Methods for the analysis of oxylipins in plants

Metabolomic analysis of patient plasma yields evidence of plant-like α-linolenic acid metabolism in Plasmodium falciparum

Metabolomics offers a powerful means to investigate human malaria parasite biology and host-parasite interactions at the biochemical level, and to discover novel therapeutic targets and biomarkers of infection. Here, we used an approach based on liquid chromatography and mass spectrometry to perform an untargeted metabolomic analysis of metabolite extracts from Plasmodium falciparum-infected and uninfected patient plasma samples, and from an enriched population of in vitro cultured P. falciparum-infected and uninfected erythrocytes. Statistical modeling robustly segregated infected and uninfected samples based on metabolite species with significantly different abundances. Metabolites of the α-linolenic acid (ALA) pathway, known to exist in plants but not known to exist in P. falciparum until now, were enriched in infected plasma and erythrocyte samples. In vitro labeling with (13)C-ALA showed evidence of plant-like ALA pathway intermediates in P. falciparum. Ortholog searches using ALA pathway enzyme sequences from 8 available plant genomes identified several genes in the P. falciparum genome that were predicted to potentially encode the corresponding enzymes in the hitherto unannotated P. falciparum pathway. These data suggest that our approach can be used to discover novel facets of host/malaria parasite biology in a high-throughput manner.

MarVis-Filter: ranking, filtering, adduct and isotope correction of mass spectrometry data

Statistical ranking, filtering, adduct detection, isotope correction, and molecular formula calculation are essential tasks in processing mass spectrometry data in metabolomics studies. In order to obtain high-quality data sets, a framework which incorporates all these methods is required. We present the MarVis-Filter software, which provides well-established and specialized methods for processing mass spectrometry data. For the task of ranking and filtering multivariate intensity profiles, MarVis-Filter provides the ANOVA and Kruskal-Wallis tests with adjustment for multiple hypothesis testing. Adduct and isotope correction are based on a novel algorithm which takes the similarity of intensity profiles into account and allows user-defined ionization rules. The molecular formula calculation utilizes the results of the adduct and isotope correction. For a comprehensive analysis, MarVis-Filter provides an interactive interface to combine data sets deriving from positive and negative ionization mode. The software is exemplarily applied in a metabolic case study, where octadecanoids could be identified as markers for wounding in plants.

Analysis of plant galactolipids by reversed-phase high-performance liquid chromatography/mass spectrometry with accurate mass measurement

The composition of plant membrane lipids was investigated by reversed-phase high performance liquid chromatography mass spectrometry with accurate mass measurement. The data dependent methods for the analysis of monogalactosyldiacylglycerols (MGDGs) and digalactosyldiacylglycerols (DGDGs) have been developed. The optimised chromatographic systems were based on a 2.0 mm i.d. Nucleosil C18 column with methanol/water (MGDGs) or acetonitrile/methanol/water (DGDGs) gradients. The galactolipids were ionised by electrospray operated in the positive ion mode and identified based on their MS/MS spectra. High resolution spectra with accurate masses were found to be essential for correct interpretation of the MS data. The elution order of non-oxidised MGDGs and DGDGs followed the equivalent carbon numbers. The methods were applied for detailed characterisation of the MGDGs and DGDGs in the leaves of Arabidopsis thaliana and Melissa officinalis.

Advances in methods for the determination of biologically relevant lipid peroxidation products

Lipid peroxidation is recognized to be an important contributor to many chronic diseases, especially those of an inflammatory pathology. In addition to their value as markers of oxidative damage, lipid peroxidation products have also been shown to have a wide variety of biological and cell signalling effects. In view of this, accurate and sensitive methods for the measurement of lipid peroxidation products are essential. Although some assays have been described for many years, improvements in protocols are continually being reported and, with recent advances in instrumentation and technology, highly specialized and informative techniques are increasingly used. This article gives an overview of the most currently used methods and then addresses the recent advances in some specific approaches. The focus is on analysis of oxysterols, F(2)-isoprostanes and oxidized phospholipids by gas chromatography or liquid chromatography mass spectrometry techniques and immunoassays for the detection of 4-hydroxynonenal.

The genuine ligand of a jasmonic acid receptor: improved analysis of jasmonates is now required

Jasmonic acid (JA), its metabolites, such as the methyl ester or amino acid conjugates as well as its precursor 12-oxophytodienoic acid (OPDA) are lipid-derived signals. JA, OPDA and JA-amino acid conjugates are known to function as signals in plant stress responses and development. More recently, formation of JA-amino acid conjugates and high biological activity of JA-Isoleucine (JA-Ile) were found to be essential in JA signaling. A breakthrough was the identification of JAZ proteins which interact with the F-box protein COI1 if JA-Ile is bound. This interaction leads to proteasomal degradation of JAZs being negative regulators of JA-induced transcription. Surprisingly, a distinct stereoisomer of JA-Ile, the (+)-7-iso-JA-Ile [(3R,7S) form] is most active. Coronatine, a bacterial phytotoxine with an identical stereochemistry at the cyclopentanone ring, has a similar bioactivity. This was explained by the recent identification of COI1 as the JA receptor and accords well with molecular modeling studies. Whereas over the last two decades JA was quantified to describe any JA dependent process, now we have to take into account a distinct stereoisomer of JA-Ile. Until recently a quantitative analysis of (+)-7-iso-JA-Ile was missing presumable due to its equilibration to (-)-JA-Ile. Now such an analysis was achieved. These aspects will be discussed based on our new knowledge on JA perception and signaling.

Jasmonates: structural requirements for lipid-derived signals active in plant stress responses and development

Jasmonates are lipid-derived signals that mediate plant stress responses and development processes. Enzymes participating in biosynthesis of jasmonic acid (JA) (1, 2) and components of JA signaling have been extensively characterized by biochemical and molecular-genetic tools. Mutants of Arabidopsis and tomato have helped to define the pathway for synthesis of jasmonoyl-isoleucine (JA-Ile), the active form of JA, and to identify the F-box protein COI1 as central regulatory unit. However, details of the molecular mechanism of JA signaling have only recently been unraveled by the discovery of JAZ proteins that function in transcriptional repression. The emerging picture of JA perception and signaling cascade implies the SCF(COI1) complex operating as E3 ubiquitin ligase that upon binding of JA-Ile targets JAZ repressors for degradation by the 26S-proteasome pathway, thereby allowing the transcription factor MYC2 to activate gene expression. The fact that only one particular stereoisomer, (+)-7-iso-JA-l-Ile (4), shows high biological activity suggests that epimerization between active and inactive diastereomers could be a mechanism for turning JA signaling on or off. The recent demonstration that COI1 directly binds (+)-7-iso-JA-l-Ile (4) and thus functions as JA receptor revealed that formation of the ternary complex COI1-JA-Ile-JAZ is an ordered process. The pronounced differences in biological activity of JA stereoisomers also imply strict stereospecific control of product formation along the JA biosynthetic pathway. The pathway of JA biosynthesis has been unraveled, and most of the participating enzymes are well-characterized. For key enzymes of JA biosynthesis the crystal structures have been established, allowing insight into the mechanisms of catalysis and modes of substrate binding that lead to formation of stereospecific products.