Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics.

The quality of rice in terms not only of its nutritional value but also in terms of its aroma and flavour is becoming increasingly important in modern rice breeding where global targets are focused on both yield stability and grain quality. In the present paper we have exploited advanced, multi-platform metabolomics approaches to determine the biochemical differences in 31 rice varieties from a diverse range of genetic backgrounds and origin. All were grown under the specific local conditions for which they have been bred and all aspects of varietal identification and sample purity have been guaranteed by local experts from each country. Metabolomics analyses using 6 platforms have revealed the extent of biochemical differences (and similarities) between the chosen rice genotypes. Comparison of fragrant rice varieties showed a difference in the metabolic profiles of jasmine and basmati varieties. However with no consistent separation of the germplasm class. Storage of grains had a significant effect on the metabolome of both basmati and jasmine rice varieties but changes were different for the two rice types. This shows how metabolic changes may help prove a causal relationship with developing good quality in basmati rice or incurring quality loss in jasmine rice in aged grains. Such metabolomics approaches are leading to hypotheses on the potential links between grain quality attributes, biochemical composition and genotype in the context of breeding for improvement. With this knowledge we shall establish a stronger, evidence-based foundation upon which to build targeted strategies to support breeders in their quest for improved rice varieties.

Merits of random forests emerge in evaluation of chemometric classifiers by external validation.

Real-world applications will inevitably entail divergence between samples on which chemometric classifiers are trained and the unknowns requiring classification. This has long been recognized, but there is a shortage of empirical studies on which classifiers perform best in 'external validation' (EV), where the unknown samples are subject to sources of variation relative to the population used to train the classifier. Survey of 286 classification studies in analytical chemistry found only 6.6% that stated elements of variance between training and test samples. Instead, most tested classifiers using hold-outs or resampling (usually cross-validation) from the same population used in training. The present study evaluated a wide range of classifiers on NMR and mass spectra of plant and food materials, from four projects with different data properties (e.g., different numbers and prevalence of classes) and classification objectives. Use of cross-validation was found to be optimistic relative to EV on samples of different provenance to the training set (e.g., different genotypes, different growth conditions, different seasons of crop harvest). For classifier evaluations across the diverse tasks, we used ranks-based non-parametric comparisons, and permutation-based significance tests. Although latent variable methods (e.g., PLSDA) were used in 64% of the surveyed papers, they were among the less successful classifiers in EV, and orthogonal signal correction was counterproductive. Instead, the best EV performances were obtained with machine learning schemes that coped with the high dimensionality (914-1898 features). Random forests confirmed their resilience to high dimensionality, as best overall performers on the full data, despite being used in only 4.5% of the surveyed papers. Most other machine learning classifiers were improved by a feature selection filter (ReliefF), but still did not out-perform random forests.

Metabolite profiling of sesquiterpene lactones from Lactuca species. Major latex components are novel oxalate and sulfate conjugates of lactucin and its derivatives.

Wounding leaves or stems of Lactuca species releases a milky latex onto the plant surface. We have examined the constituents of latex from Lactuca sativa (lettuce) cv. Diana. The major components were shown to be novel 15-oxalyl and 8-sulfate conjugates of the guaianolide sesquiterpene lactones, lactucin, deoxylactucin, and lactucopicrin. The oxalates were unstable, reverting to the parent sesquiterpene lactone on hydrolysis. Oxalyl derivatives have been reported rarely from natural sources. The sulfates were stable and are the first reported sesquiterpene sulfates from plants. Unusual tannins based on 4-hydroxyphenylacetyl conjugates of glucose were also identified. Significant qualitative and quantitative variation was found in sesquiterpene lactone profiles in different lettuce varieties and in other Lactuca spp. The proportions of each conjugate in latex also changed depending on the stage of plant development. A similar profile was found in chicory, in which oxalyl conjugates were identified, but the 8-sulfate conjugates were notably absent. The presence of the constitutive sesquiterpene lactones was not correlated with resistance to pathogens but may have a significant bearing on the molecular basis of the bitter taste of lettuce and related species. The induced sesquiterpene lactone phytoalexin, lettucenin A, was found in the Lactuca spp. but not in chicory.

Gibberellin-photoaffinity labelling of two polypeptides in plant plasma membranes.

Two polypeptides of M(r) 68 kDa and 18 kDa were gibberellin (GA)-photoaffinity labelled in vitro in plasma membrane preparations from oat (Avena sativa L.) aleurone and from leaves and stems of wild-type and GA-sensitivity mutants of different species. Labelling of these polypeptides could be competed by biologically active, but not by inactive, GAs, indicating the likely biological significance of these interactions. On 2-dimensional gels the radiolabelled polypeptides were each resolved as one intensely labelled low abundance spot with a slightly lower pl form adjacent to it. There was a strong pH dependency for both labelling events, which correlated well with pH values at which GA are known to be most biologically active. A semi-dwarf GA-sensitivity mutant of sweet pea (Lathyrus odoratus L.), lb, showed reduced photoaffinity labelling of both polypeptides compared with the wild type, Lb. In the GA-insensitive Arabidopsis thaliana mutant gai, the level of labelling was the same as in wild type, GAI. This is the first report of GA-binding proteins in plant plasma membranes. Some preliminary sequence data are given for one of the labelled polypeptides. We discuss these mutants and consider their possible roles in GA perception or action.

N4-Hexanoylspermidine, a New Polyamine-Related Compound That Accumulates during Ovary and Petal Senescence in Pea.

A previously unknown polyamine conjugate that accumulates in senescing ovaries of pea (Pisum sativum L.) was shown by mass spectrometry, nuclear magnetic resonance, and chemical synthesis to be N4-hexanoylspermidine (hexanoyl-spd) This structure was indicated by analysis of the dansylated polyamine using fast atom bombardment mass spectrometry, following purification by high-performance liquid chromatography. Furthermore, acid hydrolysis of the compound yielded spermidine and hexanoic acid. 1H-nuclear magnetic resonance suggested that spermidine was substituted at N4 in the conjugate. Hexanoyl-spd was synthesized, and its didansyl derivative was shown to have an identical mass spectrum and high-performance liquid chromatography retention time as the derivatized natural compound. Further confirmation of its structure was obtained by comparison of the synthetic and natural polyamines as trifluoroacetyl derivatives using gas chromatography-mass spectrometry. This new polyamine conjugate is present in pea ovaries at low levels at anthesis and its concentration remains low in developing seeded fruit or in parthenocarpic fruit that have been induced by application of growth regulators to emasculated flowers or by topping the plant. Conjugate levels are also low in parthenocarpic fruit induced naturally in the slender (la crys) mutant. However, levels of hexanoyl-spd increase progressively in senescing petals and ovaries, beginning at anthesis or 2 d later, respectively.

Two Transduction Pathways Mediate Rapid Effects of Abscisic Acid in Commelina Guard Cells.

Commelina guard cells can be rapidly closed by abscisic acid (ABA), and it is thought that this signal is always transduced through increases in cytosolic calcium. However, when Commelina plants were grown at 10 to 17[deg]C, most guard cells failed to exhibit any ABA-induced increase in cytosolic calcium even though all of these cells closed. At growth temperatures of 25[deg]C or above, ABA-induced closure was always associated with an increase in cytosolic calcium. This suggests that there may be two transduction routes for ABA in guard cells; only one involves increases in cytosolic calcium. Activation of either pathway on its own appears to be sufficient to cause closure. Because the rates of ABA accumulation and transport in plants grown at different temperatures are likely to be different, we synthesized and microinjected caged ABA directly into guard cells. ABA was released internally by UV photolysis and subsequently caused stomatal closure. This result suggests a possible intracellular locale for the hypothesized ABA receptor.

Large-scale purification and preliminary structural studies of MAC 182, a gibberellin-binding monoclonal antibody.

The large-scale purification of the anti-gibberellin monoclonal antibody, MAC 182, is described. N-Terminal amino acid sequences of the heavy and light chains were determined and compared with those of known antibodies. Fab-fragments were prepared and purified to a state suitable for crystallization.

Gibberellin perception and the Avena fatua aleurone: do our molecular keys fit the correct locks?

The plant hormones GA, ABA, and auxin differ from the majority of animal hormones in that they are hydrophobic weak acids. They are soluble in the inter- and intra-cellular environments of plant tissues and their neutral species can cross the plasma membrane by passive diffusion. Auxin transport is mediated by specific uptake and efflux carriers in plasma membranes, and there is some evidence for carrier-mediated uptake of GA and ABA. Because these plant hormones can cross the plasma membrane it is not a prerequisite that receptors for them should be at the protoplast surface. Nevertheless, there is substantial evidence that auxin acts at the plasma membrane, and evidence suggesting that GA may be perceived at the plasma membrane of A. fatua aleurone protoplasts has been reviewed here. It is conceivable that the plant plasma membrane might provide the means to integrate, transduce, and amplify these signals, and that such properties of the plasma membrane, rather than the permeability characteristics of these ligands, may determine the site of perception. Further progress in our understanding of signal transduction pathways that may be involved in the actions of plant hormones is likely to shed light on these questions. It has been proposed that GA receptors involved in cell elongation may be soluble rather than membrane bound. The soluble 50 kDa GA-binding protein observed in aleurone by GA4 photoaffinity labelling may be a good candidate for a soluble GA receptor.(ABSTRACT TRUNCATED AT 250 WORDS)

Gibberellin perception at the plasma membrane of Avena fatua aleurone protoplasts.

A functional assay for gibberellin (GA) receptors is described based on the induction of α-amylase gene expression in isolated aleurone protoplasts of Avena fatua L. by GA4 immobilised to Sepharose beads. A 17-thiol derivative of GA4, shown to be biologically active with aleurone protoplasts, has been coupled to epoxy-activated Sepharose 6B. This GA4-17-Sepharose induces high levels of α-amylase when incubated with isolated aleurone protoplasts, while cells of the intact aleurone layer do not respond appreciably to the immobilised GA4. In order to eliminate the possibility that GA4 may be released from the Sepharose when incubated with protoplasts, aleurone layers and isolated aleurone protoplasts have been co-incubated, and their responses to GA4, GA4-17-Sepharose and control Sepharose estimated by determining the relative amounts of α-amylase mRNA induced in each tissue. Evidence from these experiments is consistent with the view that GA417-Sepharose induces α-amylase gene expression in aleurone protoplasts by interacting with the protoplast surface. This indicates that GA receptors may be located at, or near, the external face of the aleurone plasma membrane.

New monoclonal antibodies to 3 beta-hydroxy-gibberellins.

Two new monoclonal antibodies to 3 beta-hydroxy-gibberellins are described. Monoclonal antibodies GA1-1 and GA1-2 were derived from immunizations with the hapten-protein conjugate gibberellin A1-17-KLH. Cross-reactivities with a panel of 43 gibberellins and gibberellin derivatives are compared with those of other anti-gibberellin monoclonal antibodies.

Gibberellin perception in the Avena fatua aleurone.

Gibberellins (GAs) are a class of plant hormones involved in the regulation of plant growth and development. A useful model system for studying GA-action is the aleurone layer of cereal grain. In aleurone, GA induces a considerable increase in the rates of transcription of alpha-amylase genes, and this effect can be inhibited by another plant hormone abscisic acid. We anticipate that perception of GA by aleurone cells involves an interaction between the ligand and specific receptors and that this event leads to the observed stimulation in transcription of alpha-amylase, and probably other, aleurone genes. Hormone binding assays with aleurone have not revealed a candidate receptor, and the only aspect of signal transduction that is becoming understood is the likely interaction between specific trans-acting factors and cis-elements in the GA-regulation of alpha-amylase gene transcription. This paper describes the development of novel ways for identifying GA-receptors in aleurone protoplasts of Avena fatua that are based on the use of affinity and antibody probes in functional in vivo assays for GA-receptors. The implications of our current findings are discussed in relation to models of GA-action in aleurone.

Monoclonal antibodies to 13-deoxy-gibberellins.

The production and characterization of two high affinity rat monoclonal antibodies to 13-deoxy-gibberellins is described. Hybrid myelomas were derived from rats immunized with an immunogenic keyhole limpet hemocyanin-gibberellin conjugate, linked at carbon-3 to gibberellin A(4) via a hemisuccinate bridge. The selected monoclonal antibodies were characterized by a competitive radioimmunoassay.

Preparation and characterization of monoclonal antibodies which recognise different gibberellin epitopes.

The production and characterization of high-affinity monoclonal antibodies (McAb) to gibberellins (GAs) is reported. Hybrid myelomas were derived from immunisations with conjugates in which immunogenic proteins were linked to GA1 at carbon-3 and to GA4 and GA9 at carbon-17. A series of McAb which display specificities allowing recognition of, and the discrimination between GA1, GA20, GA4 and GA9 is described. These McAb can be used in quantitative immunoassays for underivatised GAs.