The importance of worldwide linguistic and cultural diversity for climate change resilience

Local minority languages and dialects, through the local knowledge and expertise associated with them, can play major roles in analysing climate change and biodiversity loss, in facilitating community awareness of environmental crises and in setting up locally-adapted resilience and sustainability strategies. While the situation and contribution of Indigenous and Tribal Peoples are of emblematic importance, the issue of the relationships between cultural and linguistic diversity and environmental awareness and protection does not solely concern peripheral highly-specialized communities in specific ecosystems of the Global South, but constitutes a worldwide challenge, throughout all of the countries, whatever their geographical location, their economical development, or their political status. Environmental emergency and climate change resilience should therefore raise international awareness on the need to promote the survival and development of minority languages and dialects and to take into account their creativity and expertise in relation to the dynamics of their local environments.

Perspectives in Plant Abiotic Stress Signaling

State-of-the-art collections of strategies, approaches, and methods are immediately useful for ongoing characterizations or for novel discoveries in the scientific field of plant abiotic stress signaling. It must however be kept in mind that, in the future, these strategies, approaches, and methods will be facing a number of increasingly complex issues. The development of the necessary confrontation of laboratory-based knowledge on abiotic stress signaling mechanisms with real-life in natura situations of plant-stress interactions involves at least five levels of complexity: (i) plant biodiversity, (ii) the spatio-temporal heterogeneity of stress-related parameters, (iii) the unknowns of future stress-related constraints, (iv) the influence of biotic interactions, (v) the crosstalk between various signaling pathways and their final integration into physiological responses. These complexities are major bottlenecks for assessing the evolutionary, ecological, and agronomical relevance of abiotic stress signaling studies. All of the presently-described strategies, approaches, and methods will have to be gradually complemented with the development of real-time and in natura tools, with systematic application of mathematical modeling to complex interactions and with further research on the impact of stress memory mechanisms on long-term responses.

Interplay of Methodology and Conceptualization in Plant Abiotic Stress Signaling

Characterizing the mechanisms of plant sensitivity and reactivity to physicochemical cues related to abiotic stresses is of utmost importance for understanding plant-environment interactions, adaptations of the sessile lifestyle, and the evolutionary dynamics of plant species and populations. Moreover, plant communities are confronted with an environmental context of global change, involving climate changes, planetary pollutions of soils, waters and atmosphere, and additional anthropogenic changes. The mechanisms through which plants perceive abiotic stress stimuli and transduce stress perception into physiological responses constitute the primary line of interaction between the plant and the environment, and therefore between the plant and global changes. Understanding how plants perceive complex combinations of abiotic stress signals and transduce the resulting information into coordinated responses of abiotic stress tolerance is therefore essential for devising genetic, agricultural, and agroecological strategies that can ensure climate change resilience, global food security, and environmental protection. Discovery and characterization of sensing and signaling mechanisms of plant cells are usually carried out within the general framework of eukaryotic sensing and signal transduction. However, further progress depends on a close relationship between the conceptualization of sensing and signaling processes with adequate methodologies and techniques that encompass biochemical and biophysical approaches, cell biology, molecular biology, and genetics. The integration of subcellular and cellular analyses as well as the integration of in vitro and in vivo analyses are particularly important to evaluate the efficiency of sensing and signaling mechanisms in planta. Major progress has been made in the last 10-20 years with the caveat that cell-specific processes and in vivo processes still remain difficult to analyze and with the additional caveat that the range of plant models under study remains rather limited relatively to plant biodiversity and to the diversity of stress situations.

Protein-Protein Interactions in Abiotic Stress Signaling: An Overview of Biochemical and Biophysical Methods of Characterization

The identification and characterization of bona fide abiotic stress signaling proteins can occur at different levels of the complete in vivo signaling cascade or network. Knowledge of a particular abiotic stress signaling protein could theoretically lead to the characterization of complete networks through the analysis of unknown proteins that interact with the previously known protein. Such signaling proteins of interest can indeed be experimentally used as bait proteins to catch interacting prey proteins, provided that the association of bait proteins and prey proteins should yield a biochemical or biophysical signal that can be detected. To this end, several biochemical and biophysical techniques are available to provide experimental evidence for specific protein-protein interactions, such as co-immunoprecipitation, bimolecular fluorescence complementation, tandem affinity purification coupled to mass spectrometry, yeast two hybrid, protein microarrays, Förster resonance energy transfer, or fluorescence correlation spectroscopy. This array of methods can be implemented to establish the biochemical reality of putative protein-protein interactions between two proteins of interest or to identify previously unknown partners related to an initially known protein of interest. The ultimate validity of these methods however depends on the in vitro/in vivo nature of the approach and on the heterologous/homologous context of the analysis. This chapter will review the application and success of some classical methods of protein-protein interaction analysis in the field of plant abiotic stress signaling.

How does interspecific competition modify the response of grass plants against herbicide treatment? A hierarchical concentration-response approach

Ecological interactions are rarely taken into account in environmental risk assessment. The objective of this work was to assess how interspecific competition affects the way plant species react to herbicides and more specifically how it modifies the concentration-response curves that can be built using ecotoxicological bioassays. To do this, we relied on the results of ecotoxicological bioassays on six herbaceous species exposed to isoproturon under two conditions: in presence and in absence of a competitor. At the end of the experiments, eleven endpoints were measured. We modelled these data using a hierarchical modelling framework designed to assess the effects of competition on each of the four parameters of the concentration response curves (e.g. the level of response at the control or the concentration at the inflection point of the curve) simultaneously for the six species. The modelled effects could be of three types, 1) competition had no effect on the parameter, 2) competition had the same effect on the parameter for all species and 3) competition had a different effect on the parameter for each species. Our main hypothesis was that different species would react differently to competition. Results showed that about a half of the estimated parameters showed a modification under competition pressure among which only a fourth showed a species-specific effect, the three other fourth showing the same effect between the different species. Our initial hypothesis was thus not supported as species tended to react in the same way to competition. The competition effect on plants was mainly negative, thus showing that they were more affected by isoproturon under competition pressure. This study therefore establishes how competition modifies plant responses to chemical stress and how this interaction varies from one species to the other.

Local-scale dynamics of plant-pesticide interactions in a northern Brittany agricultural landscape

Soil pollution by anthropogenic chemicals is a major concern for sustainability of crop production and of ecosystem functions mediated by natural plant biodiversity. Understanding the complex effects of soil pollution requires multi-level and multi-scale approaches. Non-target and agri-environmental plant communities of field margins and vegetative filter strips are confronted with agricultural xenobiotics through soil contamination, drift, run-off and leaching events that result from chemical applications. Plant-pesticide dynamics in vegetative filter strips was studied at field scale in the agricultural landscape of a long-term ecological research network in northern Brittany (France). Vegetative filter strips effected significant pesticide abatement between the field and riparian compartments. However, comparison of pesticide usage modalities and soil chemical analysis revealed the extent and complexity of pesticide persistence in fields and vegetative filter strips, and suggested the contribution of multiple sources (yearly carry-over, interannual persistence, landscape-scale contamination). In order to determine the impact of such persistence, plant dynamics was followed in experimentally-designed vegetative filter strips of identical initial composition (Agrostis stolonifera, Anthemis tinctoria/Cota tinctoria, Centaurea cyanus, Fagopyrum esculentum, Festuca rubra, Lolium perenne, Lotus corniculatus, Phleum pratense, Trifolium pratense). After homogeneous vegetation establishment, experimental vegetative filter strips underwent rapid changes within the following two years, with Agrostis stolonifera, Festuca rubra, Lolium perenne and Phleum pratense becoming dominant and with the establishment of spontaneous vegetation. Co-inertia analysis showed that plant dynamics and soil residual pesticides could be significantly correlated, with the triazole fungicide epoxiconazole, the imidazole fungicide prochloraz and the neonicotinoid insecticide thiamethoxam as strong drivers of the correlation. However, the correlation was vegetative-filter-strip-specific, thus showing that correlation between plant dynamics and soil pesticides likely involved additional factors, such as threshold levels of residual pesticides. This situation of complex interactions between plants and soil contamination is further discussed in terms of agronomical, environmental and health issues.

Abiotic stress signalling in extremophile land plants

Plant life relies on complex arrays of environmental stress sensing and signalling mechanisms. Extremophile plants develop and grow in harsh environments with extremes of cold, heat, drought, desiccation, or salinity, which have resulted in original adaptations. In accordance with their polyphyletic origins, extremophile plants likely possess core mechanisms of plant abiotic stress signalling. However, novel properties or regulations may have emerged in the context of extremophile adaptations. Comparative omics of extremophile genetic models, such as Arabidopsis lyrata, Craterostigma plantagineum, Eutrema salsugineum, and Physcomitrella patens, reveal diverse strategies of sensing and signalling that lead to a general improvement in abiotic stress responses. Current research points to putative differences of sensing and emphasizes significant modifications of regulatory mechanisms, at the level of secondary messengers (Ca2+, phospholipids, reactive oxygen species), signal transduction (intracellular sensors, protein kinases, transcription factors, ubiquitin-mediated proteolysis) or signalling crosstalk. Involvement of hormone signalling, especially ABA signalling, cell homeostasis surveillance, and epigenetic mechanisms, also shows that large-scale gene regulation, whole-plant integration, and probably stress memory are important features of adaptation to extreme conditions. This evolutionary and functional plasticity of signalling systems in extremophile plants may have important implications for plant biotechnology, crop improvement, and ecological risk assessment under conditions of climate change.

Effect of interspecific competition on species sensitivity distribution models: Analysis of plant responses to chemical stress

Species Sensitivity Distributions (SSD) are widely used in environmental risk assessment to predict the concentration of a contaminant that is hazardous for 5% of species (HC₅). They are based on monospecific bioassays conducted in the laboratory and thus do not directly take into account ecological interactions. This point, among others, is accounted for in environmental risk assessment through an assessment factor (AF) that is applied to compensate for the lack of environmental representativity. In this study, we aimed to assess the effects of interspecific competition on the responses towards isoproturon of plant species representative of a vegetated filter strip community, and to assess its impact on the derived SSD and HC₅ values. To do so, we realized bioassays confronting six herbaceous species to a gradient of isoproturon exposure in presence and absence of a competitor. Several modelling approaches were applied to see how they affected the results, using different critical effect concentrations and investigating different ways to handle multiple endpoints in SSD. At the species level, there was a strong trend toward organisms being more sensitive to isoproturon in presence of a competitor than in its absence. At the community level, this trend was also observed in the SSDs and HC₅ values were always lower in presence of a competitor (1.12-11.13 times lower, depending on the modelling approach). Our discussion questions the relevance of SSD and AF as currently applied in environmental risk assessment.

Restoring public trust in science with the help of the humanities

A thorough analysis of the underlying worldviews and anthropologies of science and the language it uses could help to maintain the rigour of science and public trust in research.

Stress signalling dynamics of the mitochondrial electron transport chain and oxidative phosphorylation system in higher plants

BACKGROUND

Mitochondria play a diversity of physiological and metabolic roles under conditions of abiotic or biotic stress. They may be directly subjected to physico-chemical constraints, and they are also involved in integrative responses to environmental stresses through their central position in cell nutrition, respiration, energy balance and biosyntheses. In plant cells, mitochondria present various biochemical peculiarities, such as cyanide-insensitive alternative respiration, and, besides integration with ubiquitous eukaryotic compartments, their functioning must be coupled with plastid functioning. Moreover, given the sessile lifestyle of plants, their relative lack of protective barriers and present threats of climate change, the plant cell is an attractive model to understand the mechanisms of stress/organelle/cell integration in the context of environmental stress responses.

SCOPE

The involvement of mitochondria in this integration entails a complex network of signalling, which has not been fully elucidated, because of the great diversity of mitochondrial constituents (metabolites, reactive molecular species and structural and regulatory biomolecules) that are linked to stress signalling pathways. The present review analyses the complexity of stress signalling connexions that are related to the mitochondrial electron transport chain and oxidative phosphorylation system, and how they can be involved in stress perception and transduction, signal amplification or cell stress response modulation.

CONCLUSIONS

Plant mitochondria are endowed with a diversity of multi-directional hubs of stress signalling that lead to regulatory loops and regulatory rheostats, whose functioning can amplify and diversify some signals or, conversely, dampen and reduce other signals. Involvement in a wide range of abiotic and biotic responses also implies that mitochondrial stress signalling could result in synergistic or conflicting outcomes during acclimation to multiple and complex stresses, such as those arising from climate change.

Species- and organ-specific responses of agri-environmental plants to residual agricultural pollutants

Soil pollution by anthropogenic chemicals is a major concern for sustainability of crop production and of ecosystem functions mediated by natural plant biodiversity. The complex effects on plants are however difficult to apprehend. Plant communities of field margins, vegetative filter strips or rotational fallows are confronted with agricultural pollutants through residual soil contamination and/or through drift, run-off and leaching events that result from chemical applications. Exposure to xenobiotics and heavy metals causes biochemical, physiological and developmental effects. However, the range of doses, modalities of exposure, metabolization of contaminants into derived xenobiotics, and combinations of contaminants result in variable and multi-level effects. Understanding these complex plant-pollutant interactions cannot directly rely on toxicological or agronomical approaches that focus on the effects of field-rate pesticide applications. It must take into account exposure at root level, sublethal concentrations of bioactive compounds and functional biodiversity of the plant species that are affected. The present study deals with agri-environmental plant species of field margins, vegetative filter strips or rotational fallows in European agricultural landscapes. Root and shoot physiological and growth responses were compared under controlled conditions that were optimally adjusted for each plant species. Contrasted responses of growth inhibition, no adverse effect or growth enhancement depended on species, organ and nature of contaminant. However, all of the agricultural contaminants under study (pesticides, pesticide metabolites, heavy metals, polycyclic aromatic hydrocarbons) had significant effects under conditions of sublethal exposure on at least some of the plant species. The fungicide tebuconazole and polycyclic aromatic hydrocarbon fluoranthene, which gave highest levels of responses, induced both activation or inhibition effects, in different plant species or in different organs of the same plant species. These complex effects are discussed in terms of dynamics of agri-environmental plants and of ecological consequences of differential root-shoot growth under conditions of soil contamination.

Involvement of polyamines in sucrose-induced tolerance to atrazine-mediated chemical stress in Arabidopsis thaliana

Treatment of Arabidopsis thaliana seedlings with the PSII-inhibiting herbicide atrazine results in xenobiotic and oxidative stress, developmental arrest, induction of senescence and cell death processes. In contrast, exogenous sucrose supply confers a high level of atrazine stress tolerance, in relation with genome-wide modifications of transcript levels and regulation of genes involved in detoxification, defense and repair. However, the regulation mechanisms related to exogenous sucrose, involved in this sucrose-induced tolerance, are largely unknown. Characterization of these mechanisms was carried out through a combination of transcriptomic, metabolic, functional and mutant analysis under different conditions of atrazine exposure. Exogenous sucrose was found to differentially regulate genes involved in polyamine synthesis. ARGININE DECARBOXYLASE ADC1 and ADC2 paralogues, which encode the rate-limiting enzyme (EC 4.1.1.19) of the first step of polyamine biosynthesis, were strongly upregulated by sucrose treatment in the presence of atrazine. Such regulation occurred concomitantly with significant changes of major polyamines (putrescine, spermidine, spermine). Physiological characterization of a mutant affected in ADC activity and exogenous treatments with sucrose, putrescine, spermidine and spermine further showed that modification of polyamine synthesis and of polyamine levels could play adaptive roles in response to atrazine stress, and that putrescine and spermine had antagonistic effects, especially in the presence of sucrose. This interplay between sucrose, putrescine and spermine is discussed in relation with survival and anti-death mechanisms in the context of chemical stress exposure.

Pivotal roles of environmental sensing and signaling mechanisms in plant responses to climate change

Climate change reshapes the physiology and development of organisms through phenotypic plasticity, epigenetic modifications, and genetic adaptation. Under evolutionary pressures of the sessile lifestyle, plants possess efficient systems of phenotypic plasticity and acclimation to environmental conditions. Molecular analysis, especially through omics approaches, of these primary lines of environmental adjustment in the context of climate change has revealed the underlying biochemical and physiological mechanisms, thus characterizing the links between phenotypic plasticity and climate change responses. The efficiency of adaptive plasticity under climate change indeed depends on the realization of such biochemical and physiological mechanisms, but the importance of sensing and signaling mechanisms that can integrate perception of environmental cues and transduction into physiological responses is often overlooked. Recent progress opens the possibility of considering plant phenotypic plasticity and responses to climate change through the perspective of environmental sensing and signaling. This review aims to analyze present knowledge on plant sensing and signaling mechanisms and discuss how their structural and functional characteristics lead to resilience or hypersensitivity under conditions of climate change. Plant cells are endowed with arrays of environmental and stress sensors and with internal signals that act as molecular integrators of the multiple constraints of climate change, thus giving rise to potential mechanisms of climate change sensing. Moreover, mechanisms of stress-related information propagation lead to stress memory and acquired stress tolerance that could withstand different scenarios of modifications of stress frequency and intensity. However, optimal functioning of existing sensors, optimal integration of additive constraints and signals, or memory processes can be hampered by conflicting interferences between novel combinations and novel changes in intensity and duration of climate change-related factors. Analysis of these contrasted situations emphasizes the need for future research on the diversity and robustness of plant signaling mechanisms under climate change conditions.

Low doses of triazine xenobiotics mobilize ABA and cytokinin regulations in a stress- and low-energy-dependent manner

The extent of residual contaminations of pesticides through drift, run-off and leaching is a potential threat to non-target plant communities. Arabidopsis thaliana responds to low doses of the herbicide atrazine, and of its degradation products, desethylatrazine and hydroxyatrazine, not only in the long term, but also under conditions of short-term exposure. In order to investigate underlying molecular mechanisms of low-dose responses and to decipher commonalities and specificities between different chemical treatments, parallel transcriptomic studies of the early effects of the atrazine-desethylatrazine-hydroxyatrazine chemical series were undertaken using whole-genome microarrays. All of the triazines under study produced coordinated and specific changes in gene expression. Hydroxyatrazine-responsive genes were mainly linked to root development, whereas atrazine and desethylatrazine mostly affected molecular signaling networks implicated in stress and hormone responses. Analysis of signaling-related genes, promoter sites and shared-function interaction networks highlighted the involvement of energy-, stress-, abscisic acid- and cytokinin-regulated processes, and emphasized the importance of cold-, heat- and drought-related signaling in the perception of low doses of triazines. These links between low-dose xenobiotic impacts and stress-hormone crosstalk pathways give novel insights into plant-pesticide interactions and plant-pollution interactions that are essential for toxicity evaluation in the context of environmental risk assessment.

Plant-Pesticide Interactions and the Global Chloromethane Budget

Ecological, signaling, metabolic, and chemical processes in plant-microorganism systems and in plant-derived material may link the use of chlorinated pesticides in the environment with plant chloromethane emission. This neglected factor should be taken into account to assess global planetary budgets of chloromethane and impacts on atmospheric ozone depletion.

Root-level exposure reveals multiple physiological toxicity of triazine xenobiotics in Arabidopsis thaliana

Herbicides are pollutants of great concern due to environmental ubiquity resulting from extensive use in modern agriculture and persistence in soil and water. Studies at various spatial scales have also highlighted frequent occurrences of major herbicide breakdown products in the environment. Analysis of plant behavior toward such molecules and their metabolites under conditions of transient or persistent soil pollution is important for toxicity evaluation in the context of environmental risk assessment. In order to understand the mechanisms underlying the action of such environmental contaminants, the model plant Arabidopsis thaliana, which has been shown to be highly responsive to pesticides and other xenobiotics, was confronted with varying levels of the widely-used herbicide atrazine and of two of its metabolites, desethylatrazine and hydroxyatrazine, which are both frequently detected in water streams of agriculturally-intensive areas. After 24h of exposure to varying concentrations covering the range of triazine concentrations detected in the environment, root-level contaminations of atrazine, desethylatrazine and hydroxyatrazine were found to affect early growth and development in various dose-dependent and differential manners. Moreover, these differential effects of atrazine, desethylatrazine and hydroxyatrazine pointed to the involvement of distinct mechanisms directly affecting respiration and root development. The consequences of the identification of additional targets, in addition to the canonical photosystem II target, are discussed in relation with the ecotoxicological assessment of environmental xenobiotic contamination.

Herbicide-related signaling in plants reveals novel insights for herbicide use strategies, environmental risk assessment and global change assessment challenges

Herbicide impact is usually assessed as the result of a unilinear mode of action on a specific biochemical target with a typical dose-response dynamics. Recent developments in plant molecular signaling and crosstalk between nutritional, hormonal and environmental stress cues are however revealing a more complex picture of inclusive toxicity. Herbicides induce large-scale metabolic and gene-expression effects that go far beyond the expected consequences of unilinear herbicide-target-damage mechanisms. Moreover, groundbreaking studies have revealed that herbicide action and responses strongly interact with hormone signaling pathways, with numerous regulatory protein-kinases and -phosphatases, with metabolic and circadian clock regulators and with oxidative stress signaling pathways. These interactions are likely to result in mechanisms of adjustment that can determine the level of sensitivity or tolerance to a given herbicide or to a mixture of herbicides depending on the environmental and developmental status of the plant. Such regulations can be described as rheostatic and their importance is discussed in relation with herbicide use strategies, environmental risk assessment and global change assessment challenges.

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress

Lolium perenne, which is a major component of pastures, lawns, and grass strips, can be exposed to xenobiotic stresses due to diffuse and residual contaminations of soil. L. perenne was recently shown to undergo metabolic adjustments in response to sub-toxic levels of xenobiotics. To gain insight in such chemical stress responses, a de novo transcriptome analysis was carried out on leaves from plants subjected at the root level to low levels of xenobiotics, glyphosate, tebuconazole, and a combination of the two, leading to no adverse physiological effect. Chemical treatments influenced significantly the relative proportions of functional categories and of transcripts related to carbohydrate processes, to signaling, to protein-kinase cascades, such as Serine/Threonine-protein kinases, to transcriptional regulations, to responses to abiotic or biotic stimuli and to responses to phytohormones. Transcriptomics-based expressions of genes encoding different types of SNF1 (sucrose non-fermenting 1)-related kinases involved in sugar and stress signaling or encoding key metabolic enzymes were in line with specific qRT-PCR analysis or with the important metabolic and regulatory changes revealed by metabolomic analysis. The effects of pesticide treatments on metabolites and gene expression strongly suggest that pesticides at low levels, as single molecule or as mixture, affect cell signaling and functioning even in the absence of major physiological impact. This global analysis of L. perenne therefore highlighted the interactions between molecular regulation of responses to xenobiotics, and also carbohydrate dynamics, energy dysfunction, phytohormones and calcium signaling.

Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics

The phyllosphere, which lato sensu consists of the aerial parts of plants, and therefore primarily, of the set of photosynthetic leaves, is one of the most prevalent microbial habitats on earth. Phyllosphere microbiota are related to original and specific processes at the interface between plants, microorganisms and the atmosphere. Recent -omics studies have opened fascinating opportunities for characterizing the spatio-temporal structure of phyllosphere microbial communities in relation with structural, functional, and ecological properties of host plants, and with physico-chemical properties of the environment, such as climate dynamics and trace gas composition of the surrounding atmosphere. This review will analyze recent advances, especially those resulting from environmental genomics, and how this novel knowledge has revealed the extent of the ecosystemic impact of the phyllosphere at the interface between plants and atmosphere. Highlights • The phyllosphere is one of the most prevalent microbial habitats on earth. • Phyllosphere microbiota colonize extreme, stressful, and changing environments. • Plants, phyllosphere microbiota and the atmosphere present a dynamic continuum. • Phyllosphere microbiota interact with the dynamics of volatile organic compounds and atmospheric trace gasses.

Metabolic profiling of Lolium perenne shows functional integration of metabolic responses to diverse subtoxic conditions of chemical stress

Plant communities are confronted with a great variety of environmental chemical stresses. Characterization of chemical stress in higher plants has often been focused on single or closely related stressors under acute exposure, or restricted to a selective number of molecular targets. In order to understand plant functioning under chemical stress conditions close to environmental pollution conditions, the C3 grass Lolium perenne was subjected to a panel of different chemical stressors (pesticide, pesticide degradation compound, polycyclic aromatic hydrocarbon, and heavy metal) under conditions of seed-level or root-level subtoxic exposure. Physiological and metabolic profiling analysis on roots and shoots revealed that all of these subtoxic chemical stresses resulted in discrete physiological perturbations and complex metabolic shifts. These metabolic shifts involved stressor-specific effects, indicating multilevel mechanisms of action, such as the effects of glyphosate and its degradation product aminomethylphosphonic acid on quinate levels. They also involved major generic effects that linked all of the subtoxic chemical stresses with major modifications of nitrogen metabolism, especially affecting asparagine, and of photorespiration, especially affecting alanine and glycerate. Stress-related physiological effects and metabolic adjustments were shown to be integrated through a complex network of metabolic correlations converging on Asn, Leu, Ser, and glucose-6-phosphate, which could potentially be modulated by differential dynamics and interconversion of soluble sugars (sucrose, trehalose, fructose, and glucose). Underlying metabolic, regulatory, and signalling mechanisms linking these subtoxic chemical stresses with a generic impact on nitrogen metabolism and photorespiration are discussed in relation to carbohydrate and low-energy sensing.

Low environmentally relevant levels of bioactive xenobiotics and associated degradation products cause cryptic perturbations of metabolism and molecular stress responses in Arabidopsis thaliana

Anthropic changes and chemical pollution confront wild plant communities with xenobiotic combinations of bioactive molecules, degradation products, and adjuvants that constitute chemical challenges potentially affecting plant growth and fitness. Such complex challenges involving residual contamination and mixtures of pollutants are difficult to assess. The model plant Arabidopsis thaliana was confronted by combinations consisting of the herbicide glyphosate, the fungicide tebuconazole, the glyphosate degradation product aminomethylphosphonic acid (AMPA), and the atrazine degradation product hydroxyatrazine, which had been detected and quantified in soils of field margins in an agriculturally intensive region. Integrative analysis of physiological, metabolic, and gene expression responses was carried out in dose-response experiments and in comparative experiments of varying pesticide combinations. Field margin contamination levels had significant effects on plant growth and metabolism despite low levels of individual components and the presence of pesticide degradation products. Biochemical and molecular analysis demonstrated that these less toxic degradation products, AMPA and hydroxyatrazine, by themselves elicited significant plant responses, thus indicating underlying mechanisms of perception and transduction into metabolic and gene expression changes. These mechanisms may explain observed interactions, whether positive or negative, between the effects of pesticide products (AMPA and hydroxyatrazine) and the effects of bioactive xenobiotics (glyphosate and tebuconazole). Finally, the metabolic and molecular perturbations induced by low levels of xenobiotics and associated degradation products were shown to affect processes (carbon balance, hormone balance, antioxidant defence, and detoxification) that are likely to determine environmental stress sensitivity.

Physiology and toxicology of hormone-disrupting chemicals in higher plants

Higher plants are exposed to natural environmental organic chemicals, associated with plant-environment interactions, and xenobiotic environmental organic chemicals, associated with anthropogenic activities. The effects of these chemicals result not only from interaction with metabolic targets, but also from interaction with the complex regulatory networks of hormone signaling. Purpose-designed plant hormone analogues thus show extensive signaling effects on gene regulation and are as such important for understanding plant hormone mechanisms and for manipulating plant growth and development. Some natural environmental chemicals also act on plants through interference with the perception and transduction of endogenous hormone signals. In a number of cases, bioactive xenobiotics, including herbicides that have been designed to affect specific metabolic targets, show extensive gene regulation effects, which are more in accordance with signaling effects than with consequences of metabolic effects. Some of these effects could be due to structural analogies with plant hormones or to interference with hormone metabolism, thus resulting in situations of hormone disruption similar to animal cell endocrine disruption by xenobiotics. These hormone-disrupting effects can be superimposed on parallel metabolic effects, thus indicating that toxicological characterisation of xenobiotics must take into consideration the whole range of signaling and metabolic effects. Hormone-disruptive signaling effects probably predominate when xenobiotic concentrations are low, as occurs in situations of residual low-level pollutions. These hormone-disruptive effects in plants may thus be of importance for understanding cryptic effects of low-dosage xenobiotics, as well as the interactive effects of mixtures of xenobiotic pollutants.

Xenobiotic sensing and signalling in higher plants

Anthropogenic changes and chemical pollution confront plant communities with various xenobiotic compounds or combinations of xenobiotics, involving chemical structures that are at least partially novel for plant species. Plant responses to chemical challenges and stimuli are usually characterized by the approaches of toxicology, ecotoxicology, and stress physiology. Development of transcriptomics and proteomics analysis has demonstrated the importance of modifications to gene expression in plant responses to xenobiotics. It has emerged that xenobiotic effects could involve not only biochemical and physiological disruption, but also the disruption of signalling pathways. Moreover, mutations affecting sensing and signalling pathways result in modifications of responses to xenobiotics, thus confirming interference or crosstalk between xenobiotic effects and signalling pathways. Some of these changes at gene expression, regulation and signalling levels suggest various mechanisms of xenobiotic sensing in higher plants, in accordance with xenobiotic-sensing mechanisms that have been characterized in other phyla (yeast, invertebrates, vertebrates). In higher plants, such sensing systems are difficult to identify, even though different lines of evidence, involving mutant studies, transcription factor analysis, or comparative studies, point to their existence. It remains difficult to distinguish between the hypothesis of direct xenobiotic sensing and indirect sensing of xenobiotic-related modifications. However, future characterization of xenobiotic sensing and signalling in higher plants is likely to be a key element for determining the tolerance and remediation capacities of plant species. This characterization will also be of interest for understanding evolutionary dynamics of stress adaptation and mechanisms of adaptation to novel stressors.

Carbon dynamics, development and stress responses in Arabidopsis: involvement of the APL4 subunit of ADP-glucose pyrophosphorylase (starch synthesis)

An Arabidopsis thaliana T-DNA insertional mutant was identified and characterized for enhanced tolerance to the singlet-oxygen-generating herbicide atrazine in comparison to wild-type. This enhanced atrazine tolerance mutant was shown to be affected in the promoter structure and in the regulation of expression of the APL4 isoform of ADP-glucose pyrophosphorylase, a key enzyme of the starch biosynthesis pathway, thus resulting in decrease of APL4 mRNA levels. The impact of this regulatory mutation was confirmed by the analysis of an independent T-DNA insertional mutant also affected in the promoter of the APL4 gene. The resulting tissue-specific modifications of carbon partitioning in plantlets and the effects on plantlet growth and stress tolerance point out to specific and non-redundant roles of APL4 in root carbon dynamics, shoot-root relationships and sink regulations of photosynthesis. Given the effects of exogenous sugar treatments and of endogenous sugar levels on atrazine tolerance in wild-type Arabidopsis plantlets, atrazine tolerance of this apl4 mutant is discussed in terms of perception of carbon status and of investment of sugar allocation in xenobiotic and oxidative stress responses.

Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics

Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.

Natural variation reveals relationships between pre-stress carbohydrate nutritional status and subsequent responses to xenobiotic and oxidative stress in Arabidopsis thaliana

BACKGROUND

Soluble sugars are involved in responses to stress, and act as signalling molecules that activate specific or hormone cross-talk transduction pathways. Thus, exogenous sucrose treatment efficiently induces tolerance to the herbicide atrazine in Arabidopsis thaliana plantlets, at least partially through large-scale modifications of expression of stress-related genes.

METHODS

Availability of sugars in planta for stress responses is likely to depend on complex dynamics of soluble sugar accumulation, sucrose-starch partition and organ allocation. The question of potential relationships between endogenous sugar levels and stress responses to atrazine treatment was investigated through analysis of natural genetic accessions of A. thaliana. Parallel quantitative and statistical analysis of biochemical parameters and of stress-sensitive physiological traits was carried out on a set of 11 accessions.

KEY RESULTS

Important natural variation was found between accessions of A. thaliana in pre-stress shoot endogenous sugar levels and responses of plantlets to subsequent atrazine stress. Moreover, consistent trends and statistically significant correlations were detected between specific endogenous sugar parameters, such as the pre-stress end of day sucrose level in shoots, and physiological markers of atrazine tolerance.

CONCLUSIONS

These significant relationships between endogenous carbohydrate metabolism and stress response therefore point to an important integration of carbon nutritional status and induction of stress tolerance in plants. The specific correlation between pre-stress sucrose level and greater atrazine tolerance may reflect adaptive mechanisms that link sucrose accumulation, photosynthesis-related stress and sucrose induction of stress defences.

Differential patterns of reactive oxygen species and antioxidative mechanisms during atrazine injury and sucrose-induced tolerance in Arabidopsis thaliana plantlets

BACKGROUND

Besides being essential for plant structure and metabolism, soluble carbohydrates play important roles in stress responses. Sucrose has been shown to confer to Arabidopsis seedlings a high level of tolerance to the herbicide atrazine, which causes reactive oxygen species (ROS) production and oxidative stress. The effects of atrazine and of exogenous sucrose on ROS patterns and ROS-scavenging systems were studied. Simultaneous analysis of ROS contents, expression of ROS-related genes and activities of ROS-scavenging enzymes gave an integrative view of physiological state and detoxifying potential under conditions of sensitivity or tolerance.

RESULTS

Toxicity of atrazine could be related to inefficient activation of singlet oxygen (1O2) quenching pathways leading to 1O2 accumulation. Atrazine treatment also increased hydrogen peroxide (H2O2) content, while reducing gene expressions and enzymatic activities related to two major H2O2-detoxification pathways. Conversely, sucrose-protected plantlets in the presence of atrazine exhibited efficient 1O2 quenching, low 1O2 accumulation and active H2O2-detoxifying systems.

CONCLUSION

In conclusion, sucrose protection was in part due to activation of specific ROS scavenging systems with consequent reduction of oxidative damages. Importance of ROS combination and potential interferences of sucrose, xenobiotic and ROS signalling pathways are discussed.

Purification of glutamate dehydrogenase from liver and brain

Two alternative procedures are described for the purification of the major form of glutamate dehydrogenase (L-glutamate-NAD(P)+ oxidoreductase (deaminating), EC 1.4.1.3: GDH) from ox liver and brain. The first involves affinity chromatography on a column of the allosteric inhibitor GTP bound to Sepharose, whereas the other uses a bifunctional ligand (bis-NAD+) composed of two NAD+ molecules linked together by a spacer arm to precipitate the enzyme in the presence of the substrate analogue glutarate. In both procedures the affinity steps are preceded by ammonium sulfate precipitation and ion exchange chromatography on DEAE cellulose. Procedures for the synthesis of GTP-Sepharose and bis-NAD+ are described and the ancillary procedures, including the assay of GDH activity and the determination of protein concentration, are also presented.

Genome-wide interacting effects of sucrose and herbicide-mediated stress in Arabidopsis thaliana: novel insights into atrazine toxicity and sucrose-induced tolerance

Background

Soluble sugars, which play a central role in plant structure and metabolism, are also involved in the responses to a number of stresses, and act as metabolite signalling molecules that activate specific or hormone-crosstalk transduction pathways. The different roles of exogenous sucrose in the tolerance of Arabidopsis thaliana plantlets to the herbicide atrazine and oxidative stress were studied by a transcriptomic approach using CATMA arrays.

Results

Parallel situations of xenobiotic stress and sucrose-induced tolerance in the presence of atrazine, of sucrose, and of sucrose plus atrazine were compared. These approaches revealed that atrazine affected gene expression and therefore seedling physiology at a much larger scale than previously described, with potential impairment of protein translation and of reactive-oxygen-species (ROS) defence mechanisms. Correlatively, sucrose-induced protection against atrazine injury was associated with important modifications of gene expression related to ROS defence mechanisms and repair mechanisms. These protection-related changes of gene expression did not result only from the effects of sucrose itself, but from combined effects of sucrose and atrazine, thus strongly suggesting important interactions of sucrose and xenobiotic signalling or of sucrose and ROS signalling.

Conclusion

These interactions resulted in characteristic differential expression of gene families such as ascorbate peroxidases, glutathione-S-transferases and cytochrome P450s, and in the early induction of an original set of transcription factors. These genes used as molecular markers will eventually be of great importance in the context of xenobiotic tolerance and phytoremediation.

Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana

Helitrons are a class of prolific transposable elements in the Arabidopsis thaliana genome. Although 37 families were identified after the recent discovery of Helitrons, no systematic classification is available because of the high variability of helitronic sequences. Since transposition proteins are assumed to interact with Helitron termini, a Helitron model was formalized based on terminus characterization in order to carry out an exhaustive analysis of all possible combinations of the pairs of termini present. This combinatorics approach resulted in the discovery of a number of new Helitron elements corresponding to termini associations from distinct previously-described Helitron families. The occurrence matrix of termini combinations yielded a structure that revealed clusters of Helitron families.

Involvement of the ethylene-signalling pathway in sugar-induced tolerance to the herbicide atrazine in Arabidopsis thaliana seedlings

Soluble sugars can induce tolerance to otherwise lethal concentrations of the herbicide atrazine in Arabidopsis thaliana seedlings. This sugar-induced tolerance involves modifications of gene expression which are likely to be related to sugar and xenobiotic signal transduction. Since it has been suggested that ethylene- and sugar-signalling pathways may interact, the effects of glucose (Glc) and sucrose (Suc) on seedling growth and tolerance to atrazine were analysed in etr1-1, ein2-1, ein4, and sis1/ctr1-12 ethylene-signalling mutant backgrounds, where key steps of ethylene signal transduction are affected. Both ethylene-insensitive and ethylene-constitutive types of mutants were found to be affected in sugar-induced chlorophyll accumulation and root growth and in sugar-induced tolerance to atrazine. Interactions between ethylene and sugars were thus shown to take place during enhancement of seedling growth by low-to-moderate (up to 80 mM) sugar concentrations. The strong impairment of sugar-induced atrazine tolerance in etr1-1, ein2-1, and ein4 mutants demonstrated that this tolerance required active signalling pathways and could not be ascribed to mere metabolic effects nor to mere growth enhancement. Sugar-induced atrazine tolerance thus seemed to involve activation by sugar and atrazine of hexokinase-independent sugar signalling pathways and of ethylene signalling pathways, resulting in derepression of hexokinase-mediated Glc repression and in induction of protection mechanisms against atrazine injury.

Sucrose amendment enhances phytoaccumulation of the herbicide atrazine in Arabidopsis thaliana

Growth in the presence of sucrose was shown to confer to Arabidopsis thaliana (thale cress or mustard weed) seedlings, under conditions of in vitro culture, a high level of tolerance to the herbicide atrazine and to other photosynthesis inhibitors. This tolerance was associated with root-to-shoot transfer and accumulation of atrazine in shoots, which resulted in significant decrease of herbicide levels in the growth medium. In soil microcosms, application of exogenous sucrose was found to confer tolerance and capacity to accumulate atrazine in Arabidopsis thaliana plants grown on atrazine-contaminated soil, and resulted in enhanced decontamination of the soil. Application of sucrose to plants grown on herbicide-polluted soil, which increases plant tolerance and xenobiotic absorption, thus appears to be potentially useful for phytoremediation.

The pleiotropic Arabidopsis frd mutation with altered coordination of chloroplast biogenesis, cell size and differentiation, organ size and number

In higher plants, plastid development must be tightly coordinated with cell and organ development. In this paper, a novel T-DNA-mutagenized Arabidopsis line showing chlorotic leaves and minute stature was identified in a genetic screen for altered chloroplast development. The mutation corresponded to a single locus on chromosome IV and was associated with insertion of the T-DNA. This locus was named FARFADET and resulted in pleiotropic effects on chloroplast biogenesis, cell size and differentiation, organ size and number. Thus, in contrast with previously described chlorotic mutants, frd mutants were affected not only in chloroplast development and chlorophyll accumulation, but also in cell and organ development. Alteration of differentiation affected different cell types such as leaf epidermal cells, trichomes, mesophyll cells, and columella cells. A major effect on mesophyll cell differentiation was the lack of palisadic parenchyma and absence of grana stacks. Moreover, meristem size and lateral meristem initiation were affected. Genetic and molecular characterisation showed that the T-DNA insertion generated 41 bp deletion in a potential miRNA precursor. The predicted miRNA target genes were involved in plant development and stress. It is therefore hypothesized that the frd mutation had affected coordination of cell developmental span and the control of the division-differentiation balance.

Domain organization within repeated DNA sequences: application to the study of a family of transposable elements

MOTIVATION

The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of TEs, which provides the main mechanism of mutation in some genomes, is an essential component of genome evolution. In this study we introduce a new concept of domain, a segmentation unit useful for describing the architecture of different copies of TEs. Our method extracts occurrences of a terminus-defined family of TEs, aligns the sequences, finds the domains in the alignment and searches the distribution of each domain in sequences. After a classification step relative to the presence or the absence of domains, the method results in a graphical view of sequences segmented into domains.

RESULTS

Analysis of the new non-autonomous TE AtREP21 in the model plant Arabidopsis thaliana reveals copies of very different sizes and various combinations of domains which show the potential of our method.

AVAILABILITY

DomainOrganizer web page is available at www.irisa.fr/symbiose/DomainOrganizer/.

Sugar-induced tolerance to the herbicide atrazine in Arabidopsis seedlings involves activation of oxidative and xenobiotic stress responses

Exogenous sucrose confers to Arabidopsis seedlings a very high level of tolerance to the herbicide atrazine that cannot be ascribed to photoheterotrophic growth. Important differences of atrazine tolerance between sucrose and glucose treatments showed that activation of chloroplast biogenesis per se could not account for induced tolerance. Sucrose-induced acquisition of defence mechanisms was shown by the gene expression pattern of a chloroplastic iron superoxide dismutase and by enhancement of whole-cell glucose-6-phosphate dehydrogenase activity. Activation of these defence mechanisms depended on both soluble sugar and atrazine. Moreover, acquisition of sucrose protection was shown to unmask atrazine-induced gene expression, such as that of a cytosolic glutathione-S-transferase, which remained otherwise cryptic because of the lethal effects of atrazine in the absence of soluble sugars.

Involvement of soluble sugars in reactive oxygen species balance and responses to oxidative stress in plants

Soluble sugars, especially sucrose, glucose, and fructose, play an obviously central role in plant structure and metabolism at the cellular and whole-organism levels. They are involved in the responses to a number of stresses, and they act as nutrient and metabolite signalling molecules that activate specific or hormone-crosstalk transduction pathways, thus resulting in important modifications of gene expression and proteomic patterns. Various metabolic reactions and regulations directly link soluble sugars with the production rates of reactive oxygen species, such as mitochondrial respiration or photosynthesis regulation, and, conversely, with anti-oxidative processes, such as the oxidative pentose-phosphate pathway and carotenoid biosynthesis. Moreover, stress situations where soluble sugars are involved, such as chilling, herbicide injury, or pathogen attack, are related to important changes in reactive oxygen species balance. These converging or antagonistic relationships between soluble sugars, reactive oxygen species production, and anti-oxidant processes are generally confirmed by current transcriptome analyses, and suggest that sugar signalling and sugar-modulated gene expression are related to the control of oxidative stress. All these links place soluble carbohydrates in a pivotal role in the pro-oxidant and antioxidant balance, and must have constrained the selection of adaptive mechanisms involving soluble sugars and preventing de-regulation of reactive oxygen species production. Finally, in line with the specific role of sucrose in oxygenic photosynthetic organisms, this role of soluble sugars in oxidative stress regulation seems to entail differential effects of glucose and sucrose, which emphasizes the unresolved issue of characterizing sucrose-specific signalling pathways.

Characterization of the two arginine decarboxylase (polyamine biosynthesis) paralogues of the endemic subantarctic cruciferous species Pringlea antiscorbutica and analysis of their differential expression during development and response to environmental stress

Arginine decarboxylase (ADC) is a key enzyme involved in the synthesis of polyamines, which have been implicated in developmental processes and stress responses in higher plants. An ancestral ADC gene appears to have been duplicated at the origin of the Brassicaceae family, thus yielding two paralogues in the derived taxa. ADC gene structure was investigated in Pringlea antiscorbutica R. Br., a geographically isolated Brassicaceae species that is endemic from the subantarctic region. P. antiscorbutica exhibits several biochemical and physiological adaptations related to this cold and harsh environment, including high levels of polyamines, which is unusual in higher plants, and especially high levels of agmatine, the product of the ADC-catalysed reaction. Various ADC clones were obtained from P. antiscorbutica. Sequence and phylogenetic analysis showed that all these clones fitted with the presence of two paralogues, PaADC1 and PaADC2, in P. antiscorbutica. Expression of these ADC paralogues was analyzed in P. antiscorbutica during vegetative development and response to stress. Whereas PaADC2 was expressed at both seedling and mature stages, PaADC1 transcripts were hardly detected during early development and were significantly expressed in mature plants. Moreover, PaADC2, but not PaADC1, expression was up-regulated in response to chilling and salt stress at seedling stage. Analysis of 5' regulatory regions of these ADC genes revealed several differences in putative cis-regulatory elements, which could be associated with specific expression patterns. These results were compared to ADC paralogue expression in Arabidopsis thaliana and are discussed in the evolutionary context of genetic diversity resulting from gene duplication.

Differential gene expression of ARGININE DECARBOXYLASE ADC1 and ADC2 in Arabidopsis thaliana: characterization of transcriptional regulation during seed germination and seedling development

•  In plants, polyamines can generally be synthesized by the ornithine decarboxylase and arginine decarboxylase pathways. However, the model plant Arabidopsis thaliana appears to possess only the arginine decarboxylase pathway. As two paralogous ARGININE DECARBOXYLASE (ADC) genes are present in Arabidopsis, we investigated differential expression and potential differences of promoter activity during seedling development and under specific stress conditions. •  Promoter activities were studied in stable homozygotic transformants harbouring promoter::reporter gene fusions. •  Under temperate conditions, ADC2 promoter activity was strongly associated with seed germination, root and leaf development, whereas ADC1 promoter activity was low during vegetative development. Light, sucrose and ethylene were shown to be important regulators of ADC2 promoter activity. By contrast, in roots and leaves of plantlets subjected to chilling treatment the ADC1 paralogue showed high promoter activity whereas ADC2 promoter activity was considerably decreased. •  In situations of seed germination, root development and response to chilling, the modifications of promoter activities were associated with changes in mRNA levels, emphasizing the involvement of transcriptional regulation in ARGININE DECARBOXYLASE gene expression.

Characterization of environmental stress responses during early development of Pringlea antiscorbutica in the field at Kerguelen

•  Early development of Kerguelen cabbage (Pringlea antiscorbutica) was studied in the Kerguelen archipelago, its natural habitat, and under laboratory conditions. Polyamines, which are involved in developmental processes and responses to stress in several plant species, were used as markers of physiological status of P. antiscorbutica seedlings. •  Analysis under laboratory conditions of responses to low water availability and to salinity enabled identification of major environmental constraints restricting seedling development in the subantarctic region. •  Salt stress was found to modify polyamine distribution between seedling organs, in controlled experiments and in the field, thus indicating that polyamine responses to salt stress were functional in the field at Kerguelen. By contrast, exposure to low water availability induced different polyamine responses in controlled experiments and in the field. •  The present work thus shows that, under certain conditions, polyamine concentrations can be used as a marker of specific stress responses of seedlings in the field. Discrepancies are discussed in terms of growth conditions in the laboratory and of combined stresses in natural habitats.

Involvement of polyamines in the interacting effects of low temperature and mineral supply on Pringlea antiscorbutica (Kerguelen cabbage) seedlings

Pringlea antiscorbutica, which is the sole endemic crucifer in the subantarctic zone, undergoes seedling development in a harsh and cold environment. Since, at the mature stage, this species exhibits several adaptations linked to cold tolerance such as high polyamine levels, potential adaptations and polyamine response were investigated in seedlings. In order to assess the specificity of responses, P. antiscorbutica was compared with Arabidopsis thaliana, which is characterized by a life cycle preventing cold exposure at seedling stage. P. antiscorbutica and A. thaliana seedlings were found to have strikingly contrasted responses to temperature changes and to mineral nutrition. Whereas A. thaliana seedlings showed the typical growth arrest of chilling-sensitive plants, P. antiscorbutica seedlings showed optimal root growth at low temperature (5/10 degrees C) and temperate conditions caused the early arrest of root growth. Cold tolerance was associated with increased levels of polyamines or with maintenance of high levels of polyamines. Comparison of both species showed that polyamine levels could be a significant marker of chilling tolerance in seedlings. Treatments with varying mineral supply showed a positive relationship between root growth rate and variations of agmatine and putrescine endogenous contents in roots of P. antiscorbutica. This may be the first demonstration that, even under conditions of accumulation induced by environmental stress, polyamine levels can still be correlated with developmental processes. Com parison of mineral supply and temperature effects strongly indicated a trade-off of polyamine involvement between development and response to stress.

Involvement of polyamines in root development at low temperature in the subantarctic cruciferous species Pringlea antiscorbutica

Polyamine involvement in root development at low temperature was studied in seedlings of Pringlea antiscorbutica R. Br. This unique endemic cruciferous species from the subantarctic zone is subjected to strong environmental constraints and shows high polyamine contents. In the present study, free polyamine levels were modified by inhibitors of polyamine biosynthesis (D-arginine, difluoromethylornithine, cyclohexylammonium, and methylglyoxal-bis-guanylhydrazone) and variations of the endogenous pools were compared to changes in root growth. The arginine decarboxylase pathway, rather than that of ornithine decarboxylase, seemed to play a major role in polyamine synthesis in Pringlea antiscorbutica seedlings. Root, but not shoot, phenotypes were greatly affected by these treatments, which modified polyamine endogenous levels according to their expected effects. A positive correlation was found between agmatine level and growth rate of the primary root. Spermidine and spermine contents also showed positive correlations with primary root growth whereas the putrescine level showed neutral or negative effects on this trait. Free polyamines were therefore found to be differentially involved in the phenotypic plasticity of root architecture. A comparison of developmental effects and physiological concentrations suggested that agmatine and spermine in particular may play a significant role in the control of root development.

Genome-wide distribution and potential regulatory functions of AtATE, a novel family of miniature inverted-repeat transposable elements in Arabidopsis thaliana

A study of transgenic promoter::beta-glucuronidase lines showed that the promoters of the two Arabidopsis ARGININE DECARBOXYLASE paralogues, ADC1 and ADC2, exhibited extremely different patterns of activity. One major feature of the promoter of ADC1 was the presence of a novel transposable element, which was shown to possess all of the characteristics of Miniature Inverted-repeat Transposable Elements (MITEs), and to be present in 26 full-length copies and 1617 partial copies and fragments distributed throughout the Arabidopsis genome. TRANSFAC analysis showed that this transposable element possesses a significant number of transcription-factor binding motifs. A bioinformatics approach based on a suffix-tree compilation was used to obtain an exhaustive description of exact copy numbers and positions of the element in the Arabidopsis genome. The distribution among the chromosomes was non-random, and a significant number of copies were found in regions flanking genes. Full-length copies of the transposable element were detected in the immediate vicinity of 22 genes, either upstream or downstream.

The mitochondrial isovaleryl-coenzyme a dehydrogenase of arabidopsis oxidizes intermediates of leucine and valine catabolism

We recently identified a cDNA encoding a putative isovaleryl-coenzyme A (CoA) dehydrogenase in Arabidopsis (AtIVD). In animals, this homotetrameric enzyme is located in mitochondria and catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA as an intermediate step in the leucine (Leu) catabolic pathway. Expression of AtIVD:smGFP4 fusion proteins in tobacco (Nicotiana tabacum) protoplasts and biochemical studies now demonstrate the in vivo import of the plant isovaleryl-CoA dehydrogenase (IVD) into mitochondria and the enzyme in the matrix of these organelles. Two-dimensional separation of mitochondrial proteins by blue native and SDS-PAGE and size determination of the native and overexpressed proteins suggest homodimers to be the dominant form of the plant IVD. Northern-blot hybridization and studies in transgenic Arabidopsis plants expressing Ativd promoter:gus constructs reveal strong expression of this gene in seedlings and young plants grown in the absence of sucrose, whereas promoter activity in almost all tissues is strongly inhibited by exogeneously added sucrose. Substrate specificity tests with AtIVD expressed in Escherichia coli indicate a strong preference toward isovaleryl-CoA but surprisingly also show considerable activity with isobutyryl-CoA. This strongly indicates a commitment of the enzyme in Leu catabolism, but the activity observed with isobutyryl-CoA also suggests a parallel involvement of the enzyme in the dehydrogenation of intermediates of the valine degradation pathway. Such a dual activity has not been observed with the animal IVD and may suggest a novel connection of the Leu and valine catabolism in plants.

Purification, characterization and cloning of isovaleryl-CoA dehydrogenase from higher plant mitochondria

Between the different types of Acyl-CoA dehydrogenases (ACADs), those specific for branched chain acyl-CoA derivatives are involved in the catabolism of amino acids. In mammals, isovaleryl-CoA dehydrogenase (IVD), an enzyme of the leucine catabolic pathway, is a mitochondrial protein, as other acyl-CoA dehydrogenases involved in fatty acid beta-oxidation. In plants, fatty acid beta-oxidation takes place mainly in peroxisomes, and the cellular location of the enzymes involved in the catabolism of branched-chain amino acids had not been definitely assigned. Here, we describe that highly purified potato mitochondria have important IVD activity. The enzyme was partially purified and cDNAs from two different genes were obtained. The partially purified enzyme has enzymatic constant values with respect to isovaleryl-CoA comparable to those of the mammalian enzyme. It is not active towards straight-chain acyl-CoA substrates tested, but significant activity was also found with isobutyryl-CoA, implying an additional role of the enzyme in the catabolism of valine. The present study confirms recent reports that in plants IVD activity resides in mitochondria and opens the way to a more detailed study of amino-acid catabolism in plant development.

Mechanisms of primordium formation during adventitious root development from walnut cotyledon explants

In walnut (Juglans regia L.), an otherwise difficult-to-root species, explants of cotyledons have been shown to generate complete roots in the absence of exogenous growth regulators. In the present study, this process of root formation was shown to follow a pattern of adventitious, rather than primary or lateral, ontogeny: (i) the arrangement of vascular bundles in the region of root formation was of the petiole type; (ii) a typical root primordium was formed at the side of the procambium within a meristematic ring of actively dividing cells located around each vascular bundle; (iii) the developing root apical meristem was connected in a lateral way with the vascular bundle of the petiole. This adventitious root formation occurred in three main stages of cell division, primordium formation and organization of apical meristem. These stages were characterized by expression of LATERAL ROOT PRIMORDIUM-1 and CHALCONE SYNTHASE genes, which were found to be sequentially expressed during the formation of the primordium. Activation of genes related to root cell differentiation started at the early stage of primordium formation prior to organization of the root apical meristem. The systematic development of adventitious root primordia at a precise site gave indications on the positional and biochemical cues that are necessary for adventitious root formation.

Higher-plant medium- and short-chain acyl-CoA oxidases: identification, purification and characterization of two novel enzymes of eukaryotic peroxisomal beta-oxidation

Medium- and short-chain acyl-CoA oxidases were identified in and subsequently purified from dark-grown maize plantlets. The oxidase showing preference for medium-chain fatty acyl-CoAs (C10-C14) was purified to homogeneity. The oxidase showing preference for short-chain fatty acyl-CoAs (C4-C8) was purified over 150-fold. Various catalytic properties confirmed these enzymes to be true acyl-CoA oxidases. They produced trans-2-enoyl-CoA and H2O2 from the saturated acyl-CoA, as verified by various independent assay techniques. They also exhibited FAD-dependent activity; i.e. removal of loosely bound FAD by gel filtration markedly reduced activity, which could be restored upon re-addition of FAD. They showed apparent Km values between 2 and 10 microM for the acyl-CoA substrate giving maximal activity, no activity with the corresponding free fatty acid, high pH optima (8.3-8.6) and a peroxisomal subcellular location. The medium-chain acyl-CoA oxidase was determined to be a monomeric protein with a molecular mass of 62 kDa. The short-chain acyl-CoA oxidase was shown to have a native molecular mass of 60 kDa, but exhibited a labile multimeric structure, as indicated by the elution of multiple peaks of activity during several chromatographic steps, and ultimately by the purification of a subunit of molecular mass 15 kDa. The medium- and short-chain acyl-CoA oxidases were demonstrated to be distinct from the maize equivalent of the cucumber glyoxysomal long-chain acyl-CoA oxidase previously purified and characterized [Kirsch, Loffler and Kindl (1986) J. Biol. Chem. 261, 8570-8575]. The maize long-chain acyl-CoA oxidase was partially purified to permit determination of its substrate specificity; it showed activity with a broad range of acyl-CoAs of chain length greater than C8, and maximal activity with C16. The implications of the existence of multiple acyl-CoA oxidases in the regulation of plant peroxisomal beta-oxidation are discussed.