Catabolism of branched chain amino acids supports respiration but not volatile synthesis in tomato fruits

Physiological, Metabolome and Gene Expression Analyses Reveal the Accumulation and Biosynthesis Pathways of Soluble Sugars and Amino Acids in Sweet Sorghum under Osmotic Stresses

Water scarcity is a major environmental constraint on plant growth in arid regions. Soluble sugars and amino acids are essential osmolytes for plants to cope with osmotic stresses. Sweet sorghum is an important bioenergy crop and forage with strong adaptabilities to adverse environments; however, the accumulation pattern and biosynthesis basis of soluble sugars and amino acids in this species under osmotic stresses remain elusive. Here, we investigated the physiological responses of a sweet sorghum cultivar to PEG-induced osmotic stresses, analyzed differentially accumulated soluble sugars and amino acids after 20% PEG treatment using metabolome profiling, and identified key genes involved in the biosynthesis pathways of soluble sugars and amino acids using transcriptome sequencing. The results showed that the growth and photosynthesis of sweet sorghum seedlings were significantly inhibited by more than 20% PEG. After PEG treatments, the leaf osmotic adjustment ability was strengthened, while the contents of major inorganic osmolytes, including K+ and NO3-, remained stable. After 20% PEG treatment, a total of 119 and 188 differentially accumulated metabolites were identified in the stems and leaves, respectively, and the accumulations of soluble sugars such as raffinose, trehalose, glucose, sucrose, and melibiose, as well as amino acids such as proline, leucine, valine, serine, and arginine were significantly increased, suggesting that these metabolites should play key roles in osmotic adjustment of sweet sorghum. The transcriptome sequencing identified 1711 and 4978 DEGs in the stems, as well as 2061 and 6596 DEGs in the leaves after 20% PEG treatment for 6 and 48 h, respectively, among which the expressions of genes involved in biosynthesis pathways of sucrose (such as SUS1, SUS2, etc.), trehalose (including TPS6), raffinose (such as RAFS2 and GOLS2, etc.), proline (such as P5CS2 and P5CR), leucine and valine (including BCAT2), and arginine (such as ASS and ASL) were significantly upregulated. These genes should be responsible for the large accumulation of soluble sugars and amino acids under osmotic stresses. This study deepens our understanding of the important roles of individual soluble sugars and amino acids in the adaptation of sweet sorghum to water scarcity.

OsBCAT2, a gene responsible for the degradation of branched-chain amino acids, positively regulates salt tolerance by promoting the synthesis of vitamin B5

Salt stress negatively affects rice growth, development and yield. Metabolic adjustments contribute to the adaptation of rice under salt stress. Branched-chain amino acids (BCAA) are three essential amino acids that cannot be synthesized by humans or animals. However, little is known about the role of BCAA in response to salt stress in plants. Here, we showed that BCAAs may function as scavengers of reactive oxygen species (ROS) to provide protection against damage caused by salinity. We determined that branched-chain aminotransferase 2 (OsBCAT2), a protein responsible for the degradation of BCAA, positively regulates salt tolerance. Salt significantly induces the expression of OsBCAT2 rather than BCAA synthesis genes, which indicated that salt mainly promotes BCAA degradation and not de novo synthesis. Metabolomics analysis revealed that vitamin B5 (VB5) biosynthesis pathway intermediates were higher in the OsBCAT2-overexpressing plants but lower in osbcat2 mutants under salt stress. The salt stress-sensitive phenotypes of the osbcat2 mutants are rescued by exogenous VB5, indicating that OsBCAT2 affects rice salt tolerance by regulating VB5 synthesis. Our work provides new insights into the enzymes involved in BCAAs degradation and VB5 biosynthesis and sheds light on the molecular mechanism of BCAAs in response to salt stress.

S. A, Raveendran AP, Chaudhary A, Shanmugam A, Arunachalam A. Comparative transcriptomic and weighted gene co-expression network analysis to identify the core genes in the cultivars of Musa acuminata under both infected and chemical perturbated conditions

Banana is a high nutrient crop, which ranks fourth in terms of gross value production. Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4), is considered the most destructive disease leading to the complete loss of production of the Cavendish cultivars Berangan, Brazilian and Williams, which are vulnerable to the infection of FocTR4. However, the treatment with benzothiadiazole, a synthetic salicylic analog, is aimed to induce resistance in plants. Thus, the treatments pertaining to the banana plants subjected to the Foc infection within the chosen cultivars were compared with chemically treated samples obtained at different time intervals for a short duration (0-4 days). The integrated omics analyses considering the parameters of WGCNA, functional annotation, and protein-protein interactions revealed that many pathways have been negatively influenced in Cavendish bananas under FocTR4 infections and the number of genes influenced also increased over time in Williams cultivar. Furthermore, elevation in immune response and resistance genes were also observed in the roots of the Cavendish banana.

Dually biofortified cisgenic tomatoes with increased flavonoids and branched-chain amino acids content

Higher dietary intakes of flavonoids may have a beneficial role in cardiovascular disease prevention. Additionally, supplementation of branched-chain amino acids (BCAAs) in vegan diets can reduce risks associated to their deficiency, particularly in older adults, which can cause loss of skeletal muscle strength and mass. Most plant-derived foods contain only small amounts of BCAAs, and those plants with high levels of flavonoids are not eaten broadly. Here we describe the generation of metabolically engineered cisgenic tomatoes enriched in both flavonoids and BCAAs. In this approach, coding and regulatory DNA elements, all derived from the tomato genome, were combined to obtain a herbicide-resistant version of an acetolactate synthase (mSlALS) gene expressed broadly and a MYB12-like transcription factor (SlMYB12) expressed in a fruit-specific manner. The mSlALS played a dual role, as a selectable marker as well as being key enzyme in BCAA enrichment. The resulting cisgenic tomatoes were highly enriched in Leucine (21-fold compared to wild-type levels), Valine (ninefold) and Isoleucine (threefold) and concomitantly biofortified in several antioxidant flavonoids including kaempferol (64-fold) and quercetin (45-fold). Comprehensive metabolomic and transcriptomic analysis of the biofortified cisgenic tomatoes revealed marked differences to wild type and could serve to evaluate the safety of these biofortified fruits for human consumption.

Research progress on branched-chain amino acid aminotransferases

Branched-chain amino acid aminotransferases, widely present in natural organisms, catalyze bidirectional amino transfer between branched-chain amino acids and branched-chain α-ketoacids in cells. Branched-chain amino acid aminotransferases play an important role in the metabolism of branched-chain amino acids. In this paper, the interspecific evolution and biological characteristics of branched-chain amino acid aminotransferases are introduced, the related research of branched-chain amino acid aminotransferases in animals, plants, microorganisms and humans is summarized and the molecular mechanism of branched-chain amino acid aminotransferase is analyzed. It has been found that branched-chain amino acid metabolism disorders are closely related to various diseases in humans and animals and plants, such as diabetes, cardiovascular diseases, brain diseases, neurological diseases and cancer. In particular, branched-chain amino acid aminotransferases play an important role in the development of various tumors. Branched-chain amino acid aminotransferases have been used as potential targets for various cancers. This article reviews the research on branched-chain amino acid aminotransferases, aiming to provide a reference for clinical research on targeted therapy for various diseases and different cancers.

The dissection of tomato flavor: biochemistry, genetics, and omics

Flavor and quality are the major drivers of fruit consumption in the US. However, the poor flavor of modern commercial tomato varieties is a major cause of consumer dissatisfaction. Studies in flavor research have informed the role of volatile organic compounds in improving overall liking and sweetness of tomatoes. These studies have utilized and applied the tools of molecular biology, genetics, biochemistry, omics, machine learning, and gene editing to elucidate the compounds and biochemical pathways essential for good tasting fruit. Here, we discuss the progress in identifying the biosynthetic pathways and chemical modifications of important tomato volatile compounds. We also summarize the advances in developing highly flavorful tomato varieties and future steps toward developing a "perfect tomato".

Metabolomics approach to identify key volatile aromas in Thai colored rice cultivars

In addition to white jasmine rice, Thailand has many native-colored rice varieties with numerous health benefits and the potential to become a global economic crop. However, the chemical characteristics of aromatic substances in native-colored rice are still mostly unknown. This study aimed to identify the key volatile aroma compounds and the biosynthetic pathways possibly involved in their formation in Thai native-colored rice varieties, and thus leading to the search for potential genetic markers for breeding colored rice with better aromatic properties. Twenty-three rice varieties in four categories: aromatic white, aromatic black, non-aromatic black, and non-aromatic red, were investigated (n=10 per variety). Seed husks were removed before the analysis of rice volatile aromas by static headspace gas chromatography-mass spectrometry. Untargeted metabolomics approach was used to discover the key volatile compounds in colored rice. Forty-eight compounds were detected. Thirty-eight of the 48 compounds significantly differed among groups at p<0.05, 28 of which at p<0.0001, with the non-aromatic black and red rice containing much lower content of most volatile constituents than the aromatic black and white rice. Focusing on the aromatic black rice, the samples appeared to contain high level of both compound groups of aldehydes (3-methylbutanal, 2-methylbutanal, 2-methylpropanal, pentanal, hexanal) and alcohols (butane-2,3-diol, pentan-1-ol, hexan-1-ol). Biosynthetically, these distinctive black-rice volatile compounds were proposed to be formed from the metabolic degradation of branched-chain amino acids (L-leucine, L-isoleucine and L-valine) and polyunsaturated fatty acids (linoleic acid and α-linolenic acid), involving the branched-chain aminotransferases and keto-acid decarboxylases and the 9-lipoxygonases and 13-lipoxygeases, respectively. The proposed degradative pathways of amino acids and fatty acids were well agreed with the profiles key volatile compounds detected in the Thai native-colored rice varieties.

Targeted approaches to improve tomato fruit taste

Tomato (Solanum lycopersicum) is the most valuable fruit and horticultural crop species worldwide. Compared with the fruits of their progenitors, those of modern tomato cultivars are, however, often described as having unsatisfactory taste or lacking flavor. The flavor of a tomato fruit arises from a complex mix of tastes and volatile metabolites, including sugars, acids, amino acids, and various volatiles. However, considerable differences in fruit flavor occur among tomato varieties, resulting in mixed consumer experiences. While tomato breeding has traditionally been driven by the desire for continual increases in yield and the introduction of traits that provide a long shelf-life, consumers are prepared to pay a reasonable premium for taste. Therefore, it is necessary to characterize preferences of tomato flavor and to define its underlying genetic basis. Here, we review recent conceptual and technological advances that have rendered this more feasible, including multi-omics-based QTL and association analyses, along with the use of trained testing panels, and machine learning approaches. This review proposes how the comprehensive datasets compiled to date could allow a precise rational design of tomato germplasm resources with improved organoleptic quality for the future.

Effects of methyl salicylate pre-treatment on the volatile profiles and key gene expressions in tomatoes stored at low temperature

Tomato is one of the most widely cultivated horticultural plants in the world, while the key volatile compounds of tomato fruits generally derive from fatty acid, carotenoid, phenylalanine, and branched-chain amino acid pathways. As an important endogenous signal molecule, methyl salicylate (MeSA) plays a crucial role in the fruit ripening process of plant. Recently, it has been demonstrated that MeSA can maintain the flavor quality of full ripe tomatoes after cold-storage preservation. However, few research teams attempted to investigate the effects of MeSA plus low temperature treatment on the different volatile biosynthetic pathways of tomatoes previously. Therefore, in this study, the effects of methyl salicylate pre-treatment (0.05 mM MeSA, 24 h) on the volatile profile and flavor-related key gene expressions of tomato fruits stored at 10°C were evaluated for the first time. Our results showed that the loss of volatile compounds in low temperature-treated tomato fruits could be effectively alleviated by MeSA pre-treatment. Although MeSA had no remarkable effect on the formation of carotenoid pathway- and branched-chain amino acid pathway-related volatiles in tomatoes subjected to low temperature, the content of fatty acid pathway-related volatiles (including cis-3-hexenal, hexanal, and trans-2-hexenal) in full red fruits of 10°C MeSA group was remarkably higher than that of 10°C control group. Furthermore, MeSA pre-treatment significantly up-regulated the expression of LOXC or LOXD gene in low temperature-treated fruits at breaker or full red stage, respectively. In conclusion, pre-treatment with MeSA might avoid the loss of aromatic compounds in tomato fruits stored at low temperature by activating the fatty acid pathway.

Investigation of Biosynthetic Precursors of 3-Isobutyl-2-Methoxypyrazine Using Stable Isotope Labeling Studies in Bell Pepper Fruits (Capsicum annuum L.)

The biosynthesis of 3-isobutyl-2-methoxypyrazine (IBMP) in bell pepper fruits (Capsicum annuum L.) was investigated by in vivo feeding experiments with stable isotope-labeled precursors. Volatiles were extracted using headspace solid-phase microextraction (HS-SPME) and analyzed by comprehensive two-dimensional gas chromatography (GC×GC) coupled to a time-of-flight mass spectrometer (ToF-MS). Feeding experiments revealed incorporation of l-leucine and α-ketoisocaproic acid (α-KIC) as well as glycine and glyoxylic acid into IBMP. Furthermore, it has been shown that de novo biosynthesis of IBMP occurs in pericarp tissues of unripe bell pepper fruits, whereas pericarp tissues of ripe bell pepper fruits showed no capability of IBMP biosynthesis.

Amino acids metabolism as a source for aroma volatiles biosynthesis

Aroma volatiles are essential for plant ecological fitness and reproduction. Plants produce and use volatiles to attract pollinators and seed dispersers, repel herbivores and recruit their natural enemies, and communicate with other plants. Amino acids and their biosynthetic intermediates play key roles as precursors for the biosynthesis of plant volatiles. Different plants utilize different strategies and biosynthetic pathways to meet their specific biological needs. This review focuses on the different biosynthetic pathways that plants utilize to form amino acid-derived aroma volatiles, emphasizing their common and unique aspects and stressing the importance of the limiting enzymes residing in the primary-specialized metabolism interface. We also briefly review how biotechnology has used this interface and point to promising future directions for improving the quality of agricultural produce and the production of key volatiles.

Floral Scents and Fruit Aromas: Functions, Compositions, Biosynthesis, and Regulation

Floral scents and fruit aromas are crucial volatile organic compounds (VOCs) in plants. They are used in defense mechanisms, along with mechanisms to attract pollinators and seed dispersers. In addition, they are economically important for the quality of crops, as well as quality in the perfume, cosmetics, food, drink, and pharmaceutical industries. Floral scents and fruit aromas share many volatile organic compounds in flowers and fruits. Volatile compounds are classified as terpenoids, phenylpropanoids/benzenoids, fatty acid derivatives, and amino acid derivatives. Many genes and transcription factors regulating the synthesis of volatiles have been discovered. In this review, we summarize recent progress in volatile function, composition, biosynthetic pathway, and metabolism regulation. We also discuss unresolved issues and research perspectives, providing insight into improvements and applications of plant VOCs.

A flavin-dependent monooxygenase produces nitrogenous tomato aroma volatiles using cysteine as a nitrogen source

Aroma is an important factor in consumer perception and acceptance of fresh tomatoes and involves a cocktail of several dozen compounds. Tomato fruits produce uncommon nitrogen-containing volatiles derived mainly from the amino acids leucine and phenylalanine. These volatiles have strong positive correlations with consumer liking. We show that an enzyme active in ripening tomatoes is responsible for the production of all nitrogenous volatiles in tomato fruit, at the expense of substrates derived from cysteine and volatile aldehydes. This discovery defines a cysteine-dependent route to nitrogenous volatiles in plants, prompting a reconsideration of the impact of sulfur metabolism on tomato flavor and quality.

Tomato (Solanum lycopersicum) produces a wide range of volatile chemicals during fruit ripening, generating a distinct aroma and contributing to the overall flavor. Among these volatiles are several aromatic and aliphatic nitrogen-containing compounds for which the biosynthetic pathways are not known. While nitrogenous volatiles are abundant in tomato fruit, their content in fruits of the closely related species of the tomato clade is highly variable. For example, the green-fruited species Solanum pennellii are nearly devoid, while the red-fruited species S. lycopersicum and Solanum pimpinellifolium accumulate high amounts. Using an introgression population derived from S. pennellii, we identified a locus essential for the production of all the detectable nitrogenous volatiles in tomato fruit. Silencing of the underlying gene (SlTNH1;Solyc12g013690) in transgenic plants abolished production of aliphatic and aromatic nitrogenous volatiles in ripe fruit, and metabolomic analysis of these fruit revealed the accumulation of 2-isobutyl-tetrahydrothiazolidine-4-carboxylic acid, a known conjugate of cysteine and 3-methylbutanal. Biosynthetic incorporation of stable isotope-labeled precursors into 2-isobutylthiazole and 2-phenylacetonitrile confirmed that cysteine provides the nitrogen atom for all nitrogenous volatiles in tomato fruit. Nicotiana benthamiana plants expressing SlTNH1 readily transformed synthetic 2-substituted tetrahydrothiazolidine-4-carboxylic acid substrates into a mixture of the corresponding 2-substituted oxime, nitro, and nitrile volatiles. Distinct from other known flavin-dependent monooxygenase enzymes in plants, this tetrahydrothiazolidine-4-carboxylic acid N-hydroxylase catalyzes sequential hydroxylations. Elucidation of this pathway is a major step forward in understanding and ultimately improving tomato flavor quality.

The role of the electron-transfer flavoprotein: ubiquinone oxidoreductase following carbohydrate starvation in Arabidopsis cell cultures

KEY MESSAGE

The functional absence of the electron-transfer flavoprotein: ubiquinone oxidoreductase (ETFQO) directly impacts electrons donation to the mitochondrial electron transport chain under carbohydrate-limiting conditions without major impacts on the respiration of cell cultures. Alternative substrates (e.g., amino acids) can directly feed electrons into the mitochondrial electron transport chain (mETC) via the electron transfer flavoprotein/electron-transfer flavoprotein: ubiquinone oxidoreductase (ETF/ETFQO) complex, which supports plant respiration during stress situations. By using a cell culture system, here we investigated the responses of Arabidopsis thaliana mutants deficient in the expression of ETFQO (etfqo-1) following carbon limitation and supplied with amino acids. Our results demonstrate that isovaleryl-CoA dehydrogenase (IVDH) activity was induced during carbon limitation only in wild-type and that these changes occurred concomit with enhanced protein content. By contrast, neither the activity nor the total amount of IVDH was altered in etfqo-1 mutants. We also demonstrate that the activities of mitochondrial complexes in etfqo-1 mutants, display a similar pattern as in wild-type cells. Our findings suggest that the defect of ETFQO protein culminates with an impaired functioning of the IVDH, since no induction of IVDH activity was observed. However, the functional absence of the ETFQO seems not to cause major impacts on plant respiration under carbon limiting conditions, most likely due to other alternative electron entry pathways.

Branched-Chain Volatiles in Fruit: A Molecular Perspective

Branched-chain volatiles (BCVs) constitute an important family of fruit volatile metabolites essential to the characteristic flavor and aroma profiles of many edible fruits. Yet in contrast to other groups of volatile organic compounds important to fruit flavor such as terpenoids, phenylpropanoids, and oxylipins, the molecular biology underlying BCV biosynthesis remains poorly understood. This lack of knowledge is a barrier to efforts aimed at obtaining a more comprehensive understanding of fruit flavor and aroma and the biology underlying these complex phenomena. In this review, we discuss the current state of knowledge regarding fruit BCV biosynthesis from the perspective of molecular biology. We survey the diversity of BCV compounds identified in edible fruits as well as explore various hypotheses concerning their biosynthesis. Insights from branched-chain precursor compound metabolism obtained from non-plant organisms and how they may apply to fruit BCV production are also considered, along with potential avenues for future research that might clarify unresolved questions regarding BCV metabolism in fruits.

The metabolic changes that effect fruit quality during tomato fruit ripening

As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

The Bacterial Microbiome of the Tomato Fruit Is Highly Dependent on the Cultivation Approach and Correlates With Flavor Chemistry

The modes of interactions between plants and plant-associated microbiota are manifold, and secondary metabolites often play a central role in plant-microbe interactions. Abiotic and biotic (including both plant pathogens and endophytes) stress can affect the composition and concentration of secondary plant metabolites, and thus have an influence on chemical compounds that make up for the taste and aroma of fruit. While the role of microbiota in growth and health of plants is widely acknowledged, relatively little is known about the possible effect of microorganisms on the quality of fruit of plants they are colonizing. In this work, tomato (Solanum lycopersicum L.) plants of five different cultivars were grown in soil and in hydroponics to investigate the impact of the cultivation method on the flavor of fruit, and to assess whether variations in their chemical composition are attributable to shifts in bacterial microbiota. Ripe fruit were harvested and used for bacterial community analysis and for the analysis of tomato volatiles, sugars and acids, all contributing to flavor. Fruit grown in soil showed significantly higher sugar content, whereas tomatoes from plants under hydroponic conditions had significantly higher levels of organic acids. In contrast, aroma profiles of fruit were shaped by the tomato cultivars, rather than the cultivation method. In terms of bacterial communities, the cultivation method significantly defined the community composition in all cultivars, with the bacterial communities in hydroponic tomatoes being more variable that those in tomatoes grown in soil. Bacterial indicator species in soil-grown tomatoes correlated with higher concentrations of volatiles described to be perceived as "green" or "pungent." A soil-grown specific reproducibly occurring ASV (amplicon sequence variants) classified as Bacillus detected solely in "Solarino" tomatoes, which were the sweetest among all cultivars, correlated with the amount of aroma-relevant volatiles as well as of fructose and glucose in the fruit. In contrast, indicator bacterial species in hydroponic-derived tomatoes correlated with aroma compounds with "sweet" and "floral" notes and showed negative correlations with glucose concentrations in fruit. Overall, our results point toward a microbiota-related accumulation of flavor and aroma compounds in tomato fruit, which is strongly dependent on the cultivation substrate and approach.

The mitochondrial pyruvate carrier (MPC) complex mediates one of three pyruvate-supplying pathways that sustain Arabidopsis respiratory metabolism

Malate oxidation by plant mitochondria enables the generation of both oxaloacetate and pyruvate for tricarboxylic acid (TCA) cycle function, potentially eliminating the need for pyruvate transport into mitochondria in plants. Here, we show that the absence of the mitochondrial pyruvate carrier 1 (MPC1) causes the co-commitment loss of its putative orthologs, MPC3/MPC4, and eliminates pyruvate transport into Arabidopsis thaliana mitochondria, proving it is essential for MPC complex function. While the loss of either MPC or mitochondrial pyruvate-generating NAD-malic enzyme (NAD-ME) did not cause vegetative phenotypes, the lack of both reduced plant growth and caused an increase in cellular pyruvate levels, indicating a block in respiratory metabolism, and elevated the levels of branched-chain amino acids at night, a sign of alterative substrate provision for respiration. 13C-pyruvate feeding of leaves lacking MPC showed metabolic homeostasis was largely maintained except for alanine and glutamate, indicating that transamination contributes to the restoration of the metabolic network to an operating equilibrium by delivering pyruvate independently of MPC into the matrix. Inhibition of alanine aminotransferases when MPC1 is absent resulted in extremely retarded phenotypes in Arabidopsis, suggesting all pyruvate-supplying enzymes work synergistically to support the TCA cycle for sustained plant growth.

Hop bitter acids: resources, biosynthesis, and applications

Diversified members of hop bitter acids (α- and β-acids) have been found in hop (Humulus lupulus). Mixtures of hop bitter acids have been traditionally applied in brewing and food industries as bitterness flavors or food additives. Recent studies have discovered novel applications of hop bitter acids and their derivatives in medicinal and pharmaceutical fields. The increasing demands of purified hop bitter acid promoted biosynthesis efforts for the heterologous biosynthesis of objective hop bitter acids by engineered microbial factories. In this study, the updated information of hop bitter acids and their representative application in brewing, food, and medicine fields are reviewed. We also speculate future trends on the development of robust microbial cell factories and biotechnologies for the biosynthesis of hop bitter acids. KEY POINTS: • Structures and applications of hop bitter acids are summarized in this study. • Biosynthesis of hop bitter acids remains challenging. • We discuss potential strategies in the microbial production of hop bitter acids.

BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Biotic and abiotic environmental stresses have limited the increase in soybean productivity. Overexpression of the molecular chaperone BiP in transgenic plants has been associated with the response to osmotic stress and drought tolerance by maintaining cellular homeostasis and delaying hypersensitive cell death. Here, we evaluated the metabolic changes in response to the hypersensitivity response (HR) caused by the non-compatible bacteria Pseudomonas syringae pv. tomato in BiP-overexpressing plants. The HR-modified metabolic profiles in BiP-overexpressing plants were significantly distinct from the wild-type untransformed. The transgenic plants displayed a lower abundance of HR-responsive metabolites as amino acids, sugars, carboxylic acids and signal molecules, including p-aminobenzoic acid (PABA) and dihydrosphingosine (DHS), when compared to infected wild-type plants. In contrast, salicylic acid (SA) biosynthetic and signaling pathways were more stimulated in transgenic plants, and both pathogenesis-related genes (PRs) and transcriptional factors controlling the SA pathway were more induced in the BiP-overexpressing lines. Furthermore, the long-chain bases (LCBs) and ceramide biosynthetic pathways showed alterations in gene expression and metabolite abundance. Thus, as a protective pathway against pathogens, HR regulation by sphingolipids and SA may account at least in part by the enhanced resistance of transgenic plants. GmNAC32 transcriptional factor was more induced in the transgenic plants and it has also been reported to regulate flavonoid synthesis in response to SA. In fact, the BiP-overexpressing plants showed an increase in flavonoids, mainly prenylated isoflavones, as precursors for phytoalexins. Our results indicate that the BiP-mediated acceleration in the hypersensitive response may be a target for metabolic engineering of plant resistance against pathogens.

Assessing Dynamic Changes of Taste-Related Primary Metabolism During Ripening of Durian Pulp Using Metabolomic and Transcriptomic Analyses

Durian is an economically important fruit of Southeast Asia. There is, however, a lack of in-depth information on the alteration of its metabolic networks during ripening. Here, we annotated 94 ripening-associated metabolites from the pulp of durian cv. Monthong fruit at unripe and ripe stages, using capillary electrophoresis- and gas chromatography- time-of-flight mass spectrometry, specifically focusing on taste-related metabolites. During ripening, sucrose content increased. Change in raffinose-family oligosaccharides are reported herein for the first time. The malate and succinate contents increased, while those of citrate, an abundant organic acid, were unchanged. Notably, most amino acids increased, including isoleucine, leucine, and valine, whereas aspartate decreased, and glutamate was unchanged. Furthermore, transcriptomic analysis was performed to analyze the dynamic changes in sugar metabolism, glycolysis, TCA cycle, and amino acid pathways to identify key candidate genes. Taken together, our results elucidate the fundamental taste-related metabolism of durian, which can be exploited to develop durian metabolic and genetic markers in the future.

The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit

Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders' germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine-derived volatiles (PHEVs) 2-phenylethanol, phenylacetaldehyde and 1-nitro-2-phenylethane. Fruits of near-isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose-hip-like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene-editing-based (CRISPR-CAS9) reverse-genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.

Shaping Durum Wheat for the Future: Gene Expression Analyses and Metabolites Profiling Support the Contribution of BCAT Genes to Drought Stress Response

Global climate change, its implications for agriculture, and the complex scenario presented by the scientific community are of worldwide concern. Drought is a major abiotic stress that can restrict plants growth and yields, thus the identification of genotypes with higher adaptability to drought stress represents one of the primary goals in breeding programs. During abiotic stress, metabolic adaptation is crucial for stress tolerance, and accumulation of specific amino acids and/or as secondary metabolites deriving from amino acid metabolism may correlate with the increased tolerance to adverse environmental conditions. This work, focused on the metabolism of branched chain-amino acids (BCAAs) in durum wheat and the role of branched-chain amino acid aminotransferases (BCATs) in stress response. The role of BCATs in plant response to drought was previously proposed for Arabidopsis, where the levels of BCAAs were altered at the transcriptional level under drought conditions, triggering the onset of defense response metabolism. However, in wheat the role of BCAAs as a trigger of the onset of the drought defense response has not been elucidated. A comparative genomic approach elucidated the composition of the BCAT gene family in durum wheat. Here we demonstrate a tissue and developmental stage specificity of BCATs regulation in the drought response. Moreover, a metabolites profiling was performed on two contrasting durum wheat cultivars Colosseo and Cappelli resulting in the detection of a specific pattern of metabolites accumulated among genotypes and, in particular, in an enhanced BCAAs accumulation in the tolerant cv Cappelli further supporting a role of BCAAs in the drought defense response. The results support the use of gene expression and target metabolomic in modern breeding to shape new cultivars more resilient to a changing climate.

Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea)

Nitrogen (N) is critical to the growth and productivity of crops. To understand the molecular mechanisms influenced by N stress, we used RNA-Sequencing (RNA-Seq) to analyze differentially expressed genes (DEGs) in root and leaf tissues of spinach. N stress negatively influenced photosynthesis, biomass accumulation, amino acid profiles, and partitioning of N across tissues. RNA-seq analysis revealed that N stress caused most transcriptomic changes in roots, identifying 1,346 DEGs. High-affinity nitrate transporters (NRT2.1, NRT2.5) and glutamine amidotransferase (GAT1) genes were strongly induced in roots in response to N deplete and replete conditions, respectively. GO and KEGG analyses revealed that the functions associated with metabolic pathways and nutrient reservoir activity were enriched due to N stress. Whereas KEGG pathway enrichment analysis indicated the upregulation of DEGs associated with DNA replication, pyrimidine, and purine metabolism in the presence of high N in leaf tissue. A subset of transcription factors comprising bHLH, MYB, WRKY, and AP2/ERF family members was over-represented in both tissues in response to N perturbation. Interesting DEGs associated with N uptake, amino acid metabolism, hormonal pathway, carbon metabolism, along with transcription factors, were highlighted. The results provide valuable information about the underlying molecular processes in response to N stress in spinach and; could serve as a resource for functional analysis of candidate genes/pathways and enhancement of nitrogen use efficiency.

Metabolomics of wheat grains generationally-exposed to cerium oxide nanoparticles

This study investigated changes in metabolite compositions over three generation exposure of wheat (Triticum aestivum) to cerium oxide nanoparticles (CeO₂-NPs) in low or high nitrogen soil. The goal was to determine if CeO₂-NPs affects grains/seeds quality across generational exposure. Seeds from plants exposed for two generations to 0 or 500 mg CeO₂-NPs per kg soil treatment were cultivated for third year in low or high nitrogen soil amended with 0 or 500 mg CeO₂-NPs per kg soil. Metabolomics identified 180 metabolites. Multivariate analysis showed that continuous generational exposure to CeO₂-NPs altered 18 and 11 metabolites in low N and high N grains, respectively. Interestingly, DNA/RNA metabolites such as thymidine, uracil, guanosine, deoxyguanosine, adenosine monophosphate were affected; a finding that has not been observed on DNA/RNA metabolites of plants exposed to nanoparticles. Nicotianamine, a metabolite playing crucial role in Fe storage in grains, decreased by 33% in grains continuously exposed for three generations to CeO₂-NPs at high N soil. Notably, these grains also exhibited a concomitant decrease of 13-16% in Fe concentration. Together these changes suggest alterations in grain quality or implications in ecosystem processes (i.e., productivity, nutrient cycling, ecosystem stability) of progeny plants generationally-exposed to CeO₂-NPs.

RNA-Seq analysis reveals an essential role of tyrosine metabolism pathway in response to root-rot infection in Gerbera hybrida

Gerbera hybrida is one of the top five cut flowers across the world, it is host for the root rot causing parasite called Phytophthora cryptogea. In this study, plantlets of healthy and root-rot pathogen-infected G. hybrida were used as plant materials for transcriptome analyis using high-throughput Illumina sequencing technique. A total 108,135 unigenes were generated with an average length of 727 nt and N50 equal to 1274 nt out of which 611 genes were identified as DEGs by DESeq analyses. Among DEGs, 228 genes were up-regulated and 383 were down-regulated. Through this annotated data and Kyoto encyclopedia of genes and genomes (KEGG), molecular interaction network, transcripts accompanying with tyrosine metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, phenylpropanoid and flavonoid biosynthesis, and plant hormone signal transduction pathways were thoroughly observed considering expression pattern. The involvement of DEGs in tyrosine metabolism pathway was validated by real-time qPCR. We found that genes related with tyrosine metabolism were activated and up-regulated against stress response. The expression of GhTAT, GhAAT, GhHPD, GhHGD and GhFAH genes was significantly increased in the leaves and petioles at four and six dpi (days post inoculation) as compared with control. The study predicts the gene sequences responsible for the tyrosine metabolism pathway and its responses against root-rot resistance in gerbera plant. In future, identification of such genes is necessary for the better understanding of rot resistance mechanism and to develop a root rot resistance strategy for ornamental plants.

From Central to Specialized Metabolism: An Overview of Some Secondary Compounds Derived From the Primary Metabolism for Their Role in Conferring Nutritional and Organoleptic Characteristics to Fruit

Fruit flavor and nutritional characteristics are key quality traits and ones of the main factors influencing consumer preference. Central carbon metabolism, also known as primary metabolism, contributes to the synthesis of intermediate compounds that act as precursors for plant secondary metabolism. Specific and specialized metabolic pathways that evolved from primary metabolism play a key role in the plant's interaction with its environment. In particular, secondary metabolites present in the fruit serve to increase its attractiveness to seed dispersers and to protect it against biotic and abiotic stresses. As a consequence, several important organoleptic characteristics, such as aroma, color, and fruit nutritional value, rely upon secondary metabolite content. Phenolic and terpenoid compounds are large and diverse classes of secondary metabolites that contribute to fruit quality and have their origin in primary metabolic pathways, while the delicate aroma of ripe fruits is formed by a unique combination of hundreds of volatiles that are derived from primary metabolites. In this review, we show that the manipulation of primary metabolism is a powerful tool to engineer quality traits in fruits, such as the phenolic, terpenoid, and volatile content. The enzymatic reactions responsible for the accumulation of primary precursors are bottlenecks in the transfer of metabolic flux from central to specialized metabolism and should be taken into account to increase the yield of the final products of the biosynthetic pathways. In addition, understanding the connection and regulation of the carbon flow between primary and secondary metabolism is a key factor for the development of fruit cultivars with enhanced organoleptic and nutritional traits.

PDC1, a pyruvate/α-ketoacid decarboxylase, is involved in acetaldehyde, propanal and pentanal biosynthesis in melon (Cucumis melo L.) fruit

Plant pyruvate decarboxylases (PDC) catalyze the decarboxylation of pyruvate to form acetaldehyde and CO₂ and are well known to play a key role in energy supply via fermentative metabolism in oxygen-limiting conditions. In addition to their role in fermentation, plant PDCs have also been hypothesized to be involved in aroma formation although, to date, there is no direct biochemical evidence for this function. We investigated the role of PDCs in fruit volatile biosynthesis, and identified a melon pyruvate decarboxylase, PDC1, that is highly expressed in ripe fruits. In vitro biochemical characterization of the recombinant PDC1 enzyme showed that it could not only decarboxylate pyruvate, but that it also had significant activity toward other straight- and branched-chain α-ketoacids, greatly expanding the range of substrates previously known to be accepted by the plant enzyme. RNAi-mediated transient and stable silencing of PDC1 expression in melon showed that this gene is involved in acetaldehyde, propanal and pentanal production, while it does not contribute to branched-chain amino acid (BCAA)-derived aldehyde biosynthesis in melon fruit. Importantly, our results not only demonstrate additional functions for the PDC enzyme, but also challenge the long standing hypothesis that PDC is involved in BCAA-derived aldehyde formation in fruit.

The Chemistry behind Tomato Quality

Tomato is one of the most widely consumed fresh vegetables in the industrialized world and an important source of healthy constituents of the human diet. Despite the unique flavor characteristics of tomatoes, which make them extremely valuable in cooking, and their recognized beneficial role in the diet, the quality of tomato was traditionally only considered in connection to external appearances. As it happened with other highly requested crops, breeding programs of tomato focused their efforts on developing new varieties with higher yields and stress resistance, with better uniformity in fruit size, brighter color and prolonged shelf life. The downside of these strategies was that organoleptic features and nutritional value were often neglected, with a detrimental effect on commercial tomatoes. Over the last years, there has been an increase in consumers’ demand for tasty and healthy products. This aspect, paired with novel and multidisciplinary approaches to tomato research, allowed both sensory and nutritional qualities to be reconsidered as valuable parameters in breeding. In this review we describe the main chemical constituents of tomato, focusing on the flavor compounds (both volatile and non-volatile compounds) and secondary metabolites. Particular attention is paid to their beneficial effects on human health and their relevance to the overall quality of tomato.

Contribution of abscisic acid to aromatic volatiles in cherry tomato (Solanum lycopersicum L.) fruit during postharvest ripening

Fruit aroma development depends on ripening. Abscisic acid (ABA) has been reported to be involved in the regulation of tomato fruit ripening. In the present study, the effects of exogenous ABA on aromatic volatiles in tomato fruit during postharvest ripening were studied. The results showed that exogenous ABA accelerated color development and ethylene production as well as the accumulation of carotenoids, total phenolics and linoleic acid in tomato fruit during ripening. Moreover, exogenous ABA increased the accumulation of volatile compounds such as 1-peten-3-one (2.06-fold), β-damascenone (1.64-fold), benzaldehyde (3.29-fold) and benzyl cyanide (4.15-fold); induced the expression of key genes implicated in the biosynthesis pathways of aromatic volatiles, including TomloxC, HPL, ADH2, LeCCD1B and SlBCAT1 (the values of the log₂ fold changes ranged from -3.02 to 2.97); and promoted the activities of lipoxygenase (LOX), hydroperoxide lyase (HPL) and alcohol dehydrogenase (ADH). In addition, the results of promoter analyses revealed that cis-acting elements involved in ABA responsiveness (ABREs) exist in 8 of the 12 key genes involved in volatile biosynthesis, suggesting that ABA potentially affects aromatic volatile emissions via the regulation of gene expression profiles.

The phytotoxicities of decabromodiphenyl ether (BDE-209) to different rice cultivars (Oryza sativa L.)

Decabromodiphenyl ether (BDE-209), as a major component of brominated flame retardants, has been detected in the agricultural soil in considerable amount. Given that BDE-209 is toxic, ubiquitous and persistent, BDE-209 might induce toxic effects on rice cultivars planted in contaminated soil. A comparative study was conducted on phytotoxicities and GC-MS based antioxidant-related metabolite levels to investigate the differences of phytotoxicities of BDE-209 to rice cultivars in Yangtze River Delta of China. Rice seedlings were treated with BDE-209 at 0, 10, 50, 100 and 500 μg/L in a hydroponic setup. Results showed that BDE-209-induced phytotoxicites were cultivar-dependent and that the antioxidant defense systems in the cultivars were disturbed differently. Among the three selected cultivars (Jiayou 5, Lianjing 7 and Yongyou 9), Jiayou 5 and Lianjing 7 displayed lower toxic effects than Yongyou 9 in terms of the growth inhibition, lipid peroxidation and DNA damage. The increases of antioxidant enzymes were significantly higher in Jiayou 5 and Lianjing 7 than those in Yongyou 9. Multivariate analysis of antioxidant-related metabolites in the three cultivars indicated that l-tryptophan and l-valine were the most important ones among 10 metabolites responsible for the separation of cultivars. The up-regulation of l-tryptophan and l-valine were likely plant strategies to increase their tolerance. The current results provided an insight into the development of rice cultivars with higher BDE-209 tolerance.

Characterization and Synergistic Effect of Antifungal Volatile Organic Compounds Emitted by the Geotrichum candidum PF005, an Endophytic Fungus from the Eggplant

Plant-associated endophytes are recognized as sources of novel bioactive molecules having diverse applications. In this study, an endophytic yeast-like fungal strain was isolated from the fruit of eggplant (Solanum melongena) and identified as Geotrichum candidum through phenotypic and genotypic characterizations. This endophytic G. candidum isolate PF005 was found to emit fruity scented volatiles. The compositional profiling of volatile organic compounds (VOCs) revealed the presence of 3-methyl-1-butanol, ethyl 3-methylbutanoate, 2-phenylethanol, isopentyl acetate, naphthalene, and isobutyl acetate in significant proportion when analyzed on a time-course basis. The VOCs from G. candidum exhibited significant mycelial growth inhibition (54%) of phytopathogen Rhizoctonia solani, besides having mild antifungal activity against a few other fungi. The source of carbon as a nutrient was found to be an important factor for the enhanced biosynthesis of antifungal VOCs. The antifungal activity against phytopathogen R. solani was improved up to 91% by feeding the G. candidum with selective precursors of alcohol and ester volatiles. Furthermore, the antifungal activity of VOCs was enhanced synergistically up to 92% upon the exogenous addition of naphthalene (1.0 mg/plate). This is the first report of G. candidum as an endophyte emitting antifungal VOCs, wherein 2-penylethanol, isopentyl acetate, and naphthalene were identified as important contributors to its antifungal activity. Possible utilization of G. candidum PF005 as a mycofumigant has been discussed based upon its antifungal activity and the qualified presumption of safety status.

Metabolomic analyses to evaluate the effect of drought stress on selected African Eggplant accessions

BACKGROUND

Drought stress is one of the main abiotic stresses that affect crops. It leads to biochemical changes that can have adverse effects on plant growth, development and productivity. African eggplants are important vegetable and fruit crops reported to adapt and thrive well under drought stress. The diversified metabolites arising due to stress have not been well defined. A gas chromatographic-mass spectrometric metabolomic approach was applied to characterize the effect of drought stress on metabolites at different stages of growth. Nineteen accessions were selected for analysis and drought was imposed by withholding water until soil moisture reached 60% field capacity. Fresh leaf tissues were sampled before stress, 2 and 4 weeks after stress and metabolite profiling done.

RESULTS

Significant changes in metabolite content were observed, and potentially important metabolites with respect to stress responses were characterized. Proline, glutamate, sucrose, fructose and tricarboxylic acid cycle metabolites were shown to be positively correlated with stress. Principal component analysis showed a clear discrimination between the different accessions, growth stages and stress/control conditions.

CONCLUSION

The results illustrate that drought stress has a significant impact on the concentrations of some metabolites, such as amino acids, sugars and organic acids, which may contribute to drought stress effects and tolerance. © 2017 Society of Chemical Industry.

The Biosynthesis of Unusual Floral Volatiles and Blends Involved in Orchid Pollination by Deception: Current Progress and Future Prospects

Flowers have evolved diverse strategies to attract animal pollinators, with visual and olfactory floral cues often crucial for pollinator attraction. While most plants provide reward (e.g., nectar, pollen) in return for the service of pollination, 1000s of plant species, particularly in the orchid family, offer no apparent reward. Instead, they exploit their often specific pollinators (one or few) by mimicking signals of female insects, food source, and oviposition sites, among others. A full understanding of how these deceptive pollination strategies evolve and persist remains an open question. Nonetheless, there is growing evidence that unique blends that often contain unusual compounds in floral volatile constituents are often employed to secure pollination by deception. Thus, the ability of plants to rapidly evolve new pathways for synthesizing floral volatiles may hold the key to the widespread evolution of deceptive pollination. Yet, until now the biosynthesis of these volatile compounds has been largely neglected. While elucidating the biosynthesis in non-model systems is challenging, nonetheless, these cases may also offer untapped potential for biosynthetic breakthroughs given that some of the compounds can be exclusive or dominant components of the floral scent and production is often tissue-specific. In this perspective article, we first highlight the chemical diversity underpinning some of the more widespread deceptive orchid pollination strategies. Next, we explore the potential metabolic pathways and biosynthetic steps that might be involved. Finally, we offer recommendations to accelerate the discovery of the biochemical pathways in these challenging but intriguing systems.

Qualitative and Quantitative Differences in Herbivore-Induced Plant Volatile Blends from Tomato Plants Infested by Either Tuta absoluta or Bemisia tabaci

Plants release a variety of volatile organic compounds that play multiple roles in the interactions with other plants and animals. Natural enemies of plant-feeding insects use these volatiles as cues to find their prey or host. Here, we report differences between the volatile blends of tomato plants infested with the whitefly Bemisia tabaci or the tomato borer Tuta absoluta. We compared the volatile emission of: (1) clean tomato plants; (2) tomato plants infested with T. absoluta larvae; and (3) tomato plants infested with B. tabaci adults, nymphs, and eggs. A total of 80 volatiles were recorded of which 10 occurred consistently only in the headspace of T. absoluta-infested plants. Many of the compounds detected in the headspace of the two herbivory treatments were emitted at different rates. Plants damaged by T. absoluta emitted at least 10 times higher levels of many compounds compared to plants damaged by B. tabaci and intact plants. The multivariate separation of T. absoluta-infested plants from those infested with B. tabaci was due largely to the chorismate-derived compounds as well as volatile metabolites of C₁₈-fatty acids and branched chain amino acids that had higher emission rates from T. absoluta-infested plants, whereas the cyclic sesquiterpenes α- and β-copaene, valencene, and aristolochene were emitted at significantly higher levels from B. tabaci-infested plants. Our findings imply that feeding by T. absoluta and B. tabaci induced emission of volatile blends that differ quantitatively and qualitatively, providing a chemical basis for the recently documented behavioral discrimination by two generalist predatory mirid species, natural enemies of T. absoluta and B. tabaci employed in biological control.

Identification, introgression, and validation of fruit volatile QTLs from a red-fruited wild tomato species

Volatile organic compounds (VOCs) are major determinants of fruit flavor, a primary objective in tomato breeding. A recombinant inbred line (RIL) population consisting of 169 lines derived from a cross between Solanum lycopersicum and a red-fruited wild tomato species Solanum pimpinellifolium accession (SP) was characterized for VOCs in three different seasons. Correlation and hierarchical cluster analyses were performed on the 52 VOCs identified, providing a tool for the putative assignation of individual compounds to metabolic pathways. Quantitative trait locus (QTL) analysis, based on a genetic linkage map comprising 297 single nucleotide polymorphisms (SNPs), revealed 102 QTLs (75% not described previously) corresponding to 39 different VOCs. The SP alleles exerted a positive effect on most of the underlying apocarotenoid volatile QTLs-regarded as desirable for liking tomato-indicating that alleles inherited from SP are a valuable resource for flavor breeding. An introgression line (IL) population developed from the same parental genotypes provided 12 ILs carrying a single SP introgression and covering 85 VOC QTLs, which were characterized at three locations. The results showed that almost half of the QTLs previously identified in the RILs maintained their effect in an IL form, reinforcing the value of these QTLs for flavor/aroma breeding in cultivated tomato.

1H NMR and GC-MS based metabolomics reveal nano-Cu altered cucumber (Cucumis sativus) fruit nutritional supply

It is imperative to study the interaction of nanoparticles residuals with crop plants in agricultural soils, due to the increased application of nanotechnology in agriculture. So far, a few studies have focused on the impact of nanoparticles on fruit quality and nutritional supply. In this work, a thorough and comprehensive analysis of metabolite changes of cucumber fruits from plants under nano-Cu stress was possible through the use of both ¹H NMR and GC-MS. The results of supervised partial least-squares discriminant analysis from both platforms showed that cucumber fruit extracts samples were clearly grouped based on the nano-Cu level in soil. This indicates that the fruit metabolite profile was influenced by exposure to nano-Cu. GC-MS data showed concentrations of some sugars, organic acids, amino acids, and fatty acids were increased or decreased by nano-Cu. Several metabolites, such as methylnicotinamide (MNA), trigonelline, imidazole, quinolinate were only detected and quantified by ¹H NMR. Our results showed that combining the two platforms provided a comprehensive understanding about the metabolites (nutrient supply) changes in cucumber fruits impacted by exposure to nano-Cu.

The influence of alternative pathways of respiration that utilize branched-chain amino acids following water shortage in Arabidopsis

During dark-induced senescence isovaleryl-CoA dehydrogenase (IVDH) and D-2-hydroxyglutarate dehydrogenase (D-2HGDH) act as alternate electron donors to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) pathway. However, the role of this pathway in response to other stresses still remains unclear. Here, we demonstrated that this alternative pathway is associated with tolerance to drought in Arabidopsis. In comparison with wild type (WT) and lines overexpressing D-2GHDH, loss-of-function etfqo-1, d2hgdh-2 and ivdh-1 mutants displayed compromised respiration rates and were more sensitive to drought. Our results demonstrated that an operational ETF/ETFQO pathway is associated with plants' ability to withstand drought and to recover growth once water becomes replete. Drought-induced metabolic reprogramming resulted in an increase in tricarboxylic acid (TCA) cycle intermediates and total amino acid levels, as well as decreases in protein, starch and nitrate contents. The enhanced levels of the branched-chain amino acids in loss-of-function mutants appear to be related to their increased utilization as substrates for the TCA cycle under water stress. Our results thus show that mitochondrial metabolism is highly active during drought stress responses and provide support for a role of alternative respiratory pathways within this response.

The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants

Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.

Amino Acid Catabolism in Plants

Amino acids have various prominent functions in plants. Besides their usage during protein biosynthesis, they also represent building blocks for several other biosynthesis pathways and play pivotal roles during signaling processes as well as in plant stress response. In general, pool sizes of the 20 amino acids differ strongly and change dynamically depending on the developmental and physiological state of the plant cell. Besides amino acid biosynthesis, which has already been investigated in great detail, the catabolism of amino acids is of central importance for adjusting their pool sizes but so far has drawn much less attention. The degradation of amino acids can also contribute substantially to the energy state of plant cells under certain physiological conditions, e.g. carbon starvation. In this review, we discuss the biological role of amino acid catabolism and summarize current knowledge on amino acid degradation pathways and their regulation in the context of plant cell physiology.

Ethylene and 1-MCP regulate major volatile biosynthetic pathways in apple fruit

The effects of ethylene and 1-methylcyclopropene (1-MCP) on apple fruit volatile biosynthesis and gene expression were investigated. Statistical analysis identified 17 genes that changed significantly in response to ethylene and 1-MCP treatments. Genes encoding branched-chain amino acid aminotransferase (BCAT), aromatic amino acid aminotransferase (ArAT) and amino acid decarboxylases (AADC) were up-regulated during ripening and further enhanced by ethylene treatment. Genes related to fatty acid synthesis and metabolism, including acyl-carrier-proteins (ACPs), malonyl-CoA:ACP transacylase (MCAT), acyl-ACP-desaturase (ACPD), lipoxygenase (LOX), hydroperoxide lyase (HPL), alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC2), β-oxidation, acyl-CoA synthetase (ACS), enoyl-CoA hydratase (ECHD), acyl-CoA dehydrogenase (ACAD), and alcohol acyltransferases (AATs) also increased during ripening and in response to ethylene treatment. Allene oxide synthase (AOS), alcohol dehydrogenase 1 (ADH1), 3-ketoacyl-CoA thiolase and branched-chain amino acid aminotransferase 2 (BCAT2) decreased in ethylene-treated fruit. Treatment with 1-MCP and ethylene generally produced opposite effects on related genes, which provides evidence that regulation of these genes is ethylene dependent.

Diet quality influences isotopic discrimination among amino acids in an aquatic vertebrate

Stable nitrogen isotopic composition of amino acids (δ (15)NAA) has recently been employed as a powerful tool in ecological food web studies, particularly for estimating the trophic position (TP) of animal species in food webs. However, the validity of these estimates depends on the consistency of the trophic discrimination factor (TDF; - Δδ (15)NAA at each shift of trophic level) among a suite of amino acids within the tissues of consumer species. In this study, we determined the TDF values of amino acids in tadpoles (the Japanese toad, Bufo japonicus) reared exclusively on one of three diets that differed in nutritional quality. The diets were commercial fish-food pellets (plant and animal biomass), bloodworms (animal biomass), and boiled white rice (plant carbohydrate), representing a balanced, protein-rich, and protein-poor diet, respectively. The TDF values of two "source amino acids" (Src-AAs), methionine and phenylalanine, were close to zero (0.3-0.5‰) among the three diets, typifying the values reported in the literature (∼0.5‰ and ∼0.4‰, respectively). However, TDF values of "trophic amino acids" (Tr-AAs) including alanine, valine, leucine, isoleucine, and glutamic acid varied by diet: for example, the glutamic acid TDF was similar to the standard value (∼8.0‰) when tadpoles were fed either the commercial pellets (8.0‰) or bloodworms (7.9‰), but when they were fed boiled rice, the TDF was significantly reduced (0.6‰). These results suggest that a profound lack of dietary protein may alter the TDF values of glutamic acid (and other Tr-AAs and glycine) within consumer species, but not the two Src-AAs (i.e., methionine and phenylalanine). Knowledge of how a nutritionally poor diet can influence the TDF of Tr- and Src-AAs will allow amino acid isotopic analyses to better estimate TP among free-roaming animals.