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In plants, exposure to high light irradiation induces various stress responses, which entail complex metabolic rearrangements. To explore these dynamics, we conducted time‐course experiments spanning 2 min to 72 h with Arabidopsis thaliana under high and control light. Comparative metabolomics, transcriptomics, redox proteomics, and stable isotope labeling on leaf rosettes identified a series of synchronous and successive responses that provide a deeper insight into well‐orchestrated mechanisms contributing to high‐light acclimation. We observed transient transcriptome downregulation related to light harvesting and electron flow before the profound remodeling of the photosynthetic apparatus. Throughout the entire time course, redox homeostasis is tightly balanced between downregulation of production and enhanced transformation of NADPH accompanied by redistribution of reducing equivalents across several subcellular compartments. In both light conditions, C4 acids such as malate and fumarate are produced via anaplerosis. In carbon units, their accumulation in vacuoles surpasses plastidic levels of starch and intensifies notably under high light. In parallel, citrate synthesis from pyruvate is significantly hindered diurnally. Isotopic labeling in 2‐oxoglutarate and glutamate suggests a moderate de novo synthesis of C5 acids from a vacuolar citrate reservoir during the light phase while they are largely renewed during the night. In the absence of a diurnal clockwise flow through the tricarboxylic acid (TCA) cycle, increased oxidation of photorespiratory glycine takes over as a source of reductants to fuel mitochondrial ATP production. These findings, along with previous research, contribute to a model integrating redox balance and linking increased carbon assimilation and nitrogen metabolism, especially in the context of an incomplete TCA cycle.

High-quality data preprocessing is essential for untargeted metabolomics experiments, where increasing dataset scale and complexity demand adaptable, robust, and reproducible software solutions. Modern preprocessing tools must evolve to integrate seamlessly with downstream analysis platforms, ensuring efficient and streamlined workflows. Since its introduction in 2005, the xcms R package has become one of the most widely used tools for LC-MS data preprocessing. Developed through an open-source, community-driven approach, xcms has maintained long-term stability while continuously expanding its capabilities and accessibility. We present recent advancements that position xcms as a central component of a modular and interoperable software ecosystem for metabolomics data analysis. Key improvements include enhanced scalability, enabling the processing of large-scale experiments with thousands of samples on standard computing hardware. These developments empower users to build comprehensive, customizable, and reproducible workflows tailored to diverse experimental designs and analytical needs. An expanding collection of tutorials, documentation, and teaching materials further supports both new and experienced users in leveraging the broader R and Bioconductor ecosystems. These resources facilitate the integration of statistical modeling, visualization tools, and domain-specific packages, extending the reach and impact of xcms workflows. Together, these enhancements solidify xcms as a cornerstone of modern metabolomics research.

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Sulfur (S) metabolism has played a critical role in the evolution of life, serving as an energy source for early biochemical pathways like dissimilatory S reduction and anoxygenic photosynthesis. Across kingdoms, S metabolism displays remarkable diversity. S-containing metabolites like glucosinolates (GLSs) in Brassicaceae and S-alk(en)ylcysteine sulfoxides in Allium species illustrate the ecological and evolutionary significance of Scontaining compounds. These metabolites contribute to defense, homeostasis, and ecological interactions, with mechanisms like enzymatic hydrolysis releasing bioactive molecules such as allicin. Further, advances in transcriptomics and biochemical studies have revealed the genetic underpinnings of S metabolism and specialized pathways in bulb-forming Allium species. The role extends to ecological interactions by modulating S-associated defense pathways. This integrative understanding of S metabolism underscores its evolutionary, physiological, and ecological importance.

Herbivores sharing host plants are often temporally and spatially separated, limiting direct interactions between them. Nevertheless, as observed in numerous aboveground study systems, they can reciprocally influence each other via systemically induced plant responses. In contrast, examples of such plant-mediated interactions between belowground herbivores are scarce; however, we postulated that they similarly occur, given the large diversity of root-interacting soil organisms. To test this hypothesis, we analyzed the performance of cabbage root fly (Delia radicum) larvae feeding on the main roots of field mustard (Brassica rapa) plants whose fine roots were infected by the root-knot nematode (Meloidogyne incognita). Simultaneously, we studied the effects of M. incognita on D. radicum-induced defense responses and the accumulation of primary metabolites in the main root. We observed that almost 1.5 times as many D. radicum adults emerged from nematode-infected plants, indicating a facilitation effect of M. incognita infection. Although we observed increases in the accumulation of proteins and two essential amino acids, the strongest effect of nematode infection was visible in the defense response to D. radicum. We observed a 1.5 times higher accumulation of the defense-related phytohormone JA-Ile in response to D. radicum on nematode-infected plants, coinciding with a 75% increase in indole glucosinolate concentrations. Contrastingly, concentrations of aliphatic glucosinolates, secondary metabolites negatively affecting D. radicum, were 10-25% lower in nematode-infected plants. We hypothesize that the attenuated aliphatic glucosinolate concentrations result from antagonistic interactions between biosynthetic pathways of both glucosinolate classes, which was reflected in the expression of key biosynthesis genes. Our results provide explicit evidence of plant-mediated interactions between belowground organisms, likely via systemically induced responses in roots.

Abstract For G-type ATP-binding cassette (ABC) transporters, a hydrophobic “di-leucine motif” as part of a hydrophobic extracellular gate has been described to separate a large substrate-binding cavity from a smaller upper cavity and proposed to act as a valve controlling drug extrusion. Here, we show that an L704F mutation in the hydrophobic extracellular gate of Arabidopsis ABCG36/PDR8/PEN3 uncouples the export of the auxin precursor indole-3-butyric acid (IBA) from that of the defense compound camalexin (CLX). Molecular dynamics simulations reveal increased free energy for CLX translocation in ABCG36L704F and reduced CLX contacts within the binding pocket proximal to the extracellular gate region. Mutation L704Y enables export of structurally related non-ABCG36 substrates, IAA, and indole, indicating allosteric communication between the extracellular gate and distant transport pathway regions. An evolutionary analysis identifies L704 as a Brassicaceae family-specific key residue of the extracellular gate that controls the identity of chemically similar substrates. In summary, our work supports the conclusion that L704 is a key residue of the extracellular gate that provides a final quality control contributing to ABCG substrate specificity, allowing for balance of growth-defense trade-offs.

Leptomonines A and B, two novel rare benzyltetrahydroisoquinoline N-oxides, were isolated from the aerial parts of Leptopyrum fumarioides (L.) Reichenb. collected in Tuv province, Mongolia. Their chemical structures, absolute configurations, and conformations were established by 2D-NMR and CD spectral analyses. Leptomonine A (1) can suppress TNF-α production and COX-2 expression in LPS-stimulated RAW 267.4 cells. This compound at a concentration of 100 μM significantly reduced the TNF-α and COX-2 levels by 36.43% and 47.10%, respectively, compared with the negative control. Moreover, leptomonine B (2) remarkably lowers COX-2 levels at the highest concentration. The docking simulations were conducted with the COX-2 enzyme and revealed the binding ability of leptomonine A (1) and leptomonine B (2) with binding energies of − 9.03 and − 8.96 kcal/mol, respectively. The interactions of these alkaloids with the targets were mainly with the hydrophobic and hydrophilic sites, which are quite similar to rofecoxib. Phytochemical investigation revealed the diversity and novelty of the natural isoquinoline alkaloids in Leptopyrum fumarioides. Two new benzyltetrahydroisoquinoline N-oxides were identified as the bioactive constituents of Leptopyrum fumarioides by assessing its anti-inflammatory effects. The findings provide scientific justification to support the traditional application of Leptopyrum fumarioides for treating liver diseases associated with inflammation.

Plants are naturally subjected to various types of biotic stresses, including pathogenic microorganisms and herbivory by insects, which trigger different signaling pathways and related defense mechanisms. Inoculation with microorganisms, such as plant growth-promoting rhizobacteria (PGPR), can be seen as a form of stress because it triggers a systemic resistance response in plants similar to that caused by insect herbivory. However, these interactions have typically been studied independently, which has limited the understanding of their combined effects. This study examines the effects of Bacillus amyloliquefaciens GB03 inoculation and Spodoptera frugiperda herbivory on the total phenolic contents of Ocimum basilicum. We also analyze the levels of endogenous phytohormones and the activity of phenylalanine ammonia-lyase (PAL), a crucial enzyme involved in the biosynthesis of phenolic defense-related metabolites. The results indicate that the total phenolic content significantly increased only in plants that were both inoculated by GB03 and damaged by larvae. Additionally, PAL activity showed an increase in plants that were damaged by larvae and in those subjected to the combined treatment of larval damage and inoculation with GB03. Regarding phytohormones, in plants damaged by insects, the levels of salicylic acid (SA) increased, regardless of whether they were inoculated or not, while the levels of jasmonic acid–isoleucine (JA-ile) rose in all treatments compared to the control. This study highlights the intricate relationships among beneficial microbes, herbivores, and plant defense mechanisms, emphasizing their potential impact on improving plant resilience and the production of secondary metabolites. Furthermore, understanding the independent effects of PGPR inoculation, beyond its interaction with herbivory, could provide valuable insights into its role as a sustainable alternative for enhancing plant defense responses and promoting crop productivity.

Results of scientific work in chemistry can usually be obtained in the form of materials and data. A big step towards transparency and reproducibility of the scientific work can be gained if scientists publish their data in research data repositories in a FAIR manner. Nevertheless, in order to make chemistry a sustainable discipline, obtaining FAIR data is insufficient and a comprehensive concept that includes preservation of materials is needed. In order to offer a comprehensive infrastructure to find and access data and materials that were generated in chemistry projects, we combined the infrastructure Chemotion repository with an archive for chemical compounds. Samples play a key role in this concept: we describe how FAIR metadata of a virtual sample representation can be used to refer to a physically available sample in a materials’ archive and to link it with the FAIR research data gained using the said sample. We further describe the measures to make the physically available samples not only FAIR through their metadata but also findable, accessible and reusable.

Microbial biological control agents are increasingly used as an alternative to synthetic pesticides. The application of these microorganisms massively affects all members of plant‐colonising microbial communities, including pathogenic fungi. In the majority of cases, the resulting competition for ecological niches is decided by the toxicity of microbial secondary metabolites (SMs) formed. In this study, we devised confrontation experiments employing the fungal maize pathogen Colletotrichum graminicola and antagonistic partners, that is the biocontrol bacterium Bacillus amyloliquefaciens and the ubiquitous ascomycete Aspergillus nidulans. Transcriptome studies uncovered strong de‐regulation of the vast majority of the C. graminicola secondary metabolite biosynthetic gene clusters (SMBGCs), with 69% and 86% of these clusters de‐regulated at confrontation sites with B. amyloliquefaciens or A. nidulans, respectively. In the biocontrol bacterium and in A. nidulans confronting the maize pathogen, 100% and 74% of the SMBGCs were transcriptionally de‐regulated, respectively. Correspondingly, non‐targeted high‐resolution LC–MS/MS revealed a large repertoire of 1738 and 1466 novel features formed in the fungus–bacterium and fungus–fungus confrontation, respectively. Surprisingly, several of these belong to chemical classes with lead structures of synthetic fungicides.