Characterization of poplar metabotypes via mass difference enrichment analysis

Abstract

Instrumentation technology for metabolomics has advanced drastically in recent years in terms of sensitivity and specificity. Despite these technical advances, data analytical strategies are still in their infancy in comparison with other 'omics'. Plants are known to possess an immense diversity of secondary metabolites. Typically, more than 70% of metabolomics data are not amenable to systems biological interpretation because of poor database coverage. Here, we propose a new general strategy for mass-spectrometry-based metabolomics that incorporates all exact mass features with known sum formulas into the evaluation and interpretation of metabolomics studies. We extend the use of mass differences, commonly used for feature annotation, by redefining them as variables that reflect the remaining 'omic' domains. The strategy uses exact mass difference network analyses exemplified for the metabolomic description of two grey poplar (Populus × canescens) genotypes that differ in their capability to emit isoprene. This strategy established a direct connection between the metabotype and the non-isoprene-emitting phenotype, as mass differences pertaining to prenylation reactions were over-represented in non-isoprene-emitting poplars. Not only was the analysis of mass differences able to grasp the known chemical biology of poplar, but it also improved the interpretability of yet unknown biochemical relationships.

Carbon limitation leads to thermodynamic regulation of aerobic metabolism

“…Biochemical transformations were inferred by calculating all possible pairwise mass differences within a sample’s spectrum and matching differences (within 1□ppm) to a list of common biochemical transformations 50 . Biochemical transformations were identified following the procedures described by Breitling et al 50 and previously employed by Bailey et al 34 , Graham et al 10,11 , Moritz et al 36 , Kaling et al 35 , and Stegen et al 12 . Briefly, pairwise mass differences between all m/z peaks in a sample were compared with a reference list of 1298 commonly observed biochemical reactions of organic matter (Supplementary Table 2).…”

“…We underscore a need for improved model structures for predicting aerobic respiration, as we observed different metabolic processes between carbon-limited and carbon-replete environments. To investigate metabolic processes involved in aerobic respiration, we calculated inferred biochemical transformations in ultrahigh-resolution OM profiles following procedures described previously 10–12,34–36 . This method relies on the mass accuracy of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and produces a count of the number of times a specific molecule (e.g., glucose, valine, glutamine, etc.)…”

Ecology and Evolution of Intraspecific Chemodiversity of Plants

“…Plant species display varying levels of intraspecific phytochemical diversity (chemodiversity) within and among populations, from very low to extraordinarily high. For example, within tree species such as Populus nigra L. (black poplar; Salicaceae) and other Populus spp., variation in phenolics and other metabolite classes is found (Boeckler et al 2013, Moritz et al 2017. Populations of herbaceous species such as Solanum dulcamara (L.) (bittersweet nightshade; Solanaceae) show pronounced differences in their glycoalkaloid profiles between individuals (Calf et al 2018).…”

“…More recently, large-scale untargeted metabolic fingerprinting and targeted profiling are used to gain a more complete picture of the overall chemodiversity in plants (Peters et al 2018). Comparative eco-metabolomics of different plant species facing an identical challenge (Schweiger et al 2014b) or plants of one species grown under different conditions (Jansen et al 2009, Kaling et al 2015, Schweiger et al 2014a) combined with multivariate statistical tools (Kuppler et al 2016, Moritz et al 2017, Schweiger et al 2014a are extremely helpful to gain a better understanding of the specificity of plant chemodiversity and of plant responses towards their environment. Only recently, eco-metabolomics approaches have also been applied to characterise native populations in the field (Clancy et al 2018, Nagler et al 2018.…”

“…Highly sensitive chemical analytical instruments allow us to analyse even small fractions of plant organs such as individual flower parts (Abdalsamee and Müller 2015), phloem sap exudates (Jakobs and Müller 2018, Stolpe et al 2017a), extrafloral nectar (Lortzing et al 2016), or trichomes (Schilmiller et al 2009. Novel strategies for the evaluation and interpretation of metabolomics data are currently developed, for example, using exact mass difference network analyses (MDiN) for the metabolomic description of different genotypes of poplar (Moritz et al 2017) and chemotypes of T. vulgare (Clancy et al 2018). Such data sets allow disentangling of biochemical mechanisms that modify herbivore interactions (Kaling et al 2018).…”