Metabolic profiling of the sink-to-source transition in developing leaves of quaking aspen

Comprehensive physiological, transcriptomic, and metabolomic analyses revealed the regulation mechanism of evergreen and cold resistance of Pinus koraiensis needles

As a significant fruit and timber tree species among conifers, Pinus koraiensis remains it evergreen status throughout the harsh winters of the north, a testament to its intricate and prolonged evolutionary adaptation. This study delves into the annual trends of physiological indicators, gene expression levels, and metabolite accumulation to dissect the seasonal adaptability of P. koraiensis needles. Chlorophyll content reaches its zenith primarily between July and September, whereas carotenoids persist until spring. Additionally, notable seasonal variations are observed in the levels of soluble sugar and protein. Transcriptome data is categorized into four distinct stages: spring (S2), summer (S3-S4), autumn (S5), and winter (S6-S1). The differential expression of transcription factor genes, including bHLH, MYB-related, AP2/ERF, C3H, and NAC, provides insights into the needles' seasonal adaptations. Analysis of chlorophyll and carotenoid metabolism, sugar metabolism, and the MAPK signaling pathway identifies PSY5 (Cluster-50735.3), AMY13 (Cluster-37114.0), pgm1 (Cluster-46022.0), and MEKK1-1 (Cluster-33069.0) may as potential key genes involved in sustaining the needle's evergreen nature and cold resistance. Ultimately, a comprehensive annual adaptability map for P. koraiensis is proposed, enhancing understanding of its responses to seasonal variations.

Tonoplast Sucrose Trafficking Modulates Starch Utilization and Water Deficit Behavior in Poplar Leaves

Leaf osmotic adjustment by the active accrual of compatible organic solutes (e.g. sucrose) contributes to drought tolerance throughout the plant kingdom. In Populus tremula x alba, PtaSUT4 encodes a tonoplast sucrose-proton symporter, whose downregulation by chronic mild drought or transgenic manipulation is known to increase leaf sucrose and turgor. While this may constitute a single drought tolerance mechanism, we now report that other adjustments which can occur during a worsening water deficit are damped when PtaSUT4 is constitutively downregulated. Specifically, we report that starch use and leaf relative water content (RWC) dynamics were compromised when plants with constitutively downregulated PtaSUT4 were subjected to a water deficit. Leaf RWC decreased more in wild-type and vector control lines than in transgenic PtaSUT4-RNAi (RNA-interference) or CRISPR (clustered regularly interspersed short palindromic repeats) knockout (KO) lines. The control line RWC decrease was accompanied by increased PtaSUT4 transcript levels and a mobilization of sucrose from the mesophyll-enriched leaf lamina into the midvein. The findings suggest that changes in SUT4 expression can increase turgor or decrease RWC as different tolerance mechanisms to reduced water availability. Evidence is presented that PtaSUT4-mediated sucrose partitioning between the vacuole and the cytosol is important not only for overall sucrose abundance and turgor, but also for reactive oxygen species (ROS) and antioxidant dynamics. Interestingly, the reduced capacity for accelerated starch breakdown under worsening water-deficit conditions was correlated with reduced ROS in the RNAi and KO lines. A role for PtaSUT4 in the orchestration of ROS, antioxidant, starch utilization and RWC dynamics during water stress and its importance in trees especially, with their high hydraulic resistances, is considered.

Potassium regulates diel leaf growth of Brassica napus by coordinating the rhythmic carbon supply and water balance

Carbon and water are two main factors limiting leaf expansion. Restriction of leaf growth by low availability of carbon or water is among the earliest visible effects of potassium (K) deficiency. It is not known how K is involved in regulating the rhythmic supply of these two substrates, which differ remarkably across the day-night cycle, affecting leaf expansion. We investigated the effects of different K regimes on the time courses of leaf expansion, carbon assimilation, carbohydrates, and hydraulic properties of Brassica napus. Potassium supply increased leaf area, predominantly by promoting night-time leaf expansion (>60%), which was mainly associated with increased availability of carbohydrates from photosynthetic carbon fixation and import from old leaves rather than improvement of leaf hydraulics. However, sufficient K improved leaf hydraulic conductance to balance diurnal evaporative water loss and increase the osmotic contribution of water-soluble carbohydrates, thereby maintaining leaf turgor and increasing the daytime expansion rate. The results also indicated an ontogenetic role of K in modifying the amplitude of circadian expansion; almost 80% of the increase in leaf area occurred before the area reached 66.9% of the mature size. Our data provide mechanistic insight into K-mediated diel coordination of rhythmic carbon supply and water balance in leaf expansion.

Characterizing the development of photosynthetic capacity in relation to chloroplast structure and mineral nutrition in leaves of three woody fruit species

Plants have evolved different developmental patterns of photosynthetic capacity to better adapt to changing environmental conditions. Natural variation in photosynthetic development offers great potential for improving crop productivity. In this study, leaf developmental patterns were characterized in three woody fruit tree species with distinct photosynthetic capacity and growth habits. Changes in the photosynthetic rate, photosystem II (PSII) efficiency, chloroplast ultrastructure, activities of photosynthetic enzymes, and contents of carbohydrates and mineral nutrients were examined at five developmental stages to explore the interspecific variation in photosynthetic development. Rapid development of photosynthetic machinery and high photosynthetic capacity were found in Indian jujube (Ziziphus mauritiana) and apple (Malus domestica), whose net CO2 assimilation rate (A) peaked at full leaf expansion (FLE). Litchi (Litchi chinensis), a delayed-greening species, showed slow development of photosynthetic competence, with A peaked after FLE. The low photosynthetic capacity of litchi during early leaf expansion was associated with its delayed chloroplast development, low accumulation of starch, and low activities of ribulose-1,5-bisphosphate carboxylase/oxygenase and NADP-glyceraldehyde-3-phosphate dehydrogenase. Correlations between mineral contents and A across leaf stages and species identified manganese as the rate-limiting nutrients in photosynthetic development in new leaves. Foliar spray of MnSO4 solution (1 g l-1) induced a short-term increase in photosynthesis in young leaves of litchi. These findings suggest that a better understanding of interspecific variation in photosynthetic development facilitates the development of new strategies for improving the photosynthetic efficiency of woody fruit trees.

The Evolution of Leaf Function during Development Is Reflected in Profound Changes in the Metabolic Composition of the Vacuole

During its development, the leaf undergoes profound metabolic changes to ensure, among other things, its growth. The subcellular metabolome of tomato leaves was studied at four stages of leaf development, with a particular emphasis on the composition of the vacuole, a major actor of cell growth. For this, leaves were collected at different positions of the plant, corresponding to different developmental stages. Coupling cytology approaches to non-aqueous cell fractionation allowed to estimate the subcellular concentrations of major compounds in the leaves. The results showed major changes in the composition of the vacuole across leaf development. Thus, sucrose underwent a strong allocation, being mostly located in the vacuole at the beginning of development and in the cytosol at maturity. Furthermore, these analyses revealed that the vacuole, rather rich in secondary metabolites and sugars in the growth phases, accumulated organic acids thereafter. This result suggests that the maintenance of the osmolarity of the vacuole of mature leaves would largely involve inorganic molecules.

Transcriptional Changes of Cell Wall Organization Genes and Soluble Carbohydrate Alteration during Leaf Blade Development of Rice Seedlings

Plant cell walls have two constituent parts with different components and developmental stages. Much of the mystery concerning the mechanisms of synthesis, decomposition, modification, and so forth, has been resolved using omics and microscopic techniques. However, it still remains to be determined how cell wall development progresses over time after leaf emergence. Our focus in the present study was to expand our knowledge of the molecular mechanisms associated with cell wall synthesis in rice leaf blade during three distinct stages (sink, sink-to-source transition, and source). The RNA-seq, quantitative reverse transcription PCR (qRT-PCR) and carbohydrate concentrations were evaluated using developing fifth leaf blades harvested at different time points. The results revealed that some of the essential genes for the primary cell wall (PCW) were highly upregulated in the sink-to-source transition compared to the sink stage, whereas those essential to the secondary cell wall (SCW) displayed relatively higher levels (p < 0.05) during the source stage. The concentrations of soluble carbohydrates differed via type rather than stage; we observed higher monosaccharides during the sink stage and higher di- and oligo-saccharides during the sink-to-source transition and source stages. In conclusion, our findings suggest that the transcriptional regulation of plant cell wall biosynthesis genes are both synchronistic with and independent of, and directly and indirectly governed by, the abundance of soluble carbohydrates in the developing leaf blade, and, finally, raffinose is likely to play a transport role comparable to sucrose.

Delayed greening in phosphorus-efficient Hakea prostrata (Proteaceae) is a photoprotective and nutrient-saving strategy

Hakea prostrata R.Br. (Proteaceae) shows a 'delayed greening' strategy of leaf development characterised by reddish young leaves that become green as they mature. This trait may contribute to efficient use of phosphorus (P) during leaf development by first investing P in the development of leaf structure followed by maturation of the photosynthetic machinery. In this study, we investigated the properties of delayed greening in a highly P-efficient species to enhance our understanding of the ecological significance of this trait as a nutrient-saving and photoprotective strategy. In glasshouse-grown plants, we assessed foliar pigments, fatty acids and nutrient composition across five leaf developmental stages. Young leaves had higher concentrations of anthocyanin, P, nitrogen (N), copper (Cu), xanthophyll-cycle pigments and saturated fatty acids than mature leaves. As leaves developed, the concentration of anthocyanins decreased, whereas that of chlorophyll and the double bond index of fatty acids increased. In mature leaves, ~60% of the fatty acids was α-linolenic acid (C18:3 n-3). Mature leaves also had higher concentrations of aluminium (Al), calcium (Ca) and manganese (Mn) than young leaves. We conclude that delayed greening in H. prostrata is a strategy that saves P as well as N and Cu through sequential allocation of these resources, first to cell production and structural development, and then to supplement chloroplast development. This strategy also protects young leaves against photodamage and oxidative stress during leaf expansion under high-light conditions.

Defoliation-induced compensatory transpiration is compromised in SUT4-RNAi Populus

The tonoplast sucrose transporter PtaSUT4 is well expressed in leaves of Populus tremula × Populus alba (INRA 717-IB4), and its inhibition by RNA-interference (RNAi) alters leaf sucrose homeostasis. Whether sucrose partitioning between the vacuole and the cytosol is modulated by PtaSUT4 for specific physiological outcomes in Populus remains unexplored. In this study, partial defoliation was used to elicit compensatory increases in photosynthesis and transpiration by the remaining leaves in greenhouse-grown poplar. Water uptake, leaf gas exchange properties, growth and nonstructural carbohydrate abundance in source and sink organs were then compared between wild-type and SUT4-RNAi lines. Partial defoliation increased maximum photosynthesis rates similarly in all lines. There was no indication that source leaf sugar levels changed differently between wild-type and RNAi plants following partial defoliation. Sink levels of hexose (glucose and fructose) and starch decreased similarly in all lines. Interestingly, plant water uptake after partial defoliation was not as well sustained in RNAi as in wild-type plants. While the compensatory increase in photosynthesis was similar between genotypes, leaf transpiration increased less robustly in RNAi than wild-type plants. SUT4-RNAi and wild-type source leaves differed constitutively in their bulk modulus of elasticity, a measure of leaf turgor, and storage water capacitance. The data demonstrate that reduced sucrose partitioning due to PtaSUT4-RNAi altered turgor control and compensatory transpiration capacity more strikingly than photosynthesis and sugar export. The results are consistent with the interpretation that SUT4 may control vacuolar turgor independently of sink carbon provisioning.

Age-Dependent Metabolic Profiles Unravel the Metabolic Relationships Within and Between Flax Leaves (Linum usitatissimum)

Flax for oil seed is a crop of increasing popularity, but its cultivation needs technical improvement. Important agronomic traits such as productivity and resistance to stresses are to be regarded as the result of the combined responses of individual organs and their inter-communication. Ultimately, these responses directly reflect the metabolic profile at the cellular level. Above ground, the complexity of the plant phenotype is governed by leaves at different developmental stages, and their ability to synthesise and exchange metabolites. In this study, the metabolic profile of differently-developed leaves was used firstly to discriminate flax leaf developmental stages, and secondly to analyse the allocation of the metabolites within and between leaves. For this purpose, the concentration of 52 metabolites, both primary and specialized, was followed by gas chromatography (GC-) and liquid chromatography coupled to mass spectrometry (LC-MS) in alternate pairs of flax leaves. On the basis of their metabolic content, three populations of leaves in different growth stages could be distinguished. Primary and specialized metabolites showed characteristic distribution patterns, and compounds similarly evolving with leaf age could be grouped by the aid of the Kohonen self-organising map (SOM) algorithm. Ultimately, visualisation of the correlations between metabolites via hierarchical cluster analysis (HCA) allowed the assessment of the metabolic fluxes characterising different leaf developmental stages, and the investigation of the relationships between primary and specialized metabolites.

Shared expression of crassulacean acid metabolism (CAM) genes pre-dates the origin of CAM in the genus Yucca

Crassulacean acid metabolism (CAM) is a carbon-concentrating mechanism that has evolved numerous times across flowering plants and is thought to be an adaptation to water-limited environments. CAM has been investigated from physiological and biochemical perspectives, but little is known about how plants evolve from C3 to CAM at the genetic or metabolic level. Here we take a comparative approach in analyzing time-course data of C3, CAM, and C3+CAM intermediate Yucca (Asparagaceae) species. RNA samples were collected over a 24 h period from both well-watered and drought-stressed plants, and were clustered based on time-dependent expression patterns. Metabolomic data reveal differences in carbohydrate metabolism and antioxidant response between the CAM and C3 species, suggesting that changes to metabolic pathways are important for CAM evolution and function. However, all three species share expression profiles of canonical CAM pathway genes, regardless of photosynthetic pathway. Despite differences in transcript and metabolite profiles between the C3 and CAM species, shared time-structured expression of CAM genes in both CAM and C3Yucca species suggests that ancestral expression patterns required for CAM may have pre-dated its origin in Yucca.

Shoot tip culture: a step towards 13C metabolite flux analysis of sink leaf metabolism

BACKGROUND

Better understanding of the physiological and metabolic status of plants can only be obtained when metabolic fluxes are accurately assessed in a growing plant. Steady state ¹³C-MFA has been established as a routine method for analysis of fluxes in plant primary metabolism. However, the experimental system needs to be improved for continuous carbon enrichment from labelled sugars into metabolites for longer periods until complex secondary metabolism reaches steady state.

RESULTS

We developed an in vitro plant culture strategy by using peppermint as a model plant with minimizing unlabelled carbon fixation where growing shoot tip was strongly dependent on labelled glucose for their carbon necessity. We optimized the light condition and detected the satisfactory phenotypical growth under the lower light intensity. Total volatile terpenes were also highest at the same light. Analysis of label incorporation into pulegone monoterpene after continuous U-¹³C₆ glucose feeding revealed nearly 100% ¹³C, even at 15 days after first leaf visibility (DALV). Label enrichment was gradually scrambled with increasing light intensity and leaf age. This study was validated by showing similar levels of label enrichment in proteinogenic amino acids. The efficiency of this method was also verified in oregano.

CONCLUSIONS

Our shoot tip culture depicted a method in achieving long term, stable and a high percentage of label accumulation in secondary metabolites within a fully functional growing plant system. It recommends the potential application for the investigations of various facets of plant metabolism by steady state ¹³C-MFA. The system also provides a greater potential to study sink leaf metabolism. Overall, we propose a system to accurately describe complex metabolic phenotypes in a growing plant.

Environmental Conditions and Species Identity Drive Metabolite Levels in Green Leaves and Leaf Litter of 14 Temperate Woody Species

Research Highlights: Leaf chemistry is a key driver of litter decomposition; however, studies directly comparing metabolites that are important for tree growth and defence across different woody species are scarce. Background and Objectives: Choosing 14 temperate woody species differing in their growth rates, nutrient demand, shade tolerance, and drought sensitivity, we hypothesized that the species would group according to their metabolite profiles based on their ecological background. Materials and Methods: We analysed total N and C, soluble amino acid, protein, and phenolic levels in green leaves and leaf litter of these species, each in two consecutive years. Results: Metabolite levels varied significantly across species and between the sampling years which differed in temperature and precipitation (i.e., colder/drier vs warmer/ wetter). Conclusions: The 14 woody species could not be grouped according to their green leaf or leaf litter metabolite profiles. In litter leaves, most of the variation was explained by total phenolics and total nitrogen levels, and in green leaves by total phenolics and total soluble amino acid levels. Local climate variation between the two consecutive years for green leaves or leaf litter led to significant differences in metabolite levels, although some of them were species-specific.

Overexpression of a cytosolic NADP+-isocitrate dehydrogenase causes alterations in the vascular development of hybrid poplars

Cytosolic NADP+-isocitrate dehydrogenase (ICDH) is one of the major enzymes involved in the production of 2-oxoglutarate for amino acid biosynthesis in plants. In most plants studied, ICDH is encoded by either one gene or a small gene family, and the protein sequence has been highly conserved during evolution, suggesting it plays different and essential roles in metabolism and differentiation. To elucidate the role of ICDH in hybrid poplar (Populus tremula x P. alba), transgenic plants overexpressing the Pinus pinaster gene were generated. Overexpression of ICDH resulted in hybrid poplar (Populus tremula × P. alba) trees with higher expression levels of the endogenous ICDH gene and higher enzyme content than control untransformed plants. Transgenic poplars also showed an increased expression of glutamine synthetase (GS1.3), glutamate decarboxylase (GAD) and other genes associated with vascular differentiation. Furthermore, these plants exhibited increased growth in height, longer internodes and enhanced vascular development in young leaves and the apical region of stem. Modifications in amino acid and organic acid content were observed in young leaves of the transgenic lines, suggesting an increased biosynthesis of amino acids for building new structures and also for transport to other sink organs, as expanding leaves or young stems. Taken together, these results support an important role of ICDH in plant growth and vascular development.

In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes

Mature oak (Quercus spp.) leaves, although abundantly available during the plants' developmental cycle, are rarely exploited as viable sources of genomic DNA. These leaves are rich in metabolites difficult to remove during standard DNA purification, interfering with downstream molecular genetics applications. The current work assessed whether in situ dark adaptation, to deplete sugar reserves and inhibit secondary metabolite synthesis could compensate for the difficulties encountered when isolating DNA from mature leaves rich in secondary metabolites. We optimized a rapid, commercial kit based method to extract genomic DNA from dark- and light-adapted leaves. We demonstrated that in situ dark adaptation increases the yield and quality of genomic DNA obtained from mature oak leaves, yielding templates of sufficiently high quality for direct downstream applications, such as PCR amplification and gene identification. The quality of templates isolated from dark-adapted pin oak leaves particularly improved the amplification of larger fragments in our experiments. From DNA extracts prepared with our optimized method, we identified for the first time partial segments of the genes encoding 18S rRNA and isoprene synthase (IspS) from pin oak (Quercus palustris), whose full genome has not yet been sequenced.

Evolutionary Divergences in Root Exudate Composition among Ecologically-Contrasting Helianthus Species

Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments.

Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development in Inga, a genus of tropical trees

Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment.

Metabolic acclimation of source and sink tissues to salinity stress in bermudagrass (Cynodon dactylon)

Salinity is one of the major environmental factors affecting plant growth and survival by modifying source and sink relationships at physiological and metabolic levels. Individual metabolite levels and/or ratios in sink and source tissues may reflect the complex interplay of metabolic activities in sink and source tissues at the whole-plant level. We used a non-targeted gas chromatography-mass spectrometry (GC-MS) approach to study sink and source tissue-specific metabolite levels and ratios from bermudagrass under salinity stress. Shoot growth rate decreased while root growth rate increased which lead to an increased root/shoot growth rate ratio under salt stress. A clear shift in soluble sugars (sucrose, glucose and fructose) and metabolites linked to nitrogen metabolism (glutamate, aspartate and asparagine) in favor of sink roots was observed, when compared with sink and source leaves. The higher shifts in soluble sugars and metabolites linked to nitrogen metabolism in favor of sink roots may contribute to the root sink strength maintenance that facilitated the recovery of the functional equilibrium between shoot and root, allowing the roots to increase competitive ability for below-ground resource capture. This trait could be considered in breeding programs for increasing salt tolerance, which would help maintain root functioning (i.e. water and nutrient absorption, Na⁺ exclusion) and adaptation to stress.

A Journey Through a Leaf: Phenomics Analysis of Leaf Growth in Arabidopsis thaliana

In Arabidopsis, leaves contribute to the largest part of the aboveground biomass. In these organs, light is captured and converted into chemical energy, which plants use to grow and complete their life cycle. Leaves emerge as a small pool of cells at the vegetative shoot apical meristem and develop into planar, complex organs through different interconnected cellular events. Over the last decade, numerous phenotyping techniques have been developed to visualize and quantify leaf size and growth, leading to the identification of numerous genes that contribute to the final size of leaves. In this review, we will start at the Arabidopsis rosette level and gradually zoom in from a macroscopic view on leaf growth to a microscopic and molecular view. Along this journey, we describe different techniques that have been key to identify important events during leaf development and discuss approaches that will further help unraveling the complex cellular and molecular mechanisms that underlie leaf growth.

Profiling of spatial metabolite distributions in wheat leaves under normal and nitrate limiting conditions

The control and interaction between nitrogen and carbon assimilatory pathways is essential in both photosynthetic and non-photosynthetic tissue in order to support metabolic processes without compromising growth. Physiological differences between the basal and mature region of wheat (Triticum aestivum) primary leaves confirmed that there was a change from heterotrophic to autotrophic metabolism. Fourier Transform Infrared (FT-IR) spectroscopy confirmed the suitability and phenotypic reproducibility of the leaf growth conditions. Principal Component-Discriminant Function Analysis (PC-DFA) revealed distinct clustering between base, and tip sections of the developing wheat leaf, and from plants grown in the presence or absence of nitrate. Gas Chromatography-Time of Flight/Mass Spectrometry (GC-TOF/MS) combined with multivariate and univariate analyses, and Bayesian network (BN) analysis, distinguished different tissues and confirmed the physiological switch from high rates of respiration to photosynthesis along the leaf. The operation of nitrogen metabolism impacted on the levels and distribution of amino acids, organic acids and carbohydrates within the wheat leaf. In plants grown in the presence of nitrate there was reduced levels of a number of sugar metabolites in the leaf base and an increase in maltose levels, possibly reflecting an increase in starch turnover. The value of using this combined metabolomics analysis for further functional investigations in the future are discussed.

Plant metabolite profiles and the buffering capacities of ecosystems

In spite of some inherent challenges, metabolite profiling is becoming increasingly popular under field conditions. It has been used successfully to address topics like species interactions, connections between growth and chemical stoichiometry or the plant's stress response. Stress exerts a particularly clear impact on plant metabolomes and has become a central topic in many metabolite profiling experiments in the fields. In contrast to phytochambers, however, external stress is often at least partially absorbed by the environment when measuring under field conditions. Such stress-buffering capacities of (agro)-ecosystems are of crucial interest given the ever-increasing anthropogenic impact on ecosystems and this review promotes the idea of using plant metabolite profiles for respective measurements. More specifically I propose to use parameters of the response of key plant species to a given stress treatment as proxies for measuring and comparing stress-buffering capacities of ecosystems. Stress response parameters accessible by metabolite profiling comprise for example the intensity or duration of the impact of stress or the ability of the plant organism to recover from this impact after a given time. Analyses of ecosystem stress-buffering capacities may improve our understanding of how ecosystems cope with stress and may improve our abilities to predict ecosystem changes.

Structural control of metabolic flux

Organisms have to continuously adapt to changing environmental conditions or undergo developmental transitions. To meet the accompanying change in metabolic demands, the molecular mechanisms of adaptation involve concerted interactions which ultimately induce a modification of the metabolic state, which is characterized by reaction fluxes and metabolite concentrations. These state transitions are the effect of simultaneously manipulating fluxes through several reactions. While metabolic control analysis has provided a powerful framework for elucidating the principles governing this orchestrated action to understand metabolic control, its applications are restricted by the limited availability of kinetic information. Here, we introduce structural metabolic control as a framework to examine individual reactions' potential to control metabolic functions, such as biomass production, based on structural modeling. The capability to carry out a metabolic function is determined using flux balance analysis (FBA). We examine structural metabolic control on the example of the central carbon metabolism of Escherichia coli by the recently introduced framework of functional centrality (FC). This framework is based on the Shapley value from cooperative game theory and FBA, and we demonstrate its superior ability to assign “share of control” to individual reactions with respect to metabolic functions and environmental conditions. A comparative analysis of various scenarios illustrates the usefulness of FC and its relations to other structural approaches pertaining to metabolic control. We propose a Monte Carlo algorithm to estimate FCs for large networks, based on the enumeration of elementary flux modes. We further give detailed biological interpretation of FCs for production of lactate and ATP under various respiratory conditions.

Insight into the functioning of metabolic control to meet changing demands is a first step in rational engineering of biological systems towards a desired behavior. Metabolic control analysis provides the means to examine the impact of change of reaction fluxes on a specific target flux based on kinetic modeling, but suffers from limitations of the kinetic approach. Here, we introduce and analyze structural metabolic control as a framework to overcome these limitations. We utilize functional centrality, a framework based on the Shapley value from cooperative game theory and flux balance analysis, to determine the contribution of individual reactions to the functions accomplished by a metabolic network. These contributions, in turn, depend on the control exerted on the remaining network. Functional centrality provides the mathematical means to gain further understanding of metabolic control. The potential applications range from facilitating strategies of rational strain design to drug target identification.

Multiplex micro-respiratory measurements of Arabidopsis tissues

Researchers often want to study the respiratory properties of individual parts of plants in response to a range of treatments. Arabidopsis is an obvious model for this work; however, because of its size, it represents a challenge for gas exchange measurements of respiration. The combination of micro-respiratory technologies with multiplex assays has the potential to bridge this gap, and make measurements possible in this model plant species. We show the adaptation of the commercial technology used for mammalian cell respiration analysis to study three critical tissues of interest: leaf sections, root tips and seeds. The measurement of respiration in single leaf discs has allowed the age dependence of the respiration rate in Arabidopsis leaves across the rosette to be observed. The oxygen consumption of single root tips from plate-grown seedlings shows the enhanced respiration of root tips and their time-dependent susceptibility to salinity. The monitoring of single Arabidopsis seeds shows the kinetics of respiration over 48 h post-imbibition, and the effect of the phytohormones gibberellic acid (GA3 ) and abscisic acid (ABA) on respiration during seed germination. These studies highlight the potential for multiplexed micro-respiratory assays to study oxygen consumption in Arabidopsis tissues, and open up new possibilities to screen and study mutants and to identify differences in ecotypes or populations of different plant species.

Proteomic analysis of grapevine (Vitis vinifera L.) leaf changes induced by transition to autotrophy and exposure to high light irradiance

Using a proteomics approach, we evaluated the response of heterotrophic and autotrophic leaves of grapevine when exposed to high light irradiation. From a total of 572 protein spots detected on two-dimensional gels, 143 spots showed significant variation caused by changes in the trophic state. High light treatment caused variation in 90 spots, and 51 spots showed variation caused by the interaction between both factors. Regarding the trophic state of the leaf, most of the proteins detected in the heterotrophic stage decreased in abundance when the leaf reached the autotrophic stage. Major differences induced by high light were detected in autotrophic leaves. In the high-light-treated autotrophic leaves several proteins involved in the oxidative stress response were up-regulated. This pattern was not observed in the high-light-treated heterotrophic leaves. This indicates that in these types of leaves other mechanisms different to the protein antioxidant system are acting to protect young leaves against the excess of light. This also suggests that these protective mechanisms rely on other sets of proteins or non-enzymatic molecules, or that differences in protein dynamics between the heterotrophic and autotrophic stages makes the autotrophic leaves more prone to the accumulation of oxidative stress response proteins.

BIOLOGICAL SIGNIFICANCE

Transition from a heterotrophic to an autotrophic state is a key period during which the anatomical, physiological and molecular characteristics of a leaf are defined. In many aspects the right functioning of a leaf at its mature stage depends on the conditions under what this transition occurs. This because apart of the genetic control, environmental factors like mineral nutrition, temperature, water supply, light etc. are also important in its control. Many anatomical and physiological changes have been described in several plant species, however in grapevine molecular data regarding changes triggered by this transition or by light stress are still scarce. In this study, we identify that the transition from heterotrophic to autotrophic state in grapevine triggers major changes in the leaf proteome, which are mainly related to processes such as protein synthesis, protein folding and degradation, photosynthesis and chloroplast development. With the exception of proteins involved in carbon fixation, that increased in abundance, most of the proteins detected during the heterotrophic stage decreased in abundance when the leaf reached its autotrophic stage. This is most likely because leaves have reached their full size and from now they have to work as a carbon source for sink organs located in other parts of the plant. Despite the potential control of this transition by light, to date, no studies using a proteomics approach have been conducted to gain a broader view of the effects of short-term high light stress. Our results indicate that short-term high light exposure has a major impact on the proteome of the autotrophic leaves, and trigger a differential accumulation of several proteins involved in the oxidative stress response. Surprisingly, heterotrophic leaves do not display this pattern which can be attributed to a lower sensitivity of these leaves to high light stimulus. In fact we discovered that heterotrophic leaves are more tolerant to light stress than autotrophic leaves. This finding is of high biological significance because it helps to understand how young leaves are able to evolve to autotrophy in areas where high light intensities are predominant. This also reveals in this type of leaves the existence of alternative mechanisms to address this stressful condition. These observations provide new insights into the molecular changes occurring during transition of leaves to autotrophy particularly when this transition occurs under high light intensities. This for example occurs during the springtime when the grapevine buds burst and the young leaves are suddenly exposed to high light intensities.

Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in Arabidopsis

Developmental senescence is a coordinated physiological process in plants and is critical for nutrient redistribution from senescing leaves to newly formed sink organs, including young leaves and developing seeds. Progress has been made concerning the genes involved and the regulatory networks controlling senescence. The resulting complex metabolome changes during senescence have not been investigated in detail yet. Therefore, we conducted a comprehensive profiling of metabolites, including pigments, lipids, sugars, amino acids, organic acids, nutrient ions, and secondary metabolites, and determined approximately 260 metabolites at distinct stages in leaves and siliques during senescence in Arabidopsis (Arabidopsis thaliana). This provided an extensive catalog of metabolites and their spatiotemporal cobehavior with progressing senescence. Comparison with silique data provides clues to source-sink relations. Furthermore, we analyzed the metabolite distribution within single leaves along the basipetal sink-source transition trajectory during senescence. Ceramides, lysolipids, aromatic amino acids, branched chain amino acids, and stress-induced amino acids accumulated, and an imbalance of asparagine/aspartate, glutamate/glutamine, and nutrient ions in the tip region of leaves was detected. Furthermore, the spatiotemporal distribution of tricarboxylic acid cycle intermediates was already changed in the presenescent leaves, and glucosinolates, raffinose, and galactinol accumulated in the base region of leaves with preceding senescence. These results are discussed in the context of current models of the metabolic shifts occurring during developmental and environmentally induced senescence. As senescence processes are correlated to crop yield, the metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence.

Constitutively elevated salicylic acid levels alter photosynthesis and oxidative state but not growth in transgenic populus

Salicylic acid (SA) has long been implicated in plant responses to oxidative stress. SA overproduction in Arabidopsis thaliana leads to dwarfism, making in planta assessment of SA effects difficult in this model system. We report that transgenic Populus tremula × alba expressing a bacterial SA synthase hyperaccumulated SA and SA conjugates without negative growth consequences. In the absence of stress, endogenously elevated SA elicited widespread metabolic and transcriptional changes that resembled those of wild-type plants exposed to oxidative stress-promoting heat treatments. Potential signaling and oxidative stress markers azelaic and gluconic acids as well as antioxidant chlorogenic acids were strongly coregulated with SA, while soluble sugars and other phenylpropanoids were inversely correlated. Photosynthetic responses to heat were attenuated in SA-overproducing plants. Network analysis identified potential drivers of SA-mediated transcriptome rewiring, including receptor-like kinases and WRKY transcription factors. Orthologs of Arabidopsis SA signaling components NON-EXPRESSOR OF PATHOGENESIS-RELATED GENES1 and thioredoxins were not represented. However, all members of the expanded Populus nucleoredoxin-1 family exhibited increased expression and increased network connectivity in SA-overproducing Populus, suggesting a previously undescribed role in SA-mediated redox regulation. The SA response in Populus involved a reprogramming of carbon uptake and partitioning during stress that is compatible with constitutive chemical defense and sustained growth, contrasting with the SA response in Arabidopsis, which is transient and compromises growth if sustained.

Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in Arabidopsis

Developmental senescence is a coordinated physiological process in plants and is critical for nutrient redistribution from senescing leaves to newly formed sink organs, including young leaves and developing seeds. Progress has been made concerning the genes involved and the regulatory networks controlling senescence. The resulting complex metabolome changes during senescence have not been investigated in detail yet. Therefore, we conducted a comprehensive profiling of metabolites, including pigments, lipids, sugars, amino acids, organic acids, nutrient ions, and secondary metabolites, and determined approximately 260 metabolites at distinct stages in leaves and siliques during senescence in Arabidopsis (Arabidopsis thaliana). This provided an extensive catalog of metabolites and their spatiotemporal cobehavior with progressing senescence. Comparison with silique data provides clues to source-sink relations. Furthermore, we analyzed the metabolite distribution within single leaves along the basipetal sink-source transition trajectory during senescence. Ceramides, lysolipids, aromatic amino acids, branched chain amino acids, and stress-induced amino acids accumulated, and an imbalance of asparagine/aspartate, glutamate/glutamine, and nutrient ions in the tip region of leaves was detected. Furthermore, the spatiotemporal distribution of tricarboxylic acid cycle intermediates was already changed in the presenescent leaves, and glucosinolates, raffinose, and galactinol accumulated in the base region of leaves with preceding senescence. These results are discussed in the context of current models of the metabolic shifts occurring during developmental and environmentally induced senescence. As senescence processes are correlated to crop yield, the metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence.

A core set of metabolite sink/source ratios indicative for plant organ productivity in Lotus japonicus

Plant growth is an important process in physiological as well as ecological respect and a number of metabolic parameters (elemental ratios as well as steady-state levels of individual metabolites) have been demonstrated to reflect this process on the whole plant level. Since plant growth is highly localized and is the result of a complex interplay of metabolic activities in sink and source organs, we propose that ratios in metabolite levels of sink and source organs are particularly well suited to characterize this process. To demonstrate such a connection, we studied organ-specific metabolite ratios from Lotus japonicus treated with mineral nutrients, salt stress or arbuscular mycorrhizal fungi. The plants were displaying a wide range of biomass and of flower/biomass ratios. In the analysis of our data we looked for correlations between shifts in sink/source metabolite ratios and plant productivity (biomass accumulated at the time of harvest). In addition we correlated shifts in metabolite ratios comparing competing generative and vegetative sink organs with shifts in productivity of the two organs (changes in flower/biomass ratios). In our analyses we observed clear shifts of carbohydrates and of compounds connected to nitrogen metabolism in favour of sink organs of particularly high productivity. These shifts were in agreement with general differences in metabolite steady-state levels when comparing sink and source organs. Our findings suggest that differentiation of sink and source organs during sampling for metabolomic experiments substantially increases the amount of information obtained from such experiments.

Coming of leaf age: control of growth by hydraulics and metabolics during leaf ontogeny

Leaf growth is the central process facilitating energy capture and plant performance. This is also one of the most sensitive processes to a wide range of abiotic stresses. Because hydraulics and metabolics are two major determinants of expansive growth (volumetric increase) and structural growth (dry matter increase), we review the interaction nodes between water and carbon. We detail the crosstalks between water and carbon transports, including the dual role of stomata and aquaporins in regulating water and carbon fluxes, the coupling between phloem and xylem, the interactions between leaf water relations and photosynthetic capacity, the links between Lockhart's hydromechanical model and carbon metabolism, and the central regulatory role of abscisic acid. Then, we argue that during leaf ontogeny, these interactions change dramatically because of uncoupled modifications between several anatomical and physiological features of the leaf. We conclude that the control of leaf growth switches from a metabolic to a hydromechanical limitation during the course of leaf ontogeny. Finally, we illustrate how taking leaf ontogeny into account provides insights into the mechanisms underlying leaf growth responses to abiotic stresses that affect water and carbon relations, such as elevated CO2, low light, high temperature and drought.

The tonoplast-localized sucrose transporter in Populus (PtaSUT4) regulates whole-plant water relations, responses to water stress, and photosynthesis

The Populus sucrose (Suc) transporter 4 (PtaSUT4), like its orthologs in other plant taxa, is tonoplast localized and thought to mediate Suc export from the vacuole into the cytosol. In source leaves of Populus, SUT4 is the predominantly expressed gene family member, with transcript levels several times higher than those of plasma membrane SUTs. A hypothesis is advanced that SUT4-mediated tonoplast sucrose fluxes contribute to the regulation of osmotic gradients between cellular compartments, with the potential to mediate both sink provisioning and drought tolerance in Populus. Here, we describe the effects of PtaSUT4-RNA interference (RNAi) on sucrose levels and raffinose family oligosaccharides (RFO) induction, photosynthesis, and water uptake, retention and loss during acute and chronic drought stresses. Under normal water-replete growing conditions, SUT4-RNAi plants had generally higher shoot water contents than wild-type plants. In response to soil drying during a short-term, acute drought, RNAi plants exhibited reduced rates of water uptake and delayed wilting relative to wild-type plants. SUT4-RNAi plants had larger leaf areas and lower photosynthesis rates than wild-type plants under well-watered, but not under chronic water-limiting conditions. Moreover, the magnitude of shoot water content, height growth, and photosynthesis responses to contrasting soil moisture regimes was greater in RNAi than wild-type plants. The concentrations of stress-responsive RFOs increased in wild-type plants but were unaffected in SUT4-RNAi plants under chronically dry conditions. We discuss a model in which the subcellular compartmentalization of sucrose mediated by PtaSUT4 is regulated in response to both sink demand and plant water status in Populus.

Multi-dimensional regulation of metabolic networks shaping plant development and performance

The metabolome is an integral part of a plant's life cycle and determines for a large part its external phenotype. It is the final, internal product of chemical interactions, obtained through developmental, genetic, and environmental inputs, and as such, it defines the state of a plant in terms of development and performance. Understanding its regulation will provide knowledge and new insights into the biochemical pathways and genetic interactions that shape the plant and its surroundings. In this review, we will focus on four dimensions that contribute to the huge diversity of metabolomes and we will illustrate how this diversity shapes the plant in terms of development and performance: (i) temporal regulation: the metabolome is extremely dynamic and temporal changes in the environment can have an immense impact on its composition; (ii) spatial regulation: metabolites can be very specific, in both quantitative and qualitative terms, to specialized organs, tissues, and cell types; (iii) environmental regulation: the metabolic profile of plants is highly dependent on environmental signals, such as light, temperature, and nutrients, and very susceptible to biotic and abiotic stresses; and (iv) genetic regulation: the biosynthesis, structure, and accumulation of metabolites have a genetic origin, and there is quantitative and qualitative variation for metabolomes within a species. We will address the contribution of these dimensions to the wide diversity of metabolomes and highlight how the multi-dimensional regulation of metabolism defines the plant's phenotype.

Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives

Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues (the metabolome). By analyzing differences between metabolomes using biostatistics (multivariate data analysis; pattern recognition), metabolites relevant to a specific phenotypic characteristic can be identified. However, the reliability of the analytical data is a prerequisite for correct biological interpretation in metabolomics analysis. In this review the challenges in quantitative metabolomics analysis with regards to analytical as well as data preprocessing steps are discussed. Recommendations are given on how to optimize and validate comprehensive silylation-based methods from sample extraction and derivatization up to data preprocessing and how to perform quality control during metabolomics studies. The current state of method validation and data preprocessing methods used in published literature are discussed and a perspective on the future research necessary to obtain accurate quantitative data from comprehensive GC-MS data is provided.

Metabolite Signature during Short-Day Induced Growth Cessation in Populus

The photoperiod is an important environmental signal for plants, and influences a wide range of physiological processes. For woody species in northern latitudes, cessation of growth is induced by short photoperiods. In many plant species, short photoperiods stop elongational growth after a few weeks. It is known that plant daylength detection is mediated by Phytochrome A (PHYA) in the woody hybrid aspen species. However, the mechanism of dormancy involving primary metabolism remains unclear. We studied changes in metabolite profiles in hybrid aspen leaves (young, middle, and mature leaves) during short-day-induced growth cessation, using a combination of gas chromatography-time-of-flight mass spectrometry, and multivariate projection methods. Our results indicate that the metabolite profiles in mature source leaves rapidly change when the photoperiod changes. In contrast, the differences in young sink leaves grown under long and short-day conditions are less distinct. We found short daylength induced growth cessation in aspen was associated with rapid changes in the distribution and levels of diverse primary metabolites. In addition, we conducted metabolite profiling of leaves of PHYA overexpressor (PHYAOX) and those of the control to find the discriminative metabolites between PHYAOX and the control under the short-day conditions. The metabolite changes observed in PHYAOX leaves, together with those in the source leaves, identified possible candidates for the metabolite signature (e.g., 2-oxo-glutarate, spermidine, putrescine, 4-amino-butyrate, and tryptophan) during short-day-induced growth cessation in aspen leaves.

Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice

Rice plants grown in paddy fields preferentially use ammonium as a source of inorganic nitrogen. Glutamine synthetase (GS) catalyses the conversion of ammonium to glutamine. Of the three genes encoding cytosolic GS in rice, OsGS1;1 is critical for normal growth and grain filling. However, the basis of its physiological function that may alter the rate of nitrogen assimilation and carbon metabolism within the context of metabolic networks remains unclear. To address this issue, we carried out quantitative comparative analyses between the metabolite profiles of a rice mutant lacking OsGS1;1 and its background wild type (WT). The mutant plants exhibited severe retardation of shoot growth in the presence of ammonium compared with the WT. Overaccumulation of free ammonium in the leaf sheath and roots of the mutant indicated the importance of OsGS1;1 for ammonium assimilation in both organs. The metabolite profiles of the mutant line revealed: (i) an imbalance in levels of sugars, amino acids and metabolites in the tricarboxylic acid cycle, and (ii) overaccumulation of secondary metabolites, particularly in the roots under a continuous supply of ammonium. Metabolite-to-metabolite correlation analysis revealed the presence of mutant-specific networks between tryptamine and other primary metabolites in the roots. These results demonstrated a crucial function of OsGS1;1 in coordinating the global metabolic network in rice plants grown using ammonium as the nitrogen source.

The sucrose transporter family in Populus: the importance of a tonoplast PtaSUT4 to biomass and carbon partitioning

Plasma membrane, proton-coupled Group II sucrose symporters (SUT) mediate apoplastic phloem loading and sucrose efflux from source leaves in Arabidopsis and agricultural crop species that have been studied to date. We now report that the most abundantly expressed SUT isoform in Populus tremula×alba, PtaSUT4, is a tonoplast (Group IV) symporter. PtaSUT4 transcripts were readily detected in conducting as well as mesophyll cells in stems and source leaves. In comparison, Group II orthologs PtaSUT1 and PtaSUT3 were very weakly expressed in leaves. Both Group II and Group IV SUT genes were expressed in secondary stem xylem of Populus. Transgenic poplars with RNAi-suppressed PtaSUT4 exhibited increased leaf-to-stem biomass ratios, elevated sucrose content in source leaves and stems, and altered phenylpropanoid metabolism. Transcript abundance of several carbohydrate-active enzymes and phenylalanine ammonia-lyases was also altered in transgenic source leaves. Nitrogen-limitation led to a down-regulation of vacuolar invertases in all plants, which resulted in an augmentation of sucrose pooling and hexose depletion in source leaves and secondary xylem of the transgenic plants. These results are consistent with a major role for PtaSUT4 in orchestrating the intracellular partitioning, and consequently, the efflux of sucrose from source leaves and the utilization of sucrose by lateral and terminal sinks. Our findings also support the idea that PtaSUT4 modulates sucrose efflux and utilization in concert with plant N-status.

Metabolomic approaches toward understanding nitrogen metabolism in plants

Plants can assimilate inorganic nitrogen (N) sources to organic N such as amino acids. N is the most important of the mineral nutrients required by plants and its metabolism is tightly coordinated with carbon (C) metabolism in the fundamental processes that permit plant growth. Increased understanding of N regulation may provide important insights for plant growth and improvement of quality of crops and vegetables because N as well as C metabolism are fundamental components of plant life. Metabolomics is a global biochemical approach useful to study N metabolism because metabolites not only reflect the ultimate phenotypes (traits), but can mediate transcript levels as well as protein levels directly and/or indirectly under different N conditions. This review outlines analytical and bioinformatic techniques particularly used to perform metabolomics for studying N metabolism in higher plants. Examples are used to illustrate the application of metabolomic techniques to the model plants Arabidopsis and rice, as well as other crops and vegetables.

Metabolic profiling reveals local and systemic responses of host plants to nematode parasitism

The plant parasitic beet cyst nematode Heterodera schachtii induces syncytial feeding structures in Arabidopsis roots. The feeding structures form strong sink tissues that have been suggested to be metabolically highly active. In the present study, metabolic profiling and gene targeted expression analyses were performed in order to study the local and systemic effects of nematode infection on the plant host. The results showed increased levels of many amino acids and phosphorylated metabolites in syncytia, as well as high accumulation of specific sugars such as 1-kestose that do not accumulate naturally in Arabidopsis roots. A correlation-based network analysis revealed highly activated and coordinated metabolism in syncytia compared to non-infected control roots. An integrated analysis of the central primary metabolism showed a clear coherence of metabolite and transcript levels, indicating transcriptional regulation of specific pathways. Furthermore, systemic effects of nematode infection were demonstrated by correlation-based network analysis as well as independent component analysis. 1-kestose, raffinose, alpha,alpha-trehalose and three non-identified analytes showed clear systemic accumulation, indicating future potential for diagnostic and detailed metabolic analyses. Our studies open the door towards understanding the complex remodelling of plant metabolism in favour of the parasitizing nematode.

Metabolomic evaluation of pulsed electric field-induced stress on potato tissue

Metabolite profiling was used to characterize stress responses of potato tissue subjected to reversible electroporation, providing insights on how potato tissue responds to a physical stimulus such as pulsed electric fields (PEF), which is an artificial stress. Wounded potato tissue was subjected to field strengths ranging from 200 to 400 V/cm, with a single rectangular pulse of 1 ms. Electroporation was demonstrated by propidium iodide staining of the cell nucleae. Metabolic profiling of data obtained through GC/TOF-MS and UPLC/TOF-MS complemented with orthogonal projections to latent structures clustering analysis showed that 24 h after the application of PEF, potato metabolism shows PEF-specific responses characterized by the changes in the hexose pool that may involve starch and ascorbic acid degradation.

Molecular phenotyping of lignin-modified tobacco reveals associated changes in cell-wall metabolism, primary metabolism, stress metabolism and photorespiration

Lignin is an important component of secondarily thickened cell walls. Cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) are two key enzymes that catalyse the penultimate and last steps in the biosynthesis of the monolignols. Downregulation of CCR in tobacco (Nicotiana tabacum) has been shown to reduce lignin content, whereas lignin in tobacco downregulated for CAD incorporates more aldehydes. We show that altering the expression of either or both genes in tobacco has far-reaching consequences on the transcriptome and metabolome. cDNA-amplified fragment length polymorphism-based transcript profiling, combined with HPLC and GC-MS-based metabolite profiling, revealed differential transcripts and metabolites within monolignol biosynthesis, as well as a substantial network of interactions between monolignol and other metabolic pathways. In general, in all transgenic lines, the phenylpropanoid biosynthetic pathway was downregulated, whereas starch mobilization was upregulated. CCR-downregulated lines were characterized by changes at the level of detoxification and carbohydrate metabolism, whereas the molecular phenotype of CAD-downregulated tobacco was enriched in transcript of light- and cell-wall-related genes. In addition, the transcript and metabolite data suggested photo-oxidative stress and increased photorespiration, mainly in the CCR-downregulated lines. These predicted effects on the photosynthetic apparatus were subsequently confirmed physiologically by fluorescence and gas-exchange measurements. Our data provide a molecular picture of a plant's response to altered monolignol biosynthesis.

Changes in the sugarcane metabolome with stem development. Are they related to sucrose accumulation?

Sucrose content increases with internode development down the stem of sugarcane. In an attempt to determine which other changes in metabolites may be linked to sucrose accumulation gas chromatography-mass spectrometry was used to obtain metabolic profiles from methanol/water extracts of four samples of different age down the stem of cultivar Q117. Extracts were derivatized with either N-methyl-N-(trimethylsilyl) trifluoracetamide (TMS) or N-methyl N-(tert-butyldimethylsilyl) trifluoroacetamide (TBS) separately in order to increase the number of metabolites that could be detected. This resulted in the measurement of 121 and 71 metabolites from the TMS and TBS derivatization, respectively. Fifty-five metabolites were identified using commercial and publicly available libraries. Statistical analysis of the metabolite profiles resulted in clustering of tissue types. Particular metabolites were correlated with the level of sucrose accumulation, which as expected increased down the stem. Metabolites, such as tricarboxylic acid cycle intermediates and amino acids, were more abundant in the M2 sample (meristem to internode 2) that was actively growing and decreased in an apparently coordinated developmentally programmed manner in more mature internodes down the stem. However, other metabolites such as trehalose and raffinose showed positive correlations with sucrose concentration. Here we discuss the technique used to measure metabolites in sugarcane and the changes in metabolite abundance down the sugarcane stem.

Metabolite profiling of Douglas-fir (Pseudotsuga menziesii) field trials reveals strong environmental and weak genetic variation

The primary objective of this study was to assess metabolomics for its capacity to discern biological variation among 10 full-sib families of a Douglas-fir tree breeding population, replicated on two sites. The differential accumulation of small metabolites in developing xylem was examined through metabolite profiles (139 metabolites common to 181 individual trees) generated by gas chromatography mass spectrometry and a series of statistical analyses that incorporated family, site, and tree growth and quantitative phenotypic wood traits (wood density, microfibril angle, wood chemistry and fiber morphology). Multivariate discriminant, canonical discriminant and factor analyses and broad-sense heritabilities revealed that metabolic and phenotypic traits alike were strongly related to site, while similar associations relating to genetic (family) structure were weak in comparison. Canonical correlation analysis subsequently identified correlations between specific phenotypic traits (i.e. tree growth, fibre morphology and wood chemistry) and metabolic traits (i.e. carbohydrate and lignin biosynthetic metabolites), demonstrating a coherent relationship between genetics, metabolism, environmental and phenotypic expression in wood-forming tissue. The association between cambial metabolites and tree phenotype, as revealed by metabolite profiling, demonstrates the value of metabolomics for systems biology approaches to understanding tree growth and secondary cell wall biosynthesis in plants.

Developmentally controlled farnesylation modulates AtNAP1;1 function in cell proliferation and cell expansion during Arabidopsis leaf development

In multicellular organisms, organogenesis requires tight control and coordination of cell proliferation, cell expansion, and cell differentiation. We have identified Arabidopsis (Arabidopsis thaliana) nucleosome assembly protein 1 (AtNAP1;1) as a component of a regulatory mechanism that connects cell proliferation to cell growth and expansion during Arabidopsis leaf development. Molecular, biochemical, and kinetic studies of AtNAP1;1 gain- or loss-of-function mutants indicate that AtNAP1;1 promotes cell proliferation or cell expansion in a developmental context and as a function of the farnesylation status of the protein. AtNAP1;1 was farnesylated and localized to the nucleus during the cell proliferation phase of leaf development when it promotes cell division. Later in leaf development, nonfarnesylated AtNAP1;1 accumulates in the cytoplasm when it promotes cell expansion. Ectopic expression of nonfarnesylated AtNAP1;1, which localized to the cytoplasm, disrupts this developmental program by promoting unscheduled cell expansion during the proliferation phase.

Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles

Grapes are grown in semiarid environments, where drought and salinity are common problems. Microarray transcript profiling, quantitative reverse transcription-PCR, and metabolite profiling were used to define genes and metabolic pathways in Vitis vinifera cv. Cabernet Sauvignon with shared and divergent responses to a gradually applied and long-term (16 days) water-deficit stress and equivalent salinity stress. In this first-of-a-kind study, distinct differences between water deficit and salinity were revealed. Water deficit caused more rapid and greater inhibition of shoot growth than did salinity at equivalent stem water potentials. One of the earliest responses to water deficit was an increase in the transcript abundance of RuBisCo activase (day 4), but this increase occurred much later in salt-stressed plants (day 12). As water deficit progressed, a greater number of affected transcripts were involved in metabolism, transport, and the biogenesis of cellular components than did salinity. Salinity affected a higher percentage of transcripts involved in transcription, protein synthesis, and protein fate than did water deficit. Metabolite profiling revealed that there were higher concentrations of glucose, malate, and proline in water-deficit-treated plants as compared to salinized plants. The metabolite differences were linked to differences in transcript abundance of many genes involved in energy metabolism and nitrogen assimilation, particularly photosynthesis, gluconeogenesis, and photorespiration. Water-deficit-treated plants appear to have a higher demand than salinized plants to adjust osmotically, detoxify free radicals (reactive oxygen species), and cope with photoinhibition.

MET-IDEA: Data Extraction Tool for Mass Spectrometry-Based Metabolomics

A current and significant limitation to metabolomics is the large-scale, high-throughput conversion of raw chromatographically coupled mass spectrometry datasets into organized data matrices necessary for further statistical processing and data visualization. This article describes a new data extraction tool, MET-IDEA (Metabolomics Ion-based Data Extraction Algorithm) which surmounts this void. MET-IDEA is compatible with a diversity of chromatographically coupled mass spectrometry systems, generates an output similar to traditional quantification methods, utilizes the sensitivity and selectivity associated with selected ion quantification, and greatly reduces the time and effort necessary to obtain large-scale organized datasets by several orders of magnitude. The functionality of MET-IDEA is illustrated using metabolomics data obtained for elicited cell culture exudates from the model legume, Medicago truncatula. The results indicate that MET-IDEA is capable of rapidly extracting semiquantitative data from raw data files, which allows for more rapid biological insight. MET-IDEA is freely available to academic users upon request.

Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period

BACKGROUND

This study analyzes metabolomic data from a rice tillering (branching) developmental profile to define a set of biomarker metabolites that reliably captures the metabolite variance of this plant developmental event, and which has potential as a basis for rapid comparative screening of metabolite profiles in relation to change in development, environment, or genotype. Changes in metabolism, and in metabolite profile, occur as a part of, and in response to, developmental events. These changes are influenced by the developmental program, as well as external factors impinging on it. Many samples are needed, however, to characterize quantitative aspects of developmental variation. A biomarker metabolite set could benefit screening of quantitative plant developmental variation by providing some of the advantages of both comprehensive metabolomic studies and focused studies of particular metabolites or pathways.

RESULTS

An appropriate set of biomarker metabolites to represent the plant developmental period including the initiation and early growth of rice tillering (branching) was obtained by: (1) determining principal components of the comprehensive metabolomic profile, then (2) identifying clusters of metabolites representing variation in loading on the first three principal components, and finally (3) selecting individual metabolites from these clusters that were known to be common among diverse organisms. The resultant set of 21 biomarker metabolites was reliable (P = 0.001) in capturing 83% of the metabolite variation in development. Furthermore, a subset of the biomarker metabolites was successful (P = 0.05) in correctly predicting metabolite change in response to environment as determined in another rice metabolomics study.

CONCLUSION

The ability to define a set of biomarker metabolites that reliably captures the metabolite variance of a plant developmental event was established. The biomarker metabolites are all commonly present in diverse organisms, so studies of their quantitative relationships can provide comparative information concerning metabolite profiles in relation to change in plant development, environment, or genotype.