Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory

Abstract

Secondary metabolite diversity is considered an important fitness determinant for plants' biotic and abiotic interactions in nature. This diversity can be examined in two dimensions. The first one considers metabolite diversity across plant species. A second way of looking at this diversity is by considering the tissue-specific localization of pathways underlying secondary metabolism within a plant. Although these cross-tissue metabolite variations are increasingly regarded as important readouts of tissue-level gene function and regulatory processes, they have rarely been comprehensively explored by nontargeted metabolomics. As such, important questions have remained superficially addressed. For instance, which tissues exhibit prevalent signatures of metabolic specialization? Reciprocally, which metabolites contribute most to this tissue specialization in contrast to those metabolites exhibiting housekeeping characteristics? Here, we explore tissue-level metabolic specialization in Nicotiana attenuata, an ecological model with rich secondary metabolism, by combining tissue-wide nontargeted mass spectral data acquisition, information theory analysis, and tandem MS (MS/MS) molecular networks. This analysis was conducted for two different methanolic extracts of 14 tissues and deconvoluted 895 nonredundant MS/MS spectra. Using information theory analysis, anthers were found to harbor the most specialized metabolome, and most unique metabolites of anthers and other tissues were annotated through MS/MS molecular networks. Tissuemetabolite association maps were used to predict tissue-specific gene functions. Predictions for the function of two UDP-glycosyltransferases in flavonoid metabolism were confirmed by virus-induced gene silencing. The present workflow allows biologists to amortize the vast amount of data produced by modern MS instrumentation in their quest to understand gene function.secondary metabolism | mass spectrometry | metabolomics | information theory | Nicotiana attenuata P lants are elegant synthetic chemists making use of their metabolic prowess to produce complex blends of structurally diverse chemicals. Commonly quoted estimates state that plants produce somewhere on the order of 200,000 chemical structures. Secondary metabolites, also referred to as specialized metabolites or natural products, contribute to the largest fraction of this structural diversity. Compared with their counterparts in central metabolism (primary metabolites), secondary metabolite groups have diversified to the extreme in plant lineages, likely as a result of the multiple ecological roles they fulfill (1). The high degree of plasticity of secondary metabolism pathways is consistent with the existence of large families of metabolism-related genes such as cytochrome P450s and UDP-glycosyltransferases in plant genomes that can create structural and chemical modifications almost without limits. The majority of metabolic gene functions remain unknown, however, either because the metabolites that they produce are unknown or signi...

Multi‐tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome

“…With the recent developments in next generation sequencing and popularization of RNA‐seq, it became feasible to perform large experiments integrating metabolomics and transcriptomics data. This combination is a powerful means of associating the phenotypic metabolic data with changes in gene expression which has been extensively used to investigate metabolic natural variation in a wide range of species and conditions (Alseekh et al ., ; Li et al ., , ; Schulz et al ., ). One important limitation of correlation‐based integration methodologies, such as the one used in this work is that, while easy to establish, they usually detect a great deal of false positives (Redestig and Costa, ).…”

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Flower-specific jasmonate signaling regulates constitutive floral defenses in wild tobacco

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Cry1Ac production is costly for native plants attacked by non‐Cry1Ac‐targeted herbivores in the field

“…Samples were extracted and injected into a Dionex UltiMate 3000 U‐HPLC system (ThermoFisher, http://www.thermofisher.com) combined with a Dionex Acclaim C 18 2.2 μm 120 Å 2.1 mm × 150 mm column, as well as a micrOTOF‐Q II mass spectrometer (Bruker Daltonik, http://www.bruker.com) equipped with an electrospray ionization source in positive ion mode, as previously described (Li et al ., ) with only the modification that samples were all extracted in 80% methanol–20% deionized water.…”