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BackgroundStarch is of great importance to humans as a food and biomaterial, and the amount and structure of starch made in plants is determined in part by starch synthase (SS) activity. Five SS isoforms, SSI, II, III, IV and Granule Bound SSI, have been identified, each with a unique catalytic role in starch synthesis. The basic mode of action of SSs is known; however our knowledge of several aspects of SS enzymology at the structural and mechanistic level is incomplete. To gain a better understanding of the differences in SS sequences that underscore their specificity, the previously uncharacterised SSIVb from wheat was cloned and extensive bioinformatics analyses of this and other SSs sequences were done.ResultsThe wheat SSIV cDNA is most similar to rice SSIVb with which it shows synteny and shares a similar exon-intron arrangement. The wheat SSIVb gene was preferentially expressed in leaf and was not regulated by a circadian clock. Phylogenetic analysis showed that in plants, SSIV is closely related to SSIII, while SSI, SSII and Granule Bound SSI clustered together and distinctions between the two groups can be made at the genetic level and included chromosomal location and intron conservation. Further, identified differences at the amino acid level in their glycosyltransferase domains, predicted secondary structures, global conformations and conserved residues might be indicative of intragroup functional associations.ConclusionBased on bioinformatics analysis of the catalytic region of 36 SSs and 3 glycogen synthases (GSs), it is suggested that the valine residue in the highly conserved K-X-G-G-L motif in SSIII and SSIV may be a determining feature of primer specificity of these SSs as compared to GBSSI, SSI and SSII. In GBSSI, the Ile485 residue may partially explain that enzyme's unique catalytic features. The flexible 380s Loop in the starch catalytic domain may be important in defining the specificity of action for each different SS and the G-X-G in motif VI could define SSIV and SSIII action particularly.

Stressful environments can alter starch biosynthesis in cereal endosperm. The aim of this review is to carefully examine how starch functional properties are altered when plants encounter environmental parameters outside of the normal range. This is important because while growers and processors require grain yield stability and product uniformity this will be challenging in an era of variable weather patterns. Being able to predict the general physico‐chemical nature of the starch as a result of growth status is a step towards the “precise” agriculture required for the 21st century. Variations in soil moisture and nutrient availability, ambient temperature, and atmospheric composition were all shown to affect starch functionality. Elevated temperature led to the most significant changes in both tropical and temperate cereals and amylose content was the most sensitive parameter under various environmental conditions. Genotypic variation appears to be a primary contributor for the response of cereal starches to environmental stress. Nonetheless, while a large amount of data from single controlled environmental stress experiment is currently available, comparably little is known about whether similar results would be achieved in multifactorial and large‐scale settings. The challenges in terms of the need for more detailed experimental descriptions to lessen the study‐to‐study discrepancies of data and to enhance their interpretability were also discussed.

The occurrence of an extra-plastidial isoform of ADP-glucose (Glc) pyrophosphorylase (AGPase) among starch-storing organs was investigated in two ways. First, the possibility that an extra-plastidial isoform arose during the domestication of cereals was studied by comparing the intracellular distribution of enzyme activity and protein in developing endosperm of noncultivated Hordeum species with that previously reported for cultivated barley (Hordeum vulgare). As in cultivated barley, the AGPase of H. vulgare subsp. spontaneum and Hordeum murinum endosperm is accounted for by a major extra-plastidial and a minor plastidial isoform. Second, the ratio of ADP-Glc to UDP-Glc was used as an indication of the intracellular location of the AGPase activity in a wide range of starch-synthesizing organs. The ratio is expected to be high in organs in which UDP-Glc and ADP-Glc are synthesized primarily in the cytosol, because the reactions catalyzed by AGPase and UDP-Glc pyrophosphorylase will be coupled and close to equilibrium. This study revealed that ADP-Glc contents and the ratio of ADP-Glc to UDP-Glc were higher in developing graminaceous endosperms than in any other starch-storing organs. Taken as a whole the results indicate that an extra-plastidial AGPase is important in ADP-Glc synthesis in graminaceous endosperms, but not in other starch-storing organs.

The expression of 7,835 genes in developing wheat caryopses was analyzed using cDNA arrays. Using a mixed model analysis of variance (ANOVA) method, 29% (2,237) of the genes on the array were identified to be differentially expressed at the 6 different time-points examined, which covers the developmental stages from coenocytic endosperm to physiological maturity. Comparison of genes differentially expressed between two time-points revealed a dynamic transcript accumulation profile with major re-programming events that occur at 3-7, 7-14 and 21-28 DPA. A k-means clustering algorithm grouped the differentially expressed genes into 10 clusters, revealing co-expression of genes involved in the same pathway such as carbohydrate and protein synthesis or preparation for desiccation. Functional annotation of genes that show peak expression at specific time-points correlated with the developmental events associated with the respective stages. Results provide information on the temporal expression during caryopsis development for a significant number of differentially expressed genes with unknown function.

In most species, the synthesis of ADP-glucose (Glc) by the enzyme ADP-Glc pyrophosphorylase (AGPase) occurs entirely within the plastids in all tissues so far examined. However, in the endosperm of many, if not all grasses, a second form of AGPase synthesizes ADP-Glc outside the plastid, presumably in the cytosol. In this paper, we show that in the endosperm of wheat (Triticum aestivum), the cytosolic form accounts for most of the AGPase activity. Using a combination of molecular and biochemical approaches to identify the cytosolic and plastidial protein components of wheat endosperm AGPase we show that the large and small subunits of the cytosolic enzyme are encoded by genes previously thought to encode plastidial subunits, and that a gene, Ta.AGP.S.1, which encodes the small subunit of the cytosolic form of AGPase, also gives rise to a second transcript by the use of an alternate first exon. This second transcript encodes an AGPase small subunit with a transit peptide. However, we could not find a plastidial small subunit protein corresponding to this transcript. The protein sequence of the purified plastidial small subunit does not match precisely to that encoded by Ta.AGP.S.1 or to the predicted sequences of any other known gene from wheat or barley (Hordeum vulgare). Instead, the protein sequence is most similar to those of the plastidial small subunits from chickpea (Cicer arietinum) and maize (Zea mays) and rice (Oryza sativa) seeds. These data suggest that the gene encoding the major plastidial small subunit of AGPase in wheat endosperm has yet to be identified.The synthesis of starch takes place inside plastids (the chloroplasts of leaves and the amyloplasts of nonphotosynthetic starch-storing organs such as seeds). The substrate for starch synthesis, ADP-Glc is synthesized by the enzyme ADP-Glc pyrophosphorylase (AGPase). AGPase catalyzes the conversion of Glc-1-P and ATP to ADP-Glc and pyrophosphate and is a heterotetrameric protein composed of two sorts of subunits referred to as the small (SSU) and large subunits (LSU; for review, see Preiss, 1991). There is evidence for the existence of multiple, tissue-specific forms of the SSU and LSU of AGPase in plants. In maize (Zea mays), for example, the SSUs of the endosperm, embryo, and leaf are encoded by three separate genes (Hannah et al., 2001). However, there is also evidence that transcripts encoding particular AGPase subunits may be expressed in more than one tissue. For, example, the transcript encoding the LSU of AGPase in barley (Hordeum vulgare) leaves is also present in the endosperm (Doan et al., 1999). At present, we do not have a complete description for any species of the nature and patterns of expression of all of the genes encoding AGPase subunits.In most species, the synthesis of ADP-Glc occurs entirely within the plastids in all tissues so far examined. However, in the endosperm of barley (Thorbjørnsen et al., 1996a), maize (Denyer et al., 1996), and rice (Oryza sativa; Sikka et al., 2001), and probably all grasses (Beckles et al., 2001...