Formation of starch in plant cells

LIKE EARLY STARVATION 1 interacts with amylopectin during starch biosynthesis

Starch is the major energy storage compound in plants. Both transient starch and long-lasting storage starch accumulate in the form of insoluble, partly crystalline granules. The structure of these granules is related to the structure of the branched polymer amylopectin: linear chains of glucose units organized in double helices that align to form semicrystalline lamellae, with branching points located in amorphous regions between them. EARLY STARVATION 1 (ESV1) and LIKE EARLY STARVATION 1 (LESV) proteins are involved in the maintenance of starch granule structure and in the phase transition of amylopectin, respectively, in Arabidopsis (Arabidopsis thaliana). These proteins contain a conserved tryptophan-rich C-terminal domain folded into an antiparallel β-sheet, likely responsible for binding of the proteins to starch, and different N-terminal domains whose structure and function are unknown. In this work, we combined biochemical and biophysical approaches to analyze the structures of LESV and ESV1 and their interactions with the different starch polyglucans. We determined that both proteins interact with amylopectin but not with amylose and that only LESV is capable of interacting with amylopectin during starch biosynthesis. While the C-terminal domain interacts with amylopectin in its semicrystalline form, the N-terminal domain of LESV undergoes induced conformational changes that are probably involved in its specific function of mediating glucan phase transition. These results clarify the specific mechanism of action of these 2 proteins in the biosynthesis of starch granules.

The activation of Chlamydomonas reinhardtii alpha amylase 2 by glutamine requires its N-terminal aspartate kinase-chorismate mutase-tyrA (ACT) domain

The coordination of assimilation pathways for all the elements that make up cellular components is a vital task for every organism. Integrating the assimilation and use of carbon (C) and nitrogen (N) is of particular importance because of the high cellular abundance of these elements. Starch is one of the most important storage polymers of photosynthetic organisms, and a complex regulatory network ensures that biosynthesis and degradation of starch are coordinated with photosynthetic activity and growth. Here, we analyzed three starch metabolism enzymes of Chlamydomonas reinhardtii that we captured by a cyclic guanosine monophosphate (cGMP) affinity chromatography approach, namely, soluble starch synthase STA3, starch-branching enzyme SBE1, and α-amylase AMA2. While none of the recombinant enzymes was directly affected by the presence of cGMP or other nucleotides, suggesting an indirect binding to cGMP, AMA2 activity was stimulated in the presence of L-glutamine (Gln). This activating effect required the enzyme's N-terminal aspartate kinase-chorismate mutase-tyrA domain. Gln is the first N assimilation product and not only a central compound for the biosynthesis of N-containing molecules but also a recognized signaling molecule for the N status. Our observation suggests that AMA2 might be a means to coordinate N and C metabolism at the enzymatic level, increasing the liberation of C skeletons from starch when high Gln levels signal an abundance of assimilated N.

Living Synthelectronics: A New Era for Bioelectronics Powered by Synthetic Biology

Bioelectronics, which converges biology and electronics, has attracted great attention due to their vital applications in human-machine interfaces. While traditional bioelectronic devices utilize nonliving organic and/or inorganic materials to achieve flexibility and stretchability, a biological mismatch is often encountered because human tissues are characterized not only by softness and stretchability but also by biodynamic and adaptive properties. Recently, a notable paradigm shift has emerged in bioelectronics, where living cells, and even viruses, modified via gene editing within synthetic biology, are used as core components in a new hybrid electronics paradigm. These devices are defined as "living synthelectronics," and they offer enhanced potential for interfacing with human tissues at informational and substance exchange levels. In this Perspective, the recent advances in living synthelectronics are summarized. First, opportunities brought to electronics by synthetic biology are briefly introduced. Then, strategic approaches to designing and making electronic devices using living cells/viruses as the building blocks, sensing components, or power sources are reviewed. Finally, the challenges faced by living synthelectronics are raised. It is believed that this paradigm shift will significantly contribute to the real integration of bioelectronics with human tissues.

3D Printing of Polysaccharide-Based Hydrogel Scaffolds for Tissue Engineering Applications: A Review

In tissue engineering, 3D printing represents a versatile technology employing inks to construct three-dimensional living structures, mimicking natural biological systems. This technology efficiently translates digital blueprints into highly reproducible 3D objects. Recent advances have expanded 3D printing applications, allowing for the fabrication of diverse anatomical components, including engineered functional tissues and organs. The development of printable inks, which incorporate macromolecules, enzymes, cells, and growth factors, is advancing with the aim of restoring damaged tissues and organs. Polysaccharides, recognized for their intrinsic resemblance to components of the extracellular matrix have garnered significant attention in the field of tissue engineering. This review explores diverse 3D printing techniques, outlining distinctive features that should characterize scaffolds used as ideal matrices in tissue engineering. A detailed investigation into the properties and roles of polysaccharides in tissue engineering is highlighted. The review also culminates in a profound exploration of 3D polysaccharide-based hydrogel applications, focusing on recent breakthroughs in regenerating different tissues such as skin, bone, cartilage, heart, nerve, vasculature, and skeletal muscle. It further addresses challenges and prospective directions in 3D printing hydrogels based on polysaccharides, paving the way for innovative research to fabricate functional tissues, enhancing patient care, and improving quality of life.

Genome Characteristics of the Endophytic Fungus Talaromyces sp. DC2 Isolated from Catharanthus roseus (L.) G. Don

Talaromyces sp. DC2 is an endophytic fungus that was isolated from the stem of Catharanthus roseus (L.) G. Don in Hanoi, Vietnam and is capable of producing vinca alkaloids. This study utilizes the PacBio Sequel technology to completely sequence the whole genome of Talaromyces sp. DC2The genome study revealed that DC2 contains a total of 34.58 Mb spanned by 156 contigs, with a GC content of 46.5%. The identification and prediction of functional protein-coding genes, tRNA, and rRNA were comprehensively predicted and highly annotated using various BLAST databases, including non-redundant (Nr) protein sequence, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Carbohydrate-Active Enzymes (CAZy) databases. The genome of DC2 has a total of 149, 227, 65, 153, 53, and 6 genes responsible for cellulose, hemicellulose, lignin, pectin, chitin, starch, and inulin degradation, respectively. The Antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analyses revealed that strain DC2 possesses 20 biosynthetic gene clusters responsible for producing secondary metabolites. The strain DC2 has also been found to harbor the DDC gene encoding aromatic L-amino acid decarboxylase enzyme. Conclusively, this study has provided a comprehensive understanding of the processes involved in secondary metabolites and the ability of the Talaromyces sp. DC2 strain to degrade plant cell walls.

Effect of incorporating white pepper (Piper nigrum L.) oleoresin on starch/alginate films

The development of films based on natural components has demonstrated their potential for food preservation. In this research, the effect of the inclusion of white pepper oleoresin (WPO) in a film made from cassava starch and sodium alginate (FWPO) on the antimicrobial, physicochemical, mechanical, optical, and structural properties was evaluated. The films were formulated with different concentrations of WPO (0.0, 0.5, 1.0 and 1.5%). The results obtained indicated that the incorporation of WPO in the film increased the antioxidant activity against the 1,1-diphenyl-2-picryl-hydrazyl radical (DPPH), and an inhibitory effect against Escherichia coli and Staphylococcus aureus bacteria was also observed. Elongation at break (EB), water vapor permeability (WVP), moisture content, solubility, and luminosity (L*) decreased significantly (p < 0.05) with the addition of WPO. On the other hand, the tensile strength (TS), the value of b* (tendency toward yellow) and the opacity increased. Scanning electron microscopy (SEM) images showed a smooth, uniform appearance, and continuous dispersion between cassava starch, alginate and WPO. FTIR spectra showed the interactions between the film components. X-ray diffraction (XRD) patterns showed that the addition of WPO did not affect the structural stability of the films. The results obtained indicate the possible use of WPO in the packaging of food products, contributing to the improvement of food quality and safety.

Functional Characterization of the MeSSIII-1 Gene and Its Promoter from Cassava

Soluble starch synthases (SSs) play important roles in the synthesis of cassava starch. However, the expression characteristics of the cassava SSs genes have not been elucidated. In this study, the MeSSIII-1 gene and its promoter, from SC8 cassava cultivars, were respectively isolated by PCR amplification. MeSSIII-1 protein was localized to the chloroplasts. qRT-PCR analysis revealed that the MeSSIII-1 gene was expressed in almost all tissues tested, and the expression in mature leaves was 18.9 times more than that in tuber roots. MeSSIII-1 expression was induced by methyljasmonate (MeJA), abscisic acid (ABA), and ethylene (ET) hormones in cassava. MeSSIII-1 expression patterns were further confirmed in proMeSSIII-1 transgenic cassava. The promoter deletion analysis showed that the -264 bp to -1 bp MeSSIII-1 promoter has basal activity. The range from -1228 bp to -987 bp and -488 bp to -264 bp significantly enhance promoter activity. The regions from -987 bp to -747 bp and -747 bp to -488 bp have repressive activity. These findings will provide an important reference for research on the potential function and transcriptional regulation mechanisms of the MeSSIII-1 gene and for further in-depth exploration of the regulatory network of its internal functional elements.

The roles of non-structural carbohydrates in fruiting: a review focusing on mango (Mangifera indica)

Reproductive development of fruiting trees, including mango (Mangifera indica L.), is limited by non-structural carbohydrates. Competition for sugars increases with cropping, and consequently, vegetative growth and replenishment of starch reserves may reduce with high yields, resulting in interannual production variability. While the effect of crop load on photosynthesis and the distribution of starch within the mango tree has been studied, the contribution of starch and sugars to different phases of reproductive development requires attention. This review focuses on mango and examines the roles of non-structural carbohydrates in fruiting trees to clarify the repercussions of crop load on reproductive development. Starch buffers the plant's carbon availability to regulate supply with demand, while sugars provide a direct resource for carbon translocation. Sugar signalling and interactions with phytohormones play a crucial role in flowering, fruit set, growth, ripening and retention, as well as regulating starch, sugar and secondary metabolites in fruit. The balance between the leaf and fruit biomass affects the availability and contributions of starch and sugars to fruiting. Crop load impacts photosynthesis and interactions between sources and sinks. As a result, the onset and rate of reproductive processes are affected, with repercussions for fruit size, composition, and the inter-annual bearing pattern.

Starch phosphorylation regulates starch granule morphological homogeneity in Arabidopsis thaliana

Starch granule morphological homogeneity presents a gap in starch research. Transitory starch granules in wild-type plants are discoid, regardless of species. Notably, while the shape of starch granules can differ among mutants, it typically remains homogeneous within a genotype. We found an Arabidopsis thaliana mutant, dpe2sex4, lacking both the cytosolic disproportionating enzyme 2 (DPE2) and glucan phosphatase SEX4, showing an unprecedented bimodal starch granule diameter distribution when grown under a light/dark rhythm. dpe2sex4 contained 2 types of starch granules: large granules and small granules. In contrast to the double starch initiation in wheat (Triticum aestivum) endosperm, where A-type granules are initiated first and B-type granules are initiated later, dpe2sex4 small and large granules developed simultaneously in the same chloroplast. Compared with the large granules, the small granules had more branched amylopectin and less surface starch-phosphate, thus having a more compact structure that may hinder starch synthesis. During plant aging, the small granules barely grew. In in vitro experiments, fewer glucosyl residues were incorporated in small granules. Under continuous light, dpe2sex4 starch granules were morphologically homogeneous. Omitting the dark phase after a 2-wk light/dark cycle by moving plants into continuous light also reduced morphological variance between these 2 types of granules. These data shed light on the impact of starch phosphorylation on starch granule morphology homogeneity.

In-Silico Identification, Characterization and Expression Analysis of Genes Involved in Resistant Starch Biosynthesis in Potato (Solanum tuberosum L.) Varieties

Potato (Solanum tuberosum L.), an important horticultural crop is a member of the family Solanaceae and is mainly grown for consumption at global level. Starch, the principal component of tubers, is one of the significant elements for food and non-food-based applications. The genes associated with biosynthesis of starch have been investigated extensively over the last few decades. However, a complete regulation pathway of constituent of amylose and amylopectin are still not deeply explored. The current in-silico study of genes related to amylose and amylopectin synthesis and their genomic organization in potato is still lacking. In the current study, the nucleotide and amino acid arrangement in genome and twenty-two genes linked to starch biosynthesis pathway in potato were analysed. The genomic structure analysis was also performed to find out the structural pattern and phylogenetic relationship of genes. The genome mining and structure analysis identified ten specific motifs and phylogenetic analysis of starch biosynthesis genes divided them into three different clades on the basis of their functioning and phylogeny. Quantitative real-time PCR (qRT-PCR) of amylose biosynthesis pathway genes in three contrast genotypes revealed the down-gene expression that leads to identify potential cultivar for functional genomic approaches. These potential lines may help to achieve higher content of resistant starch.

Mutations in starch biosynthesis genes affect chloroplast development in wheat pericarp

Starch bioengineering in cereals has produced a plethora of genotypes with new nutritional and technological functionalities. Modulation of amylose content from 0 to 100% was inversely correlated with starch digestibility and promoted a lower glycemic index in food products. In wheat, starch mutants have been reported to exhibit various side effects, mainly related to the seed phenotype. However, little is known about the impact of altered amylose content and starch structure on plant metabolism. Here, three bread wheat starch mutant lines with extreme phenotypes in starch branching and amylose content were used to study plant responses to starch structural changes. Omics profiling of gene expression and metabolic patterns supported changes, confirmed by ultrastructural analysis in the chloroplast of the immature seeds. In detail, the identification of differentially expressed genes belonging to functional categories related to photosynthesis, chloroplast and thylakoid (e.g. CURT1), the alteration in the accumulation of photosynthesis-related compounds, and the chloroplast alterations (aberrant shape, grana stacking alteration, and increased number of plastoglobules) suggested that the modification of starch structure greatly affects starch turnover in the chloroplast, triggering oxidative stress (ROS accumulation) and premature tissue senescence. In conclusion, this study highlighted a correlation between starch structure and chloroplast functionality in the wheat kernel.

PEP-ASSOCIATED PROTEIN 3 regulates rice tiller formation and grain yield by controlling chloroplast biogenesis

Plastid-encoded RNA polymerase (PEP) plays a pivotal role in chloroplast development by governing the transcription of chloroplast genes, and PEP-associated proteins (PAPs) modulate PEP transcriptional activity. Therefore, PAPs provide an intriguing target for those efforts to improve yield, by enhancing chloroplast development. In this study, we identified the rice (Oryza sativa) OsPAP3 gene and characterized its function in chloroplast development. OsPAP3 expression was light-dependent and leaf-specific, similar to the PEP-dependent chloroplast gene RUBISCO LARGE SUBUNIT (OsRbcL), and OsPAP3 protein localized to chloroplast nucleoids where PEP functions. Analysis of loss-of-function and gain-of-function mutants showed that the expression of OsPAP3 is tightly linked to chloroplast gene expression and chloroplast biogenesis in rice. Homozygous knockout mutants of OsPAP3 had fewer chloroplasts than wild type, whereas plants overexpressing OsPAP3 had more chloroplasts. Also, OsPAP3 knockout suppressed the PEP-dependent expression of chloroplast genes, but OsPAP3 overexpression increased their expression. These findings indicate that OsPAP3 regulates chloroplast biogenesis in rice by controlling the PEP-dependent expression of chloroplast genes. More importantly, data from 3 seasons of field cultivation revealed that the overexpression of OsPAP3 improves rice grain yield by approximately 25%, largely due to increased tiller formation. Collectively, these observations suggest that OsPAP3 regulates rice growth and productivity by promoting chloroplast development.

Identification of Chemicals That Abrogate Folate-Dependent Inhibition of Starch Accumulation in Non-Photosynthetic Plastids of Arabidopsis

Folate, also known as vitamin B9, is an essential cofactor for a variety of enzymes and plays a crucial role in many biological processes. We previously reported that plastidial folate prevents starch biosynthesis triggered by the influx of sugar into non-starch-accumulating plastids, such as etioplasts, and chloroplasts under darkness; hence the loss of plastidial folate induces the accumulation of starch in plastids. To understand the molecular mechanism underlying this phenomenon, we screened our in-house chemical library and searched their derivatives to identify chemicals capable of inducing starch accumulation in etioplasts. The results revealed four chemicals, compounds #120 and #375 and their derivatives, compounds #120d and #375d, respectively. The derivative compounds induced starch accumulation in etioplasts and suppressed hypocotyl elongation in dark-grown Arabidopsis seedlings. They also inhibited the post-germinative growth of seedlings under illumination. All four chemicals contained the sulfonamide group as a consensus structure. The sulfonamide group is also found in sulfa drugs, which exhibit antifolate activity, and in sulfonylurea herbicides. Further analyses revealed that compound #375d induces starch accumulation by inhibiting folate biosynthesis. By contrast, compound #120d neither inhibited folate biosynthesis nor exhibited the herbicide activity. Protein and metabolite analyses suggest that compound #120d abrogates folate-dependent inhibition of starch accumulation in etioplasts by enhancing starch biosynthesis.

Enzyme-controlled, nutritive hydrogel for mesenchymal stromal cell survival and paracrine functions

Culture-adapted human mesenchymal stromal cells (hMSCs) are appealing candidates for regenerative medicine applications. However, these cells implanted in lesions as single cells or tissue constructs encounter an ischemic microenvironment responsible for their massive death post-transplantation, a major roadblock to successful clinical therapies. We hereby propose a paradigm shift for enhancing hMSC survival by designing, developing, and testing an enzyme-controlled, nutritive hydrogel with an inbuilt glucose delivery system for the first time. This hydrogel, composed of fibrin, starch (a polymer of glucose), and amyloglucosidase (AMG, an enzyme that hydrolyze glucose from starch), provides physiological glucose levels to fuel hMSCs via glycolysis. hMSCs loaded in these hydrogels and exposed to near anoxia (0.1% pO2) in vitro exhibited improved cell viability and angioinductive functions for up to 14 days. Most importantly, these nutritive hydrogels promoted hMSC viability and paracrine functions when implanted ectopically. Our findings suggest that local glucose delivery via the proposed nutritive hydrogel can be an efficient approach to improve hMSC-based therapeutic efficacy.

Plant structural and storage glucans trigger distinct transcriptional responses that modulate the motility of Xanthomonas pathogens

IMPORTANCE

Pathogenic Xanthomonas bacteria can affect a variety of economically relevant crops causing losses in productivity, limiting commercialization and requiring phytosanitary measures. These plant pathogens exhibit high level of host and tissue specificity through multiple molecular strategies including several secretion systems, effector proteins, and a broad repertoire of carbohydrate-active enzymes (CAZymes). Many of these CAZymes act on the plant cell wall and storage carbohydrates, such as cellulose and starch, releasing products used as nutrients and modulators of transcriptional responses to support host colonization by mechanisms yet poorly understood. Here, we reveal that structural and storage β-glucans from the plant cell function as spatial markers, providing distinct chemical stimuli that modulate the transition between higher and lower motility states in Xanthomonas citri, a key virulence trait for many bacterial pathogens.

Soluble and insoluble α-glucan synthesis in yeast by enzyme suites derived exclusively from maize endosperm

Molecular mechanisms that distinguish the synthesis of semi-crystalline α-glucan polymers found in plant starch granules from the synthesis of water-soluble polymers by nonplant species are not well understood. To address this, starch biosynthetic enzymes from maize (Zea mays L.) endosperm were isolated in a reconstituted environment using yeast (Saccharomyces cerevisiae) as a test bed. Ninety strains were constructed containing unique combinations of 11 synthetic transcription units specifying maize starch synthase (SS), starch phosphorylase (PHO), starch branching enzyme (SBE), or isoamylase-type starch debranching enzyme (ISA). Soluble and insoluble branched α-glucans accumulated in varying proportions depending on the enzyme suite, with ISA function stimulating distribution into the insoluble form. Among the SS isoforms, SSIIa, SSIII, and SSIV individually supported the accumulation of glucan polymer. Neither SSI nor SSV alone produced polymers; however, synergistic effects demonstrated that both isoforms can stimulate α-glucan accumulation. PHO did not support α-glucan production by itself, but it had either positive or negative effects on polymer content depending on which SS or a combination thereof was present. The complete suite of maize enzymes generated insoluble particles resembling native starch granules in size, shape, and crystallinity. Ultrastructural analysis revealed a hierarchical assembly starting with subparticles of approximately 50 nm diameter that coalesce into discrete structures of approximately 200 nm diameter. These are assembled into semi-crystalline α-glucan superstructures up to 4 μm in length filling most of the yeast cytosol. ISA was not essential for the formation of such particles, but their abundance was increased dramatically by ISA presence.

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.

A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways

Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.

Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield

The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.

Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis

BACKGROUND

Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. Like in bread wheat, the starch and protein accumulated in the endosperm during grain development are the primary contributors to the calorific value of durum grains.

RESULTS

To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. We demonstrate the potential of our dataset to provide new insights into key processes that occur during endosperm development, using starch metabolism as an example.

CONCLUSION

We provide a valuable resource for studying endosperm development in this increasingly important crop species.

Comparisons of rice taste and starch physicochemical properties in superior and inferior grains of rice with different taste value

The difference in grain yield between superior grains (SG) on the upper part and inferior grains (IG) on the lower part of the same panicle was widely reported. To date, variations in rice taste quality between SG and IG and the related starch physicochemical properties remained poorly understood. Here, rice cultivars with different taste quality (NT, normal taste; GT, good taste) were grown to investigate the mechanism underlying taste difference between SG and IG and the correlation between cooked rice taste and starch properties. In this study, the taste value of GT rice was 32.2% higher than that of NT rice across the cultivars. The GT rice comprised a series of typical taste qualities of larger stickiness, smaller hardness, lower apparent amylose content (AAC), and lower protein content (PC). The taste quality differed among rice grains on the same panicle; SG achieved 21.9% and 17.0% higher taste value than IG in GT rice and NT rice, respectively. The higher taste value in SG was owing to the larger stickiness and lower PC. Meanwhile, SG of GT rice achieved the lowest PC (8.2%) and gluten content (5.6%), which might indicate a better health value. Additionally, larger and smoother granules, more fa (DP < 12), lower crystallinity, and larger 1045/1022 cm^-1 ratios were found in SG starch compared to IG starch. These led to a weaker swelling power and lower gelatinization enthalpy in SG starch, while gelatinization temperature and retrogression enthalpy were the opposite. Moreover, SG starch exhibited higher storage modulus, loss modulus, slowly digestible starch contents, and resistant starch contents than IG. Our results revealed a great difference in taste quality between SG and IG in rice. The larger and smoother starch granules and shorter chain length could increase the ordered structure of starch, thus improving swelling power, gelatinization properties, and rheological characteristics and facilitating better taste quality of SG over IG. Besides, the lower PC (especially gluten content), higher slowly digestible starch, and higher resistant starch content indicated a more promising health value of SG in the food industry.

LIKE EARLY STARVATION 1 and EARLY STARVATION 1 promote and stabilize amylopectin phase transition in starch biosynthesis

Starch, the most abundant carbohydrate reserve in plants, primarily consists of the branched glucan amylopectin, which forms semi-crystalline granules. Phase transition from a soluble to an insoluble form depends on amylopectin architecture, requiring a compatible distribution of glucan chain lengths and a branch-point distribution. Here, we show that two starch-bound proteins, LIKE EARLY STARVATION 1 (LESV) and EARLY STARVATION 1 (ESV1), which have unusual carbohydrate-binding surfaces, promote the phase transition of amylopectin-like glucans, both in a heterologous yeast system expressing the starch biosynthetic machinery and in Arabidopsis plants. We propose a model wherein LESV serves as a nucleating role, with its carbohydrate-binding surfaces helping align glucan double helices to promote their phase transition into semi-crystalline lamellae, which are then stabilized by ESV1. Because both proteins are widely conserved, we suggest that protein-facilitated glucan crystallization may be a general and previously unrecognized feature of starch biosynthesis.

Loss of function of SSIIIa and SSIIIb coordinately confers high RS content in cooked rice

The sedentary lifestyle and refined food consumption significantly lead to obesity, type 2 diabetes, and related complications, which have become one of the major threats to global health. This incidence could be potentially reduced by daily foods rich in resistant starch (RS). However, it remains a challenge to breed high-RS rice varieties. Here, we reported a high-RS mutant rs4 with an RS content of ~10.8% in cooked rice. The genetic study revealed that the loss-of-function SSIIIb and SSIIIa together with a strong Wx allele in the background collaboratively contributed to the high-RS phenotype of the rs4 mutant. The increased RS contents in ssIIIa and ssIIIa ssIIIb mutants were associated with the increased amylose and lipid contents. SSIIIb and SSIIIa proteins were functionally redundant, whereas SSIIIb mainly functioned in leaves and SSIIIa largely in endosperm owing to their divergent tissue-specific expression patterns. Furthermore, we found that SSIII experienced duplication in different cereals, of which one SSIII paralog was mainly expressed in leaves and another in the endosperm. SSII but not SSIV showed a similar evolutionary pattern to SSIII. The copies of endosperm-expressed SSIII and SSII were associated with high total starch contents and low RS levels in the seeds of tested cereals, compared with low starch contents and high RS levels in tested dicots. These results provided critical genetic resources for breeding high-RS rice cultivars, and the evolutionary features of these genes may facilitate to generate high-RS varieties in different cereals.

Revisiting maize Brittle endosperm-2 reveals new insights in BETL development and starchy endosperm filling

Rerouting the starch biosynthesis pathway in maize can generate specialty types, like sweet corn and waxy corn, with a drastically increasing global demand. Hence, a fine-tuning of starch metabolism is relevant to create diverse maize cultivars for end-use applications. Here, we characterized a new maize brittle endosperm mutant, referred to as bt1774, which exhibited decreased starch content but a dramatic increase of soluble sugars at maturity. Both endosperm and embryo development was impaired in bt1774 relative to the wild-type (WT), with a prominently arrested basal endosperm transfer layer (BETL). Map-based cloning revealed that BRITTLE ENDOSPERM2 (Bt2), which encodes a small subunit of ADP-glucose pyrophosphorylase (AGPase), is the causal gene for bt1774. A MuA2 element was found to be inserted into intron 2 of Bt2, leading to a severe decrease of its expression, in bt1774. This is in line with the irregular and loosely packed starch granules in the mutant. Transcriptome of endosperm at grain filling stage identified 1, 013 differentially expressed genes in bt1774, which were notably enriched in the BETL compartment, including ZmMRP1, Miniature1, MEG1, and BETLs. Gene expression of the canonical starch biosynthesis pathway was marginally disturbed in Bt1774. Combined with the residual 60% of starch in this nearly null mutant of Bt2, this data strongly suggests that an AGPase-independent pathway compensates for starch synthesis in the endosperm. Consistent with the BETL defects, zein accumulation was impaired in bt1774. Co-expression network analysis revealed that Bt2 probably has a role in intracellular signal transduction, besides starch synthesis. Altogether, we propose that Bt2 is likely involved in carbohydrate flux and balance, thus regulating both the BETL development and the starchy endosperm filling.

Pericarp starch metabolism is associated with caryopsis development and endosperm starch accumulation in common wheat

The wheat pericarp is the main component of the caryopsis at the early development stage and ultimately converts into a tissue that covers the mature caryopsis. A large number of starch granules are accumulated in the pericarp, but the production of and the role of starch granules in caryopsis development remain- elusive. In the present study, the relationship between accumulated starch granules and starch metabolism-related genes in wheat pericarp was investigated using paraffin section observations, expression analysis, and mutant analysis. Starch synthesis is initiated before anthesis and is dependent on a sucrose uptake and conversion system similar to that in the endosperm. TaPTST2 is required to initiate the production of pericarp starch granules. Pericarp starch granules gradually disappeared at the filling stage with high expression levels of genes encoding β-amylase, sucrose-phosphate synthase, and sucrose-phosphate phosphatase. As a maternal tissue adjacent to the endosperm and embryo, the pericarp plays a temporary reservoir for excess nutrients delivered into the caryopsis during the early development stage and exported at the filling stage. The pericarp contributes to the development of the endosperm and embryo as well as the accumulation of endosperm starch. The metabolism of pericarp starch may affect the weight of the wheat caryopsis.

Metabolic and transcriptomic analyses elucidate a novel insight into the network for biosynthesis of carbohydrate and secondary metabolites in the stems of a medicinal orchid Dendrobium nobile

Dendrobium nobile is an important medicinal and nutraceutical herb. Although the ingredients of D. nobile have been identified as polysaccharides, alkaloids, amino acids, flavonoids and bibenzyls, our understanding of the metabolic pathways that regulate the synthesis of these compounds is limited. Here, we used transcriptomic and metabolic analyses to elucidate the genes and metabolites involved in the biosynthesis of carbohydrate and several secondary metabolites in the stems of D. nobile. A total of 1005 metabolites and 31,745 genes were detected in the stems of D. nobile. The majority of these metabolites and genes were involved in the metabolism of carbohydrates (fructose, mannose, glucose, xylulose and starch), while some were involved in the metabolism of secondary metabolites (alkaloids, β-tyrosine, ferulic acid, 4-hydroxybenzoate and chrysin). Our predicted regulatory network indicated that five genes (AROG, PYK, DXS, ACEE and HMGCR) might play vital roles in the transition from carbohydrate to alkaloid synthesis. Correlation analysis identified that six genes (ALDO, PMM, BGLX, EGLC, XYLB and GLGA) were involved in carbohydrate metabolism, and two genes (ADT and CYP73A) were involved in secondary metabolite biosynthesis. Our analyses also indicated that phosphoenol-pyruvate (PEP) was a crucial bridge that connected carbohydrate to alkaloid biosynthesis. The regulatory network between carbohydrate and secondary metabolite biosynthesis established will provide important insights into the regulation of metabolites and biological systems in Dendrobium species.

Transcriptome and metabolome profiling identify factors potentially involved in pro-vitamin A accumulation in cassava landraces

Cassava (Manihot esculenta Crantz) is a predominant food security crop in several developing countries. Its storage roots, rich in carbohydrate, are deficient in essential micronutrients, including provitamin A carotenoids. Increasing carotenoid content in cassava storage roots is important to reduce the incidence of vitamin A deficiency, a public health problem in sub-Saharan Africa. However, cassava improvement advances slowly, mainly due to limited information on the molecular factors influencing β-carotene accumulation in cassava. To address this problem, we performed comparative transcriptomic and untargeted metabolic analyses of roots and leaves of eleven African cassava landraces ranging from white to deep yellow colour, to uncover regulators of carotenoid biosynthesis and accumulation with conserved function in yellow cassava roots. Sequence analysis confirmed the presence of a mutation, known to influence β-carotene content, in PSY transcripts of deep yellow but not of pale yellow genotypes. We identified genes and metabolites with expression and accumulation levels significantly associated with β-carotene content. Particularly an increased activity of the abscisic acid catabolism pathway together with a reduced amount of L-carnitine, may be related to the carotenoid pathway flux, higher in yellow than in white storage roots. In fact, NCED_3.1 was specifically expressed at a lower level in all yellow genotypes suggesting that it could be a potential target for increasing carotenoid accumulation in cassava. These results expand the knowledge on metabolite compositions and molecular mechanisms influencing carotenoid biosynthesis and accumulation in cassava and provide novel information for biotechnological applications and genetic improvement of cassava with high nutritional values.

Reinvention of starch for oral drug delivery system design

Starch is a polysaccharide with varying amylose-to-amylopectin ratios as a function of its biological sources. It is characterized by low shear stress resistance, poor aqueous/organic solubility and gastrointestinal digestibility which limit its ease of processing and functionality display as an oral drug delivery vehicle. Modulation of starch composition through genetic engineering primarily alters amylose-to-amylopectin ratio. Greater molecular properties changes require chemical and enzymatic modifications of starch. Acetylation reduces water solubility and enzymatic digestibility of starch. Carboxymethylation turns starch acid-insoluble and aggregative at low pHs. The summative effects are sustaining drug release in the upper gut. Acid-insoluble carboxymethylated starch can be aminated to provide an ionic character essential for hydrogel formation which further reduces its drug release. Ionic starch can coacervate with oppositely charged starch, non-starch polyelectrolyte or drug into insoluble, controlled-release complexes. Enzymatically debranched and resistant starch has a small molecular size which confers chain aggregation into a helical hydrogel network that traps the drug molecules, protecting them from biodegradation. The modified starch has been used to modulate the intestinal/colon-specific or controlled systemic delivery of oral small molecule drugs and macromolecular therapeutics. This review highlights synthesis aspects of starch and starch derivatives, and their outcomes and challenges of applications in oral drug delivery.

Effects of Post Anthesis High Temperature Stress on Carbon Partitioning and Starch Biosynthesis in a Spring Wheat (Triticum aestivum L.) Adapted to Moderate Growth Temperatures

This study investigates carbon partitioning in the developing endosperm of a European variety of spring wheat subjected to moderately elevated daytime temperatures (27°C/16°C day/night) from anthesis to grain maturity. Elevated daytime temperatures caused significant reductions in both fresh and dry weights and reduced starch content of harvested grains compared to plants grown under a 20°C/16°C day/night regime. Accelerated grain development caused by elevated temperatures was accounted for by representing plant development as thermal time (°CDPA). We examined effects of high temperature stress (HTS) on uptake and partitioning of [U-14C]-sucrose supplied to isolated endosperms. HTS caused reduced sucrose uptake into developing endosperms from the second major grain filling stage (approximately 260°CDPA) up to maturity. Enzymes involved in sucrose metabolism were unaffected by HTS, whereas key enzyme activities involved in endosperm starch deposition such as ADP-glucose pyrophosphorylase and soluble isoforms of starch synthase were sensitive to HTS throughout grain development. HTS caused a decrease in other major carbon sinks such as evolved CO2, ethanol-soluble material, cell walls and protein. Despite reductions in labelling of carbon pools caused by HTS, the relative proportions of sucrose taken up by endosperm cells allocated to each cellular pool remain unchanged, except for evolved CO2, which increased under HTS and may reflect enhanced respiratory activity. The results of this study show that moderate temperature increases in some temperate wheat cultivars can cause significant yield reductions chiefly through three effects: reduced sucrose uptake by the endosperm, reduced starch synthesis, and increased partitioning of carbon into evolved CO2.

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.

ZnO nanoparticles efficiently enhance drought tolerance in Dracocephalum kotschyi through altering physiological, biochemical and elemental contents

Using nanofertilizers in certain concentrations can be a novel method to alleviate drought stress effects in plants as a global climate problem. We aimed to determine the impacts of zinc nanoparticles (ZnO-N) and zinc sulfate (ZnSO₄) fertilizers on the improvement of drought tolerance in Dracocephalum kotschyi as a medicinal-ornamental plant. Plants were treated with three doses of ZnO-N and ZnSO₄ (0, 10, and 20 mg/l) under two levels of drought stress [50% and 100% field capacity (FC)]. Relative water content (RWC), electrolyte conductivity (EC), chlorophyll, sugar, proline, protein, superoxide dismutase (SOD), polyphenol oxidase (PPO) and, guaiacol peroxidase (GPO) were measured. Moreover, the concentration of some elements interacting with Zn was reported using the SEM-EDX method. Results indicated that foliar fertilization of D. kotschyi under drought stress with ZnO-N decreased EC, while ZnSO₄ application was less effective. Moreover, sugar and proline content as well as activity of SOD and GPO (and to some extent PPO) in treated plants by 50% FC, increased under the influence of ZnO-N. ZnSO₄ application could increase chlorophyll and protein content and PPO activity in this plant under drought stress. Based on the results, ZnO-N and then ZnSO₄ improved the drought tolerance of D. kotschyi through their positive effects on physiological and biochemical attributes changing the concentration of Zn, P, Cu, and Fe. Accordingly, due to the increased sugar and proline content and also antioxidant enzyme activity (SOD, GPO, and to some extent PPO) on enhancing drought tolerance in this plant, ZnO-N fertilization is advisable.

The PRK/Rubisco shunt strongly influences Arabidopsis seed metabolism and oil accumulation, affecting more than carbon recycling

The carbon efficiency of storage lipid biosynthesis from imported sucrose in green Brassicaceae seeds is proposed to be enhanced by the PRK/Rubisco shunt, in which ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts outside the context of the Calvin-Benson-Bassham cycle to recycle CO2 molecules released during fatty acid synthesis. This pathway utilizes metabolites generated by the nonoxidative steps of the pentose phosphate pathway. Photosynthesis provides energy for reactions such as the phosphorylation of ribulose 5-phosphate by phosphoribulokinase (PRK). Here, we show that loss of PRK in Arabidopsis thaliana (Arabidopsis) blocks photoautotrophic growth and is seedling-lethal. However, seeds containing prk embryos develop normally, allowing us to use genetics to assess the importance of the PRK/Rubisco shunt. Compared with nonmutant siblings, prk embryos produce one-third less lipids-a greater reduction than expected from simply blocking the proposed PRK/Rubisco shunt. However, developing prk seeds are also chlorotic and have elevated starch contents compared with their siblings, indicative of secondary effects. Overexpressing PRK did not increase embryo lipid content, but metabolite profiling suggested that Rubisco activity becomes limiting. Overall, our findings show that the PRK/Rubisco shunt is tightly integrated into the carbon metabolism of green Arabidopsis seeds, and that its manipulation affects seed glycolysis, starch metabolism, and photosynthesis.

Ribulose-1,5-bisphosphate regeneration in the Calvin-Benson-Bassham cycle: Focus on the last three enzymatic steps that allow the formation of Rubisco substrate

The Calvin-Benson-Bassham (CBB) cycle comprises the metabolic phase of photosynthesis and is responsible for carbon fixation and the production of sugar phosphates. The first step of the cycle involves the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) which catalyzes the incorporation of inorganic carbon into 3-phosphoglyceric acid (3PGA). The following steps include ten enzymes that catalyze the regeneration of ribulose-1,5-bisphosphate (RuBP), the substrate of Rubisco. While it is well established that Rubisco activity acts as a limiting step of the cycle, recent modeling studies and experimental evidence have shown that the efficiency of the pathway is also impacted by the regeneration of the Rubisco substrate itself. In this work, we review the current understanding of the structural and catalytic features of the photosynthetic enzymes that catalyze the last three steps of the regeneration phase, namely ribose-5-phosphate isomerase (RPI), ribulose-5-phosphate epimerase (RPE), and phosphoribulokinase (PRK). In addition, the redox- and metabolic-based regulatory mechanisms targeting the three enzymes are also discussed. Overall, this review highlights the importance of understudied steps in the CBB cycle and provides direction for future research aimed at improving plant productivity.

An analysis of sugary endosperm in sorghum: Characterization of mutant phenotypes depending on alleles of the corresponding starch debranching enzyme

Sorghum is the fifth most important cereal crop. Here we performed molecular genetic analyses of the 'SUGARY FETERITA' (SUF) variety, which shows typical sugary endosperm traits (e.g., wrinkled seeds, accumulation of soluble sugars, and distorted starch). Positional mapping indicated that the corresponding gene was located on the long arm of chromosome 7. Within the candidate region of 3.4 Mb, a sorghum ortholog for maize Su1 (SbSu) encoding a starch debranching enzyme ISA1 was found. Sequencing analysis of SbSu in SUF uncovered nonsynonymous single nucleotide polymorphisms (SNPs) in the coding region, containing substitutions of highly conserved amino acids. Complementation of the rice sugary-1 (osisa1) mutant line with the SbSu gene recovered the sugary endosperm phenotype. Additionally, analyzing mutants obtained from an EMS-induced mutant panel revealed novel alleles with phenotypes showing less severe wrinkles and higher Brix scores. These results suggested that SbSu was the corresponding gene for the sugary endosperm. Expression profiles of starch synthesis genes during the grain-filling stage demonstrated that a loss-of-function of SbSu affects the expression of most starch synthesis genes and revealed the fine-tuned gene regulation in the starch synthetic pathway in sorghum. Haplotype analysis using 187 diverse accessions from a sorghum panel revealed the haplotype of SUF showing severe phenotype had not been used among the landraces and modern varieties. Thus, weak alleles (showing sweet and less severe wrinkles), such as in the abovementioned EMS-induced mutants, are more valuable for grain sorghum breeding. Our study suggests that more moderate alleles (e.g. produced by genome editing) should be beneficial for improving grain sorghum.

New Fructokinase, OsFRK3, Regulates Starch Accumulation and Grain Filling in Rice

Plant fructokinase (FRK) guarantees the growth and development of higher plants by participating in carbohydrate metabolism. In this study, a new fructokinase, OsFRK3, was identified using bioinformatics analysis, enzyme assay, bacterial growth assay, and yeast complementation test. Then, we created OsFRK3 knockout transgenic lines (osfrk3-1 and osfrk3-2) by the CRISPR/Cas9 technology. We found that the 1000-grain weight decreased notably (approximately -3.6% and -6.1%, respectively) in osfrk3-1 and osfrk3-2. Evidently decreased grain width, grain thickness, and endosperm filling rate were detected in the osfrk3 mutants (osfrk3-1 and osfrk3-2) compared with those of the WT. In addition, the content of seed total starch was significantly decreased by 3.42 and 4.80% in osfrk3 lines, compared with that in the WT. The level of maltose was significantly reduced in the mutants, while that of sucrose and fructose was obviously increased in the mutants. The transcript levels of OsGBSS1, OsBEIIb, OsPFP1β, and OsAGPL1 were significantly decreased in the osfrk3 mutants. These results suggest that OsFRK3 may positively regulate the accumulation of starch through influencing the sugar metabolism.

Detecting variation in starch granule size and morphology by high-throughput microscopy and flow cytometry

Starch forms semi-crystalline, water-insoluble granules, the size and morphology of which vary according to biological origin. These traits, together with polymer composition and structure, determine the physicochemical properties of starch. However, screening methods to identify differences in starch granule size and shape are lacking. Here, we present two approaches for high-throughput starch granule extraction and size determination using flow cytometry and automated, high-throughput light microscopy. We evaluated the practicality of both methods using starch from different species and tissues and demonstrated their effectiveness by screening for induced variation in starch extracted from over 10,000 barley lines, yielding four with heritable changes in the ratio of large A-granules to small B-granules. Analysis of Arabidopsis lines altered in starch biosynthesis further demonstrates the applicability of these approaches. Identifying variation in starch granule size and shape will enable identification of trait-controlling genes for developing crops with desired properties, and could help optimise starch processing.

Genome-Wide Identification of the CER Gene Family and Significant Features in Climate Adaptation of Castanea mollissima

The plant cuticle is the outermost layer of the aerial organs and an important barrier against biotic and abiotic stresses. The climate varies greatly between the north and south of China, with large differences in temperature and humidity, but Chinese chestnut is found in both regions. This study investigated the relationship between the wax layer of chestnut leaves and environmental adaptation. Firstly, semi-thin sections were used to verify that there is a significant difference in the thickness of the epicuticular wax layer between wild chestnut leaves in northwest and southeast China. Secondly, a whole-genome selective sweep was used to resequence wild chestnut samples from two typical regional populations, and significant genetic divergence was identified between the two populations in the CmCER1-1, CmCER1-5 and CmCER3 genes. Thirty-four CER genes were identified in the whole chestnut genome, and a series of predictive analyses were performed on the identified CmCER genes. The expression patterns of CmCER genes were classified into three trends-upregulation, upregulation followed by downregulation and continuous downregulation-when chestnut seedlings were treated with drought stress. Analysis of cultivars from two resource beds in Beijing and Liyang showed that the wax layer of the northern variety was thicker than that of the southern variety. For the Y-2 (Castanea mollissima genome sequencing material) cultivar, there were significant differences in the expression of CmCER1-1, CmCER1-5 and CmCER3 between the southern variety and the northern one-year-grafted variety. Therefore, this study suggests that the CER family genes play a role in environmental adaptations in chestnut, laying the foundation for further exploration of CmCER genes. It also demonstrates the importance of studying the adaptation of Chinese chestnut wax biosynthesis to the southern and northern environments.

Genetic dissection of quantitative traits loci identifies new genes for gelatinization parameters of starch and amylose-lipid complex (Resistant starch 5) in bread wheat

Starch is a major component of cereal grains such as wheat. Physicochemical and functional properties of starch affect end-use food quality and nutrients. To improve cultivars that preserve superior starch quality, the genetic foundation of the wheat starch and amylose-lipid complex (ALc, Resistant starch type 5) gelatinization are needed. This genome-wide association (GWA) mapping used 192 wheat genotypes (previously reported) to generate SNPs using an enhanced version of sequencing termed ddRAD on the Illumina Hi-seq X platform and 3696 high-quality influential SNPs were filtered out. The heterozygosity and Fst ranges in five subpopulations were 0.31-0.40 and 0.18-0.30 respectively. Nucleotide diversity and PIC ranged from 0.21 (6A) to 0.32 (2A) and 0.29 (6A) to 0.39 (4D) respectively. The Shannon waiver index was 1.7 and the whole-genome LD decay was 22 Mb at r² = 0.38. Following FDR, 23 and 8 SNPs showed association with starch properties in the year 2017 and 2018, respectively while 93 and 20 SNPs were associated with ALc gelatinization in the year 2017 and 2018 respectively. The identified potential new genes (GSK3-alpha, RING-type domain-containing protein, Tetratricopeptide repeat, Hexosyltransferase, GLP, SNF1, and WRKY transcription factor) within LD range (∼16 Kb to ∼15 Mb), BLUP value, and cis and trans-position of SNPs network provide valuable information for the future wheat breeding strategy for the improvement of the starch quality trait.

Isolation, partial characterization and in vitro digestion of starch from Ariopsis peltata and Lagenandra toxicaria tuber

The starch from two aroid tuber viz. Ariopsis peltata and Lagenandra toxicaria were isolated and evaluated for their morphological, physical and chemical properties. The tubers of these plants are used as food and medicine by the indigenous communities. The starch yield from A. peltata tuber was 25 ± 1.7% with an amylose content of 10 ± 0.9%, while the tuber of L. toxicaria contained 28 ± 6.5% starch with 15 ± 0.5% of apparent amylose in it. The starch isolated from both the tubers was highly pure (99%) starch exhibiting an A-type X-ray diffraction pattern. The starch granules of L. toxicaria were of various shapes and exhibited a smooth surface without any cleft or break. While the starch granules of A. peltata were spherical with smooth surface, as well as rough surface. The breaks and clefts were apparent on the rough-surfaced granules. The gelatinization temperature range for A. peltata and L. toxicaria starch is approximately 23 °C and 19 °C respectively. A. peltata starch showed higher thermal stability compared to L. toxicaria starch and either of the starch was rapidly digestible as evident from in vitro digestion study. The physicochemical properties of both the starches render them stable to withstand extreme processing. Besides they also mimic simple sugar in digestibility. So it can be utilized as a substitute for simple sugars in brewing and pharmaceutical industries.

Using the dominant mutation gene Ae1-5180 (amylose extender) to develop high-amylose maize

Maize amylose is a type of high value-added starch used for medical, food, and chemical applications. Mutations in the starch branching enzyme (SBEIIb), with recessive ae (amylose extender) and dominant Ae1-5180 alleles, are the primary way to improve maize endosperm amylose content (AC). However, studies on Ae1-5180 mutation are scarce, and its roles in starch synthesis and breeding potential are unclear. We found that the AC of the Ae1-5180 mutant was 47.23%, and its kernels were tarnished and glassy and are easily distinguished from those of the wild type (WT), indicating that the dominant mutant has the classical characteristics of the ae mutant. Starch granules of Ae1-5180 became smaller, and higher in amount with irregular shape. The degree of amylopectin polymerisation changed to induce an increase in starch thermal stability. Compared with WT, the activity of granule-bound starch synthase and starch synthase was higher in early stages and lower in later stages, and other starch synthesis enzymes decreased during kernel development in the Ae1-5180 mutant. We successfully developed a marker (mu406) for the assisted selection of 17 Ae1-5180 near isogenic lines (NILs) according to the position of insertion of the Mu1 transposon in the SBEIIb promoter of Ae1-5180. JH214/Ae1-5180, CANS-1/Ae1-5180, CA240/Ae1-5180, and Z1698/Ae1-5180 have high breeding application potential with their higher AC (> 40%) and their 100-kernel weight decreased to < 25% compared to respective recurrent parents. Therefore, using the dominant Ae1-5180 mutant as a donor can detect the kernel phenotype and AC of Ae1-5180-NILs in advance, thereby accelerating the high-amylose breeding process.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01323-7.

Tuning heterologous glucan biosynthesis in yeast to understand and exploit plant starch diversity

Background

Starch, a vital plant-derived polysaccharide comprised of branched glucans, is essential in nutrition and many industrial applications. Starch is often modified post-extraction to alter its structure and enhance its functionality. Targeted metabolic engineering of crops to produce valuable and versatile starches requires knowledge of the relationships between starch biosynthesis, structure, and properties, but systematic studies to obtain this knowledge are difficult to conduct in plants. Here we used Saccharomyces cerevisiae as a testbed to dissect the functions of plant starch biosynthetic enzymes and create diverse starch-like polymers.

Results

We explored yeast promoters and terminators to tune the expression levels of the starch-biosynthesis machinery from Arabidopsis thaliana. We systematically modulated the expression of each starch synthase (SS) together with a branching enzyme (BE) in yeast. Protein quantification by parallel reaction monitoring (targeted proteomics) revealed unexpected effects of glucan biosynthesis on protein abundances but showed that the anticipated broad range of SS/BE enzyme ratios was maintained during the biosynthetic process. The different SS/BE ratios clearly influenced glucan structure and solubility: The higher the SS/BE ratio, the longer the glucan chains and the more glucans were partitioned into the insoluble fraction. This effect was irrespective of the SS isoform, demonstrating that the elongation/branching ratio controls glucan properties separate from enzyme specificity.

Conclusions

Our results provide a quantitative framework for the in silico design of improved starch biosynthetic processes in plants. Our study also exemplifies a workflow for the rational tuning of a complex pathway in yeast, starting from the selection and evaluation of expression modules to multi-gene assembly and targeted protein monitoring during the biosynthetic process.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01408-x.

Investigating the Impact of Polymer Length, Attachment Site, and Charge on Enzymatic Activity and Stability of Cellulase

The thermophilic cellulase Cel5a from Fervidobacterium nodosum (FnCel5a) was conjugated with neutral, cationic, and anionic polymers of increasing molecular weights. The enzymatic activity toward an anionic soluble cellulose derivative, thermal stability, and functional chemical stability of these bioconjugates were investigated. The results suggest that increasing polymer chain length for polymers compatible with the substrate enhances the positive impact of polymer conjugation on enzymatic activity. Activity enhancements of nearly 100% were observed for bioconjugates with N,N-dimethyl acrylamide (DMAm) and N,N-dimethyl acrylamide-2-(N,N-dimethylamino)ethyl methacrylate (DMAm/DMAEMA) due to proposed polymer-substrate compatibility enabled by potential noncovalent interactions. Double conjugation of two functionally distinct polymers to wild-type and mutated FnCel5a using two conjugation methods was achieved. These doubly conjugated bioconjugates exhibited similar thermal stability to the unmodified wild-type enzyme, although enzymatic activity initially gained from conjugation was lost, suggesting that chain length may be a better tool for bioconjugate activity modulation than double conjugation.

Integrated transcriptomic and metabolomic analyses revealed the regulatory mechanism of sulfur application in grain yield and protein content in wheat (Triticum aestivum L.)

Sulfur fertilizers play an important role in increasing the yield and improving the dough quality of bread wheat, but their regulatory mechanism remains unclear. In this study, 0 kg·ha^-1 (S0) and 60 kg·ha^-1 (S60) of sulfur were applied on the anthesis date; subsequently, immature wheat grains at 8, 13, and 18 days post-anthesis (DPA) were subjected to integrated transcriptomic and metabolomic analyses to investigate the changes in the gene/metabolite activity in a typical strong-gluten wheat, Gaoyou2018 (GY2018). Our data show that the S60 treatment could significantly increase the grain yield and grain protein content by 13.2 and 3.6%, respectively. The transcriptomic analysis revealed that 10,694 differentially expressed genes (DEGs) were induced by S60 from 8 to 18 DPA when compared with their corresponding no-sulfur controls, and most DEGs were mainly involved in lipid metabolism and amino acid metabolism pathways. Ninety-seven MYB transcription factors (TFs) were identified as responsive to the S60 treatment; of these, 66 showed significantly differential expression at 13 DPA, and MYB118 might participate in the process of sulfur metabolism by regulating glucosinolate synthesis. In total, 542 significantly enriched differentially expressed (DE) metabolites (DEMs) were identified following the S60 treatment, which mainly included secondary metabolites, carbohydrates, and amino acids. Several metabolites (e.g., glutathione, sucrose, GDP-alpha-D-glucose, and amino acids) exhibited altered abundances following the S60 treatment. The combination of transcriptomic and metabolomic analyses highlighted the important role of amino acid metabolism (especially cysteine, methionine, and glutathione metabolism) and starch and sucrose metabolism pathways after S60 application. Our results provide valuable information enhancing our understanding of the molecular mechanism of the response to sulfur and provide useful clues for grain protein quality formation and yield improvement in bread wheat.

β-Glucosidases as dominant dose-dependent regulators of Oryza sativa L. in response to typical organic pollutant exposures

Understanding the metabolic defense and compensation to maintain homeostasis is crucial for assessing the potential health risk of organic pollutants in crops. Currently, limited understanding is available regarding the targeted metabolic pathways and response mechanism under contaminant stress. This study showed that ciprofloxacin (CIP) at the environmental concentrations (1, 5, 25, 50 mg/L) did not significantly inhibit growth or cause severe oxidative damage to rice (Oryza sativa L.). Instead, the increment in CIP concentration induced a series of sequential metabolic disorders, which were characterized predominantly by primary and secondary metabolic disturbances, including phenylpropanoid biosynthesis, the carbohydrate, lipid and amino acid metabolism. After CIP in vivo exceeded a certain threshold level (>0.29 mg/g dry weight), β-glucosidases (BGLUs) mediated the transition from the activation of the genes related to phenylpropanoid biosynthesis to the inhibition of the genes related to carbohydrate metabolism in rice. In particular, starch and sucrose metabolism showed the most profound perturbation stressed by environmental concentrations of CIP (5 mg/L) and other tested organic pollutants (10 μg/L of tricyclazole, thiamethoxam, polybrominated diphenyl ethers, and polychlorinated biphenyls). Besides, the key genes encoding endoglucanase and BGLU were significantly downregulated (|log₂FC| > 3.0) under 100 μg/L of other tested organic pollutants, supporting the transition from the activation of secondary defense metabolism to the disruption of primary energy metabolism. Thus, in addition to bioaccumulation, changes in BGLU activity and starch and sucrose metabolism can reflect the potential adverse effects of pollutants on rice. This study explained the stepwise metabolic and transcriptional responses of rice to organic pollutants, which provided a new reference for the comprehensive evaluation of their environmental risks.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.