Ureide metabolism under abiotic stress in Arabidopsis thaliana

Metabonomics and physiology revealed the critical function of 5-Phosphoribosylamine and antioxidant enzymes in enhancing aged oat seed germination

Effective Microorganism (EM) is widely employed as a growth promoter in agricultural practices. The aging of oat seeds not only directly impairs agricultural production but also exerts adverse effects on biodiversity. The mechanism through which EM influence the germination of aging seeds remains unclear. In this experiment, the EM bacterial solution underwent pretreatment, which included the original-solution treatment (OrT), supernatant treatment (SuT), and sterile treatment (StT). Aging of oat seeds was induced using the pretreated EM bacterial solution. In this study, the EM bacterial solution facilitated the enhancement of the germination rate, germination index, and vitality index of aged seeds, with SuT demonstrating the most pronounced effects. Specifically, SuT resulted in a significant increase in APX and POD activities, while significantly reducing the malondialdehyde content. In addition, metabolic profiling highlighted the significance of 5-phosphoribosylamine in the purine metabolic pathway. Particularly in the SuT, the upregulation of 5-phosphoribosylamine facilitated the synthesis of (R)-Allantoin, consequently augmenting antioxidant enzyme activity.

OsAAH confers salt tolerance in rice seedlings

Soil salinization is becoming a great threat that reduces crop productivity worldwide. In this study, we found that rice allantoate amidohydrolase (OsAAH) expression was significantly upregulated by salt stress, and its overexpression conferred salt tolerance at the seedling stage. Compared to wild type (WT), the contents of ureides (allantoin and allantoate) were significantly increased in Osaah mutants and reduced in OsAAH overexpression lines both before and after salt treatments. Exogenous allantoin significantly promoted salt tolerance in OsAAH overexpression, but not in Osaah mutants. Subcellular localization showed that OsAAH was also localized to the peroxisomes in addition to the previously reported endoplasmic reticulum (ER). The differential expression of peroxisome-related genes was identified between Osaah mutants and WT. Furthermore, the contents of H2O2 and malondialdehyde (MDA) were significantly accumulated in Osaah mutants and reduced in OsAAH overexpression lines. The activities of antioxidant enzymes were significantly reduced in Osaah mutants and enhanced in OsAAH overexpression under NaCl treatment. The transcription factor OsABI5 could directly bind to OsAAH promoter and activate OsAAH expression. Our findings reveal that OsAAH could be induced by salt stress through the activation of OsABI5 and then confer salt tolerance by enhancing the scavenging capacity of reactive oxygen species (ROS), which contributes to rice breeding in salt tolerance.

Identification and Expression Analysis of UPS Gene Family in Potato

Ureide permeases (UPSs) mediate the transport of ureides, including allantoin and allantoate, which act as nitrogen-transporting compounds in plants and have recently been found to play a role in cellular signaling. To date, UPSs have not been reported in potato, and their identification is important for further function studies and for understanding molecular mechanisms of plant adverse responses. Based on potato genomic data, we identified 10 StUPS genes in potato (Solanum tuberosum L.). Then, we conducted a comprehensive study of the identified StUPS genes using bioinformatics methods. Genome phylogenetic and genomic localization analyses revealed that StUPSs can be classified into four categories, are highly homologous to Arabidopsis thaliana UPS members, and are distributed on three chromosomes. The six StUPS genes were investigated by RT-qPCR, and the findings indicated that all of these genes are involved in the response to several stresses, including low nitrogen, cold, ABA, salt, H2O2, and drought. This study establishes a strong theoretical framework for investigating the function of potato UPS genes, as well as the molecular mechanisms underlying the responses of these genes to various environmental stresses.

Endogenous ureides are employed as a carbon source in Arabidopsis plants exposed to carbon starvation conditions

Ureides, the degraded products of purine catabolism in Arabidopsis, have been shown to act as antioxidant and nitrogen sources. Herein we elucidate purine degraded metabolites as a carbon source using the Arabidopsis Atxdh1, Ataln, and Ataah knockout (KO) mutants vis-à-vis wild-type (WT) plants. Plants were grown under short-day conditions on agar plates containing half-strength MS medium with or without 1% sucrose. Notably, the absence of sucrose led to diminished biomass accumulation in both shoot and root tissues of the Atxdh1, Ataln, and Ataah mutants, while no such effect was observed in WT plants. Moreover, the application of sucrose resulted in a reduction of purine degradation metabolite levels, specifically xanthine and allantoin, predominantly within the roots of WT plants. Remarkably, an increase in proteins associated with the purine degradation pathway was observed in WT plants in the presence of sucrose. Lower glyoxylate levels in the roots but not in the shoot of the Atxdh1 mutant in comparison to WT, were observed under sucrose limitation, and improved by sucrose application in root, indicating that purine degradation provided glyoxylate in the root. Furthermore, the deficit of purine-degraded metabolites in the roots of mutants subjected to carbon starvation was partially mitigated through allantoin application. Collectively, these findings signify that under conditions of sucrose limitation and short-day growth, purines are primarily remobilized within the root system to augment the availability of ureides, serving as an additional carbon (as well as nitrogen) source to support plant growth.

Comparative metabolite profiling of salt sensitive Oryza sativa and the halophytic wild rice Oryza coarctata under salt stress

To better understand the salt tolerance of the wild rice, Oryza coarctata, root tissue-specific untargeted comparative metabolomic profiling was performed against the salt-sensitive Oryza sativa. Under control, O. coarctata exhibited abundant levels of most metabolites, while salt caused their downregulation in contrast to metabolites in O. sativa. Under control conditions, itaconate, vanillic acid, threonic acid, eicosanoids, and a group of xanthin compounds were comparatively abundant in O. coarctata. Similarly, eight amino acids showed constitutive abundance in O. coarctata. In contrast, under control, glycerolipid abundances were lower in O. coarctata and salt stress further reduced their abundance. Most phospholipids also showed a distribution similar to the glycerolipids. Fatty acyls were however significantly induced in O. coarctata but organic acids were prominently induced in O. sativa. Changes in metabolite levels suggest that there was upregulation of the arachidonic acid metabolism in O. coarctata. In addition, the phenylpropanoid biosynthesis as well as cutin, suberin, and wax biosynthesis were also more enriched in O. coarctata, likely contributing to its anatomical traits responsible for salt tolerance. The comparative variation in the number of metabolites like gelsemine, allantoin, benzyl alcohol, specific phospholipids, and glycerolipids may play a role in maintaining the superior growth of O. coarctata in salt. Collectively, our results offer a comprehensive analysis of the metabolite profile in the roots of salt-tolerant O. coarctata and salt-sensitive O. sativa, which confirm potential targets for metabolic engineering to improve salt tolerance and resilience in commercial rice genotypes.

cGMP functions as an important messenger involved in SlSAMS1-regulated salt stress tolerance in tomato

Salt stress adversely affects the growth, development, and yield of tomato (Solanum lycopersicum). SAM Synthetase (SAMS), which is responsible for the biosynthesis of S-adenosylmethionine (SAM, a precursor of polyamine biosynthesis), participates in plant response to abiotic stress. However, the regulatory mechanism of SAMS-mediated salt stress tolerance remains elusive. In this study, we characterized a SAMS homologue SlSAMS1 in tomato. We found that SlSAMS1 is highly expressed in tomato roots, and its expression can be induced by salt stress. Crucially, overexpression of SlSAMS1 in tomato enhances salt stress tolerance. Through metabolomic profiling, we identified some differentially accumulated metabolites, especially, a secondary messenger guanosine 3',5'-cyclic monophosphate (cGMP) which may play a key role in SlSAMS1-regulated salt tolerance. A series of physiological and biochemical data suggest that cGMP alleviates salt stress-induced growth inhibition, and potentially acts downstream of the polyamine-nitric oxide (PA-NO) signaling pathway to trigger H2O2 signaling in response to salt stress. Taken together, the study reveals that SlSAMS1 regulates tomato salt tolerance via the PA-NO-cGMP-H2O2 signal module. Our findings elucidate the regulatory pathway of SlSAMS1-induced plant response to salt stress and indicate a pivotal role of cGMP in salt tolerance.

Rhizobacteria-enhanced drought tolerance and post-drought recovery of creeping bentgrass involving differential modulation of leaf and root metabolism

Rhizobacteria that produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCd) that inhibits ethylene production may mitigate stress damages. The objectives of this study were to examine whether a novel strain of ACCd-producing bacteria, Paraburkholderia aspalathi "WSF23," promotes plant tolerance to drought stress and post-stress recovery and determine changes in metabolic profiles in leaves and roots associated with the positive ACCd-bacteria effects in cool-season perennial grass species. Creeping bentgrass (Agrostis Stolonifera L. cv. "Penncross") plants were inoculated with P. aspalathi "WSF23" and exposed to drought by withholding irrigation for 35 days, followed by re-watering for 15 days in growth chambers. Inoculated plants demonstrated increased turf quality, canopy density, and root growth during drought stress and more rapid re-growth upon re-watering. Metabolomic analysis demonstrated that inoculation with P. aspalathi "WSF 23" increased the content of metabolites in the metabolic pathways related to stress defense, including osmoregulation, cell wall stability, and antioxidant protection in both leaves and roots, as well as nitrogen metabolism in roots of creeping bentgrass exposed to drought stress. The promotion of post-stress recovery by P. aspalathi "WSF 23" was mainly associated with enhanced carbohydrate and pyrimidine metabolism and zeatin biosynthesis pathways in leaves and increased carbohydrates, biosynthesis of DNA and proteins, cellular metabolism, and TCA cycle activity in roots. These results provide insights into the metabolic pathways regulated by "WSF23," with the PGPR conferring improvements in drought stress tolerance and post-drought recovery in a perennial grass species.

Allantoin: A Potential Compound for the Mitigation of Adverse Effects of Abiotic Stresses in Plants

Stress-induced alterations vary with the species of plants, the intensity and duration of the exposure, and stressors availability in nature or soil. Purine catabolism acts as an inherent defensive mechanism against various abiotic stresses and plays a pivotal role in the stress acclimatisation of plants. The intermediate metabolite of purine catabolism, allantoin, compensates for soil nitrogen deficiency due to the low carbon/nitrogen ratio, thereby maintaining nitrogen homeostasis and supporting plant growth and development. Allantoin accounts for 90% of the total nitrogenous compound in legumes, while it contributes only 15% in non-leguminous plants. Moreover, studies on a variety of plant species have reported the differential accumulation of allantoin in response to abiotic stresses, endowing allantoin as a stress modulator. Allantoin functions as signalling molecule to stimulate stress-responsive genes (P5CS; pyrroline-5-carboxylase synthase) and ROS (reactive oxygen species) scavenging enzymes (antioxidant). Moreover, it regulates cross-talk between the abscisic acid and jasmonic acid pathway, and maintains ion homeostasis by increasing the accumulation of putrescine and/or spermine, consequently enhancing the tolerance against stress conditions. Further, key enzymes of purine catabolism (xanthine dehydrogenase and allantoinase) have also been explored by constructing various knockdown/knockout mutant lines to decipher their impact on ROS-mediated oxidative injury in plants. Thus, it is established that allantoin serves as a regulatory signalling metabolite in stress protection, and therefore a lower accumulation of allantoin also reduces plant stress tolerance mechanisms. This review gives an account of metabolic regulation and the possible contribution of allantoin as a photo protectant, osmoprotectant, and nitrogen recycler to reduce abiotic-stress-induced impacts on plants.

Salt priming induces low-temperature tolerance in sugar beet via xanthine metabolism

To understand the physiological mechanisms involved in xanthine metabolism during salt priming for improving low-temperature tolerance, salt priming (SP), xanthine dehydrogenase inhibitor (XOI), exogenous allantoin (EA), and back-supplemented EA (XOI + EA) treatments were given and the low-temperature tolerance of sugar beet was tested. Under low-temperature stress, salt priming promoted the growth of sugar beet leaves and increased the maximum quantum efficiency of PS II (Fv/Fm). However, during salt priming, either XOI or EA treatment alone increased the content of reactive oxygen species (ROS), such as superoxide anion and hydrogen peroxide, in the leaves under low-temperature stress. XOI treatment increased allantoinase activity with its gene (BvallB) expression under low-temperature stress. Compared to the XOI treatment, the EA treatment alone and the XOI + EA treatment increased the activities of antioxidant enzymes. At low temperatures, the sucrose content and the activity of key carbohydrate enzymes (AGPase, Cylnv, and FK) were significantly reduced by XOI compared to the changes under salt priming. XOI also stimulated the expression of protein phosphatase 2C and sucrose non-fermenting1-related protein kinase (BvSNRK2). The results of a correlation network analysis showed that BvallB was positively correlated with malondialdehyde, D-Fructose-6-phosphate, and D-Glucose-6-phosphate, and negatively correlated with BvPOX42, BvSNRK2, dehydroascorbate reductase, and catalase. These results suggested that salt-induced xanthine metabolism modulated ROS metabolism, photosynthetic carbon assimilation, and carbohydrate metabolism, thus enhancing low-temperature tolerance in sugar beet. Additionally, xanthine and allantoin were found to play key roles in plant stress resistance.

Transcriptomic and metabolomic analysis reveals that symbiotic nitrogen fixation enhances drought resistance in common bean

Common bean (Phaseolus vulgaris L.), one of the most important legume crops, uses atmospheric nitrogen through symbiosis with soil rhizobia, reducing the need for nitrogen fertilization. However, this legume is particularly sensitive to drought conditions, prevalent in arid regions where this crop is cultured. Therefore, studying the response to drought is important to sustain crop productivity. We have used integrated transcriptomic and metabolomic analysis to understand the molecular responses to water deficit in a marker-class common bean accession cultivated under N2 fixation or fertilized with nitrate (NO3-). RNA-seq revealed more transcriptional changes in the plants fertilized with NO3- than in the N2-fixing plants. However, changes in N2-fixing plants were more associated with drought tolerance than in those fertilized with NO3-. N2-fixing plants accumulated more ureides in response to drought, and GC/MS and LC/MS analysis of primary and secondary metabolite profiles revealed that N2-fixing plants also had higher levels of abscisic acid, proline, raffinose, amino acids, sphingolipids, and triacylglycerols than those fertilized with NO3-. Moreover, plants grown under nitrogen fixation recovered from drought better than plants fertilized with NO3-. Altogether we show that common bean plants grown under symbiotic nitrogen fixation were more protected against drought than the plants fertilized with nitrate.

Is there any direct link between hazardous trace metals and the allantoin content in some moss species?

The accumulation of allantoin and trace metals (TMs) in nine moss species was examined after the exposure to stress conditions. Both the environmental anthropopressure effect and laboratory-simulated stress conditions were monitored. Moss samples were collected from different locations, i.e. a non-TM contaminated area, an urban area, and a metalliferous area. The effect of Cd, Pb, Hg, Ni, Zn, salinity, and an acidic environment on the allantoin content was tested. Principal component analysis was performed to reveal the relationship between samples of different origin. Large differences in the metal and allantoin accumulation capability of mosses were noted between samples harvested from the different locations. Seven species were considered as potential metal accumulators, as they exhibited tolerance to elevated levels of heavy metals. The observed TM effect on the allantoin accumulation indicated TM pollution as an important environmental factor that can significantly influence the content of this compound in mosses. Further studies on the contribution of various environmental factors and individual characteristics of plant species are highly expected to recognize the trend in the accumulation of specialized metabolites and TMs in response to hazardous growth conditions.

Assessment of functional relevance of genes associated with local temperature variables in Arabidopsis thaliana

How likely genetic variations associated with environment identified in silico from genome wide association study are functionally relevant to environmental adaptation has been largely unexplored experimentally. Here we analyzed top 29 genes containing polymorphisms associated with local temperature variation (minimum, mean, maximum) among 1129 natural accessions of Arabidopsis thaliana. Their loss-of-function mutants were assessed for growth and stress tolerance at five temperatures. Twenty genes were found to affect growth or tolerance at one or more of these temperatures. Significantly, genes associated with maximum temperature more likely have a detect a function at higher temperature, while genes associated with minimum temperature more likely have a function at lower temperature. In addition, gene variants are distributed more frequently at geographic locations where they apparently offer an enhanced growth or tolerance for five genes tested. Furthermore, variations in a large proportion of the in silico identified genes associated with minimum or mean-temperatures exhibited a significant association with growth phenotypes experimentally assessed at low temperature for a small set of natural accessions. This study shows a functional relevance of gene variants associated with environmental variables and supports the feasibility of the use of local temperature factors in investigating the genetic basis of temperature adaptation.

A Role for Allantoate Amidohydrolase (AtAAH) in the Germination of Arabidopsis thaliana Seeds

Seed dormancy is a very complex trait controlled by interactions between genetic and environmental factors. Nitrate is inversely correlated with seed dormancy in Arabidopsis. This is explained by the fact that seed dry storage (after-ripening) reduces the need for nitrogen for germination. When nitrate is absorbed by plants, it is first reduced to nitrite and then to ammonium for incorporation into amino acids, nucleic acids and chlorophyll. Previously, we showed that ALLANTOATE AMIDOHYDROLASE (AtAAH) transcripts are up-regulated in imbibed dormant seeds compared with after-ripened seeds. AAH is an enzyme in the uric acid catabolic pathway which catalyzes the hydrolysis of allantoate to yield CO2, NH3 and S-ureidoglycine. This pathway is the final stage of purine catabolism, and functions in plants and some bacteria to provide nitrogen, particularly when other nitrogen sources are depleted. Ataah mutant seeds are more dormant and accumulate high levels of allantoate, allantoin and urea, whereas energy-related metabolites and several amino acids are lower upon seed imbibition in comparison with Columbia-0. AtAAH expression could be detected during the early stages of seed development, with a transient increase around 8 d after pollination. AtAAH expression is the highest in mature pollen. The application of exogenous potassium nitrate can partly complement the higher dormancy phenotype of the Ataah mutant seeds, whereas other nitrogen sources cannot. Our results indicate that potassium nitrate does not specifically overcome the alleviated dormancy levels in Ataah mutant seeds, but promotes germination in general. Possible pathways by which AtAAH affects seed germination are discussed.

Metabolomics reveals primary response of wheat (Triticum aestivum) to irrigation with oilfield produced water

The reuse of oilfield produced water (PW) for agricultural irrigation has received increased attention for utility in drought-stricken regions. It was recently demonstrated that PW irrigation can affect physiological processes in food crops. However, metabolomic evaluations are important to further discern specific mechanisms of how PW may contribute as a plant-environmental stressor. Herein, the primary metabolic responses of wheat irrigated with PW and matching salinity controls were investigated. Non-targeted gas chromatography mass spectrometry (GC-MS) metabolomics was combined with multivariate analysis and revealed that PW irrigation altered the primary metabolic profiles of both wheat leaf and grain. Over 600 compounds (183 annotated metabolites) were detected that varied between controls (salinity control and tap water) and PW irrigated plants. While some of these changed metabolites are related to salinity stress, over half were found to be unique to PW. The primary metabolites exhibiting changes in abundance in leaf and grain tissues were amines/amino acids, organic acids, and saccharides. Metabolite pathway analysis revealed that amino acid metabolism, sugar metabolism, and nitrogen remobilization are all impacted by PW irrigation, independent of regular plant responses to salinity stress. These data, when combined with prior physiological studies, support a multi-faceted, physio-metabolic response of wheat to the unique stressor imposed by irrigation with PW.

Allantoin overaccumulation enhances production of metabolites under excess of metals but is not tightly regulated by nitric oxide

The aln-3 mutant overaccumulating allantoin and respective wild type (WT) strain of Arabidopsis thaliana were exposed to cadmium (Cd) or mercury (Hg) with or without nitric oxide (NO) donor (sodium nitroprusside, SNP) to study cross-talk, metabolic and oxidative changes between these nitrogen sources (organic vs. inorganic). The aln-3 accumulated over 10-fold more allantoin than WT with the effect of Cd and Hg differing in leaf and root tissue: aln-3 contained more ascorbic acid and phytochelatins when treated with Cd or Hg and more Cd in both organs. SNP depleted leaf Cd and root Hg accumulation in aln3 but had a positive impact on the amount of metabolites typically in WT plants, indicating potentially negative relation between allantoin and NO. In agreement, aln-3 roots showed lower NO signals in control or metal treatments, but higher ROS signal, and SNP had more pronounced impact in WT roots. Flavonol glycosides were more abundant in aln-3 and were affected more by metals than by SNP. Malate was the most affected Krebs acid with strong reaction to SNP and Hg treatment. Data indicate that allantoin overaccumulation influences the accumulation of specific metabolites but nitric oxide has a greater impact on the metabolite profile in WT.

Chrysanthemum × grandiflora leaf and root transcript profiling in response to salinity stress

As high soil salinity threatens the growth and development of plants, understanding the mechanism of plants' salt tolerance is critical. The Chrysanthemum × grandiflora is a newly developed species with a strong salt resistance that possesses multiple genes controlling its quantitative salt resistance. Because of this multigene control, we chose to investigate the plant stress genes overall responses at the transcriptome level. C. grandiflora were treated with a 200 mM NaCl solution for 12 h to study its effect on the roots and leaves via Illumina RNA sequencing. PAL, CYP73A, and 4CL in the phenylpropanoid biosynthesis pathway were upregulated in roots and leaves. In the salicylic acid signal transduction pathway, TGA7 was upregulated in the roots and leaves, while in the jasmonic acid signal transduction pathway, TIFY9 was upregulated in the roots and leaves. In the ion transporter gene, we identified HKT1 that showed identical expression patterns in the roots and leaves. The impact of NaCl imposition for 12 h was largely due to osmotic effect of salinity on C. grandiflora, and most likely the transcript abundance changes in this study were due to the osmotic effect. In order to verify the accuracy of the Illumina sequencing data, we selected 16 DEGs for transcription polymerase chain reaction (qRT-PCR) analysis. qRT-PCR and transcriptome sequencing analysis revealed that the transcriptome sequencing results were reliable.

Altering ureide transport in nodulated soybean results in whole-plant adjustments of metabolism, assimilate partitioning, and sink strength

Legumes develop a symbiotic relationship with bacteria that are housed in root nodules and fix atmospheric di-nitrogen (N2) to ammonia. In soybean (Glycine max (L.) Merr.) nodules, the final products of nitrogen (N) fixation are amino acids, and the ureides allantoin and allantoic acid that also serve as the major long-distance N transport forms. Recently, we have shown that increased expression of UPS1 (ureide permease 1) in soybean nodules results in enhanced ureide export from nodules with positive effects on N fixation and seed yield. Here, we demonstrate that changes in the ureide transport processes trigger alterations in allantoin and allantoic acid pools and partitioning throughout the transgenic plants. They further result in adjustments in amino acid availability in, and translocation to, root and shoot sinks. In addition, leaf carbon (C) capture, assimilation and allocation to sinks are improved, accommodating the increased nodule function, and root and shoot growth. Overall, we demonstrate that enhanced ureide partitioning in nodulated soybean leads to a complex rebalancing of N and C acquisition, metabolism, and transport processes with positive consequences for above- and below-ground vegetative biomass, and whole-plant N and C gains.

Ureides are accumulated similarly in response to UV-C irradiation and wounding in Arabidopsis leaves but are remobilized differently during recovery

Purine degradation products have been shown to play roles in plant response to stresses such as drought, salinity, extended dark, nitrogen deficiency, and pathogen infection. In this study, we used Arabidopsis wild-type (WT) and an Atxdh1-knockout mutant defective in xanthine dehydrogenase1 (XDH1) to examine the role of degraded purine metabolites in the responses to wounding or UV-C stress applied to the middle leaves of the plant. Wounding or UV-C stress in the mutant resulted in lower fresh-weight, increased senescence symptoms, and increased cell death compared to WT plants. In addition, WT plants exhibited lower levels of oxidative stress indicators, reactive oxygen species, and malondialdehyde in their leaves than the mutant. Notably, transcripts and proteins functioning in the purine degradation pathway were regulated in such a way that it led to enhanced ureide levels in WT leaves 24h after applying the UV-C or wound stress. However, different remobilization of the accumulated ureides was observed after 72h of stress. In plants treated with UV-C, the concentration of allantoin was highest in young leaves, whereas in wounded plants it was lowest in these leaves and instead accumulated mainly in the middle leaves that had been wounded. These results indicated that in WT plants treated with UV-C, ureides were remobilized from the lower older and damaged leaves to support young leaf growth during the recovery period from stress. After wounding, however, whilst some ureides were remobilized to the young leaves, more remained in the wounded middle leaves to function as antioxidants and/or healing agents.

Data-Independent-Acquisition-Based Proteomic Approach towards Understanding the Acclimation Strategy of Oleaginous Microalga Microchloropsis gaditana CCMP526 in Hypersaline Conditions

Salinity is one of the significant factors that affect growth and cellular metabolism, including photosynthesis and lipid accumulation, in microalgae and higher plants. Microchloropsis gaditana CCMP526 can acclimatize to different salinity levels by accumulating compatible solutes, carbohydrates, and lipids as energy storage molecules. We used proteomics to understand the molecular basis for acclimation of M. gaditana to increased salinity levels [55 and 100 PSU (practical salinity unit)]. Correspondence analysis was used for the identification of salinity-responsive proteins (SRPs). The highest number of salinity-induced proteins was observed in 100 PSU. Gene ontology enrichment analysis revealed a separate path of acclimation for cells exposed to 55 and 100 PSU. Osmolyte and lipid biosynthesis were upregulated in hypersaline conditions. Concomitantly, lipid oxidation pathways were also upregulated in hypersaline conditions, providing acetyl-CoA for energy metabolism through the tricarboxylic acid cycle. Carbon fixation and photosynthesis were tightly regulated, while chlorophyll biosynthesis was affected in hypersaline conditions. Importantly, temporal proteome analysis of salinity-induced M. gaditana revealed vital SRPs which could be used for engineering salinity resilient microalgal strains for improved productivity in hypersaline culture conditions.

Silicon alleviates salinity stress in licorice (Glycyrrhiza uralensis) by regulating carbon and nitrogen metabolism

Salt stress is one of the key factors that limits the cultivation of Glycyrrhiza uralensis Fisch. (G. uralensis) in the northern part of China. In this study, three salt treatments (including 21, 42 and 63 ds/m NaCl/kg dry soil) and four Si (silicon) concentrations (including 0, 1.4, 2.8 and 4.2 ds/m SiO₂/kg K₂SiO₃ in dry soil) were tested using G. uralensis as the plant material in a pot experiment with three replications. The results showed that the application of various concentrations of Si increased sucrose synthetase (SS), sucrose phosphate synthetase (SPS) and glutamine synthetase (GS), as well as nitrate reductase (NR) activities, and promoted carbon and nitrogen metabolism. Si application also increased the root dry weight of G. uralensis. Multilevel comparative analysis showed that the application of 2.8 ds/m SiO₂ was the optimum rate for improved growth and yield of G. uralensis under different salt levels. This study provides important information that can form the basis for the cultivation of high-yielding and high-quality G. uralensis in saline soils.

Exogenous allantoin improves the salt tolerance of sugar beet by increasing putrescine metabolism and antioxidant activities

Allantoin as a nitrogen metabolite can improve the salt tolerance in plants, but its mechanism of action remain elusive. Herein, the effects of pretreatment with exogenous allantoin in salt tolerance were investigated in sugar beet. The seedlings were subjected to salt stress (300 mM Na⁺) without or with different allantoin concentrations (0.01, 0.1, and 1 mM). The effects of allantoin on plant growth, homeostasis, oxidative damage, osmoregulation, and polyamine metabolism were studied. The results showed that salt stress inhibited the net photosynthetic rate and plant growth, and caused oxidative damage. However, these adverse effects were mitigated by exogenous allantoin in a dose-dependent manner, especially at 0.1 mM. Allantoin reduced the accumulation of ROS by increasing the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), and AsA content. Under salt stress, allantoin reduced the root concentrations of free putrescine (Put) but increased the free spermine (Spm) in leaves and roots. Furthermore, allantoin decreased the Na⁺/K⁺ ratio and promoted the accumulation of betaine and soluble sugars in leaves and roots. Under salinity conditions, allantoin may enhance the antioxidant system and improve ion homeostasis by enhancing putrescine and/or spermine accumulation. In addition, Pearson's correlation and principal component analysis (PCA) established correlations between physiological parameters, and significant differences between different concentrations of allantoin were observed. In total, exogenous allantoin effectively reduced the oxidative damage and ion toxicity in sugar beet, caused by salinity, this finding would be helpful in improving salt tolerance in plant.

Ureide metabolism in Arabidopsis thaliana is modulated by C:N balance

Plants can respond and adapt to changes in the internal content of carbon and nitrogen by using organic compounds that widely differ in their carbon/nitrogen ratio. Among them, the amides asparagine and glutamine are believed to be preferred by most plants, including Arabidopsis. However, increases in the ureides allantoin and/or allantoate concentrations have been observed in different plant species under several environmental conditions. In this work, changes in the ratio between carbon skeletons and reduced nitrogen were investigated by varying the concentrations of nitrogen and sucrose in the growth media. Allantoin accumulation was observed when plants were grown in media with high ammonia concentrations. This increase was reverted by adding sucrose as additional carbon source. Moreover, mutant plants with a decreased capability to degrade allantoin showed a compromised growth compared to WT in ammonia supplemented media. Together, our results indicate that allantoin accumulation is induced by low carbon/nitrogen ratio and suggest that its degradation is critical for proper plant growth and development.

Role of ureides in source-to-sink transport of photoassimilates in non-fixing soybean

Nitrogen (N)-fixing soybean plants use the ureides allantoin and allantoic acid as major long-distance transport forms of N, but in non-fixing, non-nodulated plants amino acids mainly serve in source-to-sink N allocation. However, some ureides are still synthesized in roots of non-fixing soybean, and our study addresses the role of ureide transport processes in those plants. In previous work, legume ureide permeases (UPSs) were identified that are involved in cellular import of allantoin and allantoic acid. Here, UPS1 from common bean was expressed in the soybean phloem, which resulted in enhanced source-to-sink transport of ureides in the transgenic plants. This was accompanied by increased ureide synthesis and elevated allantoin and allantoic acid root-to-sink transport. Interestingly, amino acid assimilation, xylem transport, and phloem partitioning to sinks were also strongly up-regulated. In addition, photosynthesis and sucrose phloem transport were improved in the transgenic plants. These combined changes in source physiology and assimilate partitioning resulted in increased vegetative growth and improved seed numbers. Overall, the results support that ureide transport processes in non-fixing plants affect source N and carbon acquisition and assimilation as well as source-to-sink translocation of N and carbon assimilates with consequences for plant growth and seed development.

Determination of Ureides Content in Plant Tissues

The ureides allantoin and allantoate are the main organic nitrogen compounds transported in several legumes, predominantly from N₂ fixation. Moreover, recent studies point out a remarkable role for allantoin during several stress responses of plants other than legumes. The goal of this protocol is to determine ureides concentration in different plant tissues. Ureides are extracted from plant material by boiling it in phosphate buffer. The allantoin and allantoate present in the supernatants are subjected to alkaline-acidic hydrolysis to glyoxylate. The glyoxylate is converted into glycoxylic acid phenylhydrazone, that is then oxidized to red-colored 1,5-diphenylformazan. The absorbance of supernatants is measured using a spectrophotometer at 520 nm. Ureides concentration can be inferred by using a glyoxylate calibration curve. Ureide quantification of different tissues of Arabidopsis thaliana and soybean plants were carried out following this protocol.

Transcriptomic and metabolomic analyses reveal mechanisms of adaptation to salinity in which carbon and nitrogen metabolism is altered in sugar beet roots

BACKGROUND

Beta vulgaris L. is one of the main sugar-producing crop species and is highly adaptable to saline soil. This study explored the alterations to the carbon and nitrogen metabolism mechanisms enabling the roots of sugar beet seedlings to adapt to salinity.

RESULTS

The ionome, metabolome, and transcriptome of the roots of sugar beet seedlings were evaluated after 1 day (short term) and 7 days (long term) of 300 mM Na+ treatment. Salt stress caused reactive oxygen species (ROS) damage and ion toxicity in the roots. Interestingly, under salt stress, the increase in the Na+/K+ ratio compared to the control ratio on day 7 was lower than that on day 1 in the roots. The transcriptomic results showed that a large number of differentially expressed genes (DEGs) were enriched in various metabolic pathways. A total of 1279 and 903 DEGs were identified on days 1 and 7, respectively, and were mapped mainly to 10 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most of the genes were involved in carbon metabolism and amino acid (AA) biosynthesis. Furthermore, metabolomic analysis revealed that sucrose metabolism and the activity of the tricarboxylic acid (TCA) cycle increased in response to salt stress. After 1 day of stress, the content of sucrose decreased, whereas the content of organic acids (OAs) such as L-malic acid and 2-oxoglutaric acid increased. After 7 days of salt stress, nitrogen-containing metabolites such as AAs, betaine, melatonin, and (S)-2-aminobutyric acid increased significantly. In addition, multiomic analysis revealed that the expression of the gene encoding xanthine dehydrogenase (XDH) was upregulated and that the expression of the gene encoding allantoinase (ALN) was significantly downregulated, resulting in a large accumulation of allantoin. Correlation analysis revealed that most genes were significantly related to only allantoin and xanthosine.

CONCLUSIONS

Our study demonstrated that carbon and nitrogen metabolism was altered in the roots of sugar beet plants under salt stress. Nitrogen metabolism plays a major role in the late stages of salt stress. Allantoin, which is involved in the purine metabolic pathway, may be a key regulator of sugar beet salt tolerance.

Transcriptomic Response to Water Deficit Reveals a Crucial Role of Phosphate Acquisition in a Drought-Tolerant Common Bean Landrace

Drought is one of the most critical factors limiting legume crop productivity. Understanding the molecular mechanisms of drought tolerance in the common bean is required to improve the yields of this important crop under adverse conditions. In this work, RNA-seq analysis was performed to compare the transcriptome profiles of drought-stressed and well-irrigated plants of a previously characterized drought-tolerant common bean landrace. The analysis revealed responses related with the abscisic acid signaling, including downregulation of a phosphatase 2C (PP2C) and an abscisic acid-8' hydroxylase, and upregulation of several key transcription factors and genes involved in cell wall remodeling, synthesis of osmoprotectants, protection of photosynthetic apparatus, and downregulation of genes involved in cell expansion. The results also highlighted a significant proportion of differentially expressed genes related to phosphate starvation response. In addition, the moderate detrimental effects of drought in the biomass of these tolerant plants were abolished by the addition of phosphate, thus indicating that, besides the ABA-mediated response, acquisition of phosphate could be crucial for the drought tolerance of this common bean genotype. These results provided information about the mechanisms involved in drought response of common bean response that could be useful for enhancing the drought tolerance of this important crop legume.

Biochemical and Molecular Characterization of PvNTD2, a Nucleotidase Highly Expressed in Nodules from Phaseolus vulgaris

Nucleotides are molecules of great importance in plant physiology. In addition to being elementary units of the genetic material, nucleotides are involved in bio-energetic processes, play a role as cofactors, and are also components of secondary metabolites and the hormone cytokinin. The common bean (Phaseolus vulgaris) is a legume that transports the nitrogen fixed in nodules as ureides, compounds synthetized from purine nucleotides. The first step in this pathway is the removal of the 5’-phosphate group by a phosphatase. In this study, a gene that codes for a putative nucleotidase (PvNTD2) has been identified in P. vulgaris. The predicted peptide contains the conserved domains for haloacid dehalogenase-like hydrolase superfamily. The protein has been overexpressed in Escherichia coli, and the purified protein showed molybdate-resistant phosphatase activity with nucleoside monophosphates as substrates, confirming that the identified gene codes for a nucleotidase. The optimum pH for the activity was 7–7.5. The recombinant enzyme did not show special affinity for any particular nucleotide, although the behaviour with AMP was different from that with the other nucleotides. The activity was inhibited by adenosine, and a regulatory role for this nucleoside was proposed. The expression pattern of PvNTD2 shows that it is ubiquitously expressed in all the tissues analysed, with higher expression in nodules of adult plants. The expression was maintained during leaf ontogeny, and it was induced during seedling development. Unlike PvNTD1, another NTD previously described in common bean, the high expression of PvNTD2 was maintained during nodule development, and its possible role in this organ is discussed.

Plant peroxisomes at the crossroad of NO and H2 O2 metabolism

Plant peroxisomes are subcellular compartments involved in many biochemical pathways during the life cycle of a plant but also in the mechanism of response against adverse environmental conditions. These organelles have an active nitro-oxidative metabolism under physiological conditions but this could be exacerbated under stress situations. Furthermore, peroxisomes have the capacity to proliferate and also undergo biochemical adaptations depending on the surrounding cellular status. An important characteristic of peroxisomes is that they have a dynamic metabolism of reactive nitrogen and oxygen species (RNS and ROS) which generates two key molecules, nitric oxide (NO) and hydrogen peroxide (H₂ O₂ ). These molecules can exert signaling functions by means of post-translational modifications that affect the functionality of target molecules like proteins, peptides or fatty acids. This review provides an overview of the endogenous metabolism of ROS and RNS in peroxisomes with special emphasis on polyamine and uric acid metabolism as well as the possibility that these organelles could be a source of signal molecules involved in the functional interconnection with other subcellular compartments.

Comparative transcriptome analysis reveals unique genetic adaptations conferring salt tolerance in a xerohalophyte

Most studies on salt tolerance in plants have been conducted using glycophytes like Arabidopsis thaliana (L.) Heynh., with limited resistance to salinity. The xerohalophyte Zygophyllum xanthoxylum (Bunge) Engl. is a salt-accumulating desert plant that efficiently transports Na+ into vacuoles to manage salt and exhibits increased growth under salinity conditions, suggesting a unique transcriptional response compared with glycophytes. We used transcriptome profiling by RNA-seq to compare gene expression in roots of Z. xanthoxylum and A. thaliana under 50 mM NaCl treatments. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis suggested that 50 mM NaCl was perceived as a stimulus for Z. xanthoxylum whereas a stress for A. thaliana. Exposure to 50 mM NaCl caused metabolic shifts towards gluconeogenesis to stimulate growth of Z. xanthoxylum, but triggered defensive systems in A. thaliana. Compared with A. thaliana, a vast array of ion transporter genes was induced in Z. xanthoxylum, revealing an active strategy to uptake Na+ and nutrients from the environment. An ascorbate-glutathione scavenging system for reactive oxygen species was also crucial in Z. xanthoxylum, based on high expression of key enzyme genes. Finally, key regulatory genes for the biosynthesis pathways of abscisic acid and gibberellin showed distinct expression patterns between the two species and auxin response genes were more active in Z. xanthoxylum compared with A. thaliana. Our results provide an important framework for understanding unique patterns of gene expression conferring salt resistance in Z. xanthoxylum.

Relationship between ureidic/amidic metabolism and antioxidant enzymatic activities in legume seedlings

Ureides are nitrogenous compounds with a special function in some legume under nitrogen fixing conditions, the ureidic legumes. In this group, ureides are the predominant nitrogen transport molecule from nodules to the upper part, whereas amidic legumes use amides as nitrogen transport compounds. In this study, the ureide levels have been analysed in seedlings from four ureidic and four amidic legume plants. It has been found that the differentiation among ureide and amide plants already exists in seedlings during early seedling development, with high levels of ureide and allantoinase activity in cotyledons and embryonic axes from ureide plants. Since ureides have been implicated in the response of plant to several stress, total hydrosoluble antioxidant capacity and the levels of several antioxidant activities have been determined and compared among these two legume groups. The total antioxidant capacity did not follow any differential pattern in cotyledons or embryonic axes for the analysed plants. The levels of superoxide dismutase, guaiacol peroxidase and ascorbate peroxidase in both embryonic axes and cotyledons are statistical different between amide and ureide seedlings, whereas the catalase activity was similar among these groups of plants. We discuss than amides and ureides could follow different strategies to protect against oxidation.

Allantoin attenuates cadmium-induced toxicity in cucumber plants

Concentration-dependent responses of cucumber plants to cadmium (Cd, 5-15 µM) and/or allantoin (Alla, 10-1000 µM) have been investigated to detect a possible protective role of Alla under Cd excess. After 14 days of exposure, Alla often considerably reversed Cd-induced inhibition of growth and reduction of the content of photosynthetic pigments. Higher Alla doses depleted the Cd amount in shoots, which could be related to citric acid (increase in the shoots but depletion in the roots in Cd+Alla treatments) rather than to phytochelatins (Alla had a negative impact on the phytochelatin accumulation). An increase in the Alla concentration suppressed Cd-induced spatial H₂O₂ appearance, which does not seem to be related to antioxidative enzymes (low impact of Alla on catalase, ascorbate peroxidase, and guaiacol peroxidase). On the contrary, shoot glutathione and mainly ascorbic acid accumulation strongly increased in Cd+Alla treatments, indicating their prominent role in Alla-induced amelioration of Cd-stimulated oxidative stress and growth retardation. Similarly, phenolic metabolites (total soluble phenols and flavonols) were slightly influenced by Alla and their antioxidative action was not expected. We conclude that Alla-mediated attenuation of Cd-induced toxicity relies on enhanced accumulation of glutathione and ascorbate in the shoot tissue mainly, rather than on elevated antioxidative enzyme activities.

Opposite fates of the purine metabolite allantoin under water and nitrogen limitations in bread wheat

Degradation of nitrogen-rich purines is tightly and oppositely regulated under drought and low nitrogen supply in bread wheat. Allantoin is a key target metabolite for improving nitrogen homeostasis under stress. The metabolite allantoin is an intermediate of the catabolism of purines (components of nucleotides) and is known for its housekeeping role in nitrogen (N) recycling and also for its function in N transport and storage in nodulated legumes. Allantoin was also shown to differentially accumulate upon abiotic stress in a range of plant species but little is known about its role in cereals. To address this, purine catabolic pathway genes were identified in hexaploid bread wheat and their chromosomal location was experimentally validated. A comparative study of two Australian bread wheat genotypes revealed a highly significant increase of allantoin (up to 29-fold) under drought. In contrast, allantoin significantly decreased (up to 22-fold) in response to N deficiency. The observed changes were accompanied by transcriptional adjustment of key purine catabolic genes, suggesting that the recycling of purine-derived N is tightly regulated under stress. We propose opposite fates of allantoin in plants under stress: the accumulation of allantoin under drought circumvents its degradation to ammonium (NH₄⁺) thereby preventing N losses. On the other hand, under N deficiency, increasing the NH₄⁺ liberated via allantoin catabolism contributes towards the maintenance of N homeostasis.

There is a direct link between allantoin concentration and cadmium tolerance in Arabidopsis

Allantoin, an important intermediate of ureide metabolism, has been the subject of investigation recently due to its dual function in nitrogen recycling and abiotic stress response in plants. Allantoin appears to be the dominant ureide accumulating in response to different abiotic stresses, and mutants containing elevated allantoin concentrations exhibit a stress-tolerant phenotype due to limited reactive oxygen species (ROS) generation. Here we describe the involvement of allantoin in stress response and attempt to explain the regulatory mechanism(s) underlying allantoin function in plants. Growth of wild type Col-0 seedlings in the presence of exogenous allantoin improved root elongation in response to Cd treatment. Allantoin treatment of Col-0 seeds increases superoxide dismutase activity causing an enhanced seed germination and seedling growth following Cd exposure. Additionally, allantoinase-overexpressed (ALNox) lines, with lower levels of allantoin, exhibited more susceptibility to Cd treatment than Col-0 Arabidopsis, implying that there is a positive correlation between allantoin concentration and Cd resistance in plants. Growing ABA-insensitive (abi) mutants on allantoin-containing media and comparison between abi mutants and their wild-type backgrounds demonstrated that the potential regulatory function of allantoin does not require ABA at germination but may be ABA-dependent at later stages of seedling growth, suggesting a potential crosstalk between allantoin-mediated stress response and ABA signalling pathway in plants.

Effect of Long-Term Strontium Exposure on the Content of Phytoestrogens and Allantoin in Soybean

Abiotic stress, including metal excess, can modify plant metabolism. Here we investigated the influence of long-term strontium exposure (12 weeks, 0.5⁻4.0 mM Sr) on the content of phytoestrogens and allantoin as well as the mineral composition in soybean. Seven phytoestrogens were identified in the soybean: daidzin, glycitin, genistin, malonyldaidzin, malonylgenistin, daidzein, and coumestrol. The results showed that both malonyldaidzin and malonylgenistin were dominant phytoestrogens; however, the roots contained a relatively high amount of daidzein. It was found that strontium reduced the phytoestrogen content and decreased the antioxidant capacity. Strontium evoked depletion of the sum of all phytoestrogens by 40⁻70% in the leaves, 25⁻50% in the stems and in the seeds, depending on the strontium concentration. In the roots, 0.5 and 4.0 mM of strontium decreased the total phytoestrogen content by 25 and 55%, respectively, while 2.0 mM of strontium did not exert an effect on their accumulation. On the other hand, strontium ions induced allantoin accumulation mainly in the roots. Strontium was preferentially accumulated in the leaves, with a slight impact on macro- and micro-nutrients. Our research showed strontium-secondary metabolites interaction in the soybean, which can be useful for obtaining a natural pharmaceutical product containing both strontium and phytoestrogens for remediation of postmenopausal osteoporosis.

Disruption of ureide degradation affects plant growth and development during and after transition from vegetative to reproductive stages

BACKGROUND

The ureides allantoin and allantoate are major metabolic intermediates of purine catabolism with high nitrogen-to-carbon ratios. Ureides play a key role in nitrogen utilization in ureide-type legumes, but their effects on growth and development in non-legume plants are poorly understood. Here, we examined the effects of knocking out genes encoding ureide-degrading enzymes, allantoinase (ALN) and allantoate amidohydrolase (AAH), on the vegetative-to-reproductive transition and subsequent growth of Arabidopsis plants.

RESULTS

The ureide-degradation mutants (aln and aah) showed symptoms similar to those of nitrogen deficiency: early flowering, reduced size at maturity, and decreased fertility. Consistent with these phenotypes, carbon-to-nitrogen ratios and nitrogen-use efficiencies were significantly decreased in ureide-degradation mutants; however, adding nitrogen to irrigation water did not alleviate the reduced growth of these mutants. In addition to nitrogen status, levels of indole-3-acetic acid and gibberellin in five-week-old plants were also affected by the aln mutations. To test the possibility that ureides are remobilized from source to sink organs, we measured ureide levels in various organs. In wild-type plants, allantoate accumulated predominantly in inflorescence stems and siliques; this accumulation was augmented by disruption of its catabolism. Mutants lacking ureide transporters, ureide permeases 1 and 2 (UPS1 and UPS2), exhibited phenotypes similar to those of the ureide-degradation mutants, but had decreased allantoate levels in the reproductive organs. Transcript analysis in wild-type plants suggested that genes involved in allantoate synthesis and ureide transport were coordinately upregulated in senescing leaves.

CONCLUSIONS

This study demonstrates that ureide degradation plays an important role in supporting healthy growth and development in non-legume Arabidopsis during and after transition from vegetative to reproductive stages.

Exogenous allantoin increases Arabidopsis seedlings tolerance to NaCl stress and regulates expression of oxidative stress response genes

Allantoin is a nitrogenous compound derived from purine catabolism that contributes to nitrogen recycling in plants. Accumulation of allantoin in plant tissues and a potential role in protection of plants from abiotic stress conditions has been identified. The present work shows that application of exogenous allantoin increased stress tolerance of Arabidopsis seedlings when germinated on, or subjected to the media containing NaCl. Allantoin-induced tolerance to NaCl stress was associated with decreased production of superoxide and hydrogen peroxide in seedlings. To understand the molecular mechanism, the effect of exogenous allantoin treatment on expression of several stress-related genes was investigated. Exogenous allantoin altered the expression of several antioxidant encoding genes and upregulated the expression of two genes involved in oxidative stress tolerance, SOS1 and RCD1, in the presence or absence of NaCl. Allantoin increased the NaCl tolerance of abscisic acid insensitive mutants, suggesting that it can function independently of abscisic acid signaling. These results provide additional evidence for the role of allantoin in enhancing plants tolerance to oxidative stress.

Exploring traditional aus-type rice for metabolites conferring drought tolerance

BACKGROUND

Traditional varieties and landraces belonging to the aus-type group of rice (Oryza sativa L.) are known to be highly tolerant to environmental stresses, such as drought and heat, and are therefore recognized as a valuable genetic resource for crop improvement. Using two aus-type (Dular, N22) and two drought intolerant irrigated varieties (IR64, IR74) an untargeted metabolomics analysis was conducted to identify drought-responsive metabolites associated with tolerance.

RESULTS

The superior drought tolerance of Dular and N22 compared with the irrigated varieties was confirmed by phenotyping plants grown to maturity after imposing severe drought stress in a dry-down treatment. Dular and N22 did not show a significant reduction in grain yield compared to well-watered control plants, whereas the intolerant varieties showed a significant reduction in both, total spikelet number and grain yield. The metabolomics analysis was conducted with shoot and root samples of plants at the tillering stage at the end of the dry-down treatment. The data revealed an overall higher accumulation of N-rich metabolites (amino acids and nucleotide-related metabolites allantoin and uridine) in shoots of the tolerant varieties. In roots, the aus-type varieties were characterised by a higher reduction of metabolites representative of glycolysis and the TCA cycle, such as malate, glyceric acid and glyceric acid-3-phosphate. On the other hand, the oligosaccharide raffinose showed a higher fold increase in both, shoots and roots of the sensitive genotypes. The data further showed that, for certain drought-responsive metabolites, differences between the contrasting rice varieties were already evident under well-watered control conditions.

CONCLUSIONS

The drought tolerance-related metabolites identified in the aus-type varieties provide a valuable set of protective compounds and an entry point for assessing genetic diversity in the underlying pathways for developing drought tolerant rice and other crops.

A Nitrogen Molecular Sensing System, Comprised of the ALLANTOINASE and UREIDE PERMEASE 1 Genes, Can Be Used to Monitor N Status in Rice

Nitrogen (N) is an essential nutrient for plant growth and development, but its concentration in the soil is often insufficient for optimal crop production. Consequently, improving N utilization in crops is considered as a major target in agricultural biotechnology. However, much remains to be learnt about crop N metabolism for application. In this study, we have developed a molecular sensor system to monitor the N status in rice (Oryza sativa). We first examined the role of the ureide, allantoin, which is catabolized into allantoin-derived metabolites and used as an N source under low N conditions. The expression levels of two genes involved in ureide metabolism, ALLANTOINASE (OsALN) and UREIDE PERMEASE 1 (OsUPS1), were highly responsive to the N status. OsALN was rapidly up-regulated under low N conditions, whereas OsUPS1 was up-regulated under high N conditions. Taking advantage of the responses of these two genes to N status, we generated transgenic rice plants harboring the molecular N sensors, proALN::ALN-LUC2 and proUPS1::UPS1-LUC2, comprising the gene promoters driving expression of the luciferase reporter. We observed that expression of the transgenes mimicked transcriptional regulation of the endogenous OsALN and OsUPS1 genes in response to exogenous N status. Importantly, the molecular N sensors showed similar levels of specificity to nitrate and ammonium, from which we infer their sensing abilities. Transgenic rice plants expressing the proUPS1::UPS1-LUC2 sensor showed strong luminescence under high exogenous N conditions (>1 mM), whereas transgenic plants expressing the proALN::ALN-LUC2 sensor showed strong luminescence under low exogenous N conditions (<0.1 mM). High exogenous N (>1 mM) substantially increased internal ammonium and nitrate levels, whereas low exogenous N (<0.1 mM) had no effect on internal ammonium and nitrate levels, indicating the luminescence signals of molecular sensors reflect internal N status in rice. Thus, proALN::ALN-LUC2 and proUPS1::UPS1-LUC2 represent N molecular sensors that operate over a physiological and developmental range in rice.

Nucleases activities during French bean leaf aging and dark-induced senescence

During leaf senescence resources are managed, with nutrients mobilized from older leaves to new sink tissues. The latter implies a dilemma in terms of resource utilization, the leaf senescence should increase seed quality whereas delay in senescence should improve the seed yield. Increased knowledge about nutrient recycling during leaf senescence could lead to advances in agriculture and improved seed quality. Macromolecules mobilized during leaf senescence include proteins and nucleic acids. Although nucleic acids have been less well studied than protein degradation, they are possible reservoirs of nitrogen and phosphorous. The present study investigated nuclease activities and gene expression patterns of five members of the S1/P1 family in French bean (Phaseolus vulgaris L. cv.)Page: 2 during leaf senescence. An in-gel assay was used to detect nuclease activity during natural and dark-induced senescence, with single-stranded DNA (ssDNA) used as a substrate. The results revealed two nucleases (glycoproteins), with molecular masses of 34 and 39kDa in the senescent leaves. The nuclease activities were higher at a neutral than at an acidic pH. EDTA treatment inhibited the activities of the nucleases, and the addition of zinc resulted in the recovery of these activities. Both the 34 and 39kDa nucleases were able to use RNA and double-stranded DNA (dsDNA) as substrates, although their activities were low when dsDNA was used as a substrate. In addition, two ribonucleases with molecular masses of 14 and 16kDa, both of which could only utilize RNA as a substrate, were detected in the senescent leaves. Two members of the S1/P1 family, PVN2 and PVN5, were expressed under the experimental conditions, suggesting that these two genes were involved in senescence. The nuclease activity of the glycoproteins and gene expression were similar under both natural senescence and dark-induced senescence conditions.

Allantoin contributes to the stress response in cadmium-treated Arabidopsis roots

Ureides are nitrogen-rich compounds, derived from purine catabolism. A dual role for ureides, and for allantoin in particular, in both nitrogen recycling and the abiotic stress response has been recently identified. Previous work on the effect of allantoin on cadmium (Cd)-exposed Arabidopsis revealed that high concentration of allantoin in allantoinase-negative mutant (aln-3) leaves alleviates Cd toxicity via inducing antioxidant mechanisms in these plants. In the present study, we evaluate whether allantoin has a similar protective role in roots. Both wild type and aln-3 roots contain higher amounts of internal Cd compared to leaves. Likewise, aln-3 roots are more resistant to Cd, reflected in fresh and dry weight, and stimulated antioxidant enzyme activity, including superoxide dismutase (SOD) and catalase (CAT), resulting in lower reactive oxygen species concentration. In contrast with wild-type leaves, high levels of Cd in Col-0 roots reduces transcript abundance of uricase, leading to a significant decline in allantoin level of treated roots at 1000 and 1500 μM CdCl₂. This metabolite change is also accompanied by decreasing the activity of antioxidant enzymes (SOD and CAT). Additionally, contrary to wild-type leaves, root genotype has a significant effect on CAT activity under Cd treatment, suggesting the possible different sources of damage and oxidative stress response in these two tissues.

NmeA, a novel efflux transporter specific for nucleobases and nucleosides, contributes to metal resistance in Aspergillus nidulans

Through Minos transposon mutagenesis we obtained A. nidulans mutants resistant to 5-fluorouracil due to insertions into the upstream region of the uncharacterized gene nmeA, encoding a Major Facilitator Superfamily (MFS) transporter. Minos transpositions increased nmeA transcription, which is otherwise extremely low under all conditions tested. To dissect the function of NmeA we used strains overexpressing or genetically lacking the nmeA gene. Strains overexpressing NmeA are resistant to toxic purine analogues, but also, to cadmium, zinc and borate, whereas an isogenic nmeAΔ null mutant exhibits increased sensitivity to these compounds. We provide direct evidence that nmeA overexpression leads to efflux of adenine, xanthine, uric acid and allantoin, the latter two being intermediate metabolites of purine catabolism that are toxic when accumulated cytoplasmically due to relevant genetic lesions. By using a functional GFP-tagged version we show that NmeA is a plasma membrane transporter. Homology modeling and docking approaches identified a single purine binding site and a tentative substrate translocation trajectory in NmeA. Orthologues of NmeA are present in all Aspergilli and other Eurotiomycetes, but are absent from other fungi or non-fungal organisms. NmeA is thus the founding member of a new class of transporters essential for fungal success under specific toxic conditions.

Temporal impact of the vascular wilt pathogen Verticillium dahliae on tomato root proteome

The soil-borne fungus Verticillium dahliae is the causal agent of wilting disease and affects a wide range of plant species worldwide. Here, we report on the time-resolved analysis of the tomato root proteome in response to fungal colonization. Tomato (Solanum lycopersicum cv. Hildares) was inoculated with V. dahliae at the two-leaf stage and roots were harvested at 7, 14 and 21 days post inoculation (dpi). In order to identify proteins related to the fungal spread at the different time points, a subsequent proteome analysis by two-dimensional differential gel electrophoresis (2D-DIGE) was conducted on samples from three independent experiments. Hierarchical clustering and k-means clustering of identified proteins distinguished early and late responses to fungal colonization. The results underline that plant defense and adaptation responses are timely coordinated. Proteins involved in oxidative stress were down-regulated at 7 dpi but induced 21 dpi indicating versatile reactive oxygen species signaling interacting with salicylic acid defence signaling at that stage of infection. Drought-stress proteins were induced at 21 dpi, reflecting the beginning of wilting symptoms. Notably, two proteins involved in energy-generating pathways were induced throughout all sampling dates and may reflect the increase in metabolic activity to maintain root growth and, concurrently, activate defense responses.

BIOLOGICAL SIGNIFICANCE

Mounting of defense responses requires a substantial flux of carbon and nitrogen from primary to secondary metabolites. In-depth understanding of these key metabolic pathways required for growth and defense responses, especially at proteome level, will allow the development of breeding strategies for crops where Verticillium tolerance is absent. Our data show early and late responses of tomato root proteins towards pathogen infection and identify primary metabolism enzymes affected by V. dahliae. Those proteins represent candidates for plant improvement.

Allantoin Increases Cadmium Tolerance in Arabidopsis via Activation of Antioxidant Mechanisms

Plants apply various molecular, physiological and morphological strategies in response to undesirable environmental conditions. One of the possible responses which may contribute to surviving stressful conditions is the accumulation of ureides. Ureides are recognized as important nitrogen-rich compounds involved in recycling nitrogen in plants to support growth and reproduction. Amongst them, allantoin not only serves as a transportable nitrogen-rich compound, but has also been suggested to protect plants from abiotic stresses via minimizing oxidative damage. This work focuses on the effect of cadmium (Cd) on ureide metabolism in Arabidopsis, in order to clarify the potential role of allantoin in plant tolerance to heavy metals. In response to Cd treatment, allantoin levels increase in Arabidopsis thaliana, ecotype Col-0, due to reduced allantoinase (ALN) gene expression and enzyme activity. This coincides with increases in uricase (UO) transcripts. UO and ALN encode the enzymes for the production and degradation of allantoin, respectively. ALN-negative aln-3 Arabidopsis mutants with elevated allantoin levels demonstrate resistance to soil-applied CdCl₂, up to 1,500 μM. Although aln-3 mutants take up and store more Cd within their leaf tissue, they contain less damaging superoxide radicals. The protective mechanism of aln-3 mutants appears to involve enhancing the activity of antioxidant enzymes such as superoxide dismutase and ascorbate peroxidase.