Early response of plant cell to carbon deprivation: in vivo 31P-NMR spectroscopy shows a quasi-instantaneous disruption on cytosolic sugars, phosphorylated intermediates of energy metabolism, phosphate partitioning, and intracellular pHs

Life at the conservative end of the leaf economics spectrum: intergeneric variation in the allocation of phosphorus to biochemical fractions in species of Banksia (Proteaceae) and Hakea (Proteaceae)

In severely phosphorus (P)-impoverished environments, plants have evolved to use P very efficiently. Yet, it is unclear how P allocation in leaves contributes to their photosynthetic P-use efficiency (PPUE) and position along the leaf economics spectrum (LES). We address this question in 10 species of Banksia and Hakea, two highly P-efficient Proteaceae genera. We characterised traits in leaves of Banksia and Hakea associated with the LES: leaf mass per area, light-saturated photosynthetic rates, P and nitrogen concentrations, and PPUE. We also determined leaf P partitioning to five biochemical fractions (lipid, nucleic acid, metabolite, inorganic and residual P) and their possible association with the LES. For both genera, PPUE was negatively correlated with fractional allocation of P to lipids, but positively correlated with that to metabolites. For Banksia only, PPUE was negatively correlated with residual P, highlighting a strategy contrasting to that of Hakea. Phosphorus-allocation patterns significantly explained PPUE but were not linked to the resource acquisition vs resource conservation gradient defined by the LES. We conclude that distinct P-allocation patterns enable species from different genera to achieve high PPUE and discuss the implications of different P investments. We surmise that different LES axes representing different ecological strategies coexist in extremely P-impoverished environments.

Plant Heterotrophic Cultures: No Food, No Growth

Plant cells are capable of uptaking exogenous organic substances. This inherited trait allows the development of heterotrophic cell cultures in various plants. The most common of them are Nicotiana tabacum and Arabidopsis thaliana. Plant cells are widely used in academic studies and as factories for valuable substance production. The repertoire of compounds supporting the heterotrophic growth of plant cells is limited. The best growth of cultures is ensured by oligosaccharides and their cleavage products. Primarily, these are sucrose, raffinose, glucose and fructose. Other molecules such as glycerol, carbonic acids, starch, and mannitol have the ability to support growth occasionally, or in combination with another substrate. Culture growth is accompanied by processes of specialization, such as elongation growth. This determines the pattern of the carbon budget. Culture ageing is closely linked to substrate depletion, changes in medium composition, and cell physiological rearrangements. A lack of substrate leads to starvation, which results in a decrease in physiological activity and the mobilization of resources, and finally in the loss of viability. The cause of the instability of cultivated cells may be the non-optimal metabolism under cultural conditions or the insufficiency of internal regulation.

Boron contributes to excessive aluminum tolerance in trifoliate orange (Poncirus trifoliata (L.) Raf.) by inhibiting cell wall deposition and promoting vacuole compartmentation

Boron (B) is an indispensable micronutrient for plant growth that can also alleviate aluminum (Al) toxicity. However, limited data are available on the underlying mechanisms behind this phenomenon. Here, we found that a certain range of B application could alleviate the inhibitory effects of Al toxicity on citrus. Transcriptome analysis revealed that several Al stress-responsive genes and pathways were differentially affected and enriched, such as coding for the secretion of organic acid and the distribution of Al in subcellular components after B addition. Specifically, B application enhanced rhizosphere pH and induced malate exudation by expressing PtALMT4 and PtALMT9 genes occurred in Al-treated root, which ultimately reduced the absorption of Al and coincided with down-regulated the expression of PtNrat1. Moreover, B supply suppressed the pectin methyl-esterase (PME) activity and displayed a lower level of PtPME2 expression, while enhanced the PtSTAR1 expression, which is responsible for reducing cell wall (CW) Al deposition. Boron addition enhanced the PtALS1 and PtALS3 expression, accompanied by a higher proportion of vacuolar Al compartmentation during Al exposure. Collectively, the protective effects of B on root injury induced by Al is mainly by subsiding the Al uptake in the root apoplast and compartmentalizing Al into vacuole.

Potential Networks of Nitrogen-Phosphorus-Potassium Channels and Transporters in Arabidopsis Roots at a Single Cell Resolution

Nitrogen (N), phosphorus (P), and potassium (K) are three major macronutrients essential for plant life. These nutrients are acquired and transported by several large families of transporters expressed in plant roots. However, it remains largely unknown how these transporters are distributed in different cell-types that work together to transfer the nutrients from the soil to different layers of root cells and eventually reach vasculature for massive flow. Using the single cell transcriptomics data from Arabidopsis roots, we profiled the transcriptional patterns of putative nutrient transporters in different root cell-types. Such analyses identified a number of uncharacterized NPK transporters expressed in the root epidermis to mediate NPK uptake and distribution to the adjacent cells. Some transport genes showed cortex- and endodermis-specific expression to direct the nutrient flow toward the vasculature. For long-distance transport, a variety of transporters were shown to express and potentially function in the xylem and phloem. In the context of subcellular distribution of mineral nutrients, the NPK transporters at subcellular compartments were often found to show ubiquitous expression patterns, which suggests function in house-keeping processes. Overall, these single cell transcriptomic analyses provide working models of nutrient transport from the epidermis across the cortex to the vasculature, which can be further tested experimentally in the future.

Recent insights into the metabolic adaptations of phosphorus-deprived plants

Inorganic phosphate (Pi) is an essential macronutrient required for many fundamental processes in plants, including photosynthesis and respiration, as well as nucleic acid, protein, and membrane phospholipid synthesis. The huge use of Pi-containing fertilizers in agriculture demonstrates that the soluble Pi levels of most soils are suboptimal for crop growth. This review explores recent advances concerning the understanding of adaptive metabolic processes that plants have evolved to alleviate the negative impact of nutritional Pi deficiency. Plant Pi starvation responses arise from complex signaling pathways that integrate altered gene expression with post-transcriptional and post-translational mechanisms. The resultant remodeling of the transcriptome, proteome, and metabolome enhances the efficiency of root Pi acquisition from the soil, as well as the use of assimilated Pi throughout the plant. We emphasize how the up-regulation of high-affinity Pi transporters and intra- and extracellular Pi scavenging and recycling enzymes, organic acid anion efflux, membrane remodeling, and the remarkable flexibility of plant metabolism and bioenergetics contribute to the survival of Pi-deficient plants. This research field is enabling the development of a broad range of innovative and promising strategies for engineering phosphorus-efficient crops. Such cultivars are urgently needed to reduce inputs of unsustainable and non-renewable Pi fertilizers for maximum agronomic benefit and long-term global food security and ecosystem preservation.

Mutation of the chloroplast-localized phosphate transporter OsPHT2;1 reduces flavonoid accumulation and UV tolerance in rice

Phosphorus (P) is an essential macronutrient required for plant development and production. The mechanisms regulating phosphate (Pi) uptake are well established, but the function of chloroplast Pi homeostasis is poorly understood in Oryza sativa (rice). PHT2;1 is one of the transporters/translocators mediating Pi import into chloroplasts. In this study, to gain insight into the role of OsPHT2;1-mediated stroma Pi, we analyzed OsPHT2;1 function in Pi utilization and photoprotection. Our results showed that OsPHT2;1 was induced by Pi starvation and light exposure. Cell-based assays showed that OsPHT2;1 localized to the chloroplast envelope and functioned as a low-affinity Pi transporter. The ospht2;1 had reduced Pi accumulation, plant growth and photosynthetic rates. Metabolite profiling revealed that 52.6% of the decreased metabolites in ospht2;1 plants were flavonoids, which was further confirmed by 40% lower content of total flavonoids compared with the wild type. As a consequence, ospht2;1 plants were more sensitive to UV-B irradiation. Moreover, the content of phenylalanine, the precursor of flavonoids, was also reduced, and was largely associated with the repressed expression of ADT1/MTR1. Furthermore, the ospht2;1 plants showed decreased grain yields at relatively high levels of UV-B irradiance. In summary, OsPHT2;1 functions as a chloroplast-localized low-affinity Pi transporter that mediates UV tolerance and rice yields at different latitudes.

Boron mitigates citrus root injuries by regulating intracellular pH and reactive oxygen species to resist H+-toxicity

Boron (B)-deficiency and H⁺-toxicity are important limiting factors for plants growth in acid soils. High B supply may reduce H⁺-toxicity-induced inhibition of growth in citrus. Trifoliate orange rootstock seedlings were irrigated with nutrient solution containing either 0 μM or 10 μM H₃BO₃ at two pH levels (pH4 (H⁺-toxicity) and pH6 (normal)). The results showed that H⁺-toxicity without B severely hampered main root elongation. Simultaneously, oxidative damage caused by H⁺-toxicity led to severe damage to the apical structure of root such as root crown abscission. However, B application promoted the root length, root cell viability and reduced cell wall (CW) thickness of root tips under H⁺-toxicity. Additionally, B application reduced the H⁺-toxicity-induced reactive oxygen species (ROS) accumulation in roots as characterized by lower fluorescence intensity of H₂O₂ and O₂^- staining. Moreover, ³¹P-NMR (³¹P nuclear magnetic resonance) spectra revealed B application regulated the pH of vacuoles and cytoplasm in root tips by reducing phosphoenolpyruvate carboxykinase (PEPCase) activity while enhancing NADP malic enzyme (NADP-ME) activity during H⁺-toxicity. Collectively, our results demonstrate that B supply alleviates H⁺-toxicity and promotes root growth by reducing ROS accumulation, attenuating intracellular acidic microenvironment to ensure normal chemical reactions in root tip cells.

Tribute Roland Douce, 1939-2018

On November 4, 2018, Roland Douce, Professor Emeritus at the University of Grenoble, France, died at the age of 79. In Grenoble, where he spent most of his scientific career, Roland Douce created a world-renowned school of plant science, studying the structure, functions, and interactions of plant organelles involved in photosynthesis, respiration, and photorespiration. His main achievements concern the chemical and functional characterization of chloroplast envelope membranes, the demonstration of the uniqueness of plant mitochondria, and the integration of metabolism within the plant cell, among manifold activities. Roland Douce devoted his whole life to science and research with passion and enthusiasm: he was a true charismatic leader.

Heterologous expression and kinetic characterization of the α, β and αβ blend of the PPi-dependent phosphofructokinase from Citrus sinensis

This work reports the molecular cloning and heterologous expression of the genes coding for α and β subunits of pyrophosphate-dependent phosphofructokinase (PPi-PFK) from orange. When expressed individually, both recombinant subunits were produced as highly purified monomeric proteins able to phosphorylate fructose-6-phosphate at the expenses of PPi (specific activity of 0.075 and 0.017 units. mg^-1 for α and β subunits, respectively). On the other hand, co-expression rendered a α₃β₃ hexamer with specific activity three orders of magnitude higher than the single subunits. All the conformations of the enzyme were characterized with respect to its kinetic properties and sensitivity to the regulator fructose-2,6-bisphosphate. A thorough review of current knowledge on the matter indicates that this is the first report of the recombinant production of active plant PPi-PFK and the characterization of its different conformations. This is a main contribution for future studies focused to better understand the enzyme properties and how it accomplishes its relevant role in plant metabolism.

Arabidopsis thaliana plants challenged with uranium reveal new insights into iron and phosphate homeostasis

Uranium (U) is a naturally occurring radionuclide that is toxic to plants. It is known to interfere with phosphate nutrition and to modify the expression of iron (Fe)-responsive genes. The transporters involved in the uptake of U from the environment are unknown. Here, we addressed whether IRT1, a high-affinity Fe²⁺ transporter, could contribute to U uptake in Arabidopsis thaliana. An irt1 null mutant was grown hydroponically in different conditions of Fe bioavailability and phosphate supply, and challenged with uranyl. Several physiological parameters (fitness, photosynthesis) were measured to evaluate the response to U treatment. We found that IRT1 is not a major route for U uptake in our experimental conditions. However, the analysis of irt1 indicated that uranyl interferes with Fe and phosphate homeostasis at different levels. In phosphate-sufficient conditions, the absence of the cation chelator EDTA in the medium has drastic consequences on the physiology of irt1, with important symptoms of Fe deficiency in chloroplasts. These effects are counterbalanced by U, probably because the radionuclide competes with Fe for complexation with phosphate and thus releases active Fe for metabolic and biogenic processes. Our study reveals that challenging plants with U is useful to decipher the complex interplay between Fe and phosphate.

Plant metabolism as studied by NMR spectroscopy

The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.

Intracellular transport and compartmentation of phosphate in plants

Phosphate (Pi) is an essential macronutrient with structural and metabolic roles within every compartment of the plant cell. Intracellular Pi transporters direct Pi to each organelle and also control its exchange between subcellular compartments thereby providing the means to coordinate compartmented metabolic processes, including glycolysis, photosynthesis, and respiration. In this review we summarize recent advances in the identification and functional analysis of Pi transporters that localize to vacuoles, chloroplasts, non-photosynthetic plastids, mitochondria, and the Golgi apparatus. Electrical potentials across intracellular membranes and the pH of subcellular environments will also be highlighted as key factors influencing the energetics of Pi transport, and therefore pose limits for Pi compartmentation.

Quantitative Imaging of FRET-Based Biosensors for Cell- and Organelle-Specific Analyses in Plants

Genetically encoded Förster resonance energy transfer (FRET)-based biosensors have been used to report relative concentrations of ions and small molecules, as well as changes in protein conformation, posttranslational modifications, and protein-protein interactions. Changes in FRET are typically quantified through ratiometric analysis of fluorescence intensities. Here we describe methods to evaluate ratiometric imaging data acquired through confocal microscopy of a FRET-based inorganic phosphate biosensor in different cells and subcellular compartments of Arabidopsis thaliana. Linear regression was applied to donor, acceptor, and FRET-derived acceptor fluorescence intensities obtained from images of multiple plants to estimate FRET ratios and associated location-specific spectral correction factors with high precision. FRET/donor ratios provided a combination of high dynamic range and precision for this biosensor when applied to the cytosol of both root and leaf cells, but lower precision when this ratiometric method was applied to chloroplasts. We attribute this effect to quenching of donor fluorescence because high precision was achieved with FRET/acceptor ratios and thus is the preferred ratiometric method for this organelle. A ligand-insensitive biosensor was also used to distinguish nonspecific changes in FRET ratios. These studies provide a useful guide for conducting quantitative ratiometric studies in live plants that is applicable to any FRET-based biosensor.

The Ca2+-Regulation of the Mitochondrial External NADPH Dehydrogenase in Plants Is Controlled by Cytosolic pH

NADPH is a key reductant carrier that maintains internal redox and antioxidant status, and that links biosynthetic, catabolic and signalling pathways. Plants have a mitochondrial external NADPH oxidation pathway, which depends on Ca²⁺ and pH in vitro, but concentrations of Ca²⁺ needed are not known. We have determined the K_0.5(Ca²⁺) of the external NADPH dehydrogenase from Solanum tuberosum mitochondria and membranes of E. coli expressing Arabidopsis thaliana NDB1 over the physiological pH range using O₂ and decylubiquinone as electron acceptors. The K_0.5(Ca²⁺) of NADPH oxidation was generally higher than for NADH oxidation, and unlike the latter, it depended on pH. At pH 7.5, K_0.5(Ca²⁺) for NADPH oxidation was high (≈100 μM), yet 20-fold lower K_0.5(Ca²⁺) values were determined at pH 6.8. Lower K_0.5(Ca²⁺) values were observed with decylubiquinone than with O₂ as terminal electron acceptor. NADPH oxidation responded to changes in Ca²⁺ concentrations more rapidly than NADH oxidation did. Thus, cytosolic acidification is an important activator of external NADPH oxidation, by decreasing the Ca²⁺-requirements for NDB1. The results are discussed in relation to the present knowledge on how whole cell NADPH redox homeostasis is affected in plants modified for the NDB1 gene.

Live imaging of inorganic phosphate in plants with cellular and subcellular resolution

Despite variable and often scarce supplies of inorganic phosphate (Pi) from soils, plants must distribute appropriate amounts of Pi to each cell and subcellular compartment to sustain essential metabolic activities. The ability to monitor Pi dynamics with subcellular resolution in live plants is, therefore, critical for understanding how this essential nutrient is acquired, mobilized, recycled, and stored. Fluorescence indicator protein for inorganic phosphate (FLIPPi) sensors are genetically encoded fluorescence resonance energy transfer-based sensors that have been used to monitor Pi dynamics in cultured animal cells. Here, we present a series of Pi sensors optimized for use in plants. Substitution of the enhanced yellow fluorescent protein component of a FLIPPi sensor with a circularly permuted version of Venus enhanced sensor dynamic range nearly 2.5-fold. The resulting circularly permuted FLIPPi sensor was subjected to a high-efficiency mutagenesis strategy that relied on statistical coupling analysis to identify regions of the protein likely to influence Pi affinity. A series of affinity mutants was selected with dissociation constant values of 0.08 to 11 mm, which span the range for most plant cell compartments. The sensors were expressed in Arabidopsis (Arabidopsis thaliana), and ratiometric imaging was used to monitor cytosolic Pi dynamics in root cells in response to Pi deprivation and resupply. Moreover, plastid-targeted versions of the sensors expressed in the wild type and a mutant lacking the PHOSPHATE TRANSPORT4;2 plastidic Pi transporter confirmed a physiological role for this transporter in Pi export from root plastids. These circularly permuted FLIPPi sensors, therefore, enable detailed analysis of Pi dynamics with subcellular resolution in live plants.

Hexokinase 1 is required for glucose-induced repression of bZIP63, At5g22920, and BT2 in Arabidopsis

Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes (bZIP63, At5g22920, BT2, MGD2, and TPS9) in Arabidopsis thaliana. In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/ transporting proteins (adg1, sex1, sus1-4, sus5/6, and tpt2), including also hexokinase1 (HXK1) loss- and gain-of-function plants-gin2.1 and oe3.2, respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63, At5g22920, and BT2. The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Overall, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63, At5g22920, and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression.

The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation

Understanding the mechanisms that allow plants to respond to variable and reduced availability of inorganic phosphate is of increasing agricultural importance because of the continuing depletion of the rock phosphate reserves that are used to combat inadequate phosphate levels in the soil. Changes in gene expression, protein levels, enzyme activities and metabolite levels all point to a reconfiguration of the central metabolic network in response to reduced availability of inorganic phosphate, but the metabolic significance of these changes can only be assessed in terms of the fluxes supported by the network. Steady-state metabolic flux analysis was used to define the metabolic phenotype of a heterotrophic Arabidopsis thaliana cell culture grown on a Murashige and Skoog medium containing 0, 1.25 or 5 mm inorganic phosphate. Fluxes through the central metabolic network were deduced from the redistribution of (13) C into metabolic intermediates and end products when cells were labelled with [1-(13) C], [2-(13) C], or [(13) C6 ]glucose, in combination with (14) C measurements of the rates of biomass accumulation. Analysis of the flux maps showed that reduced levels of phosphate in the growth medium stimulated flux through phosphoenolpyruvate carboxylase and malic enzyme, altered the balance between cytosolic and plastidic carbohydrate oxidation in favour of the plastid, and increased cell maintenance costs. We argue that plant cells respond to phosphate deprivation by reconfiguring the flux distribution through the pathways of carbohydrate oxidation to take advantage of better phosphate homeostasis in the plastid.

Molecular insights into how a deficiency of amylose affects carbon allocation--carbohydrate and oil analyses and gene expression profiling in the seeds of a rice waxy mutant

BACKGROUND

Understanding carbon partitioning in cereal seeds is of critical importance to develop cereal crops with enhanced starch yields for food security and for producing specified end-products high in amylose, β-glucan, or fructan, such as functional foods or oils for biofuel applications. Waxy mutants of cereals have a high content of amylopectin and have been well characterized. However, the allocation of carbon to other components, such as β-glucan and oils, and the regulation of the altered carbon distribution to amylopectin in a waxy mutant are poorly understood. In this study, we used a rice mutant, GM077, with a low content of amylose to gain molecular insight into how a deficiency of amylose affects carbon allocation to other end products and to amylopectin. We used carbohydrate analysis, subtractive cDNA libraries, and qPCR to identify candidate genes potentially responsible for the changes in carbon allocation in GM077 seeds.

RESULTS

Carbohydrate analysis indicated that the content of amylose in GM077 seeds was significantly reduced, while that of amylopectin significantly rose as compared to the wild type BP034. The content of glucose, sucrose, total starch, cell-wall polysaccharides and oil were only slightly affected in the mutant as compared to the wild type. Suppression subtractive hybridization (SSH) experiments generated 116 unigenes in the mutant on the wild-type background. Among the 116 unigenes, three, AGP, ISA1 and SUSIBA2-like, were found to be directly involved in amylopectin synthesis, indicating their possible roles in redirecting carbon flux from amylose to amylopectin. A bioinformatics analysis of the putative SUSIBA2-like binding elements in the promoter regions of the upregulated genes indicated that the SUSIBA2-like transcription factor may be instrumental in promoting the carbon reallocation from amylose to amylopectin.

CONCLUSION

Analyses of carbohydrate and oil fractions and gene expression profiling on a global scale in the rice waxy mutant GM077 revealed several candidate genes implicated in the carbon reallocation response to an amylose deficiency, including genes encoding AGPase and SUSIBA2-like. We believe that AGP and SUSIBA2 are two promising targets for classical breeding and/or transgenic plant improvement to control the carbon flux between starch and other components in cereal seeds.

Respiratory carbon fluxes in leaves

Leaf respiration is a major metabolic process that drives energy production and growth. Earlier works in this field were focused on the measurement of respiration rates in relation to carbohydrate content, photosynthesis, enzymatic activities or nitrogen content. Recently, several studies have shed light on the mechanisms describing the regulation of respiration in the light and in the dark and on associated metabolic flux patterns. This review will highlight advances made into characterizing respiratory fluxes and provide a discussion of metabolic respiration dynamics in relation to important biological functions.

High-resolution plant metabolomics: from mass spectral features to metabolites and from whole-cell analysis to subcellular metabolite distributions

The main goal of metabolomics is the comprehensive qualitative and quantitative analysis of the time- and space-resolved distribution of all metabolites present in a given biological system. Because metabolite structures, in contrast to transcript and protein sequences, are not directly deducible from the genomic DNA sequence, the massive increase in genomic information is only indirectly of use to metabolomics, leaving compound annotation as a key problem to be solved by the available analytical techniques. Furthermore, as metabolites vary widely in both concentration and chemical behavior, there is no single analytical procedure allowing the unbiased and comprehensive structural elucidation and determination of all metabolites present in a given biological system. In this review the different approaches for targeted and non-targeted metabolomics analysis will be described with special emphasis on mass spectrometry-based techniques. Particular attention is given to approaches which can be employed for the annotation of unknown compounds. In the second part, the different experimental approaches aimed at tissue-specific or subcellular analysis of metabolites are discussed including a range of non-mass spectrometry based technologies.

A simple and efficient method for the long-term preservation of plant cell suspension cultures

BACKGROUND

The repeated weekly subculture of plant cell suspension is labour intensive and increases the risk of variation from parental cells lines. Most of the procedures to preserve cultures are based on controlled freezing/thawing and storage in liquid nitrogen. However, cells viability after unfreezing is uncertain. The long-term storage and regeneration of plant cell cultures remains a priority.

RESULTS

Sycamore (Acer pseudoplatanus) and Arabidopsis cell were preserved over six months as suspensions cultures in a phosphate-free nutrient medium at 5°C. The cell recovery monitored via gas exchange measurements and metabolic profiling using in vitro and in vivo 13C- and 31P-NMR took a couple of hours, and cell growth restarted without appreciable delay. No measurable cell death was observed.

CONCLUSION

We provide a simple method to preserve physiologically homogenous plant cell cultures without subculture over several months. The protocol based on the blockage of cell growth and low culture temperature is robust for heterotrophic and semi-autotrophic cells and should be adjustable to cell lines other than those utilised in this study. It requires no specialized equipment and is suitable for routine laboratory use.

Expression pattern and putative function of EXL1 and homologous genes in Arabidopsis

The Arabidopsis EXORDIUM-LIKE1 (EXL1) gene (At1g35140) is required for adaptation to carbon (C)- and energy-limiting growth conditions. An exl1 loss of function mutant showed diminished biomass production in a low total irradiance growth regime, impaired survival during extended night, and impaired survival of anoxia stress. We show here additional expression data and discuss the putative roles of EXL1. We hypothesize that EXL1 suppresses brassinosteroid-dependent growth and controls C allocation in the cell. In-depth expression analysis of homologous genes suggests that the EXL2 (At5g64260) and EXL4 (At5g09440) genes play similar roles.

Role of phosphatidic acid in plant galactolipid synthesis

Phosphatidic acid (PA) is a precursor metabolite for phosphoglycerolipids and also for galactoglycerolipids, which are essential lipids for formation of plant membranes. PA has in addition a main regulatory role in a number of developmental processes notably in the response of the plant to environmental stresses. We review here the different pools of PA dispatched at different locations in the plant cell and how these pools are modified in different growth conditions, particularly during plastid membrane biogenesis and when the plant is exposed to phosphate deprivation. We analyze how these modifications can affect galactolipid synthesis by tuning the activity of MGD1 enzyme allowing a coupling of phospho- and galactolipid metabolisms. Some mechanisms are considered to explain how physicochemical properties of PA allow this lipid to act as a central internal sensor in plant physiology.