Profiling of Stable Isotope Enrichment in Specialized Metabolites Using Liquid Chromatography and Multiplexed Nonselective Collision-Induced Dissociation

Tandem Mass Spectrum Similarity-Based Network Analysis Using 13C-Labeled and Non-labeled Metabolome Data to Identify the Biosynthetic Pathway of the Blood Pressure-Lowering Asparagus Metabolite Asparaptine A

The biosynthetic pathway of asparaptine, a naturally occurring inhibitor of angiotensin-converting enzyme (ACE) in vitro, is largely unknown in Asparagus officinalis. To determine which metabolites are involved in the pathway, we performed tandem mass spectrum similarity-based metabolome network analysis using ¹³C-labeled and non-labeled valine-fed asparagus calluses. We revealed that S-(2-carboxy-n-propyl)-cysteine as an intermediate and two new metabolites as asparaptine analogues, lysine- and histidine-type conjugates, are involved in the pathway. Asparaptine was therefore renamed asparaptine A (arginine type), and the two analogues were named asparaptines B (lysine type) and C (histidine type). Oral feeding of asparaptine A to a hypertensive mouse breed showed that this metabolite lowers both the blood pressure and heart rate within 2 h and the effect of asparaptine A wears off after 2 days. These results suggest that asparaptine A may not only have effects as an ACE inhibitor but also have β-antagonistic effects.

Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research

Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites. Here we discuss current common strategies for UHPLC-HRMS-based metabolomics, with a focus on expanding metabolome coverage.

Effect of uncouplers of oxidative phosphorylation on metabolism of propionate in liver explants from dairy cows

Our objective was to determine the effects of uncouplers of oxidative phosphorylation on the metabolism of propionate in liver tissue of dairy cows in the postpartum period. A total of 8 primiparous dairy cows were biopsied for liver tissue explants in 2 block-design experiments. Cows were 5.9 ± 2.8 (mean ± SD) days in milk, and the 2 experiments were run concurrently. Treatments for experiment 1 were 10 μM 2,4-dinitrophenol methyl ether (DNPME) or propylene carbonate (vehicle control). Treatments for experiment 2 were 5 mM sodium salicylate (SAL) or no treatment (control). Explants were incubated in 2.5 mM [¹³C₃]propionate with treatments and terminated after 0.5, 15, and 60 min of exposure to tracer. Treatment with DNPME had no effects on measured metabolites compared with control. Treatment with SAL increased total ¹³C% enrichment of succinate (3.03 vs. 2.45%), but tended to decrease total ¹³C% enrichment of fumarate (2.86 vs. 3.10%) and decreased total ¹³C% enrichment of malate (3.96 vs. 4.58%) compared with the control. Treatment with DNPME appeared to have no effects on hepatic propionate metabolism, and treatment with SAL may impair the succinate dehydrogenase reaction.

Effects of propionate concentration on short-term metabolism in liver explants from dairy cows in the postpartum period

Our objective was to determine the temporal effects of increasing supply of propionate on propionate metabolism in liver tissue of dairy cows in the postpartum (PP) period. A total of 6 dairy cows [primiparous: n = 3, 9.00 ± 1.00 d PP (mean ± SD) and multiparous: n = 3; 4.67 ± 1.15 d PP] were biopsied for liver explants in a block-design experiment. Explants were treated with 3 concentrations of [¹³C₃]sodium propionate of 1, 2, or 4 mM. Explants were incubated in 2 mL of Medium 199 supplemented with 1% BSA, 0.6 mM oleic acid, 2 mM sodium l-lactate, 0.2 mM sodium pyruvate, and 0.5 mMl-glutamine at 38°C and sampled at 0.5, 15, and 60 min. Increasing the concentration of [¹³C₃]propionate increased total ¹³C% enrichment of propionyl coenzyme A (CoA), succinate, fumarate, malate, and citrate with time. Concentration of propionate did not affect total ¹³C% enrichment of hepatic glucose or acetyl CoA, but total ¹³C% enrichment increased with time for hepatic glucose. The ¹³C labeling from propionate was incorporated into acetyl CoA, but increased concentrations of propionate did not result in greater labeling of acetyl CoA. However, increases in ¹³C% enrichment of [M+4]citrate and [M+5]citrate concentrations of [¹³C₃]propionate indicate propionate conversion to acetyl CoA and subsequent entry of acetyl CoA into the tricarboxylic acid cycle in dairy cows in the PP period. This research presents evidence that despite an increase in hepatic acetyl CoA concentration and general consensus on the upregulation of gluconeogenesis of dairy cows during the PP period, carbon derived from propionate contributes to the pool of acetyl CoA, which increases as concentration of propionate increases, in addition to stimulating oxidation of acetyl CoA from other sources. Because of the hypophagic effects of propionate, but importance of propionate as a glucose precursor, a balance of propionate supply to dairy cows could lead to improvements in dry matter intake, and subsequently, health and production in dairy cows.

An Integrated Analytical Approach Reveals Trichome Acylsugar Metabolite Diversity in the Wild Tomato Solanum pennellii

Acylsugars constitute an abundant class of pest- and pathogen-protective Solanaceae family plant-specialized metabolites produced in secretory glandular trichomes. Solanum pennellii produces copious triacylated sucrose and glucose esters, and the core biosynthetic pathway producing these compounds was previously characterized. We performed untargeted metabolomic analysis of S. pennellii surface metabolites from accessions spanning the species range, which indicated geographic trends in the acylsugar profile and revealed two compound classes previously undescribed from this species, tetraacylglucoses and flavonoid aglycones. A combination of ultrahigh-performance liquid chromatography–high resolution mass spectrometry (UHPLC–HR-MS) and NMR spectroscopy identified variations in the number, length, and branching pattern of acyl chains, and the proportion of sugar cores in acylsugars among accessions. The new dimensions of acylsugar variation revealed by this analysis further indicate variation in the biosynthetic and degradative pathways responsible for acylsugar accumulation. These findings provide a starting point for deeper investigation of acylsugar biosynthesis, an understanding of which can be exploited through crop breeding or metabolic engineering strategies to improve the endogenous defenses of crop plants.

Higher dimensional metabolomics using stable isotope labeling for identifying the missing specialized metabolism in plants

The exact mechanics of specialized metabolism and its importance throughout plant evolution remain mysterious. Specialized metabolites and their corresponding biosynthetic genes are crucial to understand the reason for the prevalence of certain metabolism. Even though mass spectrometry-based metabolomics has enabled us to acquire data about the structural properties of unknown specialized metabolites as well as known metabolites and their corresponding isomers/analogs, extensive analytical approaches are still required. Herein, we review the most advanced analytical approaches using stable isotope labeling that can be used to identify the unknown specialized metabolites.

A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines

Natural products (NPs) and traditional medicines (TMs) are used for treatment of various diseases and also to develop new drugs. However, identification of drug leads within the immense biodiversity of living organisms is a challenging task that requires considerable time, labor, and computational resources as well as the application of modern analytical instruments. LC-MS platforms are widely used for both drug discovery and quality control of TMs and food supplements. Moreover, a large dataset generated during LC-MS analysis contains valuable information that could be extracted and handled by means of various data mining and statistical tools. Novel sophisticated LC-MS based approaches are being introduced every year. Therefore, this review is prepared for the scientists specialized in pharmacognosy and analytical chemistry of NPs as well as working in related areas, in order to navigate them in the world of diverse LC-MS based techniques and strategies currently employed for NP discovery and dereplication, quality control, pattern recognition and sample comparison, and also in targeted and untargeted metabolomic studies. The suggested classification system includes the following LC-MS based procedures: elemental composition determination, isotopic fine structure analysis, mass defect filtering, de novo identification, clustering of the compounds in Molecular Networking (MN), diagnostic fragment ion (or neutral loss) filtering, manual dereplication using MS/MS data, database-assisted peak annotation, annotation of spectral trees, MS fingerprinting, feature extraction, bucketing of LC-MS data, peak profiling, predicted metabolite screening, targeted quantification of biomarkers, quantitative analysis of multi-component system, construction of chemical fingerprints, multi-targeted and untargeted metabolite profiling.

Novel applications of mass spectrometry-based metabolomics in herbal medicines and its active ingredients: Current evidence

Current evidence shows that herbal medicines could be beneficial for the treatment of various diseases. However, the complexities present in chemical compositions of herbal medicines are currently an obstacle for the progression of herbal medicines, which involve unclear bioactive compounds, mechanisms of action, undetermined targets for therapy, non-specific features for drug metabolism, etc. To overcome those issues, metabolomics can be a great to improve and understand herbal medicines from the small-molecule metabolism level. Metabolomics could solve scientific difficulties with herbal medicines from a metabolic perspective, and promote drug discovery and development. In recent years, mass spectrometry-based metabolomics was widely applied for the analysis of herbal constituents in vivo and in vitro. In this review, we highlight the value of mass spectrometry-based metabolomics and metabolism to address the complexity of herbal medicines in systems pharmacology, and to enhance their biomedical value in biomedicine, to shed light on the aid that mass spectrometry-based metabolomics can offer to the investigation of its active ingredients, especially, to link phytochemical analysis with the assessment of pharmacological effect and therapeutic potential. © 2019 Wiley Periodicals, Inc. Mass Spec Rev.

Metabolomics 20 years on: what have we learned and what hurdles remain?

The term metabolome was coined in 1998, by analogy to genome, transcriptome and proteome. The first research papers using the terms metabolomics, metabonomics, metabolic profiling or metabolite profiling were published shortly thereafter. In this short review we reflect on the major achievements brought about by the use of these approaches, and document the knowledge and technology gaps that are currently constraining its further development. Finally, we detail why we think that the time is ripe to refocus our efforts on the understanding of metabolic function.

High Enrichment [13 C]-Labeling of Plants Grown Hydroponically from Seed to Seed in a Controlled 13 C-Carbon Dioxide Atmosphere Enclosure

In vivo isotopic labeling empowers proteomic and metabolomic analyses to resolve relationships between the molecular composition, environment, and phenotype of an organism. Carbon-13 is particularly useful for plant labeling as it can be introduced via 13 CO2 gas and readily assimilated into plant metabolic systems through natural carbon fixation. While short-term labeling experiments can be performed within a simple sealed enclosure, long-term growth in an isolated environment raises many challenges beyond nutrient availability and buildup of metabolic waste. Viable growth conditions must be maintained by means that do not compromise the integrity of the carbon-13 enrichment. To address these issues, an automated growth chamber equipped with countermeasures to neutralize stresses and ensure high isotopic enrichment throughout the life cycle of the plant has been developed. The following describes this growth chamber and its use in an example 130-day growth of ten soybean plants to full maturity, achieving 100% carbon-13 enrichment of new seed tissue. © 2018 by John Wiley & Sons, Inc.

Biosynthesis of floral scent 2-phenylethanol in rose flowers

Plants emit chemically diverse volatile compounds for attracting pollinators or putting up a chemical defense against herbivores. 2-Phenylethanol (2PE) is one of the abundantly emitted scent compounds in rose flowers. Feeding experiments with l-[2H8]phenylalanine into rose flowers and subsequent analysis using gas chromatography–mass spectrometry analysis revealed the hypothetical biosynthetic intermediates to [2H8]-2PE, and the biochemical and genetic analyses elucidated the principal pathway to [2H8]-2PE. We recently found season-specific 2PE pathway producing [2H7]-2PE from l-[2H8]phenylalanine. This is a unique example where the dominant pathway to a specific compound changes with the seasons. This review focuses on the biosynthesis of floral volatiles and their regulation to adapt to the changes in the environment.

Recent advances in stable isotope-enabled mass spectrometry-based plant metabolomics

Methods employing isotope labeled compounds have been an important part of the bioanalytical canon for many decades. The past fifteen years have seen the development of many new approaches using stable (non-radioactive) isotopes as labels for high-throughput bioanalytical, 'omics-scale' measurements of metabolites (metabolomics) and proteins (proteomics). This review examines stable isotopic labeling approaches that have been developed for labeling whole intact plants, plant tissues, or crude extracts of plant materials with stable isotopes (mainly using ²H, ¹³C, ¹⁵N, ¹⁸O or ³⁴S). The application of metabolome-scale labeling for improving metabolite annotation, metabolic pathway elucidation, and relative quantification in mass spectrometry-based metabolomics of plants is also reviewed.

Metabolomics-Inspired Insight into Developmental, Environmental and Genetic Aspects of Tomato Fruit Chemical Composition and Quality

Tomato was one of the first plant species to be evaluated using metabolomics and remains one of the best characterized, with tomato fruit being both an important source of nutrition in the human diet and a valuable model system for the development of fleshy fruits. Additionally, given the broad habitat range of members of the tomato clade and the extensive use of exotic germplasm in tomato genetic research, it represents an excellent genetic model system for understanding both metabolism per se and the importance of various metabolites in conferring stress tolerance. This review summarizes technical approaches used to characterize the tomato metabolome to date and details insights into metabolic pathway structure and regulation that have been obtained via analysis of tissue samples taken under different developmental or environmental circumstance as well as following genetic perturbation. Particular attention is paid to compounds of importance for nutrition or the shelf-life of tomatoes. We propose furthermore how metabolomics information can be coupled to the burgeoning wealth of genome sequence data from the tomato clade to enhance further our understanding of (i) the shifts in metabolic regulation occurring during development and (ii) specialization of metabolism within the tomato clade as a consequence of either adaptive evolution or domestication.