Search

Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem-environment barrier called the periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied at higher resolution. We dissected the stem of silver birch (Betula pendula) into eight major tissue types, and characterized these by a combined transcriptomics and metabolomics approach. We further analyzed the varying bark types within the Betulaceae family. The two meristems had a distinct contribution to the stem transcriptomic landscape. Furthermore, inter- and intraspecies analyses illustrated the unique molecular profile of the phellem. We identified multiple tissue-specific metabolic pathways, such as the mevalonate/betulin biosynthesis pathway, that displayed differential evolution within the Betulaceae. A detailed analysis of suberin and betulin biosynthesis pathways identified a set of underlying regulators and highlighted the important role of local, small-scale gene duplication events in the evolution of metabolic pathways. This work reveals the transcriptome and metabolic diversity among bark tissues and provides insights to its development and evolution, as well as its biotechnological applications. Published version

The Arabidopsis mutant rcd1 is tolerant to methyl viologen (MV). MV enhances the Mehler reaction, i.e. electron transfer from Photosystem I (PSI) to O2, generating reactive oxygen species (ROS) in the chloroplast. To study the MV tolerance of rcd1, we first addressed chloroplast thiol redox enzymes potentially implicated in ROS scavenging. NADPH-thioredoxin oxidoreductase type C (NTRC) was more reduced in rcd1. NTRC contributed to the photosynthetic and metabolic phenotypes of rcd1, but did not determine its MV tolerance. We next tested rcd1 for alterations in the Mehler reaction. In rcd1, but not in the wild type, the PSI-to-MV electron transfer was abolished by hypoxic atmosphere. A characteristic feature of rcd1 is constitutive expression of mitochondrial dysfunction stimulon (MDS) genes that affect mitochondrial respiration. Similarly to rcd1, in other MDS-overexpressing plants hypoxia also inhibited the PSI-to-MV electron transfer. One possible explanation is that the MDS gene products may affect the Mehler reaction by altering the availability of O2. In green tissues, this putative effect is masked by photosynthetic O2 evolution. However, O2 evolution was rapidly suppressed in MV-treated plants. Transcriptomic meta-analysis indicated that MDS gene expression is linked to hypoxic response not only under MV, but also in standard growth conditions. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.

A comparative transcriptomic study and a single-cell metabolome analysis were combined to determine whether parenchymal ray cells contribute to the biosynthesis of monolignols in the lignifying xylem of Norway spruce (Picea abies). Ray parenchymal cells may function in the lignification of upright tracheids by supplying monolignols. To test this hypothesis, parenchymal ray cells and upright tracheids were dissected with laser-capture microdissection from tangential cryosections of developing xylem of spruce trees. The transcriptome analysis revealed that among the genes involved in processes typical for vascular tissues, genes encoding cell wall biogenesis-related enzymes were highly expressed in both developing tracheids and ray cells. Interestingly, most of the shikimate and monolignol biosynthesis pathway-related genes were equally expressed in both cell types. Nonetheless, 1,073 differentially expressed genes were detected between developing ray cells and tracheids, among which a set of genes expressed only in ray cells was identified. In situ single cell metabolomics of semi-intact plants by picoliter pressure probe-electrospray ionization-mass spectrometry detected monolignols and their glycoconjugates in both cell types, indicating that the biosynthetic route for monolignols is active in both upright tracheids and parenchymal ray cells. The data strongly support the hypothesis that in developing xylem, ray cells produce monolignols that contribute to lignification of tracheid cell walls. Transcriptomics combined with single-cell metabolomics give new information on the role of rays in lignification of developing xylem in Norway spruce.

Six potato cultivars grown in Turkey in boron-prone areas and differing in their tolerance towards high boron were studied to reveal whether boron causes oxidative stress. To assess stress level, chlorophyll fluorescence and growth parameters were measured. Oxidative damage was assessed as malondialdehyde level, and antioxidant protection was evaluated as ascorbate (AA), dehydroascorbate, reduced glutathione (GSH) and oxidized glutathione amounts and superoxide dismutase, catalase, ascorbate peroxidase (APX) and glutathione reductase (GR) activities. High boron stress affected photosynthesis negatively in a threshold-dependent manner and inhibited growth. No pronounced changes in oxidation of lipids occurred in any cultivar. Activation of APX suggested the involvement of an ascorbic acid–reduced glutathione cycle in the protection against oxidative stress caused by high boron. Efficient work of this antioxidant system was probably hindered by boron complexation with NAD(P)+/NAD(P)H and resulted in...

Organellar reactive oxygen species (ROS) signalling is a key mechanism that promotes the onset of defensive measures in stress-exposed plants. The underlying molecular mechanisms and feedback regulation loops, however, still remain poorly understood. Our previous work has shown that a specific regulatory B'γ subunit of protein phosphatase 2A (PP2A) is required to control organellar ROS signalling and associated metabolic adjustments in Arabidopsis thaliana. Here, we addressed the mechanisms through which PP2A-B'γ impacts on organellar metabolic crosstalk and ROS homeostasis in leaves. Genetic, biochemical and pharmacological approaches, together with a combination of data-dependent acquisition (DDA) and selected reaction monitoring (SRM) MS techniques, were utilized to assess PP2A-B'γ-dependent adjustments in Arabidopsis thaliana. We show that PP2A-B'γ physically interacts with the cytoplasmic form of aconitase, a central metabolic enzyme functionally connected with mitochondrial respiration, oxidative stress responses and regulation of cell death in plants. Furthermore, PP2A-B'γ impacts ROS homeostasis by controlling the abundance of specific alternative oxidase isoforms, AOX1A and AOX1D, in leaf mitochondria. We conclude that PP2A-B'γ-dependent regulatory actions modulate the functional status of metabolic enzymes that essentially contribute to intracellular ROS signalling and metabolic homeostasis in plants.

Previous reports have connected non-symbiotic and truncated hemoglobins (Hbs) to metabolism of nitric oxide (NO), an important signalling molecule involved in wood formation. We have studied the capability of poplar (Populus tremula × tremuloides) Hbs PttHb1 and PttTrHb proteins alone or with a flavin-protein reductase to relieve NO cytotoxicity in living cells. Complementation tests in a Hb-deficient, NO-sensitive yeast (Saccharomyces cerevisiae) Δyhb1 mutant showed that neither PttHb1 nor PttTrHb alone protected cells against NO. To study the ability of Hbs to interact with a reductase, ferredoxin NADP(+) oxidoreductase PtthFNR was characterized by sequencing and proteomics. To date, by far the greatest number of the known dual-targeted plant proteins are directed to chloroplasts and mitochondria. We discovered a novel variant of hFNR that lacks the plastid presequence and resides in cytosol. The coexpression of PttHb1 and PtthFNR partially restored NO resistance of the yeast Δyhb1 mutant, whereas PttTrHb coexpressed with PtthFNR failed to rescue growth. YFP fusion proteins confirmed the interaction between PttHb1 and PtthFNR in plant cells. The structural modelling results indicate that PttHb1 and PtthFNR are able to interact as NO dioxygenase. This is the first report on dual targeting of central plant enzyme FNR to plastids and cytosol.

Oxygen deprivation, in line with other stress conditions, is accompanied by reactive oxygen (ROS) and nitrogen species (RNS) formation and is characterised by a set of metabolic changes collectively named as the 'oxidative stress response'. The controversial induction of oxidative metabolism under the lack of oxygen is necessitated by ROS and RNS signaling in the induction of adaptive responses, and inevitably results in oxidative damage. To prevent detrimental effects of oxidative stress, the levels of ROS and NO are tightly controlled on transcriptional, translational and metabolic levels. Hypoxia triggers the induction of genes responsible for ROS and NO handling and utilization (respiratory burst oxidase, non-symbiotic hemoglobins, several cytochromes P450, mitochondrial dehydrogenases, and antioxidant-related transcripts). The level of oxygen in the tissue is also under metabolic control via multiple mechanisms: Regulation of glycolytic and fermentation pathways to manage pyruvate availability for respiration, and adjustment of mitochondrial electron flow through NO and ROS balance. Both adaptive strategies are controlled by energy status and aim to decrease the respiratory capacity and to postpone complete anoxia. Besides local oxygen concentration, ROS and RNS formation is controlled by an array of antioxidants. Hypoxic treatment leads to the upregulation of multiple transcripts associated with ascorbate, glutathione and thioredoxin metabolism. The production of ROS and NO is an integral part of the response to oxygen deprivation which encompasses several levels of metabolic regulation to sustain redox signaling and to prevent oxidative damage.

Plant mitochondria differ from their mammalian counterparts in many respects, which are due to the unique and variable surroundings of plant mitochondria. In green leaves, plant mitochondria are surrounded by ample respiratory substrates and abundant molecular oxygen, both resulting from active photosynthesis, while in roots and bulky rhizomes and fruit carbohydrates may be plenty, whereas oxygen levels are falling. Several enzymatic complexes in mitochondrial electron transport chain (ETC) are capable of reactive oxygen species (ROS) formation under physiological and pathological conditions. Inherently connected parameters such as the redox state of electron carriers in the ETC, ATP synthase activity and inner mitochondrial membrane potential, when affected by external stimuli, can give rise to ROS formation via complexes I and III, and by reverse electron transport (RET) from complex II. Superoxide radicals produced are quickly scavenged by superoxide dismutase (MnSOD), and the resulting H(2)O(2) is detoxified by peroxiredoxin-thioredoxin system or by the enzymes of ascorbate-glutathione cycle, found in the mitochondrial matrix. Arginine-dependent nitric oxide (NO)-releasing activity of enzymatic origin has been detected in plant mitochondria. The molecular identity of the enzyme is not clear but the involvement of mitochondria-localized enzymes responsible for arginine catabolism, arginase and ornithine aminotransferase has been shown in the regulation of NO efflux. Besides direct control by antioxidants, mitochondrial ROS production is tightly controlled by multiple redundant systems affecting inner membrane potential: NAD(P)H-dependent dehydrogenases, alternative oxidase (AOX), uncoupling proteins, ATP-sensitive K(+) channel and a number of matrix and intermembrane enzymes capable of direct electron donation to ETC. NO removal, on the other hand, takes place either by reactions with molecular oxygen or superoxide resulting in peroxynitrite, nitrite or nitrate ions or through interaction with non-symbiotic hemoglobins or glutathione. Mitochondrial ROS and NO production is tightly controlled by multiple redundant systems providing the regulatory mechanism for redox homeostasis and specific ROS/NO signaling.

Organellar reactive oxygen species (ROS) signalling is a key mechanism that promotes the onset of defensive measures in stress-exposed plants. The underlying molecular mechanisms and feedback regulation loops, however, still remain poorly understood. Our previous work has shown that a specific regulatory B'γ subunit of protein phosphatase 2A (PP2A) is required to control organellar ROS signalling and associated metabolic adjustments in Arabidopsis thaliana. Here, we addressed the mechanisms through which PP2A-B'γ impacts on organellar metabolic crosstalk and ROS homeostasis in leaves. Genetic, biochemical and pharmacological approaches, together with a combination of data-dependent acquisition (DDA) and selected reaction monitoring (SRM) MS techniques, were utilized to assess PP2A-B'γ-dependent adjustments in Arabidopsis thaliana. We show that PP2A-B'γ physically interacts with the cytoplasmic form of aconitase, a central metabolic enzyme functionally connected with mitochondrial respiration, oxidative stress responses and regulation of cell death in plants. Furthermore, PP2A-B'γ impacts ROS homeostasis by controlling the abundance of specific alternative oxidase isoforms, AOX1A and AOX1D, in leaf mitochondria. We conclude that PP2A-B'γ-dependent regulatory actions modulate the functional status of metabolic enzymes that essentially contribute to intracellular ROS signalling and metabolic homeostasis in plants.

Hydrogen peroxide (H 2 O 2 ) was detected cytochemically in plant tissues during anoxia and re-oxygenation by transmission electron microscopy using its reaction with cerium chloride to produce electron dense precipitates of cerium perhydroxides. Anoxia-tolerant yellow flag iris (Iris pseudacorus) and rice (Oryza sativa), and anoxia-intolerant wheat (Triticum aestivum) and garden iris (Iris germanica) were used in the experiments. In all plants tested, anoxia and re-oxygenation increased H 2 O 2 in plasma membranes and the apoplast. In the anoxia-tolerant species the response was delayed in time, and in highly tolerant I. pseudacorus plasma membrane associated H 2 O 2 was detected only after 45 d of oxygen deprivation. Quantification of cerium precipitates showed a statistically significant increase in the amount of H 2 O 2 caused by anoxia in wheat root meristematic tissue, but not in the anoxia-tolerant I. pseudacorus rhizome parenchyma. Formation of H 2 O 2 under anoxia is considered mainly an enzymatic process (confirmed by an enzyme inhibition analysis) and is due to the trace amount of dissolved oxygen (below 10 - 5 M) present in the experimental system. The data suggest oxidative stress is an integral part of oxygen deprivation stress, and emphasize the importance of the apoplast and plasma membrane in the development of the anoxic stress response.

Global gene expression data were analyzed to search for the genes related to oxidative stress response, to examine the differences between hypoxia and anoxia, and to reveal new components of oxygen deprivation response escaped from the previous analyses. Gene Set Z-score (GSZ) was used to report gene ontology (GO) classes that showed significant regulation and also partial up- and downregulation in Arabidopsis anoxic and hypoxic microarray data sets. Under both anoxia and hypoxia significant upregulation was reported for anaerobic respiration, response to low oxygen levels, and response to hypoxia. Comparable high GSZ scores were shown for several oxidative stress-related GO classes and for functional groups of biological processes known to involve oxygen radical formation such as: cellular respiration, wounding, and response to high light and UV-B. Availability of oxygen in hypoxic experimental sets was marked by upregulation of several oxygenases, including ACC-oxidase responsible for ethylene synthesis. Consistent strong induction of several Fe-dependent ketoglutarate oxygenases (FeKGO) in the majority of hypoxic conditions analyzed suggests an important and yet unidentified function for these enzymes. Based on metabolic and gene expression studies we suggest that FeKGO may function in a bypass route for part of the TCA cycle (citrate-isocitrate) inhibited under hypoxia. This would incorporate 2-ketoglutarate supplied by activated GABA shunt and form succinate, a TCA cycle and mitochondrial electron transport chain substrate. FeKGO turnover is sustained by the putative route coupled to ascorbate–monodehydroascorbate cycling and hemoglobin-dependent NO elimination. The analysis strongly supports earlier findings that formation of activated oxygen and oxidative stress is an integral part of the response to oxygen deprivation. Several novel functional gene groups were highlighted by the analysis: upregulation of cysteamine dioxygenase activity and FeKGO and downregulation of circadian rhythm-related genes.

Numerous investigations link oxidative damage with differ-ent environmental and biotic stresses, such as heavy metalstress (Howlett and Avery 1997), ice encasement (Hethering-ton et al. 1987), senescence (Gidrol et al. 1989), salt stress(Guetadahan et al. 1997), anoxia (Chirkova et al. 1998), andthe hypersensitive response (Goodman 1994). Oxidativedamage can be detected by lipid peroxidation (LP), which isa natural metabolic process under normal conditions. It canbe divided into three stages: initiation, propagation, andtermination (Schiach 1992, Shewfelt and Purvis 1995). Theinitiation phase includes generation of reactive oxygen spe-cies (ROS) such as the superoxide anion, hydrogen peroxide,singlet oxygen, or the hydroxyl radical. ROS are byproductsof electron transport in chloroplasts, mitochondria, andplasma membranes (Elstner 1987). The imposition of stressresults in the elevation of ROS levels (Foyer et al. 1994,Alscher et al. 1997) and successively leads to lipid peroxida-tion and degradation. Polyunsaturated fatty acids (PUFA,the main components of membrane lipids) are susceptible toperoxidation as substrates. Hydroxyl radicals and singletoxygen can react with the methylene groups of PUFAforming conjugated dienes, lipid peroxy radicals, and hy-droperoxides (Smirnoff 1995). The peroxy radicals can in-volve new molecules of PUFA in the process thus initiatingthe propagation phase (Frankel 1985).For each stage of this free radical chain reaction, plantcells have a defense system eliminating ROS and toxicproducts of LP (Buettner 1993, Smirnoff 1995). Undersevere stress conditions, elevated levels of free radicals canbreak down the defense mechanisms of the cell.However, until now it is not quite clear whether peroxida-tion can be considered a cause of membrane damage andmetabolic disorders, or a secondary effect of these processes.This problem arises from controversial observations con-cerning the mechanisms and products of LP in plant tissues.Recently, a new comprehensive model for lipid peroxidationin plant tissues has been developed (Shewfelt and Purvis1995). This model emphasizes the importance of chemicalrather than biochemical processes in the oxidative stress.Free radicals are regarded as a common link between many

In this chapter, we discuss the metabolic changes relevant for the production of reactive oxygen and nitrogen species (ROS and RNS) in plant tissues during oxygen deprivation. It is notable too, that at times the oxidative damage does not take place during the oxygen deficiency period but only after the restoration of normal oxygen supply to the tissues. This is mainly due to the fact that ROS may be formed immediately after oxygen re-enters the tissues. The level of oxygen in the tissues naturally depends on the outside concentration and diffusion rate but is also under metabolic control. Two hypotheses on the regulation of internal O2 concentration in the cells through the control of respiration rely on a regulation of glycolytic pathway and pyruvate availability and mitochondrial electron transport chain by NO and ROS balance. Both adaptive strategies aim to decrease the respiratory capacity and to postpone complete anoxia. This chapter also describes the interaction of the many antioxidants found in plant tissues and oxidative stress and oxidative damage caused by waterlogging and oxygen deprivation. If the antioxidative protection is still capable of detoxifying the ROS formed, damage is minimal, but if not, then considerable damage can take place very suddenly. Many of the ROS and RNS species act as signalling agents acting in the regulation of metabolic events leading to tolerance or, e.g. in the case of aerenchyma development, into programmed cell death. The balance between O2 transport to hypoxic tissues, regulatory adaptations, anoxic metabolites, ROS–RNS chemistry and signalling, determines the survival of plants under waterlogging and oxygen deprivation.

Oxidative stress is induced by a wide range of environmental factors including UV stress, pathogen invasion (hypersensitive reaction), herbicide action and oxygen shortage. Oxygen deprivation stress in plant cells is distinguished by three physiologically different states: transient hypoxia, anoxia and reoxygenation. Generation of reactive oxygen species (ROS) is characteristic for hypoxia and especially for reoxygenation. Of the ROS, hydrogen peroxide (H(2)O(2)) and superoxide (O(2)(.-)) are both produced in a number of cellular reactions, including the iron-catalysed Fenton reaction, and by various enzymes such as lipoxygenases, peroxidases, NADPH oxidase and xanthine oxidase. The main cellular components susceptible to damage by free radicals are lipids (peroxidation of unsaturated fatty acids in membranes), proteins (denaturation), carbohydrates and nucleic acids. Consequences of hypoxia-induced oxidative stress depend on tissue and/or species (i.e. their tolerance to anoxia), on membrane properties, on endogenous antioxidant content and on the ability to induce the response in the antioxidant system. Effective utilization of energy resources (starch, sugars) and the switch to anaerobic metabolism and the preservation of the redox status of the cell are vital for survival. The formation of ROS is prevented by an antioxidant system: low molecular mass antioxidants (ascorbic acid, glutathione, tocopherols), enzymes regenerating the reduced forms of antioxidants, and ROS-interacting enzymes such as SOD, peroxidases and catalases. In plant tissues many phenolic compounds (in addition to tocopherols) are potential antioxidants: flavonoids, tannins and lignin precursors may work as ROS-scavenging compounds. Antioxidants act as a cooperative network, employing a series of redox reactions. Interactions between ascorbic acid and glutathione, and ascorbic acid and phenolic compounds are well known. Under oxygen deprivation stress some contradictory results on the antioxidant status have been obtained. Experiments on overexpression of antioxidant production do not always result in the enhancement of the antioxidative defence, and hence increased antioxidative capacity does not always correlate positively with the degree of protection. Here we present a consideration of factors which possibly affect the effectiveness of antioxidant protection under oxygen deprivation as well as under other environmental stresses. Such aspects as compartmentalization of ROS formation and antioxidant localization, synthesis and transport of antioxidants, the ability to induce the antioxidant defense and cooperation (and/or compensation) between different antioxidant systems are the determinants of the competence of the antioxidant system.

Under stress conditions, mitochondria sense metabolic changes, e.g. in pH, cytoplasmic Ca 2+ , energy status, and reactive oxygen species (ROS), and respond by induction of the permeability transition pore (PTP) and by releasing cytochrome c, thus initiating the programmed cell death (PCD) cascade in animal cells. In plant cells, the presence of all the components of the cascade has not yet been shown. In wheat (Triticum aestivum L.) root mitochondria, the onset of anoxia caused rapid dissipation of the inner membrane potential, initial shrinkage of the mitochondrial matrix and the release of previously accumulated Ca 2+ .C a 2+ uptake by mitochondria was dependent on the presence of inorganic phosphate. Treatment of mitochondria with high micromolar and millimolar Ca 2+ (but not Mg 2+ ) concentrations induced high amplitude swelling, indicative of PTP opening. Alterations in mitochondrial volume were confirmed by transmission electron microscopy. Mitochondrial swelling was not sensitive to cyclosporin A (CsA)—an inhibitor of mammalian PTP. The release of cytochrome c was monitored under lack of oxygen. Anoxia alone failed to induce cytochrome c release from mitochondria. Oxygen deprivation and Ca2+ ions together caused cytochrome c release in a CsA-insensitive manner. This process correlated positively with Ca2+ concentration and required Ca2+ localization in the mitochondrial matrix. Functional characteristics of wheat root mitochondria, such as membrane potential, Ca2+ transport, swelling, and cytochrome c release under lack of oxygen are discussed in relation to PCD.a 2002 Annals of Botany Company

The redox potential of the cell, as well as the antioxidant status of the tissue, are considered to be important regulatory constituents in an adaptive response in plants. Here the involvement of active antioxidants ascorbic acid (AA), reduced glutathione (GSH) and α- and β-tocopherols in reactive oxygen species scavenging, and the effect of anoxic stress on their reduction state were studied in 4 anoxia-tolerant and -intolerant plant species: Iris germanica L., Iris pseudacorus L., wheat (Triticum aestivum L. cv. Leningradka) and rice (Oryza sativa L. cv. VNIIR). The initial antioxidant content (both AA and GSH) was higher in the rhizomes of the more anoxia-tolerant Iris spp., as compared with that of the roots of the cereals. The predominant form of ascorbate was dehydroascorbic acid (DHA) in the cereals and AA in the Iris spp. Imposition of anoxia with subsequent reoxygenation resulted in an overall depletion of the reduced forms of antioxidants. No concurrent increase in oxidised forms (DHA and conjugated glutathione) was observed in anoxic samples. «-tocopherol content in Iris spp. was in the range 1-2 μg g -1 fresh weight, while β-tocopherol content was higher in the anoxia-intolerant I. germanica (7.2 μg g -1 fresh weight) as compared with the tolerant I. pseudacorus (1.5 μg g -1 fresh weight). In I. pseudacorus, a significant decrease in α- and β-tocopherol levels was observed only after long-term (45 days) anoxia. The results suggested exclusion of AA and GSH from the redox cycling under prolonged anoxia, and a concomitant decrease in the redox state, as well as an anoxia-induced depletion of α- and β-tocopherols.