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The regulatory nucleotide, guanosine 3’, 5’-bis(pyrophosphate; ppGpp)—originally identified in Escherichia coli—controls gene expression and enzyme activities in the bacteria and plastids of plant cells. We recently reported that the ppGpp over-producing mutant of Arabidopsis thaliana had a larger shoot weight than wild type (WT), especially under nutrient-deficient conditions. However, the mechanisms behind the influence of ppGpp on plant growth and biomass remain elusive. To understand the impact of the ppGpp accumulation on plant growth, we characterized metabolic changes in the ppGpp-overproducing mutant upon transition from nitrogen-rich to nitrogen-limiting concentrations. We found that the fresh weight of the mutant was significantly larger than WT when the total nitrogen source (KNO3 and NH4NO3) concentration was below 0.9 mM. When the nitrogen content in the medium decreased, aromatic and branched-chain amino acids increased in WT due to accelerated protein degradation and/or attenuated protein synthesis. These amino-acid levels in the ppGpp over-accumulating mutant decreased upon nitrogen deficiency. The results suggest that the ppGpp-overaccumulation affects amino-acid and protein homeostasis and facilitates growth under nitrogen-limiting conditions.

Arbuscular mycorrhizal (AM) fungal extraradical hyphae exude their metabolites into the soil. Root exudate metabolites are affected by plant species and P status. However, the effect of P status on AM hyphal exudate metabolites has been unknown. This study aimed to examine hyphal exudate metabolite composition of two AM fungal species and their response to P deficiency through metabolite profiling. Rhizophagus clarus and R. irregularis were grown in a two-compartment in vitro culture system of Linum usitatissimum roots on solid modified Strullu-Romand medium in combination with two P levels (3 µM (P3) and 30 µM (P30)). Hyphal exudates were collected from the hyphal compartment at 118 days after inoculation (DAI). The metabolite composition of the hyphal exudates was determined by capillary electrophoresis/time-of-flight mass spectrometry, resulting in the identification of a total of 141 metabolites at 118 DAI. In the hyphal exudates of R. clarus, the concentrations of 18 metabolites, including sugars, amino acids, and organic acids, were significantly higher (p < 0.05) under P3 than under P30 conditions. In contrast, the concentrations of 10 metabolites, including sugar and amino acids, in the hyphal exudates of R. irregularis were significantly lower (p < 0.05) under P3 than under P30 conditions. These findings suggest that the extraradical hyphae of AM fungi exude diverse metabolites of which concentrations are affected by P conditions and differ between AM fungal species.

Key messageOverexpressing Nicotinamidase 3 gene, and the exogenous application of its metabolite nicotinic acid (NA), enhance drought stress tolerance and increase biomass in Arabidopsis thaliana.With progressive global climatic changes, plant productivity is threatened severely by drought stress. Deciphering the molecular mechanisms regarding genes responsible for balancing plant growth and stress amelioration could imply multiple possibilities for future sustainable goals. Nicotinamide adenine dinucleotide (NAD) biosynthesis and recycling/ distribution is a crucial feature for plant growth. The current study focuses on the functional characterization of nicotinamidase 3 (NIC3) gene, which is involved in the biochemical conversion of nicotinamide (NAM) to nicotinic acid (NA) in the salvage pathway of NAD biosynthesis. Our data show that overexpression of NIC3 gene enhances drought stress tolerance and increases plant growth. NIC3-OX plants accumulated more NA as compared to WT plants. Moreover, the upregulation of several genes related to plant growth/stress tolerance indicates that regulating the NAD salvage pathway could significantly enhance plant growth and drought stress tolerance. The exogenous application of nicotinic acid (NA) showed a similar phenotype as the effect of overexpressing NIC3 gene. In short, we contemplated the role of NIC3 gene and NA application in drought stress tolerance and plant growth. Our results would be helpful in engineering plants with enhanced drought stress tolerance and increased growth potential.

Fermenting seaweed with koji fungi transforms its chemical composition, generating bioactive compounds absent in the raw material. We previously reported that the fungal fermentation of the edible red alga Pyropia yezoensis (Nori) produces betaine structural analogs (such as betaine, stachydrine, and carnitine), which are of particular interest because of their physiological roles and potential health benefits. Using metabolomic profiling, we compared non-fermented Nori with powders fermented by three industrially important fungi: Aspergillus luchuensis mut. kawachii (white koji fungus), Aspergillus oryzae (yellow koji fungus), and Monascus purpureus (red koji fungus). All fermentations enhanced the levels of betaine and carnitine, but stachydrine production was unique to the yellow koji fungus. Precursor patterns revealed distinct metabolic strategies: the yellow koji fungus exhibited an intermediate detectable choline oxidation route and strong proline methylation, the white koji fungus rapidly converted choline without intermediate accumulation, and the red koji fungus favored carnitine and proline but produced little stachydrine. Fermentation also shifted the methylation balance toward a state that supports methyl-dependent pathways. These findings reveal clear species-specific strategies for the production of betaine structural analogs, providing a mechanistic basis for understanding the metabolic divergence among koji fungi and guiding the targeted design of functional seaweed products.

Plants release various metabolites from roots and root exudates contribute to differences in stress tolerance among plant species. Plant and soil microbes have complex interactions that are affected by biotic and abiotic factors. The purpose of this study was to examine the differences in metabolites in root exudates of rice (Oryza sativa) cultivars and their correlation with bacterial populations in the rhizosphere. Two rice cultivars (O. sativa cv. Akamai and O. sativa cv. Koshihikari) were grown in soils fertilized with 0 g P kg−1 (− P) or 4.8 g P kg−1 (+ P). Root exudates and root-attached soil were collected at 13 and 20 days after transplanting (DAT) and their metabolites and bacterial community structure were determined. The exudation of proline, serine, threonine, valine and 4-coumarate were increased under low P conditions in both cultivars. There was a positive correlation between the concentration of pantothenate in root exudates and the representation of members of the genera Clostridium and Sporosarcina, which were negatively correlated with root dry weight. Gracilibacter, Opitutus, Pelotomaculum, Phenylobacterium and Oxobacter were positively correlated with root dry weight and presence of allantoin, 2-aminobtyrate and GlcNac. This study provides new information about the response of plants and rhizosphere soil bacteria to low P conditions.

Liver fibrosis results from chronic liver injury triggered by factors such as viral infection, excess alcohol intake, and lipid accumulation. However, the mechanisms underlying liver fibrosis are not fully understood. Here, we demonstrate that the expression of fibroblast growth factor 18 ( Fgf18 ) is elevated in mouse livers following the induction of chronic liver fibrosis models. Deletion of Fgf18 in hepatocytes attenuates liver fibrosis; conversely, overexpression of Fgf18 promotes liver fibrosis. Single-cell RNA sequencing reveals that overexpression of Fgf18 in hepatocytes results in an increase in the number of Lrat + hepatic stellate cells (HSCs), thereby inducing fibrosis. Mechanistically, FGF18 stimulates the proliferation of HSCs by inducing the expression of Ccnd1 . Moreover, the expression of FGF18 is correlated with the expression of profibrotic genes, such as COL1A1 and ACTA2 , in human liver biopsy samples. Thus, FGF18 promotes liver fibrosis and could serve as a therapeutic target to treat liver fibrosis. Fibroblast growth factor (FGF)18 plays pleiotropic roles, including bone development and carcinogenesis, however, its precise role in liver fibrosis remains incompletely understood. Here, the authors show that FGF18 promotes liver fibrosis by stimulating hepatic stellate cell proliferation, without concomitant upregulation of profibrotic genes.

Metabolites in the fruits of edible plants include sweet sugars, visually appealing pigments, various products with human nutritional value, and biologically active plant hormones. Although quantities of these metabolites vary during fruit development and ripening because of cell division and enlargement, there are few reports describing the actual dynamics of these changes. Therefore, we applied multiple metabolomic techniques to identify the changes in metabolite levels during the development and ripening of pear fruits (Pyrus communis L. 'La France'). We quantified and classified over 250 metabolites into six groups depending on their specific patterns of variation during development and ripening. Approximately half the total number of metabolites, including histidine and malate, accumulated transiently around the blooming period, during which cells are actively dividing, and then decreased either rapidly or slowly. Furthermore, the amounts of sulfur-containing amino acids also increased in pear fruits around 3-4 months after the blooming period, when fruit cells are enlarging, but virtually disappeared from ripened fruits. Some metabolites, including the plant hormone abscisic acid, accumulated particularly in the receptacle prior to blooming and/or fruit ripening. Our results show several patterns of variation in metabolite levels in developing and ripening pear fruits, and provide fundamental metabolomic data that is useful for understanding pear fruit physiology and enhancing the nutritional traits of new cultivars.

Key MessageIntegrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava.Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid, and indole-3-acetic acid conjugated with aspartic acid on tuberous root development. An integrated analysis of metabolites and gene expression indicated the expression levels of several genes encoding enzymes involved in starch biosynthesis and sucrose metabolism are up-regulated during tuberous root development, which is consistent with the accumulation of starch, sugar phosphates, and nucleotides. An integrated analysis of phytohormones and gene transcripts revealed a relationship among AUX signaling, CK signaling, and BR signaling, with AUX, CK, and BR inducing tuberous root development. In contrast, ABA and JA inhibited tuberous root development. These phenomena might represent the differences between stem tubers (e.g., potato) and root tubers (e.g., cassava). On the basis of these results, a phytohormonal regulatory model for tuberous root development was constructed. This model may be useful for future phytohormonal studies involving cassava.

Aims Root exudates of soybean grown under low-, normal-, and high-K + conditions were evaluated using metabolomics. Methods Two soybean cultivars, ‘Satonohohoemi’ (low-K-tolerant) and ‘Tachinagaha’ (low-K sensitive), were hydroponically grown with 6 (K6), 60 (K60), and 120 (K120) mg K L −1 for 7 and 14 days after transplanting (DAT). Root exudates were collected, and metabolites were evaluated using capillary electrophoresis time-of-flight mass spectrometry. Results Rroot K concentration was lower in K6 and higher in K120 compared to K60. Number of metabolites detected in ‘Satonohohoemi’ and ‘Tachinagaha’ was 43 and 39, respectively. Score plot of the principal component analysis (PCA) showed a clear grouping of the root exudate metabolites based one three K concentrations and two sampling times, with the first PCA accounting for 65.7% and 71.5% of the variance for the ‘Satonohohoemi’ and ‘Tachinagaha’, respectively. High-K conditions enhanced release of root exudate metabolites to rhizosphere in both soybean cultivars from 18% to 42%. However, low-K conditions resulted in a 1.2-fold increase and a 2.5-fold decrease in the release of root exudate metabolites in ‘Tachinagaha’ and ‘Satonohohoemi’, respectively, at 7 and 14 DAT. Conclusions These results reveal that soybean roots exude many metabolites in response to high- and low-K conditions. The number of increased metabolites was higher after long-term (14 DAT) compared to that of the short-term (7 DAT) of exposure of high- and low-K conditions. Soybean cultivars differ in the capacity to release metabolites by altering the exudation of specific metabolites for a better adaptation to the high- and low-K conditions.

Edible algae Neopyropia yezoensis is used as “Nori”, its dried sheet product, in Japanese cuisine. Its lipid components reportedly improve hepatic steatosis in obese db/db mice. In this study, we prepared “Nori powder (NP)” and “fermented Nori powder (FNP)” to utilize the functional lipids contained in “Nori” and examined their nutraceutical effects in vivo. Male db/db mice were fed a basal AIN-76 diet, a 10% NP-supplemented diet, or a 10% FNP-supplemented diet for 4 weeks. We detected eicosapentaenoic acid (EPA) present in both NP and FNP in the serum and liver of db/db mice in a dose-dependent manner. The NP diet reduced hepatic triglyceride accumulation (by 58%) in db/db mice by modulating gene expression, which resulted in the inhibition of lipogenic enzyme activity. Additionally, NP intake significantly suppressed the expression of inflammatory genes in the liver and hepatic injury marker levels in the sera (by 26%) of db/db mice. The FNP diet also led to a marked reduction in hepatic triglyceride accumulation (by 50%) and hepatic injury (by 28%) in db/db mice, and the mechanism of these alleviative actions was similar to that of the NP diet. Although the EPA content of FNP was one-third that of NP, metabolomic analysis revealed that bioactive betaine analogs, such as stachydrine, betaine, and carnitine, were detected only in FNP. In conclusion, we suggest that (1) mechanical processing of “Nori” makes its lipid components readily absorbable by the body to exert their lipid-lowering effects, and (2) fermentation of “Nori” produces anti-inflammatory molecules and lipid-lowering molecules, which together with the lipid components, can exert hepatic steatosis-alleviating effects.