Variations on a theme: synthesis and modification of plant benzoic acids

Mechanistic insight into the impact of polystyrene microparticle on submerged plant during asexual propagules germination to seedling: Internalization in functional organs and alterations of physiological phenotypes

Asexual reproduction is one of the most important propagations in aquatic plants. However, there is a lack of information about the growth-limiting mechanisms induced by microplastics on the submerged plant during asexual propagule germination to seedling. Hence, we investigated the effects of two sizes (2 µm, 0.2 µm) and three concentrations (0.5 mg/L, 5 mg/L, and 50 mg/L) of polystyrene microplastics (PSMPs) on Potamogeton crispus turion germination and seedling growth. Both PSMPs sizes were found in P. crispus seedling tissues. Metabolic profile alterations were observed in leaves, particularly affecting secondary metabolic pathways and ATP-binding cassette transporters. Metal elements are indispensable cofactors for photosynthesis; however, alterations in the metabolic profile led to varying degrees of reduced concentrations in magnesium, iron, copper, and zinc within P. crispus. Therefore, the maximum quantum yield of photosystem II significantly decreased in all concentrations with 0.2 µm-PSMPs, and at 50 mg/L with 2 µm-PSMPs. These findings reveal that internalization of microplastics, nutrient absorption inhibition, and metabolic changes contribute to the negative impact on P. crispus seedlings.

Deciphering Aphanomyces euteiches-pea-biocontrol bacterium interactions through untargeted metabolomics

Aphanomyces euteiches causes root rot in pea, leading to significant yield losses. However, the metabolites involved in this pathosystem have not been thoroughly studied. This study aimed to fill this gap and explore mechanisms of bacterial suppression of A. euteiches via untargeted metabolomics using pea grown in a controlled environment. Chemical isotope labeling (CIL), followed by liquid chromatography-mass spectrometry (LC-MS), was used for metabolite separation and detection. Univariate and multivariate analyses showed clear separation of metabolites from pathogen-treated pea roots and roots from other treatments. A three-tier approach positively or putatively identified 5249 peak pairs or metabolites. Of these, 403 were positively identified in tier 1; 940 were putatively identified with high confidence in tier 2. There were substantial changes in amino acid pool, and fatty acid and phenylpropanoid pathway products. More metabolites, including salicylic and jasmonic acids, were upregulated than downregulated in A. euteiches-infected roots. 1-aminocyclopropane-1-carboxylic acid and 12-oxophytodienoic acid were upregulated in A. euteiches + bacterium-treated roots compared to A. euteiches-infected roots. A great number of metabolites were up- or down-regulated in response to A. euteiches infection compared with the control and A. euteiches + bacterium-treated plants. The results of this study could facilitate improved disease management.

Biochemical Pathways of Salicylic Acid Derived from l-Phenylalanine in Plants with Different Basal SA Levels

As a plant hormone, salicylic acid (SA) has diverse regulatory roles in plant growth and stress resistance. Although SA is widely found in plants, there is substantial variation in basal SA among species. Tea plant is an economically important crop containing high contents of SA whose synthesis pathway remains unidentified. The phenylalanine ammonia-lyase (PAL) pathway is responsible for basal SA synthesis in plants. In this study, isotopic tracing and enzymatic assay experiments were used to verify the SA synthesis pathway in tea plants and evaluate the variation in phenylalanine-derived SA formation among 11 plant species with different levels of SA. The results indicated that SA could be synthesized via PAL in tea plants and conversion efficiency from benzoic acid to SA might account for variation in basal SA among plant species. This research lays the foundation for an improved understanding of the molecular regulatory mechanism for SA biosynthesis.

Pour some sugar on me: The diverse functions of phenylpropanoid glycosylation

The phenylpropanoid metabolism is the source of a vast array of specialized metabolites that play diverse functions in plant growth and development and contribute to all aspects of plant interactions with their surrounding environment. These compounds protect plants from damaging ultraviolet radiation and reactive oxygen species, provide mechanical support for the plants to stand upright, and mediate plant-plant and plant-microorganism communications. The enormous metabolic diversity of phenylpropanoids is further expanded by chemical modifications known as "decorative reactions", including hydroxylation, methylation, glycosylation, and acylation. Among these modifications, glycosylation is the major driving force of phenylpropanoid structural diversification, also contributing to the expansion of their properties. Phenylpropanoid glycosylation is catalyzed by regioselective uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs), whereas glycosyl hydrolases known as β-glucosidases are the major players in deglycosylation. In this article, we review how the glycosylation process affects key physicochemical properties of phenylpropanoids, such as molecular stability and solubility, as well as metabolite compartmentalization/storage and biological activity/toxicity. We also summarize the recent knowledge on the functional implications of glycosylation of different classes of phenylpropanoid compounds. A balance of glycosylation/deglycosylation might represent an essential molecular mechanism to regulate phenylpropanoid homeostasis, allowing plants to dynamically respond to diverse environmental signals.

Effects of Signal Peptide and Chaperone Co-Expression on Heterologous Protein Production in Escherichia coli

Various host systems have been employed to increase the yield of recombinant proteins. However, some recombinant proteins were successfully produced at high yields but with no functional activities. To achieve both high protein yield and high activities, molecular biological strategies have been continuously developed. This work describes the effect of signal peptide (SP) and co-expression of molecular chaperones on the production of active recombinant protein in Escherichia coli. Extracellular enzymes from Bacillus subtilis, including β-1,4-xylanase, β-1,4-glucanase, and β-mannanase constructed with and without their signal peptides and intracellular enzymes from Pseudomonas stutzeri ST201, including benzoylformate decarboxylase (BFDC), benzaldehyde dehydrogenase (BADH), and d-phenylglycine aminotransferase (d-PhgAT) were cloned and overexpressed in E. coli BL21(DE3). Co-expression of molecular chaperones with all enzymes studied was also investigated. Yields of β-1,4-xylanase (Xyn), β-1,4-glucanase (Cel), and β-mannanase (Man), when constructed without their N-terminal signal peptides, increased 1112.61-, 1.75-, and 1.12-fold, respectively, compared to those of spXyn, spCel, and spMan, when constructed with their signal peptides. For the natural intracellular enzymes, the chaperones, GroEL-GroES complex, increased yields of active BFDC, BADH, and d-PhgAT, up to 1.31-, 4.94- and 37.93-fold, respectively, and also increased yields of Man and Xyn up to 1.53- and 3.46-fold, respectively, while other chaperones including DnaK-DnaJ-GrpE and Trigger factor (Tf) showed variable effects with these enzymes. This study successfully cloned and overexpressed extracellular and intracellular enzymes in E. coli BL21(DE3). When the signal peptide regions of the secretory enzymes were removed, yields of active enzymes were higher than those with intact signal peptides. In addition, a higher yield of active enzymes was obtained, in general, when these enzymes were co-expressed with appropriate chaperones. Therefore, E. coli can produce cytoplasmic and secretory enzymes effectively if only the enzyme coding sequence without its signal peptide is used and appropriate chaperones are co-expressed to assist in correct folding.

Variable lignin structure revealed in Populus leaves

Lignin has long been a trait of interest, especially in bioenergy feedstocks such as Populus. While the stem lignin of Populus is well studied, foliar lignin has received significantly less consideration. To this end, leaves from 11 field grown, natural variant Populus trichocarpa genotypes were investigated by NMR, FTIR, and GC-MS. Five of these genotypes were sufficiently irrigated, and the other six genotypes were irrigated at a reduced rate (59% of the potential evapotranspiration for the site) to induce drought treatment. Analysis by HSQC NMR revealed highly variable lignin structure among the samples, especially for the syringyl/guaiacyl (S/G) ratio, which ranged from 0.52-11.9. Appreciable levels of a condensed syringyl lignin structure were observed in most samples. The same genotype subjected to different treatments exhibited similar levels of condensed syringyl lignin, suggesting this was not a response to stress. A cross peak of δ_C/δ_H 74.6/5.03, consistent with the erythro form of the β-O-4 linkage, was observed in genotypes where significant syringyl units were present. Principle component analysis revealed that FTIR absorbances associated with syringyl units (830 cm^-1, 1317 cm^-1) greatly contributed to variability between samples. Additionally, the ratio of 830/1230 cm^-1 peak intensities were reasonably correlated (p-value < 0.05) with the S/G ratio determined by NMR. Analysis by GC-MS revealed significant variability of secondary metabolites such as tremuloidin, trichocarpin, and salicortin. Additionally, salicin derivatives were found to be well correlated with NMR results, which has been previously hypothesized. These results highlight previously unexplored nuance and variability associated with foliage tissue of poplar.

Potentiating Biosynthesis of Alkaloids and Polyphenolic Substances in Catharanthus roseus Plant Using ĸ-Carrageenan

Catharanthus roseus is a medicinal plant that produces indole alkaloids, which are utilized in anticancer therapy. Vinblastine and vincristine, two commercially important antineoplastic alkaloids, are mostly found in the leaves of Catharanthus roseus. ĸ-carrageenan has been proven as plant growth promoting substance for a number of medicinal and agricultural plants. Considering the importance of ĸ-carrageenan as a promoter of plant growth and phytochemical constituents, especially alkaloids production in Catharanthus roseus, an experiment was carried out to explore the effect of ĸ-carrageenan on the plant growth, phytochemicals content, pigments content, and production of antitumor alkaloids in Catharanthus roseus after planting. Foliar application of ĸ-carrageenan (at 0, 400, 600 and 800 ppm) significantly improved the performance of Catharanthus roseus. Phytochemical analysis involved determining the amount of total phenolics (TP), flavonoids (F), free amino acids (FAA), alkaloids (TAC) and pigments contents by spectrophotometer, minerals by ICP, amino acids, phenolic compounds and alkaloids (Vincamine, Catharanthine, Vincracine (Vincristine), and vinblastine) analysis uses HPLC. The results indicated that all examined ĸ-carrageenan treatments led to a significant (p ≤ 0.05) increase in growth parameters compared to the untreated plants. Phytochemical examination indicates that the spray of ĸ-carrageenan at 800 mg L^-1 increased the yield of alkaloids (Vincamine, Catharanthine and Vincracine (Vincristine)) by 41.85 μg/g DW, total phenolic compounds by 3948.6 μg gallic/g FW, the content of flavonoids 951.3 μg quercetin /g FW and carotenoids content 32.97 mg/g FW as compared to the control. An amount of 400 ppm ĸ-carrageenan treatment gave the best contents of FAA, Chl a, Chl b and anthocyanin. The element content of K, Ca, Cu, Zn and Se increased by treatments. Amino acids constituents and phenolics compounds contents were altered by ĸ-carrageenan.

Virtual and In Vitro Screening of Natural Products Identifies Indole and Benzene Derivatives as Inhibitors of SARS-CoV-2 Main Protease (Mpro)

The rapid spread of the coronavirus disease 2019 (COVID-19) resulted in serious health, social, and economic consequences. While the development of effective vaccines substantially reduced the severity of symptoms and the associated deaths, we still urgently need effective drugs to further reduce the number of casualties associated with SARS-CoV-2 infections. Machine learning methods both improved and sped up all the different stages of the drug discovery processes by performing complex analyses with enormous datasets. Natural products (NPs) have been used for treating diseases and infections for thousands of years and represent a valuable resource for drug discovery when combined with the current computation advancements. Here, a dataset of 406,747 unique NPs was screened against the SARS-CoV-2 main protease (M^pro) crystal structure (6lu7) using a combination of ligand- and structural-based virtual screening. Based on 1) the predicted binding affinities of the NPs to the M^pro, 2) the types and number of interactions with the M^pro amino acids that are critical for its function, and 3) the desirable pharmacokinetic properties of the NPs, we identified the top 20 candidates that could potentially inhibit the M^pro protease function. A total of 7 of the 20 top candidates were subjected to in vitro protease inhibition assay and 4 of them (4/7; 57%), including two beta carbolines, one N-alkyl indole, and one Benzoic acid ester, had significant inhibitory activity against M^pro protease. These four NPs could be developed further for the treatment of COVID-19 symptoms.

Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.

Multiomics analysis reveals the mechanisms underlying the different floral colors and fragrances of Rosa hybrida cultivars

The color and fragrance of rose flowers affect their commercial value. However, several rose varieties with new floral colors developed by the bud mutation method lost their fragrance during the breeding process, raising the question: Is there a relationship between floral color and aroma traits? Rose cultivar 'Yellow Island' (YI) with intensely aroma and yellow petals, while its bud mutant 'Past Feeling' (PF) with light aroma and pink petals mixing some yellow, two cultivars were used to explore this question using multiomics approaches. We investigated the genomic polymorphisms between PF and YI by whole-genome resequencing. 71 differentially abundant metabolites and 155 related differentially expressed genes identified in petals between PF and YI. From this, we constructed a model of metabolic changes affecting floral color and fragrance integrating shikimate, terpenoid, carotenoid, and green leaf volatile metabolites and predicted the associated key genes and transcription factors. This study provides a reference for understanding the molecular mechanism of variation in rose floral color and aroma traits.

Machine learning enables prediction of metabolic system evolution in bacteria

Evolution prediction is a long-standing goal in evolutionary biology, with potential impacts on strategic pathogen control, genome engineering, and synthetic biology. While laboratory evolution studies have shown the predictability of short-term and sequence-level evolution, that of long-term and system-level evolution has not been systematically examined. Here, we show that the gene content evolution of metabolic systems is generally predictable by applying ancestral gene content reconstruction and machine learning techniques to ~3000 bacterial genomes. Our framework, Evodictor, successfully predicted gene gain and loss evolution at the branches of the reference phylogenetic tree, suggesting that evolutionary pressures and constraints on metabolic systems are universally shared. Investigation of pathway architectures and meta-analysis of metagenomic datasets confirmed that these evolutionary patterns have physiological and ecological bases as functional dependencies among metabolic reactions and bacterial habitat changes. Last, pan-genomic analysis of intraspecies gene content variations proved that even "ongoing" evolution in extant bacterial species is predictable in our framework.

Siloxane-containing derivatives of benzoic acid: chemical transformation of the carboxyl group

This research presents a scalable method for chemical transformation of Si-containing derivatives of benzoic acid to a wide range of corresponding esters, thioesters, amides, etc. Some of them form HOF-like structures in the crystalline state.

Unraveling the metabolic effects of benzophenone-3 on the endosymbiotic dinoflagellate Cladocopium goreaui

As a well-known pseudo-persistent environmental pollutant, oxybenzone (BP-3) and its related organic ultraviolet (UV) filters have been verified to directly contribute to the increasing mortality rate of coral reefs. Previous studies have revealed the potential role of symbiotic Symbiodiniaceae in protecting corals from the toxic effects of UV filters. However, the detailed protection mechanism(s) have not been explained. Here, the impacts of BP-3 on the symbiotic Symbiodiniaceae Cladocopium goreaui were explored. C. goreaui cells exhibited distinct cell growth at different BP-3 doses, with increasing growth at the lower concentration (2 mg L^-1) and rapid death at a higher concentration (20 mg L^-1). Furthermore, C. goreaui cells showed a significant BP-3 uptake at the lower BP-3 concentration. BP-3 absorbing cells exhibited elevated photosynthetic efficiency, and decreased cellular carbon and nitrogen contents. Besides, the derivatives of BP-3 and aromatic amino acid metabolism highly responded to BP-3 absorption and biodegradation. Our physiological and metabolic results reveal that the symbiotic Symbiodiniaceae could resist the toxicity of a range of BP-3 through promoting cell division, photosynthesis, and reprogramming amino acid metabolism. This study provides novel insights into the influences of organic UV filters to coral reef ecosystems, which urgently needs increasing attention and management.

Microbial synthesis of 4-hydroxybenzoic acid from renewable feedstocks

4-Hydroxybenzoic acid (4HBA) and its esterified forms can be used as preservatives in the pharmaceutical and food industries. Here, we reported the establishment of a coenzyme-A (CoA) free multi-enzyme cascade in Escherichia coli to utilize biobased _L-tyrosine for efficient synthesis of 4HBA. The multi-enzyme cascade contains _L-amino acid deaminase from Proteus mirabilis, hydroxymandelate synthase from Amycolatopsis orientalis, (S)-mandelate dehydrogenase and benzoylformate decarboxylase from Pseudomonas putida, and aldehyde dehydrogenase from Saccharomyces cerevisiae. The whole-cell biocatalysis afforded the synthesis of 128 ± 1 mM of 4HBA (17.7 ± 0.1 g/L) from 150 mM _L-tyrosine with > 85% conversion within 96 h. In addition, the artificial enzymatic cascade also allowed the synthesis of benzoic acid from 100 mM _L-phenylalanine with a conversion ∼ 90%. In summary, our research offers a sustainable alternative for synthesizing 4HBA and benzoic acid from renewable feedstocks.

Epichloë gansuensis Increases the Tolerance of Achnatherum inebrians to Low-P Stress by Modulating Amino Acids Metabolism and Phosphorus Utilization Efficiency

In the long-term evolutionary process, Achnatherum inebrians and seed-borne endophytic fungi, Epichloë gansuensis, formed a mutually beneficial symbiosis relationship, and Epichloë gansuensis has an important biological role in improving the tolerance of host grasses to abiotic stress. In this work, we first assessed the effects of Epichloë gansuensis on dry weight, the content of C, N, P and metal ions, and metabolic pathway of amino acids, and phosphorus utilization efficiency (PUE) of Achnatherum inebrians at low P stress. Our results showed that the dry weights, the content of alanine, arginine, aspartic acid, glycine, glutamine, glutamic acid, L-asparagine, lysine, phenylalanine, proline, serine, threonine, and tryptophan were higher in leaves of Epichloë gansuensis-infected (E+) Achnatherum inebrians than Epichloë gansuensis-uninfected (E−) Achnatherum inebrians at low P stress. Further, Epichloë gansuensis increased C content of roots compared to the root of E− plant at 0.01 mM P and 0.5 mM P; Epichloëgansuensis increased K content of leaves compared to the leaf of E− plant at 0.01 mM P and 0.5 mM P. Epichloëgansuensis reduced Ca content of roots compared to the root of E− plant at 0.01 mM P and 0.5 mM P; Epichloë gansuensis reduced the content of Mg and Fe in leaves compared to the leaf of E− plant at 0.01 mM P and 0.5 mM P. In addition, at low P stress, Epichloë gansuensis most probably influenced aspartate and glutamate metabolism; valine, leucine, and isoleucine biosynthesis in leaves; and arginine and proline metabolism; alanine, aspartate, and glutamate metabolism in roots. Epichloë gansuensis also affected the content of organic acid and stress-related metabolites at low P stress. In conclusion, Epichloë gansuensis improves Achnatherum inebrians growth at low P stress by regulating the metabolic pathway of amino acids, amino acids content, organic acid content, and increasing PUE.

Cytosolic aromatic aldehyde dehydrogenase provides benzoic acid for xanthone biosynthesis in Hypericum

Benzoic acid is a building block of a multitude of well-known plant natural products, such as paclitaxel and cocaine. Its simple chemical structure contrasts with its complex biosynthesis. Hypericum species are rich in polyprenylated benzoic acid-derived xanthones, which have received attention due to their biological impact on human health. The upstream biosynthetic sequence leading to xanthones is still incomplete. To supply benzoic acid for xanthone biosynthesis, Hypericum calycinum cell cultures use the CoA-dependent non-β-oxidative pathway, which starts with peroxisomal cinnamate CoA-ligase (HcCNL). Here, we use the xanthone-producing cell cultures to identify the transcript for benzaldehyde dehydrogenase (HcBD), a pivotal player in the non-β-oxidative pathways. In addition to benzaldehyde, the enzyme efficiently catalyzes the oxidation of trans-cinnamaldehyde in vitro. The enzymatic activity is strictly dependent on the presence of NAD⁺ as co-factor. HcBD is localized to the cytosol upon ectopic expression of reporter fusion constructs. HcBD oxidizes benzaldehyde, which moves across the peroxisome membrane, to form benzoic acid. Increases in the HcCNL and HcBD transcript levels precede the elicitor-induced xanthone accumulation. The current work addresses a crucial step in the yet incompletely understood CoA-dependent non-β-oxidative route of benzoic acid biosynthesis. Addressing this step may offer a new biotechnological tool to enhance product formation in biofactories.

A metabolite roadmap of the wood-forming tissue in Populus tremula

Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.

A promiscuous coenzyme A ligase provides benzoyl-coenzyme A for xanthone biosynthesis in Hypericum

Benzoic acid-derived compounds, such as polyprenylated benzophenones and xanthones, attract the interest of scientists due to challenging chemical structures and diverse biological activities. The genus Hypericum is of high medicinal value, as exemplified by H. perforatum. It is rich in benzophenone and xanthone derivatives, the biosynthesis of which requires the catalytic activity of benzoate-coenzyme A (benzoate-CoA) ligase (BZL), which activates benzoic acid to benzoyl-CoA. Despite remarkable research so far done on benzoic acid biosynthesis in planta, all previous structural studies of BZL genes and proteins are exclusively related to benzoate-degrading microorganisms. Here, a transcript for a plant acyl-activating enzyme (AAE) was cloned from xanthone-producing Hypericum calycinum cell cultures using transcriptomic resources. An increase in the HcAAE1 transcript level preceded xanthone accumulation after elicitor treatment, as previously observed with other pathway-related genes. Subcellular localization of reporter fusions revealed the dual localization of HcAAE1 to cytosol and peroxisomes owing to a type 2 peroxisomal targeting signal. This result suggests the generation of benzoyl-CoA in Hypericum by the CoA-dependent non-β-oxidative route. A luciferase-based substrate specificity assay and the kinetic characterization indicated that HcAAE1 exhibits promiscuous substrate preference, with benzoic acid being the sole aromatic substrate accepted. Unlike 4-coumarate-CoA ligase and cinnamate-CoA ligase enzymes, HcAAE1 did not accept 4-coumaric and cinnamic acids, respectively. The substrate preference was corroborated by in silico modeling, which indicated valid docking of both benzoic acid and its adenosine monophosphate intermediate in the HcAAE1/BZL active site cavity.

Phenolic metabolism in the hornwort Anthoceros agrestis: 4-coumarate CoA ligase and 4-hydroxybenzoate CoA ligase

4-Coumarate coenzyme A ligase and 4-hydroxybenzoate coenzyme A ligase from the hornwort Anthoceros agrestis expressed in E. coli were characterized on biochemical and molecular levels and showed interesting substrate specificities. Acyl-activating enzymes are associated with the biosynthesis or degradation of various metabolic products such as lipids, amino acids, sugars, and natural compounds. In this work, cDNA sequences encoding 4-coumarate coenzyme A ligase (4CL) and 4-hydroxybenzoate coenzyme A ligase (4HBCL) were amplified from the hornwort Anthoceros agrestis. The coding sequences were expressed in E. coli and purified by Ni-chelate chromatography. The CoA ligases exhibited different substrate specificities. 4CL catalyzed the activation of 4-coumaric acid, 3-coumaric acid, 2-coumaric acid, caffeic acid, isoferulic acid, ferulic acid, and cinnamic acid but lacked activities towards sinapic acid and benzoic acids. In contrast, 4HBCL preferred 4-hydroxybenzoic acid and benzoic acid, but also accepted other benzoic acid derivatives except salicylic acid and 3-aminosalicylic acid. Furthermore, 4HBCL also activated isoferulic acid, cinnamic acid, 2-coumaric acid, 3-coumaric acid, 4-coumaric acid and caffeic acid, but lacked affinity for ferulic acid and sinapic acid. These substrate specificities could be related to the phenolic compounds identified in Anthoceros agrestis.

Metabolomic markers and physiological adaptations for high phosphate utilization efficiency in rice

Utilizing phosphate more efficiently is crucial for sustainable crop production. Highly efficient rice (Oryza sativa) cultivars have been identified and this study aims to identify metabolic markers associated with P utilization efficiency (PUE). P deficiency generally reduced leaf P concentrations and CO₂ assimilation rates but efficient cultivars were reducing leaf P concentrations further than inefficient ones while maintaining similar CO₂ assimilation rates. Adaptive changes in carbon metabolism were detected but equally in efficient and inefficient cultivar groups. Groups furthermore did not differ with respect to partial substitutions of phospholipids by sulfo- and galactolipids. Metabolites significantly more abundant in the efficient group, such as sinapate, benzoate and glucoronate, were related to antioxidant defence and may help alleviating oxidative stress caused by P deficiency. Sugar alcohols ribitol and threitol were another marker metabolite for higher phosphate efficiency as were several amino acids, especially threonine. Since these metabolites are not known to be associated with P deficiency, they may provide novel clues for the selection of more P efficient genotypes. In conclusion, metabolite signatures detected here were not related to phosphate metabolism but rather helped P efficient lines to keep vital processes functional under the adverse conditions of P starvation.

The role of salicylic acid and gibberellin signaling in plant responses to abiotic stress with an emphasis on heavy metals

Salicylic acid (SA) and gibberellins (GAs), as two important plant growth hormones, play a key role in increasing plant tolerance to abiotic stress. They contribute to the increased plant antioxidant activities in ROS scavenging, which is related to the enzymes involved in H₂O₂-detoxifying. In photosynthetic cycles, the endogenous form of these phytohormones enhances photosynthetic properties such as stomatal conductance, net photosynthesis (PN), photosynthetic oxygen evolution, and efficiency of carboxylation. Furthermore, in cell cycle, they are able to influence division and expansion of cell growth in plants under stress, leading to increased growth of radicle cells in a meristem, and ultimately contributing to the increased germination rate and lengths of shoot and root in the stress-affected plants. In the case of crosstalk between SA and GA, exogenous GA₃ can upregulate biosynthesis of SA and consequently result in rising levels of SA, enhancing plant defense response to environmental abiotic stresses. The aim of this paper was to investigate the mechanisms related to GA and SA phytohormones in amelioration of abiotic stress, in particular, heavy metal stress.

Evidence from stable-isotope labeling that catechol is an intermediate in salicylic acid catabolism in the flowers of Silene latifolia (white campion)

A stable isotope-assisted mass spectrometry-based platform was utilized to demonstrate that the plant hormone, salicylic acid, is catabolized to catechol, a widespread secondary plant compound. The phytohormone salicylic acid (SA) plays a central role in the overall plant defense program, as well as various other aspects of plant growth and development. Although the biosynthetic steps toward SA are well documented, how SA is catabolized in plants remains poorly understood. Accordingly, in this study a series of stable isotope feeding experiments were performed with Silene latifolia (white campion) to explore possible routes of SA breakdown. S. latifolia flowers that were fed a solution of [²H₆]-salicylic acid emitted the volatile and potent pollinator attractant, 1,2-dimethoxybenzene (veratrole), which contained the benzene ring-bound deuterium atoms. Extracts from these S. latifolia flowers revealed labeled catechol as a possible intermediate. After feeding flowers with [²H₆]-catechol, the stable isotope was recovered in veratrole as well as its precursor, guaiacol. Addition of a trapping pool of guaiacol in combination with [²H₆]-salicylic acid resulted in the accumulation of the label into catechol. Finally, we provide evidence for catechol O-methyltransferase enzyme activity in a population of S. latifolia that synthesizes veratrole from guaiacol. This activity was absent in non-veratrole emitting flowers. Taken together, these results imply the conversion of salicylic acid to veratrole in the following reaction sequence: salicylic acid > catechol > guaiacol > veratrole. This catabolic pathway for SA may also be embedded in other lineages of the plant kingdom, particularly those species which are known to accumulate catechol.

Arabidopsis SMALL DEFENSE-ASSOCIATED PROTEIN 1 Modulates Pathogen Defense and Tolerance to Oxidative Stress

Salicylic acid (SA) and reactive oxygen species (ROS) are known to be key modulators of plant defense. However, mechanisms of molecular signal perception and appropriate physiological responses to SA and ROS during biotic or abiotic stress are poorly understood. Here we report characterization of SMALL DEFENSE-ASSOCIATED PROTEIN 1 (SDA1), which modulates defense against bacterial pathogens and tolerance to oxidative stress. sda1 mutants are compromised in defense gene expression, SA accumulation, and defense against bacterial pathogens. External application of SA rescues compromised defense in sda1 mutants. sda1 mutants are also compromised in tolerance to ROS-generating chemicals. Overexpression of SDA1 leads to enhanced resistance against bacterial pathogens and tolerance to oxidative stress. These results suggest that SDA1 regulates plant immunity via the SA-mediated defense pathway and tolerance to oxidative stress. SDA1 encodes a novel small plant-specific protein containing a highly conserved seven amino acid (S/G)WA(D/E)QWD domain at the N-terminus that is critical for SDA1 function in pathogen defense and tolerance to oxidative stress. Taken together, our studies suggest that SDA1 plays a critical role in modulating both biotic and abiotic stresses in Arabidopsis (Arabidopsis thaliana) and appears to be a plant-specific stress responsive protein.

A rapid UHPLC-QqQ-MS/MS method for the simultaneous qualitation and quantitation of coumarins, furocoumarins, flavonoids, phenolic acids in pummelo fruits

The impact of secondary metabolites on fruit quality, plant growth and human health has led to an increased demand for analytical methods to characterize and quantify these metabolites in recent years. A versatile, sensitive and rapid method based on UHPLC-QqQ-MS/MS was developed for simultaneous qualitation and quantitation of coumarins, furocoumarins, flavonoids and phenolic acids. The chromatographic elution and multiple reaction monitoring mode transitions were optimized to achieve good separation and accurate quantitation of 47 analytes, including 13 groups of isomers, during a single 13 min chromatographic run. This method was validated with good precision and recoveries, wide linear ranges and low limits of detection and quantitation (0.014-1.50 μg L-1). The validated method was further applied to quantify the analytes in flavedo, albedo and pulp from two pummelo varieties, C. grandis 'Shatianyu' and C. grandis 'Guanximiyu'. This method combines high sensitivity, good selectivity, and short chromatographic run time.

Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation

Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color are key traits for many floricultural crops. Volatile organic compounds (VOCs) play vital roles in pollinator attraction, defense, and interaction with the environment. Recent progress in omics technology has led to the isolation of genes encoding candidate enzymes responsible for the biosynthesis and regulatory circuits of plant VOCs. Uncovering the biosynthetic pathways and regulatory mechanisms underlying the production of floral scents is necessary not only for a better understanding of the function of relevant genes but also for the generation of new cultivars with desirable traits through molecular breeding approaches. However, little is known about the pathways responsible for floral scents in orchids because of their long life cycle as well as the complex and large genome; only partial terpenoid pathways have been reported in orchids. Here, we review the biosynthesis and regulation of floral volatile compounds in orchids. In particular, we focused on the genes responsible for volatile compounds in various tissues and developmental stages in Cymbidium orchids. We also described the emission of orchid floral volatiles and their function in pollination ecology. Taken together, this review will provide a broad scope for the study of orchid floral scents.

Naturally occurring benzoic, sorbic, and propionic acid in vegetables

Benzoic, sorbic and propionic acid are used as preservatives in foods and can also be naturally present in processed foods. The levels of preservatives in 939 vegetables were determined. Benzoic and sorbic acid were analysed by high-performance liquid chromatography with a diode-array detector and further confirmed by liquid chromatography-tandem mass spectrometry, whereas propionic acid was analysed using a gas chromatography-flame ionization detector and further confirmed by gas chromatography-mass spectrometry. Benzoic and propionic acid were found in 10.9% and 36.2%, respectively, of the samples. In contrast, sorbic acid was not found in any of the samples. The highest amounts of benzoic and propionic acid were found in perilla leaves (0.33-298 mg kg^-1) and ginseng (<LOD-32.8 mg kg^-1), respectively. The background concentration ranges of naturally occurring preservatives in vegetables determined in this study could be used for inspection services of standard criteria to address consumer complaints or trade disputes.

Mechanism and kinetic study of the reaction of benzoic acid with OH, NO3 and SO4− radicals in the atmosphere

Benzoic acid (BA) is one of the most common organic acids in the Earth’s atmosphere and an important component of atmospheric aerosol particles. The reaction mechanism of OH, NO₃ and SO₄⁻ radicals with BA in atmospheric water droplets and that of OH radicals with BA in the atmosphere were studied in this paper. The results show that in atmospheric water droplets the potential barriers of the elementary addition reactions of BA with OH radicals are lower than those of elementary abstraction reactions, and the potential barriers of OH-initiated reactions are less than for NO₃ and SO₄⁻ reactions. The initiation reactions of OH radicals and BA are exothermic, but the abstraction reactions of NO₃ and SO₄⁻ are endothermic processes. Among the products, 6-hydroxybenzoic acid (6-HBA) and 4,6-dihydroxybenzoic acid (4,6-DHBA) are the most stable, while 3-hydroxybenzoic acid (3-HBA) and 3,5-dihydroxybenzoic acid (3,5-DHBA) are much less stable and, thus, much less abundant compared to 6-HBA and 4,6-DHBA. The initiation and subsequent degradation of BA with OH radicals in the gas phase were calculated. The products of addition and abstraction reactions of BA with OH radicals can be further oxidized and degraded by O₂/NO. According to the results of kinetic calculations, the total reaction rate constant of OH radicals with BA at 298.15 K in atmospheric water droplets is 2.35 × 10⁻¹¹ cm³ per molecule per s. The relationship between reaction rate constants, temperature and altitude were also investigated and discussed in the present study.

We present a study of benzoic acid with OH, NO³ and SO₄⁻ radicals in the atmospheric environment.

Transcriptome analysis of Polianthes tuberosa during floral scent formation

Polianthes tuberosa is a popular ornamental plant. Its floral scent volatiles mainly consist of terpenes and benzenoids that emit a charming fragrance. However, our understanding of the molecular mechanism responsible for the floral scent of P. tuberosa is limited. Using transcriptome sequencing and de novo assembly, a total of 228,706,703 high-quality reads were obtained, which resulted in the identification of 96,906 unigenes (SRA Accession Number SRP126470, TSA Acc. No. GGEA00000000). Approximately 41.85% of the unigenes were functionally annotated using public databases. A total of 4,694 differentially expressed genes (DEGs)were discovered during flowering. Gas chromatography-mass spectrometry analysis revealed that the majority of the volatiles comprised benzenoids and small amounts of terpenes. Homology analysis identified 13 and 17 candidate genes associated with terpene and benzenoid biosynthesis, respectively. Among these, PtTPS1, PtDAHPSs, PtPAL1, and PtBCMT2 might play important roles in regulating the formation of floral volatiles. The data generated by transcriptome sequencing provide a critical resource for exploring concrete characteristics as well as for supporting functional genomics studies. The results of the present study also lay the foundation for the elucidation of the molecular mechanism underlying the regulation of floral scents in monocots.

Two-dimensional analysis provides molecular insight into flower scent of Lilium 'Siberia'

Lily is a popular flower around the world not only because of its elegant appearance, but also due to its appealing scent. Little is known about the regulation of the volatile compound biosynthesis in lily flower scent. Here, we conducted an approach combining two-dimensional analysis and weighted gene co-expression network analysis (WGCNA) to explore candidate genes regulating flower scent production. In the approach, changes of flower volatile emissions and corresponding gene expression profiles at four flower developmental stages and four circadian times were both captured by GC-MS and RNA-seq methods. By overlapping differentially-expressed genes (DEGs) that responded to flower scent changes in flower development and circadian rhythm, 3,426 DEGs were initially identified to be candidates for flower scent production, of which 1,270 were predicted as transcriptional factors (TFs). The DEGs were further correlated to individual flower volatiles by WGCNA. Finally, 37, 41 and 90 genes were identified as candidate TFs likely regulating terpenoids, phenylpropanoids and fatty acid derivatives productions, respectively. Moreover, by WGCNA several genes related to auxin, gibberellins and ABC transporter were revealed to be responsible for flower scent production. Thus, this strategy provides an important foundation for future studies on the molecular mechanisms involved in floral scent production.

Volatile compounds from beneficial or pathogenic bacteria differentially regulate root exudation, transcription of iron transporters, and defense signaling pathways in Sorghum bicolor

Our results show that Sorghum bicolor is able to recognize bacteria through its volatile compounds and differentially respond to beneficial or pathogens via eliciting nutritional or defense adaptive traits. Plants establish beneficial, harmful, or neutral relationships with bacteria. Plant growth promoting rhizobacteria (PGPR) emit volatile compounds (VCs), which may act as molecular cues influencing plant development, nutrition, and/or defense. In this study, we compared the effects of VCs produced by bacteria with different lifestyles, including Arthrobacter agilis UMCV2, Bacillus methylotrophicus M4-96, Sinorhizobium meliloti 1021, the plant pathogen Pseudomonas aeruginosa PAO1, and the commensal rhizobacterium Bacillus sp. L2-64, on S. bicolor. We show that VCs from all tested bacteria, except Bacillus sp. L2-64, increased biomass and chlorophyll content, and improved root architecture, but notheworthy A. agilis induced the release of attractant molecules, whereas P. aeruginosa activated the exudation of growth inhibitory compounds by roots. An analysis of the expression of iron-transporters SbIRT1, SbIRT2, SbYS1, and SbYS2 and genes related to plant defense pathways COI1 and PR-1 indicated that beneficial, pathogenic, and commensal bacteria could up-regulate iron transporters, whereas only beneficial and pathogenic species could induce a defense response. These results show how S. bicolor could recognize bacteria through their volatiles profiles and highlight that PGPR or pathogens can elicit nutritional or defensive traits in plants.

Metabolomics analysis of rice responses to salinity stress revealed elevation of serotonin, and gentisic acid levels in leaves of tolerant varieties

A GC-MS based analytical approach was undertaken to understand the metabolomic responses of seedlings of 2 salt sensitive (Sujala and MTU 7029) and 2 tolerant varieties (Bhutnath, and Nonabokra) of indica rice (Oryza sativa L.) to NaCl induced stress. The 4 varieties responded differently to NaCl treatment with respect to the conserved primary metabolites (sugars, polyols, amino acids, organic acids and certain purine derivatives) of the leaf of rice seedlings. However, there were significant differences in salt induced production of chorismic acid derivatives. Serotonin level was increased in both the salt tolerant varieties in response to NaCl induced stress. In both the salt tolerant varieties, increased production of the signaling molecule gentisic acid in response to NaCl treatment was noticed. Salt tolerant varieties also produced increased level of ferulic acid and vanillic acid. In the salt sensitive varieties, cinnamic acid derivatives, 4-hydroxycinnamic acid (in Sujala) and 4-hydroxybenzoic acid (in MTU 7029), were elevated in the leaves. So increased production of the 2 signaling molecules serotonin and gentisic acid may be considered as 2 important biomarker compounds produced in tolerant varieties contributing toward NaCl tolerance.

Improvement of drought tolerance of soybean plants by using methyl jasmonate

Methyl jasmonate (MeJA) is a naturally occurring plant growth regulator and play vital roles in plant defense and many developmental processes such as root growth and seed germination. This study was undertaken to study the possible role of using methyl jasmonate to alleviate the adverse effect of water stress on soybean genotypes (Giza 22 and 35). The results showed that water stress reduced shoot length, fresh and dry weights of shoot and root, photosynthetic pigments, relative water content and oil content in the shoots of all soybean genotypes. On the other hand, there was a considerable increase in cell wall fractionation, saturated and unsaturated fatty acids, flavonoids, phenolic acid and sugar fraction content in the shoots of the soybean genotypes in response to the water stress. Foliar spray with methyl jasmonate increased all the above parameters as compared to stressed plants. The results investigate the important role of MeJA in alleviation of water stress in soybean plants and suggest that MeJA could be used for improving plant growth under water stress as a potential growth regulator. The soybean genotypes Giza 22 was found to be more resistant to water stress than Giza 35.

Redirection of metabolite biosynthesis from hydroxybenzoates to volatile terpenoids in green hairy roots of Daucus carota

A metabolic shift in green hairy root cultures of carrot from phenylpropanoid/benzenoid biosynthesis toward volatile isoprenoids was observed when compared with the metabolite profile of normal hairy root cultures. Hairy roots cultures of Daucus carota turned green under continuous illumination, while the content of the major phenolic compound p-hydroxybenzoic acid (p-HBA) was reduced to half as compared to normal hairy roots cultured in darkness. p-Hydroxybenzaldehyde dehydrogenase (HBD) activity was suppressed in the green hairy roots. However, comparative volatile analysis of 14-day-old green hairy roots revealed higher monoterpene and sesquiterpene contents than found in normal hairy roots. Methyl salicylate content was higher in normal hairy roots than in green ones. Application of clomazone, an inhibitor of 1-deoxy-D-xylulose 5-phosphate synthase (DXS), reduced the amount of total monoterpenes and sesquiterpenes in green hairy roots compared to normal hairy roots. However, methyl salicylate content was enhanced in both green and normal hairy roots treated with clomazone as compared to their respective controls. Because methyl-erythritol 4-phosphate (MEP) and phenylpropanoid pathways, respectively, contribute to the formation of monoterpenes and phenolic acids biosynthesis, the activities of enzymes regulating those pathways were measured in terms of their in vitro activities, in both green and normal hairy root cultures. These key enzymes were 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), an early regulatory enzyme of the MEP pathway, pyruvate kinase (PK), an enzyme of primary metabolism related to the MEP pathway, shikimate dehydrogenase (SKDH) which is involved in biosynthesis of aromatic amino acids, and phenylalanine ammonia-lyase (PAL) that catalyzes the first step of phenylpropanoid biosynthesis. Activities of DXR and PK were higher in green hairy roots as compared to normal ones, whereas the opposite trend was observed for SKDH and PAL activities. Gene expression analysis of DXR and PAL showed trends similar to those for the respective enzyme activities. Based on these observations, we suggest a possible redirection of metabolites from the primary metabolism toward isoprenoid biosynthesis, limiting the phenolic biosynthetic pathway in green hairy roots grown under continuous light.

Insights into molecular and metabolic events associated with fruit response to post-harvest fungal pathogens

Due to post-harvest losses more than 30% of harvested fruits will not reach the consumers' plate. Fungal pathogens play a key role in those losses, as they cause most of the fruit rots and the customer complaints. Many of the fungal pathogens are already present in the unripe fruit but remain quiescent during fruit growth until a particular phase of fruit ripening and senescence. The pathogens sense the developmental change and switch into the devastating necrotrophic life style that causes fruit rotting. Colonization of unripe fruit by the fungus initiates defensive responses that limit fungal growth and development. However, during fruit ripening several physiological processes occur that correlate with increased fruit susceptibility. In contrast to plant defenses in unripe fruit, the defense posture of ripe fruit entails a different subset of defense responses that will end with fruit rotting and losses. This review will focus on several aspects of molecular and metabolic events associated with fleshy fruit responses induced by post-harvest fungal pathogens during fruit ripening.

Transcriptome profiling provides new insights into the formation of floral scent in Hedychium coronarium

BACKGROUND

Hedychium coronarium is a popular ornamental plant in tropical and subtropical regions because its flowers not only possess intense and inviting fragrance but also enjoy elegant shape. The fragrance results from volatile terpenes and benzenoids presented in the floral scent profile. However, in this species, even in monocots, little is known about the underlying molecular mechanism of floral scent production.

RESULTS

Using Illumina platform, approximately 81 million high-quality reads were obtained from a pooled cDNA library. The de novo assembly resulted in a transcriptome with 65,591 unigenes, 50.90% of which were annotated using public databases. Digital gene expression (DGE) profiling analysis revealed 7,796 differential expression genes (DEGs) during petal development. GO term classification and KEGG pathway analysis indicated that the levels of transcripts changed significantly in "metabolic process", including "terpenoid biosynthetic process". Through a systematic analysis, 35 and 33 candidate genes might be involved in the biosynthesis of floral volatile terpenes and benzenoids, respectively. Among them, flower-specific HcDXS2A, HcGPPS, HcTPSs, HcCNL and HcBCMT1 might play critical roles in regulating the formation of floral fragrance through DGE profiling coupled with floral volatile profiling analyses. In vitro characterization showed that HcTPS6 was capable of generating β-farnesene as its main product. In the transcriptome, 1,741 transcription factors (TFs) were identified and 474 TFs showed differential expression during petal development. It is supposed that two R2R3-MYBs with flower-specific and developmental expression might be involved in the scent production.

CONCLUSIONS

The novel transcriptome and DGE profiling provide an important resource for functional genomics studies and give us a dynamic view of biological process during petal development in H. coronarium. These data lay the basis for elucidating the molecular mechanism of floral scent formation and regulation in monocot. The results also provide the opportunities for genetic modification of floral scent profile in Hedychium.

Transcriptome and metabolome reprogramming in Vitis vinifera cv. Trincadeira berries upon infection with Botrytis cinerea

Vitis vinifera berries are sensitive towards infection by the necrotrophic pathogen Botrytis cinerea, leading to important economic losses worldwide. The combined analysis of the transcriptome and metabolome associated with fungal infection has not been performed previously in grapes or in another fleshy fruit. In an attempt to identify the molecular and metabolic mechanisms associated with the infection, peppercorn-sized fruits were infected in the field. Green and veraison berries were collected following infection for microarray analysis complemented with metabolic profiling of primary and other soluble metabolites and of volatile emissions. The results provided evidence of a reprogramming of carbohydrate and lipid metabolisms towards increased synthesis of secondary metabolites involved in plant defence, such as trans-resveratrol and gallic acid. This response was already activated in infected green berries with the putative involvement of jasmonic acid, ethylene, polyamines, and auxins, whereas salicylic acid did not seem to be involved. Genes encoding WRKY transcription factors, pathogenesis-related proteins, glutathione S-transferase, stilbene synthase, and phenylalanine ammonia-lyase were upregulated in infected berries. However, salicylic acid signalling was activated in healthy ripening berries along with the expression of proteins of the NBS-LRR superfamily and protein kinases, suggesting that the pathogen is able to shut down defences existing in healthy ripening berries. Furthermore, this study provided metabolic biomarkers of infection such as azelaic acid, a substance known to prime plant defence responses, arabitol, ribitol, 4-amino butanoic acid, 1-O-methyl- glucopyranoside, and several fatty acids that alone or in combination can be used to monitor Botrytis infection early in the vineyard.

Synthetic plant defense elicitors

To defend themselves against invading pathogens plants utilize a complex regulatory network that coordinates extensive transcriptional and metabolic reprogramming. Although many of the key players of this immunity-associated network are known, the details of its topology and dynamics are still poorly understood. As an alternative to forward and reverse genetic studies, chemical genetics-related approaches based on bioactive small molecules have gained substantial popularity in the analysis of biological pathways and networks. Use of such molecular probes can allow researchers to access biological space that was previously inaccessible to genetic analyses due to gene redundancy or lethality of mutations. Synthetic elicitors are small drug-like molecules that induce plant defense responses, but are distinct from known natural elicitors of plant immunity. While the discovery of some synthetic elicitors had already been reported in the 1970s, recent breakthroughs in combinatorial chemical synthesis now allow for inexpensive high-throughput screens for bioactive plant defense-inducing compounds. Along with powerful reverse genetics tools and resources available for model plants and crop systems, comprehensive collections of new synthetic elicitors will likely allow plant scientists to study the intricacies of plant defense signaling pathways and networks in an unparalleled fashion. As synthetic elicitors can protect crops from diseases, without the need to be directly toxic for pathogenic organisms, they may also serve as promising alternatives to conventional biocidal pesticides, which often are harmful for the environment, farmers and consumers. Here we are discussing various types of synthetic elicitors that have been used for studies on the plant immune system, their modes-of-action as well as their application in crop protection.

A familiar ring to it: biosynthesis of plant benzoic acids

Plant benzoic acids (BAs) are building blocks or important structural elements for numerous primary and specialized metabolites, including plant hormones, cofactors, defense compounds, and attractants for pollinators and seed dispersers. Many natural products derived from plant BAs or containing benzoyl/benzyl moieties are also of medicinal or nutritional value to humans. Biosynthesis of BAs in plants is a network involving parallel and intersecting pathways spread across multiple subcellular compartments. In this review, a current overview on the metabolism of plant BAs is presented with a focus on the recent progress made on isolation and functional characterization of genes encoding biosynthetic enzymes and intracellular transporters. In addition, approaches for deciphering the complex interactions between pathways of the BAs network are discussed.

Metabolomic insights into the bioconversion of isonitrosoacetophenone in Arabidopsis thaliana and its effects on defense-related pathways

Plants are constantly exposed to numerous biotic or abiotic stress factors throughout their life-cycle. Pathogens and pathogen-derived molecules are the best studied inducers of plant defense responses, but synthetic and naturally occurring molecules have also been used to induce various types of resistance in plants. Here, an oxime molecule, 2-isonitrosoacetophenone (INAP), related to the stress metabolite citaldoxime, was used to trigger metabolic changes in the metabolome of treated Arabidopsis thaliana plants as monitored by UHPLC-MS in conjunction with principal component analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA). The chemometric methods revealed metabolites found to be significantly present in response to the treatment. These include bioconversion products (2-keto-2-phenylacetaldoxime-glycoside and l-mandelonitrile-glycoside) as well as those of which the levels are affected by the treatment (benzoic acid and derivatives, other phenylpropanoid-derived compounds and glucosinolates). Using in planta bacterial growth evaluations, INAP treatment was furthermore found to induce an anti-microbial environment in vivo.

Biosynthesis and metabolism of β-d-salicin: A novel molecule that exerts biological function in humans and plants

β-d-Salicin 1 (Mahdi et al. [8]) is an interesting medicinal phytochemical that exhibits cross functions in plants and humans immunologically. This molecule 1 (Mahdi et al. [8]) has attracted the attention of scientists in various interdisciplinary fields, including chemistry, pharmacology and medicine. The biological cross functions of β-d-salicin 1 (Mahdi et al. [8]) serve in plant survival and healing processes via salicylic acid 2 (Pierpont [23]). Thus, this raise a question whether plant biosynthesis and human metabolism crosstalk to induce therapy via molecular recognition. If so, biotechnology and bioinformatics are significant techniques for new strategies in drug development. Thus, understanding the biosynthesis, metabolism and the cross-molecular setting of recognition may encourage further discussion and research on its medicinal and biological activity virtues.

Expression profiles of key phenylpropanoid genes during Vanilla planifolia pod development reveal a positive correlation between PAL gene expression and vanillin biosynthesis

In Vanilla planifolia pods, development of flavor precursors is dependent on the phenylpropanoid pathway. The distinctive vanilla aroma is produced by numerous phenolic compounds of which vanillin is the most important. Because of the economic importance of vanilla, vanillin biosynthetic pathways have been extensively studied but agreement has not yet been reached on the processes leading to its accumulation. In order to explore the transcriptional control exerted on these pathways, five key phenylpropanoid genes expressed during pod development were identified and their mRNA accumulation profiles were evaluated during pod development and maturation using quantitative real-time PCR. As a prerequisite for expression analysis using qRT-PCR, five potential reference genes were tested, and two genes encoding Actin and EF1 were shown to be the most stable reference genes for accurate normalization during pod development. For the first time, genes encoding a phenylalanine ammonia-lyase (VpPAL1) and a cinnamate 4-hydroxylase (VpC4H1) were identified in vanilla pods and studied during maturation. Among phenylpropanoid genes, differential regulation was observed from 3 to 8 months after pollination. VpPAL1 was gradually up-regulated, reaching the maximum expression level at maturity. In contrast, genes encoding 4HBS, C4H, OMT2 and OMT3 did not show significant increase in expression levels after the fourth month post-pollination. Expression profiling of these key phenylpropanoid genes is also discussed in light of accumulation patterns for key phenolic compounds. Interestingly, VpPAL1 gene expression was shown to be positively correlated to maturation and vanillin accumulation.

Proteome analysis of peroxisomes from etiolated Arabidopsis seedlings identifies a peroxisomal protease involved in β-oxidation and development

Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.

Metabolomic analysis of isonitrosoacetophenone-induced perturbations in phenolic metabolism of Nicotiana tabacum cells

Plants have developed biochemical and molecular responses to adapt to different stress environments. One of the characteristics of the multi-component defence response is the production of defence-related metabolites. Plant defences can be triggered by various stimuli, including synthetic or naturally occurring molecules, especially those derived from pathogens. In the current study, Nicotiana tabacum cell suspensions were treated with isonitrosoacetophenone (INAP), a subcomponent of a plant-derived stress metabolite with anti-fungal and anti-oxidant properties, in order to investigate the effect thereof on cellular metabolism. Subsequent metabolomic-based analyses were employed to evaluate changes in the metabolome. UPLC-MS in conjunction with multivariate data analyses was found to be an appropriate approach to study the effect of chemical inducers like INAP on plant metabolism in this model system. Principal component analysis (PCA) indicated that INAP is capable of inducing time-dependent metabolic perturbations in the cultured cells. Orthogonal projection to latent structures discriminant analysis (OPLS-DA) revealed metabolites of which the levels are affected by INAP, and eight of these were tentatively annotated from the mass spectral data and online databases. These metabolites are known in the context of plant stress- and defence responses and include benzoic- or cinnamic acid derivatives that are either glycosylated or quinilated as well as flavonoid derivatives. The results indicate that INAP affects the shikimate-, phenylpropanoid- and flavonoid pathways, the products of which may subsequently lead to an anti-oxidant environment in vivo.

HPLC Quantification of Phenolic Acids from Vetiveria zizanioides (L.) Nash and Its Antioxidant and Antimicrobial Activity

Extraction procedure was standardized and for the soluble, glycoside, and wall-bound fractions of phenolic acids from Vetiveria zizanioides. The water soluble alkaline extract which represents the cell wall-bound fraction contained the highest amount of phenolic acids (2.62 ± 1.2 μM/g fwt GA equivalents). Increased phenolic content in the cell wall indicates more lignin deposition which has an important role in plant defense and stress mitigation. Antioxidant property expressed as percentage TEAC value obtained by ABTS assay was correlated with the amount of phenolic acids and showed a Pearson's coefficient 0.988 (significant at 0.01 level). The compounds p-coumaric acid, p-dihydroxybenzoic acid, and ferulic acid were detected in the acidic extracts by HPLC analysis. The plant extracts exhibited considerable antimicrobial activity against tested bacterial and fungal strains.