Developmental stage-specific metabolite signatures in Arabidopsis thaliana under optimal and mild nitrogen limitation

Applying an NMR-based metabolomic workflow to unveil strawberry molecular mechanisms in vernalization

Nuclear Magnetic Resonance (NMR) is a mature technique in metabolomics due to its non-invasive, highly reproducible, and inherently quantitative nature. However, difficulties in data analysis hinder its standardization in research. Herein, we propose an NMR-based metabolomic workflow that comprises data preprocessing, metabolite annotation, and data analysis. In this work, we apply such workflow to study vernalization, which is a critical process for crop development with largely unknown molecular mechanisms. Our findings suggest that sugar mobility, accessibility, and increased photosynthetic activity support plant viability post-vernalization. In other words, these processes ensure successful transplanting of the plant, highlighting the importance of sufficient cold exposure for flowering, fruiting, and ripening. This study demonstrates that the proposed workflow is suitable to capture metabolic changes in plant development. Such methodology underscores the potential of NMR-based metabolomics as a powerful tool for crop monitoring, aiding in improved agricultural practices and yield optimization.

Carbon and nitrogen signaling regulate FLOWERING LOCUS C and impact flowering time in Arabidopsis

The timing of flowering in plants is modulated by both carbon (C) and nitrogen (N) signaling pathways. In a previous study, we established a pivotal role of the sucrose-signaling trehalose 6-phosphate pathway in regulating flowering under N-limited short-day conditions. In this work, we show that both wild-type Arabidopsis (Arabidopsis thaliana) plants grown under N-limited conditions and knock-down plants of TREHALOSE PHOSPHATE SYNTHASE 1 induce FLOWERING LOCUS C (FLC) expression, a well-known floral repressor associated with vernalization. When exposed to an extended period of cold, a flc mutant fails to respond to N availability and flowers at the same time under N-limited and full-nutrition conditions. Our data suggest that SUCROSE NON-FERMENTING 1 RELATED KINASE 1-dependent trehalose 6-phosphate-mediated C signaling and a mechanism downstream of N signaling (likely involving NIN-LIKE PROTEIN 7) impact the expression of FLC. Collectively, our data underscore the existence of a multi-factor regulatory system in which the C and N signaling pathways jointly govern the regulation of flowering in plants.

Comprehensive LC-MS/MS analysis of nitrogen-related plant metabolites

We have developed and validated a novel LC-MS/MS method for simultaneously analyzing amino acids, biogenic amines, and their acetylated and methylated derivatives in plants. This method involves a one-step extraction of 2-5 mg of lyophilized plant material followed by fractionation of different biogenic amine forms, and exploits an efficient combination of hydrophilic interaction liquid chromatography (HILIC), reversed phase (RP) chromatography with pre-column derivatization, and tandem mass spectrometry (MS). This approach enables high-throughput processing of plant samples, significantly reducing the time needed for analysis and its cost. We also present a new synthetic route for deuterium-labeled polyamines. The LC-MS/MS method was rigorously validated by quantifying levels of nitrogen-related metabolites in seedlings of seven plant species, including Arabidopsis, maize, and barley, all of which are commonly used model organisms in plant science research. Our results revealed substantial variations in the abundance of these metabolites between species, developmental stages, and growth conditions, particularly for the acetylated and methylated derivatives and the various polyamine fractions. However, the biological relevance of these plant metabolites is currently unclear. Overall, this work contributes significantly to plant science by providing a powerful analytical tool and setting the stage for future investigations into the functions of these nitrogen-related metabolites in plants.

The transcription factor HSFA7b controls thermomemory at the shoot apical meristem by regulating ethylene biosynthesis and signaling in Arabidopsis

The shoot apical meristem (SAM) is responsible for overall shoot growth by generating all aboveground structures. Recent research has revealed that the SAM displays an autonomous heat stress (HS) memory of a previous non-lethal HS event. Considering the importance of the SAM for plant growth, it is essential to determine how its thermomemory is mechanistically controlled. Here, we report that HEAT SHOCK TRANSCRIPTION FACTOR A7b (HSFA7b) plays a crucial role in this process in Arabidopsis, as the absence of functional HSFA7b results in the temporal suppression of SAM activity after thermopriming. We found that HSFA7b directly regulates ethylene response at the SAM by binding to the promoter of the key ethylene signaling gene ETHYLENE-INSENSITIVE 3 to establish thermotolerance. Moreover, we demonstrated that HSFA7b regulates the expression of ETHYLENE OVERPRODUCER 1 (ETO1) and ETO1-LIKE 1, both of which encode ethylene biosynthesis repressors, thereby ensuring ethylene homeostasis at the SAM. Taken together, these results reveal a crucial and tissue-specific role for HSFA7b in thermomemory at the Arabidopsis SAM.

Biomass allocation in response to accession recognition in Arabidopsis thaliana depends on nutrient availability and plant age

Many organisms have evolved to identify and respond to differences in genetic relatedness between conspecifics, allowing them to select between competitive and facilitative strategies to improve fitness. Due to their sessile nature, plants frequently draw from the same pool of nutrients, and the ability to limit competition between closely related conspecifics would be advantageous. Studies with Arabidopsis thaliana have confirmed that plants can detect variations at the accession level and alter their root system architecture (RSA) in response, presumably for regulating nutrient uptake. The phenotypic impact of this accession-recognition on the RSA is influenced by nutrient availability, underscoring the importance of plant-plant recognition in their growth and fitness. Thus far, these observations have been limited to short-term studies (<21 days) of only the RSA of this model angiosperm. Here we exploit nutrient-mediated regulation of accession-recognition to observe how this plant-plant recognition phenomenon influences growth from germination to flowering in A. thaliana. Our work identifies root and shoot traits that are affected by nutrient-mediated accession recognition. By coupling phenotypic assays to mass spectrometry-based studies of primary metabolite distribution, we provide preliminary insight into the biochemical underpinnings of the changes observed during these plant-plant responses. Most notably that late-stage changes in sucrose metabolism in members of the same accession drove early flowering. This work underscores the need to evaluate accession-recognition under the context of nutrient availability and consider responses throughout the plant's life, not simply at the earliest stages of interaction.