Improved growth and stress tolerance in the Arabidopsis oxt1 mutant triggered by altered adenine metabolism

Global omics study of Tetraselmis chuii reveals time-related metabolic adaptations upon oxidative stress

Microalgae species encounter oxidative stress in their natural environments, prompting the development of species-specific adaptation mechanisms. Understanding these mechanisms can offer valuable insights for biotechnological applications in microalgal metabolic manipulation. In this study, we investigated the response of Tetraselmis chuii, an industrially important microalga, to H2O2-induced oxidative stress. Exposure to 0.5-mM H2O2 resulted in reduced cell viability, and higher concentrations led to a drastic decline. After 1 h of exposure to H2O2, photosynthetic capacity (Qy) was negatively impacted, and this reduction intensified after 6 h of continuous stress. Global multi-omics analysis revealed that T. chuii rapidly responded to H2O2-induced oxidative stress within the first hour, causing significant changes in both transcriptomic and metabolomic profiles. Among the cellular functions negatively affected were carbon and energy flow, with photosynthesis-related PSBQ having a 2.4-fold downregulation, pyruvate kinase decreased by 1.5-fold, and urea content reduced by threefold. Prolonged exposure to H2O2 incurred a high energy cost, leading to unsuccessful attempts to enhance carbon metabolism, as depicted, for example, by the upregulation of photosystems-related PETC and PETJ by more than twofold. These findings indicate that T. chuii quickly responds to oxidative stress, but extended exposure can have detrimental effects on its cellular functions. KEY POINTS: • 0.5-mM H2O2-induced oxidative stress strongly affects T. chuii • Distinct short- and long-term adaptation mechanisms are induced • Major metabolic adaptations occur within the first hour of exposure.

Phosphoribosyltransferases and Their Roles in Plant Development and Abiotic Stress Response

Glycosylation is a widespread glycosyl modification that regulates gene expression and metabolite bioactivity in all life processes of plants. Phosphoribosylation is a special glycosyl modification catalyzed by phosphoribosyltransferase (PRTase), which functions as a key step in the biosynthesis pathway of purine and pyrimidine nucleotides, histidine, tryptophan, and coenzyme NAD(P)⁺ to control the production of these essential metabolites. Studies in the past decades have reported that PRTases are indispensable for plant survival and thriving, whereas the complicated physiological role of PRTases in plant life and their crosstalk is not well understood. Here, we comprehensively overview and critically discuss the recent findings on PRTases, including their classification, as well as the function and crosstalk in regulating plant development, abiotic stress response, and the balance of growth and stress responses. This review aims to increase the understanding of the role of plant PRTase and also contribute to future research on the trade-off between plant growth and stress response.

Identification of compounds with activity against Trypanosoma cruzi within a collection of synthetic nucleoside analogs

Introduction

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi, and it is the most important neglected tropical disease in the Americas. Two drugs are available to treat the infection, but their efficacy in the chronic stage of the disease, when most cases are diagnosed, is reduced. Their tolerability is also hindered by common adverse effects, making the development of safer and efficacious alternatives a pressing need. T. cruzi is unable to synthesize purines de novo, relying on a purine salvage pathway to acquire these from its host, making it an attractive target for the development of new drugs.

Methods

We evaluated the anti-parasitic activity of 23 purine analogs with different substitutions in the complementary chains of their purine rings. We sequentially screened the compounds' capacity to inhibit parasite growth, their toxicity in Vero and HepG2 cells, and their specific capacity to inhibit the development of amastigotes. We then used in-silico docking to identify their likely targets.

Results

Eight compounds showed specific anti-parasitic activity, with IC₅₀ values ranging from 2.42 to 8.16 μM. Adenine phosphoribosyl transferase, and hypoxanthine-guanine phosphoribosyl transferase, are their most likely targets.

Discussion

Our results illustrate the potential role of the purine salvage pathway as a target route for the development of alternative treatments against T. cruzi infection, highlithing the apparent importance of specific substitutions, like the presence of benzene groups in the C8 position of the purine ring, consistently associated with a high and specific anti-parasitic activity.

A plastid nucleoside kinase is involved in inosine salvage and control of purine nucleotide biosynthesis

In nucleotide metabolism, nucleoside kinases recycle nucleosides into nucleotides-a process called nucleoside salvage. Nucleoside kinases for adenosine, uridine, and cytidine have been characterized from many organisms, but kinases for inosine and guanosine salvage are not yet known in eukaryotes and only a few such enzymes have been described from bacteria. Here we identified Arabidopsis thaliana PLASTID NUCLEOSIDE KINASE 1 (PNK1), an enzyme highly conserved in plants and green algae belonging to the Phosphofructokinase B family. We demonstrate that PNK1 from A. thaliana is located in plastids and catalyzes the phosphorylation of inosine, 5-aminoimidazole-4-carboxamide-1-β-d-ribose (AICA ribonucleoside), and uridine but not guanosine in vitro, and is involved in inosine salvage in vivo. PNK1 mutation leads to increased flux into purine nucleotide catabolism and, especially in the context of defective uridine degradation, to over-accumulation of uridine and UTP as well as growth depression. The data suggest that PNK1 is involved in feedback regulation of purine nucleotide biosynthesis and possibly also pyrimidine nucleotide biosynthesis. We additionally report that cold stress leads to accumulation of purine nucleotides, probably by inducing nucleotide biosynthesis, but that this adjustment of nucleotide homeostasis to environmental conditions is not controlled by PNK1.

Histological, metabolomic and transcriptomic analyses reveal mechanisms of cold acclimation of the Moso bamboo (Phyllostachys edulis) leaf

The Moso bamboo (Phyllostachys edulis) leaf copes well with cold winters in southeastern China. However, until now, there has been almost no research on its adaptation mechanisms to cold weather. Herein, we found that the Moso bamboo leaf has evolved several anatomical structures that may play a role in enhancing its cold tolerance. These structures include fewer fusiform cells, smaller bulliform cells, lower stomata density and many more trichomes, as well as lower relative water content than in the leaf of a cold-sensitive bamboo species, Bambusa ventricosa. Untargeted metabolomic analysis revealed that the winter leaf of Moso bamboo had 10- to 1000-fold higher stress-resistant metabolites such as glutathione, trehalose and ascorbic acid than the leaf of B. ventricosa on both warm and cold days. In contrast to the leaves that grew on a warm day, some metabolites such as glutathione and trehalose increased dramatically in the leaves of Moso bamboo that grew on a cold day. However, they unexpectedly decreased in the leaf of B. ventricosa growing at cold temperatures. Transcriptome analysis revealed a cold stress response network that includes trehalose, glutathione, flavonoid metabolism, DNA repair, reactive oxygen species degradation, stress-associated genes and abiotic stress-related plant hormones such as jasmonic acid, abscisic acid and ethylene. The potential mediator transcription factors, such as EREBP, HSF, MYB, NAC and WRYK, were also significantly upregulated in Moso bamboo leaves growing at cold temperatures. Interestingly, many newly identified genes were involved in the transcriptome of the winter leaf of the Moso bamboo. Most of these new genes have not even been annotated yet. The above results indicate that the Moso bamboo leaf has evolved special histological structures, metabolic pathways and a cold stress-tolerant transcriptome to adapt to the cold weather in its distribution areas.

Transcriptomic and Metabolomic Analyses of the Effects of Exogenous Trehalose on Heat Tolerance in Wheat

Trehalose can improve the tolerance of plants to various types of environmental stress. Nonetheless, information respecting the molecular networks of wheat seedlings to exogenous trehalose under heat stress is limited. Here, two wheat varieties pretreated with exogenous trehalose were selected to explore the molecular mechanism by which trehalose improves the heat tolerance of wheat (Triticum aestivum L.). The results indicated that exogenous trehalose improved the physiological state of wheat seedlings under heat stress. Through RNA sequencing and metabolomics analysis, the genes and metabolites specifically expressed in trehalose pretreatment were identified. After heat stress, there were 18,352 differentially expressed genes (DEGs) in the control and trehalose-treated (H_vs_TreH) groups of Yangmai 18 and 9045 DEGs in Yannong 19. Functional annotation and enrichment analyses showed that the DEGs in the two wheat varieties were mainly involved in carbohydrate metabolism and biosynthesis of secondary metabolites. Through a liquid chromatography–mass spectrometry platform, 183 differential metabolites in H_vs_TreH groups of Yangmai 18 and 77 differential metabolites in Yannong 19 were identified. Compared with the control group, many protective metabolites, such as amino acids, purines, phenylpropanoids and flavonoids, showed significant differences under heat stress. The results indicated that exogenous trehalose protected the wheat biomembrane system, enhanced carbohydrate metabolism and signal transduction, strengthened the activity of the tricarboxylic acid cycle (TCA cycle), regulated purine metabolism, gene expression and metabolite accumulation in the phenylpropanoid biosynthesis and flavonoid biosynthesis pathways, thus improving the heat tolerance of wheat.

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.

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

Diclofenac modified the root system architecture of Arabidopsis via interfering with the hormonal activities of auxin

Diclofenac, a pharmaceutical and personal care product, is accumulating in various environmental matrices worldwide. Increased irrigation has facilitated an influx of environmental diclofenac into agricultural products, which potentially threatens non-target living organisms. In this study, we demonstrated that diclofenac modified the growth and root developmental processes of plants by disturbing the activity of auxin, a group of major phytohormones. Exogenous diclofenac treatment retarded growth and induced oxidative stress in young seedlings of Arabidopsis thaliana. In the developmental perspective, diclofenac altered the root system architecture, which was also similarly observed under exogenous IAA (a natural form of phytoalexins) treatment. The effects of diclofenac on the root development of A. thaliana were mediated through canonical auxin signaling pathways. However, when diclofenac and IAA were treated in combination, diclofenac suppressed the activity of IAA in root system architecture. At the molecular level, diclofenac significantly inhibited the activity of IAA upregulating the expression of early auxin-responsive marker genes. In conclusion, diclofenac modified the root development of A. thaliana via interfering with the activities of natural auxin. These results indicate that diclofenac could potentially act as an environmental contaminant disturbing the natural developmental processes of plants.

Proteomic analysis reveals the role of exogenous cysteine in alleviating chromium stress in maize seedlings

Cysteine (Cys) is incorporated into several compounds which are involved in detoxification of heavy metals. It is evident from recent studies that Cys is effective in alleviating the toxicity of heavy metals. Nevertheless, little is known about the Cys-mediated alleviation of chromium (Cr) toxicity. In our study, the impacts of exogenous Cys on Cr-stressed maize (Zea mays L.) were examined by using physiological and proteomic analyses. The results showed that Cr (100 µM) increased the accumulation of hydrogen peroxide, decreased cell viability, enhanced lipid peroxidation and consequently inhibited plant growth. The application of Cys (500 µM) attenuated the adverse effects of Cr on seedling growth. Cys supplementation to Cr treated plants decreased Cr accumulation in the shoots and increased Cr accumulation in roots. Cys treatment also modulated the activities of antioxidant enzymes and increased endogenous Cys content. Sixty proteins in root tissue were significantly affected by exogenous Cys under Cr stress using two-dimensional electrophoresis. Forty-six differentially expressed proteins were successfully identified by MALDI-TOF/TOF mass spectrometry. These differentially expressed proteins were involved in various biological pathways such as stress response (41.3%), energy and carbohydrate metabolism (21.7%), protein metabolism (6.5%), amino acid metabolism (6.5%), and others of unknown functions. The defense response-related proteins including glutathione peroxidase, glutathione S-transferases, pathogenesis-related proteins, glyoxalases and superoxide dismutase were differently regulated by Cys suggesting their roles in the Cys-mediated Cr tolerance.

Nitric oxide regulates watermelon (Citrullus lanatus) responses to drought stress

The role of exogenous nitric oxide (NO) application in alleviating drought stress responses by enhancing the antioxidant activities in plants is well established for several species. However, none of the studies reported its role in protecting the watermelon genotypes from drought stress. In this study, we aimed to observe the effect of NO application on the physiological and biochemical responses of the two watermelon (Citrullus lanatus var. lanatus) genotypes grown under drought stress conditions by treating the plants with 15% polyethylene glycol 6000 (PEG 6000) and 100 µM sodium nitroprusside (SNP), which is a NO donor in Hoagland solution. Among the two genotypes, one genotype, KAR 98 was drought tolerant; while another, KAR 147 was drought sensitive. Drought stress showed a decrease in the growth parameters of both the genotypes; however, as expected it was higher in the susceptible genotype, KAR 147. NO application could not prevent the reductions in the growth parameters; however, it reduced the increment in malondialdehyde (MDA) content caused by the drought stress in both watermelon genotypes. Moreover, while drought stress condition reduced the ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), and peroxidase (POX) activities in both genotypes, NO + PEG application increased the APX activity in the tolerant genotype, KAR 98. Though the obtained results does not show the direct involvement of NO in increasing drought tolerance of watermelon plants, the increase in the APX antioxidant enzyme activity on NO application under drought stress confirmed its role in protecting the watermelon genotypes from the oxidative damage caused by the drought stress. Moreover, it can be concluded that the effect of NO application on watermelons' responses towards drought stress condition may vary according to the specific genotypes. As to date none of the studies reported the effect of NO application on the antioxidant activity of watermelon genotypes under drought stress, the present study may provide information about the mechanisms that can be focused to improve drought stress tolerance of watermelon genotypes.

Exogenous ascorbic acid induces systemic heat stress tolerance in tomato seedlings: transcriptional regulation mechanism

The current study was devoted to assessing the impact of exogenous ascorbic acid (AsA) in inducing systemic thermotolerance against acute heat stress in tomato (Solanum lycopersicum) seedlings. There were four treatment groups including untreated control (CK), heat-stressed tomato (HS: exposure to 40 °C for 8 h), and treated with ascorbic acid (0.5 mM AsA), and the last group includes both the exogenous application of ascorbic acid and heat stress (AsA + HS). The HS led to leaf curling and mild wilting while plants treated with AsA displayed similar phenotype with control plants, approving that AsA eliminated the injurious effects of the heat stress. The oxidative damage to cell components was confirmed by higher levels of hydrogen peroxide, lipid peroxidation, electrolyte leakage, total oxidant status, and oxidative stress index. Moreover, acute heat stress significantly reduced the photosynthetic pigment contents, and nutrient contents in tomato seedling leaves. In contrast, ascorbic acid postulated a priming effect on tomato roots and, substantially, alleviated heat stress effects on seedlings through reducing the oxidative damage and increasing the contents of ascorbic acid, proline, photosynthetic pigments, and upregulation of heat shock proteins in leaves. Ascorbic acid seems to be a key signaling molecule which enhanced the thermotolerance of tomato plants.

Metabolome Profiling Supports the Key Role of the Spike in Wheat Yield Performance

Although the relevance of spike bracts in stress acclimation and contribution to wheat yield was recently revealed, the metabolome of this organ and its response to water stress is still unknown. The metabolite profiles of flag leaves, glumes and lemmas were characterized under contrasting field water regimes in five durum wheat cultivars. Water conditions during growth were characterized through spectral vegetation indices, canopy temperature and isotope composition. Spike bracts exhibited better coordination of carbon and nitrogen metabolisms than the flag leaves in terms of photorespiration, nitrogen assimilation and respiration paths. This coordination facilitated an accumulation of organic and amino acids in spike bracts, especially under water stress. The metabolomic response to water stress also involved an accumulation of antioxidant and drought tolerance related sugars, particularly in the spikes. Furthermore, certain cell wall, respiratory and protective metabolites were associated with genotypic outperformance and yield stability. In addition, grain yield was strongly predicted by leaf and spike bracts metabolomes independently. This study supports the role of the spike as a key organ during wheat grain filling, particularly under stress conditions and provides relevant information to explore new ways to improve wheat productivity including potential biomarkers for yield prediction.

A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana

Oxidative stress can lead to plant growth retardation, yield loss, and death. The atr7 mutant of Arabidopsis thaliana exhibits pronounced tolerance to oxidative stress. Using positional cloning, confirmed by knockout and RNA interference (RNAi) lines, we identified the atr7 mutation and revealed that ATR7 is a previously uncharacterized gene with orthologs in other seed plants but with no homology to genes in lower plants, fungi or animals. Expression of ATR7-GFP fusion shows that ATR7 is a nuclear-localized protein. RNA-seq analysis reveals that transcript levels of genes encoding abiotic- and oxidative stress-related transcription factors (DREB19, HSFA2, ZAT10), chromatin remodelers (CHR34), and unknown or uncharacterized proteins (AT5G59390, AT1G30170, AT1G21520) are elevated in atr7. This indicates that atr7 is primed for an upcoming oxidative stress via pathways involving genes of unknown functions. Collectively, the data reveal ATR7 as a novel seed plants-specific nuclear regulator of oxidative stress response.

A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress

Abiotic stresses cause oxidative damage in plants. Here, we demonstrate that foliar application of an extract from the seaweed Ascophyllum nodosum, SuperFifty (SF), largely prevents paraquat (PQ)-induced oxidative stress in Arabidopsis thaliana. While PQ-stressed plants develop necrotic lesions, plants pre-treated with SF (i.e., primed plants) were unaffected by PQ. Transcriptome analysis revealed induction of reactive oxygen species (ROS) marker genes, genes involved in ROS-induced programmed cell death, and autophagy-related genes after PQ treatment. These changes did not occur in PQ-stressed plants primed with SF. In contrast, upregulation of several carbohydrate metabolism genes, growth, and hormone signaling as well as antioxidant-related genes were specific to SF-primed plants. Metabolomic analyses revealed accumulation of the stress-protective metabolite maltose and the tricarboxylic acid cycle intermediates fumarate and malate in SF-primed plants. Lipidome analysis indicated that those lipids associated with oxidative stress-induced cell death and chloroplast degradation, such as triacylglycerols (TAGs), declined upon SF priming. Our study demonstrated that SF confers tolerance to PQ-induced oxidative stress in A. thaliana, an effect achieved by modulating a range of processes at the transcriptomic, metabolic, and lipid levels.

Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value

Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the first genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing effort produced nearly 80 million clean reads assembled into 124,723 unitranscripts. Careful annotation and comparison with public databases revealed homologs to genes with a key role in important metabolic pathways linked to abiotic stress tolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis, α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identified. We also used the transcriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 proved polymorphic and represent the first set of SSR markers for the genus Capparis. This transcriptome will be an important contribution to future studies and breeding programs for this orphan crop, aiding to the development of improved varieties to sustain agriculture in arid conditions.

Network Analyses and Data Integration of Proteomics and Metabolomics From Leaves of Two Contrasting Varieties of Sugarcane in Response to Drought

Uncovering the molecular mechanisms involved in the responses of crops to drought is crucial to understand and enhance drought tolerance mechanisms. Sugarcane (Saccharum spp.) is an important commercial crop cultivated mainly in tropical and subtropical areas for sucrose and ethanol production. Usually, drought tolerance has been investigated by single omics analysis (e.g. global transcripts identification). Here we combine label-free quantitative proteomics and metabolomics data (GC-TOF-MS), using a network-based approach, to understand how two contrasting commercial varieties of sugarcane, CTC15 (tolerant) and SP90-3414 (susceptible), adjust their leaf metabolism in response to drought. To this aim, we propose the utilization of regularized canonical correlation analysis (rCCA), which is a modification of classical CCA, and explores the linear relationships between two datasets of quantitative variables from the same experimental units, with a threshold set to 0.99. Light curves revealed that after 4 days of drought, the susceptible variety had its photosynthetic capacity already significantly reduced, while the tolerant variety did not show major reduction. Upon 12 days of drought, photosynthesis in the susceptible plants was completely reduced, while the tolerant variety was at a third of its rate under control conditions. Network analysis of proteins and metabolites revealed that different biological process had a stronger impact in each variety (e.g. translation in CTC15, generation of precursor metabolites, response to stress and energy in SP90-3414). Our results provide a reference data set and demonstrate that rCCA can be a powerful tool to infer experimentally metabolite-protein or protein-metabolite associations to understand plant biology.

The impact of Genetically Modified (GM) crops in modern agriculture: A review

Genetic modification in plants was first recorded 10,000 years ago in Southwest Asia where humans first bred plants through artificial selection and selective breeding. Since then, advancements in agriculture science and technology have brought about the current GM crop revolution. GM crops are promising to mitigate current and future problems in commercial agriculture, with proven case studies in Indian cotton and Australian canola. However, controversial studies such as the Monarch Butterfly study (1999) and the Séralini affair (2012) along with current problems linked to insect resistance and potential health risks have jeopardised its standing with the public and policymakers, even leading to full and partial bans in certain countries. Nevertheless, the current growth rate of the GM seed market at 9.83-10% CAGR along with promising research avenues in biofortification, precise DNA integration and stress tolerance have forecast it to bring productivity and prosperity to commercial agriculture.

Purine salvage in plants

Purine bases and nucleosides are produced by turnover of nucleotides and nucleic acids as well as from some cellular metabolic pathways. Adenosine released from the S-adenosyl-L-methionine cycle is linked to many methyltransferase reactions, such as the biosynthesis of caffeine and glycine betaine. Adenine is produced by the methionine cycles, which is related to other biosynthesis pathways, such those for the production of ethylene, nicotianamine and polyamines. These purine compounds are recycled for nucleotide biosynthesis by so-called "salvage pathways". However, the salvage pathways are not merely supplementary routes for nucleotide biosynthesis, but have essential functions in many plant processes. In plants, the major salvage enzymes are adenine phosphoribosyltransferase (EC 2.4.2.7) and adenosine kinase (EC 2.7.1.20). AMP produced by these enzymes is converted to ATP and utilised as an energy source as well as for nucleic acid synthesis. Hypoxanthine, guanine, inosine and guanosine are salvaged to IMP and GMP by hypoxanthine/guanine phosphoribosyltransferase (EC 2.4.2.8) and inosine/guanosine kinase (EC 2.7.1.73). In contrast to de novo purine nucleotide biosynthesis, synthesis by the salvage pathways is extremely favourable, energetically, for cells. In addition, operation of the salvage pathway reduces the intracellular levels of purine bases and nucleosides which inhibit other metabolic reactions. The purine salvage enzymes also catalyse the respective formation of cytokinin ribotides, from cytokinin bases, and cytokinin ribosides. Since cytokinin bases are the active form of cytokinin hormones, these enzymes act to maintain homeostasis of cellular cytokinin bioactivity. This article summarises current knowledge of purine salvage pathways and their possible function in plants and purine salvage activities associated with various physiological phenomena are reviewed.

Effects of Combined Low Glutathione with Mild Oxidative and Low Phosphorus Stress on the Metabolism of Arabidopsis thaliana

Plants possess highly sensitive mechanisms that monitor environmental stress levels for a dose-dependent fine-tuning of their growth and development. Differences in plant responses to severe and mild abiotic stresses have been recognized. Although many studies have revealed that glutathione can contribute to plant tolerance to various environmental stresses, little is known about the relationship between glutathione and mild abiotic stress, especially the effect of stress-induced altered glutathione levels on the metabolism. Here, we applied a systems biology approach to identify key pathways involved in the gene-to-metabolite networks perturbed by low glutathione content under mild abiotic stress in Arabidopsis thaliana. We used glutathione synthesis mutants (cad2-1 and pad2-1) and plants overexpressing the gene encoding γ-glutamylcysteine synthetase, the first enzyme of the glutathione biosynthetic pathway. The plants were exposed to two mild stress conditions-oxidative stress elicited by methyl viologen and stress induced by the limited availability of phosphate. We observed that the mutants and transgenic plants showed similar shoot growth as that of the wild-type plants under mild abiotic stress. We then selected the synthesis mutants and performed multi-platform metabolomics and microarray experiments to evaluate the possible effects on the overall metabolome and the transcriptome. As a common oxidative stress response, several flavonoids that we assessed showed overaccumulation, whereas the mild phosphate stress resulted in increased levels of specific kaempferol- and quercetin-glycosides. Remarkably, in addition to a significant increased level of sugar, osmolytes, and lipids as mild oxidative stress-responsive metabolites, short-chain aliphatic glucosinolates over-accumulated in the mutants, whereas the level of long-chain aliphatic glucosinolates and specific lipids decreased. Coordinated gene expressions related to glucosinolate and flavonoid biosynthesis also supported the metabolite responses in the pad2-1 mutant. Our results suggest that glutathione synthesis mutants accelerate transcriptional regulatory networks to control the biosynthetic pathways involved in glutathione-independent scavenging metabolites, and that they might reconfigure the metabolic networks in primary and secondary metabolism, including lipids, glucosinolates, and flavonoids. This work provides a basis for the elucidation of the molecular mechanisms involved in the metabolic and transcriptional regulatory networks in response to combined low glutathione content with mild oxidative and nutrient stress in A. thaliana.

De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

BACKGROUND

Arundo donax has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited.

RESULTS

We used RNA sequencing (RNA-Seq) to de novo assemble and characterize the A. donax leaf transcriptome. The sequencing generated 1249 million clean reads that were assembled using single-k-mer and multi-k-mer approaches into 62,596 unique sequences (unitranscripts) with an N50 of 1134 bp. TransDecoder and Trinotate software suites were used to obtain putative coding sequences and annotate them by mapping to UniProtKB/Swiss-Prot and UniRef90 databases, searching for known transcripts, proteins, protein domains, and signal peptides. Furthermore, the unitranscripts were annotated by mapping them to the NCBI non-redundant, GO and KEGG pathway databases using Blast2GO. The transcriptome was also characterized by BLAST searches to investigate homologous transcripts of key genes involved in important metabolic pathways, such as lignin, cellulose, purine, and thiamine biosynthesis and carbon fixation. Moreover, a set of homologous transcripts of key genes involved in stomatal development and of genes coding for stress-associated proteins (SAPs) were identified. Additionally, 8364 simple sequence repeat (SSR) markers were identified and surveyed. SSRs appeared more abundant in non-coding regions (63.18%) than in coding regions (36.82%). This SSR dataset represents the first marker catalogue of A. donax. 53 SSRs (PolySSRs) were then predicted to be polymorphic between ecotype-specific assemblies, suggesting genetic variability in the studied ecotypes.

CONCLUSIONS

This study provides the first publicly available leaf transcriptome for the A. donax bioenergy crop. The functional annotation and characterization of the transcriptome will be highly useful for providing insight into the molecular mechanisms underlying its extreme adaptability. The identification of homologous transcripts involved in key metabolic pathways offers a platform for directing future efforts in genetic improvement of this species. Finally, the identified SSRs will facilitate the harnessing of untapped genetic diversity. This transcriptome should be of value to ongoing functional genomics and genetic studies in this crop of paramount economic importance.

Apoplastic Nucleoside Accumulation in Arabidopsis Leads to Reduced Photosynthetic Performance and Increased Susceptibility Against Botrytis cinerea

Interactions between plant and pathogen often occur in the extracellular space and especially nucleotides like ATP and NAD have been identified as key players in this scenario. Arabidopsis mutants accumulating nucleosides in the extracellular space were generated and studied with respect to susceptibility against Botrytis cinerea infection and general plant fitness determined as photosynthetic performance. The mutants used are deficient in the main nucleoside uptake system ENT3 and the extracellular nucleoside hydrolase NSH3. When grown on soil but not in hydroponic culture, these plants markedly accumulate adenosine and uridine in leaves. This nucleoside accumulation was accompanied by reduced photosystem II efficiency and altered expression of photosynthesis related genes. Moreover, a higher susceptibility toward Botrytis cinerea infection and a reduced induction of pathogen related genes PR1 and WRKY33 was observed. All these effects did not occur in hydroponically grown plants substantiating a contribution of extracellular nucleosides to these effects. Whether reduced general plant fitness, altered pathogen response capability or more direct interactions with the pathogen are responsible for these observations is discussed.

PfsR is a key regulator of iron homeostasis in Synechocystis PCC 6803

Iron is an essential cofactor in numerous cellular processes. The iron deficiency in the oceans affects the primary productivity of phytoplankton including cyanobacteria. In this study, we examined the function of PfsR, a TetR family transcriptional regulator, in iron homeostasis of the cyanobacterium Synechocystis PCC 6803. Compared with the wild type, the pfsR deletion mutant displayed stronger tolerance to iron limitation and accumulated significantly more chlorophyll a, carotenoid, and phycocyanin under iron-limiting conditions. The mutant also maintained more photosystem I and photosystem II complexes than the wild type after iron deprivation. In addition, the activities of photosystem I and photosystem II were much higher in pfsR deletion mutant than in wild-type cells under iron-limiting conditions. The transcripts of pfsR were enhanced by iron limitation and inactivation of the gene affected pronouncedly expression of fut genes (encoding a ferric iron transporter), feoB (encoding a ferrous iron transporter), bfr genes (encoding bacterioferritins), ho genes (encoding heme oxygenases), isiA (encoding a chlorophyll-binding protein), and furA (encoding a ferric uptake regulator). The iron quota in pfsR deletion mutant cells was higher than in wild-type cells both before and after exposure to iron limitation. Electrophoretic mobility shift assays showed that PfsR bound to its own promoter and thereby auto-regulated its own expression. These data suggest that PfsR is a critical regulator of iron homeostasis.

Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis

Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members.