Comparative physiological, metabolomic, and transcriptomic analyses reveal developmental stage-dependent effects of cluster bagging on phenolic metabolism in Cabernet Sauvignon grape berries.

BACKGROUND: Light conditions significantly influence grape berry ripening and the accumulation of phenolic compounds, but the underlying molecular basis remains partially understood. Here, we applied integrated transcriptomics and pathway-level metabolomics analyses to investigate the effect of cluster bagging during various developmental stages on phenolic metabolism in Cabernet Sauvignon grapes. RESULTS: Bagging treatments had limited effects on berry quality attributes at harvest and did not consistently affect phenolic acid biosynthesis between seasons. Significantly elevated flavan-3-ol and flavonol contents were detected in re-exposed berries after bagging during early-developmental stages, while bagging after véraison markedly inhibited skin anthocyanin accumulation. Several anthocyanin derivatives and flavonol glycosides were identified as marker phenolic metabolites for distinguishing bagged and non-bagged grapes. Coordinated transcriptional changes in the light signaling components CRY2 and HY5/HYHs, transcription regulator MYBA1, and enzymes LAR, ANR, UFGT and FLS4, coincided well with light-responsive biosynthesis of the corresponding flavonoids. The activation of multiple hormone signaling pathways after both light exclusion and re-exposure treatments was inconsistent with the changes in phenolic accumulation, indicating a limited role of plant hormones in mediating light/darkness-regulated phenolic biosynthesis processes. Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. CONCLUSIONS: Altogether, our findings provide novel insights into the understanding of berry phenolic biosynthesis under light/darkness and practical guidance for improving grape features.

Microbial production of O-methylated flavanones from methylated phenylpropanoic acids in engineered Escherichia coli.

Methylated flavonoids possess improved bioactivities compared to their unmethylated counterparts. In this study, for the efficient production of O-methylated flavonoids from simple methylated phenylpropanoic acids, a recombinant Escherichia coli strain expressing 4-coumarate:coenzyme A ligase (4CL) from Oryza sativa and chalcone synthase (CHS) from Hordeum vulgare was constructed; this strain produced significant amount of homoeriodictyol (~ 52 mg/L) as well as a few amount of hesperetin (0.4 mg/L), respectively, from ferulic acid and 4-methylcaffeic acid. This demonstrates, for the first time, that the scarce but valuable methylated flavanones can be successfully produced from methylated phenylpropanoic acids in a microbial host via an artificial biosynthetic pathway consisting of 4CL and CHS that can accept O-methylated precursors.

Effects of growth temperature and carbon dioxide enrichment on soybean seed components at different stages of development.

Soybean plants were grown to maturity in controlled environment chambers and at the onset of flowering three temperature treatments were imposed that provided optimum [28/24 °C], low [22/18 °C] or high [36/32 °C] chamber air temperatures. In addition, plants were treated continuously with either 400 or 800 µmol mol-1 CO2. Seeds were harvested at 42, 53, 69 and 95 days after planting (i.e., final maturity). This study quantified 51 metabolites in developing soybean seeds, plus total lipids and proteins were measured at maturity. About 80% of measured soluble carbohydrates, amines and organic acids decreased to low levels in mature seeds, although important exceptions were raffinose, ribose/arabinose, citrate and all eight fatty acids. This suggested that the metabolism of young seeds supported lipid and protein synthesis. A total of 35 and 9 metabolites differed among temperature and CO2 treatments, respectively, and treatment effects were predominately observed on the first and second samplings. However, shikimate, pinitol and oleate were increased by high temperature treatments in mature seeds. The above results indicated that CO2 enrichment primarily altered metabolite levels during the initial stages of seed development and this was likely due to enhanced photosynthate formation in leaves.

Short-chain aliphatic ester synthesis using Thermobifida fusca cutinase.

Short-chain aliphatic esters are commonly used as fruit flavorings in the food industry. In this study, Thermobifida fusca (T. fusca) cutinase was used for the synthesis of aliphatic esters, and the maximum yield of ethyl caproate reached 99.2% at a cutinase concentration of 50U/ml, 40°C, and water content of 0.5%, representing the highest ester yield to date. The cutinase-catalyzed esterification displayed strong tolerance for water content (up to 8%) and acid concentration (up to 0.8M). At substrate concentrations ⩽0.8M, the ester yield remained above 80%. Moreover, ester yields of more than 98% and 95% were achieved for acids of C3-C8 and alcohols of C1-C6, respectively, indicating extensive chain length selectivity of the cutinase. These results demonstrate the superior ability of T. fusca cutinase to catalyze the synthesis of short-chain esters. This study provides the basis for industrial production of short-chain esters using T. fusca cutinase.

Analysis of phenolic compounds and antioxidant abilities of extracts from germinating Vitis californica seeds submitted to cold stress conditions and recovery after the stress.

The material for this study consisted of stratified seeds of Vitis californica submitted to germination under optimum conditions (+25 °C) or under chill stress (+10 °C), also followed by recovery. It has been determined that the germinating seeds contain considerable amounts of tannins, catechins as well as phenolic acids such as gallic, p-coumaric, caffeic and ferulic acids. Gallic acid appeared in the highest amount in the germinating seeds (from 42.40-204.00 µg/g of fresh weight (FW)), followed by caffeic acid (from 6.62-20.13 µg/g FW), p-coumaric acid (from 2.59-5.41 µg/g FW), and ferulic acid (from 0.56-0.92 µg/g FW). The phenolic acids occurred mostly in the ester form. Under chill stress, the germinating seeds were determined to contain an elevated total amount of phenolics, as well as raised levels of condensed tannins, catechins, gallic acid, and gafeic acid. The levels of p-coumoric and ferulic acids were found to have decreased. In extracts isolated from a sample exposed to low temperature, increased antioxidant activity and reduction potential were also demonstrated. Tissue of the germinating seeds which underwent post-stress recovery was found to have less total phenolics.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins.

Secondary metabolite profile in induced tetraploids of wild Solanum commersonii Dun.

The main aim of this work was to study the leaf secondary metabolite profiles of artificially induced tetraploids (2n=4x=48) of Solanum commersonii, a diploid (2n=2x=24) wild potato species. The tetraploid genotypes of S. commersonii were produced by oryzalin treatment. Both HPLC-UV and LC/MS analyses revealed that there were no qualitative differences in the metabolite profiles between the diploid S. commersonii and its tetraploids. By contrast, the results showed that the phenylpropanoid content was generally significantly higher in the tetraploids than in the diploid S. commersonii. Concerning the glycoalkaloids (GAs), the results provided evidence that the content of minor GAs (solanidenediol triose, solanidadienol lycotetraose, and solanidenol lycotetraose) was higher in tetraploids than in the diploid progenitor, while the content of major GAs (dehydrodemissine and dehydrocommersonine) was significantly higher in diploid S. commersonii than in its tetraploid genotypes. The results are discussed from the practical perspective of potato biodiversity enhancement.

Effects of dam and/or seqA mutations on the fatty acid and phospholipid membrane composition of Salmonella enterica serovar Typhimurium.

We examined the phospholipids (Phls) and the membrane fatty acid (FA) composition in Salmonella enterica serovar Typhimurium dam and/or seqA mutants. Phosphatidylglycerol, phosphatidylethanolamine (PE), and cardiolipin (CL) are the major Phls present in all the strains and accounted for greater than 95% of the total lipid phosphorus. Phosphatidic acid and phosphatidylserine are the minor ones. The seqA mutant showed a decrease in PE and an increase in CL and phosphatidylglycerol proportion compared with the wild-type strain. The same changes were observed with the seqA dam double mutant. However, the dam mutation caused an unusual accumulation of CL with a significant decrease in the PE content, compared with the isogenic wild-type strain. FA composition of the total lipids and the different fractions containing Phls have been determined. The major saturated FAs (SFAs) and unsaturated FAs (UFAs) found were C(14:0), C(16:0) and C(16:1w7), C(18:1w9), respectively. Cyclic FAs, cyc(17:0) and cyc(19:0), were also present in appreciable amounts. Moreover, dam and/or seqA mutations caused a decrease in UFA/SFA ratio and there was a progressive reduction in the content of C(16:1w7) and C(18:1w9), going through the order seqA, dam/seqA, and dam mutants. This decrease in UFA content was compensated for in all strains by an increase in the corresponding C(17-) and C(19-) cyclic FAs. So these UFAs were converted to their cyclopropane derivatives, which resulted in a low UFA/SFA ratio. SeqA and Dam proteins might regulate FA biosynthesis and Phls composition of Salmonella enterica serovar Typhimurium.

Metabolism of berry anthocyanins to phenolic acids in humans.

We studied the metabolism of berry anthocyanins to phenolic acids in six human subjects by giving them bilberry-lingonberry puree with and without oat cereals. Puree + cereals contained 1435 micromol of anthocyanins and 339 micromol of phenolic acids. The urinary excretion of measured 18 phenolic acids increased 241 micromol during the 48 h follow-up after the puree + cereals supplementation. The excretion peak of dietary phenolic acids was observed at 4-6 h after the puree + cereals supplementation and 2 h earlier after the supplementation of the puree alone. Homovanillic and vanillic acids were the most abundant metabolites, and they were partly produced from anthocyanins. No gallic acid, a fragmentation product of delphinidin glycosides, was detected, and only a very low amount of malvidin glycosides was possibly metabolized to syringic acid. Although anthocyanins were partly fragmented to phenolic acids, still a large part of metabolites remained unknown.

Lichen photobionts show tolerance against lichen acids produced by lichen mycobionts.

In order to determine the allelopathic nature of lichen acids produced by lichen mycobionts, we compared lichen photobionts with other photosynthetic organisms in terms of inhibition of photosynthetic electron transport around photosystem II (PSII) by representative lichen acids. Whereas at the thylakoid level we found no clear difference in tolerance against lichen acids between lichen photobionts and other species, at the cellular level lichen photobionts showed strong tolerance as compared with other species. These findings suggest the presence of a lichen acid-specific exclusion or detoxification mechanism in lichen photobiont cells.

Isolation of a thermophilic and halophilic tyrosol-degrading Geobacillus from a Tunisian high-temperature oil field.

An aerobic, thermophilic, halotolerant and Gram-positive bacterium, designated strain C5, was isolated from a high-temperature oil field, located in Sfax, Tunisia, after enrichment on tyrosol. Strain C5 grew between 25 and 70 degrees C and optimally at 50 degrees C. It grew in the presence of 0-12% (w/v) NaCl, with optimum growth at 3% (w/v) NaCl. Strain C5 was able to degrade tyrosol aerobically, in the presence of 30 g L(-1) NaCl and under warm conditions (55 degrees C). The degradation of tyrosol proceeded via p-hydroxyphenylacetic and 3,4-dihydroxyphenylacetic acids. The products were confirmed by HPLC and GC-MS analyses. Strain C5 was also found to degrde a wide range of other aromatic compounds, including benzoic, p-hydroxybenzoic, protocatechuic, vanillic, p-hydroxyphenylacetic, 3,4-dihydroxyphenylacetic, cinnamic and ferulic acids, phenol and m-cresol. Moreover, strain C5 was grown on diesel and crude oil as sole carbon and energy sources. Strain C5 was also able to utilize several carbohydrates. Phenotypic characteristics and phylogenetic analysis of the 16S rRNA gene sequence of strain C5 revealed that it was related to members of the genus Geobacillus, being most closely related to the type strain of G. pallidus (99% sequence similarity). In addition, we report on growth of the type strain of G. pallidus on different aromatic compounds and hydrocarbons.

Clinical applications of urinary organic acids. Part 2. Dysbiosis markers.

Part 1 of this series focused on urinary organic acids as markers of detoxification; part 2 focuses on dysbiosis markers. Intestinal microbial growth is accompanied by the release of products of their metabolism that may be absorbed and excreted in urine. Several organic acids are known to be specific products of bacterial metabolic action on dietary polyphenols or unassimilated amino acids or carbohydrates. Associated gastrointestinal or neurological symptoms may result from irritation of the intestinal mucosa or systemic distribution of absorbed neurotoxic products. Detection of abnormally elevated levels of these products is a useful diagnostic tool for patients with gastrointestinal or toxicological symptoms. Test profiles of urinary organic acids associated with microbial overgrowth can include benzoate, hippurate, phenylacetate, phenylpropionate, cresol, hydroxybenzoate, hydroxyphenylacetate, hydroxyphenylpropionate and 3,4-dihydroxyphenylpropionate, indican, tricarballylate, D-lactate, and D-arabinitol. Effective treatments for the associated microbial overgrowths may be directed at reducing microbial populations, introducing favorable microbes, and restoring intestinal mucosal integrity.

Elimination of resin acids by advanced oxidation processes and their impact on subsequent biodegradation.

Wood pulping and paper production generate a considerable amount of wastewater, containing many pollutants among them resin and fatty acids. Resin acids contribute substantially to effluent toxicity and were identified to be detrimental to microorganisms of activated sludge and in particular to bacteria in anaerobic wastewater treatment system and other forms of aquatic life. The objective of the present study was to check the applicability of the ozone and advanced oxidation processes (AOPs) to eliminate resin acids from aqueous solutions and to determine the ozone dose required. Furthermore, an investigation of the influence of the oxidation methods on subsequent biological destruction of the byproducts was performed. Aqueous solution of the resin acids: abietic, dehydroabietic and isopimaric acids with different initial composition were subjected to ozonation or AOP processes at different ozone doses. After ozonation or advanced oxidation pretreatment the model solutions were biodegraded in aerated vessels containing activated sludge. During ozonation of the resin acids aqueous solutions the resin acids were almost eliminated, however the reduction of chemical oxygen demand (COD) was rather low. The ozone dose required to obtain reduction of resin acids >90% was in the range of 0.1-0.7mgO(3)/mgCOD, depending on the composition and concentration of model solutions. The toxicity of ozonated resin acids solutions decreased with increasing applied ozone dose up to about 0.3-0.5mgO(3)/mgCOD, thereafter increased. Ozonation and other AOP processes did not increase the rate of biodegradation of resin acids model solutions in aerated activated sludge systems compared to not pretreated solutions.

The conformational study of two carbocyclic nucleosides: why carbocyclic nucleic acids (CarNAs) form more stable duplexes with RNA than DNA does.

Replacement of the furanose moiety of DNA with a cyclopentane ring produces a modified sugar analogue: Carbocyclic nucleic acid (CarNA). UV melting-temperature experiments demonstrate that the incorporation of 2'-deoxycarbaguanosine ((c)G) and 2'-deoxyaristeromycin ((c)A) of carbocyclic nucleosides into a DNA strand increases the stability of the CarNA/RNA hybrid. Circular Dichroism (CD) study indicates that the CarNA/RNA hybrid adopts an A-like conformation. To elucidate the molecular basis of the increased stability of the CarNA/RNA, the conformation of (c)G and (c)A were examined by (1)H NMR conformational analysis of (3)J(HH) coupling constants and ab initio molecular orbital (MO) calculations. These results show that the populations of N-type of (c)G and (c)A are higher than those of dG and dA, respectively, at different temperatures [For example, 37% (N%) of (c)G vs. 28%of dG, 36% (N%) of (c)A vs. 25% of dA at 278 K], which suggest that the cyclopentane rings of (c)G and (c)A prefer the N-type conformation in two-state N-S pseudorotional equilibrium in comparison with the furanose rings of dG and dA. The DeltaH degrees of (c)G (DeltaH degrees = - 0.43 kcal mol(-1)) and (c)A (DeltaH degrees = - 0.41kcal mol(-1)) are lower than that of dG (dG = - 1.8 kcal mol(-1)) and dA (dA = - 1.0 kcal mol(-1)), respectively, which suggest that the gauche effect in the (c)A and (c)G driving N-S pseudorotional equilibrium to S-type is reduced by replacement of the 4'-oxygen by a CH(2) group. These results suggest that the preferred N-type of the (c)G and (c)A leads to the A-like conformation, which contributes to the stability of CarNA/RNA hybrid.