MetaboHUB

Species-specific feedback between plants and soil microbial communities is an important driver of vegetation dynamics. Arbuscular mycorrhizal (AM) fungi colonise most terrestrial plants but are not expected to generate specific feedbacks due to low host specificity. We tested whether variation in mycorrhizal associations and associated rhizosphere metabolomes among co-existing temperate grassland species leads to species-specific plant-soil feedback. More mycorrhizal plant species showed more divergent plant-soil feedback: they experienced reduced growth and mycorrhizal colonisation in soils originating from weakly mycorrhizal species, but feedback became neutral in soil from species with similar mycorrhizal strategies. The species with the most self-promoting soil feedback was characterised by strong metabolome shifts related to stress and immune responses following soil inoculum manipulation, while the metabolomes of species with more negative feedback were unresponsive. This study demonstrates that AM fungi can generate species-specific plant-soil feedback, which can be predicted from plant mycorrhizal strategies and rhizosphere chemistry.

• High temperature triggers stage-dependent shifts in berry polyphenol dynamics. • Heat treatment at ripening causes a rise then fall in berry polyphenol contents. • Cabernet-Sauvignon shows earlier and longer polyphenol responses than Merlot. • Phenolic acids and flavanols show distinct cultivar- and time-specific responses. • Fine-scale sampling captures transient heat-induced changes in berry composition. High temperature is a major abiotic stress that profoundly affects grape berry development and secondary metabolism. This study investigated the temporal dynamics of polyphenolic compounds in Vitis vinifera cv. Cabernet Sauvignon (CS) and Merlot berries subjected to berry‑scale heat treatments (HT) under greenhouse conditions. HT was applied at both the herbaceous and ripening stages. Polyphenolic profiles were only marginally altered during the herbaceous stage, whereas a markedly broader response was observed during the ripening stage. In both cultivars, HT induced a characteristic “increase-then-decrease” pattern in polyphenol accumulation, with CS exhibiting an earlier onset of the induction and a more delayed decline phase than Merlot. Furthermore, transient variations in specific phenolic classes, particularly phenolic acids and flavanols, displayed distinct cultivar‑ and time‑dependent signatures under HT. Taken together, these results reveal both conserved and cultivar‑specific responses to heat stress and highlight the critical importance of high temporal resolution for capturing transient yet biologically meaningful changes in grape berry composition.

Broomrapes (Phelipanche and Orobanche spp.) and witchweeds (Striga spp.) are parasitic weeds that are increasingly threatening crops worldwide. Seeds of these species rely on host-derived signals such as strigolactones to germinate. While cytokinins were also reported as germination inducers of witchweeds, their role during germination of broomrapes remains unexplored. Our study shows that some but not all cytokinins stimulate Striga hermonthica germination independently of strigolactones, and that high concentrations of bioactive cytokinins trigger Striga seedlings to differentiate into fully extruded embryo-like structures. In contrast, cytokinin free bases but not ribosylated or glycosylated conjugates are extremely potent inhibitors of broomrapes germination. Germination inhibition upon the cytokinin signaling inhibitor PI-55 and inhibitor of cytokinin degradation INCYDE suggest that the cytokinin perception and degradation machinery is conserved in parasitic weeds. In Phelipanche ramosa, gene expression analyses combined with targeted quantification of cytokinin contents revealed that strigolactones first induce an increase in ABA catabolism, then a modification of the cytokinin endogenous pool in favor of inactive conjugates. Overall, this study provides valuable insights into the hormonal interplay governing seed germination in broomrapes and witchweeds, paving the way for future studies aimed at developing novel strategies for parasitic weed control.

Abstract In the glucose-free environment of the midgut of the tsetse fly vector, the procyclic forms ofTrypanosoma bruceiprimarily consume proline to feed its central carbon and energy metabolism. In this context, the parasite produces through gluconeogenesis glucose 6- phosphate (G6P), the precursor of essential metabolic pathways, from proline catabolism. We showed here that the parasite uses three different enzymes to perform the key gluconeogenic reaction producing fructose 6-phosphate (F6P) from fructose 1,6-bisphosphate, (i) fructose-1,6- bisphosphatase (FBPase), the canonical enzyme performing this reaction, (ii) sedoheptulose- 1,7-bisphosphatase (SBPase) and (iii) more surprisingly ATP-dependent phosphofructokinase (PFK), an enzyme considered to irreversibly catalyse the opposite reaction involved in glycolysis. These three enzymes, as well as six other glycolytic/gluconeogenic enzymes, are located in peroxisome-related organelles, named glycosomes. Incorporation of13C-enriched glycerol (a more effective alternative to proline for monitoring gluconeogenic activity) into F6P and G6P was more affected in the PFK null mutant than in the FBPase null mutant, suggesting the PFK contributes at least as much as FBPase to gluconeogenesis. We also showed that glucose deprivation did not affect the quantities of PFK substrates and products, whereas a 500-fold increase in the substrate/product ratio was expected for PFK to carry out the gluconeogenic reaction. In conclusion, we showed for the first time that ATP-dependent PFK can functionin vivoin the gluconeogenic direction, even in the presence of FBPase activity. This particular feature, which precludes loss of ATP through a futile cycle involving PFK and FBPase working simultaneously in the glycolytic and gluconeogenic directions, respectively, is probably due to the supramolecular organisation of the metabolic pathway within glycosomes to overcome thermodynamic barriers through metabolic channelling.

Urban vegetation provides many ecosystem services like heat island mitigation. However, urban trees are subjected to the stresses that they are meant to alleviate, with drought being a main constraint. We investigated the drought response strategy of plane trees (Platanus × hispanica), focusing on stomatal regulation and metabolic remodelling. To address this question, a semi-controlled experiment was performed in an urban site with fourteen plane trees grown in containers. From May to June 2022, those trees were physiologically characterized in response to a controlled edaphic drought completed by a targeted metabolome analysis focused on amino acids, sugars, polyols and organic acids. Early P. × hispanica response to drought consisted in stomatal closure limiting carbon assimilation and osmotic adjustment, which was likely related to malate and trehalose accumulation. Both allowed the maintenance of stem water potential and Relative Water Content. As the drought became severe, when the extractable soil water content (eSWC) dropped below 30%, a non-stomatal limitation of photosynthesis was observed and was associated with photosynthetic apparatus damage (reduced chlorophyll content and decrease in Fv/Fm) and a further decline in carbon assimilation. When eSWC decreased below 25%, severe drought induced defoliation. Together, these results highlight the isohydric strategy of P. × hispanica, based notably on osmotic adjustment and explain its resistance to drought combined with other urban constraints. In the context of climatic change in cities, it would be interesting to analyse the impact of successive drought cycles in the long term, aiming for sustainable planning and management of urban trees.

Acute intermittent porphyria is an inherited error of heme synthesis. The underlying pathophysiology, involving mainly hepatic heme synthesis, is poorly understood despite its occurrence, and the severity of acute porphyria attack is still difficult to control. A better understanding of the interactions between heme synthesis and global metabolism would improve the management of AIP patients. An untargeted metabolomic analysis was performed on the urine of 114 patients with overt AIP and asymptomatic carriers using liquid chromatography coupled to high-resolution mass spectrometry. The collected data were analyzed by combining univariate and multivariate analyses. A total of 239 metabolites were annotated in urine samples by matching chromatographic and mass spectral characteristics with those from our chemical library. Twenty-six metabolites, including porphyrin precursors, intermediates of tryptophan or glycine metabolism and, unexpectedly, bile acids, showed significant concentration differences between the phenotypic groups. Dysregulation of bile acid metabolism was confirmed by targeted quantitative analysis, which revealed an imbalance in favor of hydrophobic bile acids associated with changes in conjugation, which was more pronounced in the severe phenotype. Using a random forest model, the cholic acid/chenodeoxycholic acid ratio enables the differential classification of severe patients from other patients with a diagnostic accuracy of 84%. The analysis of urine samples revealed significant modifications in the metabolome of AIP patients. Alteration in bile acids provides new insights into the pathophysiology of chronic complications, such as primary liver cancer, while also providing new biomarker candidates for predicting the most severe phenotypes.

Background & aimDietary shifts replacing animal protein (AP) with plant protein (PP) sources have been associated with lowering cardiometabolic risk (CMR), but underlying mechanisms are poorly characterized. This nutritional intervention aims to characterize the metabolic changes induced by diets containing different proportions of AP and PP sources in males at CMR. DesignThis study is a 4-week, crossover, randomized, controlled-feeding trial in which 19 males with CMR followed two diets providing either 36% for the control diet (CON-D) or 64% for the flexitarian diet (FLEX-D) of total protein intake from PP sources. Plasma nontargeted metabolomes (LC-MS method) were measured in the fasted state and after a high-fat challenge meal at the end of each intervention arm. Lipogenesis and protein synthesis fluxes, flow-mediated dilatation (FMD) and gluco-lipidic responses were assessed after the challenge meal. Data were analyzed with mixed models, and univariate and multivariate models for metabolomics data. ResultsIn both arms CMR improved with time, with decreased body weight (-0.9%), insulin resistant (-34%, HOMA-IR, Homeostatic Model Assessment for Insulin Resistance) and low-density lipoproteins (LDL)-cholesterol (-11%). Diet had no effect on FMD or metabolic fluxes, but a trend was observed for a stronger decrease in HOMA-IR and lower postprandial glucose after FLEX-D vs CON-D. The abundance of 21 and 37 metabolites differed between diets at fasted and fed states, respectively, including food intake biomarkers of AP (methylhistidine, eicosapentaenoic acid, hydroxyprolines) and PP sources (trigonelline, N-acetyl-ornithine). In fasted or fed states, indole acrylic acid and indole propionic acid, both products of tryptophan catabolism, were higher after FLEX-D vs CON-D, while the indispensable amino acids-related metabolites alpha-aminoadipic acid, hydroxymethylbutyric acids and propionylcarnitine were lower. In the postprandial state only, the ω-oxidation products dodecanedioic, tetradecanedioic and hexadecanedioic acids were higher after FLEX-D vs CON-D. ConclusionsDespite little changes in risk factors after 4 wk, this study evidenced subtle metabolic adaptations in amino acids and lipid metabolism and gut microbiota activity occurring after higher PP source intake that may be beneficial to CMR. ClinicalTrials.gov study identifierNCT04236518 Clinical Trial RegistryNCT04236518 on ClinicalTrials.gov

Enzymatic parameters are classically determined in vitro, under conditions that are far from those encountered in cells, casting doubt on their physiological relevance. We developed a generic approach combining tools from synthetic and systems biology to measure enzymatic parameters in vivo. In the context of a synthetic carotenoid pathway in Saccharomyces cerevisiae, we focused on a phytoene synthase and three phytoene desaturases, which are difficult to study in vitro. We designed, built, and analyzed a collection of yeast strains mimicking substantial variations in substrate concentration by strategically manipulating the expression of geranyl-geranyl pyrophosphate (GGPP) synthase. We successfully determined in vivo Michaelis-Menten parameters (KM, Vmax, and kcat) for GGPP-converting phytoene synthase from absolute metabolomics, fluxomics and proteomics data, highlighting differences between in vivo and in vitro parameters. Leveraging the versatility of the same set of strains, we then extracted enzymatic parameters for two of the three phytoene desaturases. Our approach demonstrates the feasibility of assessing enzymatic parameters directly in vivo, providing a novel perspective on the kinetic characteristics of enzymes in real cellular conditions.

Dedifferentiated and Well-differentiated liposarcoma are characterized by a systematic amplification of the Murine Double Minute 2 (MDM2) oncogene. We demonstrate that p53-independent metabolic functions of chromatin-bound MDM2 are exacerbated in liposarcoma and mediate an addiction to serine metabolism to sustain tumor growth. However, the origin of exogenous serine remains unclear. Here, we show that elevated serine levels in mice harboring liposarcoma-patient derived xenograft, released by distant muscle is essential for liposarcoma cell survival. Repressing interleukine-6 expression, or treating liposarcoma cells with Food and Drugs Administration (FDA) approved anti-interleukine-6 monoclonal antibody, decreases de novo serine synthesis in muscle, impairs proliferation, and increases cell death in vitro and in vivo. This work reveals a metabolic crosstalk between muscle and liposarcoma tumor and identifies anti-interleukine-6 as a plausible treatment for liposarcoma patients.