The molecular structures of starch components and their contribution to the architecture of starch granules: A comprehensive review

Characterization Methods for Starch-Based Materials: State of the Art and Perspectives

Improving starch-containing materials, whether food, animal feed, high-tech biomaterials, or engineering plastics, is best done by understanding how biosynthetic processes and any subsequent processing control starch structure, and how this structure controls functional properties. Starch structural characterization is central to this. This review examines how information on the three basic levels of the complex multi-scale structure of starch – individual chains, the branching structure of isolated molecules, and the way these molecules form various crystalline and amorphous arrangements – can be obtained from experiment. The techniques include fluorophore-assisted carbohydrate electrophoresis, multiple-detector size-exclusion chromatography, and various scattering techniques (light, X-ray, and neutron). Some examples are also given to show how these data provide mechanistic insight into how biosynthetic processes control the structure and how the various structural levels control functional properties.

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

Background

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol.

Description

PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available.

Conclusion

PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

Integral Proteins in Plant Oil Bodies

Hydrophobic storage neutral lipids are stably preserved in specialized organelles termed oil bodies in the aqueous cytosolic compartment of plant cells via encapsulation with surfactant molecules including phospholipids and integral proteins. To date, three classes of integral proteins, termed oleosin, caleosin, and steroleosin, have been identified in oil bodies of angiosperm seeds. Proposed structures, targeting traffic routes, and biological functions of these three integral oil-body proteins were summarized and discussed. In the viewpoint of evolution, isoforms of oleosin and caleosin are found in oil bodies of pollens as well as those of more primitive species; moreover, caleosin- and steroleosin-like proteins are also present in other subcellular locations besides oil bodies. Technically, artificial oil bodies of structural stability similar to native ones were successfully constituted and seemed to serve as a useful tool for both basic research studies and biotechnological applications.

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.

Pullulanase: role in starch hydrolysis and potential industrial applications

The use of pullulanase (EC 3.2.1.41) has recently been the subject of increased applications in starch-based industries especially those aimed for glucose production. Pullulanase, an important debranching enzyme, has been widely utilised to hydrolyse the α-1,6 glucosidic linkages in starch, amylopectin, pullulan, and related oligosaccharides, which enables a complete and efficient conversion of the branched polysaccharides into small fermentable sugars during saccharification process. The industrial manufacturing of glucose involves two successive enzymatic steps: liquefaction, carried out after gelatinisation by the action of α-amylase; saccharification, which results in further transformation of maltodextrins into glucose. During saccharification process, pullulanase has been used to increase the final glucose concentration with reduced amount of glucoamylase. Therefore, the reversion reaction that involves resynthesis of saccharides from glucose molecules is prevented. To date, five groups of pullulanase enzymes have been reported, that is, (i) pullulanase type I, (ii) amylopullulanase, (iii) neopullulanase, (iv) isopullulanase, and (v) pullulan hydrolase type III. The current paper extensively reviews each category of pullulanase, properties of pullulanase, merits of applying pullulanase during starch bioprocessing, current genetic engineering works related to pullulanase genes, and possible industrial applications of pullulanase.

Immersion mode material pocket dynamic mechanical analysis (IMP-DMA): a novel tool to study gelatinisation of purified starches and starch-containing plant materials

There is a clear need for improved methods for the study of the physical changes that occur in slurries and sol-gel systems that have significant water content. In this paper a novel immersion mode material pocket form of dynamic mechanical analysis (IMP-DMA) has been designed, combining material pocket technology to provide physical support to a powdered sample within an immersion bath. IMP-DMA allows the mechanical response of a powder during heating to be monitored in excess water. IMP-DMA was evaluated using a range of starch samples loaded as a slurry into a solid steel pocket, the mechanical responses of these samples were monitored as a function of temperature, and values for modulus and tanδ peaks were found to correspond well with events occurring at both the onset and peak gelatinisation temperatures as measured by differential scanning calorimetry (DSC) (e.g. wheat starch has an onset and peak DSC temperature of 49.3 °C and 57.2 °C, respectively, and shows a peak in tanδ at 52.8 °C and a modulus peak at 57.7 °C). Some limitations were found in the ability of DMA to detect transitions in starches with low or high amylose contents. IMP-DMA was shown to be an effective tool for monitoring the changes in starch structure that occur during gelatinisation, both in purified starches and in more complex starch-containing food materials. Thus, a new hyphenated form of DMA is now available that permits the thermally induced transitions of particle water dispersions to be characterised.

Characterisation of large scale structures in starch granules via small-angle neutron and X-ray scattering

Small angle scattering (SAS) techniques have a distinguished track record in illuminating the semi-crystalline lamellar structure of the starch granule. To date, there have been few attempts to use SAS techniques to characterise larger-scale structures reported from imaging techniques such as growth rings, blocklets or pores, nor how these structures would modulate the well-known scattering arising from the semi-crystalline lamellar structure. In this study, SAS data collected over an extended q range were gathered from dry and hydrated starch powders from varied botanical sources. The use of neutrons and X-rays, as well as comparing dry and hydrated granules, allowed different levels of contrast in scattering length density to be probed and therefore selected structural regions to be highlighted. The lowest q range, 0.002-0.04 Å(-1), was found to be dominated by scattering from the starch granules themselves, especially in the dry powders; however an inflection point from a low contrast structure was observed at 0.035 Å(-1). The associated scattering was interpreted within a unified scattering framework with the inflexion point correlating with a structure with radius of gyration ~90 Å - a size comparable to small blocklets or superhelices. In hydrated starches, it is observed that there is an inflection point between lamellar and q(-4) power-law scattering regions at approximately 0.004 Å(-1) which may correlate with growth rings and large blocklets. The implications of these findings on existing models of starch lamellar scattering are discussed.

Phase transitions of pea starch over a wide range of water content

The phase transitions of pea starch over a wide range of water content were investigated by differential scanning calorimetry (DSC). Swelling of starch granules increased progressively with increasing water content. The main endotherm G broadened progressively with increasing water content up to 94.5 wt % (water:starch ratio 15:1), above which it became too broad to define. The corresponding peak and conclusion temperatures and enthalpy change increased with increasing water content. Scanning electron microscopy (SEM) showed that, at a water:starch ratio of 2:1 (water content of 70.7 wt %), starch granules only swelled partially with discernible granular contours still clearly evident. The results of swelling power tests and SEM images revealed that the endotherm G obtained at a water:starch ratio of 2:1 represented only partial swelling of starch granules. The transition from a narrow to broad endotherm G was interpreted to reflect the thermal transition behavior progressing from limited swelling to maximum swelling and then partial dissolution and leaching of starch polymers from the granules.

Increased laforin and laforin binding to glycogen underlie Lafora body formation in malin-deficient Lafora disease

The solubility of glycogen, essential to its metabolism, is a property of its shape, a sphere generated through extensive branching during synthesis. Lafora disease (LD) is a severe teenage-onset neurodegenerative epilepsy and results from multiorgan accumulations, termed Lafora bodies (LB), of abnormally structured aggregation-prone and digestion-resistant glycogen. LD is caused by loss-of-function mutations in the EPM2A or EPM2B gene, encoding the interacting laforin phosphatase and malin E3 ubiquitin ligase enzymes, respectively. The substrate and function of malin are unknown; an early counterintuitive observation in cell culture experiments that it targets laforin to proteasomal degradation was not pursued until now. The substrate and function of laforin have recently been elucidated. Laforin dephosphorylates glycogen during synthesis, without which phosphate ions interfere with and distort glycogen construction, leading to LB. We hypothesized that laforin in excess or not removed following its action on glycogen also interferes with glycogen formation. We show in malin-deficient mice that the absence of malin results in massively increased laforin preceding the appearance of LB and that laforin gradually accumulates in glycogen, which corresponds to progressive LB generation. We show that increasing the amounts of laforin in cell culture causes LB formation and that this occurs only with glycogen binding-competent laforin. In summary, malin deficiency causes increased laforin, increased laforin binding to glycogen, and LB formation. Furthermore, increased levels of laforin, when it can bind glycogen, causes LB. We conclude that malin functions to regulate laforin and that malin deficiency at least in part causes LB and LD through increased laforin binding to glycogen.

Two carbon fluxes to reserve starch in potato (Solanum tuberosum L.) tuber cells are closely interconnected but differently modulated by temperature

Parenchyma cells from tubers of Solanum tuberosum L. convert several externally supplied sugars to starch but the rates vary largely. Conversion of glucose 1-phosphate to starch is exceptionally efficient. In this communication, tuber slices were incubated with either of four solutions containing equimolar [U-¹⁴C]glucose 1-phosphate, [U-¹⁴C]sucrose, [U-¹⁴C]glucose 1-phosphate plus unlabelled equimolar sucrose or [U-¹⁴C]sucrose plus unlabelled equimolar glucose 1-phosphate. C¹⁴-incorporation into starch was monitored. In slices from freshly harvested tubers each unlabelled compound strongly enhanced ¹⁴C incorporation into starch indicating closely interacting paths of starch biosynthesis. However, enhancement disappeared when the tubers were stored. The two paths (and, consequently, the mutual enhancement effect) differ in temperature dependence. At lower temperatures, the glucose 1-phosphate-dependent path is functional, reaching maximal activity at approximately 20 °C but the flux of the sucrose-dependent route strongly increases above 20 °C. Results are confirmed by in vitro experiments using [U-¹⁴C]glucose 1-phosphate or adenosine-[U-¹⁴C]glucose and by quantitative zymograms of starch synthase or phosphorylase activity. In mutants almost completely lacking the plastidial phosphorylase isozyme(s), the glucose 1-phosphate-dependent path is largely impeded. Irrespective of the size of the granules, glucose 1-phosphate-dependent incorporation per granule surface area is essentially equal. Furthermore, within the granules no preference of distinct glucosyl acceptor sites was detectable. Thus, the path is integrated into the entire granule biosynthesis. In vitro C¹⁴C-incorporation into starch granules mediated by the recombinant plastidial phosphorylase isozyme clearly differed from the in situ results. Taken together, the data clearly demonstrate that two closely but flexibly interacting general paths of starch biosynthesis are functional in potato tuber cells.

The plastidial glucan, water dikinase (GWD) catalyses multiple phosphotransfer reactions

The plant genome encodes at least two distinct and evolutionary conserved plastidial starch-related dikinases that phosphorylate a low percentage of glucosyl residues at the starch granule surface. Esterification of starch favours the transition of highly ordered α-glucans to a less ordered state and thereby facilitates the cleavage of interglucose bonds by hydrolases. Metabolically most important is the phosphorylation at position C6, which is catalysed by the glucan, water dikinase (GWD). The reactions mediated by recombinant wild-type GWD from Arabidopsis thaliana (AtGWD) and from Solanum tuberosum (StGWD) were studied. Two mutated proteins lacking the conserved histidine residue that is indispensible for glucan phosphorylation were also included. The wild-type GWDs consume approximately 20% more ATP than is required for glucan phosphorylation. Similarly, although incapable of phosphorylating α-glucans, the two mutated dikinase proteins are capable of degrading ATP. Thus, consumption of ATP and phosphorylation of α-glucans are not strictly coupled processes but, to some extent, occur as independent phosphotransfer reactions. As revealed by incubation of the GWDs with [γ-(33) P]ATP, the consumption of ATP includes the transfer of the γ-phosphate group to the GWD protein but this autophosphorylation does not require the conserved histidine residue. Thus, the GWD proteins possess two vicinal phosphorylation sites, both of which are transiently phosphorylated. Following autophosphorylation at both sites, native dikinases flexibly use various terminal phosphate acceptors, such as water, α-glucans, AMP and ADP. A model is presented describing the complex phosphotransfer reactions of GWDs as affected by the availability of the various acceptors.

Deciphering starch quality of rice kernels using metabolite profiling and pedigree network analysis

The physiological properties of rice grains are immediately obvious to consumers. High-coverage metabolomic characterization of the rice diversity research set predicted a negative correlation between fatty acid and lipid levels and amylose/total starch ratio (amylose ratio), but the reason for this is unclear. To obtain new insight into the relationships among the visual phenotypes of rice kernels, starch granule structures, amylose ratios, and metabolite changes, we investigated the metabolite changes of five Japonica cultivars with various amylose ratios and two knockout mutants (e1, a Starch synthase IIIa (SSIIIa)-deficient mutant and the SSIIIa/starch branching enzyme (BE) double-knockout mutant 4019) by using mass spectrometry-based metabolomics techniques. Scanning electron microscopy clearly showed that the two mutants had unusual starch granule structures. The metabolomic compositions of two cultivars with high amylose ratios (Hoshiyutaka and Yumetoiro) exhibited similar patterns, while that of the double-knockout mutant, which has an extremely high amylose ratio, differed. Rice pedigree network analysis of the cultivars and the mutants provided insight into the association between metabolic-trait properties and their underlying genetic basis in rice breeding in Japan. Multidimensional scaling analysis revealed that the Hoshiyutaka and Yumetoiro cultivars were Indica-like, yet they are classified as Japonica subpopulations. Exploring metabolomic traits is a powerful way to follow rice genetic traces and breeding history.

Theory of the origin, evolution, and nature of life

Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics

BACKGROUND

Increasing awareness of limitations to natural resources has set high expectations for plant science to deliver efficient crops with increased yields, improved stress tolerance, and tailored composition. Collections of representative varieties are a valuable resource for compiling broad breeding germplasms that can satisfy these diverse needs.

RESULTS

Here we show that the untargeted high-coverage metabolomic characterization of such core collections is a powerful approach for studying the molecular backgrounds of quality traits and for constructing predictive metabolome-trait models. We profiled the metabolic composition of kernels from field-grown plants of the rice diversity research set using 4 complementary analytical platforms. We found that the metabolite profiles were correlated with both the overall population structure and fine-grained genetic diversity. Multivariate regression analysis showed that 10 of the 17 studied quality traits could be predicted from the metabolic composition independently of the population structure. Furthermore, the model of amylose ratio could be validated using external varieties grown in an independent experiment.

CONCLUSIONS

Our results demonstrate the utility of metabolomics for linking traits with quantitative molecular data. This opens up new opportunities for trait prediction and construction of tailored germplasms to support modern plant breeding.

Integrated functions among multiple starch synthases determine both amylopectin chain length and branch linkage location in Arabidopsis leaf starch

This study assessed the impact on starch metabolism in Arabidopsis leaves of simultaneously eliminating multiple soluble starch synthases (SS) from among SS1, SS2, and SS3. Double mutant ss1- ss2- or ss1- ss3- lines were generated using confirmed null mutations. These were compared to the wild type, each single mutant, and ss1- ss2- ss3- triple mutant lines grown in standardized environments. Double mutant plants developed similarly to the wild type, although they accumulated less leaf starch in both short-day and long-day diurnal cycles. Despite the reduced levels in the double mutants, lines containing only SS2 and SS4, or SS3 and SS4, are able to produce substantial amounts of starch granules. In both double mutants the residual starch was structurally modified including higher ratios of amylose:amylopectin, altered glucan chain length distribution within amylopectin, abnormal granule morphology, and altered placement of α(1→6) branch linkages relative to the reducing end of each linear chain. The data demonstrate that SS activity affects not only chain elongation but also the net result of branch placement accomplished by the balanced activities of starch branching enzymes and starch debranching enzymes. SS3 was shown partially to overlap in function with SS1 for the generation of short glucan chains within amylopectin. Compensatory functions that, in some instances, allow continued residual starch production in the absence of specific SS classes were identified, probaby accomplished by the granule bound starch synthase GBSS1.

Emerging roles of engineered nanomaterials in the food industry

Nanoscience is the study of phenomena and the manipulation of materials at the atomic or molecular level. Nanotechnology involves the design, production and use of structures through control of the size and shape of the materials at the nanometre scale. Nanotechnology in the food sector is an emerging area with considerable research and potential products. There is particular interest in the definition and regulation of engineered nanomaterials. This term covers three classes of nanomaterials: natural and processed nanostructures in foods; particulate nanomaterials metabolized or excreted on digestion; and particulate nanomaterials not broken down on digestion, which accumulate in the body. This review describes examples of these classes and their likely status in the food industry.