Metabolic footprinting study of white spruce somatic embryogenesis using NMR spectroscopy

Identification of Metabolic Pathways Differentially Regulated in Somatic and Zygotic Embryos of Maritime Pine

Embryogenesis is a complex phase of conifer development involving hundreds of genes, and a proper understanding of this process is critical not only to produce embryos with different applied purposes but also for comparative studies with angiosperms. A global view of transcriptome dynamics during pine somatic and zygotic embryogenesis is currently missing. Here, we present a genome-wide transcriptome analysis of somatic and zygotic embryos at three developmental stages to identify conserved biological processes and gene functions during late embryogenesis. Most of the differences became more significant as the developmental process progressed from early to cotyledonary stages, and a higher number of genes were differentially expressed in somatic than in zygotic embryos. Metabolic pathways substantially affected included those involved in amino acid biosynthesis and utilization, and this difference was already observable at early developmental stages. Overall, this effect was found to be independent of the line (genotype) used to produce the somatic embryos. Additionally, transcription factors differentially expressed in somatic versus zygotic embryos were analyzed. Some potential hub regulatory genes were identified that can provide clues as to what transcription factors are controlling the process and to how the observed differences between somatic and zygotic embryogenesis in conifers could be regulated.

Current Proteomic and Metabolomic Knowledge of Zygotic and Somatic Embryogenesis in Plants

Embryogenesis is the primary developmental program in plants. The mechanisms that underlie the regulation of embryogenesis are an essential research subject given its potential contribution to mass in vitro propagation of profitable plant species. Somatic embryogenesis (SE) refers to the use of in vitro techniques to mimic the sexual reproduction program known as zygotic embryogenesis (ZE). In this review, we synthesize the current state of research on proteomic and metabolomic studies of SE and ZE in angiosperms (monocots and dicots) and gymnosperms. The most striking finding was the small number of studies addressing ZE. Meanwhile, the research effort focused on SE has been substantial but disjointed. Together, these research gaps may explain why the embryogenic induction stage and the maturation of the somatic embryo continue to be bottlenecks for efficient and large-scale regeneration of plants. Comprehensive and integrative studies of both SE and ZE are needed to provide the molecular foundation of plant embryogenesis, information which is needed to rationally guide experimental strategies to solve SE drawbacks in each species.

Polyphenol oxidase (PPO) arm of catecholamine pathway catalyzes the conversion of L-tyrosine to L-DOPA in Mucuna pruriens (L.) DC var. pruriens: An integrated pathway analysis using field grown and in vitro callus cultures

Mucuna pruriens (L.) DC var. pruriens is the natural source for _L-DOPA, precursor of the neurotransmitter dopamine, used widely in the treatment of Parkinson's disease. However, _L-DOPA synthesis in plants is mediated either by Catecholamine (CA) pathway or alternate pathway catalyzed by Cytochrome P450 (CYP450) class of enzymes. Interestingly, the CA pathway itself can be initiated either by tyrosine hydroxylase (TH) or polyphenol oxidase (PPO). The CA pathway mediated synthesis of _L-DOPA has not yet been proved in M. pruriens albeit strong indications. Therefore, the present investigation is focused on metabolite analysis of major intermediates of CA pathway up to the formation of dopamine and expression analysis of the selected genes, in different tissues and callus cultures. The four major intermediates, _L-tyrosine, tyramine, _L-DOPA and dopamine, were detected using NMR spectroscopy and quantified by HPLC in the callus cultures and in different tissues of the field plant, respectively. The various stages of leaf tissue were also analyzed for metabolite profiling. The relative amount of intermediates detected during the ontogeny of leaf indicates that PPO mediated conversion of _L-tyrosine to dopamine through _L-DOPA is relatively higher compared to dopamine production from tyramine. Among the two possible enzymes, activity of PPO was 6.5-fold more than TH in metabolically active young leaves compared to intermediate leaves. The gene expression profiles comprising upstream genes of _L-tyrosine synthesis and downstream up to dopamine synthesis shows strong correlation with _L-DOPA synthesis. The study validates CA pathway mediated synthesis of _L-DOPA with PPO as candidate enzyme, in M. pruriens.

Cold deacclimation mechanisms and reacclimation potential in flower buds of blackcurrant (Ribes nigrum)

As a consequence of global climate change, cold acclimation and deacclimation cycles are becoming increasingly frequent during winter in temperate regions. However, little is known about plant deacclimation and in particular reacclimation mechanisms, although deacclimation resistance and the ability to reacclimate may have wide-ranging consequences regarding plant productivity in a changing climate. Here, we report time-dependent responses of freezing tolerance, respiration rates, metabolite contents (high-resolution magic angle spinning NMR) and fatty acid levels (gas chromatography) in flower buds of two ecodormant Ribes nigrum cultivars exposed to three different deacclimation temperatures followed by a reacclimation treatment at 4°C. The data reveal that despite differences in the progression of deacclimation, the capacity of blackcurrant flower buds to reharden in late winter is virtually non-existing, implying that increasingly irregular temperature patterns is critical for blackcurrant fruit yield. The early phase of deacclimation is associated with a transient increase in respiration and decreasing contents of amino acids, tricarboxylic acid (TCA) cycle intermediates and sugars, indicating an increased need for carbon sources and respiratory energy production for the activation of growth. Decreasing sugar levels may additionally cause loss of freezing tolerance. Deacclimation also involves desaturation of membrane lipids, which likely also contributes to decreased freezing tolerance but may also reflect biosynthesis of signaling molecules stimulating growth and floral organ differentiation. These data provide new insights into the under-researched deacclimation mechanisms and the ability of blackcurrant to reacclimate following different advancements of deacclimation and contribute to our understanding of plant responses to increasingly irregular temperature patterns.

Metabolome and Transcriptome Association Analysis Reveals Dynamic Regulation of Purine Metabolism and Flavonoid Synthesis in Transdifferentiation during Somatic Embryogenesis in Cotton

Plant regeneration via somatic embryogenesis (SE) is a key step during genetic engineering. In the current study, integrated widely targeted metabolomics and RNA sequencing were performed to investigate the dynamic metabolic and transcriptional profiling of cotton SE. Our data revealed that a total of 581 metabolites were present in nonembryogenic staged calli (NEC), primary embryogenic calli (PEC), and initiation staged globular embryos (GE). Of the differentially accumulated metabolites (DAMs), nucleotides, and lipids were specifically accumulated during embryogenic differentiation, whereas flavones and hydroxycinnamoyl derivatives were accumulated during somatic embryo development. Additionally, metabolites related to purine metabolism were significantly enriched in PEC vs. NEC, whereas in GE vs. PEC, DAMs were remarkably associated with flavonoid biosynthesis. An association analysis of the metabolome and transcriptome data indicated that purine metabolism and flavonoid biosynthesis were co-mapped based on the Kyoto encyclopedia of genes and genomes (KEGG) database. Moreover, purine metabolism-related genes associated with signal recognition, transcription, stress, and lipid binding were significantly upregulated. Moreover, several classic somatic embryogenesis (SE) genes were highly correlated with their corresponding metabolites that were involved in purine metabolism and flavonoid biosynthesis. The current study identified a series of potential metabolites and corresponding genes responsible for SE transdifferentiation, which provides a valuable foundation for a deeper understanding of the regulatory mechanisms underlying cell totipotency at the molecular and biochemical levels.

Metabolic Fingerprinting of Dormant and Active Flower Primordia of Ribes nigrum Using High-Resolution Magic Angle Spinning NMR

Global warming may modify the timing of dormancy release and spring growth of buds of temperate fruit crops. Environmental regulation of the activity-dormancy cycle in perennial plants remains poorly understood at the metabolic level. Especially, the fine-scale metabolic dynamics in the meristematic zone within buds has received little attention. In this work we performed metabolic profiling of intact floral primordia of Ribes nigrum isolated from buds differing in dormancy status using high-resolution magic angle spinning (HR-MAS) NMR. The technique proved useful in monitoring different groups of metabolites, e.g., carbohydrates and amino acids, in floral primordia and allowed metabolic separation of primordia from endo- and ecodormant buds. In addition, due to its nondestructive character, HR-MAS NMR may provide novel insights into cellular compartmentation of individual biomolecules that cannot be obtained using liquid-state NMR. Out results show that HR-MAS NMR may be an important method for metabolomics of intact plant structures.

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.

Elucidation of the polyamine biosynthesis pathway during Brazilian pine (Araucaria angustifolia) seed development

Polyamines (PAs), such as spermidine and spermine, as well as amino acids that are substrates for their biosynthesis, are known to be essential for plant development. However, little is known about the gene expression and metabolic switches associated with the ornithine/arginine and PA biosynthetic pathway during seed development in conifers. To understand these metabolic switches, the enzyme activity of arginine decarboxylase and ornithine decarboxylase, as well as the contents of PAs and amino acids were evaluated in three Araucaria angustifolia (Bertol. Kuntze) seed developmental stages in combination with expression profile analyses of genes associated with the ornithine/arginine and PA biosynthetic pathway. Twelve genes were selected for further analysis and it was shown that the expression profiles of AaADC and AaSAMDC were up-regulated during zygotic embryo development. Polyamines and amino acids were found to accumulate differently in embryos and megagametophytes, and the transition from the globular to the cotyledonary stage was marked by an increase in free and conjugated spermidine and spermine contents. Putrescine is made from arginine, which was present at low content at the late embryogenesis stage, when high content of citrulline was observed. Differences in amino acids, PAs and gene expression profiles of biosynthetic genes at specific seed stages and at each seed transition stage were investigated, providing insights into molecular and physiological aspects of conifer embryogenesis for use in future both basic and applied studies.

Molecular Aspects of Conifer Zygotic and Somatic Embryo Development: A Review of Genome-Wide Approaches and Recent Insights

Genome-wide profiling (transcriptomics, proteomics, metabolomics) is providing unprecedented opportunities to unravel the complexity of coordinated gene expression during embryo development in trees, especially conifer species harboring "giga-genome." This knowledge should be critical for the efficient delivery of improved varieties through seeds and/or somatic embryos in fluctuating markets and to cope with climate change. We reviewed "omics" as well as targeted gene expression studies during both somatic and zygotic embryo development in conifers and tentatively puzzled over the critical processes and genes involved at the specific developmental and transition stages. Current limitations to the interpretation of these large datasets are going to be lifted through the ongoing development of comprehensive genome resources in conifers. Nevertheless omics already confirmed that master regulators (e.g., transcription and epigenetic factors) play central roles. As in model angiosperms, the molecular regulation from early to late embryogenesis may mainly arise from spatiotemporal modulation of auxin-, gibberellin-, and abscisic acid-mediated responses. Omics also showed the potential for the development of tools to assess the progress of embryo development or to build genotype-independent, predictive models of embryogenesis-specific characteristics.

Arginine supplementation and exposure time affects polyamine and glucose metabolism in primary liver cells isolated from Atlantic salmon

Arginine has been demonstrated to enhance glucose and lipid oxidation in mammals through activation of polyamine turnover. We aimed to investigate how arginine affects energy utilization through polyamine metabolism and whether this effect is time dependent. Primary liver cells were isolated from Atlantic salmon (2.2 kg body weight) fed diets containing 25.5 (low arginine, LA) or 36.1 (high arginine, HA) g arginine/kg dry matter for 12 weeks, to investigate the effect of long-term arginine supplementation. The cells were cultured for 24 h in L-15 medium to which either alpha-difluoromethylornithine (DFMO) or N (1),N (11)-diethylnorspermine (DENSPM) was added. Analysis of the medium by nuclear magnetic resonance revealed significant differences between the two dietary groups as well as between cells exposed to DFMO and DENSPM, with decreased glucose, fumarate and lactate concentrations in media of the HA cells. Liver cells from fish fed the HA diet had higher spermidine/spermine-N1-acetyltransferase protein abundance and lower adenosine triphosphate concentration as compared to the LA-fed fish, while gene expression was not affected by either diet or treatment. Primary liver cells isolated from salmon fed a commercial diet and cultured in L-15 media with or without arginine supplementation (1.82 or 3.63 mM) for 48 h, representing short-term effect of arginine supplementation, showed differential expression of genes for apoptosis and polyamine synthesis due to arginine supplementation or inhibition by DFMO. Overall, arginine concentration and exposure time affected energy metabolism and gene regulation more than inhibition or activation of key enzymes of polyamine metabolism, suggesting a polyamine-independent influence of arginine on cellular energy metabolism and survival.

Metabolite profiling reveals clear metabolic changes during somatic embryo development of Norway spruce (Picea abies)

Progress on industrial-scale propagation of conifers by somatic embryogenesis has been hampered by the differences in developmental capabilities between cell lines, which are limiting the capture of genetic gains from breeding programs. In this study, we investigated the metabolic events occurring during somatic embryo development in Norway spruce to establish a better understanding of the fundamental metabolic events required for somatic embryo development. Three embryogenic cell lines of Norway spruce (Picea abies (L.) Karst) with different developmental capabilities were studied during somatic embryo development from proliferation of proembryogenic masses to mature somatic embryos. The three different cell lines displayed normal, aberrant and blocked somatic embryo development. Metabolite profiles from four development stages in each of the cell lines were obtained using combined gas chromatography-mass spectrometry. Multivariate discriminant analyses of the metabolic data revealed significant metabolites (P  ≤  0.05) for each development stage and transition. The results suggest that endogenous auxin and sugar signaling affects initial stages of somatic embryo development. Furthermore, the results highlight the importance of a timed stress response and the presence of stimulatory metabolites during late stages of embryo development.

(1)H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in (1)H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

(1)H NMR metabolomics identification of markers of hypoxia-induced metabolic shifts in a breast cancer model system

Hypoxia can promote invasive behavior in cancer cells and alters the response to therapeutic intervention as a result of changes in the expression many genes, including genes involved in intermediary metabolism. Although metabolomics technologies are capable of simultaneously measuring a wide range of metabolites in an untargeted manner, these methods have been relatively under utilized in the study of cancer cell responses to hypoxia. Thus, (1)H NMR metabolomics was used to examine the effects of hypoxia in the MDA-MB-231 human breast cancer cell line, both in vitro and in vivo. Cell cultures were compared with respect to their metabolic responses during growth under either hypoxic (1% O(2)) or normoxic conditions. Orthogonal partial least squares discriminant analysis (OPLS-DA) was used to identify a set of metabolites that were responsive to hypoxia. Via intracardiac administration, MDA-MB-231 cells were also used to generate widespread metastatic disease in immuno-compromised mice. Serum metabolite analysis was conducted to compare animals with and without a large tumor burden. Intriguingly, using a cross-plot of the OPLS loadings, both the in vitro and in vivo samples yielded a subset of metabolites that were significantly altered by hypoxia. These included primarily energy metabolites and amino acids, indicative of known alterations in energy metabolism, and possibly protein synthesis or catabolism. The results suggest that the metabolite pattern identified might prove useful as a marker for intra-tumoral hypoxia.

Separating the inseparable: the metabolomic analysis of plant-pathogen interactions

Plant-microbe interactions-whether pathogenic or symbiotic-exert major influences on plant physiology and productivity. Analysis of such interactions represents a particular challenge to metabolomic approaches due to the intimate association between the interacting partners coupled with a general commonality of metabolites. We here describe an approach based on co-cultivation of Arabidopsis cell cultures and bacterial plant pathogens to assess the metabolomes of both interacting partners, which we refer to as dual metabolomics.

Oxidative parameters of embryo culture media may predict treatment outcome in in vitro fertilization: a novel applicable tool for improving embryo selection

OBJECTIVE

To examine whether the oxidative status of an individual embryo before transfer may predict chances of implantation.

DESIGN

A prospective laboratory study.

SETTING

An IVF unit in a university-affiliated hospital.

PATIENT(S)

One hundred thirty-three women undergoing IVF-ET treatment cycles.

INTERVENTION(S)

Before ET, 10 μL of embryo culture medium was retrieved individually from each embryo and the oxidative status assessed by the thermochemiluminescence (TCL) analyzer.

MAIN OUTCOME MEASURE(S)

The occurrence of pregnancy. Two parameters were recorded: the TCL amplitude after 50 seconds (H1) and the TCL ratio. These were compared with demographic, clinical, and laboratory parameters and treatment outcome. All data underwent statistical analysis.

RESULT(S)

Altogether 284 embryos were transferred in 133 ET cycles. Forty-one pregnancies occurred (31%). For embryos transferred after 72 hours (77 transfers), the highest H1 levels in each group of transferred embryos correlated with the occurrence of pregnancy. The combination of maximal intracohort H1 level <210 counts per second with a TCL ratio of ≤ 80% had a positive predictive value of 70.6% for the occurrence of pregnancy.

CONCLUSION(S)

The oxidative status of the early embryo in IVF is associated with the chances of implantation. Assessment of the oxidative status of embryos in culture media before transfer may serve as an applicable tool for improving embryo selection in light of the legal limitations of the number of transferred embryos allowed.

Shoot differentiation from protocorm callus cultures of Vanilla planifolia (Orchidaceae): proteomic and metabolic responses at early stage

BACKGROUND

Vanilla planifolia is an important Orchid commercially cultivated for the production of natural vanilla flavour. Vanilla plants are conventionally propagated by stem cuttings and thus causing injury to the mother plants. Regeneration and in vitro mass multiplication are proposed as an alternative to minimize damage to mother plants. Because mass production of V. planifolia through indirect shoot differentiation from callus culture is rare and may be a successful use of in vitro techniques for producing somaclonal variants, we have established a novel protocol for the regeneration of vanilla plants and investigated the initial biochemical and molecular mechanisms that trigger shoot organogenesis from embryogenic/organogenic callus.

RESULTS

For embryogenic callus induction, seeds obtained from 7-month-old green pods of V. planifolia were inoculated on MS basal medium (BM) containing TDZ (0.5 mg l(-1)). Germination of unorganized mass callus such as protocorm -like structure (PLS) arising from each seed has been observed. The primary embryogenic calli have been formed after transferring on BM containing IAA (0.5 mg l(-1)) and TDZ (0.5 mg l(-1)). These calli were maintained by subculturing on BM containing IAA (0.5 mg l(-1)) and TDZ (0.3 mg l(-1)) during 6 months and formed embryogenic/organogenic calli. Histological analysis showed that shoot organogenesis was induced between 15 and 20 days after embryogenic/organogenic calli were transferred onto MS basal medium with NAA (0.5 mg l(-1)). By associating proteomics and metabolomics analyses, the biochemical and molecular markers responsible for shoot induction have been studied in 15-day-old calli at the stage where no differentiating part was visible on organogenic calli. Two-dimensional electrophoresis followed by matrix-assisted laser desorption ionization time-of-flight-tandem mass spectrometry (MALDI-TOF-TOF-MS) analysis revealed that 15 protein spots are significantly expressed (P < 0.05) at earlier stages of shoot differentiation. The majority of these proteins are involved in amino acid-protein metabolism and photosynthetic activity. In accordance with proteomic analysis, metabolic profiling using 1D and 2D NMR techniques showed the importance of numerous compounds related with sugar mobilization and nitrogen metabolism. NMR analysis techniques also allowed the identification of some secondary metabolites such as phenolic compounds whose accumulation was enhanced during shoot differentiation.

CONCLUSION

The subculture of embryogenic/organogenic calli onto shoot differentiation medium triggers the stimulation of cell metabolism principally at three levels namely (i) initiation of photosynthesis, glycolysis and phenolic compounds synthesis; (ii) amino acid-protein synthesis, and protein stabilization; (iii) sugar degradation. These biochemical mechanisms associated with the initiation of shoot formation during protocorm-like body (PLB) organogenesis could be coordinated by the removal of TDZ in callus maintenance medium. These results might contribute to elucidate the complex mechanism that leads to vanilla callus differentiation and subsequent shoot formation into PLB organogenesis. Moreover, our results highlight an early intermediate metabolic event in vanillin biosynthetic pathway with respect to secondary metabolism. Indeed, for the first time in vanilla tissue culture, phenolic compounds such as glucoside A and glucoside B were identified. The degradation of these compounds in specialized tissue (i.e. young green beans) probably contributes to the biosynthesis of glucovanillin, the parent compound of vanillin.

Dual metabolomics: a novel approach to understanding plant-pathogen interactions

One of the most well-characterised plant pathogenic interactions involves Arabidopsis thaliana and the bacteria Pseudomonas syringae pathovar tomato (Pst). The standard Pst inoculation procedure involves infiltration of large populations of bacteria into plant leaves which means that metabolite changes cannot be readily assigned to the host or pathogen. A plant cell-pathogen co-culture based approach has been developed where the plant and pathogen cells are separated after 12h of co-culture via differential filtering and centrifugation. Fourier transform infrared (FT-IR) spectroscopy was employed to assess the intracellular metabolomes (metabolic fingerprints) of both host and pathogen and their extruded (extracellular) metabolites (metabolic footprints) under conditions relevant to disease and resistance. We propose that this system will enable the metabolomic profiling of the separated host and pathogen (i.e. 'dual metabolomics') and will facilitate the modelling of reciprocal responses.