PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.

INTRODUCTION: Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories. OBJECTIVES: To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management. METHODS: We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles. RESULTS: PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases. CONCLUSION: PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest .

Genetic and lipidomic analyses suggest that Nostoc punctiforme, a plant-symbiotic cyanobacterium, does not produce sphingolipids.

Sphingolipids, a class of amino-alcohol-based lipids, are well characterized in eukaryotes and in some anaerobic bacteria. However, the only sphingolipids so far identified in cyanobacteria are two ceramides (i.e., an acetylsphingomyelin and a cerebroside), both based on unbranched, long-chain base (LCB) sphingolipids in Scytonema julianum and Moorea producens , respectively. The first step in de novo sphingolipid biosynthesis is the condensation of l-serine with palmitoyl-CoA to produce 3-keto-diyhydrosphingosine (KDS). This reaction is catalyzed by serine palmitoyltransferase (SPT), which belongs to a small family of pyridoxal phosphate-dependent α-oxoamine synthase (AOS) enzymes. Based on sequence similarity to molecularly characterized bacterial SPT peptides, we identified a putative SPT (Npun_R3567) from the model nitrogen-fixing, plant-symbiotic cyanobacterium, Nostoc punctiforme strain PCC 73102 (ATCC 29133). Gene expression analysis revealed that Npun_R3567 is induced during late-stage diazotrophic growth in N. punctiforme . However, Npun_R3567 could not produce the SPT reaction product, 3-keto-diyhydrosphingosine (KDS), when heterologously expressed in Escherichia coli . This agreed with a sphingolipidomic analysis of N. punctiforme cells, which revealed that no LCBs or ceramides were present. To gain a better understanding of Npun_R3567, we inferred the phylogenetic position of Npun_R3567 relative to other bacterial AOS peptides. Rather than clustering with other bacterial SPTs, Npun_R3567 and the other cyanobacterial BioF homologues formed a separate, monophyletic group. Given that N. punctiforme does not appear to possess any other gene encoding an AOS enzyme, it is altogether unlikely that N. punctiforme is capable of synthesizing sphingolipids. In the context of cross-kingdom symbiosis signalling in which sphingolipids are emerging as important regulators, it appears unlikely that sphingolipids from N. punctiforme play a regulatory role during its symbiotic association with plants.

The impact of chitosan on the early metabolomic response of wheat to infection by Fusarium graminearum.

BACKGROUND: Chitosan has shown potential for the control of Fusarium head blight (FHB) disease caused by Fusarium graminearum. The objective of this study was to compare the effect of chitosan hydrochloride applied pre- or post-fungal inoculation on FHB and to better understand its' mode of action via an untargeted metabolomics study. RESULTS: Chitosan inhibited fungal growth in vitro and, when sprayed on the susceptible wheat cultivar Remus 24 hours pre-inoculation with F. graminearum, it significantly reduced the number of infected spikelets at 7, 14 and 21 days post-inoculation. Chitosan pre-treatment also increased the average grain weight per head, the number of grains per head and the 1000-grain weight compared to the controls sprayed with water. No significant impact of chitosan on grain yield was observed when the plants were sprayed 24 hours post-inoculation with F. graminearum, even if it did result in a reduced number of infected spikelets at every time point. An untargeted metabolomic study using UHPLC-QTOF-MS on wheat spikes revealed that spraying the spikes with both chitosan and F. graminearum activated known FHB resistance pathways (e.g. jasmonic acid). Additionally, more metabolites were up- or down-regulated when both chitosan and F. graminearum spores were sprayed on the spikes (117), as compared with chitosan (51) or F. graminearum on their own (32). This included a terpene, a terpenoid and a liminoid previously associated with FHB resistance. CONCLUSIONS: In this study we showed that chitosan hydrochloride inhibited the spore germination and hyphal development of F. graminearum in vitro, triggered wheat resistance against infection by F. graminearum when used as a pre-inoculant, and highlighted metabolites and pathways commonly and differentially affected by chitosan, the pathogen and both agents. This study provides insights into how chitosan might provide protection or stimulate wheat resistance to infection by F. graminearum. It also unveiled new putatively identified metabolites that had not been listed in previous FHB or chitosan-related metabolomic studies.

Metabotyping of 30 maize hybrids under early-sowing conditions reveals potential marker-metabolites for breeding.

INTRODUCTION: In Northern Europe, maize early-sowing used to maximize yield may lead to moderate damages of seedlings due to chilling without visual phenotypes. Genetic studies and breeding for chilling tolerance remain necessary, and metabolic markers would be particularly useful in this context. OBJECTIVES: Using an untargeted metabolomic approach on a collection of maize hybrids, our aim was to identify metabolite signatures and/or metabolites associated with chilling responses at the vegetative stage, to search for metabolites differentiating groups of hybrids based on silage-earliness, and to search for marker-metabolites correlated with aerial biomass. METHODS: Thirty genetically-diverse maize dent inbred-lines (Zea mays) crossed to a flint inbred-line were sown in a field to assess metabolite profiles upon cold treatment induced by a modification of sowing date, and characterized with climatic measurements and phenotyping. RESULTS: NMR- and LC-MS-based metabolomic profiling revealed the biological variation of primary and specialized metabolites in young leaves of plants before flowering-stage. The effect of early-sowing on leaf composition was larger than that of genotype, and several metabolites were associated to sowing response. The metabolic distances between genotypes based on leaf compositional data were not related to the genotype admixture groups, and their variability was lower under early-sowing than normal-sowing. Several metabolites or metabolite-features were related to silage-earliness groups in the normal-sowing condition, some of which were confirmed the following year. Correlation networks involving metabolites and aerial biomass suggested marker-metabolites for breeding for chilling tolerance. CONCLUSION: After validation in other experiments and larger genotype panels, these marker-metabolites can contribute to breeding.

Specificity of lipoxygenase pathways supports species delineation in the marine diatom genus Pseudo-nitzschia.

Oxylipins are low-molecular weight secondary metabolites derived from the incorporation of oxygen into the carbon chains of polyunsaturated fatty acids (PUFAs). Oxylipins are produced in many prokaryotic and eukaryotic lineages where they are involved in a broad spectrum of actions spanning from stress and defense responses, regulation of growth and development, signaling, and innate immunity. We explored the diversity in oxylipin patterns in the marine planktonic diatom Pseudo-nitzschia. This genus includes several species only distinguishable with the aid of molecular markers. Oxylipin profiles of cultured strains were obtained by reverse phase column on a liquid chromatograph equipped with UV photodiode detector and q-ToF mass spectrometer. Lipoxygenase compounds were mapped on phylogenies of the genus Pseudo-nitzschia inferred from the nuclear encoded hyper-variable region of the LSU rDNA and the plastid encoded rbcL. Results showed that the genus Pseudo-nitzschia exhibits a rich and varied lipoxygenase metabolism of eicosapentaenoic acid (EPA), with a high level of specificity for oxylipin markers that generally corroborated the genotypic delineation, even among genetically closely related cryptic species. These results suggest that oxylipin profiles constitute additional identification tools for Pseudo-nitzschia species providing a functional support to species delineation obtained with molecular markers and morphological traits. The exploration of the diversity, patterns and plasticity of oxylipin production across diatom species and genera will also provide insights on the ecological functions of these secondary metabolites and on the selective pressures driving their diversification.

LIPOXYGENASE PRODUCTS IN MARINE DIATOMS: A CONCISE ANALYTICAL METHOD TO EXPLORE THE FUNCTIONAL POTENTIAL OF OXYLIPINS(1).

Oxylipins are oxygenated derivatives of polyunsaturated fatty acids (PUFAs) that act as chemical mediators in many ecological and physiological processes in marine and freshwater diatoms. The occurrence and distribution of these molecules are relatively widespread within the lineage with considerable species-specific differences due to the variability of both the fatty acids recognized as substrates and the enzymatic transformations. The present review provides a general introduction to recent studies on diatom oxylipins and describes an analytical method for the detection and assessment of these elusive molecules in laboratory and field samples. This methodology is based on selective enrichment of the oxylipin fraction by solvent extraction, followed by parallel acquisition of full-scan UV and tandem mass spectra on reverse phase liquid chromatography (LC) peaks. The analytical procedure enables identification of potential genetic differences, enzymatic regulation, and ecophysiological conditions that result in different oxylipin signatures, thus providing an effective tool for probing the functional relevance of this class of lipids in plankton communities. Examples of oxylipin measurements in field samples are also provided as a demonstration of the analytical potential of the methodology.

15S-lipoxygenase metabolism in the marine diatom Pseudo-nitzschia delicatissima.

In recent years, oxylipins (lipoxygenase-derived oxygenated fatty acid products) have been reported in several bloom-forming marine diatoms. Despite increasing attention on the ecophysiological role of these molecules in marine environments, their biosynthesis is largely unknown in these microalgae. Biochemical methods, including tandem mass spectrometry, nuclear magnetic resonance and radioactive probes were used to identify structures, enzymatic activities and growth-dependent modulation of oxylipin biosynthesis in the pennate diatom Pseudo-nitzschia delicatissima. Three major compounds, 15S-hydroxy-(5Z,8Z,11Z,13E,17Z)-eicosapentaenoic acid (15S-HEPE), 15-oxo-5Z,9E,11E,13E-pentadecatetraenoic acid and 13,14-threo-13R-hydroxy-14S,15S-trans-epoxyeicosa-5Z,8Z,11Z,17Z-tetraenoic acid (13,14-HEpETE), were produced by three putative biochemical pathways triggered by eicosapentaenoic acid-dependent 15S lipoxygenase. Oxylipin production increases along the growth curve, with remarkable changes that precede the demise of the culture. At least one of the compounds, namely 15-oxoacid, is formed only in the stationary phase immediately before the collapse of the culture. Synthesis and regulation of phyco-oxylipins seem to correspond to a signaling mechanism that governs adaptation of diatoms along the growth curve until bloom termination. Factors triggering the process are unknown but synthesis of 15-oxoacid, constrained within a time-window of a few days just before the collapse of the culture, implies the involvement of a physiological control not directly dependent on distress or death of diatom cells.

LOX-induced lipid peroxidation mechanism responsible for the detrimental effect of marine diatoms on zooplankton grazers.

Some marine diatoms negatively affect the reproduction of dominant zooplankton grazers such as copepods, thus compromising the transfer of energy through the marine food chains. In this paper, the metabolic mechanism that leads to diatom-induced toxicity is investigated in three bloom-forming microalgae. We show that copepod dysfunctions can be induced by highly reactive oxygen species (hROS) and a blended mixture of diatom products, including fatty acid hydroperoxides (FAHs); these compounds display teratogenic and proapoptotic properties. The process is triggered by the early onset of lipoxygenase activities that elicit the synthesis of species-specific products, the basic structures of which were established (1-20); these compounds boost oxidative stress by massive lipid peroxidation. Our study might explain past laboratory and field results showing how diatoms damage zooplankton grazers even in the absence of polyunsaturated aldehydes, a class of molecules that has been formerly implicated in mediating the toxic activity of diatoms on copepods.

Chloroplastic glycolipids fuel aldehyde biosynthesis in the marine diatom Thalassiosira rotula.

Enzymatic preparations and specialized analytical tools have shown that chloroplast-derived glycolipids are the main substrates for the biosynthetic pathway that produces antiproliferative polyunsaturated aldehydes in broken cells of the marine diatom Thalassiosira rotula. This process, which is associated with the formation of free fatty acids and lyso compounds from polar lipids but not triglycerides, is largely dependent on glycolipid hydrolytic activity, rather than phospholipase A(2) as previously suggested. Preliminary characterization of lipolytic enzymes has revealed protein bands of 40-45 kDa. Under native conditions these proteins seem to be associated with soluble aggregates that have an apparent molecular weight of approximately 200 kDa. The biochemical process, which is similar to that described in the algal-bloom forming diatom Skeletonema costatum, suggests a mechanism based on decompartmentalization and mixing of preexisting enzymes and substrates.