Glutamine Metabolism, Sensing and Signaling in Plants

Pathogen-induced root glutamine concentration is a determinant of the outcome of the Medicago truncatula-Aphanomyces euteiches interaction

MAIN CONCLUSION

Our work highlights that glutamine plays a central role in contributing to the outcome of disease in the Medicago truncatula-Aphanomyces euteiches interaction when modulating plant N supply. Nitrogen (N) is essential for the growth of plants and microorganisms. The quantity and quality of N supply can impact plant development but also its interaction with pathogens. Our previous work showed that N modulated Medicago truncatula (Mt) susceptibility to the oomycete pathogen Aphanomyces euteiches (Ae) when plants were grown in vitro and glutamine (Gln) was proposed to mediate this effect of N on plant disease. Using more than 30 lines representative of Mt diversity, we show here that pathogen-induced root Gln concentrations are correlated with higher susceptibility to Ae. N modulation of the response to Ae of the partially resistant Mt A17 genotype was associated with changes in the expression of MtGS1 genes encoding cytosolic glutamine synthetases (GSs). This raises the question of the importance of Gln during Mt/Ae interaction and a possible role of cytosolic GS in mediating Mt susceptibility to Ae. Interestingly, exogenous Gln induced a higher susceptibility of the A17 line to Ae and induced a metabolic profile of inoculated A17 roots similar to that of a susceptible genotype. RNAseq experiments highlighted a higher expression of numerous plant defense genes in non-inoculated roots on Gln. On the pathogen side, a higher expression of genes encoding proteases and a lower expression of genes encoding elicitins as well as a better growth of Ae on Gln could explain the higher susceptibility of Mt on Gln. Altogether our results highlight the delicate balance between plant immunity, pathogen growth and virulence in contributing to the outcome of disease when modulating N supply and that Gln plays a central role in this process.

Metabolites in Cellular Leachate as Biomarkers for the Nature and Severity of Injury Following a Short vs. Prolonged Freezing Stress

Freeze injury is typically quantified by measuring electrolyte leakage from plant tissues exposed to a freeze-thaw cycle, whereby higher leakage indicates greater injury. The severity of stress is also assessed by the ability (or lack thereof) of the injured tissue to recover, wherein reduced leakage during the post-thaw period relative to right after thaw indicates recoverable injury. In this study, spinach leaves were injured to various degrees by freezing them for different durations at a fixed sub-zero temperature. We explored the cellular nature of freeze-thaw injury by comparing the profiles of cellular metabolites that were leaked from reversibly and/or irreversibly injured leaves. A total of 47 metabolites were, thus, detected in the leachate, including 8 sugars, 20 amino acids, GABA, uracil, adenine, palmitic acid, ferulic, coumaric acid, and other organic/inorganic acids involved in primary and secondary metabolism (e.g., citric acid, phosphoric acid, coumaric acid, etc.). Combined multivariate metabolome analysis, including principal component analysis, hierarchical clustering, and partial least square discriminant analysis, together identified 14 key metabolites mainly responsible for distinguishing the reversible vs. irreversible injury. These metabolites are also indicators for various lesions, including structural/functional perturbations to cellular components (cell wall, chloroplast, vacuole, plasma membrane, nucleic acids), disruption of metabolic homeostasis (antioxidant system, cytoplasmic pH, Kreb's cycle), protein degradation, and hypoxia.

Morphophysiological and proteomic profiling unveiling mechanisms underlying nitrogen use efficiency in popcorn (Zea mays var. everta)

In this study we hypothesize that the contrasting nitrogen use efficiency (NUE) between popcorn (Zea mays var. everta) inbred lines P2 (high NUE) and L80 (low NUE) is driven by distinct morphophysiological responses and proteomic profiles found in leaves and roots. To elucidate the mechanisms involved, plants were cultivated in a greenhouse under high (100% N) and low (10% N) nitrogen conditions, in a randomized complete block design with two factorial treatment arrangements and seven blocks. Morphological and physiological traits such as photochemical and non-photochemical quenching, quantum yield of photosystem II, and potential photosynthesis were evaluated. Compared to L80, under low N, P2 exhibited 25.9% greater leaf area, 22.4% taller plants, 21.7% thicker stems and 113% higher shoot dry mass, as well as higher values of photochemical and non-photochemical quenching and quantum yield of photosystem II that drove to a maximum photosynthesis 16.5% higher than L80. Comparative proteomic analysis of the leaves identified 215 differentially accumulated proteins (DAPs) in P2 and 168 DAPs in L80, while in roots, 127 DAPs were observed in P2 and 172 in L80. Notably, in leaves, the response to oxidative stress, energy metabolism, and photosynthesis represented the main differences between P2 and L80. In roots, the nitrate transport, ammonium assimilation, and amino acid metabolism appear to have contributed to the improved NUE in P2. Consequently, this study provides valuable insights into the molecular mechanisms underlying NUE and opens avenues for molecular breeding aimed at selecting superior genotypes for the development of a more sustainable agriculture.

Transcription-metabolism analysis of various signal transduction pathways in Brassica chinensis L. exposed to PLA-MPs

Biodegradable plastics, regarded as an ideal substitute for traditional plastics, are increasingly utilized across various industries. However, due to their unique degradation properties, they can generate microplastics (MPs) at a faster rate, potentially posing a threat to plant development. This study employed transcriptomics and metabolomics to investigate the effects of polylactic acid microplastics (PLA-MPs) on the physiological and biochemical characteristics of Brassica chinensis L. over different periods. The findings indicated that exposure to varying concentrations of PLA-MPs had distinct influences on the growth and development of Brassica chinensis L. Transcriptomic analysis showed different concentrations of PLA-MPs directly influenced the expression of genes associated with plant hormones, such as SnRK2 and BnaA01g27170D. In addition, it was observed that these PLA-MPs also impacted plant growth and development by modulating the expression of other genes, eg. related to sulfur metabolism and glycerophosphate metabolism. Metabolomic analysis demonstrated alterations levels of metabolites such as L-glutamine, and arginine in response to PLA-MPs, which influenced pathways related to vitamin B6 metabolism, the one-carbon folate pool, glycerophospholipid metabolism, and cysteine. This study offers new insights into the potential impacts of biodegradable microplastics (BMPs) on plants and underscores the need for further investigation into the potentially more significant effects of BMPs on terrestrial ecosystems.

Extreme heat affects blueberry pollen nutrition, bee health, and plant reproduction

Extreme heat events are increasingly common, and if these align with pollen development, they can alter pollen nutrient composition. However, no studies have examined how the timing of heat relative to bud development affects the role of pollen in plant pollination and bee health. To explore this, we exposed highbush blueberry plants to extreme heat (37.5 °C) or normal (25 °C) conditions for 4 h across several floral bud stages. Pollen was analyzed for protein, carbohydrate, and amino acid content. We found that blueberry floral buds vary in their sensitivity to heat, with bud swell being the most heat-sensitive developmental stage with significant reductions in pollen protein, total and several individual amino acids. When pollen from blueberry plants exposed to the same conditions was fed to Osmia lignaria larvae, we found that individuals fed heat-stressed pollen were 7 times more likely to die compared to those fed non-stressed pollen. Blueberry flowers exposed to the same conditions were used for a hand pollination study, where we observed a 39% reduction in fruit set following heat stress at bud swell. This study reveals how extreme heat can disrupt both plant pollination and bee survival through changes in pollen nutritional composition.

UHPLC-HRMS/MS-Based Metabolic Profiling and Quantification of Phytochemicals in Different Parts of Coccinia grandis (L.) Voigt

Coccinia grandis (L.) Voigt (C. grandis), a member of the Cucurbitaceae family, is recognized for its phytochemicals that possess antioxidant and antidiabetic properties, along with a wide array of nutritional and health-promoting benefits. However, a comprehensive investigation of the phytochemical profiles and biologically active constituents in different parts of C. grandis has not yet been reported. Therefore, this study aimed to evaluate the phytochemical constituents of three distinct parts of C. grandis (fruit, leaves, and stem) at the same growth stage. The phytochemicals in C. grandis were identified using UHPLC-HRMS-based untargeted metabolomics, followed by a quantitative analysis of the primary metabolites. The qualitative analysis revealed 60 secondary metabolites, including phenolic compounds (6 hydroxybenzoic acids, 22 hydroxycinnamic acids, 2 coumarins, 1 flavanone, 1 flavanonol, 2 flavones, 22 flavonols, and 2 lignans) and triterpenes (2 cucurbitacins). Furthermore, nine plant hormones and 30 amino acids were successfully identified. The quantitative analysis of 32 types of secondary metabolites indicated that the leaves contained the highest total amounts of flavonoids (501.37 mg/100 g) and hydroxycinnamic acids (1148.23 mg/100 g). Additionally, the analysis of amino acids revealed a total of 20 types, with the leaf extract exhibiting the highest total amounts of both essential and nonessential amino acids, followed by the fruit and stem extracts. In conclusion, the analysis of the primary and secondary metabolite composition and content of various parts of C. grandis demonstrated that the leaf extract replace with had the greatest functionality, suggesting its potential utility in the development of health functional foods.

Effects of nanoplastics on the growth, transcription, and metabolism of rice (Oryza sativa L.) and synergistic effects in the presence of iron plaque and humic acid

Nanoplastics (NPs) can adversely affect living organisms. However, the uptake of NPs by plants and the physiological and molecular mechanisms underlying NP-mediated plant growth remain unclear, particularly in the presence of iron minerals and humic acid (HA). In this study, we investigated NP accumulation in rice (Oryza sativa L.) and the physiological effects of exposure to polystyrene NPs (0, 20, and 100 mg L-1) in the presence of iron plaque (IP) and HA. NPs were absorbed on the root surface and entered cells, and confocal laser scanning microscopy confirmed NP uptake by the roots. NP treatments decreased root superoxide dismutase (SOD) activity (28.9-44.0%) and protein contents (31.2-38.6%). IP and HA (5 and 20 mg L-1) decreased the root protein content (20.44-58.3% and 44.2-45.2%, respectively) and increased the root lignin content (22.3-27.5% and 19.2-29.6%, respectively) under NP stress. IP inhibited the NP-induced decreasing trend of SOD activity (19.2-29.5%), while HA promoted this trend (48.7-50.3%). Transcriptomic and metabolomic analysis (Control, 100NPs, and IP-100NPs-20HA) showed that NPs inhibited arginine biosynthesis, and alanine, aspartate, and glutamate metabolism and activated phenylpropanoid biosynthesis related to lignin. The coexistence of IP and HA had positive effects on the amino acid metabolism and phenylpropanoid biosynthesis induced by NPs. Regulation of genes and metabolites involved in nitrogen metabolism and secondary metabolism significantly altered the levels of protein and lignin in rice roots. These findings provide a scientific basis for understanding the environmental risk of NPs under real environmental conditions.

Heterologous biosynthesis of betanin triggers metabolic reprogramming in tobacco

Engineering of a specialized metabolic pathway in plants is a promising approach to produce high-value bioactive compounds to address the challenges of climate change and population growth. Understanding the interaction between the heterologous pathway and the native metabolic network of the host plant is crucial for optimizing the engineered system and maximizing the yield of the target compound. In this study, we performed transcriptomic, metabolomic and metagenomic analysis of tobacco (Nicotiana tabacum) plants engineered to produce betanin, an alkaloid pigment that is found in Caryophyllaceae plants. Our data reveals that, in a dose-dependent manor, the biosynthesis of betanin promotes carbohydrate metabolism and represses nitrogen metabolism in the leaf, but enhances nitrogen assimilation and metabolism in the root. By supplying nitrate or ammonium, the accumulation of betanin increased by 1.5-3.8-fold in leaves and roots of the transgenic plants, confirming the pivotal role of nitrogen in betanin production. In addition, the rhizosphere microbial community is reshaped to reduce denitrification and increase respiration and oxidation, assistant to suppress nitrogen loss. Our analysis not only provides a framework for evaluating the pleiotropic effects of an engineered metabolic pathway on the host plant, but also facilitates the development of novel strategies to balance the heterologous process and the native metabolic network for the high-yield and nutrient-efficient production of bioactive compounds in plants.

Metabolic profiling and spatial metabolite distribution in wild soybean (G. soja) and cultivated soybean (G. max) seeds

Wild soybeans retain many substances significantly reduced or lost in cultivars during domestication. This study utilized LC-MS to analyze metabolites in the seed coats and embryos of wild and cultivated soybeans. 866 and 815 metabolites were identified in the seed extracts of both soybean types, with 35 and 10 significantly differing metabolites in the seed coat and embryos, respectively. The upregulated metabolites in wild soybeans are linked to plant defense, stress responses, and nitrogen cycling. MALDI-MSI results further elucidated the distribution of these differential metabolites in the cotyledons, hypocotyls, and radicles. In addition to their role in physiological processes like growth and response to environmental stimuli, the prevalent terpenoids, lipids, and flavonoids present in wild soybeans exhibit beneficial bioactivities, including anti-inflammatory, antibacterial, anticancer, and cardiovascular disease prevention properties. These findings underscore the potential of wild soybeans as a valuable resource for enhancing the nutritional and ecological adaptability of cultivated soybeans.

An integration of physiology, transcriptomics, and proteomics reveals carbon and nitrogen metabolism responses in alfalfa (Medicago sativa L.) exposed to titanium dioxide nanoparticles

Nanoparticle (NP) pollution has negative impacts and is a major global environmental problem. However, the molecular response of alfalfa (Medicago sativa L.) to titanium dioxide nanoparticles (TiO2 NPs) is limited. Herein, the dual effects of TiO2 NPs (0-1000 mg L-1) on carbon (C) and nitrogen (N) metabolisms in alfalfa were investigated. The results showed that 500 mg L-1 TiO2 NPs (Ti-500) had the highest phytotoxicity in the C/N metabolizing enzymes; and it significantly increased total soluble sugar, starch, sucrose, and sucrose-phosphate synthase. Furthermore, obvious photosynthesis responses were found in alfalfa exposed to Ti-500. By contrast, 100 mg L-1 TiO2 NPs (Ti-100) enhanced N metabolizing enzymes. RNA-seq analyses showed 4265 and 2121 differentially expressed genes (DEGs) in Ti-100 and Ti-500, respectively. A total of 904 and 844 differentially expressed proteins (DEPs) were identified in Ti-100 and Ti-500, respectively. Through the physiological, transcriptional, and proteomic analyses, the DEGs and DEPs related to C/N metabolism, photosynthesis, chlorophyll synthesis, starch and sucrose metabolism, and C fixation in photosynthetic organisms were observed. Overall, TiO2 NPs at low doses improve photosynthesis and C/N regulation, but high doses can cause toxicity. It is valuable for the safe application of NPs in agriculture.

Acetic acid: a cheap but chief metabolic regulator for abiotic stress tolerance in plants

As sessile organisms, plants constantly face a variety of abiotic stresses, such as drought, salinity, and metal/metalloid toxicity, all of which possess significant threats to plant growth and yield potential. Improving plant resilience to such abiotic stresses bears paramount importance in practicing sustainable agriculture worldwide. Acetic acid/acetate has been recognized as an important metabolite with multifaceted roles in regulating plant adaptation to diverse abiotic stresses. Recent studies have elucidated that acetic acid can potentiate plants' inherent mechanisms to withstand the adverse effects of abiotic stresses through the regulation of lipid metabolism, hormone signaling, epigenetic changes, and physiological defense mechanisms. Numerous studies also underpin the potential use of acetic acid in boosting crop production under unfavorable environmental conditions. This review provides a comprehensive update on the understanding of how acetic acid regulates plant photosynthesis, acts as an antitranspirant, detoxifies reactive oxygen species to alleviate oxidative stress, interacts with phytohormones to regulate physiological processes, and improves soil fertility and microbial diversity, with a specific focus on drought, salinity, and metal toxicity. We also highlight the eco-friendly and economic potential of acetic acid that may attract farmers from developing countries to harness the benefits of acetic acid application for boosting abiotic stress resistance in crops. Given that acetic acid is a widely accessible, inexpensive, and eco-friendly compound, the revelation of acetic acid-mediated regulatory pathways and its crosstalk with other signaling molecules will have significant importance in developing a sustainable strategy for mitigating abiotic stresses in crops.

Glutamine induces lateral root initiation, stress responses, and disease resistance in Arabidopsis

The production of glutamine (Gln) from NO3- and NH4+ requires ATP, reducing power, and carbon skeletons. Plants may redirect these resources to other physiological processes using Gln directly. However, feeding Gln as the sole nitrogen (N) source has complex effects on plants. Under optimal concentrations, Arabidopsis (Arabidopsis thaliana) seedlings grown on Gln have similar primary root lengths, more lateral roots, smaller leaves, and higher amounts of amino acids and proteins compared to those grown on NH4NO3. While high levels of Gln accumulate in Arabidopsis seedlings grown on Gln, the expression of GLUTAMINE SYNTHETASE1;1 (GLN1;1), GLN1;2, and GLN1;3 encoding cytosolic GS1 increases and expression of GLN2 encoding chloroplastic GS2 decreases. These results suggest that Gln has distinct effects on regulating GLN1 and GLN2 gene expression. Notably, Arabidopsis seedlings grown on Gln have an unexpected gene expression profile. Compared with NH4NO3, which activates growth-promoting genes, Gln preferentially induces stress- and defense-responsive genes. Consistent with the gene expression data, exogenous treatment with Gln enhances disease resistance in Arabidopsis. The induction of Gln-responsive genes, including PATHOGENESIS-RELATED1, SYSTEMIC ACQUIRED RESISTANCE DEFICIENT1, WRKY54, and WALL ASSOCIATED KINASE1, is compromised in salicylic acid (SA) biosynthetic and signaling mutants under Gln treatments. Together, these results suggest that Gln may partly interact with the SA pathway to trigger plant immunity.

Nitrate Signaling and Its Role in Regulating Flowering Time in Arabidopsis thaliana

Plant growth is coordinated with the availability of nutrients that ensure its development. Nitrate is a major source of nitrogen (N), an essential macronutrient for plant growth. It also acts as a signaling molecule to modulate gene expression, metabolism, and a variety of physiological processes. Recently, it has become evident that the calcium signal appears to be part of the nitrate signaling pathway. New key players have been discovered and described in Arabidopsis thaliana (Arabidopsis). In addition, knowledge of the molecular mechanisms of how N signaling affects growth and development, such as the nitrate control of the flowering process, is increasing rapidly. Here, we review recent advances in the identification of new components involved in nitrate signal transduction, summarize newly identified mechanisms of nitrate signaling-modulated flowering time in Arabidopsis, and suggest emerging concepts and existing open questions that will hopefully be informative for further discoveries.

Metabolome and Transcriptome Association Analysis Reveals Mechanism of Synthesis of Nutrient Composition in Quinoa (Chenopodium quinoa Willd.) Seeds

Quinoa (Chenopodium quinoa Willd.) seeds are rich in nutrition, superior to other grains, and have a high market value. However, the biosynthesis mechanisms of protein, starch, and lipid in quinoa grain are still unclear. The objective of this study was to ascertain the nutritional constituents of white, yellow, red, and black quinoa seeds and to employ a multi-omics approach to analyze the synthesis mechanisms of these nutrients. The findings are intended to furnish a theoretical foundation and technical support for the biological breeding of quinoa in China. In this study, the nutritional analysis of white, yellow, red, and black quinoa seeds from the same area showed that the nutritional contents of the quinoa seeds were significantly different, and the protein content increased with the deepening of color. The protein content of black quinoa was the highest (16.1 g/100 g) and the lipid content was the lowest (2.7 g/100 g), among which, linoleic acid was the main fatty acid. A combined transcriptome and metabolome analysis exhibited that differentially expressed genes were enriched in "linoleic acid metabolism", "unsaturated fatty acid biosynthesis", and "amino acid biosynthesis". We mainly identified seven genes involved in starch synthesis (LOC110716805, LOC110722789, LOC110738785, LOC110720405, LOC110730081, LOC110692055, and LOC110732328); five genes involved in lipid synthesis (LOC110701563, LOC110699636, LOC110709273, LOC110715590, and LOC110728838); and nine genes involved in protein synthesis (LOC110710842, LOC110720003, LOC110687170, LOC110716004, LOC110702086, LOC110724454 LOC110724577, LOC110704171, and LOC110686607). The data presented in this study based on nutrient, transcriptome, and metabolome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa, and provide candidate genes for further genetic improvements to improve the nutritional value of quinoa seeds.

Integrating Targeted Metabolomics and Targeted Proteomics to Study the Responses of Wheat Plants to Engineered Nanomaterials

This manuscript presents a multiomics investigation into the metabolic and proteomic responses of wheat to molybdenum (Mo)- and copper (Cu)-based engineered nanomaterials (ENMs) exposure via root and leaf application methods. Wheat plants underwent a four-week growth period with a 16 h photoperiod (light intensity set at 150 μmol·m-2·s-1), at 22 °C and 60% humidity. Six distinct treatments were applied, including control conditions alongside exposure to Mo- and Cu-based ENMs through both root and leaf routes. The exposure dosage amounted to 6.25 mg of the respective element per plant. An additional treatment with a lower dose (0.6 mg Mo/plant) of Mo ENM exclusively through the root system was introduced upon the detection of phytotoxicity. Utilizing LC-MS/MS analysis, 82 metabolites across various classes and 24 proteins were assessed in different plant tissues (roots, stems, leaves) under diverse treatments. The investigation identified 58 responsive metabolites and 19 responsive proteins for Cu treatments, 71 responsive metabolites, and 24 responsive proteins for Mo treatments, mostly through leaf exposure for Cu and root exposure for Mo. Distinct tissue-specific preferences for metabolite accumulation were revealed, highlighting the prevalence of organic acids and fatty acids in stem or root tissues, while sugars and amino acids were abundant in leaves, mirroring their roles in energy storage and photosynthesis. Joint-pathway analysis was conducted and unveiled 23 perturbed pathways across treatments. Among these, Mo exposure via roots impacted all identified pathways, whereas exposure via leaf affected 15 pathways, underscoring the reliance on exposure route of metabolic and proteomic responses. The coordinated response observed in protein and metabolite concentrations, particularly in amino acids, highlighted a dynamic and interconnected proteomic-to-metabolic-to-proteomic relationship. Furthermore, the contrasting expression patterns observed in glutamate dehydrogenase (upregulation at 1.38 ≤ FC ≤ 1.63 with high Mo dose, and downregulation at 0.13 ≤ FC ≤ 0.54 with low Mo dose) and its consequential impact on glutamine expression (7.67 ≤ FC ≤ 39.60 with high Mo dose and 1.50 ≤ FC ≤ 1.95 with low Mo dose) following Mo root exposure highlighted dose-dependent regulatory trends influencing proteins and metabolites. These findings offer a multidimensional understanding of plant responses to ENMs exposure, guiding agricultural practices and environmental safety protocols while advancing knowledge on nanomaterial impacts on plant biology.

Glutamine as sole nitrogen source prevents induction of nitrate transporter gene NRT2.4 and affects amino acid metabolism in Arabidopsis

Plants assimilate inorganic nitrogen (N) to glutamine. Glutamine is the most abundant amino acid in most plant species, the N-supplying precursor of all N-containing compounds in the cell and the first organic nitrogen molecule formed from inorganic nitrogen taken up by the roots. In addition to its role in plant nutrition, glutamine most likely also has a function as a signaling molecule in the regulation of nitrogen metabolism. We investigated whether glutamine influences the high-affinity transporter system for nitrate uptake. Therefore, we analyzed the expression of the nitrate transporter NRT2.4, which is inducible by N deficiency, in Arabidopsis thaliana grown under different nitrogen starvation scenarios, comparing nitrate or glutamine as the sole nitrogen source. Using the reporter line ProNRT2.4:GFP and two independent knockout lines, nrt2.4-1 and nrt2.4-2, we analyzed gene expression and amino acid profiles. We showed that the regulation of NRT2.4 expression depends on available nitrogen in general, for example on glutamine as a nitrogen source, and not specifically on nitrate. In contrast to high nitrate concentrations, amino acid profiles changed to an accumulation of amino acids containing more than one nitrogen during growth in high glutamine concentrations, indicating a switch to nitrogen storage metabolism. Furthermore, we demonstrated that the nrt2.4-2 line shows unexpected effects on NRT2.5 gene expression and the amino acids profile in shoots under high glutamine supply conditions compared to Arabidopsis wild type and nrt2.4-1, suggesting non-NRT2.4-related metabolic consequences in this knockout line.

Metabolic changes during wheat microspore embryogenesis induction using the highly responsive cultivar Svilena

Androgenetically-derived haploids can be obtained by inducing embryogenesis in microspores. Thus, full homozygosity is achieved in a single generation, oppositely to conventional plant breeding programs. Here, the metabolite profile of embryogenic microspores of Triticum aestivum was acquired and integrated with transcriptomic existing data from the same samples in an effort to identify the key metabolic processes occurring during the early stages of microspore embryogenesis. Primary metabolites and transcription profiles were identified at three time points: prior to and immediately following a low temperature pre-treatment given to uninuclear microspores, and after the first nuclear division. This is the first time an integrative -omics analysis is reported in microspore embryogenesis in T. aestivum. The key findings were that the energy produced during the pre-treatment was obtained from the tricarboxylic acid (TCA) cycle and from starch degradation, while starch storage resumed after the first nuclear division. Intermediates of the TCA cycle were highly demanded from a very active amino acid metabolism. The transcription profiles of genes encoding enzymes involved in amino acid synthesis differed from the metabolite profiles. The abundance of glutamine synthetase was correlated with that of glutamine. Cytosolic glutamine synthetase isoform 1 was found predominantly after the nuclear division. Overall, energy production was shown to represent a major component of the de-differentiation process induced by the pre-treatment, supporting a highly active amino acid metabolism.