Chloroplastic ascorbate modifies plant metabolism and may act as a metabolite signal regardless of oxidative stress

Ascorbate (Asc) is a major plant metabolite that plays crucial roles in various processes, from reactive oxygen scavenging to epigenetic regulation. However, to what extent and how Asc modulates metabolism is largely unknown. We investigated the consequences of chloroplastic and total cellular Asc deficiencies by studying chloroplastic Asc transporter mutant lines lacking PHOSPHATE TRANSPORTER 4; 4 and the Asc-deficient vtc2-4 mutant of Arabidopsis (Arabidopsis thaliana). Under regular growth conditions, both Asc deficiencies caused minor alterations in photosynthesis, with no apparent signs of oxidative damage. In contrast, metabolomics analysis revealed global and largely overlapping alterations in the metabolome profiles of both Asc-deficient mutants, suggesting that chloroplastic Asc modulates plant metabolism. We observed significant alterations in amino acid metabolism, particularly in arginine metabolism, activation of nucleotide salvage pathways, and changes in secondary metabolism. In addition, proteome-wide analysis of thermostability revealed that Asc may interact with enzymes involved in arginine metabolism, the Calvin-Benson cycle, and several photosynthetic electron transport components. Overall, our results suggest that, independent of oxidative stress, chloroplastic Asc modulates the activity of diverse metabolic pathways in vascular plants and may act as an internal metabolite signal.

Characterization of the Bax Inhibitor-1 Family in Cauliflower and Functional Analysis of BobBIL4

The Bax inhibitor-1 (BI-1) gene family, which is important for plant growth, development, and stress tolerance, remains largely unexplored in cauliflower. In this study, we identified and characterized cauliflower BI-1 family genes. Based on aligned homologous sequences and collinearity with Arabidopsis genes, we identified nine cauliflower BI-1 genes, which encode proteins that varied in length, molecular weight, isoelectric point, and predicted subcellular localization, including the Golgi apparatus, plasma membrane, and various compartments within the chloroplast. Phylogenetic analyses detected evolutionary conservation and divergence among these genes. Ten structural motifs were identified, with Motif 5 found to be crucial for inhibiting apoptosis. According to the cis-regulatory elements in their promoters, these genes likely influence hormone signaling and stress responses. Expression profiles among tissues highlighted the functional diversity of these genes, with particularly high expression levels observed in the silique and root. Focusing on BobBIL4, we investigated its role in brassinosteroid (BR)-mediated root development and salt stress tolerance. BobBIL4 expression levels increased in response to BR and salt treatments. The functional characterization of this gene in Arabidopsis revealed that it enhances root growth and salinity tolerance. These findings provide insights into BI-1 gene functions in cauliflower while also highlighting the potential utility of BobBIL4 for improving crop stress resistance.

Cell death in bryophytes: emerging models to study core regulatory modules and conserved pathways

This review summarizes recent progress in our current understanding of the mechanisms underlying the cell death pathways in bryophytes, focusing on conserved pathways and particularities in comparison to angiosperms. Regulated cell death (RCD) plays key roles during essential processes along the plant life cycle. It is part of specific developmental programmes and maintains homeostasis of the organism in response to unfavourable environments. Bryophytes could provide valuable models to study developmental RCD processes as well as those triggered by biotic and abiotic stresses. Some pathways analogous to those present in angiosperms occur in the gametophytic haploid generation of bryophytes, allowing direct genetic studies. In this review, we focus on such RCD programmes, identifying core conserved mechanisms and raising new key questions to analyse RCD from an evolutionary perspective.

Biomolecular interaction of purified recombinant Arabidopsis thaliana's alternative oxidase 1A with TCA cycle metabolites: Biophysical and molecular docking studies

In higher plants, the mitochondrial alternative oxidase (AOX) pathway plays an essential role in maintaining the TCA cycle/cellular carbon and energy balance under various physiological and stress conditions. Though the activation of AOX pathway upon exogenous addition of α-ketoacids/TCA cycle metabolites [pyruvate, α-ketoglutarate (α-KG), oxaloacetic acid (OAA), succinate and malic acid] to isolated mitochondria is known, the molecular mechanism of interaction of these metabolites with AOX protein is limited. The present study is designed to understand the biomolecular interaction of pure recombinant Arabidopsis thaliana AOX1A with TCA cycle metabolites under in vitro conditions using various biophysical and molecular docking studies. The binding of α-KG, fumaric acid and OAA to rAtAOX1A caused conformational change in the microenvironment of tryptophan residues as evidenced by red shift in the synchronous fluorescence spectra (∆λ = 60 nm). Besides, a decrease in conventional fluorescence emission spectra, tyrosine specific synchronous fluorescence spectra (∆λ = 15 nm) and α-helical content of CD spectra revealed the conformation changes in rAtAOX1A structure associated with binding of various TCA cycle metabolites. Further, surface plasmon resonance (SPR) and microscale thermophoresis (MST) studies revealed the binding affinity, while docking studies identified binding pocket residues, respectively, for these metabolites on rAtAOX1A.

COI1 dependent jasmonic acid signalling positively modulates ROS scavenging system in transgenic hairy root culture of tomato

Reactive oxygen species (ROS) production is a routine event in plants. ROS function as signalling molecules in regulating plant development and defence. However, their accumulation beyond threshold leads to toxicity. Hence, plants are evolved with specialized ROS scavenging system involving phytohormones (synthesis and signalling), enzymes and metabolites. To understand the role of phytohormone jasmonic acid (JA) signalling in ROS scavenging, tomato coronatine insensitive 1 (SlCOI1), a key gene in JA signalling, was silenced and overexpressed in tomato transgenic hairy roots (HR) under the constitutive promoter. Targeted metabolomics of transgenic HR revealed accumulation of phenolic acids including ferulic acid, coumaric acid, vanillic acid, and flavonoid catechin in SlCOI1 overexpressed line. Moreover, osmolyte amino acids proline, asparagine, and glutamine showed a positive co-relation with transgenic overexpression of SlCOI1. Ascorbic acid-glutathione, a crucial antioxidant system was found to be influenced by COI1-mediated JA signalling. The expression of genes encoding enzymes superoxide dismutase 1, ascorbate peroxidase 1, and dehydroascorbate reductase 2 was found to be down and upregulated in SlCOI1 silenced and overexpressed lines, respectively. Methyl jasmonate and Fusarium oxysporum f.sp. lycopersici crude extract treatment further confirmed the regulatory role of COI1-mediated JA signalling in regulation of enzymatic components involved in ROS scavenging. The COI1-mediated JA signalling could also elevate the expression of RESPIRATORY BURST OXIDASE HOMOLOG-B gene which is involved in ROS wave signal generation. The present study underscores the role of COI1-mediated JA signalling in modulating enzymatic and non-enzymatic components of ROS scavenging system and pathogen associated molecular pattern triggered immunity.

Plant Life with and without Oxygen: A Metabolomics Approach

Oxygen deficiency is an environmental challenge which affects plant growth, the development and distribution in land and aquatic ecosystems, as well as crop yield losses worldwide. The capacity to exist in the conditions of deficiency or the complete lack of oxygen depends on a number of anatomic, developmental and molecular adaptations. The lack of molecular oxygen leads to an inhibition of aerobic respiration, which causes energy starvation and the acceleration of glycolysis passing into fermentations. We focus on systemic metabolic alterations revealed with the different approaches of metabolomics. Oxygen deprivation stimulates the accumulation of glucose, pyruvate and lactate, indicating the acceleration of the sugar metabolism, glycolysis and lactic fermentation, respectively. Among the Krebs-cycle metabolites, only the succinate level increases. Amino acids related to glycolysis, including the phosphoglycerate family (Ser and Gly), shikimate family (Phe, Tyr and Trp) and pyruvate family (Ala, Leu and Val), are greatly elevated. Members of the Asp family (Asn, Lys, Met, Thr and Ile), as well as the Glu family (Glu, Pro, Arg and GABA), accumulate as well. These metabolites are important members of the metabolic signature of oxygen deficiency in plants, linking glycolysis with an altered Krebs cycle and allowing alternative pathways of NAD(P)H reoxidation to avoid the excessive accumulation of toxic fermentation products (lactate, acetaldehyde, ethanol). Reoxygenation induces the downregulation of the levels of major anaerobically induced metabolites, including lactate, succinate and amino acids, especially members of the pyruvate family (Ala, Leu and Val), Tyr and Glu family (GABA and Glu) and Asp family (Asn, Met, Thr and Ile). The metabolic profiles during native and environmental hypoxia are rather similar, consisting in the accumulation of fermentation products, succinate, fumarate and amino acids, particularly Ala, Gly and GABA. The most intriguing fact is that metabolic alterations during oxidative stress are very much similar, with plant response to oxygen deprivation but not to reoxygenation.

Methyl jasmonate redirects the dynamics of carbohydrates and amino acids toward the lignans accumulation in Linum album cells

Linum album accumulates lignans e.g., podophyllotoxin (PTOX) and 6-methoxy podophyllotoxin (6MPTOX). This study was aimed to figure out how different concentrations of MeJA (0, 50, 100, 150, and 200 μM) by affecting on free sugars and amino acids contents induce lignans accumulation in L. album cells. Results revealed that hydrogen peroxide (H₂O₂) content increased at 50μM, while it decreased at the high levels of MeJA (150 and 200 μM). Also, increasing trend of nitric oxide (NO) and lipid peroxidation levels peaked at 200 μM MeJA. An increased antioxidant enzymes activity was also observed in the treated cells. Moreover, an increase in rhamnose/xylose, glucose, and mannose was detected at 150 and 200 μM MeJA compared to the control. These compounds provide energy source and carbon skeleton for amino acids biosynthesis. Our results emphasized variations in amino acids levels in the presence of MeJA, where Phe level shifts along with synthesizing phenolics. Likewise, MeJA treatment switch on phenyl-ammonia lyase (PAL) and tyrosine-ammonia lyase (TAL) activities that regenerate phenolic compounds. Changes in phenolic acids (cinnamic, coumaric, caffeic, ferulic, and salicylic acid) and flavonoids (catechin, vitexin, myricetin, and kaempferol) were observed under MeJA treatment. Eventually, MeJA induced lignans production except for lariciresinol (LARI), so that the highest amounts of PTOX and 6MPTOX were analyzed at 50 μM, which were 4 and 5 time of control, respectively. Conclusively, it can be suggested that MeJA-induced oxidative status change redirects free sugars and amino acids toward the production of phenolic compounds especially lignans in L. album cells.

Effect of ascorbate and hydrogen peroxide on hormone and metabolite levels during post-germination growth in wheat

The modulation of hormone and metabolite levels by ascorbate (ASA) and hydrogen peroxide (H₂ O₂ ) was compared during post-germination growth in shoots of wheat. Treatment with ASA resulted in a greater reduction of growth than the addition of H₂ O₂ . ASA also had a larger effect on the redox state of the shoot tissues as shown by the higher ASA and glutathione (GSH) levels, lower glutathione disulfide (GSSG) content and GSSG/GSH ratio compared to the H₂ O₂ treatment. Apart from common responses (i.e., increase of cis-zeatin and its O-glucosides), the contents of several compounds related to cytokinin (CK) and abscisic acid (ABA) metabolism were greater after ASA application. These differences in the redox state and hormone metabolism following the two treatments may be responsible for their distinct influence on various metabolic pathways. Namely, the glycolysis and citrate cycle were inhibited by ASA and they were not affected by H₂ O₂ , while the amino acid metabolism was induced by ASA and repressed by H₂ O₂ based on the changes in the level of the related carbohydrates, organic and amino acids. The first two pathways produce reducing power, while the last one needs it; therefore ASA, as a reductant may suppress and induce them, respectively. H₂ O₂ as an oxidant had different effect, namely it did not alter glycolysis and citrate cycle, and inhibited the formation of amino acids.

Cytochrome b 5: A versatile electron carrier and regulator for plant metabolism

Cytochrome b ₅ (CB5) is a small heme-binding protein, known as an electron donor delivering reducing power to the terminal enzymes involved in oxidative reactions. In plants, the CB5 protein family is substantially expanded both in its isoform numbers and cellular functions, compared to its yeast and mammalian counterparts. As an electron carrier, plant CB5 proteins function not only in fatty acid desaturation, hydroxylation and elongation, but also in the formation of specialized metabolites such as flavonoids, phenolic esters, and heteropolymer lignin. Furthermore, plant CB5s are found to interact with different non-catalytic proteins such as ethylene signaling regulator, cell death inhibitor, and sugar transporters, implicating their versatile regulatory roles in coordinating different metabolic and cellular processes, presumably in respect to the cellular redox status and/or carbon availability. Compared to the plentiful studies on biochemistry and cellular functions of mammalian CB5 proteins, the cellular and metabolic roles of plant CB5 proteins have received far less attention. This article summarizes the fragmentary information pertaining to the discovery of plant CB5 proteins, and discusses the conventional and peculiar functions that plant CB5s might play in different metabolic and cellular processes. Gaining comprehensive insight into the biological functions of CB5 proteins could offer effective biotechnological solutions to tailor plant chemodiversity and cellular responses to environment stimuli.

Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View

Abiotic stresses rewire plant central metabolism to maintain metabolic and energy homeostasis. Metabolites involved in the plant central metabolic network serve as a hub for regulating carbon and energy metabolism under various stress conditions. In this review, we introduce recent metabolomics techniques used to investigate the dynamics of metabolic responses to abiotic stresses and analyze the trend of publications in this field. We provide an updated overview of the changing patterns in central metabolic pathways related to the metabolic responses to common stresses, including flooding, drought, cold, heat, and salinity. We extensively review the common and unique metabolic changes in central metabolism in response to major abiotic stresses. Finally, we discuss the challenges and some emerging insights in the future application of metabolomics to study plant responses to abiotic stresses.

Early gene expression response of barley root tip to toxic concentrations of cadmium

Already a short-term Cd treatment induces changes in gene expression in barley root tips via IAA and ROS signaling during mild and severe Cd stress, respectively. Even a short, 30 min, Cd treatment of roots induced a considerable alteration in gene expression in the barley root tips within an hour after the treatments. The very early activation of MYB1 transcription factor expression is partially regulated by auxin signaling in mildly stressed seedlings. An increase in allene oxide cyclase and NADPH oxidase expression was a distinguishing feature of root tips response to mild Cd stress and their expression is activated via IAA signaling. Meanwhile, early changes in the level of dehydrin transcripts were detected in moderately and severely stressed root tips, and their induction is related to altered ROS homeostasis in cells. The early activation of glutathione peroxidase expression by mild Cd stress indicates the involvement of IAA in the signaling process. In contrast, early ascorbate peroxidase expression was induced only with Cd treatment causing severe stress and ROS play central roles in its induction. The expression of cysteine protease was activated similarly in both mildly and severely Cd-stressed roots; consequently, both increased IAA and ROS levels take part in the regulation of cysteine protease expression. The Cd-evoked accumulation of BAX Inhibitor-1 mRNA was characteristic for moderately and severely stressed roots. Whereas decreased IAA level did not affect its expression, rotenone-mediated ROS depletion markedly reduced the Cd-induced expression of BAX Inhibitor-1. An early increase of alternative oxidase levels in the root tip cells indicated that the reduction of mitochondrial superoxide generation is an important component of barley root response to severe Cd stress.

Oxidative Stress-Induced Alteration of Plant Central Metabolism

Oxidative stress is an integral component of various stress conditions in plants, and this fact largely determines the substantial overlap in physiological and molecular responses to biotic and abiotic environmental challenges. In this review, we discuss the alterations in central metabolism occurring in plants experiencing oxidative stress. To focus on the changes in metabolite profile associated with oxidative stress per se, we primarily analyzed the information generated in the studies based on the exogenous application of agents, inducing oxidative stress, and the analysis of mutants displaying altered oxidative stress response. Despite of the significant variation in oxidative stress responses among different plant species and tissues, the dynamic and transient character of stress-induced changes in metabolites, and the strong dependence of metabolic responses on the intensity of stress, specific characteristic changes in sugars, sugar derivatives, tricarboxylic acid cycle metabolites, and amino acids, associated with adaptation to oxidative stress have been detected. The presented analysis of the available data demonstrates the oxidative stress-induced redistribution of metabolic fluxes targeted at the enhancement of plant stress tolerance through the prevention of ROS accumulation, maintenance of the biosynthesis of indispensable metabolites, and production of protective compounds. This analysis provides a theoretical basis for the selection/generation of plants with improved tolerance to oxidative stress and the development of metabolic markers applicable in research and routine agricultural practice.

Comparative Proteomics Analysis Reveals Unique Early Signaling Response of Saccharomyces cerevisiae to Oxidants with Different Mechanism of Action

The early signaling events involved in oxidant recognition and triggering of oxidant-specific defense mechanisms to counteract oxidative stress still remain largely elusive. Our discovery driven comparative proteomics analysis revealed unique early signaling response of the yeast Saccharomyces cerevisiae on the proteome level to oxidants with a different mechanism of action as early as 3 min after treatment with four oxidants, namely H₂O₂, cumene hydroperoxide (CHP), and menadione and diamide, when protein abundances were compared using label-free quantification relying on a high-resolution mass analyzer (Orbitrap). We identified significant regulation of 196 proteins in response to H₂O₂, 569 proteins in response to CHP, 369 proteins in response to menadione and 207 proteins in response to diamide. Only 17 proteins were common across all treatments, but several more proteins were shared between two or three oxidants. Pathway analyses revealed that each oxidant triggered a unique signaling mechanism associated with cell survival and repair. Signaling pathways mostly regulated by oxidants were Ran, TOR, Rho, and eIF2. Furthermore, each oxidant regulated these pathways in a unique way indicating specificity of response to oxidants having different modes of action. We hypothesize that interplay of these signaling pathways may be important in recognizing different oxidants to trigger different downstream MAPK signaling cascades and to induce specific responses.

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era

Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.

Genotypic difference in secondary metabolism-related enzyme activities and their relative gene expression patterns, osmolyte and plant hormones in wheat

Salinity and drought are the two most important and frequently co-occurring abiotic factors. A greenhouse pot experiment was carried out on two contrasting wheat genotypes (Jimai22, salt tolerant; Yangmai20, salt sensitive) to analyze the effect of drought (4% soil moisture content, D) and salinity (100 mM NaCl, S) either individually or combined on secondary metabolism-related enzyme activities and osmolytes. Results showed that drought, salinity and their combination (D + S) caused increases in phenylalanine ammonialyase (PAL, EC 4.3.1.24) activities compared with controls with a greater enhancement in Jimai22 than Yangmai20. Polyphenol peroxidase (PPO, EC 1.14.18.1) and shikimate dehydrogenase (SKDH, EC 1.1.1.25) activities increased more in Jimai22 both under salinity alone and D + S stresses. The D + S combination increased cinnamyl alcohol dehydrogenase (CAD, EC 1.1.1.195) activity and glycine betaine (GB) under both 10 and 4% soil moisture contents (SMC), and elevated abscisic acid (ABA), indole-3-acetic acid (IAA) and flavonoid contents at 4% SMC in Jimai22, contents of the compounds remained unchanged in Yangmai20. The treatment with salinity alone at both SMCs significantly increased callose and flavonoid contents in Jimai22 more than in Yangmai20, as compared to controls. In addition, the total phenol content at 4% SMC increased in the salt-tolerant genotype more. Moreover, total tocopherol under salinity alone and D + S at 4% SMC and chitinase activity under salinity at both SMC remarkably increased in Jimai22 while non-significant change observed in Yangmai20. Also, the expression of genes related to secondary metabolism (PAL, PPO, CAD, SKDH, and GB) was more induced in Jimai22 than Yangmai20 under D + S, and lower accumulation of H₂ O₂ and O₂ ^- also occurred. Our findings suggest that high tolerance to D + S stress in Jimai22 was closely related to enhanced secondary metabolism-related enzyme activities and osmolytes such as PAL, CAD, PPO, SKDH, GB, total tocopherol, callose, plant hormones and their transcript level, which may beneficial to lower the reactive oxygen species (ROS) accumulation.

Radiation metabolomics in the quest of cardiotoxicity biomarkers: the review

Purpose: Ionizing radiation is a risk factor to the whole organism, including the heart. Cardiac damage is considered to be a late effect of radiation exposure. While the acute cardiotoxicity of high doses is well characterized, the knowledge about nature and magnitude of the cardiac risk following lower doses exposure is incomplete. It has been shown that the cardiotoxic effects of radiation are source-, dose- and time-dependent. This paper provides an overview on these dependencies with regard to the molecular responses at the cellular and tissue levels. Main focus is put on the Nuclear Magnetic Resonance (NMR)-based and Mass Spectrometry (MS)-based metabolomic approaches in search of toxicity markers of relatively small doses of radiation.Conclusions: Available literature indicates that radiation exposure affects metabolites associated with: energy production, degradation of proteins and cell membranes, expression of proteins and stress response. Such effects are common for both animal and human studies. However, the specific metabolic response depends on several factors, including the examined organ. Radiation metabolomics can be used to explain the mechanisms of development of radiation-induced heart disease and to find an organ-specific biomarker of radiation exposure. The main aim of this review was to collect the information on the human cardiotoxicity biomarkers. In addition it also summarizes results of the studies on the metabolic responses to ionizing radiation for other organs, as well as the comparative data concerning animal studies.

Metabolomics in Plant Stress Physiology

Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.

Uncovering Bax inhibitor-1 dual role in the legume-rhizobia symbiosis in common bean roots

Bax-inhibitor 1 (BI-1) is a cell death suppressor conserved in all eukaryotes that modulates cell death in response to abiotic stress and pathogen attack in plants. However, little is known about its role in the establishment of symbiotic interactions. Here, we demonstrate the functional relevance of an Arabidopsis thaliana BI-1 homolog (PvBI-1a) to symbiosis between the common bean (Phaseolus vulgaris) and Rhizobium tropici. We show that the changes in expression of PvBI-1a observed during early symbiosis resemble those of some defence response-related proteins. By using gain- and loss-of-function approaches, we demonstrate that the overexpression of PvBI-1a in the roots of common bean increases the number of rhizobial infection events (and therefore the final number of nodules per root), but induces the premature death of nodule cells, affecting their nitrogen fixation efficiency. Nodule morphological alterations are known to be associated with changes in the expression of genes tied to defence, autophagy, and vesicular trafficking. Results obtained in the present work suggest that BI-1 has a dual role in the regulation of programmed cell death during symbiosis, extending our understanding of its critical function in the modulation of host immunity while responding to beneficial microbes.

In vivo detection of protein cysteine sulfenylation in plastids

Protein cysteine thiols are post-translationally modified under oxidative stress conditions. Illuminated chloroplasts are one of the important sources of hydrogen peroxide (H₂ O₂ ) and are highly sensitive to environmental stimuli, yet a comprehensive view of the oxidation-sensitive chloroplast proteome is still missing. By targeting the sulfenic acid YAP1C-trapping technology to the plastids of light-grown Arabidopsis cells, we identified 132 putatively sulfenylated plastid proteins upon H₂ O₂ pulse treatment. Almost half of the sulfenylated proteins are enzymes of the amino acid metabolism. Using metabolomics, we observed a reversible decrease in the levels of the amino acids Ala, Asn, Cys, Gln, Glu, His, Ile, Leu, Lys, Phe, Ser, Thr and Val after H₂ O₂ treatment, which is in line with an anticipated decrease in the levels of the glycolysis and tricarboxylic acid metabolites. Through the identification of an organelle-tailored proteome, we demonstrated that the subcellular targeting of the YAP1C probe enables us to study in vivo cysteine sulfenylation at the organellar level. All in all, the identification of these oxidation events in plastids revealed that several enzymes of the amino acid metabolism rapidly undergo cysteine oxidation upon oxidative stress.

Consequences of Oxidative Stress on Plant Glycolytic and Respiratory Metabolism

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are present at low and controlled levels under normal conditions. These reactive molecules can increase to high levels under various biotic and abiotic conditions, resulting in perturbation of the cellular redox state that can ultimately lead to oxidative or nitrosative stress. In this review, we analyze the various effects that result from alterations of redox homeostasis on plant glycolytic pathway and tricarboxylic acid (TCA) cycle. Most documented modifications caused by ROS or RNS are due to the presence of redox-sensitive cysteine thiol groups in proteins. Redox modifications include Cys oxidation, disulfide bond formation, S-glutathionylation, S-nitrosylation, and S-sulfhydration. A growing number of proteomic surveys and biochemical studies document the occurrence of ROS- or RNS-mediated modification in enzymes of glycolysis and the TCA cycle. In a few cases, these modifications have been shown to affect enzyme activity, suggesting an operational regulatory mechanism in vivo. Further changes induced by oxidative stress conditions include the proposed redox-dependent modifications in the subcellular distribution of a putative redox sensor, NAD-glyceraldehyde-3P dehydrogenase and the micro-compartmentation of cytosolic glycolytic enzymes. Data from the literature indicate that oxidative stress may induce complex changes in metabolite pools in central carbon metabolism. This information is discussed in the context of our understanding of plant metabolic response to oxidative stress.

Arabidopsis Bax inhibitor-1 interacts with enzymes related to very-long-chain fatty acid synthesis

Bax inhibitor-1 (BI-1) is a widely conserved cell death regulator that confers resistance to environmental stress in plants. Previous studies suggest that Arabidopsis thaliana BI-1 (AtBI-1) modifies sphingolipids by interacting with cytochrome b₅ (AtCb5), an electron-transfer protein. To reveal how AtBI-1 regulates sphingolipid synthesis, we screened yeast sphingolipid-deficient mutants and identified yeast ELO2 and ELO3 as novel enzymes that are essential for AtBI-1 function. ELO2 and ELO3 are condensing enzymes that synthesize very-long-chain fatty acids (VLCFAs), major fatty acids in plant sphingolipids. In Arabidopsis, we identified four ELO homologs (AtELO1-AtELO4), localized in the endoplasmic reticulum membrane. Of those AtELOs, AtELO1 and AtELO2 had a characteristic histidine motif and were bound to AtCb5-B. This result suggests that AtBI-1 interacts with AtELO1 and AtELO2 through AtCb5. AtELO2 and AtCb5-B also interact with KCR1, PAS2, and CER10, which are essential for the synthesis of VLCFAs. Therefore, AtELO2 may participate in VLCFA synthesis with AtCb5 in Arabidopsis. In addition, our co-immunoprecipitation/mass spectrometry analysis demonstrated that AtBI-1 forms a complex with AtELO2, KCR1, PAS2, CER10, and AtCb5-D. Furthermore, AtBI-1 contributes to the rapid synthesis of 2-hydroxylated VLCFAs in response to oxidative stress. These results indicate that AtBI-1 regulates VLCFA synthesis by interacting with VLCFA-synthesizing enzymes.

New insights into the phylogeny of the TMBIM superfamily across the tree of life: Comparative genomics and synteny networks reveal independent evolution of the BI and LFG families in plants

The Transmembrane BAX Inhibitor Motif containing (TMBIM) superfamily, divided into BAX Inhibitor (BI) and Lifeguard (LFG) families, comprises a group of cytoprotective cell death regulators conserved in prokaryotes and eukaryotes. However, no research has focused on the evolution of this superfamily in plants. We identified 685 TMBIM proteins in 171 organisms from Archaea, Bacteria, and Eukarya, and provided a phylogenetic overview of the whole TMBIM superfamily. Then, we used orthology and synteny network analyses to further investigate the evolution and expansion of the BI and LFG families in 48 plants from diverse taxa. Plant BI family forms a single monophyletic group; however, monocot BI sequences transposed to another genomic context during evolution. Plant LFG family, which expanded trough whole genome and tandem duplications, is subdivided in LFG I, LFG IIA, and LFG IIB major phylogenetic groups, and retains synteny in angiosperms. Moreover, two orthologous groups (OGs) are shared between bryophytes and seed plants. Other several lineage-specific OGs are present in plants. This work clarifies the phylogenetic classification of the TMBIM superfamily across the three domains of life. Furthermore, it sheds new light on the evolution of the BI and LFG families in plants providing a benchmark for future research.

The Wheat Bax Inhibitor-1 Protein Interacts with an Aquaporin TaPIP1 and Enhances Disease Resistance in Arabidopsis

Bax inhibitor-1 (BI-1) is an endoplasmic reticulum (ER)-resident cell death suppressor evolutionarily conserved in eukaryotes. The ability of BI-1 to inhibit the biotic and abiotic stresses have been well-studied in Arabidopsis, while the functions of wheat BI-1 are largely unknown. In this study, the wheat BI-1 gene TaBI-1.1 was isolated by an RNA-seq analysis of Fusarium graminearum (Fg)-treated wheat. TaBI-1.1 expression was induced by a salicylic acid (SA) treatment and down-regulated by an abscisic acid (ABA) treatment. Based on β-glucuronidase (GUS) staining, TaBI-1.1 was expressed in mature leaves and roots but not in the hypocotyl or young leaves. Constitutive expression of TaBI-1.1 in Arabidopsis enhanced its resistance to Pseudomonas syringae pv. Tomato (Pst) DC3000 infection and induced SA-related gene expression. Additionally, TaBI-1.1 transgenic Arabidopsis exhibited an alleviation of damage caused by high concentrations of SA and decreased the sensitivity to ABA. Consistent with the phenotype, the RNA-seq analysis of 35S::TaBI-1.1 and Col-0 plants showed that TaBI-1.1 was involved in biotic stresses. These results suggested that TaBI-1.1 positively regulates SA signals and plays important roles in the response to biotic stresses. In addition, TaBI-1.1 interacted with the aquaporin TaPIP1, and both them were localized to ER membrane. Furthermore, we demonstrated that TaPIP1 was up-regulated by SA treatment and TaPIP1 transgenic Arabidopsis enhanced the resistance to Pst DC3000 infection. Thus, the interaction between TaBI-1.1 and TaPIP1 on the ER membrane probably occurs in response to SA signals and defense response.

Comparative Metabolomic Analysis of the Cambium Tissue of Non-transgenic and Multi-Gene Transgenic Poplar (Populus × euramericana 'Guariento')

Poplar, a model for woody plant research, is the most widely distributed tree species in the world. Metabolites are the basis of phenotypes, allowing an intuitive and effective understanding of biological processes and their mechanisms. However, metabolites in non-transgenic and multi-gene transgenic poplar remains poorly characterized, especially in regards of the influences on quantity and in the analysis of the relative abundance of metabolites after the introduction of multi stress-related genes. In this study, we investigated the cambium metabolomes of one non-transgenic (D5-0) and two multi-gene (vgb, SacB, ERF36, BtCry3A, and OC-I) transgenic lines (D5-20 and D5-21) of hybrid poplar (Populus × euramericana 'Guariento') using both gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). We aimed to explore the effects of the exogenous genes on metabolite composition and to screen out metabolites with important biological functions. Finally, we identified 239 named metabolites and determined their relative abundance. Among these, 197 metabolites had a different abundance across the three lines. These methabolites spanned nine primary and 44 secondary metabolism pathways. Arginine and glutamate, as substrates and intermediates in nitrogen metabolism, and important in growth and stress-related processes, as well as sucrose, uridine diphosphate glucose, and their derivatives, precursors in cell wall pathways, and catechol, relevant to insect resistance, differed greatly between the genetically modified and non-transgenic poplar. These findings may provide a basis for further study of cambium metabolism, and fully understand metabolites associated with stress response.

Urea application promotes amino acid metabolism and membrane lipid peroxidation in Azolla

A pot experiment was conducted to evaluate the effect of urea on nitrogen metabolism and membrane lipid peroxidation in Azolla pinnata. Compared to controls, the application of urea to A. pinnata resulted in a 44% decrease in nitrogenase activity, no significant change in glutamine synthetase activity, 660% higher glutamic-pyruvic transaminase, 39% increase in free amino acid levels, 22% increase in malondialdehyde levels, 21% increase in Na⁺/K⁺- levels, 16% increase in Ca²⁺/Mg²⁺-ATPase levels, and 11% decrease in superoxide dismutase activity. In terms of H₂O₂ detoxifying enzymes, peroxidase activity did not change and catalase activity increased by 64% in urea-treated A. pinnata. These findings suggest that urea application promotes amino acid metabolism and membrane lipid peroxidation in A. pinnata.

Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles

Transcript and metabolite profiling were performed on leaves from six rice cultivars under high night temperature (HNT) condition. Six genes were identified as central for HNT response encoding proteins involved in transcription regulation, signal transduction, protein-protein interactions, jasmonate response and the biosynthesis of secondary metabolites. Sensitive cultivars showed specific changes in transcript abundance including abiotic stress responses, changes of cell wall-related genes, of ABA signaling and secondary metabolism. Additionally, metabolite profiles revealed a highly activated TCA cycle under HNT and concomitantly increased levels in pathways branching off that could be corroborated by enzyme activity measurements. Integrated data analysis using clustering based on one-dimensional self-organizing maps identified two profiles highly correlated with HNT sensitivity. The sensitivity profile included genes of the functional bins abiotic stress, hormone metabolism, cell wall, signaling, redox state, transcription factors, secondary metabolites and defence genes. In the tolerance profile, similar bins were affected with slight differences in hormone metabolism and transcription factor responses. Metabolites of the two profiles revealed involvement of GABA signaling, thus providing a link to the TCA cycle status in sensitive cultivars and of myo-inositol as precursor for inositol phosphates linking jasmonate signaling to the HNT response specifically in tolerant cultivars.

Melatonin restricts Pb-induced PCD by enhancing BI-1 expression in tobacco suspension cells

Melatonin is a conserved substance, which was discovered in the evolutionary distant organisms like bacteria, plants, invertebrates and vertebrates. Recent studies have shown that melatonin despite its possible role in photoperiod processes, has been found to be a direct free radical scavenger and an indirect antioxidant. In this report the impact of exogenous melatonin on the Bax inhibitor-1 (BI-1) expression level in Nicotiana tabacum L. line Bright Yellow 2 (BY-2) suspension cells exposed to lead was examined. BI-1 is a well-conserved protein in plants and animals that serves as the inhibitor of mammalian proapoptotic proteins as well as plant ROS-induced cell death. Our results showed that pretreatment with 200 nm melatonin, expressing BI-1 and fortified tobacco suspension cells against damages induced by lead. The obtained results revealed, that melatonin significantly increases BY-2 cells proliferation and protects BY-2 cells against death. Moreover, the conducted analyses showed for the first time that the protective effect of melatonin may be connected not only with its antioxidant properties but also with its direct impact on elevating BI-1 expression and lead-induced programmed cell death (PCD) restriction.

Transcriptional regulator PrqR plays a negative role in glucose metabolism and oxidative stress acclimation in Synechocystis sp. PCC 6803

Plant and cyanobacteria can perceive signals from soluble sugar and reactive oxygen species (ROS) and then coordinate gene expression under stress acclimation, but the underlying mechanism remains unclear. In this study, we found that the transcriptional factor PrqR (Slr0895) in Synechocystis can perceive signals from ROS generated after shifting from prolonged darkness with glucose into high-light. The deletion mutant (DprqR) showed increased growth rate and decreased ROS content, whereas the complementary strain (CprqR) restored the growth characteristics, phenotypes and ROS status of WT, thereby establishing PrqR as a negative regulator of ROS.LC/GC-MS-based metabolic profiling also showed active ROS mitigation in DprqR mutant. Further study by qRT-PCR, ChIP-PCR and deletion of both prqR and prqA (DprqR-DprqA mutant) revealed that PrqR exerts this negative regulation of ROS removal by controlling the expression of sodB and prqA (slr0896). Furthermore, PrqR also found to control glucose metabolism by regulating a positive regulator of glucose metabolism, sigE, and its regulons. Results suggest that PrqR was involved in perceiving signals from ROS under physiological condition, as well as in regulating stress removal and glucose metabolism.

Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress

Metabolomics is one omics approach that can be used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include analysis of a wide range of chemical species with diverse physical properties, from ionic inorganic compounds to biochemically derived hydrophilic carbohydrates, organic and amino acids, and a range of hydrophobic lipid-related compounds. This complexitiy brings huge challenges to the analytical technologies employed in current plant metabolomics programs, and powerful analytical tools are required for the separation and characterization of this extremely high compound diversity present in biological sample matrices. The use of mass spectrometry (MS)-based analytical platforms to profile stress-responsive metabolites that allow some plants to adapt to adverse environmental conditions is fundamental in current plant biotechnology research programs for the understanding and development of stress-tolerant plants. In this review, we describe recent applications of metabolomics and emphasize its increasing application to study plant responses to environmental (stress-) factors, including drought, salt, low oxygen caused by waterlogging or flooding of the soil, temperature, light and oxidative stress (or a combination of them). Advances in understanding the global changes occurring in plant metabolism under specific abiotic stress conditions are fundamental to enhance plant fitness and increase stress tolerance. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:620-649, 2016.

Profiling of acidic (amino and phenolic acids) and phenylpropanoids production in response to methyl jasmonate-induced oxidative stress in Scrophularia striata suspension cells

A metabolic profiling including calculation of energy cost of amino acids biosynthesis in cultured cells of Scrophularia striata showed that methyl jasmonate-inducible oxidative stress elicited secondary metabolites formation derived from phenylalanine and tyrosine and increased energy cost for these amino acids biosynthesis. Understanding of the metabolic pathways in cell culture of Scrophularia striata, an aromatic plant species, facilitates means of production of pharmaceutical metabolites under oxidative stress. In this study, we evaluated the effects of MeJA on the S. striata metabolic pathway and the responses to oxidative stress. Exposure to methyl jasmonate (MeJA) affects plant growth, effectively induces production of reactive oxygen species (ROS) and inserts oxidative stress at the cellular level which results in alteration of primary metabolites and production of phenylepropanoid compounds. Cells treated with MeJA indicated increase in the activities of three antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT), guaiacol peroxidase (GPx) as well as intracellular H2O2 and MDA contents compared with mock-treated cells. High performance liquid chromatography (HPLC)-based metabolome analysis revealed dynamic metabolic changes in oxidatively stressed S. striata cells, e.g., general phenylpropanoid pathway, phenylethanoid-glycosides, lignans, and increased energy cost of biosynthesis and accumulation of amino acids. Furthermore, principal component analysis (PCA)-derived score plots demonstrated that MeJA affects cellular metabolism in S. striata cells and significantly alters metabolite composition under MeJA-inducible oxidative stress. These observations suggest that MeJA-elicited cell suspension cultures of S. striata balanced the production of primary and secondary metabolites in coordination with ROS-scavenging system.

Integrated metabolomics and phytochemical genomics approaches for studies on rice

Metabolomics is widely employed to monitor the cellular metabolic state and assess the quality of plant-derived foodstuffs because it can be used to manage datasets that include a wide range of metabolites in their analytical samples. In this review, we discuss metabolomics research on rice in order to elucidate the overall regulation of the metabolism as it is related to the growth and mechanisms of adaptation to genetic modifications and environmental stresses such as fungal infections, submergence, and oxidative stress. We also focus on phytochemical genomics studies based on a combination of metabolomics and quantitative trait locus (QTL) mapping techniques. In addition to starch, rice produces many metabolites that also serve as nutrients for human consumers. The outcomes of recent phytochemical genomics studies of diverse natural rice resources suggest there is potential for using further effective breeding strategies to improve the quality of ingredients in rice grains.

Pseudomonas syringae pv. tomato OxyR Is Required for Virulence in Tomato and Arabidopsis

Reactive oxygen species (ROS) have been shown to have a crucial role in plant defense responses and signaling pathways. In addition, ROS also have direct toxicity against pathogens. However, the molecular mechanisms of plant ROS in the direct effects against pathogens is still unclear. To investigate the function of plant ROS in the interactions of plant and bacterial pathogens, we focused on oxyR, encoding an oxidative stress-regulated transcription factor in Pseudomonas syringae pv. tomato DC3000 (DC3000), and generated an ΔoxyR mutant. The DC3000 ΔoxyR mutant showed high sensitivity to oxidative stress in comparison with wild type and the complemented line. The host plants of DC3000, including tomato and Arabidopsis inoculated with the ΔoxyR mutant, clearly showed reduced disease symptoms as well as reduced bacterial populations. Expression profiles of DC3000 genes revealed that OxyR could regulate the expression of genes encoding ROS-detoxifying enzymes, including catalases (KatB and KatG), in response to ROS. We also demonstrated that the expression of katB could be regulated by OxyR during the infection of DC3000 in Arabidopsis. These results suggest that OxyR has an important role in the virulence of DC3000 by regulating the expression of genes related to oxidative stress.

Overexpression of BAX INHIBITOR-1 Links Plasma Membrane Microdomain Proteins to Stress

BAX INHIBITOR-1 (BI-1) is a cell death suppressor widely conserved in plants and animals. Overexpression of BI-1 enhances tolerance to stress-induced cell death in plant cells, although the molecular mechanism behind this enhancement is unclear. We recently found that Arabidopsis (Arabidopsis thaliana) BI-1 is involved in the metabolism of sphingolipids, such as the synthesis of 2-hydroxy fatty acids, suggesting the involvement of sphingolipids in the cell death regulatory mechanism downstream of BI-1. Here, we show that BI-1 affects cell death-associated components localized in sphingolipid-enriched microdomains of the plasma membrane in rice (Oryza sativa) cells. The amount of 2-hydroxy fatty acid-containing glucosylceramide increased in the detergent-resistant membrane (DRM; a biochemical counterpart of plasma membrane microdomains) fraction obtained from BI-1-overexpressing rice cells. Comparative proteomics analysis showed quantitative changes of DRM proteins in BI-1-overexpressing cells. In particular, the protein abundance of FLOTILLIN HOMOLOG (FLOT) and HYPERSENSITIVE-INDUCED REACTION PROTEIN3 (HIR3) markedly decreased in DRM of BI-1-overexpressing cells. Loss-of-function analysis demonstrated that FLOT and HIR3 are required for cell death by oxidative stress and salicylic acid, suggesting that the decreased levels of these proteins directly contribute to the stress-tolerant phenotypes in BI-1-overexpressing rice cells. These findings provide a novel biological implication of plant membrane microdomains in stress-induced cell death, which is negatively modulated by BI-1 overexpression via decreasing the abundance of a set of key proteins involved in cell death.

High night temperature strongly impacts TCA cycle, amino acid and polyamine biosynthetic pathways in rice in a sensitivity-dependent manner

Global climate change combined with asymmetric warming can have detrimental effects on the yield of crop plants such as rice (Oryza sativa L.). Little is known about metabolic responses of rice to high night temperature (HNT) conditions. Twelve cultivars with different HNT sensitivity were used to investigate metabolic changes in the vegetative stage under HNT compared to control conditions. Central metabolism, especially TCA cycle and amino acid biosynthesis, were strongly affected particularly in sensitive cultivars. Levels of several metabolites were correlated with HNT sensitivity. Furthermore, pool sizes of some metabolites negatively correlated with HNT sensitivity under control conditions, indicating metabolic pre-adaptation in tolerant cultivars. The polyamines putrescine, spermidine and spermine showed increased abundance in sensitive cultivars under HNT conditions. Correlations between the content of polyamines and 75 other metabolites indicated metabolic shifts from correlations with sugar-phosphates and 1-kestose under control to correlations with sugars and amino and organic acids under HNT conditions. Increased expression levels of ADC2 and ODC1, genes encoding enzymes catalysing the first committed steps of putrescine biosynthesis, were restricted to sensitive cultivars under HNT. Additionally, transcript levels of eight polyamine biosynthesis genes were correlated with HNT sensitivity. Responses to HNT in the vegetative stage result in distinct differences between differently responding cultivars with a dysregulation of central metabolism and an increase of polyamine biosynthesis restricted to sensitive cultivars under HNT conditions and a pre-adaptation of tolerant cultivars already under control conditions with higher levels of potentially protective compatible solutes.

Comparison of three generic vancomycin products using liquid chromatography-mass spectrometry and an online tool

PURPOSE

Three different generic vancomycin products were compared using liquid chromatography-mass spectrometry (LC-MS) and open-access metabolomic tools.

METHODS

Single-lot samples of vancomycin hydrochloride from three different manufacturers (Hospira, APP Pharmaceuticals, and Pfizer) were reconstituted and injected into a high-resolution LC-MS system. The mass spectral fingerprints were compared for similarity of nonvancomycin B components using the XCMS Online system through Scripps University. Significance was defined as a p of ≤0.01 and a fold change of ≥1.5. The concentration of vancomycin B in each product was also measured using LC-MS on days 0, 1, 2, 4, 7, 10, and 14.

RESULTS

Qualitative comparisons of the products using the XCMS Online interface indicated the presence of significant differences among the products at the time of reconstitution; however, these variations seemed to converge after 14 days of storage. The concentration profiles of vancomycin B during refrigerated storage did not differ significantly among the three products. XCMS Online analyses revealed that the Pfizer and Hospira products were the most similar to each other.

CONCLUSION

While there were no significant differences found in the concentration of vancomycin B among Pfizer, APP, and Hospira products, there were differences in their initial mass spectral analysis after reconstitution. Liquid chromatography-tandem mass spectrometry profiles of the ions or isotopes present in the three products showed significant differences in impurities such as crystalline degradation product (CDP)-1 and CDP intermediate. After 14 days of refrigerated storage, the differences among the products converged, and fewer distinct features could be detected.

Characterization and study of transgenic cultivars by capillary and microchip electrophoresis

Advances in biotechnology have increased the demand for suitable analytical techniques for the analysis of genetically modified organisms. Study of the substantial equivalence, discrimination between transgenic and non-transgenic cultivars, study of the unintended effects caused by a genetic modification or their response to diverse situations or stress conditions (e.g., environmental, climatic, infections) are some of the concerns that need to be addressed. Capillary electrophoresis (CE) is emerging as an alternative to conventional techniques for the study and characterization of genetically modified organisms. This article reviews the most recent applications of CE for the analysis and characterization of transgenic cultivars in the last five years. Different strategies have been described depending on the level analyzed (DNA, proteins or metabolites). Capillary gel electrophoresis (CGE) has shown to be particularly useful for the analysis of DNA fragments amplified by PCR. Metabolites and proteins have been mainly separated using capillary zone electrophoresis (CZE) using UV and MS detection. Electrophoretic chips have also proven their ability in the analysis of transgenic cultivars and a section describing the new applications is also included.

Comparative metabolomic analysis of wild type and mads3 mutant rice anthers

Rice (Oryza sativa L.) MADS3 transcription factor regulates the homeostasis of reactive oxygen species (ROS) during late anther development, and one MADS3 mutant, mads3-4, has defective anther walls, aborted microspores and complete male sterility. Here, we report the untargeted metabolomic analysis of both wild type and mads3-4 mature anthers. Mutation of MADS3 led to an unbalanced redox status and caused oxidative stress that damages lipid, protein, and DNA. To cope with oxidative stress in mads3-4 anthers, soluble sugars were mobilized and carbohydrate metabolism was shifted to amino acid and nucleic acid metabolism to provide substrates for the biosynthesis of antioxidant proteins and the repair of DNA. Mutation of MADS3 also affected other aspects of rice anther development such as secondary metabolites associated with cuticle, cell wall, and auxin metabolism. Many of the discovered metabolic changes in mads3-4 anthers were corroborated with changes of expression levels of corresponding metabolic pathway genes. Altogether, this comparative metabolomic analysis indicated that MADS3 gene affects rice anther development far beyond the ROS homeostasis regulation.

Arabidopsis Bax inhibitor-1 promotes sphingolipid synthesis during cold stress by interacting with ceramide-modifying enzymes

Bax inhibitor-1 (BI-1) is a widely conserved cell death suppressor localized in the endoplasmic reticulum membrane. Our previous results revealed that Arabidopsis BI-1 (AtBI-1) interacts with not only Arabidopsis cytochrome b 5 (Cb5), an electron transfer protein, but also a Cb5-like domain (Cb5LD)-containing protein, Saccharomyces cerevisiae fatty acid 2-hydroxylase 1, which 2-hydroxylates sphingolipid fatty acids. We have now found that AtBI-1 binds Arabidopsis sphingolipid Δ8 long-chain base (LCB) desaturases AtSLD1 and AtSLD2, which are Cb5LD-containing proteins. The expression of both AtBI-1 and AtSLD1 was increased by cold exposure. However, different phenotypes were observed in response to cold treatment between an atbi-1 mutant and a sld1sld2 double mutant. To elucidate the reasons behind the difference, we analyzed sphingolipids and found that unsaturated LCBs in atbi-1 were not altered compared to wild type, whereas almost all LCBs in sld1sld2 were saturated, suggesting that AtBI-1 may not be necessary for the desaturation of LCBs. On the other hand, the sphingolipid content in wild type increased in response to low temperature, whereas total sphingolipid levels in atbi-1 were unaltered. In addition, the ceramide-modifying enzymes AtFAH1, sphingolipid base hydroxylase 2 (AtSBH2), acyl lipid desaturase 2 (AtADS2) and AtSLD1 were highly expressed under cold stress, and all are likely to be related to AtBI-1 function. These findings suggest that AtBI-1 contributes to synthesis of sphingolipids during cold stress by interacting with AtSLD1, AtFAH1, AtSBH2 and AtADS2.

The metabolic response of cultured tomato cells to low oxygen stress

The storage of fruits and vegetables under a controlled atmosphere can induce low oxygen stress, which can lead to post-harvest losses through the induction of disorders such as core breakdown and browning. To gain better understanding of the metabolic response of plant organs to low oxygen, cultured tomato cells (Lycopersicum esculentum) were used as a model system to study the metabolic stress response to low oxygen (0 and 1 kPa O2). By adding 13C labelled glucose, changes in the levels of polar metabolites and their 13C label accumulation were quantified. Low oxygen stress altered the metabolite profile of tomato cells, with the accumulation of the intermediates of glycolysis in addition to increases in lactate and sugar alcohols. 13C label data showed reduced label accumulation in almost all metabolites except lactate and some sugar alcohols. The results showed that low oxygen stress in tomato cell culture activated fermentative metabolism and sugar alcohol synthesis while inhibiting the activity of the TCA cycle and the biosynthesis of metabolites whose precursors are derived from central metabolism, including fluxes to most organic acids, amino acids and sugars.

Rice suspension cultured cells are evaluated as a model system to study salt responsive networks in plants using a combined proteomic and metabolomic profiling approach

Salinity is one of the major abiotic stresses affecting plant productivity but surprisingly, a thorough understanding of the salt-responsive networks responsible for sustaining growth and maintaining crop yield remains a significant challenge. Rice suspension culture cells (SCCs), a single cell type, were evaluated as a model system as they provide a ready source of a homogenous cell type and avoid the complications of multicellular tissue types in planta. A combination of growth performance, and transcriptional analyses using known salt-induced genes was performed on control and 100 mM NaCl cultured cells to validate the biological system. Protein profiling was conducted using both DIGE- and iTRAQ-based proteomics approaches. In total, 106 proteins were identified in DIGE experiments and 521 proteins in iTRAQ experiments with 58 proteins common to both approaches. Metabolomic analysis provided insights into both developmental changes and salt-induced changes of rice SCCs at the metabolite level; 134 known metabolites were identified, including 30 amines and amides, 40 organic acids, 40 sugars, sugar acids and sugar alcohols, 21 fatty acids and sterols, and 3 miscellaneous compounds. Our results from proteomic and metabolomic studies indicate that the salt-responsive networks of rice SCCs are extremely complex and share some similarities with thee cellular responses observed in planta. For instance, carbohydrate and energy metabolism pathways, redox signaling pathways, auxin/indole-3-acetic acid pathways and biosynthesis pathways for osmoprotectants are all salt responsive in SCCs enabling cells to maintain cellular function under stress condition. These data are discussed in the context of our understanding of in planta salt-responses.

The characteristics of Bax inhibitor-1 and its related diseases

Bax inhibitor-1 (BI-1) is an evolutionarily-conserved endoplasmic reticulum protein. The expression of BI-1 in mammalian cells suppresses apoptosis induced by Bax, a pro-apoptotic member of the Bcl-2 family. BI-1 has been shown to be associated with calcium (Ca(2+)) levels, reactive oxygen species (ROS) production, cytosolic acidification, and autophagy as well as endoplasmic reticulum stress signaling pathways. According to both in vitro and clinical studies, BI-1 promotes the characteristics of cancers. In other diseases, BI-1 has also been shown to regulate insulin resistance, adipocyte differentiation, hepatic dysfunction and depression. However, the roles of BI-1 in these disease conditions are not fully consistent among studies. Until now, the molecular mechanisms of BI-1 have not directly explained with regard to how these conditions can be regulated. Therefore, this review investigates the physiological role of BI-1 through molecular mechanism studies and its application in various diseases.

Development of an LC-MS/MS method for the analysis of free sphingoid bases using 4-fluoro-7-nitrobenzofurazan (NBD-F)

The molecular species of sphingoid bases were tagged with the fluorescent amino group reagent, 4-fluoro-7-nitrobenzofurazan (NBD-F). The NBD-sphingoid bases were analyzed by a highly selective and sensitive liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) technique capable of reliable detection of several fmol of the derivatives. Lipid extracts from plant samples were derivatized with NBD-F, and all nine species of free sphingoid bases present in plant sphingolipids were separated and quantified for the first time; a complete baseline resolution was achieved for cis-8 and trans-8 isomers of sphingoid bases by reversed phase HPLC on a C18 column. The extraction and derivatization procedures and LC-MS/MS method can facilitate the progress of the studies for seeking the active components of sphingoid bases species in response to biological challenges.

Unlocking Triticeae genomics to sustainably feed the future

The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.

A review of the "Omics" approach to biomarkers of oxidative stress in Oryza sativa

Physiological and ecological constraints that cause the slow growth and depleted production of crops have raised a major concern in the agriculture industry as they represent a possible threat of short food supply in the future. The key feature that regulates the stress signaling pathway is always related to the reactive oxygen species (ROS). The accumulation of ROS in plant cells would leave traces of biomarkers at the genome, proteome, and metabolome levels, which could be identified with the recent technological breakthrough coupled with improved performance of bioinformatics. This review highlights the recent breakthrough in molecular strategies (comprising transcriptomics, proteomics, and metabolomics) in identifying oxidative stress biomarkers and the arising opportunities and obstacles observed in research on biomarkers in rice. The major issue in incorporating bioinformatics to validate the biomarkers from different omic platforms for the use of rice-breeding programs is also discussed. The development of powerful techniques for identification of oxidative stress-related biomarkers and the integration of data from different disciplines shed light on the oxidative response pathways in plants.

The role of plant Bax inhibitor-1 in suppressing H2O2-induced cell death

Hydrogen peroxide (H2O2) is known to be a typical endogenous signaling molecule that triggers programmed cell death in plants and metazoan. In this respect, they seem to share the mechanism of cell death caused by H2O2 and other reactive oxygen species (ROS). Bax inhibitor-1 (BI-1) is a well-conserved protein in plants and animals that serves as the inhibitor of mammalian proapoptotic proteins as well as plant ROS-induced cell death. As a target of H2O2, mitochondrion is considered to be an organelle of the primary ROS generation and perception. Thus, analysis of mitochondrial behavior in relation to functional roles of regulatory proteins (e.g., BI-1) will lead us to understand the core mechanisms of cell death regulation conserved in eukaryotes. In this chapter, we first introduce techniques of analyzing H2O2- (and ROS-) mediated changes in mitochondrial behavior. Next, we describe our understanding of the functions of plant BI-1 in regulation of ROS-induced cell death, with a technical basis for assessment of tolerance to ROS-mediated cell death in model plant systems.

The use of metabolomics to dissect plant responses to abiotic stresses

Plant metabolism is perturbed by various abiotic stresses. As such the metabolic network of plants must be reconfigured under stress conditions in order to allow both the maintenance of metabolic homeostasis and the production of compounds that ameliorate the stress. The recent development and adoption of metabolomics and systems biology approaches enable us not only to gain a comprehensive overview, but also a detailed analysis of crucial components of the plant metabolic response to abiotic stresses. In this review we introduce the analytical methods used for plant metabolomics and describe their use in studies related to the metabolic response to water, temperature, light, nutrient limitation, ion and oxidative stresses. Both similarity and specificity of the metabolic responses against diverse abiotic stress are evaluated using data available in the literature. Classically discussed stress compounds such as proline, γ-amino butyrate and polyamines are reviewed, and the widespread importance of branched chain amino acid metabolism under stress condition is discussed. Finally, where possible, mechanistic insights into metabolic regulatory processes are discussed.

Changes in the contents of metabolites and enzyme activities in rice plants responding to Rhizoctonia solani Kuhn infection: activation of glycolysis and connection to phenylpropanoid pathway

Rhizoctonia solani Kuhn causes sheath blight disease in rice, and genetic resistance against it is the most desirable characteristic. Current improvement efforts are based on analysis of polygenic quantitative trait loci (QTLs), but interpretation is limited by the lack of information on the changes in metabolic pathways. Our previous studies linked activation of the glycolytic pathway to enhanced generation of lignin in the phenylpropanoid pathway. The current studies investigated the regulation of glycolysis by examining the time course of changes in enzymatic activities and metabolite contents. The results showed that the activities of all glycolytic enzymes as well as fructose-6-phosphate (F-6-P), fructose-1,6-bisphosphate (F-1,6-P(2)), dihydroxyacetone phosphate (DHAP), glyceraldehyde-3-phosphate (GAP), 3-phosphoglycerate (3-PG), phosphoenolpyruvate (PEP) and pyruvate contents increased. These results combined with our previous findings that the expression of phosphoglucomutase (PGM), triosephosphate isomerase (TPI), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), enolase and pyruvate kinase (PK) increased after infection suggested that the additional establishment of glycolysis in the cytosol compartment occurred after infection. Further evidence for this was our recent findings that the increase in expression of the 6-phosphofructokinase (PFK) plastid isozyme Os06g05860 was accompanied by an increase in expression of three cytosolic PFK isozymes, i.e. Os01g09570, Os01g53680 and Os04g39420, as well as pyrophosphate-dependent phosphofrucokinase (PFP) isozymes Os08g25720 (α-subunit) and Os06g13810 (β-subunit) in infected rice plants of the resistant line. The results also showed that the reactions catalysed by PFK/PFP, aldolase, GAPDH + phosphoglycerate kinase (PGK) and PK in leaf sheaths of R. solani-infected rice plants were non-equilibrium reactions in vivo. This study showed that PGM, phosphoglucose isomerase (PGI), TPI and phosphoglycerate mutase (PGmu) + enolase could be regulated through coarse control whereas, PFK/PFP, aldolase, GAPDH + PGK and PK could be regulated through coarse and fine controls simultaneously.

Chemical PARP inhibition enhances growth of Arabidopsis and reduces anthocyanin accumulation and the activation of stress protective mechanisms

Poly-ADP-ribose polymerase (PARP) post-translationally modifies proteins through the addition of ADP-ribose polymers, yet its role in modulating plant development and stress responses is only poorly understood. The experiments presented here address some of the gaps in our understanding of its role in stress tolerance and thereby provide new insights into tolerance mechanisms and growth. Using a combination of chemical and genetic approaches, this study characterized phenotypes associated with PARP inhibition at the physiological level. Molecular analyses including gene expression analysis, measurement of primary metabolites and redox metabolites were used to understand the underlying processes. The analysis revealed that PARP inhibition represses anthocyanin and ascorbate accumulation under stress conditions. The reduction in defense is correlated with enhanced biomass production. Even in unstressed conditions protective genes and molecules are repressed by PARP inhibition. The reduced anthocyanin production was shown to be based on the repression of transcription of key regulatory and biosynthesis genes. PARP is a key factor for understanding growth and stress responses of plants. PARP inhibition allows plants to reduce protection such as anthocyanin, ascorbate or Non-Photochemical-Quenching whilst maintaining high energy levels likely enabling the observed enhancement of biomass production under stress, opening interesting perspectives for increasing crop productivity.