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Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus , making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L−1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common P erm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that P erm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (P kasOP* and P 41) enabled strong constitutive expression during the entire process. Using P kasOP* , several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L−1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3′-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L−1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin. • Nybomycin is a promising antibiotic against multi-resistant S. aureus. • Genomic studies identified the minimal nybomycin gene cluster. • Streamlined chassis Streptomyces albidoflavus Del14 used for production. • Systematic engineering of primary and secondary pathways. • Engineered S. albidoflavus NYB-11 forms nybomycin up to 12 mg L−1 [ABSTRACT FROM AUTHOR]

The chorismic acid synthetase AroC is the key enzyme for the synthesis of aromatic compounds in the shikimic acid pathway. Identifying the characteristics of aroC gene in Brevibacillus brevis and its transcriptional regu lators will lay a foundation for the study of the mechanism of action of Brevibacillus brevis. The aroC gene was cloned from Brevibacillus brevis FJAT-0809-GLX, and then the bioinformatics analysis and the prediction of transcription factor were carried out. The sequence length of aroC gene in Brevibacillus brevis FJAT-0809-GLX was 1164 bp, and the GenBank accession number was OR475562. The aroC gene sequence of Brevibacillus brevis FJAT-0809-GLX had the highest homology with that of Brevibacillus brevis NBRC 100599, which was 98. 88%. The amino acid sequence of AroC had the highest homology with Brevibacillus brevis HNCS-1, which was 100%. Its encoded protein was a hydrophilic protein without signal peptide, which was located in the cytoplasm. A total of 23 transcription factors targeting BbaroC were identified from 10 species, with 12 and 3 transcription factors predicted from Escherichia coli (Strain KI2 MG1655) and Bacillus subtilis (Strain 168), respectively. BbaroC may play an important role in the production of antibacterial active substances of Brevibacillus brevis, which would provide basis for its wide application in agriculture. [ABSTRACT FROM AUTHOR]

Essential oils (EOs) are concentrated liquids extracted from various parts of plants and can be classified based on their phytochemical compounds. Terpenes and terpenoids have a wide range of biological activities, including anticancer, anti-inflammatory, antimicrobial, antioxidant, and antiallergic properties. Terpenes are plant-based compounds commonly used in the pharmaceutical, food, biofuel, and chemical industries by humans. In synthetic biology, genomic resources and emerging tools facilitate the production of high-quality terpenoids in plants and microbes. Terpenoids, however, are difficult to produce in large quantities due to their complex chemical structures and the limited amounts found in plants. The regulation of terpenoid biosynthesis has gradually emerged as a research priority. This review presents an overview of the biological activities, synthesis pathways, and key enzymes involved in the biosynthetic pathways and regulation of terpenes or terpenoids. This review will also include references for further research on molecular regulation, biological advancements, and increasing the content of terpenes or terpenoids in plants. [ABSTRACT FROM AUTHOR]

In order to find new targets to solve the problem of bacterial resistance caused by antibiotic abuse, the differences in the bactericidal phenotypes of Escherichia coli wild-type BW25113 (WT) and ydiB gene knockout strain(ΔydiB) were compared by comparing the aminoglycoside antibiotics (gentamicin, tobramycin, streptomycin, amikacin and mycifradin), quinolones antibiotics (ofloxacin and ciprofloxacin) and beta-lactam antibiotics (ampicillin and carbenicillin). And by further testing the bactericidal phenotype of aminoglycoside antibiotics represented by gentamicin against the over-expression strains BW25113-pCA24N and BW25113-pCA24N (ydiB} T the importance of ydiB gene to bacterial resistance was confirmed. The results showed that compared with Escherichia coli wild-type BW25113 (WT), the ydiB gene knockout strain (ΔydiB} was only resistant to aminoglycoside antibiotics, and it was found that the over-expression strain BW25113-PCA24N (.ydiB) could restore the sensitivity to gentamicin. Therefore, it was proved that ydiB gene was a key gene for the action of aminoglycoside antibiotics and was expected to become a new target for the action of aminoglycoside antibiotics. [ABSTRACT FROM AUTHOR]

Glyphosate is a nonselective herbicide of systemic action that inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase, thus compromising amino acid production and consequently the growth and development of susceptible plants. The objective of this study was to evaluate the hormetic effect of glyphosate on the morphology, physiology, and biochemistry of coffee plants. Coffee seedlings (Coffea arabica cv Catuaí Vermelho IAC-144) were transplanted into pots filled with a mixture of soil and substrate and subjected to ten doses of glyphosate: 0, 11.25, 22.5, 45, 90, 180, 360, 720, 1440, and 2880 g acid equivalent (ae) ha−1. Evaluations were performed using the morphological, physiological, and biochemical variables. Data analysis for the confirmation of hormesis occurred with the application of mathematical models. The hormetic effect of glyphosate on coffee plant morphology was determined by the variables plant height, number of leaves, leaf area, and leaf, stem, and total dry mass. Doses from 14.5 to 30 g ae ha−1 caused the highest stimulation. In the physiological analyses, the highest stimulation was observed upon CO2 assimilation, transpiration, stomatal conductance, carboxylation efficiency, intrinsic water use efficiency, electron transport rate, and photochemical efficiency of photosystem II at doses ranging from 4.4 to 55 g ae ha−1. The biochemical analyses revealed significant increases in the concentrations of quinic acid, salicylic acid, caffeic acid, and coumaric acid, with maximum stimulation at doses between 3 and 140 g ae ha−1. Thus, the application of low doses of glyphosate has positive effects on the morphology, physiology, and biochemistry of coffee plants. [ABSTRACT FROM AUTHOR]

Glyphosate is a nonselective herbicide of systemic action that inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase, thus compromising amino acid production and consequently the growth and development of susceptible plants. The objective of this study was to evaluate the hormetic effect of glyphosate on the morphology, physiology, and biochemistry of coffee plants. Coffee seedlings (Coffea arabica cv Catuaí Vermelho IAC-144) were transplanted into pots filled with a mixture of soil and substrate and subjected to ten doses of glyphosate: 0, 11.25, 22.5, 45, 90, 180, 360, 720, 1440, and 2880 g acid equivalent (ae) ha−1. Evaluations were performed using the morphological, physiological, and biochemical variables. Data analysis for the confirmation of hormesis occurred with the application of mathematical models. The hormetic effect of glyphosate on coffee plant morphology was determined by the variables plant height, number of leaves, leaf area, and leaf, stem, and total dry mass. Doses from 14.5 to 30 g ae ha−1 caused the highest stimulation. In the physiological analyses, the highest stimulation was observed upon CO2 assimilation, transpiration, stomatal conductance, carboxylation efficiency, intrinsic water use efficiency, electron transport rate, and photochemical efficiency of photosystem II at doses ranging from 4.4 to 55 g ae ha−1. The biochemical analyses revealed significant increases in the concentrations of quinic acid, salicylic acid, caffeic acid, and coumaric acid, with maximum stimulation at doses between 3 and 140 g ae ha−1. Thus, the application of low doses of glyphosate has positive effects on the morphology, physiology, and biochemistry of coffee plants.

The laxative properties of senna are attributed to the presence of sennosides produced in the plant. The low production level of sennosides in the plant is an important impediment to their growing demand and utilization. Understanding biosynthetic pathways helps to engineer them in terms of enhanced production. The biosynthetic pathways of sennoside production in plants are not completely known yet. However, attempts to get information on genes and proteins engaged in it have been made which decode involvement of various pathways including shikimate pathway. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) is a key enzyme involved in sennosides production through the shikimate pathway. Unfortunately, there is no information available on proteomic characterization of DAHPS enzyme of senna (caDAHPS) resulting in lack of knowledge about its role. We for the first time characterized DAHPS enzyme of senna using in-silico analysis. To the best of our knowledge this is the first attempt to identify the coding sequence of caDAHPS by cloning and sequencing. We found Gln179, Arg175, Glu462, Glu302, Lys357 and His420 amino acids in the active site of caDAHPS through molecular docking. followed by molecular dynamic simulation. The amino acid residues, Lys182, Cys136, His460, Leu304, Gly333, Glu334, Pro183, Asp492 and Arg433 at the surface interact with PEP by van der Waals bonds imparting stability to the enzyme-substrate complex. Docking results were further validated by molecular dynamics. The presented in-silico analysis of caDAHPS will generate opportunities to engineer the sennoside biosynthesis in plants.Communicated by Ramaswamy H. Sarma.

In light of climate change and risks of food insecurity, it is becoming increasingly important to preserve plant germplasm in genebanks. Storage of seeds, particularly via cryopreservation, is one of the most proficient methods for ex situ plant germplasm conservation. Whilst seed cryo-banking can have little, to no, or even beneficial effects on subsequent seedling vigor in some species, it can lead to a number of plant abnormalities (morphological and physiological). This study investigated the effects of maize seed cryopreservation on seedling growth (until 14 d) and levels of selected amino acids produced in the shikimate pathway, a major link between primary and secondary metabolism. Seed cryopreservation reduced FW in recovered seedlings, reduced caffeic acid (2.5-fold decrease), and increased levels of all other shikimate pathway–related compounds assessed: phenylalanine (2.9-fold increase), tyrosine (2.6-fold increase), and shikimic (2.1-fold increase) and protocathecuic (3.1-fold increase) acids in cotyledons. Our results suggest that maize seed cryopreservation results in seedlings that exhibit signs of an 'overly' efficient and caffeic acid–deficient shikimate pathway, possibly related to their reduced growth during a highly vulnerable growth stage. However, these metabolic abnormalities manifested most severely in the maternal (cotyledonary), as opposed to vegetative (roots, stems, and leaves), tissues and hence are likely to disappear when the seedlings shed the cotyledons and become completely autotrophic. [ABSTRACT FROM AUTHOR]

The use of mixed nitrate and ammonium as a nitrogen source can improve plant growth. Here, we used metabolomics and transcriptomics to study the underlying mechanisms. Maize plants were grown hydroponically in the presence of three forms of nitrogen (nitrate alone, 75%/25% nitrate/ammonium, and ammonium alone). Plants grown with mixed nitrogen had a higher photosynthetic rate than those supplied only with nitrate, and had the highest leaf area and shoot and root biomass among the three nitrogen treatments. In shoot and root, the concentration of nitrogenous compounds (ammonium, glutamine, and asparagine) and carbohydrates (sucrose, glucose, and fructose) in plants with a mixed nitrogen supply was higher than that with nitrate supply, but lower than that with ammonium supply. The activity of the related enzymes (glutamate synthase, asparagine synthase, phosphoenolpyruvate carboxylase, invertase, and ADP-glucose pyrophosphorylase) changed accordingly. Specifically, the mixed nitrogen source enhanced auxin synthesis via the shikimic acid pathway, as indicated by the higher levels of phosphoenolpyruvate and tryptophan compared with the other two treatments. The expression of corresponding genes involving auxin synthesis and response was up-regulated. Supply of only ammonium resulted in high levels of glutamine and asparagine, starch, and trehalose hexaphosphate. We conclude that, in addition to increased photosynthesis, mixed nitrogen supply enhances leaf growth via increasing auxin synthesis to build a large sink for carbon and nitrogen utilization, which, in turn, facilitates further carbon assimilation and nitrogen uptake. [ABSTRACT FROM AUTHOR]

Secondary phenolic metabolites are defined as valuable natural products synthesized by different organisms that are not essential for growth and development. These compounds play an essential role in plant defense mechanisms and an important role in the pharmaceutical, cosmetics, food, and agricultural industries. Despite the vast chemical diversity of natural compounds, their content in plants is very low, and, as a consequence, this eliminates the possibility of the production of these interesting secondary metabolites from plants. Therefore, microorganisms are widely used as cell factories by industrial biotechnology, in the production of different non-native compounds. Among microorganisms commonly used in biotechnological applications, yeast are a prominent host for the diverse secondary metabolite biosynthetic pathways. Saccharomyces cerevisiae is often regarded as a better host organism for the heterologous production of phenolic compounds, particularly if the expression of different plant genes is necessary.

Abstract: Glyphosate has been shown to affect the development of plant disease in several ways. Plants utilize phenolic and other shikimic acid pathway‐derived compounds as part of their defense against pathogens, and glyphosate inhibits the biosynthesis of these compounds via its mode of action. Several studies have shown a correlation between enhanced disease and suppression of phenolic compound production after glyphosate. Glyphosate‐resistant crop plants have also been studied for changes in resistance as a result of carrying the glyphosate resistance trait. The evidence indicates that neither the resistance trait nor application of glyphosate to glyphosate‐resistant plants increases susceptibility to disease. The only exceptions to this are cases where glyphosate has been shown to reduce rust diseases on glyphosate‐resistant crops, supporting a fungicidal role for this chemical. Finally, glyphosate treatment of weeds or volunteer crops can cause a temporary increase in soil‐borne pathogens that may result in disease development if crops are planted too soon after glyphosate application. © 2017 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

A wide range of commercially relevant aromatic chemicals can be synthesized via the shikimic acid pathway. Thus, this pathway has been the target of diverse metabolic engineering strategies. In the present work, an optimized yeast strain for production of the shikimic acid pathway intermediate 3-dehydroshikimate (3-DHS) was generated, which is a precursor for the production of the valuable compounds cis, cis-muconic acid (CCM) and gallic acid (GA). Production of CCM requires the overexpression of the heterologous enzymes 3-DHS dehydratase AroZ, protocatechuic acid (PCA) decarboxylase AroY and catechol dioxygenase CatA. The activity of AroY limits the yield of the pathway. This repertoire of enzymes was expanded by a novel fungal decarboxylase. Introducing this enzyme into the pathway in the optimized strain, a titer of 1244 mg L-1 CCM could be achieved, yielding 31 mg g-1 glucose. This represents the highest yield of this compound reported in Saccharomyces cerevisiae to date. To demonstrate the applicability of the optimized strain for production of other compounds from 3-DHS, we overexpressed AroZ together with a mutant of a para-hydroxybenzoic acid hydroxylase with improved substrate specificity for PCA, PobAY385F. Thereby, we could demonstrate the production of GA for the first time in S. cerevisiae. [ABSTRACT FROM AUTHOR]

The phenolic compounds are part of one of the most abundant groups within the secondary metabolites. These are biosynthesized in plants by means of routes such as shikimic acid and acetate-malonate. In this review, they are mentioned some groups of polyphenols that are originated in vegetables by means of these routes. Through the route of the shikimate they can produce aromatic acids such as chorismic acid, preferential, quinic, gallic acid that can be building blocks of many other more functionalized compounds. Also, cinnamic acid can obtain groups as diverse as coumarins, chalcones, flavonols, flavanones, lignins, lignans. If the reference is made to the acetate-malonate route, simple phenols such as 6-methylsalicylic acid and other derivatives such as orsellinic acid and derivatives can be generated. Due to the applicative importance of polyphenols, some chemical synthesis methods have been proposed to obtain them, some of which are mentioned in this document. Because of the variety of chemical structure some research results are presented where the biological activity of polyphenols was studied, as reports of antioxidant, antimicrobial, anticancer activities, and other biological activities. Phenolic compounds are a very diverse group of secondary metabolites, which have been and will continue to be studied, mainly through their biological activity, and the need to understand their biosynthesis in plants and other organisms. [ABSTRACT FROM AUTHOR]

Saccharomyces cerevisiae has been extensively engineered for optimising its performance as a microbial cell factory to produce valuable aromatic compounds and their derivatives as bulk and fine chemicals. The production of heterologous aromatic molecules in yeast is achieved via engineering of the aromatic amino acid biosynthetic pathway. This pathway is connected to two pathways of the central carbon metabolism, and is highly regulated at the gene and protein level. These characteristics impose several challenges for tailoring it, and various modifications need to be applied in order to redirect the carbon flux towards the production of the desired compounds. This minireview addresses the metabolic engineering approaches targeting the central carbon metabolism, the shikimate pathway and the tyrosine and phenylalanine biosynthetic pathway of S. cerevisiae for biosynthesis of aromatic chemicals and their derivatives from glucose. [ABSTRACT FROM AUTHOR]

Abstract: The application of postharvest abiotic stresses is an effective strategy to activate the primary and secondary metabolism of plants inducing the accumulation of antioxidant phenolic compounds. In the present study, the effect of water stress applied alone and in combination with wounding stress on the activation of primary (shikimic acid) and secondary (phenylpropanoid) metabolic pathways related with the accumulation of phenolic compound in plants was evaluated. Carrot (Daucus carota) was used as model system for this study, and the effect of abiotic stresses was evaluated at the gene expression level and on the accumulation of metabolites. As control of the study, whole carrots were stored under the same conditions. Results demonstrated that water stress activated the primary and secondary metabolism of carrots, favoring the lignification process. Likewise, wounding stress induced higher activation of the primary and secondary metabolism of carrots as compared to water stress alone, leading to higher accumulation of shikimic acid, phenolic compounds and lignin. Additional water stress applied on wounded carrots exerted a synergistic effect on the wound-response at the gene expression level. For instance, when wounded carrots were treated with water stress, the tissue showed 20- and 14-fold increases in the relative expression of 3-deoxy-D-arabino-heptulosanate synthase and phenylalanine ammonia-lyase genes, respectively. However, since lignification was increased, lower accumulation of phenolic compounds was detected. Indicatively, at 48 h of storage, wounded carrots treated with water stress showed ~31% lower levels of phenolic compounds and ~23% higher lignin content as compared with wounded controls. In the present study, it was demonstrated that water stress is one of the pivotal mechanism of the wound-response in carrot. Results allowed the elucidation of strategies to induce the accumulation of specific primary or secondary metabolites when plants are treated with water stress alone or when additional water stress is applied on wounded tissue. If the accumulation of a specific primary or secondary metabolite were desirable, it would be recommended to apply both stresses to accelerate their biosynthesis. However, strategies such as the use of enzymatic inhibitors to block the carbon flux and enhance the accumulation of specific compounds should be designed.

Flavonoids are the main flavor components and functional ingredients in tea, and the shikimic acid pathway is considered as one of the most important pathways in flavonoid biosynthesis, but little was known about the function of regulatory genes in the metabolism phenolic compounds in tea plant ( Camellia sinensis), especially related genes in shikimic acid pathway. The dynamic changes of catechin (predominant flavonoid) contents were analyzed in this study, and four genes ( CsPPT, CsDAHPS, CsSDH and CsCS) involving in shikimic acid pathway in C. sinensis albino cultivar 'Baicha 1' were cloned and characterized. The full-length cDNA sequences of these genes were obtained using reverse transcription-PCR and rapid amplification of cDNA ends. At the albinistic stage, the amounts of all catechins decreased to the lowest levels, when epigallocatechin gallate was the highest, whereas gallocatechin-3-O-gallate the lowest. Gene expression patterns analyzed by qRT-PCR showed that CsPPT and CsDAHPS were highly expressed in flowers and buds, while CsSDH and CsCS showed high expression levels in buds and leaves. It was also found that the transcript abundance of shikimic acid biosynthetic genes followed a tightly regulated biphasic pattern, and was affected by albinism. The transcript levels of CsPPT and CsDAHPS were decreased at albinistic stage followed elevated expression, whereas CsSDH and CsCS were increased only at re-greening stage. Taken together, these findings suggested that these four genes in C. sinensis may play different roles in shikimic acid biosynthesis and these genes may have divergent functions. [ABSTRACT FROM AUTHOR]

OBJECTIVE: To examine the skin whitening capabilities of shikimic acid pathway compounds and find the most effective molecule to be used as the active ingredient for skin whitening products. MATERIALS AND METHODS: Skin whitening is the practice of using chemical substances to lighten skin tone by the lessening the concentration of melanin. The whitening efficacy of shikimic acid pathway compounds was evaluated. Eight compounds in the shikimic acid pathway were chosen for this study: benzoic acid, p-coumaric acid, vanillic acid, syringic acid, quinic acid, shikimic acid, orcinol monohydrate, and phenyl pyruvic acid. We measured the tyrosinase inhibitory capacity of the compounds in the animal model of zebrafish and also evaluated the compounds' anti-oxidant activities using the DPPH radical scavenging, and ABTS+ free radical scavenging tests. Compounds' cytotoxicity effects were also evaluated. RESULTS: Amongst eight shikimic acid pathway compounds used in this study, shikimic acid was the most potent tyrosinase-inhibitor and the most efficient compound to be used as an active ingredient for skin whitening. Shikimic acid revealed a good radical scavenging activity (RAS) with low cell toxicity. CONCLUSIONS: Promising results obtained in this study may open a new window of opportunity to introduce another compound to be used in the skin-whiting cosmetics industry. [ABSTRACT FROM AUTHOR]

Upon herbivory, plants activate complex biochemical pathways that result in an array of defense responses including the emission of a novel blend of volatile organic compounds (VOCs). These compounds mediate the recruitment of predators and parasitoids that exert biological control of the attacking herbivore. Genetic manipulation of a particular trait to improve agricultural plant varieties may affect other traits as a result of possible pleiotropy or insertional mutations, which in turn can affect the interaction of the plant with other organisms. Changes in herbivore-induced VOC emissions are known to occur in transgenic plants engineered to express resistance to insects (mainly Bt-plants), not only as a result of modified insect behavior but also as a result of altered resource allocation. Transgenic glyphosate-resistant plants express a variant of the enzyme EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) that is insensitive to the herbicide glyphosate. This enzyme is essential in metabolic routes that result in the synthesis of amino acids and secondary metabolites. We addressed whether the constitutive and Anticarsia gemmatalis-induced emissions of VOCs from a transgenic soybean line differ from those of the isoline, and whether changes may interfere in the foraging behavior of the predatory bug Podisus nigrispinus. Analyses showed that both herbivory and genotype influenced VOC emissions. In addition, the genotype affected the herbivore-induced VOC emission. Larger emissions were measured in the transgenic line than the non-transgenic line upon herbivory. The bioassays showed that P. nigrispinus significantly discriminated only between the odors of undamaged and damaged plants of the non-transgenic line. No preference was observed for herbivore-damaged plants of any of the two lines over the other. The results from this study suggest that despite a greater emission of volatiles the predators are less able to discriminate between herbivore-damaged and undamaged transgenic plants. This condition does not necessarily increase the preference of the predator for damaged non-transgenic plants over transgenic plants. This study opens possibilities for new studies of chemical ecology in tritrophic systems to assess the effect of transgenic glyphosate-resistant plants. [ABSTRACT FROM AUTHOR]

[Display omitted] • Evaluated humic substance formation differences in different materials composting. • To confirm the effect of shikimic acid pathway (SAP) to humic substance formation. • Identified the core bacteria related to converting SAP products to humic substance. • Identified the key impact factors of humic substance formation. • A new idea for promoting humic substance formation in composting was proposed. This study aimed to evaluate differences in humic substance (HS) formation based on the shikimic acid pathway (SAP) during five different materials composting. The results showed that compared with other three materials, gallic acid, protocatechuic acid and shikimic acid of the SAP products in lawn waste (LW) and garden waste (GW) compost decreased significantly. Furthermore, as important indicators for evaluating humification, humic acid and degree of polymerization increased by 39.4%, 79.5% and 21.8%, 87.9% in LW and GW, respectively. Correlation analysis showed that SAP products were strongly correlated with HS fractions in LW and GW. Meanwhile, network analysis indicated that more core bacteria associated with both SAP products and HS were identified in LW and GW. Finally, the structural equation model proved that SAP had more significant contribution to humification improvement in LW and GW. These findings provided theoretical foundation and feasible actions to improve compost quality by the SAP. [ABSTRACT FROM AUTHOR]

Coffee is a popular roasted beverage that provides health benefits through phenolic antioxidants. However, roasting effect on antioxidant activity remains inconclusive, and changes of phenolic composition in coffee beans occurring upon roasting could provide valuable information about the health attributes of phenolic compounds in coffee. This study aims to determine antioxidant activity, total phenolic content, purpurogallin and other phenolic compounds in coffees from different geographic origins with different roasting degrees. In coffee extracts, antioxidant activity and total phenolic content ranged from 63.9 to 92.0 mg Trolox equivalents per gram dry weight of coffee, and 36.0–57.7 mg gallic acid equivalents per gram dry weight of coffee, respectively. However, both antioxidant activity and total phenolic content did not correlate with roasting degree (p > 0.05). Chlorogenic acid decreased (p < 0.0001) with increased roasting degree, while shikimic acid, caffeic acid, gallic acid, pyrogallol, and purpurogallin increased (p < 0.0001) correspondingly. Roasting could therefore enhance the formation of purpurogallin and other phenolic compounds, which compensates for the decreased antioxidant activity due to the breakdown of chlorogenic acid. In addition, gallic acid, pyrogallol, and purpurogallin were not detected in green coffee beans and could be converted from other phenolic compounds during roasting. • Antioxidant activity and total phenolic content did not correlate with roasting. • Chlorogenic acid decreased with increased roasting degree. • Gallic acid, pyrogallol, and purpurogallin were not detected in green coffee beans. • Gallic acid, pyrogallol, and purpurogallin were formed during coffee roasting. • The formed phenolics could compensate for the decreased antioxidant capacity. [ABSTRACT FROM AUTHOR]

[Display omitted] • The key factors affecting shikimic acid (SA) pathway were identified. • The key influencing factors of each metabolite were obviously different. • Only the SA content in lawn waste could be affected by physicochemical factors. • The more complex environment, the more factors that restrict protocatechuic acid. • A new direction for improving SA metabolic intensity during composting. Metabolites of shikimic acid (SA) pathway can be used as humic substance (HS) precursors. Due to the complexity of SA anabolism, there were few studies on SA pathway during composting. The aim of this study was to identify the key drivers of SA pathway during different materials composting. During composting, the SA, protocatechuic acid (PA) and gallic acid (GA) decreased by 57.09%, 72.27% and 54.04% on average, respectively. The structural equation model showed that SA had key driving factors (organic matter and pH) during lawn waste composting. In addition, the complexity of material structure was the main factor affecting PA driving factors. The factors and degree of influence on GA varied with different materials. Accordingly, this study provided theoretical support for the improvement of SA metabolic intensity by single material and mixed material composting, and further provided a new direction for future HS research. [ABSTRACT FROM AUTHOR]

The application of postharvest abiotic stresses is an effective strategy to activate the primary and secondary metabolism of plants inducing the accumulation of antioxidant phenolic compounds. In the present study, the effect of water stress applied alone and in combination with wounding stress on the activation of primary (shikimic acid) and secondary (phenylpropanoid) metabolic pathways related with the accumulation of phenolic compound in plants was evaluated. Carrot (Daucus carota) was used as model system for this study, and the effect of abiotic stresses was evaluated at the gene expression level and on the accumulation of metabolites. As control of the study, whole carrots were stored under the same conditions. Results demonstrated that water stress activated the primary and secondary metabolism of carrots, favoring the lignification process. Likewise, wounding stress induced higher activation of the primary and secondary metabolism of carrots as compared to water stress alone, leading to higher accumulation of shikimic acid, phenolic compounds, and lignin. Additional water stress applied on wounded carrots exerted a synergistic effect on the wound-response at the gene expression level. For instance, when wounded carrots were treated with water stress, the tissue showed 20- and 14-fold increases in the relative expression of 3-deoxy-D-arabino-heptulosanate synthase and phenylalanine ammonia-lyase genes, respectively. However, since lignification was increased, lower accumulation of phenolic compounds was detected. Indicatively, at 48 h of storage, wounded carrots treated with water stress showed ~31% lower levels of phenolic compounds and ~23% higher lignin content as compared with wounded controls. In the present study, it was demonstrated that water stress is one of the pivotal mechanism of the wound-response in carrot. Results allowed the elucidation of strategies to induce the accumulation of specific primary or secondary metabolites when plants are treated with water stress alone or when additional water stress is applied on wounded tissue. If the accumulation of a specific primary or secondary metabolite were desirable, it would be recommended to apply both stresses to accelerate their biosynthesis. However, strategies such as the use of enzymatic inhibitors to block the carbon flux and enhance the accumulation of specific compounds should be designed. [ABSTRACT FROM AUTHOR]

Background: The shikimic acid (SA) pathway is a fundamental route to synthesize aromatic building blocks for cell growth and metabolic processes, as well as for fermentative production of various aromatic compounds. Genes encoding enzymes of SA pathway are not continuous on genome and they are differently regulated. Results: In this study, efforts were made to construct continuous genetic modules of SA pathway that are regulated by a same Ptac promoter. Firstly, aro genes [aroG (NCgl2098), aroB (NCgl1559), aroD (NCgl0408) and aroE (NCgl1567)] from Corynebacterium glutamicum and ribosome binding site (RBS) libraries that were tailored for the above genes were obtained, and the strength of each RBS in the 4 libraries was quantified. Secondly, 9 genetic modules were built up from the RBS libraries, a previously characterized ribozyme insulator (RiboJ) and transcriptional promoter (Ptac) and terminator, and aroG, aroB, aroD and aroE. The functionality and efficiency of the constructed genetic modules were evaluated in C. glutamicum by determination of SA synthesis. Results showed that C. glutamicum RES167ΔaroK carrying a genetic module produced 4.3 g/L of SA, which was 54 folds higher compared to that of strain RES167ΔaroK (80 mg/L, without the genetic module) during fermentation in 250-mL flasks. The same strain produced 7.4, and 11.3 g/L of SA during 5-L batch and fed-batch fermentations, respectively, which corresponding to SA molar yields of 0.39 and 0.24 per mole sucrose consumption. Conclusion: These results demonstrated that the constructed SA pathway modules are effective in increasing SA synthesis in C. glutamicum, and they might be useful for fermentative production of aromatic compounds derived from SA pathway. [ABSTRACT FROM AUTHOR]

[Display omitted] • Significant effect of herbicide stress on catecholamine content. • Stimulation of catecholamine metabolism after contact with pesticide. • Effects of pesticides on vitamin B3 and B9 content. Japanese radish Daikon (Raphanus sativus) sprouts were exposed, under the model plant growing conditions, to herbicide stress induced by triketone herbicides (mesotrione and sulcotrione) as well as degradation products (4-methylsulfonyl-2-nitrobenzoic acid, amino-4-(methylsulfonyl)benzoic acid, 2-chloro-4-mesylbenzoic acid and cyclohexane-1,3-dione). Changes in the content of selected l -tyrosine metabolites (dopamine, tyramine, normetanephrine) and catecholamine synthesis cofactors (water-soluble vitamins) were monitored in plant tissues using high-performance liquid chromatography. Normetanephrine content increased up to 0.13 mg per gram of sprouts, 1500-fold higher than in the control sample. Tyramine and dopamine content increased by 50 % and 100 %, respectively. These changes corresponded with changes in the content of B3 and B9 vitamins. It has been proved that contact of the plant with this group of herbicides and theirs degradation products leads to a disturbance in the l -tyrosine metabolism. Consequently, this also leads to significant changes in the quality of foods of plant origin. [ABSTRACT FROM AUTHOR]

Type II dehydroquinase (DHQ2) is the third enzyme of the shikimic acid pathway, and it has been the effective target for tuberculosis (TB). So far, developing multiple potent inhibitors of the DHQ2 ofMycobacterium tuberculosis(DHQ2-Mt) has been considered to be the new therapy to TB. Molecular dynamics simulations followed by molecular mechanics-generalised Born surface area were carried out to calculate the free binding energy and to determine the affinity ability of the four chosen inhibitor molecules,L1,L2,L3andL4. Energy decomposition analyses show the electrostatic interaction and van der Waals interaction of the ligands to every residue of the DHQ2-Mt. The results suggest that some important residues have different interactions with the four ligands, such as Arg19 and Tyr24. These interactions may have an effect on the ligand binding affinity. The binding affinity of monosubstituted inhibitor is higher than that of disubstituted inhibitor, due to some important interactions with the DHQ2-Mt residues. These computational works will be significant to the theoretical research in the future. [ABSTRACT FROM AUTHOR]

Background: A central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete shikimic acid pathway, whereas metazoans lacking this pathway require a dietary source of these compounds. The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes. Using Hidden Markov Model profiles (HMM profiles) to identify all known enzymes of the pathway, we report the presence of genes encoding shikimate pathway enzymes in the hypothetical proteomes constructed from the genomes of 488 sequenced prokaryotes. Results: Amongst free-living prokaryotes most Bacteria possess, as expected, genes encoding a complete shikimic acid pathway, whereas of the culturable Archaea, only one was found to have a complete complement of recognisable enzymes in its predicted proteome. It may be that in the Archaea, the primary amino-acid sequences of enzymes of the pathway are highly divergent and so are not detected by HMM profiles. Alternatively, structurally unrelated (non-orthologous) proteins might be performing the same biochemical functions as those encoding recognized genes of the shikimate pathway. Most surprisingly, 30% of host-associated (mutualistic, commensal and pathogenic) bacteria likewise do not possess a complete shikimic acid pathway. Many of these microbes show some degree of genome reduction, suggesting that these host-associated bacteria might sequester essential aromatic compounds from a parasitised host, as a 'shared metabolic adaptation' in mutualistic symbiosis, or obtain them from other consorts having the complete biosynthetic pathway. The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic pathways. Conclusions: These results challenge the conventional belief that the shikimic acid pathway is universal and essential in prokaryotes. The possibilities that non-orthologous enzymes catalyse reactions in this pathway (especially in the Archaea), or that there exist specific uptake mechanisms for the acquisition of shikimate intermediates or essential pathway products, warrant further examination to better understand the precise metabolic attributes of host-beneficial and pathogenic bacteria. [ABSTRACT FROM AUTHOR]

Abstract: The theoretical 2H-distribution in the aromatic ring of phenylpropanoids can be predicted from that of their precursors – erythrose-4-phosphate, phosphoenolpyruvate and NADPH – and by invoking the mechanism of the NIH-shift and implied deuterium isotope effects. For each position in the non-oxygenated ring, the predicted natural 2H-abundance is in excellent agreement with experimental data obtained from quantitative 2H NMR-measurements on natural compounds, especially concerning the relative 2H-abundances p > o ⩾ m. For the p-hydroxylated derivatives, the experimentally determined 2H-abundance sequence order m > o can also be deduced, assuming an anisotropic migration (intramolecular isotope effect) of the p-hydrogen atom to the two differently 2H-substituted m-positions during the NIH-shift (intramolecular hydrogen transfer) and an in vivo deuterium kinetic isotope effect of ∼1.20 on the final hydrogen elimination from the proposed ketodiene intermediate. The predicted 2H-distribution pattern of methyl salicylate 10, a representative of an o-hydroxylated natural compound, is in excellent agreement with that reported from 2H NMR analyses. However, for salicyl alcohol, minor differences between the theoretical and experimentally determined pattern are found that cannot yet be satisfactorily explained. On the other hand, a very good agreement is found between the theoretical and experimental pattern of coumarin, provided a deuterium kinetic isotope effect of ∼1.30 is assumed for the elimination of the H-atoms from the ketodiene intermediate. The secondary m-hydroxylation of p-coumaric acid in the biosynthesis of vanillin seems to proceed without large isotope effects. Parallel differences are also observed for the 18O-kinetic isotope effects on the corresponding monooxygenase-catalysed reactions. The results demonstrate convincingly that the mechanisms of these general reactions of the phenylpropanoid biosynthetic pathway are identical and follow general principles. Small observed differences between the 2H-patterns of individual natural aromatic compounds originating from the same hydroxylation type can therefore be assigned to differences of the patterns of the precursors, the extent and the orientation of the hydrogen migration, and the kinetic isotope effect on the final hydrogen elimination. The evidence for the existence of general systematic rules governing isotopic patterns in the shikimic acid pathway and its subsequent reactions is further supported by the recently reported13C-distribution pattern of vanillin, which is also in agreement with that predicted from the precursors. Hence, it is apparent that the systematics of the isotope patterns of phenylpropanoids are in line with the generally accepted biosynthetic reactions in the shikimic acid pathway and that this knowledge can strengthen their value as an essential support for the distinction of natural and synthetic aromatic compounds. [Copyright &y& Elsevier]

Secondary phenolic metabolites are defined as valuable natural products synthesized by different organisms that are not essential for growth and development. These compounds play an essential role in plant defense mechanisms and an important role in the pharmaceutical, cosmetics, food, and agricultural industries. Despite the vast chemical diversity of natural compounds, their content in plants is very low, and, as a consequence, this eliminates the possibility of the production of these interesting secondary metabolites from plants. Therefore, microorganisms are widely used as cell factories by industrial biotechnology, in the production of different non-native compounds. Among microorganisms commonly used in biotechnological applications, yeast are a prominent host for the diverse secondary metabolite biosynthetic pathways. Saccharomyces cerevisiae is often regarded as a better host organism for the heterologous production of phenolic compounds, particularly if the expression of different plant genes is necessary. [ABSTRACT FROM AUTHOR]