Integrating metabolomics and transcriptomics data to discover a biocatalyst that can generate the amine precursors for alkamide biosynthesis.

The Echinacea genus is exemplary of over 30 plant families that produce a set of bioactive amides, called alkamides. The Echinacea alkamides may be assembled from two distinct moieties, a branched-chain amine that is acylated with a novel polyunsaturated fatty acid. In this study we identified the potential enzymological source of the amine moiety as a pyridoxal phosphate-dependent decarboxylating enzyme that uses branched-chain amino acids as substrate. This identification was based on a correlative analysis of the transcriptomes and metabolomes of 36 different E. purpurea tissues and organs, which expressed distinct alkamide profiles. Although no correlation was found between the accumulation patterns of the alkamides and their putative metabolic precursors (i.e., fatty acids and branched-chain amino acids), isotope labeling analyses supported the transformation of valine and isoleucine to isobutylamine and 2-methylbutylamine as reactions of alkamide biosynthesis. Sequence homology identified the pyridoxal phosphate-dependent decarboxylase-like proteins in the translated proteome of E. purpurea. These sequences were prioritized for direct characterization by correlating their transcript levels with alkamide accumulation patterns in different organs and tissues, and this multi-pronged approach led to the identification and characterization of a branched-chain amino acid decarboxylase, which would appear to be responsible for generating the amine moieties of naturally occurring alkamides.

Identification and characterization of wheat drought-responsive MYB transcription factors involved in the regulation of cuticle biosynthesis.

A plant cuticle forms a hydrophobic layer covering plant organs, and plays an important role in plant development and protection from environmental stresses. We examined epicuticular structure, composition, and a MYB-based regulatory network in two Australian wheat cultivars, RAC875 and Kukri, with contrasting cuticle appearance (glaucousness) and drought tolerance. Metabolomics and microscopic analyses of epicuticular waxes revealed that the content of ß-diketones was the major compositional and structural difference between RAC875 and Kukri. The content of ß-diketones remained the same while those of alkanes and primary alcohols were increased by drought in both cultivars, suggesting that the interplay of all components rather than a single one defines the difference in drought tolerance between cultivars. Six wheat genes encoding MYB transcription factors (TFs) were cloned; four of them were regulated in flag leaves of both cultivars by rapid dehydration and/or slowly developing cyclic drought. The involvement of selected MYB TFs in the regulation of cuticle biosynthesis was confirmed by a transient expression assay in wheat cell culture, using the promoters of wheat genes encoding cuticle biosynthesis-related enzymes and the SHINE1 (SHN1) TF. Two functional MYB-responsive elements, specifically recognized by TaMYB74 but not by other MYB TFs, were localized in the TdSHN1 promoter. Protein structural determinants underlying the binding specificity of TaMYB74 for functional DNA cis-elements were defined, using 3D protein molecular modelling. A scheme, linking drought-induced expression of the investigated TFs with downstream genes that participate in the synthesis of cuticle components, is proposed.

PIN6 is required for nectary auxin response and short stamen development.

The PIN family of proteins is best known for its involvement in polar auxin transport and tropic responses. PIN6 (At1g77110) is one of the remaining PIN family members in Arabidopsis thaliana to which a biological function has not yet been ascribed. Here we report that PIN6 is a nectary-enriched gene whose expression level is positively correlated with total nectar production in Arabidopsis, and whose function is required for the proper development of short stamens. PIN6 accumulates in internal membranes consistent with the ER, and multiple lines of evidence demonstrate that PIN6 is required for auxin-dependent responses in nectaries. Wild-type plants expressing auxin-responsive DR5:GFP or DR5:GUS reporters displayed intense signal in lateral nectaries, but pin6 lateral nectaries showed little or no signal for these reporters. Further, exogenous auxin treatment increased nectar production more than tenfold in wild-type plants, but nectar production was not increased in pin6 mutants when treated with auxin. Conversely, the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) reduced nectar production in wild-type plants by more than twofold, but had no significant effect on pin6 lines. Interestingly, a MYB57 transcription factor mutant, myb57-2, closely phenocopied the loss-of-function mutant pin6-2. However, PIN6 expression was not dependent on MYB57, and RNA-seq analyses of pin6-2 and myb57-2 mutant nectaries showed little overlap in terms of differentially expressed genes. Cumulatively, these results demonstrate that PIN6 is required for proper auxin response and nectary function in Arabidopsis. These results also identify auxin as an important factor in the regulation of nectar production, and implicate short stamens in the maturation of lateral nectaries.

Alkaloids and athlete immune function: caffeine, theophylline, gingerol, ephedrine, and their congeners.

Plant alkaloids are found in foods, beverages, and supplements consumed by athletes for daily nutrition, performance enhancement, and immune function improvement. This paper examined possible immunomodulatory roles of alkaloids in exercise contexts, with a focus on human studies. Four representative groups were scrutinized: (a) caffeine (guaranine, mateine); (b) theophylline and its isomers, theobromine and paraxanthine; (c) ginger alkaloids including gingerols and shogaol; and (d) ephedra alkaloids such as ephedrine and pseudoephedrine. Emerging or prospective alkaloid sources (Goji berry, Noni berry, and bloodroot) were also considered. Human in vitro and in vivo studies on alkaloids and immune function were often conflicting. Caffeine may be immunomodulatory in vivo depending on subject characteristics, exercise characteristics, and immune parameters measured. Caffeine may exhibit antioxidant capacities. Ginger may exert in vivo anti-inflammatory effects in certain populations, but it is unclear whether these effects are due to alkaloids or other biochemicals. Evidence for an immunomodulatory role of alkaloids in energy drinks, cocoa, or ephedra products in vivo is weak to nonexistent. For alkaloid sources derived from plants, variability in the reviewed studies may be due to the presence of unrecognized alkaloids or non-alkaloid compounds (which may themselves be immunomodulatory), and pre-experimental factors such as agricultural or manufacturing differences. Athletes should not look to alkaloids or alkaloid-rich sources as a means of improving immune function given their inconsistent activities, safety concerns, and lack of commercial regulation.

Biological origins of normal-chain hydrocarbons: a pathway model based on cuticular wax analyses of maize silks.

Long-chain normal hydrocarbons (e.g. alkanes, alkenes and dienes) are rare biological molecules and their biosynthetic origins are obscure. Detailed analyses of the surface lipids that accumulate on maize silks have revealed that these hydrocarbons constitute a large portion (>90%) of the cuticular waxes that coat this organ, which contrasts with the situation on maize seedling leaves, where the cuticular waxes are primary alcohols and aldehydes. The normal hydrocarbons that occur on silks are part of a homologous series of alkanes, alkenes and dienes of odd-number carbon atoms, ranging between 19 and 33 in number. The alkenes and dienes consist of a homologous series, each of which has double bonds situated at defined positions of the alkyl chains: alkenes have double bonds situated at the sixth, ninth or 12th positions, and dienes have double bonds situated at the sixth and ninth, or ninth and twelfth positions. Finding a homologous series of unsaturated aldehydes and fatty acids suggests that these alkenes and dienes are biosynthesized by a series of parallel pathways of fatty-acid elongation and desaturation reactions, which are followed by sequential reduction and decarbonylation. In addition, the silk cuticular waxes contain metabolically related unsaturated long-chain methylketones, which probably arise via a decarboxylation mechanism. Finally, metabolite profiling analyses of the cuticular waxes of two maize inbred lines (B73 and Mo17), and their genetic hybrids, have provided insights into the genetic control network of these biosynthetic pathways, and that the genetic regulation of these pathways display best-parent heterotic effects.

Platform biochemicals for a biorenewable chemical industry.

The chemical industry is currently reliant on a historically inexpensive, petroleum-based carbon feedstock that generates a small collection of platform chemicals from which highly efficient chemical conversions lead to the manufacture of a large variety of chemical products. Recently, a number of factors have coalesced to provide the impetus to explore alternative renewable sources of carbon. Here we discuss the potential impact on the chemical industry of shifting from non-renewable carbon sources to renewable carbon sources. This change to the manufacture of chemicals from biological carbon sources will provide an opportunity for the biological research community to contribute fundamental knowledge concerning carbon metabolism and its regulation. We discuss whether fundamental biological research into metabolic processes at a holistic level, made possible by completed genome sequences and integrated with detailed structural understanding of biocatalysts, can change the chemical industry from being dependent on fossil-carbon feedstocks to using biorenewable feedstocks. We illustrate this potential by discussing the prospect of building a platform technology based upon a concept of combinatorial biosynthesis, which would explore the enzymological flexibilities of polyketide biosynthesis.

Human blood mononuclear cell in vitro cytokine response before and after two different strenuous exercise bouts in the presence of bloodroot and Echinacea extracts.

The purpose of this multidisciplinary investigation was to characterize cytokine production by human blood mononuclear cells after 2 contrasting exercise bouts (a maximal graded oxygen consumption [VO(2)max] test and 90 min of cycling at 85% of ventilatory threshold [VT]) when stimulated in vitro with extracts from bloodroot (Sanguinaria canadensis), coneflower (Echinacea tennesseensis), or solvent vehicle controls. Blood was sampled pre- and post-exercise. Production of TNF, IL-1beta, and IL-10 were measured at 24, 48, and 72 h, respectively. In the VO(2)max test there was a main effect of exercise such that exercise increased cytokine synthesis and a main effect of stimulant such that bloodroot extracts significantly increased cytokine production compared to other stimulants or controls. In the 90-min bout, there was a main effect of exercise for TNF and IL-1beta (but not IL-10) such that exercise decreased cytokine synthesis and a main effect of stimulant such that bloodroot extracts significantly increased cytokine production compared to other stimulants or controls, with exercisexstimulant interactions for both IL-1beta and IL-10. A similar though weaker effect was seen with Echinacea extracts; subsequent biochemical analyses suggested this was related to alkamide decay during 3 years undisturbed storage at ultralow (-80 degrees C) temperature. In this study, the VO(2)max test was associated with enhanced cytokine production whereas the 90-min cycling at 85% VT was associated with suppressed cytokine production. Bloodroot extracts were able to increase cytokine production in both contexts. Herbal extracts purported to offset exercise-associated effects on immune activity warrant continued investigation.

Quantitative analysis of short-chain acyl-coenzymeAs in plant tissues by LC-MS-MS electrospray ionization method.

Because acyl-CoAs play major roles in numerous anabolic and catabolic pathways, the quantitative determination of these metabolites in biological tissues is paramount to understanding the regulation of these metabolic processes. Here, we report a method for the analysis of a collection of short-chain acyl-CoAs (<6 carbon chain length) from plant extracts. Identification of each individual acyl-CoA was conducted by monitoring specific mass-fragmentation ions that are derived from common chemical moieties of all Coenzyme A (CoA) derivatives, namely the adenosine triphosphate nucleotide, pantothenate and acylated cysteamine. This method is robust and quick, enabling the quantitative analysis of up to 12 different acyl-CoAs in plant metabolite extracts with minimal post-extraction processing, using a 30min chromatographic run-time.

A single-cell platform for reconstituting and characterizing fatty acid elongase component enzymes.

Fatty acids of more than 18-carbons, generally known as very long chain fatty acids (VLCFAs) are essential for eukaryotic cell viability, and uniquely in terrestrial plants they are the precursors of the cuticular lipids that form the organism's outer barrier to the environment. VLCFAs are synthesized by fatty acid elongase (FAE), which is an integral membrane enzyme system with multiple components. The genetic complexity of the FAE system, and its membrane association has hampered the biochemical characterization of FAE. In this study we computationally identified Zea mays genetic sequences that encode the enzymatic components of FAE and developed a heterologous expression system to evaluate their functionality. The ability of the maize components to genetically complement Saccharomyces cerevisiae lethal mutants confirmed the functionality of ZmKCS4, ZmELO1, ZmKCR1, ZmKCR2, ZmHCD and ZmECR, and the VLCFA profiles of the resulting strains were used to infer the ability of each enzyme component to determine the product profile of FAE. These characterizations indicate that the product profile of the FAE system is an attribute shared among the KCS, ELO, and KCR components of FAE.

Developmental changes in the metabolic network of snapdragon flowers.

Evolutionary and reproductive success of angiosperms, the most diverse group of land plants, relies on visual and olfactory cues for pollinator attraction. Previous work has focused on elucidating the developmental regulation of pathways leading to the formation of pollinator-attracting secondary metabolites such as scent compounds and flower pigments. However, to date little is known about how flowers control their entire metabolic network to achieve the highly regulated production of metabolites attracting pollinators. Integrative analysis of transcripts and metabolites in snapdragon sepals and petals over flower development performed in this study revealed a profound developmental remodeling of gene expression and metabolite profiles in petals, but not in sepals. Genes up-regulated during petal development were enriched in functions related to secondary metabolism, fatty acid catabolism, and amino acid transport, whereas down-regulated genes were enriched in processes involved in cell growth, cell wall formation, and fatty acid biosynthesis. The levels of transcripts and metabolites in pathways leading to scent formation were coordinately up-regulated during petal development, implying transcriptional induction of metabolic pathways preceding scent formation. Developmental gene expression patterns in the pathways involved in scent production were different from those of glycolysis and the pentose phosphate pathway, highlighting distinct developmental regulation of secondary metabolism and primary metabolic pathways feeding into it.

Phytochemical and immunomodulatory properties of an Echinacea laevigata (Asteraceae) tincture.

BACKGROUND: Echinacea preparations are consumed for the prevention or treatment of upper respiratory infections. OBJECTIVE: The objective of this study was to provide the first data regarding the in vitro immunomodulatory properties of the American federally endangered species Echinacea laevigata (Asteraceae). METHODS: Human peripheral blood mononuclear cells were cultured with root tinctures from E. laevigata, E. angustifolia, E. pallida, and E. purpurea. Cytokine production (tumor necrosis factor [TNF], interleukin [IL]-2, IL-10) and mononuclear cell proliferation were measured. High-performance liquid chromatography was used to assay levels of known bioactive compounds from all extracts tested to statistically determine whether there were relationships between extract phytochemical content and observed immune effects. RESULTS: E. laevigata extract was most similar to E. pallida extract and able to augment IL-10 and mononuclear cell proliferation, but not TNF or IL-2. Echinacoside, a caffeic acid derivative, correlated most strongly with results. CONCLUSIONS: This species may deserve continued investigation in both experimental and therapeutic contexts.

Identification, cloning and characterization of a GDSL lipase secreted into the nectar of Jacaranda mimosifolia.

The presence and function of several proteins secreted into floral nectars has been described in recent years. Here we report the presence of at least eight distinct proteins secreted into the floral nectar of the tropical tree Jacaranda mimosifolia (Bignoniaceae). Steps were initiated to identify and characterize these proteins in order to determine potential functions. The N-terminal sequence of the major Jacaranda nectar protein, JNP1, at 43 kDa contained similarity with members of the plant GDSL lipase/esterase gene family. Based upon this sequence, a full-length cDNA was isolated and predicted to encode a mature protein of 339 amino acids with a molecular mass of 37 kDa. Both raw nectar and heterologously expressed JNP1 displayed lipase/esterase activities. Interestingly, J. mimosifolia flowers produce an opaque, white colored nectar containing spherical, lipophilic particles approximately 5 microm in diameter and smaller. GS-MS analysis also identified the accumulation of free fatty acids within the nectar. It is proposed that JNP1 hydrolyzes Jacaranda nectar lipids with the concomitant release of free fatty acids. Potential functions of JNP1 in relation to pollinator attraction and prevention of microbial growth within nectar are briefly discussed.

Characterization of two GL8 paralogs reveals that the 3-ketoacyl reductase component of fatty acid elongase is essential for maize (Zea mays L.) development.

Prior analyses established that the maize (Zea mays L.) gl8a gene encodes 3-ketoacyl reductase, a component of the fatty acid elongase required for the biosynthesis of very long chain fatty acids (VLCFAs). A paralogous gene, gl8b, has been identified that is 96% identical to gl8a. The gl8a and gl8b genes map to syntenic chromosomal regions, have similar, but not identical, expression patterns, and encode proteins that are 97% identical. Both of these genes are required for the normal accumulation of cuticular waxes on seedling leaves. The chemical composition of the cuticular waxes from gl8a and gl8b mutants indicates that these genes have at least overlapping, if not redundant, functions in cuticular wax biosynthesis. Although gl8a and gl8b double mutant kernels have endosperms that cannot be distinguished from wild-type siblings, these kernels are non-viable because their embryos fail to undergo normal development. Double mutant kernels accumulate substantially reduced levels of VLCFAs. VLCFAs are components of a variety of compounds, for example, cuticular waxes, suberin, and sphingolipids. Consistent with their essential nature in yeast, the accumulation of the ceramide moiety of sphingolipids is substantially reduced and their fatty acid composition altered in gl8a and gl8b double mutant kernels relative to wild-type kernels. Hence, we hypothesize that sphingolipids or other VLCFA-containing compounds are essential for normal embryo development.