Lysine catabolism: a stress and development super-regulated metabolic pathway

The Metabolomics Response of Solanum melongena L. Leaves to Various Forms of Pb

Due to activities like mining and smelting, lead (Pb) enters the atmosphere in various forms in coarse and fine particles. It enters plants mainly through leaves, and goes up the food chain. In this study, PbXn (nano-PbS, mic-PbO and PbCl2) was applied to eggplant (Solanum melongena L.) leaves, and 379 differential metabolites were identified and analyzed in eggplant leaves using liquid chromatography-mass spectrometry. Multivariate statistical analysis revealed that all three Pb treatments significantly altered the metabolite profile. Compared with nano-PbS, mic-PbO and PbCl2 induced more identical metabolite changes. However, the alterations in metabolites related to the TCA cycle and pyrimidine metabolism, such as succinic acid, citric acid and cytidine, were specific to PbCl2. The number of differential metabolites induced by mic-PbO and PbCl2 was three times that of nano-PbS, even though the amount of nano-PbS absorbed by leaves was ten times that of PbO and seven times that of PbCl2. This suggests that the metabolic response of eggplant leaves to Pb is influenced by both concentration and form. This study enhances the current understanding of plants' metabolic response to Pb, and demonstrates that the metabolomics map provides a more comprehensive view of a plant's response to specific metals.

N-hydroxypipecolic acid primes plants for enhanced microbial pattern-induced responses

The bacterial elicitor flagellin induces a battery of immune responses in plants. However, the rates and intensities by which metabolically-related defenses develop upon flagellin-sensing are comparatively moderate. We report here that the systemic acquired resistance (SAR) inducer N-hydroxypipecolic acid (NHP) primes Arabidopsis thaliana plants for strongly enhanced metabolic and transcriptional responses to treatment by flg22, an elicitor-active peptide fragment of flagellin. While NHP powerfully activated priming of the flg22-induced accumulation of the phytoalexin camalexin, biosynthesis of the stress hormone salicylic acid (SA), generation of the NHP biosynthetic precursor pipecolic acid (Pip), and accumulation of the stress-inducible lipids γ-tocopherol and stigmasterol, it more modestly primed for the flg22-triggered generation of aromatic and branched-chain amino acids, and expression of FLG22-INDUCED RECEPTOR-KINASE1. The characterization of the biochemical and immune phenotypes of a set of different Arabidopsis single and double mutants impaired in NHP and/or SA biosynthesis indicates that, during earlier phases of the basal immune response of naïve plants to Pseudomonas syringae infection, NHP and SA mutually promote their biosynthesis and additively enhance camalexin formation, while SA prevents extraordinarily high NHP levels in later interaction periods. Moreover, SA and NHP additively contribute to Arabidopsis basal immunity to bacterial and oomycete infection, as well as to the flagellin-induced acquired resistance response that is locally observed in plant tissue exposed to exogenous flg22. Our data reveal mechanistic similarities and differences between the activation modes of flagellin-triggered acquired resistance in local tissue and the SAR state that is systemically induced in plants upon pathogen attack. They also corroborate that the NHP precursor Pip has no independent immune-related activity.

Metabolite profiling of susceptible and resistant wheat (Triticum aestivum) cultivars responding to Puccinia striiformis f. sp. tritici infection

BACKGROUND

Puccinia striiformis f. sp. tritici (Pst) is an economically devasting disease that is prominent in cereal crops such as wheat (Triticum aestivum). The fungal pathogen can cause approximately 30-70% losses in crop productivity and yields. Pst has become difficult to manage due to its ease of transmission through wind dispersal over long distances, and intercontinental dispersal has been previously reported. The ease of transmission has resulted in further destruction because of new and more virulent strains infecting crops previously resistant to a different strain.

RESULTS

In this study, a liquid chromatography-mass spectrometry-based untargeted metabolomics approach, in combination with multivariate data analytical tools, was used to elucidate the mechanistic nature of the defence systems of a Pst-resistant and a susceptible wheat cultivar infected with P. striiformis. We also investigated the time-dependant metabolic reconfiguration of infected plants over a four-week period. The untargeted metabolomic analysis revealed a time-course metabolic reprogramming involving phenylpropanoids (majority flavonoids), amino acids, lipids, benzoic acids, TCA cycle intermediates and benzoxazinoids responding to Pst infection. Interestingly, the results do not show a linear course for the decrease and increase (up-/down-regulation) of said classes of metabolites, but rather the up- or down-regulation of specific metabolites in response to the pathogen infection. The resistant Koonap cultivar had an abundance of phenolic compounds such as rutin, isoorintin-7-O-glucoside and luteolin-6-C-hexoside-O-hexoside. These compounds showed a decrease over time in control Koonap plants compared to an increase in Pst-infected plants. These metabolites were down-regulated in the susceptible Gariep cultivar, which could serve as biomarkers for plant responses to biotic stress and resistance against Pst.

CONCLUSIONS

Overall, an LC-MS-based metabolomics approach allowed for the metabolic profiling and analysis of the impact of plant-pathogen interactions on the overall plant metabolome and provided a real-time snapshot of the differential significant metabolic perturbations occurring in wheat plants responding to the Pst pathogen. The Pst-resistant Koonap cultivar showed a rapid accumulation of defence metabolites in response to pathogen infection compared to the susceptible Gariep cultivar. These findings provide insight into the mechanistic biochemical nature of plant-microbe interactions and the prospects of metabolic engineering for improved plant tolerance and resistance to biotic stresses.

Redox state and metabolic responses to severe heat stress in lenok Brachymystax lenok (Salmonidae)

In order to provide new insights into the physiological responses of lenok (Brachymystax lenok: Salmonidae) to acute and severe heat stress (25°C, 48 h), dynamic changes in redox state and metabolic responses are studied combined biochemical index and non-targeted metabolome. Nicotinamide adenine dinucleotide (NAD⁺) consumption causes significant increases in ratio of reduced NADH to NAD⁺ and ratio of reduced nicotinamide adenine dinucleotide phosphate (NADPH) to NADP⁺, which induced the redox imbalance in heat stressed lenok. Lowered reduced glutathione/oxidized glutathione (GSH/GSSG) ratios suggested that more oxidized conditions occurred in heat-stressed lenok, leading to membrane lipid oxidation. The first few hours of heat stress promoted the activity of enzymes involved in anaerobic glycolysis (hexokinase, pyruvate kinase, lactic dehydrogenase) and glutamicpyruvic transaminase and glutamic oxaloacetic transaminase, which might lead to consumption of many carbohydrates and amino acid catabolism. These enzyme activities decreased with time in a possible compensatory strategy to manage anabolic and catabolic metabolism, maintaining the redox homeostasis. After 48 h of recovery, NAD⁺, carbohydrate levels and enzyme activities had returned to control levels, whereas many amino acids were consumed for repair and new synthesis. GSH remained at levels lower than controls, and the more oxidized conditions had not recovered, aggravating oxidative damage. Glutamic acid, glutamine, lysine and arginine may play important roles in survival of heat-stressed lenok.

In Vivo Detection of Glutamate in Tomatoes by an Enzyme-Based Electrochemical Biosensor

The in vivo and on-site detection of key physiology parameters in plants will be of great relevance for precision agriculture and food technology. In this work, a sensitive enzymatic glutamate sensor was successfully developed. To enhance the conductivity and catalytic ability and to fix the glutamate oxidase, Au-Pt nanoparticles were first deposited on screen-printed electrodes, and then carboxylated graphene oxide and carboxylated multiwalled carbon nanotubes were fabricated for the synthesis of the electrode. The detection range of the glutamate sensor is widest (2 μM to 16 mM) up to date, and its detection limit is relatively low (0.14 μM). A number of standard curves were built in the pH range of 3.5-7.5, which can be applied in various plants and fruits. Using this sensor, the glutamate level in tomatoes was determined in vivo. This glutamate sensor has important practical value in precision agriculture. Our strategy also provides a way to establish the detection modes for other biomolecules in plants.

The Hidden Potential of High-Throughput RNA-Seq Re-Analysis, a Case Study for DHDPS, Key Enzyme of the Aspartate-Derived Lysine Biosynthesis Pathway and Its Role in Abiotic and Biotic Stress Responses in Soybean

DHDPS is a key enzyme in the aspartate-derived lysine biosynthesis pathway and an evident object of study for biofortification strategies in plants. DHDPS isoforms with novel regulatory properties in Medicago truncatula were demonstrated earlier and hypothesized to be involved in abiotic and biotic stress responses. Here, we present a phylogenetic analysis of the DHPDS gene family in land plants which establishes the existence of a legume-specific class of DHDPS, termed DHDPS B-type, distinguishable from the DHDPS A-type commonly present in all land plants. The G. max genome comprises two A-type DHDPS genes (Gm.DHDPS-A1; Glyma.09G268200, Gm.DHDPS-A2; Glyma.18G221700) and one B-type (Gm.DHDPS-B; Glyma.03G022300). To further investigate the expression pattern of the G. max DHDPS isozymes in different plant tissues and under various stress conditions, 461 RNA-seq experiments were exploited and re-analyzed covering two expression atlases, 13 abiotic and 5 biotic stress studies. Gm.DHDPS-B is seen almost exclusively expressed in roots and nodules in addition to old cotyledons or senescent leaves while both DHDPS A-types are expressed constitutively in all tissues analyzed with the highest expression in mature seeds. Furthermore, Gm.DHDPS-B expression is significantly upregulated in some but not all stress responses including salt stress, flooding, ethylene or infection with Phytophthora sojae and coincides with downregulation of DHDPS A-types. In conclusion, we demonstrate the potential of an in-depth RNA-seq re-analysis for the guidance of future experiments and to expand on current knowledge.

Metabonomics study of liver and kidney subacute toxicity induced by garidi-5 in rats

Objective

Metabonomics was used to analyze and explore the biomarkers and possible mechanisms of liver and kidney subacute toxicity induced by garidi-5 in rats.

Methods

Taking garidi-5 as the target drug and SD rats as the research objects, each administration group except the normal group was intragastric administration of the corresponding drug solution for 28 d. The serum, liver and kidney samples of rats were detected by metabolomics and characterized by principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) to identify the sensitive markers and metabolic pathways of liver and kidney subacute toxicity.

Results

Metabolomics analysis showed that compared with the normal group (Z), the 52, 64 and 54 different metabolites were identified in the serum, liver and kidney samples of garidi-5 high dose group (GG), which were mainly enriched in ABC transporters, arginine and proline metabolism, nicotinate and nicotinamide metabolism, central carbon metabolism in cancer pathways.

Conclusion

The preliminarily suggested that garidi-5 can damage the liver and kidney by affecting the ABC transporters, arginine and proline metabolism, nicotinate and nicotinamide metabolism pathways, etc. Trimethylamine N-oxide, l-pyroglutamic acid, glycine-betaine, xanthine, glutathione, l-leucine, cytidine, l-arginine, spermidine, urea, 5-aminovaleric acid, creatine, l-glutamic acid, 1-methylnicotinamide and S-adenosyl-l-methionine can be used as potential biomarkers of liver and kidney toxicity sensitivity.

Deep Untargeted Metabolomics Analysis to Further Characterize the Adaptation Response of Gliricidia sepium (Jacq.) Walp. to Very High Salinity Stress

The multipurpose tree Gliricidia sepium (Jacq.) Walp. adapts to a very high level of salt stress (≥20 dS m^-1) and resumes the production of new leaves around 2 weeks after losing all leaves due to abrupt salinity stress. The integration of metabolome and transcriptome profiles from gliricidia leaves points to a central role of the phenylpropanoid biosynthesis pathway in the short-term response to salinity stress. In this study, a deeper untargeted metabolomics analysis of the leaves and roots of young gliricidia plants was conducted to characterize the mechanism(s) behind this adaptation response. The polar and lipidic fractions from leaf and root samples were extracted and analyzed on a UHPLC.ESI.Q-TOF.HRMS system. Acquired data were analyzed using the XCMS Online, and MetaboAnalyst platforms, via three distinct and complementary strategies. Together, the results obtained first led us to postulate that these plants are salt-excluding plants, which adapted to high salinity stress via two salt-excluding mechanisms, starting in the canopy-severe defoliation-and concluding in the roots-limited entry of Na. Besides that, it was possible to show that the phenylpropanoid biosynthesis pathway plays a role throughout the entire adaptation response, starting in the short term and continuing in the long one. The roots metabolome analysis revealed 11 distinct metabolic pathways affected by salt stress, and the initial analysis of the two most affected ones-steroid biosynthesis and lysine biosynthesis-led us also to postulate that the accumulation of lignin and some phytosterols, as well as lysine biosynthesis-but not degradation, play a role in promoting the adaptation response. However, additional studies are necessary to investigate these hypotheses.

Gene Expression and Metabolic Analyses of Nontransgenic and AtPAP1 Transgenic Tobacco Infected with Potato Virus X (PVX)

Potato virus X (PVX), a species of the genus Potexvirus, is a plant pathogenic virus that causes severe symptoms such as mild mosaic, crinkling, necrosis, and mottling on leaves. The objectives of the present study were to investigate the effect of PVX virus infection on the metabolic system in nontransgenic and Arabidopsis thaliana production of anthocyanin pigment 1 (AtPAP1) transgenic tobacco using transcript expression analysis and metabolic profiling. Potato virus X inoculation increased the gene expression of phenylpropanoid and flavonoid biosynthesis and the production of chlorogenic acid, p-coumaric acid, benzoic acid, rutin, quercetin, and kaempferol in nontransgenic tobacco leaves. However, in the AtPAP1 transgenic tobacco leaves, PVX inoculation decreased the expression of AtPAP1 and phenylpropanoid and flavonoid biosynthesis genes, and the production of phenolics and anthocyanin also declined. In contrast, the levels of amino acids and tricarboxylic acid (TCA) cycle intermediates increased after infection in the AtPAP1 transgenic plant leaves. To date, these results have not been reported previously. We suggest that PVX infection decreases AtPAP1 expression, leading to the downregulation of phenylpropanoid and flavonoid biosynthesis in transgenic plants.

Integrated analysis about the effects of heat stress on physiological responses and energy metabolism in Gymnocypris chilianensis

The temperature of the rivers in the Qilian Mountains, China varies widely from day to night, and Gymnocypris chilianensis living in these rivers may experience a change of 10 °C to 20 °C within a day. To explore the mechanisms underlying G. chilianensis responses to heat stress, we conducted an acute temperature stress experiment. In response to heat stress, levels of antioxidant enzymes (SOD\CAT\MDA) first increased and then decreased with time, but T-AOC levels only decreased. The activities of key glycolytic enzymes HK and PFK in the liver also first increased and then decreased and transaminase (AST/ALT) activity increased significantly. We obtained 5350 significantly different genes through transcriptome sequencing with enrichment pathways including primarily glycine, serine and threonine metabolism, cysteine and methionine metabolism, tryptophan metabolism, fructose and mannose metabolism, steroid hormone biosynthesis, and fatty acid degradation. A total of 457 differential metabolites were identified in the liver under thermal stress, most of which are involved in biochemical pathways of amino acid metabolism. Biosynthesis of amino acids indicated that G. chilianensis maintained physiological homeostasis by enhancing glucose metabolism and regulating lipid and amino acid metabolism pathways under thermal stress. We also randomly selected 12 key response genes for validation using qRT-PCR. This is the first study describing the mechanisms underlying responses to thermal stress in G. chilianensis, and may also provide reference data for the study of environmental mutations in indigenous fish in the Qinghai-Tibet Plateau and Qilian Mountains.

How do rice seedlings of landrace Pokkali survive in saline fields after transplantation? Physiology, biochemistry, and photosynthesis

Rice, one of the most important staple food crops in the world, is highly sensitive to soil salinity at the seedling stage. The ultimate yield of this crop is a function of the number of seedlings surviving after transplantation in saline water. Oryza sativa cv. IR64 is a high-yielding salinity-sensitive variety, while Pokkali is a landrace traditionally cultivated by the local farmers in the coastal regions in India. However, the machinery responsible for the seedling-stage tolerance in Pokkali is not understood. To bridge this gap, we subjected young seedlings of these contrasting genotypes to salinity and performed detailed investigations about their growth parameters, ion homeostasis, biochemical composition, and photosynthetic parameters after every 24 h of salinity for three days. Taken together, all the physiological and biochemical indicators, such as proline accumulation, K⁺/Na⁺ ratio, lipid peroxidation, and electrolyte leakage, clearly revealed significant differences between IR64 and Pokkali under salinity, establishing their contrasting nature at this stage. In response to salinity, the F_v/F_m ratio (maximum quantum efficiency of Photosystem II as inferred from Chl a fluorescence) and the energy conserved for the electron transport after the reduction of Q_A (the primary electron acceptor of PSII), to Q_A^-, and reduction of the end electron acceptor molecules towards the PSI (Photosystem I) electron acceptor side was higher in Pokkali than IR64 plants. These observations reflect a direct contribution of photosynthesis towards seedling-stage salinity tolerance in rice. These findings will help to breed high-yielding crops for salinity prone agricultural lands.

Root Metabolite Differences in Two Maize Varieties Under Lead (Pb) Stress

To assess root metabolic differences of maize varieties in their response to lead (Pb) stress, the lead-tolerant variety Huidan No. 4 and the lead-sensitive variety Ludan No. 8 were tested under Pb-free and Pb-stressed conditions. Changes in metabolites were measured using ultra-performance liquid chromatography-mass spectrometry. Pb stress changed the levels of the amino acids proline, glutamine, lysine, and arginine in both varieties, whereas glutamate and phenylalanine levels changed only in Huidan No. 4. Pb stress altered cystine, valine, methionine, and tryptophan levels only in Ludan No. 8. Therefore, the synthesis and decomposition of amino acids may affect the response of maize to Pb stress. The degree of change in differential metabolites for Huidan No. 4 was greater than that for Ludan No. 8. In cell wall subcellular components, increases in superoxide dismutase (SOD), peroxidases (PODs), and Pb concentrations were greater in Huidan No. 4 than in Ludan No. 8. Therefore, the greater Pb tolerance of Huidan No. 4 could be due to better sequestration of Pb in cell walls and more effective removal of reactive oxygen species (ROS) from the plant. The levels of certain metabolites only increased in Ludan No. 8, indicating that Pb-sensitive varieties may use different metabolic pathways to cope with Pb stress. Both varieties showed increased levels of some metabolites related to antioxidant protection and osmotic regulation. This study provides an understanding of maize Pb tolerance mechanisms and a basis for further development of tools for use in maize breeding.

Engineering a feedback inhibition-insensitive plant dihydrodipicolinate synthase to increase lysine content in Camelina sativa seeds

Camelina sativa (camelina) is emerging as an alternative oilseed crop due to its short growing cycle, low input requirements, adaptability to less favorable growing environments and a seed oil profile suitable for biofuel and industrial applications. Camelina meal and oil are also registered for use in animal and fish feeds; however, like meals derived from most cereals and oilseeds, it is deficient in certain essential amino acids, such as lysine. In higher plants, the reaction catalyzed by dihydrodipicolinate synthase (DHDPS) is the first committed step in the biosynthesis of lysine and is subject to regulation by lysine through feedback inhibition. Here, we report enhancement of lysine content in C. sativa seed via expression of a feedback inhibition-insensitive form of DHDPS from Corynebacterium glutamicums (CgDHDPS). Two genes encoding C. sativa DHDPS were identified and the endogenous enzyme is partially insensitive to lysine inhibition. Site-directed mutagenesis was used to examine the impact of alterations, alone and in combination, present in lysine-desensitized DHDPS isoforms from Arabidopsis thaliana DHDPS (W53R), Nicotiana tabacum (N80I) and Zea mays (E84K) on C. sativa DHDPS lysine sensitivity. When introduced alone, each of the alterations decreased sensitivity to lysine; however, enzyme specific activity was also affected. There was evidence of molecular or structural interplay between residues within the C. sativa DHDPS allosteric site as coupling of the W53R mutation with the N80V mutation decreased lysine sensitivity of the latter, but not to the level with the W53R mutation alone. Furthermore, the activity and lysine sensitivity of the triple mutant (W53R/N80V/E84T) was similar to the W53R mutation alone or the C. glutamicum DHDPS. The most active and most lysine-insensitive C. sativa DHDPS variant (W53R) was not inhibited by free lysine up to 1 mM, comparable to the C. glutamicums enzyme. Seed lysine content increased 13.6 -22.6% in CgDHDPS transgenic lines and 7.6–13.2% in the mCsDHDPS lines. The high lysine-accumulating lines from this work may be used to produce superior quality animal feed with improved essential amino acid profile.

Host Gamma-Aminobutyric Acid Metabolic Pathway Is Involved in Resistance Against Rhizoctonia solani

Rhizoctonia solani is a highly destructive necrotrophic fungal pathogen having a diverse host range, including rice and tomato. Previously R. solani infection has been found to cause large-scale readjustment in host primary metabolism and accumulation of various stress-associated metabolites such as gamma-aminobutyric acid (GABA) in rice. In this study, we report upregulation of GABA pathway genes during pathogenesis of R. solani in rice and tomato. The exogenous application of GABA provided partial resistance against R. solani infection in both the hosts. Furthermore, by using the virus-induced gene silencing approach, we knocked down the expression of some of the tomato genes involved in GABA biosynthesis (glutamate decarboxylase) and GABA catabolism (GABA-transaminase and succinic semialdehyde dehydrogenase) to study their role in host defense against R. solani infection. The silencing of each of these genes increased disease susceptibility in tomato. Overall the results from gene expression analysis, exogenous chemical application, and gene silencing studies suggest that the GABA pathway plays a positive role in plant defense against necrotrophic pathogen R. solani.

Rethinking of the Roles of Endophyte Symbiosis and Mycotoxin in Oxytropis Plants

Plants in the Oxytropis genus can live with the endophytic fungi Alternaria sect. Undifilum. Swainsonine, the mycotoxin produced by the endophyte render the host plant toxic and this has been detrimental to grazing livestock in both China and U.S.A. Despite previous efforts, many questions remain to be solved, such as the transmission mode and life cycle of host–endophyte symbiont, the biosynthesis pathway of swainsonine, and in particular the ecological role and evolution of such symbiosis. In this review, we compile the literature to synthesize ideas on the diversity of the symbiosis and propagation of the endophyte. We further compare the previous work from both Alternaria sect. Undifilum and other swainsonine producing fungi to orchestrate a more comprehensive biosynthesis pathway of swainsonine. We also connect swainsonine biosynthesis pathway with that of its precursor, lysine, and link this to a potential role in modulating plant stress response. Based on this we hypothesize that this host–endophyte co-evolution originated from the needs for host plant to adapt for stress. Validation of this hypothesis will depend on future research on endophytic symbiosis in Oxytropis and help in better understanding the roles of plant–endophyte symbiosis in non-Poaceae species.

Transcriptomic and metabolomic insights into the adaptive response of Salix viminalis to phenanthrene

Polycyclic aromatic hydrocarbons (PAHs) are widespread, persistent environmental pollutants. They exert toxic effects at different developmental stages of plants. Plant defense mechanisms against PAHs are poorly understood. To this end, transcriptomics and widely targeted metabolomic sequencing were used to study the changes in gene expression and metabolites that occur in the roots of Salix viminalis subjected to phenanthrene stress. Significant variations in genes and metabolites were observed between treatment groups and the control group. Thirteen amino acids and key genes involved in their biosynthesis were upregulated exposed to phenanthrene. Cysteine biosynthesis was upregulated. Sucrose, inositol galactoside, and mellidiose were the main carbohydrates that were largely accumulated. Glutathione biosynthesis was enhanced in order to scavenge reactive oxygen species and detoxify the phenanthrene. Glucosinolate and flavonoid biosynthesis were upregulated. The production of pinocembrin, apigenin, and epigallocatechin increased, which may play a role in antioxidation to resist phenanthrene stress. In addition, levels of six amino acids and N,N'-(p-coumaroyl)-cinnamoyl-caffeoyl-spermidine were significantly increased, which may have helped protect the plant against phenanthrene stress. These results demonstrated that S. viminalis had a positive defense strategy in response to phenanthrene challenge. Subsequent defense-related reactions may have also occurred within 24 h of phenanthrene exposure. The findings of the present study would be useful in elucidating the molecular mechanisms regulating plant responses to PAH challenges and would help guide crop and plant breeders in enhancing PAH resistance.

Metabolite Profile of Xylem Sap in Cotton Seedlings Is Changed by K Deficiency

Xylem sap, belonging to the plant apoplast, not only provides plant tissues with inorganic and organic substances but also facilitates communication between the roots and the leaves and coordinates their development. This study investigated the effects of potassium (K) deficiency on the morphology and the physiology of cotton seedlings as well as pH, mineral nutrient contents, and metabolites of xylem sap. In particular, we compared changes in root-shoot communication under low K (LK) and normal K (NK, control) levels. Compared to control, LK stress significantly decreased seedling biomass (leaf, stem, and root dry weight; stem and root length; root surface area and root volume) and the levels of K, Na (sodium), Mg (magnesium), Fe (iron), and Zn (zinc) in xylem sap. A total of 82 metabolites in sap analyzed by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) showed significant differences between the two conditions; among these, 38 were up-regulated more than 2-fold, while the others were down-regulated less than 0.5-fold. In particular, several metabolites found in the cell membrane including three cholines (glycerophosphatecholine, 2-hexenylcholine, and caproylcholine) and desglucocoroloside and others such as malondialdehyde, α-amino acids and derivatives, sucrose, and sugar alcohol significantly increased under LK stress, indicating that cell membranes were damaged and protein metabolism was abnormal. It is worth noting that glycerophosphocholine was up-regulated 29-fold under LK stress, indicating that it can be used as an important signal of root-shoot communication. Furthermore, in pathway analyses, 26 metabolites were matched to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways; L-aspartic acid, which was associated with 10 KEGG pathways, was the most involved metabolite. Overall, K deficiency reduced the antioxidant capacity of cotton seedlings and led to a metabolic disorder including elevated levels of primary metabolites and inhibited production of secondary metabolites. This eventually resulted in decreased biomass of cotton seedlings under LK stress. This study lays a solid foundation for further research on targeted metabolites and signal substances in the xylem sap of cotton plants exposed to K deficiency.

Effect of glutamate on Pyricularia oryzae infection of rice monitored by changes in photosynthetic parameters and antioxidant metabolism

Considering the importance of blast caused by Pyricularia oryzae in the decrease of rice yield worldwide, this study aimed to assess the photosynthetic performance [leaf gas exchange and chlorophyll (Chl) a fluorescence parameters as well as the photosynthetic pigments concentration], the activities of antioxidant enzymes [ascorbate peroxidase, catalase (CAT), peroxidase (POX), superoxide dismutase (SOD), glutathione peroxidase (GPX), glutathione reductase (GR) and glutathione-S-transferase] and concentrations of hydrogen peroxide (H₂ O₂ ) and malondialdehyde (MDA) in the leaves of rice plants non-supplied (-Glu) or supplied (+Glu) with glutamate (Glu) and non-infected or infected by P. oryzae. Blast severity was reduced in the leaves of +Glu plants. On the infected leaves of +Glu plants, the values for internal CO₂ concentration were lower while the values for net carbon assimilation rate, stomatal conductance as well as for the concentrations of Chl a, Chl b and carotenoids were higher in comparison to infected leaves of -Glu plants. The functionality of the photosynthetic apparatus was preserved in the infected leaves of +Glu plants. The activities of CAT, GPX, GR, POX and SOD increased in the infected leaves of both -Glu and +Glu plants compared to their non-inoculated counterparts, but their activities were lower for +Glu plants. The lower activity of these antioxidative enzymes was triggered by the reduced hydrogen peroxide concentration in the infected leaves of +Glu plants resulting in lower MDA concentration. It can be concluded that photosynthesis was less impaired in infected plants supplied with glutamate due to the lower biochemical constraints for CO₂ fixation. Moreover, there was a need for lower activity of reactive oxygen species scavenging enzymes in infected leaves of plants supplied with glutamate due to the lower oxidative stress imposed by P. oryzae infection.

Lysine, Lysine-Rich, Serine, and Serine-Rich Proteins: Link Between Metabolism, Development, and Abiotic Stress Tolerance and the Role of ncRNAs in Their Regulation

Lysine (Lys) is indispensable nutritionally, and its levels in plants are modulated by both transcriptional and post-transcriptional control during plant ontogeny. Animal glutamate receptor homologs have been detected in plants, which may participate in several plant processes through the Lys catabolic products. Interestingly, a connection between Lys and serotonin metabolism has been established recently in rice. 2-Aminoadipate, a catabolic product of Lys appears to play a critical role between serotonin accumulation and the color of rice endosperm/grain. It has also been shown that expression of some lysine-methylated proteins and genes encoding lysine-methyltransferases (KMTs) are regulated by cadmium even as it is known that Lys biosynthesis and its degradation are modulated by novel mechanisms. Three complex pathways co-exist in plants for serine (Ser) biosynthesis, and the relative preponderance of each pathway in relation to plant development or abiotic stress tolerance are being unfolded slowly. But the phosphorylated pathway of L-Ser biosynthesis (PPSB) appears to play critical roles and is essential in plant metabolism and development. Ser, which participates indirectly in purine and pyrimidine biosynthesis and plays a pivotal role in plant metabolism and signaling. Also, L-Ser has been implicated in plant responses to both biotic and abiotic stresses. A large body of information implicates Lys-rich and serine/arginine-rich (SR) proteins in a very wide array of abiotic stresses. Interestingly, a link exists between Lys-rich K-segment and stress tolerance levels. It is of interest to note that abiotic stresses largely influence the expression patterns of SR proteins and also the alternative splicing (AS) patterns. We have checked if any lncRNAs form a cohort of differentially expressed genes from the publicly available PPSB, sequence read archives of NCBI GenBank. Finally, we discuss the link between Lys and Ser synthesis, catabolism, Lys-proteins, and SR proteins during plant development and their myriad roles in response to abiotic stresses.

Metabolic Effects of Elevated CO2 on Wheat Grain Development and Composition

The increase in the atmospheric CO₂ concentration is predicted to influence wheat production and grain quality and nutritional properties. In the present study, durum wheat (Triticum durum Desf. cv. Sula) was grown under two different CO₂ (400 versus 700 μmol mol^-1) concentrations to examine effects on the crop yield and grain quality at different phenological stages (from grain filling to maturity). Exposure to elevated CO₂ significantly increased aboveground biomass and grain yield components. Growth at elevated CO₂ diminished the elemental N content as well as protein and free amino acids, with a typical decrease in glutamine, which is the most represented amino acid in grain proteins. Such a general decrease in nitrogenous compounds was associated with altered kinetics of protein accumulation, N remobilization, and N partitioning. Our results highlight important modifications of grain metabolism that have implications for its nutritional quality.

Global metabolic responses of the lenok (Brachymystax lenok) to thermal stress

High temperature is a powerful stressor for fish living in natural and artificial environments, especially for cold water species. Understanding the impact of thermal stress on physiological processes of fish is crucial for better cultivation and fisheries management. However, the metabolic mechanism of cold water fish to thermal stress is still not completely clear. In this study, a NMR-based metabonomic strategy in combination with high-throughput RNA-Seq was employed to investigate global metabolic changes of plasma and liver in a typical cold water fish species lenok (Brachymystax lenok) subjected to a sub-lethal high temperature. Our results showed that thermal stress caused multiple dynamic metabolic alterations of the lenok with prolonged stress, including repression of energy metabolism, shifts in lipid metabolism, alterations in amino acid metabolism, changes in choline and nucleotide metabolisms. Specifically, thermal stress induced an activation of glutamate metabolism, indicating that glutamate could be an important biomarker associated with thermal stress. Evidence from Hsp 70 gene expression, blood biochemistry and histology confirmed that high temperature exposure had negative effects on health of the lenok. These findings imply that thermal stress has a severe adverse effect on fish health and demonstrate that the integrated analyses combining NMR-based metabonomics and transcriptome strategy is a powerful approach to enhance our understanding of metabolic mechanisms of fish to thermal stress.

Filamentous cyanobacteria triples oil production in seawater-based medium supplemented with industrial waste: monosodium glutamate residue

BACKGROUND

To overcome the daunting technical and economic barriers of algal biofuels, we evaluated whether seawater can be a viable medium for economically producing filamentous Spirulina subsalsa as feedstock, using monosodium glutamate residue (MSGR) produced by the glutamate extraction process as an inexpensive nutrient source.

RESULTS

Spirulina subsalsa cannot grow in pure seawater, but exhibited faster biomass accumulation in seawater supplemented with MSGR than in freshwater medium (modified Zarrouk medium). Introducing seawater into media ensured this cyanobacterium obtained high lipid productivity (120 mg/L/day) and suffered limited bacterial infections during growth. Moreover, the yields of protein, carotenoids and phytols were also improved in seawater mixed with MSGR. S. subsalsa exhibited high biomass and lipid productivity in bag bioreactors with 5- and 10-L medium, demonstrating the potential of this cultivation method for scaling up. Moreover, seawater can produce more biomass through medium reuse. Reused seawater medium yielded 72% of lipid content compared to pristine medium. The reason that S. subsalsa grew well in seawater with MSGR is its proficient adaptation to salinity, which included elongation and desaturation of fatty acids, accumulation of lysine and methionine, and secretion of sodium. The nutrients provided by MSGR, like organic materials, played an important role in these responses.

CONCLUSION

Spirulina subsalsa has an efficient system to adapt to saline ambiance in seawater. When supplemented with MSGR, seawater is a great potential medium to produce S. subsalsa in large scale as biofuel feedstock. Meanwhile, value-added products can be derived from the ample protein and pigments that can broaden the range of biomass application and improve this biorefinery economics.

Knock-Down of the Phosphoserine Phosphatase Gene Effects Rather N- Than S-Metabolism in Arabidopsis thaliana

The aim of present study was to elucidate the significance of the phosphorylated pathway of Ser production for Cys biosynthesis in leaves at day and night and upon cadmium (Cd) exposure. For this purpose, Arabidopsis wildtype plants as control and its psp mutant knocked-down in phosphoserine phosphatase (PSP) were used to test if (i) photorespiratory Ser is the dominant precursor of Cys synthesis in autotrophic tissue in the light, (ii) the phosphorylated pathway of Ser production can take over Ser biosynthesis in leaves at night, and (iii) Cd exposure stimulates Cys and glutathione (GSH) biosynthesis and effects the crosstalk of S and N metabolism, irrespective of the Ser source. Glycine (Gly) and Ser contents were not affected by reduction of the psp transcript level confirming that the photorespiratory pathway is the main route of Ser synthesis. The reduction of the PSP transcript level in the mutant did not affect day/night regulation of sulfur fluxes while day/night fluctuation of sulfur metabolite amounts were no longer observed, presumably due to slower turnover of sulfur metabolites in the mutant. Enhanced contents of non-protein thiols in both genotypes and of GSH only in the psp mutant were observed upon Cd treatment. Mutation of the phosphorylated pathway of Ser biosynthesis caused an accumulation of alanine, aspartate, lysine and a decrease of branched-chain amino acids. Knock-down of the PSP gene induced additional defense mechanisms against Cd toxicity that differ from those of WT plants.

Genome-wide identification and characterization of seed storage proteins (SSPs) of foxtail millet (Setaria italica (L.) P. Beauv.)

We report the identification of 47 foxtail millet (Setaria italica (L.) P. Beauv.) seed storage proteins (SSPs) consisting of 14 albumins, 12 prolamins, 18 globulins and 3 glutelins using computational approaches and compared their essential amino acid composition with 225 SSPs of rice, barley, sorghum and maize. Comparative analysis revealed several unique foxtail millet SSPs containing high amounts of essential amino acids. These include three 2s-albumin proteins containing 11.9%, 10.9%, 9.82% lysine, one 10-kDa prolamin containing 20% methionine residues and one each 7S-globulin, 10-kDa prolamin, alpha-zein proteins containing 9.2% threonine, 9.35% phenylalanine and 2.5% tryptophan, respectively. High lysine containing albumins and high methionine containing prolamins were also detected in other cereals indicating that these SSPs are widespread in cereals. Phylogenetic studies revealed that the foxtail millet SSPs are closer to sorghum and maize. The lysine-rich albumins and the methionine-rich prolamins formed a separate cluster. Motif analysis of lysine-rich albumins displayed several lysine containing conserved motifs across cereals including foxtail millet. The 10-kDa prolamin protein containing 20% methionine was unique as it lacked the characteristic repeat motifs of methionine found in the high methionine containing zeins and kafirins. The motif "NPAAFWQQQQLL" was uniquely repeated in the foxtail millet high tryptophan prolamin protein. The findings of the present study provide new insights in foxtail millet seed storage protein characterization and their nutritional importance in terms of essential amino acid composition.

Comparative physiological and metabolomics analysis of wheat (Triticum aestivum L.) following post-anthesis heat stress

Genetic improvement for stress tolerance requires a solid understanding of biochemical processes involved with different physiological mechanisms and their relationships with different traits. The objective of this study was to demonstrate genetic variability in altered metabolic levels in a panel of six wheat genotypes in contrasting temperature regimes, and to quantify the correlation between those metabolites with different traits. In a controlled environment experiment, heat stress (35:28 ± 0.08°C) was initiated 10 days after anthesis. Flag leaves were collected 10 days after heat treatment to employ an untargeted metabolomics profiling using LC-HRMS based technique called IROA. High temperature stress produced significant genetic variations for cell and thylakoid membrane damage, and yield related traits. 64 known metabolites accumulated 1.5 fold of higher or lower due to high temperature stress. In general, metabolites that increased the most under heat stress (L-tryptophan, pipecolate) showed negative correlation with different traits. Contrary, the metabolites that decreased the most under heat stress (drummondol, anthranilate) showed positive correlation with the traits. Aminoacyl-tRNA biosysnthesis and plant secondary metabolite biosynthesis pathways were most impacted by high temperature stress. The robustness of metabolic change and their relationship with phenotypes renders those metabolites as potential bio-markers for genetic improvement.

Measurement of metabolite variations and analysis of related gene expression in Chinese liquorice (Glycyrrhiza uralensis) plants under UV-B irradiation

Plants respond to UV-B irradiation (280–315 nm wavelength) via elaborate metabolic regulatory mechanisms that help them adapt to this stress. To investigate the metabolic response of the medicinal herb Chinese liquorice (Glycyrrhiza uralensis) to UV-B irradiation, we performed liquid chromatography tandem mass spectrometry (LC-MS/MS)-based metabolomic analysis, combined with analysis of differentially expressed genes in the leaves of plants exposed to UV-B irradiation at various time points. Fifty-four metabolites, primarily amino acids and flavonoids, exhibited changes in levels after the UV-B treatment. The amino acid metabolism was altered by UV-B irradiation: the Asp family pathway was activated and closely correlated to Glu. Some amino acids appeared to be converted into antioxidants such as γ-aminobutyric acid and glutathione. Hierarchical clustering analysis revealed that various flavonoids with characteristic groups were induced by UV-B. In particular, the levels of some ortho-dihydroxylated B-ring flavonoids, which might function as scavengers of reactive oxygen species, increased in response to UV-B treatment. In general, unigenes encoding key enzymes involved in amino acid metabolism and flavonoid biosynthesis were upregulated by UV-B irradiation. These findings lay the foundation for further analysis of the mechanism underlying the response of G. uralensis to UV-B irradiation.

Flavin Monooxygenase-Generated N-Hydroxypipecolic Acid Is a Critical Element of Plant Systemic Immunity

Following a previous microbial inoculation, plants can induce broad-spectrum immunity to pathogen infection, a phenomenon known as systemic acquired resistance (SAR). SAR establishment in Arabidopsis thaliana is regulated by the Lys catabolite pipecolic acid (Pip) and flavin-dependent-monooxygenase1 (FMO1). Here, we show that elevated Pip is sufficient to induce an FMO1-dependent transcriptional reprogramming of leaves that is reminiscent of SAR. In planta and in vitro analyses demonstrate that FMO1 functions as a pipecolate N-hydroxylase, catalyzing the biochemical conversion of Pip to N-hydroxypipecolic acid (NHP). NHP systemically accumulates in plants after microbial attack. When exogenously applied, it overrides the defect of NHP-deficient fmo1 in acquired resistance and acts as a potent inducer of plant immunity to bacterial and oomycete infection. Our work has identified a pathogen-inducible L-Lys catabolic pathway in plants that generates the N-hydroxylated amino acid NHP as a critical regulator of systemic acquired resistance to pathogen infection.

Deciphering physio-biochemical, yield, and nutritional quality attributes of water-stressed radish (Raphanus sativus L.) plants grown from Zn-Lys primed seeds

Water shortage appears to be expedited under the current climate change scenario worldwide. The present work was aimed to investigate the effects of zinc-chelated lysine (Zn-Lys) on germination and yield of water stressed radish plants. The research was comprised of two studies where the effect of Zn-Lys seed priming on germination attributes under PEG-induced water stress was investigated in the first experiment. In the second experiment, growth, physio-biochemical, and yield responses of water-stressed radish plants raised from Zn-Lys primed seeds were recorded. The seeds pre-conditioned with 0, 1.5, 3, 4.5, or 6 mg kg^-1 of Zn-Lys was grown in petri-dishes and pots. Priming treatments significantly improved the germination attributes under water stress. Plants raised from primed seeds exhibited significant improvements in plant biomass production, leaf photosynthetic pigments, final root yield, and nutritional quality. Furthermore, the activities of superoxide dismutase (SOD) and peroxidase (POD) were increased, while the melondialdehyde (MDA) content decreased. Root flavonoids, ascorbic acid, carotenoids, protein, carbohydrates, fiber and lysine content were significantly improved due to Zn-Lys seed priming, both under water-stressed and non-stressed conditions. Moreover, plant's mineral nutrients such as K and Ca as well as Mg, Fe, P, and Zn of final harvested roots were also improved due to Zn-Lys seed priming. Overall, for the induction of drought tolerance and nutritional quality, Zn-Lys regimes of 3 and 4.5 mg kg^-1 were most effective. It can be inferred that the Zn-Lys priming maintained a potential balance of nutrient uptake and translocation by preventing drought-induced lipid peroxidation of membranes.

Mapping the Arabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions

Metabolic genome-wide association studies (mGWAS), whereupon metabolite levels are regarded as traits, can help unravel the genetic basis of metabolic networks. A total of 309 Arabidopsis accessions were grown under two independent environmental conditions (control and stress) and subjected to untargeted LC-MS-based metabolomic profiling; levels of the obtained hydrophilic metabolites were used in GWAS. Our two-condition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci (p ≤ 1.0E-08), 24.39% of which were environment-specific. Interestingly, differently from natural variation in Arabidopsis primary metabolites, which tends to be controlled by a large number of small-effect loci, we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites. The two-condition-based GWAS was followed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment. Through this integrative approach, we selected 70 key candidate associations between structural genes and metabolites, and experimentally validated eight novel associations, two of them showing differential genetic regulation in the two environments studied. We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different abiotic environments for identifying metabolite-gene associations, providing novel global insights into the metabolic landscape of Arabidopsis.

Metabolomics Reveals Cu(OH)2 Nanopesticide-Activated Anti-oxidative Pathways and Decreased Beneficial Antioxidants in Spinach Leaves

While the use of nanopesticides in modern agriculture continues to increase, their effects on crop plants are still poorly understood. Here, 4 week old spinach plants grown in an artificial medium were exposed via foliar spray to Cu(OH)₂ nanopesticide (0.18 and 18 mg/plant) or Cu ions (0.15 and 15 mg/plant) for 7 days. A gas chromatography-time-of-flight-mass spectrometry metabolomics approach was applied to assess metabolic alterations induced by Cu(OH)₂ nanopesticide in spinach leaves. Exposure to Cu(OH)₂ nanopesticide and copper ions induced alterations in the metabolite profiles of spinach leaves. Compared to the control, exposure to 18 mg of Cu(OH)₂ nanopesticide induced significant reduction (29-85%) in antioxidant or defense-associated metabolites including ascorbic acid, α-tocopherol, threonic acid, β-sitosterol, 4-hydroxybutyric acid, ferulic acid, and total phenolics. The metabolic pathway for ascorbate and aldarate was disturbed in all exposed spinach plants (nanopesticide and Cu²⁺). Cu²⁺ is responsible for the reduction in antioxidants and perturbation of the ascorbate and aldarate metabolism. However, nitrogen metabolism perturbation was nanopesticide-specific. Spinach biomass and photosynthetic pigments were not altered, indicating that metabolomics can be a rapid and sensitive tool for the detection og earlier nanopesticide effects. Consumption of antioxidants during the antioxidant defense process resulted in reduction of the nutritional value of exposed spinach.

Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi-SlPH tomato line with reduced fruit acidity and higher pH

Background

The destructive phytopathogen Colletotrichum gloeosporioides causes anthracnose disease in fruit. During host colonization, it secretes ammonia, which modulates environmental pH and regulates gene expression, contributing to pathogenicity. However, the effect of host pH environment on pathogen colonization has never been evaluated. Development of an isogenic tomato line with reduced expression of the gene for acidity, SlPH (Solyc10g074790.1.1), enabled this analysis. Total RNA from C. gloeosporioides colonizing wild-type (WT) and RNAi–SlPH tomato lines was sequenced and gene-expression patterns were compared.

Results

C. gloeosporioides inoculation of the RNAi–SlPH line with pH 5.96 compared to the WT line with pH 4.2 showed 30% higher colonization and reduced ammonia accumulation. Large-scale comparative transcriptome analysis of the colonized RNAi–SlPH and WT lines revealed their different mechanisms of colonization-pattern activation: whereas the WT tomato upregulated 13-LOX (lipoxygenase), jasmonic acid and glutamate biosynthesis pathways, it downregulated processes related to chlorogenic acid biosynthesis II, phenylpropanoid biosynthesis and hydroxycinnamic acid tyramine amide biosynthesis; the RNAi–SlPH line upregulated UDP-D-galacturonate biosynthesis I and free phenylpropanoid acid biosynthesis, but mainly downregulated pathways related to sugar metabolism, such as the glyoxylate cycle and L-arabinose degradation II. Comparison of C. gloeosporioides gene expression during colonization of the WT and RNAi–SlPH lines showed that the fungus upregulates ammonia and nitrogen transport and the gamma-aminobutyric acid metabolic process during colonization of the WT, while on the RNAi–SlPH tomato, it mainly upregulates the nitrate metabolic process.

Conclusions

Modulation of tomato acidity and pH had significant phenotypic effects on C. gloeosporioides development. The fungus showed increased colonization on the neutral RNAi–SlPH fruit, and limited colonization on the WT acidic fruit. The change in environmental pH resulted in different defense responses for the two tomato lines. Interestingly, the WT line showed upregulation of jasmonate pathways and glutamate accumulation, supporting the reduced symptom development and increased ammonia accumulation, as the fungus might utilize glutamate to accumulate ammonia and increase environmental pH for better expression of pathogenicity factors. This was not found in the RNAi–SlPH line which downregulated sugar metabolism and upregulated the phenylpropanoid pathway, leading to host susceptibility.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3961-6) contains supplementary material, which is available to authorized users.

Test for l-glutamate inhibition of growth of Alternaria alternata by inducing resistance in tomato fruit

Although numerous studies have reported the involvement of glutamate in plant abiotic stress, relatively little is known about the role of glutamate in plant defence against pathogens. To gain further knowledge, we investigated the effect of glutamate on Alternaria alternata in tomato fruit. A multidisciplinary approach was pursued, combining exogenous glutamate applications, enzymatic activity measurements and real-time quantitative PCR analysis. The results showed glutamate significantly reduced the disease incidence in tomato caused by A. alternata, by inducing resistance (Duncan's test, p<0.05). A large variety of defence-related enzymes and genes involved in the glutamine synthetase/glutamate synthase cycle, energy-generated metabolism, such as the γ-aminobutyric acid shunt, glycolysis and the tricarboxylic acid cycle, and the salicylic acid signalling pathway were activated by glutamate. The activation of these pathways as mentioned above might play a potential role in the resistance mechanisms underpinning glutamate-induced plant immunity.

Improving protein content and quality by over-expressing artificially synthetic fusion proteins with high lysine and threonine constituent in rice plants

Rice grains are rich in starch but low in protein with very low level of both lysine and threonine. Thus, it is important to further improve protein quality and quantity, especially to increase lysine and threonine content in rice grains. We artificially synthesized two new genes by fusing endogenous rice genes with lysine (K)/threonine (T) motif (TKTKK) coding sequences. They were designated as TKTKK1 and TKTKK2 and their encoded proteins consist of 73.1% and 83.5% of lysine/threonine, respectively. These two genes were under the control of 35S promoter and were independently introduced into the rice genome to generate transgenic plants. Our data showed that overexpression of TKTKK1 generated stable proteins with expected molecular weight and the transgenic rice seeds significantly increased lysine, threonine, total amino acids and crude protein content by 33.87%, 21.21%, 19.43% and 20.45%, respectively when compared with wild type control; significant improvement was also observed in transgenic rice seeds overexpressing TKTKK2. However, limited improvement in protein quality and quantity was observed in transgenic seeds carrying tandom array of these two new genes. Our data provide the basis and alternative strategy on further improving protein quality and quantity in other crops or vegetable plants by synthetic biology.

Development of high-lysine rice via endosperm-specific expression of a foreign LYSINE RICH PROTEIN gene

BACKGROUND

Lysine (Lys) is considered to be the first limiting essential amino acid in rice. Although there have been extensive efforts to improve the Lys content of rice through traditional breeding and genetic engineering, no satisfactory products have been achieved to date.

RESULTS

We expressed a LYSINE-RICH PROTEIN gene (LRP) from Psophocarpus tetragonolobus (L.) DC using an endosperm-specific GLUTELIN1 promoter (GT1) in Peiai64S (PA64S), an elite photoperiod-thermo sensitive male sterility (PTSMS) line. The expression of the foreign LRP protein was confirmed by Western blot analysis. The Lys level in the transgenic rice seeds increased more than 30 %, the total amount of other amino acids also increased compared to wild-type. Persistent investigation of amino acids in 3 generations showed that the Lys content was significantly increased in seeds of transgenic rice. Furthermore, Lys content in the hybrid of the transgenic plants also had an approximate 20 % increase compared to hybrid control. At the grain-filling stage, we monitored the transcript abundance of many genes encoding key enzymes involved in amino acid metabolism, and the results suggested that reduced amino acid catabolism led to the accumulation of amino acids in the transgenic plants. The genetically engineered rice showed unfavorable grain phenotypes compared to wild-type, however, its hybrid displayed little negative effects on grain.

CONCLUSIONS

Endosperm-specific expression of foreign LRP significantly increased the Lys content in the seeds of transgenic plant, and the the Lys increase was stably heritable with 3 generation investigation. The hybrid of the transgenic plants also showed significant increases of Lys content in the seeds. These results indicated that expression of LRP in rice seeds may have promising applications in improving Lys levels in rice.

De Novo Assembly and Comparative Transcriptome Analysis Provide Insight into Lysine Biosynthesis in Toona sinensis Roem

Toona sinensis Roem is a popular leafy vegetable in Chinese cuisine and is also used as a traditional Chinese medicine. In this study, leaf samples were collected from the same plant on two development stages and then used for high-throughput Illumina RNA-sequencing (RNA-Seq). 125,884 transcripts and 54,628 unigenes were obtained through de novo assembly. A total of 25,570 could be annotated with known biological functions, which indicated that the T. sinensis leaves and shoots were undergoing multiple developmental processes especially for active metabolic processes. Analysis of differentially expressed unigenes between the two libraries showed that the lysine biosynthesis was an enriched KEGG pathway, and candidate genes involved in the lysine biosynthesis pathway in T. sinensis leaves and shoots were identified. Our results provide a primary analysis of the gene expression files of T. sinensis leaf and shoot on different development stages and afford a valuable resource for genetic and genomic research on plant lysine biosynthesis.

Improving Nutritional Quality of Plant Proteins Through Genetic Engineering

Humans and animals are unable to synthesize essential amino acids such as branch chain amino acids methionine (Met), lysine (Lys) and tryptophan (Trp). Therefore, these amino acids need to be supplied through the diets. Several essential amino acids are deficient or completely lacking among crops used for human food and animal feed. For example, soybean is deficient in Met; Lys and Trp are lacking in maize. In this mini review, we will first summarize the roles of essential amino acids in animal nutrition. Next, we will address the question: “What are the amino acids deficient in various plants and their biosynthesis pathways?” And: “What approaches are being used to improve the availability of essential amino acids in plants?” The potential targets for metabolic engineering will also be discussed, including what has already been done and what remains to be tested.

New Insight into the Mechanism and Function of Autophagy in Plant Cells

Autophagy is a degradation pathway that is conserved throughout eukaryotic organisms and plays important roles in the tolerance of abiotic and biotic stresses. It functions as a housekeeping process to remove unwanted cell components under normal conditions, and is induced during stress and senescence to break down damaged cellular contents and to recycle materials. The target components are engulfed into specialized transport structures termed autophagosomes and are subsequently delivered to the vacuole for degradation. Here, we review milestones in the study of autophagy in plants, discuss recent advances in our understanding of the mechanism and physiological roles of plant autophagy, and highlight potential future directions of research.

Molecular and physiological changes in response to salt stress in Citrus macrophylla W plants overexpressing Arabidopsis CBF3/DREB1A

Plant stress induced by high salinity has leading to an important reduction in crop yields. Due to their tropical origin, citrus fruits are highly sensitive to salts. Rootstocks are the root system of fruit trees, regulating ion uptake and transport to the canopy. Therefore, increasing their salt tolerance could improve the salt tolerance of the fruit tree. For this, we genetically-transformed an important rootstock for lemon, Citrus macrophylla W, to constitutively express the CBF3/DREB1A gene from Arabidopsis, a well-studied salinity tolerance transcription factor. Transgenic lines showed normal size, with no dwarfism. Under salt stress, some transgenic lines showed greater growth, similar accumulation of chloride and sodium in the leaves and better stomatal conductance, in comparison to wild-type plants. Quantitative real-time analyses showed a similar expression of several CBF3/DREB1A target genes, such as COR15A, LEA 4/5, INV, SIP1, P5CS, GOLS, ADC2 and LKR/SDH, in transgenic lines and wild type plants, with the exception of INV that shows increased expression in line 4C15. Under salt stress, all measured transcript increased in both wild type and transgenics lines, with the exception of INV. Altogether, these results suggest a higher salt tolerance of transgenic C. macrophylla plants induced by the overexpression of AtCBF3/DREB1A.

Developmental, nutritional and hormonal anomalies of weightlessness-grown wheat

The behavior of water in weightlessness, as occurs in orbiting spacecraft, presents multiple challenges for plant growth. Soils remain saturated, impeding aeration, and leaf surfaces remain wet, impeding gas exchange. Herein we report developmental and biochemical anomalies of "Super Dwarf" wheat (Triticum aestivum L.) grown aboard Space Station Mir during the 1996-97 "Greenhouse 2" experiment. Leaves of Mir-grown wheat were hyperhydric, senesced precociously and accumulated aromatic and branched-chain amino acids typical of tissues experiencing oxidative stress. The highest levels of stress-specific amino acids occurred in precociously-senescing leaves. Our results suggest that the leaf ventilation system of the Svet Greenhouse failed to remove sufficient boundary layer water, thus leading to poor gas exchange and onset of oxidative stress. As oxidative stress in plants has been observed in recent space-flight experiments, we recommend that percentage water content in apoplast free-spaces of leaves be used to evaluate leaf ventilation effectiveness. Mir-grown plants also tillered excessively. Crowns and culms of these plants contained low levels of abscisic acid but high levels of cytokinins. High ethylene levels may have suppressed abscisic acid synthesis, thus permitting cytokinins to accumulate and tillering to occur.

A targeted metabolomics approach toward understanding metabolic variations in rice under pesticide stress

Diazinon insecticide is widely applied throughout rice (Oryza sativa L.) fields in Iran. However, concerns are now being raised about its potential adverse impacts on rice fields. In this study, a time-course metabolic change in rice plants was investigated after diazinon treatment using gas chromatography-mass spectrometry (GC-MS), and subsequently the statistical strategy of random forest (RF) was performed in order to find the stress-associated effects. According to the results, a wide range of metabolites were dynamically varied as a result of the plant response to diazinon such as biosynthesis and metabolism of sugars, amino acids, organic acids, and phenylpropanoids, all correlating with the exposure time. Plant response was involved in multiple metabolic pathways, most of which were correlated with the exposure time. In this study, RF was explored as a potential multivariate method for GC-MS analysis of metabolomics data of rice (O. sativa L.) plants under diazinon stress; more than 31 metabolites were quantitatively determined, and time-course metabolic response of the plant during different days after treatment was measured. Results demonstrated RF as a potential multivariate method for GC-MS analysis of changes in plant metabolome under insecticide stress.

Regulation of amino acid metabolic enzymes and transporters in plants

Amino acids play several critical roles in plants, from providing the building blocks of proteins to being essential metabolites interacting with many branches of metabolism. They are also important molecules that shuttle organic nitrogen through the plant. Because of this central role in nitrogen metabolism, amino acid biosynthesis, degradation, and transport are tightly regulated to meet demand in response to nitrogen and carbon availability. While much is known about the feedback regulation of the branched biosynthesis pathways by the amino acids themselves, the regulation mechanisms at the transcriptional, post-transcriptional, and protein levels remain to be identified. This review focuses mainly on the current state of our understanding of the regulation of the enzymes and transporters at the transcript level. Current results describing the effect of transcription factors and protein modifications lead to a fragmental picture that hints at multiple, complex levels of regulation that control and coordinate transport and enzyme activities. It also appears that amino acid metabolism, amino acid transport, and stress signal integration can influence each other in a so-far unpredictable fashion.

Altered growth and improved resistance of Arabidopsis against Pseudomonas syringae by overexpression of the basic amino acid transporter AtCAT1

Amino acid transporters in plants are crucial for distributing amino acids between plant organs and cellular compartments. The H(+)-coupled plasma membrane transporter CAT1 (cationic amino acid transporter 1) facilitates the high-affinity uptake of basic amino acids. The uptake of lysine (Lys) via the roots was not altered in loss-of-function mutants, in accordance with the minor expression of CAT1 in roots, but plants ectopically overexpressing CAT1 incorporated Lys at higher rates. Exogenous Lys inhibited the primary root of Arabidopsis, whereas lateral roots were stimulated. These effects were augmented by the presence or absence of CAT1. Furthermore, the total biomass of soil-grown plants ectopically overexpressing CAT1 was reduced and the time to flowering was accelerated. These effects were accompanied by only minor changes in the overall amino acid profile. Interestingly, CAT1 belongs to a specific small cluster of nitrogen-containing metabolite transporter genes that are rapidly up-regulated upon infection with Pseudomonas syringae and that may participate in the systemic response of plants to pathogen attack. The overexpression of CAT1 indeed enhanced the resistance to the hemibiotrophic bacterial pathogen P. syringae via a constitutively activated salicylic acid (SA) pathway, which is consistent with the developmental defects and the resistance phenotype.

Metabolic changes in Avena sativa crowns recovering from freezing

Extensive research has been conducted on cold acclimation and freezing tolerance of fall-sown cereal plants due to their economic importance; however, little has been reported on the biochemical changes occurring over time after the freezing conditions are replaced by conditions favorable for recovery and growth such as would occur during spring. In this study, GC-MS was used to detect metabolic changes in the overwintering crown tissue of oat (Avena sativa L.) during a fourteen day time-course after freezing. Metabolomic analysis revealed increases in most amino acids, particularly proline, 5-oxoproline and arginine, which increased greatly in crowns that were frozen compared to controls and correlated very significantly with days after freezing. In contrast, sugar and sugar related metabolites were little changed by freezing, except sucrose and fructose which decreased dramatically. In frozen tissue all TCA cycle metabolites, especially citrate and malate, decreased in relation to unfrozen tissue. Alterations in some amino acid pools after freezing were similar to those observed in cold acclimation whereas most changes in sugar pools after freezing were not. These similarities and differences suggest that there are common as well as unique genetic mechanisms between these two environmental conditions that are crucial to the winter survival of plants.

New insights into the regulation of plant immunity by amino acid metabolic pathways

Besides defence pathways regulated by classical stress hormones, distinct amino acid metabolic pathways constitute integral parts of the plant immune system. Mutations in several genes involved in Asp-derived amino acid biosynthetic pathways can have profound impact on plant resistance to specific pathogen types. For instance, amino acid imbalances associated with homoserine or threonine accumulation elevate plant immunity to oomycete pathogens but not to pathogenic fungi or bacteria. The catabolism of Lys produces the immune signal pipecolic acid (Pip), a cyclic, non-protein amino acid. Pip amplifies plant defence responses and acts as a critical regulator of plant systemic acquired resistance, defence priming and local resistance to bacterial pathogens. Asp-derived pyridine nucleotides influence both pre- and post-invasion immunity, and the catabolism of branched chain amino acids appears to affect plant resistance to distinct pathogen classes by modulating crosstalk of salicylic acid- and jasmonic acid-regulated defence pathways. It also emerges that, besides polyamine oxidation and NADPH oxidase, Pro metabolism is involved in the oxidative burst and the hypersensitive response associated with avirulent pathogen recognition. Moreover, the acylation of amino acids can control plant resistance to pathogens and pests by the formation of protective plant metabolites or by the modulation of plant hormone activity.

Pipecolic acid enhances resistance to bacterial infection and primes salicylic acid and nicotine accumulation in tobacco

Distinct amino acid metabolic pathways constitute integral parts of the plant immune system. We have recently identified pipecolic acid (Pip), a lysine-derived non-protein amino acid, as a critical regulator of systemic acquired resistance (SAR) and basal immunity to bacterial infection in Arabidopsis thaliana. In Arabidopsis, Pip acts as an endogenous mediator of defense amplification and priming. For instance, Pip conditions plants for effective biosynthesis of the phenolic defense signal salicylic acid (SA), accumulation of the phytoalexin camalexin, and expression of defense-related genes. Here, we show that tobacco plants respond to leaf infection by the compatible bacterial pathogen Pseudomonas syringae pv tabaci (Pstb) with a significant accumulation of several amino acids, including Lys, branched-chain, aromatic, and amide group amino acids. Moreover, Pstb strongly triggers, alongside the biosynthesis of SA and increases in the defensive alkaloid nicotine, the production of the Lys catabolites Pip and α-aminoadipic acid. Exogenous application of Pip to tobacco plants provides significant protection to infection by adapted Pstb or by non-adapted, hypersensitive cell death-inducing P. syringae pv maculicola. Pip thereby primes tobacco for rapid and strong accumulation of SA and nicotine following bacterial infection. Thus, our study indicates that the role of Pip as an amplifier of immune responses is conserved between members of the rosid and asterid groups of eudicot plants and suggests a broad practical applicability for Pip as a natural enhancer of plant disease resistance.

Cadaverine: a lysine catabolite involved in plant growth and development

The cadaverine (Cad) a diamine, imino compound produced as a lysine catabolite is also implicated in growth and development of plants depending on environmental condition. This lysine catabolism is catalyzed by lysine decarboxylase, which is developmentally regulated. However, the limited role of Cad in plants is reported, this review is tempted to focus the metabolism and its regulation, transport and responses, interaction and cross talks in higher plants. The Cad varied presence in plant parts/products suggests it as a potential candidate for taxonomic marker as well as for commercial exploitation along with growth and development.