MetaCom Metabolomics Facility

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.

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.

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.

A bottleneck in the development of new anti-cancer drugs is the recognition of their mode of action (MoA). We combined metabolomics and machine learning to predict MoAs of novel anti-proliferative drug candidates, focusing on human prostate cancer cells (PC-3). As proof of concept, we studied 38 drugs with known effects on 16 key processes of cancer metabolism, profiling low molecular weight intermediates of the central carbon and cellular energy metabolism (CCEM) by LC-MS/MS. These metabolic patterns unveiled distinct MoAs, enabling accurate MoA predictions for novel agents by machine learning. We validate the transferability of MoA predictions from PC-3 to two other cancer cell models and show that correct predictions are still possible, but at the expense of prediction quality. Furthermore, metabolic profiles of treated cells yield insights into intracellular processes, exemplified for drugs inducing different types of mitochondrial dysfunction. Specifically, we predict that pentacyclic triterpenes inhibit oxidative phosphorylation and affect phospholipid biosynthesis, as supported by respiration parameters, lipidomics, and molecular docking. Using biochemical insights from individual drug treatments, our approach offers new opportunities, including the optimization of combinatorial drug applications.

A bottleneck in the development of new anti‐cancer drugs is the recognition of their mode of action (MoA). Metabolomics combined with machine learning allowed to predict MoAs of novel anti‐proliferative drug candidates, focusing on human prostate cancer cells (PC‐3). As proof of concept, 38 drugs are studied with known effects on 16 key processes of cancer metabolism, profiling low molecular weight intermediates of the central carbon and cellular energy metabolism (CCEM) by LC‐MS/MS. These metabolic patterns unveiled distinct MoAs, enabling accurate MoA predictions for novel agents by machine learning. The transferability of MoA predictions based on PC‐3 cell treatments is validated with two other cancer cell models, i.e., breast cancer and Ewing\'s sarcoma, and show that correct MoA predictions for alternative cancer cells are possible, but still at some expense of prediction quality. Furthermore, metabolic profiles of treated cells yield insights into intracellular processes, exemplified for drugs inducing different types of mitochondrial dysfunction. Specifically, it is predicted that pentacyclic triterpenes inhibit oxidative phosphorylation and affect phospholipid biosynthesis, as confirmed by respiration parameters, lipidomics, and molecular docking. Using biochemical insights from individual drug treatments, this approach offers new opportunities, including the optimization of combinatorial drug applications.

The 2-pyrone moiety is present in a wide range of structurally diverse natural products with various biological activities. The plant biosynthetic routes towards these compounds mainly depend on the activity of either type III polyketide synthase-like 2-pyrone synthases or hydroxylating 2-oxoglutarate dependent dioxygenases. In the present study, the substrate specificity of these enzymes is investigated by a systematic screening using both natural and artificial substrates with the aims of efficiently forming (new) products and understanding the underlying catalytic mechanisms. In this framework, we focused on the in vitro functional characterization of a 2-pyrone synthase Gh2PS2 from Gerbera x hybrida and two dioxygenases AtF6’H1 and AtF6’H2 from Arabidopsis thaliana using a set of twenty aromatic and aliphatic CoA esters as substrates. UHPLC-ESI-HRMSn based analyses of reaction intermediates and products revealed a broad substrate specificity of the enzymes, enabling the facile \"green\" synthesis of this important class of natural products and derivatives in a one-step/one-pot reaction in aqueous environment without the need for halogenated or metal reagents and protective groups. Using protein modelling and substrate docking we identified amino acid residues that seem to be important for the observed product scope.

Background  In viticulture, iron (Fe) chlorosis is a common abiotic stress that impairs plant development and leads to yield and quality losses. Under low availability of the metal, the applied N form (nitrate and ammonium) can play a role in promoting or mitigating Fe deficiency stresses. However, the processes involved are not clear in grapevine. Therefore, the aim of this study was to investigate the response of two grapevine rootstocks to the interaction between N forms and Fe uptake. This process was evaluated in a hydroponic experiment using two ungrafted grapevine rootstocks Fercal (Vitis berlandieri x V. vinifera) tolerant to deficiency induced Fe chlorosis and Couderc 3309 (V. riparia x V. rupestris) susceptible to deficiency induced Fe chlorosis. Results  The results could differentiate Fe deficiency effects, N-forms effects, and rootstock effects. Interveinal chlorosis of young leaves appeared earlier on 3309 C from the second week of treatment with NO3−/NH4+ (1:0)/-Fe, while Fercal leaves showed less severe symptoms after four weeks of treatment, corresponding to decreased chlorophyll concentrations lowered by 75% in 3309 C and 57% in Fercal. Ferric chelate reductase (FCR) activity was by trend enhanced under Fe deficiency in Fercal with both N combinations, whereas 3309 C showed an increase in FCR activity under Fe deficiency only with NO3−/NH4+ (1:1) treatment. With the transcriptome analysis, Gene Ontology (GO) revealed multiple biological processes and molecular functions that were significantly regulated in grapevine rootstocks under Fe-deficient conditions, with more genes regulated in Fercal responses, especially when both forms of N were supplied. Furthermore, the expression of genes involved in the auxin and abscisic acid metabolic pathways was markedly increased by the equal supply of both forms of N under Fe deficiency conditions. In addition, changes in the expression of genes related to Fe uptake, regulation, and transport reflected the different responses of the two grapevine rootstocks to different N forms. Conclusions  Results show a clear contribution of N forms to the response of the two grapevine rootstocks under Fe deficiency, highlighting the importance of providing both N forms (nitrate and ammonium) in an appropriate ratio in order to ease the rootstock responses to Fe deficiency.

Methylerythritol cyclodiphosphate (MEcPP) is an intermediate in the biosynthesis of isoprenoids in plant plastids and in bacteria, and acts as a stress signal in plants. Here, we show that MEcPP regulates biofilm formation in Escherichia coli K-12 MG1655. Increased MEcPP levels, triggered by genetic manipulation or oxidative stress, inhibit biofilm development and production of fimbriae. Deletion of fimE, encoding a protein known to downregulate production of adhesive fimbriae, restores biofilm formation in cells with elevated MEcPP levels. Limited proteolysis-coupled mass spectrometry (LiP-MS) reveals that MEcPP interacts with the global regulatory protein H-NS, which is known to repress transcription of fimE. MEcPP prevents the binding of H-NS to the fimE promoter. Therefore, our results indicate that MEcPP can regulate biofilm formation by modulating H-NS activity and thus reducing fimbriae production. Further research is needed to test whether MEcPP plays similar regulatory roles in other bacteria.

Diterpenoids form a diverse group of natural products, many of which are or could become pharmaceuticals or industrial chemicals. The modular character of diterpene biosynthesis and the promiscuity of the enzymes involved make combinatorial biosynthesis a promising approach to generate libraries of diverse diterpenoids. Here, we report on the combinatorial assembly in yeast of ten diterpene synthases producing (+)-copalyldiphosphate-derived backbones and four cytochrome P450 oxygenases (CYPs) in diverse combinations. This resulted in the production of over 200 diterpenoids. Based on literature and chemical database searches, 162 of these compounds can be considered new-to-Nature. The CYPs accepted most substrates they were given but remained regioselective with few exceptions. Our results provide the basis for the systematic exploration of the diterpenoid chemical space in yeast using sequence databases.