25. The starch granules from the storage root of transgenic plants showed cracking on the hilum, while those from wild-type plants appeared to be typical sweetpotato starch. In accordance with these observations, the expression of SSII in the storage roots of the sweetpotato cultivar with low pasting temperature starch (QS) was notably lower than in cultivars with normal starch. Moreover, nucleotide sequence analysis suggested that most of the SSII transcripts in the cultivar with low pasting temperature starch were inactive alleles. These results clearly indicate that the activity of SSII in sweetpotato storage roots, like those in other plants, affects the pasting properties of starch through alteration of the amylopectin structure.

Starch granule initiation in Arabidopsis requires the presence of either class IV or class III starch synthases

The mechanisms underlying starch granule initiation remain unknown. We have recently reported that mutation of soluble starch synthase IV (SSIV) in Arabidopsis thaliana results in restriction of the number of starch granules to a single, large, particle per plastid, thereby defining an important component of the starch priming machinery. In this work, we provide further evidence for the function of SSIV in the priming process of starch granule formation and show that SSIV is necessary and sufficient to establish the correct number of starch granules observed in wild-type chloroplasts. The role of SSIV in granule seeding can be replaced, in part, by the phylogenetically related SSIII. Indeed, the simultaneous elimination of both proteins prevents Arabidopsis from synthesizing starch, thus demonstrating that other starch synthases cannot support starch synthesis despite remaining enzymatically active. Herein, we describe the substrate specificity and kinetic properties of SSIV and its subchloroplastic localization in specific regions associated with the edges of starch granules. The data presented in this work point to a complex mechanism for starch granule formation and to the different abilities of SSIV and SSIII to support this process in Arabidopsis leaves.