Structure and function of enzymes involved in the biosynthesis of phenylpropanoids

Changes in rice allelopathy and rhizosphere microflora by inhibiting rice phenylalanine ammonia-lyase gene expression

Gene expression of phenylalanine ammonia-lyase (PAL) in allelopathic rice PI312777 was inhibited by RNA interference (RNAi). Transgenic rice showed lower levels of PAL gene expression and PAL activity than wild type rice (WT). The concentrations of phenolic compounds were lower in the root tissues and root exudates of transgenic rice than in those of wild type plants. When barndyardgrass (BYG) was used as the receiver plant, the allelopathic potential of transgenic rice was reduced. The sizes of the bacterial and fungal populations in rice rhizospheric soil at the 3-, 5-, and 7-leaf stages were estimated by using quantitative PCR (qPCR), which showed a decrease in both populations at all stages of leaf development analyzed. However, PI312777 had a larger microbial population than transgenic rice. In addition, in T-RFLP studies, 14 different groups of bacteria were detected in WT and only 6 were detected in transgenic rice. This indicates that there was less rhizospheric bacterial diversity associated with transgenic rice than with WT. These findings collectively suggest that PAL functions as a positive regulator of rice allelopathic potential.

Protein changes during ethanol induced seed germination in Aconitum heterophyllum

Aconitum heterophyllum is a high altitude medicinal plant that has become endangered due to overexploitation for their aconitins. The most effective, conventional propagation method for any plant species is by seed. However, in Aconitum seed germination is erratic, and seedling survival is low. In the present study results have been discussed on the possible implication of ethanol treatment on removal of barriers on radical emergence in terms of protein changes. Eighty seven percent of seed germination was achieved in Aconitum with ethanol treatment. Comparative 2-DE analysis of ethanol treated and untreated seed protein profiles in Phase II of germination revealed 40 differentially expressed proteins. Twenty-seven out of 40 proteins were induced, 5 were increased and 8 were repressed. Mass spectrometry and subsequent identification confirmed that these proteins were involved in metabolism, DNA regulation, stress tolerance and plasmamembrane/cell wall biosynthesis/extension processes. These protein changes might be responsible for physiological and physical changes, respectively, resulted in increase in germination percentage. Further, characterization of these proteins will be of great help in understanding the molecular mechanism lying behind enhanced germination in response to ethanol treatment.

An emerging understanding of mechanisms governing insect herbivory under elevated CO2

By changing the chemical composition of foliage, the increase in atmospheric CO(2) is fundamentally altering insect herbivory. The responses of folivorous insects to these changes is, however, highly variable. In this review we highlight emerging mechanisms by which increasing CO(2) alters the defense chemistry and signaling of plants. The response of allelochemicals affecting insect performance varies under elevated CO(2), and results suggest this is driven by changes in plant hormones. Increasing CO(2) suppresses the production of jasmonates and ethylene and increases the production of salicylic acid, and these differential responses of plant hormones affect specific secondary chemical pathways. In addition to changes in secondary chemistry, elevated CO(2) decreases rates of water loss from leaves, increases temperature and feeding rates, and alters nutritional content. New insights into the mechanistic responses of secondary chemistry to elevated CO(2) increase our ability to predict the ecological and evolutionary responses of plants attacked by insects.

Identification and bioanalysis of natural products from insect symbionts and pathogens

: With the development of several novel methods in genome sequencing, molecular biology, and analytical chemistry a new area of natural product chemistry is currently starting that allows the analysis of minute amounts of complex biological samples. The combination of these methods, as discussed in this review, also enables the analysis of bacteria living in symbiosis or being pathogenic to insects, which might be the largest reservoir for novel microbes associated with higher organisms due to the huge number of insect species.

Plant glandular trichomes as targets for breeding or engineering of resistance to herbivores

Glandular trichomes are specialized hairs found on the surface of about 30% of all vascular plants and are responsible for a significant portion of a plant's secondary chemistry. Glandular trichomes are an important source of essential oils, i.e., natural fragrances or products that can be used by the pharmaceutical industry, although many of these substances have evolved to provide the plant with protection against herbivores and pathogens. The storage compartment of glandular trichomes usually is located on the tip of the hair and is part of the glandular cell, or cells, which are metabolically active. Trichomes and their exudates can be harvested relatively easily, and this has permitted a detailed study of their metabolites, as well as the genes and proteins responsible for them. This knowledge now assists classical breeding programs, as well as targeted genetic engineering, aimed to optimize trichome density and physiology to facilitate customization of essential oil production or to tune biocide activity to enhance crop protection. We will provide an overview of the metabolic diversity found within plant glandular trichomes, with the emphasis on those of the Solanaceae, and of the tools available to manipulate their activities for enhancing the plant's resistance to pests.

The R2R3-MYB-like regulatory factor EOBI, acting downstream of EOBII, regulates scent production by activating ODO1 and structural scent-related genes in petunia

Flower scent is a highly dynamic trait, under developmental, spatial, and diurnal regulation. The mechanism governing scent production is only beginning to be unraveled. In petunia (Petunia hybrida), EMISSION OF BENZENOIDS II (EOBII) controls transcription of both the shikimate pathway-regulating MYB factor ODORANT1 (ODO1) and phenylpropanoid scent-related structural genes. A promoter-activation screen identified an R2R3-MYB-like regulatory factor of phenylpropanoid volatile biosynthesis acting downstream of EOBII, designated EOBI. EOBI silencing led to downregulation of ODO1 and numerous structural scent-related genes from both the shikimate and phenylpropanoid pathways. The ability of EOBI to directly activate ODO1, as revealed by electrophoretic mobility shift assay and yeast one-hybrid analysis, place EOBI upstream of ODO1 in regulating substrate availability for volatile biosynthesis. Interestingly, ODO1-silenced transgenic petunia flowers accumulated higher EOBI transcript levels than controls, suggesting a complex feedback loop between these regulatory factors. The accumulation pattern of EOBI transcript relative to EOBII and ODO1, and the effect of up/downregulation of EOBII on transcript levels of EOBI and ODO1, further support these factors' hierarchical relationships. The dependence of scent production on EOBI expression and its direct interaction with both regulatory and structural genes provide evidence for EOBI's wide-ranging involvement in the production of floral volatiles.

Expression patterns of a cinnamyl alcohol dehydrogenase gene involved in lignin biosynthesis and environmental stress in Ginkgo biloba

The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. A cDNA sequence encoding the CAD gene was isolated from the leaves of Ginkgo biloba L, designated as GbCAD1. The full-length cDNA of GbCAD1 was 1,494 bp containing a 1,074 bp open reading frame encoding a polypeptide of 357 amino acids with a calculated molecular mass of 38.7 kDa and an isoelectric point of 5.74. Comparative and bioinformatic analyses revealed that GbCAD1 showed extensive homology with CADs from other gymnosperm species. Southern blot analysis indicated that GbCAD1 belonged to a multi-gene family. Phylogenetic tree analysis revealed that GbCAD1 shared the same ancestor in evolution with other CADs and had a further relationship with other gymnosperm species. GbCAD1 was an enzyme being pH-dependent and temperature-sensitive, and showing a selected catalyzing. Tissue expression pattern analysis showed that GbCAD1 was constitutively expressed in stems and roots, especially in the parts of the pest and disease infection, with the lower expression being found in two- to four-year-old stem. Further analysis showed the change in lignin content had some linear correlation with the expression level of GbCAD1 mRNA in different tissues. The increased expression of GbCAD1 was detected when the seedling were treated with exogenous abscisic acid, salicylic acid, ethephon, ultraviolet and wounding. These results indicate that the GbCAD1 gene may play a role in the resistance mechanism to biotic and abiotic stresses as well as in tissue-specific developmental lignification.

Exploiting genes and functional diversity of chlorogenic acid and luteolin biosyntheses in Lonicera japonica and their substitutes

Chlorogenic acids (CGAs) and luteolin are active compounds in Lonicera japonica, a plant of high medicinal value in traditional Chinese medicine. This study provides a comprehensive overview of gene families involved in chlorogenic acid and luteolin biosynthesis in L. japonica, as well as its substitutes Lonicera hypoglauca and Lonicera macranthoides. The gene sequence feature and gene expression patterns in various tissues and buds of the species were characterized. Bioinformatics analysis revealed that 14 chlorogenic acid and luteolin biosynthesis-related genes were identified from the L. japonica transcriptome assembly. Phylogenetic analyses suggested that the function of individual gene could be differentiation and induce active compound diversity. Their orthologous genes were also recognized in L. hypoglauca and L. macranthoides genomic datasets, except for LHCHS1 and LMC4H2. The expression patterns of these genes are different in the tissues of L. japonica, L. hypoglauca and L. macranthoides. Results also showed that CGAs were controlled in the first step of biosynthesis, whereas both steps controlled luteolin in the bud of L. japonica. The expression of LJFNS2 exhibited positive correlation with luteolin levels in L. japonica. This study provides significant information for understanding the functional diversity of gene families involved in chlorogenic acid and the luteolin biosynthesis, active compound diversity of L. japonica and its substitutes, and the different usages of the three species.

Flavonoids: biosynthesis, biological functions, and biotechnological applications

Flavonoids are widely distributed secondary metabolites with different metabolic functions in plants. The elucidation of the biosynthetic pathways, as well as their regulation by MYB, basic helix-loop-helix (bHLH), and WD40-type transcription factors, has allowed metabolic engineering of plants through the manipulation of the different final products with valuable applications. The present review describes the regulation of flavonoid biosynthesis, as well as the biological functions of flavonoids in plants, such as in defense against UV-B radiation and pathogen infection, nodulation, and pollen fertility. In addition, we discuss different strategies and achievements through the genetic engineering of flavonoid biosynthesis with implication in the industry and the combinatorial biosynthesis in microorganisms by the reconstruction of the pathway to obtain high amounts of specific compounds.

First Phytochemical Evidence of Chemotypes for the Seagrass Zostera noltii

The variability of the flavonoid content of two populations of Z. noltii from different geographical zones, i.e., the Bay of Arcachon and the Bay of Cadiz, was evaluated. Samples were collected in spring and autumn at the two sites, and extracts were prepared by maceration in water. The phenolic content was fully characterized using Nuclear Magnetic Resonance (NMR), UV and Liquid Chromatography-Mass Spectrometry (LC-MS), and the concentration of the individual phenolic was determined by quantitative High-Performance Liquid Chromatography with Diode-Array Detection (HPLC-DAD). The two populations show a strong geographical differentiation in their flavonoid content. The samples from Cadiz were dominated by apigenin 7-sulfate, which represents 71% (autumn collection) and 83% (spring collection) of the total flavonoids, whereas the samples from Arcachon were characterized by diosmetin 7-sulfate (85 and 93% of the total flavonoids). Structural elucidation of the individual phenolics was assigned using the complementary information from their spectral evidence. In addition, the results were confirmed by acid hydrolysis of the flavonoid sulfates, and comparison to synthetic standards obtained by sulfation of apigenin, diosmetin and luteolin. The results represent the first experimental evidence of the existence of chemotypes within the species Z. noltii.

A versatile targeted metabolomics method for the rapid quantification of multiple classes of phenolics in fruits and beverages

Compelling evidence of the health benefits of phenolic compounds and their impact on food quality have stimulated the development of analytical methods for the identification and quantification of these compounds in different matrices in recent years. A targeted metabolomics method has been developed for the quantification of 135 phenolics, such as benzoates, phenylpropanoids, coumarins, stilbenes, dihydrochalcones, and flavonoids, in fruit and tea extracts and wine using UPLC/QqQ-MS/MS. Chromatography was optimized to achieve separation of the compounds over a period of 15 min, and MRM transitions were selected for accurate quantification. The method was validated by studying the detection and quantification limits, the linearity ranges, and the intraday and interday repeatability of the analysis. The validated method was applied to the analysis of apples, berries, green tea, and red wine, providing a valuable tool for food quality evaluation and breeding studies.

Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce

In plants, relationships between resistance to herbivorous insect pests and growth are typically controlled by complex interactions between genetically correlated traits. These relationships often result in tradeoffs in phenotypic expression. In this study we used genetical genomics to elucidate genetic relationships between tree growth and resistance to white pine terminal weevil (Pissodes strobi Peck.) in a pedigree population of interior spruce (Picea glauca, P. engelmannii and their hybrids) that was growing at Vernon, B.C. and segregating for weevil resistance. Genetical genomics uses genetic perturbations caused by allelic segregation in pedigrees to co-locate quantitative trait loci (QTLs) for gene expression and quantitative traits. Bark tissue of apical leaders from 188 trees was assayed for gene expression using a 21.8K spruce EST-spotted microarray; the same individuals were genotyped for 384 SNP markers for the genetic map. Many of the expression QTLs (eQTL) co-localized with resistance trait QTLs. For a composite resistance phenotype of six attack and oviposition traits, 149 positional candidate genes were identified. Resistance and growth QTLs also overlapped with eQTL hotspots along the genome suggesting that: 1) genetic pleiotropy of resistance and growth traits in interior spruce was substantial, and 2) master regulatory genes were important for weevil resistance in spruce. These results will enable future work on functional genetic studies of insect resistance in spruce, and provide valuable information about candidate genes for genetic improvement of spruce.

Structural basis for modification of flavonol and naphthol glucoconjugates by Nicotiana tabacum malonyltransferase (NtMaT1)

Plant HXXXD acyltransferase-catalyzed malonylation is an important modification reaction in elaborating the structural diversity of flavonoids and anthocyanins, and a universal adaptive mechanism to detoxify xenobiotics. Nicotiana tabacum malonyltransferase 1 (NtMaT1) is a member of anthocyanin acyltransferase subfamily that uses malonyl-CoA (MLC) as donor catalyzing transacylation in a range of flavonoid and naphthol glucosides. To gain insights into the molecular basis underlying its catalytic mechanism and versatile substrate specificity, we resolved the X-ray crystal structure of NtMaT1 to 3.1 Å resolution. The structure comprises two α/β mixed subdomains, as typically found in the HXXXD acyltransferases. The partial electron density map of malonyl-CoA allowed us to reliably dock the entire molecule into the solvent channel and subsequently define the binding sites for both donor and acceptor substrates. MLC bound to the NtMaT1 occupies one end of the long solvent channel between two subdomains. On superimposing and comparing the structure of NtMaT1 with that of an enzyme from anthocyanin acyltransferase subfamily from red chrysanthemum (Dm3Mat3) revealed large architectural variation in the binding sites, both for the acyl donor and for the acceptor, although their overall protein folds are structurally conserved. Consequently, the shape and the interactions of malonyl-CoA with the binding sites' amino acid residues differ substantially. These major local architectural disparities point to the independent, divergent evolution of plant HXXXD acyltransferases in different species. The structural flexibility of the enzyme and the amendable binding pattern of the substrates provide a basis for the evolution of the distinct, versatile substrate specificity of plant HXXXD acyltransferases.

Characterization of a flavonol 3-O-methyltransferase in the trichomes of the wild tomato species Solanum habrochaites

The glandular trichomes of the wild tomato species Solanum habrochaites accumulate the polymethylated flavonol aglycones, 3,7,3'-O-methyl myricetin, 3,7,3',5'-O-methyl myricetin, and 3,7,3',4',5'-O-methyl myricetin. Partially methylated flavonol aglycones and partially methylated flavonol glycones containing a methyl group at the 3 position have been previously reported from a variety of plants. The 3-O-methyltransferase (3-OMT) activity has been previously partially purified from plants, but a gene transcript encoding an enzyme capable of methylating flavonols at the 3 position has not yet been identified, nor have been such proteins purified and characterized. We previously identified two gene transcripts expressed in the glandular trichomes of S. habrochaites and showed that they encode enzymes capable of methylating myricetin at the 3' and 5' and the 7 and 4' positions, respectively. Here we report the identification of gene transcripts expressed in S. lycopersicum (cultivated tomato) and in S. habrochaites glandular trichomes that encode enzymes capable of methylating myricetin, and its partially methylated derivatives exclusively at the 3 position. The S. habrochaites gene transcript is preferentially expressed in the glandular trichomes and it encodes a protein with high similarity to the S. habrochaites, 3'/5' O-methyltransferase which is also present in glandular trichomes. Phylogenic analysis suggests that the 3-OMT activity has probably evolved from an ancestral 3'/5' methyltransferase activity. The discovery and characterization of 3-OMT provides a more complete picture of the series of reactions leading to highly methylated myricetin compounds in S. habrochaites glandular trichomes.

Genome-wide analysis of the grapevine stilbene synthase multigenic family: genomic organization and expression profiles upon biotic and abiotic stresses

BACKGROUND

Plant stilbenes are a small group of phenylpropanoids, which have been detected in at least 72 unrelated plant species and accumulate in response to biotic and abiotic stresses such as infection, wounding, UV-C exposure and treatment with chemicals. Stilbenes are formed via the phenylalanine/polymalonate-route, the last step of which is catalyzed by the enzyme stilbene synthase (STS), a type III polyketide synthase (PKS). Stilbene synthases are closely related to chalcone synthases (CHS), the key enzymes of the flavonoid pathway, as illustrated by the fact that both enzymes share the same substrates. To date, STSs have been cloned from peanut, pine, sorghum and grapevine, the only stilbene-producing fruiting-plant for which the entire genome has been sequenced. Apart from sorghum, STS genes appear to exist as a family of closely related genes in these other plant species.

RESULTS

In this study a complete characterization of the STS multigenic family in grapevine has been performed, commencing with the identification, annotation and phylogenetic analysis of all members and integration of this information with a comprehensive set of gene expression analyses including healthy tissues at differential developmental stages and in leaves exposed to both biotic (downy mildew infection) and abiotic (wounding and UV-C exposure) stresses. At least thirty-three full length sequences encoding VvSTS genes were identified, which, based on predicted amino acid sequences, cluster in 3 principal groups designated A, B and C. The majority of VvSTS genes cluster in groups B and C and are located on chr16 whereas the few gene family members in group A are found on chr10. Microarray and mRNA-seq expression analyses revealed different patterns of transcript accumulation between the different groups of VvSTS family members and between VvSTSs and VvCHSs. Indeed, under certain conditions the transcriptional response of VvSTS and VvCHS genes appears to be diametrically opposed suggesting that flow of carbon between these two competing metabolic pathways is tightly regulated at the transcriptional level.

CONCLUSIONS

This study represents an overview of the expression pattern of each member of the STS gene family in grapevine under both constitutive and stress-induced conditions. The results strongly indicate the existence of a transcriptional subfunctionalization amongst VvSTSs and provide the foundation for further functional investigations about the role and evolution of this large gene family. Moreover, it represents the first study to clearly show the differential regulation of VvCHS and VvSTS genes, suggesting the involvement of transcription factors (TFs) in both the activation and repression of these genes.

Genes of phenylpropanoid pathway are activated in early response to Fusarium attack in flax plants

Fusarium is the most common flax pathogen causing serious plant diseases and in most cases leading to plant death. To protect itself, the plant activates a number of genes and metabolic pathways, both to counteract the effects of the pathogen, and to eliminate the threat. The identification of the plant genes which respond to infection is the approach, that has been used in this study. Forty-seven flax genes have been identified by means of cDNA subtraction method as those, which respond to pathogen infection. Subtracted genes were classified into several classes and the prevalence of the genes involved in the broad spectrum of antioxidants biosynthesis has been noticed. By means of semi-quantitative RT-PCR and metabolite profiling, the involvement of subtracted genes controlling phenylpropanoid pathway in flax upon infection was positively verified. We identified the key genes of the synthesis of these compounds. At the same time we determined the level of the metabolites produced in the phenylpropanoid pathway (flavonoids, phenolic acids) in early response to Fusarium attack by means of GC-MS technique. To the best of our knowledge this is the first report to describe genes and metabolites of early flax response to pathogens studied in a comprehensive way.

The B gene of pea encodes a defective flavonoid 3',5'-hydroxylase, and confers pink flower color

The inheritance of flower color in pea (Pisum sativum) has been studied for more than a century, but many of the genes corresponding to these classical loci remain unidentified. Anthocyanins are the main flower pigments in pea. These are generated via the flavonoid biosynthetic pathway, which has been studied in detail and is well conserved among higher plants. A previous proposal that the Clariroseus (B) gene of pea controls hydroxylation at the 5' position of the B ring of flavonoid precursors of the anthocyanins suggested to us that the gene encoding flavonoid 3',5'-hydroxylase (F3'5'H), the enzyme that hydroxylates the 5' position of the B ring, was a good candidate for B. In order to test this hypothesis, we examined mutants generated by fast neutron bombardment. We found allelic pink-flowered b mutant lines that carried a variety of lesions in an F3'5'H gene, including complete gene deletions. The b mutants lacked glycosylated delphinidin and petunidin, the major pigments present in the progenitor purple-flowered wild-type pea. These results, combined with the finding that the F3'5'H gene cosegregates with b in a genetic mapping population, strongly support our hypothesis that the B gene of pea corresponds to a F3'5'H gene. The molecular characterization of genes involved in pigmentation in pea provides valuable anchor markers for comparative legume genomics and will help to identify differences in anthocyanin biosynthesis that lead to variation in pigmentation among legume species.

The role of flavonoids in the establishment of plant roots endosymbioses with arbuscular mycorrhiza fungi, rhizobia and Frankia bacteria

Flavonoids are a group of secondary metabolites derived from the phenylpropanoid pathway. They are ubiquitous in the plant kingdom and have many diverse functions including key roles at different levels of root endosymbioses. While there is a lot of information on the role of particular flavonoids in the Rhizobium-legume symbiosis, yet their exact role during the establishment of arbuscular mycorrhiza and actinorhizal symbioses still remains unclear. Within the context of the latest data suggesting a common symbiotic signaling pathway for both plant-fungal and plant bacterial endosymbioses between legumes and actinorhiza-forming fagales, this mini-review highlights some of the recent studies on the three major types of root endosymbioses. Implication of the molecular knowledge of endosymbioses signaling and genetic manipulation of flavonoid biosynthetic pathway on the development of strategies for the transfer and optimization of nodulation are also discussed.

Genome-Wide Characterization of ISR Induced in Arabidopsis thaliana by Trichoderma hamatum T382 Against Botrytis cinerea Infection

In this study, the molecular basis of the induced systemic resistance (ISR) in Arabidopsis thaliana by the biocontrol fungus Trichoderma hamatum T382 against the phytopathogen Botrytis cinerea B05-10 was unraveled by microarray analysis both before (ISR-prime) and after (ISR-boost) additional pathogen inoculation. The observed high numbers of differentially expressed genes allowed us to classify them according to the biological pathways in which they are involved. By focusing on pathways instead of genes, a holistic picture of the mechanisms underlying ISR emerged. In general, a close resemblance is observed between ISR-prime and systemic acquired resistance, the systemic defense response that is triggered in plants upon pathogen infection leading to increased resistance toward secondary infections. Treatment with T. hamatum T382 primes the plant (ISR-prime), resulting in an accelerated activation of the defense response against B. cinerea during ISR-boost and a subsequent moderation of the B. cinerea induced defense response. Microarray results were validated for representative genes by qRT-PCR. The involvement of various defense-related pathways was confirmed by phenotypic analysis of mutants affected in these pathways, thereby proving the validity of our approach. Combined with additional anthocyanin analysis data these results all point to the involvement of the phenylpropanoid pathway in T. hamatum T382-induced ISR.

Evolution of the chalcone-isomerase fold from fatty-acid binding to stereospecific catalysis

Specialized metabolic enzymes biosynthesize chemicals of ecological importance, often sharing a pedigree with primary metabolic enzymes¹. However, the lineage of the enzyme chalcone isomerase (CHI) remained a quandary. In vascular plants, CHI-catalyzed conversion of chalcones to chiral (S)-flavanones is a committed step in the production of plant flavonoids, compounds that contribute to attraction, defense², and development³. CHI operates near the diffusion limit with stereospecific control^4,5. While associated primarily with plants, the CHI-fold occurs in several other eukaryotic lineages and in some bacteria. Here we report crystal structures, ligand-binding properties, and in vivo functional characterization of a non-catalytic CHI-fold family from plants. A. thaliana contains five actively transcribed CHI-fold genes, three of which additionally encode amino-terminal chloroplast-transit sequences (cTP). These three CHI-fold proteins localize to plastids, the site of de novo fatty acid (FA) biosynthesis in plant cells. Furthermore, their expression profiles correlate with those of core FA biosynthetic enzymes, with maximal expression occurring in seeds and coinciding with increased FA storage in the developing embryo. In vitro, these proteins are Fatty Acid-binding Proteins (FAP). FAP knockout A. thaliana plants exhibit elevated alpha-linolenic acid levels and marked reproductive defects, including aberrant seed formation. Notably, the FAP discovery defines the adaptive evolution of a stereospecific and catalytically ‘perfected’ enzyme⁶ from a non-enzymatic ancestor over a defined period of plant evolution.

The role of flavonoids in root-rhizosphere signalling: opportunities and challenges for improving plant-microbe interactions

The flavonoid pathway produces a diverse array of plant compounds with functions in UV protection, as antioxidants, pigments, auxin transport regulators, defence compounds against pathogens and during signalling in symbiosis. This review highlights some of the known function of flavonoids in the rhizosphere, in particular for the interaction of roots with microorganisms. Depending on their structure, flavonoids have been shown to stimulate or inhibit rhizobial nod gene expression, cause chemoattraction of rhizobia towards the root, inhibit root pathogens, stimulate mycorrhizal spore germination and hyphal branching, mediate allelopathic interactions between plants, affect quorum sensing, and chelate soil nutrients. Therefore, the manipulation of the flavonoid pathway to synthesize specifically certain products has been suggested as an avenue to improve root-rhizosphere interactions. Possible strategies to alter flavonoid exudation to the rhizosphere are discussed. Possible challenges in that endeavour include limited knowledge of the mechanisms that regulate flavonoid transport and exudation, unforeseen effects of altering parts of the flavonoid synthesis pathway on fluxes elsewhere in the pathway, spatial heterogeneity of flavonoid exudation along the root, as well as alteration of flavonoid products by microorganisms in the soil. In addition, the overlapping functions of many flavonoids as stimulators of functions in one organism and inhibitors of another suggests caution in attempts to manipulate flavonoid rhizosphere signals.

Plastids are major regulators of light signaling in Arabidopsis

We previously provided evidence that plastid signaling regulates the downstream components of a light signaling network and that this signal integration coordinates chloroplast biogenesis with both the light environment and development by regulating gene expression. We tested these ideas by analyzing light- and plastid-regulated transcriptomes in Arabidopsis (Arabidopsis thaliana). We found that the enrichment of Gene Ontology terms in these transcriptomes is consistent with the integration of light and plastid signaling (1) down-regulating photosynthesis and inducing both repair and stress tolerance in dysfunctional chloroplasts and (2) helping coordinate processes such as growth, the circadian rhythm, and stress responses with the degree of chloroplast function. We then tested whether factors that contribute to this signal integration are also regulated by light and plastid signals by characterizing T-DNA insertion alleles of genes that are regulated by light and plastid signaling and that encode proteins that are annotated as contributing to signaling, transcription, or no known function. We found that a high proportion of these mutant alleles induce chloroplast biogenesis during deetiolation. We quantified the expression of four photosynthesis-related genes in seven of these enhanced deetiolation (end) mutants and found that photosynthesis-related gene expression is attenuated. This attenuation is particularly striking for Photosystem II subunit S expression. We conclude that the integration of light and plastid signaling regulates a number of END genes that help optimize chloroplast function and that at least some END genes affect photosynthesis-related gene expression.

Phosphorylation of FAR-RED ELONGATED HYPOCOTYL1 is a key mechanism defining signaling dynamics of phytochrome A under red and far-red light in Arabidopsis

Emerging plants have to adapt to a high ratio of far-red light (FR)/red light (R) light in the canopy before they reach the R-enriched direct sunlight. Phytochrome A (phyA) is the single dominant photoreceptor in young Arabidopsis thaliana seedlings that initiates photomorphogenesis in response to a FR-enriched environment and transduces increasing R signals to early responsive genes. To date, how phyA differentially transmits FR and R signals to downstream genes remains obscure. Here, we present a phyA pathway in which FAR-RED ELONGATED HYPOCOTYL1 (FHY1), an essential partner of phyA, directly guides phyA to target gene promoters and coactivates transcription. Furthermore, we identified two phosphorylation sites on FHY1, Ser-39 and Thr-61, whose phosphorylation by phyA under R inhibits phyA signaling at each step of its pathway. Deregulation of FHY1 phosphorylation renders seedlings colorblind to FR and R. Finally, we show that the weaker phyA response resulting from FHY1 phosphorylation ensures the seedling deetiolation process in response to a R-enriched light condition. Collectively, our results reveal FHY1 phosphorylation as a key mechanism for FR/R spectrum-specific responses in plants and an essential event for plant adaption to changing light conditions in nature.

In planta production of the highly potent resveratrol analogue pterostilbene via stilbene synthase and O-methyltransferase co-expression

Resveratrol and related stilbenes are thought to play important roles in defence responses in several plant species and have also generated considerable interest as nutraceuticals owing to their diverse health-promoting properties. Pterostilbene, a 3,5-dimethylether derivative of resveratrol, possesses properties similar to its parent compound and, additionally, exhibits significantly higher fungicidal activity in vitro and superior pharmacokinetic properties in vivo. Recombinant enzyme studies carried out using a previously characterized O-methyltransferase sequence from Sorghum bicolor (SbOMT3) demonstrated its ability to catalyse the A ring-specific 3,5-bis-O-methylation of resveratrol, yielding pterostilbene. A binary vector was constructed for the constitutive co-expression of SbOMT3 with a stilbene synthase sequence from peanut (AhSTS3) and used for the generation of stably transformed tobacco and Arabidopsis plants, resulting in the accumulation of pterostilbene in both species. A reduced floral pigmentation phenotype observed in multiple tobacco transformants was further investigated by reversed-phase HPLC analysis, revealing substantial decreases in both dihydroquercetin-derived flavonoids and phenylpropanoid-conjugated polyamines in pterostilbene-producing SbOMT3/AhSTS3 events. These results demonstrate the potential utility of this strategy for the generation of pterostilbene-producing crops and also underscore the need for the development of additional approaches for minimizing concomitant reductions in key phenylpropanoid-derived metabolites.

Harvest-inducibility of the promoter of alfalfa S-adenosyl-L-methionine: trans-caffeoyl-CoA3-O-methyltransferase gene

A major limitation on the expression of some foreign proteins in transgenic plants is the toxic effect of such proteins on the host plant resulting in inhibition of normal growth and development. A solution to this problem is to control the expression of genes for such proteins by means of inducible promoters, as is frequently done in microbial systems. A cDNA clone was obtained from subtractive hybridization of non-harvested and harvested alfalfa leaf tissue, named hi12. The hi12 cDNA was identified as part of the S-adenosyl-L-methionine: trans-caffeoyl-CoA3-O-methyltransferase gene of alfalfa, a gene encoding an essential key enzyme in lignin synthesis. The hi12 gene was strongly induced by harvesting and wounding but not by heat shock. The promoter of the hi12 gene, isolated by genomic walking, contained several stress response cis-elements. Transgenic plants of tobacco and Medicago truncatula containing the GUS gene driven by the promoter showed GUS expression following harvesting, demonstrating the activity of these regulatory regions in other plant species.

Methyl eugenol: its occurrence, distribution, and role in nature, especially in relation to insect behavior and pollination

This review discusses the occurrence and distribution (within a plant) of methyl eugenol in different plant species (> 450) from 80 families spanning many plant orders, as well as various roles this chemical plays in nature, especially in the interactions between tephritid fruit flies and plants.

Flavonoids: biosynthesis, biological functions, and biotechnological applications

Flavonoids are widely distributed secondary metabolites with different metabolic functions in plants. The elucidation of the biosynthetic pathways, as well as their regulation by MYB, basic helix-loop-helix (bHLH), and WD40-type transcription factors, has allowed metabolic engineering of plants through the manipulation of the different final products with valuable applications. The present review describes the regulation of flavonoid biosynthesis, as well as the biological functions of flavonoids in plants, such as in defense against UV-B radiation and pathogen infection, nodulation, and pollen fertility. In addition, we discuss different strategies and achievements through the genetic engineering of flavonoid biosynthesis with implication in the industry and the combinatorial biosynthesis in microorganisms by the reconstruction of the pathway to obtain high amounts of specific compounds.

Defense mechanisms against herbivory in Picea: sequence evolution and expression regulation of gene family members in the phenylpropanoid pathway

Background

In trees, a substantial amount of carbon is directed towards production of phenolics for development and defense. This metabolic pathway is also a major factor in resistance to insect pathogens in spruce. In such gene families, environmental stimuli may have an important effect on the evolutionary fate of duplicated genes, and different expression patterns may indicate functional diversification.

Results

Gene families in spruce (Picea) have expanded to superfamilies, including O-methyltransferases, cytochrome-P450, and dirigents/classIII-peroxidases. Neo-functionalization of superfamily members from different clades is reflected in expression diversification. Genetical genomics can provide new insights into the genetic basis and evolution of insect resistance in plants. Adopting this approach, we merged genotype data (252 SNPs in a segregating pedigree), gene expression levels (for 428 phenylpropanoid-related genes) and measures of susceptibility to Pissodes stobi, using a partial-diallel crossing-design with white spruce (Picea glauca). Thirty-eight expressed phenylpropanoid-related genes co-segregated with weevil susceptibility, indicating either causative or reactive effects of these genes to weevil resistance. We identified eight regulatory genomic regions with extensive overlap of quantitative trait loci from susceptibility and growth phenotypes (pQTLs) and expression QTL (eQTL) hotspots. In particular, SNPs within two different CCoAOMT loci regulate phenotypic variation from a common set of 24 genes and three resistance traits.

Conclusions

Pest resistance was associated with individual candidate genes as well as with trans-regulatory hotspots along the spruce genome. Our results showed that specific genes within the phenylpropanoid pathway have been duplicated and diversified in the conifer in a process fundamentally different from short-lived angiosperm species. These findings add to the information about the role of the phenylpropanoid pathway in the evolution of plant defense mechanisms against insect pests and provide substantial potential for the functional characterization of several not yet resolved alternative pathways in plant defenses.

Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery

BACKGROUND

Giant freshwater prawn (Macrobrachium rosenbergii or GFP), is the most economically important freshwater crustacean species. However, as little is known about its genome, 454 pyrosequencing of cDNA was undertaken to characterise its transcriptome and identify genes important for growth.

METHODOLOGY AND PRINCIPAL FINDINGS

A collection of 787,731 sequence reads (244.37 Mb) obtained from 454 pyrosequencing analysis of cDNA prepared from muscle, ovary and testis tissues taken from 18 adult prawns was assembled into 123,534 expressed sequence tags (ESTs). Of these, 46% of the 8,411 contigs and 19% of 115,123 singletons possessed high similarity to sequences in the GenBank non-redundant database, with most significant (E value < 1e(-5)) contig (80%) and singleton (84%) matches occurring with crustacean and insect sequences. KEGG analysis of the contig open reading frames identified putative members of several biological pathways potentially important for growth. The top InterProScan domains detected included RNA recognition motifs, serine/threonine-protein kinase-like domains, actin-like families, and zinc finger domains. Transcripts derived from genes such as actin, myosin heavy and light chain, tropomyosin and troponin with fundamental roles in muscle development and construction were abundant. Amongst the contigs, 834 single nucleotide polymorphisms, 1198 indels and 658 simple sequence repeats motifs were also identified.

CONCLUSIONS

The M. rosenbergii transcriptome data reported here should provide an invaluable resource for improving our understanding of this species' genome structure and biology. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs.

Diadenosine polyphosphates (Ap3A and Ap4A) behave as alarmones triggering the synthesis of enzymes of the phenylpropanoid pathway in Arabidopsis thaliana

It is known that cells under stress accumulate various dinucleoside polyphosphates, compounds suggested to function as alarmones. In plants, the phenylpropanoid pathways yield metabolites protecting these organisms against various types of stress. Observations reported in this communication link these two phenomena and provide an example of a metabolic "addressee" for an "alarm" signaled by diadenosine triphosphate (Ap3A) or diadenosine tetraphosphate (Ap4A). In response to added Ap3A or Ap4A, seedlings of Arabidopsis thaliana incubated in full nutrition medium increased both the expression of the genes for and the specific activity of phenylalanine ammonia-lyase and 4-coumarate:coenzyme A ligase, enzymes that control the beginning of the phenylpropanoid pathway. Neither adenine mononucleotides (AMP, ADP or ATP) nor adenosine evoked such effects. Reactions catalyzed in vitro by these enzymes were not affected by Ap3A or Ap4A.

Cold-field fruit extracts exert different antioxidant and antiproliferative activities in vitro

Consumption of plant phenolics in the daily diet has been recognised as lowering the risk of aging-associated diseases. A total of 11 cold-field fruits in China were evaluated for total contents of phenolics, flavonoids and anthocyanins, and antioxidant and antiproliferation activities. Total phenolic contents of the fruits extracts had a positive correlation with antioxidant activity (R2>0.7112). Among the 11 fruits, the extracts of raspberry had the highest capacities for scavenging DPPH (EC50 25.6±0.51μM TE/g FW) and ABTS+ (EC50 63.6±1.67μM TE/g FW). Proliferation of HepG2 and HT-29 cells was significantly inhibited in a dose-dependent pattern after exposure to the fruit extracts, among which lingonberry and rowanberry exhibited the highest antiproliferative activities. These results provide new knowledge on health functions of fruits and the fruits with high antioxidant contents are recommended for potential health benefits.

Transcriptome profiling and insilico analysis of Gynostemma pentaphyllum using a next generation sequencer

Gynosaponins (Gypenosides) are major phyto-chemicals in Gynostemma pentaphyllum (Thunb.), with similarities to the ginsenosides present in Panax ginseng. Gynosaponins are classified as terpenoid compounds. In G. pentaphyllum, 25% of the total gynosaponins are similar to ginsenosides. In this study, we analyzed the transcriptional levels of the G. pentaphyllum genome to identify secondary metabolite genes. The complete transcriptomes for the roots and leaves were obtained using a GS-FLX pyro-sequencer. In total, we obtained 265,340 and all reads were well annotated according to biological databases. Using insilico analysis, 84% of sequence were well annotated and we obtained most of the secondary metabolite genes that represent mono-, di-, tri- and sesquiterpenoids. From our EST, most of the terpenoid genes were noted, among those few similar genes were studied in P. ginseng and these transcripts will help to characterize more triterpenoid genes in G. pentaphyllum. Also help to compare P. ginseng and G. pentaphyllum at transcriptome level.

Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry

The incompatible pathosystem between resistant cotton (Gossypium barbadense cv. 7124) and Verticillium dahliae strain V991 was used to study the cotton transcriptome changes after pathogen inoculation by RNA-Seq. Of 32,774 genes detected by mapping the tags to assembly cotton contigs, 3442 defence-responsive genes were identified. Gene cluster analyses and functional assignments of differentially expressed genes indicated a significant transcriptional complexity. Quantitative real-time PCR (qPCR) was performed on selected genes with different expression levels and functional assignments to demonstrate the utility of RNA-Seq for gene expression profiles during the cotton defence response. Detailed elucidation of responses of leucine-rich repeat receptor-like kinases (LRR-RLKs), phytohormone signalling-related genes, and transcription factors described the interplay of signals that allowed the plant to fine-tune defence responses. On the basis of global gene regulation of phenylpropanoid metabolism-related genes, phenylpropanoid metabolism was deduced to be involved in the cotton defence response. A closer look at the expression of these genes, enzyme activity, and lignin levels revealed differences between resistant and susceptible cotton plants. Both types of plants showed an increased level of expression of lignin synthesis-related genes and increased phenylalanine-ammonia lyase (PAL) and peroxidase (POD) enzyme activity after inoculation with V. dahliae, but the increase was greater and faster in the resistant line. Histochemical analysis of lignin revealed that the resistant cotton not only retains its vascular structure, but also accumulates high levels of lignin. Furthermore, quantitative analysis demonstrated increased lignification and cross-linking of lignin in resistant cotton stems. Overall, a critical role for lignin was believed to contribute to the resistance of cotton to disease.

Transcript Accumulation Dynamics of Phenylpropanoid Pathway Genes in the Maturing Xylem and Phloem of Picea abies during Latewood Formation

In temperate regions, latewood is produced when cambial activity declines with the approach of autumnal dormancy. The understanding of the temporal (cambium activity vs dormancy) and spatial (phloem, cambial region, maturing xylem) regulation of key genes involved in the phenylpropanoid pathway during latewood formation represents a crucial step towards providing new insights into the molecular basis of xylogenesis. In this study, the temporal pattern of transcript accumulation of 12 phenylpropanoid genes (PAL1, C4H3/5, C4H4, 4CL3, 4CL4, HCT1, C3H3, CCoAOMT1, COMT2, COMT5, CCR2) was analyzed in maturing xylem and phloem of Picea abies during latewood formation. Quantitative reverse transcription-polymerase chain reaction analyses revealed a well-defined RNA accumulation pattern of genes involved in the phenylpropanoid pathway during latewood formation. Differences in the RNA accumulation patterns were detected between the different tissue types analyzed. The results obtained here demonstrated that the molecular processes involved in monolignol biosynthesis are not restricted to the cambial activity timeframe but continued after the end of cambium cell proliferation. Furthermore, since it has been shown that lignification of maturing xylem takes place in late autumn, we argue on the basis of our data that phloem could play a key role in the monolignol biosynthesis process.

The imminent role of protein engineering in synthetic biology

Protein engineering has for decades been a powerful tool in biotechnology for generating vast numbers of useful enzymes for industrial applications. Today, protein engineering has a crucial role in advancing the emerging field of synthetic biology, where metabolic engineering efforts alone are insufficient to maximize the full potential of synthetic biology. This article reviews the advancements in protein engineering techniques for improving biocatalytic properties to optimize engineered pathways in host systems, which are instrumental to achieve high titer production of target molecules. We also discuss the specific means by which protein engineering has improved metabolic engineering efforts and provide our assessment on its potential to continue to advance biology engineering as a whole.

Genome-wide comparison of two poplar genotypes with different growth rates

The ecologically dominant and economically important genus Populus, with its available full genome sequence, has become an ideal woody species for genomic study. Rapid growth is one of the primary advantageous features of Populus, and extensive physiological research has been carried out on the growth of Populus throughout the growing period among different clones. However, the molecular information related to the mechanisms of rapid growth is rather limited. In this study, an Affymetrix poplar genome array was employed to analyze the transcriptomic changes from the pre-growth to the fast-growth phase in two poplar clones (P.deltoides × P.nigra, DN2, and P.nigra × (P.deltoides × P. nigra), NE19) with different growth rates. A total of 1,695 differently expressed genes were identified between two time points in NE19 and DN2 (two-way ANOVA, P < 0.01 and fold change ≥2). Except for genes changing in common for both clones, many transcripts were regulated specifically in one genotype. After functional analysis of the differentially expressed genes, distinct biological strategies seemed to be utilized by the two genotypes to accommodate their fast-growth phase. The faster-growing clone NE19, which has a higher photosynthetic rate and larger total leaf area, emphasized growth-related primary metabolism. However, the slower-growing DN2 tended to have more up-regulated genes involved in defense-related secondary metabolism and stress response. Emphasis of such divergent biological processes in two clones may explain their significant growth differences during the fast-growth phase.

Metabolic engineering of flavonoids in plants and microorganisms

Over 9,000 flavonoid compounds have been found in various plants, comprising one of the largest families of natural products. Flavonoids are an essential factor in plant interactions with the environment, often serving as the first line of defense against UV irradiation and pathogen attacks. Flavonoids are also major nutritional compounds in foods and beverages, with demonstrated health benefits. Some flavonoids are potent antioxidants, and specific flavonoid compounds are beneficial in many physiological and pharmacological processes. Therefore, engineering of flavonoid biosynthesis in plants or in microorganisms has significant scientific and economical importance. Construction of biosynthetic pathways in heterologous systems offers promising results for large-scale flavonoid production by fermentation or bioconversion. Genomics and metabolomics now offer unprecedented tools for detailed understanding of the engineered transgenic organism and for developing novel technologies to further increase flavonoid production yields. We summarize some of the recent metabolic engineering strategies in plants and microorganisms, with a focus on applications of metabolic flux analysis. We are confident that these engineering approaches will lead to successful industrial flavonoid production in the near future.

Stimulation of acidic reduction of nitrite to nitric oxide by soybean phenolics: possible relevance to gastrointestinal host defense

This study aimed to evaluate the potential of soybean-promoted acidic nitrite reduction and to correlate this activity with the content of phenolics and with the bactericidal activity against Escherichia coli O157:H7. Extracts of embrionary axes and cotyledons enriched in phenolics increased •NO formation at acidic pH at values that were 7.1 and 4.5 times higher, respectively, when compared to the reduction of the nonenriched extracts. Among the various phenolics accumulated in the soybean extracts, five stimulated nitrite reduction in the following decreasing order of potency: epicatechin gallate, chlorogenic acid, caffeic acid, galic acid and p-coumaric acid. Extracts of embrionary axes presented higher contents of epicatechin gallate and caffeic acid, compared to that of cotyledons, indicating a positive correlation between activity of the extracts and content of phenolics with regard to nitrite reducing activity. Soybean extracts enriched in phenolics interacted synergistically with acidified nitrite to prevent E. coli O157:H7 growth. The results suggest that soybean phenolics may interfere with the metabolism of •NO in an acidic environment by accelerating the reduction of nitrite, with a potential antimicrobial effect in the stomach.

Identification of reference genes suitable for qRT-PCR in grapevine and application for the study of the expression of genes involved in pterostilbene synthesis

The recent publication of the grapevine genome sequence facilitates the use of qRT-PCR to study gene expression changes. For this approach, reference genes are commonly used to normalize data and their stability of expression should be systematically validated. Among grapevine defenses is the production of the antimicrobial stilbenic phytoalexins, notably the highly fungitoxic pterostilbene, which plays a crucial role in grapevine interaction with Plasmopara viticola and Botrytis cinerea. As a resveratrol O-methyltransferase (ROMT) gene involved in pterostilbene synthesis was recently identified, we investigated the accumulation of the corresponding transcripts to those of two other stilbene biosynthesis related genes phenylalanine ammonia lyase (PAL) and stilbene synthase (STS) in response to pathogen infection. Using three computer-based statistical methods and C(t) values or LRE method generated values as input data, we have first identified two reference genes (VATP16 and 60SRP) suitable for normalization of qPCR expression data obtained in grapevine leaves and berries infected by P. viticola and B. cinerea, respectively. Next, we have highlighted that the expression of ROMT is induced in P. viticola-infected leaves and also in B. cinerea-infected berries, confirming the involvement of pterostilbene in grapevine defenses.

Structural and biochemical elucidation of mechanism for decarboxylative condensation of beta-keto acid by curcumin synthase

The typical reaction catalyzed by type III polyketide synthases (PKSs) is a decarboxylative condensation between acyl-CoA (starter substrate) and malonyl-CoA (extender substrate). In contrast, curcumin synthase 1 (CURS1), which catalyzes curcumin synthesis by condensing feruloyl-CoA with a diketide-CoA, uses a β-keto acid (which is derived from diketide-CoA) as an extender substrate. Here, we determined the crystal structure of CURS1 at 2.32 Å resolution. The overall structure of CURS1 was very similar to the reported structures of type III PKSs and exhibited the αβαβα fold. However, CURS1 had a unique hydrophobic cavity in the CoA-binding tunnel. Replacement of Gly-211 with Phe greatly reduced the enzyme activity. The crystal structure of the G211F mutant (at 2.5 Å resolution) revealed that the side chain of Phe-211 occupied the hydrophobic cavity. Biochemical studies demonstrated that CURS1 catalyzes the decarboxylative condensation of a β-keto acid using a mechanism identical to that for normal decarboxylative condensation of malonyl-CoA by typical type III PKSs. Furthermore, the extender substrate specificity of CURS1 suggested that hydrophobic interaction between CURS1 and a β-keto acid may be important for CURS1 to use an extender substrate lacking the CoA moiety. From these results and a modeling study on substrate binding, we concluded that the hydrophobic cavity is responsible for the hydrophobic interaction between CURS1 and a β-keto acid, and this hydrophobic interaction enables the β-keto acid moiety to access the catalytic center of CURS1 efficiently.

Identification of reference genes suitable for qRT-PCR in grapevine and application for the study of the expression of genes involved in pterostilbene synthesis

The recent publication of the grapevine genome sequence facilitates the use of qRT-PCR to study gene expression changes. For this approach, reference genes are commonly used to normalize data and their stability of expression should be systematically validated. Among grapevine defenses is the production of the antimicrobial stilbenic phytoalexins, notably the highly fungitoxic pterostilbene, which plays a crucial role in grapevine interaction with Plasmopara viticola and Botrytis cinerea. As a resveratrol O-methyltransferase (ROMT) gene involved in pterostilbene synthesis was recently identified, we investigated the accumulation of the corresponding transcripts to those of two other stilbene biosynthesis related genes phenylalanine ammonia lyase (PAL) and stilbene synthase (STS) in response to pathogen infection. Using three computer-based statistical methods and C(t) values or LRE method generated values as input data, we have first identified two reference genes (VATP16 and 60SRP) suitable for normalization of qPCR expression data obtained in grapevine leaves and berries infected by P. viticola and B. cinerea, respectively. Next, we have highlighted that the expression of ROMT is induced in P. viticola-infected leaves and also in B. cinerea-infected berries, confirming the involvement of pterostilbene in grapevine defenses.

Functional analysis of the Asian soybean rust resistance pathway mediated by Rpp2

Asian soybean rust is an aggressive foliar disease caused by the obligate biotrophic fungus Phakopsora pachyrhizi. On susceptible plants, the pathogen penetrates and colonizes leaf tissue, resulting in the formation of necrotic lesions and the development of numerous uredinia. The soybean Rpp2 gene confers resistance to specific isolates of P. pachyrhizi. Rpp2-mediated resistance limits the growth of the pathogen and is characterized by the formation of reddish-brown lesions and few uredinia. Using virus-induced gene silencing, we screened 140 candidate genes to identify those that play a role in Rpp2 resistance toward P. pachyrhizi. Candidate genes included putative orthologs to known defense-signaling genes, transcription factors, and genes previously found to be upregulated during the Rpp2 resistance response. We identified 11 genes that compromised Rpp2-mediated resistance when silenced, including GmEDS1, GmNPR1, GmPAD4, GmPAL1, five predicted transcription factors, an O-methyl transferase, and a cytochrome P450 monooxygenase. Together, our results provide new insight into the signaling and biochemical pathways required for resistance against P. pachyrhizi.

The Arabidopsis PAP1 transcription factor plays an important role in the enrichment of phenolic acids in Salvia miltiorrhiza

Phenolic acids are health-promoting but low content secondary metabolites in Salvia miltiorrhiza. Here, the Arabidopsis transcription factor Production of Anthocyanin Pigment 1 (AtPAP1) was expressed in S. miltiorrhiza and improved the antioxidant capacity in transgenic plants up to 3-fold. Salvianolic acid B (Sal B) biosynthesis was strongly induced (10-fold higher) in 1 month old transgenic plantlets, a growth stage not normally characterized by significant levels of phenolic acids. This high-Sal B phenotype was stable in roots during vegetative growth, with tissues accumulating approximately 73.27 mg/g of dry weight. Total phenolics, total flavonoids, anthocyanin, and lignin were also significantly enhanced. Consistent with these biological and phytochemical changes, expression of phenolic acid biosynthetic genes was stimulated. Our results demonstrate that AtPAP1 has an additional, previously unknown, role as a transcriptional activator of phenolic acid biosynthesis in S. miltiorrhiza. The results provide a promising strategy for engineering phenolics production in economically significant medicinal plants.