Differential Off-line LC-NMR (DOLC-NMR) Metabolomics To Monitor Tyrosine-Induced Metabolome Alterations in Saccharomyces cerevisiae

Applications of chromatographic methods in metabolomics: A review

Chromatography is a robust and reliable separation method that can use various stationary phases to separate complex mixtures commonly seen in metabolomics. This review examines the types of chromatography and stationary phases that have been used in targeted or untargeted metabolomics with methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. General considerations for sample pretreatment and separations in metabolomics are considered, along with the various supports and separation formats for chromatography that have been used in such work. The types of liquid chromatography (LC) that have been most extensively used in metabolomics will be examined, such as reversed-phase liquid chromatography and hydrophilic liquid interaction chromatography. In addition, other forms of LC that have been used in more limited applications for metabolomics (e.g., ion-exchange, size-exclusion, and affinity methods) will be discussed to illustrate how these techniques may be utilized for new and future research in this field. Multidimensional LC methods are also discussed, as well as the use of gas chromatography and supercritical fluid chromatography in metabolomics. In addition, the roles of chromatography in NMR- vs. MS-based metabolomics are considered. Applications are given within the field of metabolomics for each type of chromatography, along with potential advantages or limitations of these separation methods.

Biosynthetic Profile in the Co-culture of Aspergillus sydowii and Bacillus subtilis to Produce Novel Benzoic Derivatives

Microbial co-culture simulates the natural ecosystem through the combination of artificial microbes. This approach has been widely applied in the study of activating silent genes to reveal novel secondary metabolites. However, there are still challenges in determining the biosynthetic pathways. In this study, the effects of microbial co-culture on the morphology of the microbes were verified by the morphological observation. Subsequently, through the strategy combining substrate feeding, stable isotope labeling, and gene expression analysis, the biosynthetic pathways of five benzoic acid derivatives N1-N4 and N7 were demonstrated: the secondary metabolite 10-deoxygerfelin of A. sydowii acted as an inducer to induce B. subtilis to produce benzoic acid, which was further converted into 3-OH-benzoic acid by A. sydowii. Subsequently, A. sydowii used 3-OH-benzoic acid as the substrate to synthesize the new compound N2, and then N1, N3, N4, and N7 were biosynthesized upon the upregulation of hydrolase, hydroxylase, and acyltransferase during co-culture. The plate zone analysis suggested that the biosynthesis of the newly induced compounds N1-N4 was mainly attributed to A. sydowii, and both A. sydowii and B. subtilis were indispensable for the biosynthesis of N7. This study provides an important basis for a better understanding of the interactions among microorganisms, providing new ideas for studying the biosynthetic pathways of the newly induced secondary metabolites in co-culture.

Discovery and Identification of Tastants and Taste-Modulating N-Acyl Amino Acid Derivatives in Traditional Korean Fermented Dish Kimchi Using a Sensomics Approach

Sensory-guided fractionation by means of ultrafiltration and gel permeation chromatography followed by high-performance liquid chromatography, synthesis, liquid chromatography-tandem mass spectrometry (LC-MS/MS) quantitation, and taste re-engineering experiments revealed taste-active and taste-enhancing compounds contributing to the umami, mouthful and complex taste profile of the fermented Korean dish, kimchi. Besides basic taste-active compounds, in particular, various N-acylated amino acids deriving from succinic acid and lactic acid imparted taste-modulating properties in food matrices. Taste threshold concentrations were determined to evaluate intrinsic and modulating effects. Quantitation of N-acylated amino acids in kimchi following synthesis revealed the presence of numerous derivatives showing taste-active properties. Sensory evaluation including recombination and partial addition experiments highlighted that both the N-lactoyl- and the N-succinoyl amino acid derivatives contribute to increasing the fullness, volume, and complexity of food matrices, whereas the latter directly contributes to the overall taste of kimchi in natural concentrations.

Treated Unconventional Waters Combined with Different Irrigation Strategies Affect 1H NMR Metabolic Profile of a Monovarietal Extra Virgin Olive Oil

The agricultural sector is facing a decrease in water supply and water quality at a global level and this is a problem that strictly affects all the Mediterranean olive growing areas. The aim of this work was to evaluate, for the first time, by NMR Spectroscopy and multivariate data analysis the metabolic profiling of the oils produced under different irrigation schemes. Arbosana olive oils were obtained from the use of saline reclaimed water (RW) and treated municipal wastewater (DW), combined with: full irrigation (FI) and regulated deficit irrigation (RDI). The results show a higher relative content of saturated fatty acids in EVOOs obtained from RDI strategy, regardless of the water source. Moreover, an increase in unsaturated fatty acids, a ω6/ω3 ratio content was observed in EVOOs obtained from RW when compared with DW water. Furthermore, the RW–RDI showed an increase in secoiridoid derivatives and hydroperoxides with respect to DW–RDI. A sustainable irrigation management, by combining a deficit irrigation strategy and saline reclaimed water source, could be crucial in order to overcome the problem of water scarcity and to guarantee the olive oil nutraceutical properties. The 1H NMR-based metabolomic approach proved a powerful and versatile tool for this specific investigation.

The Biosynthesis and Metabolism of the N-Acylated Aromatic Amino Acids: N-Acylphenylalanine, N-Acyltyrosine, N-Acyltryptophan, and N-Acylhistidine

The fatty acid amides are a family of lipids composed of two chemical moieties, a fatty acid and a biogenic amine linked together in an amide bond. This lipid family is structurally related to the endocannabinoid anandamide (N-arachidonoylethanolamine) and, thus, is frequently referred to as a family of endocannabinoid-related lipids. The fatty acid amide family is divided into different classes based on the conjugate amine; anandamide being a member of the N-acylethanolamine class (NAE). Another class within the fatty acid amide family is the N-acyl amino acids (NA-AAs). The focus of this review is a sub-class of the NA-AAs, the N-acyl aromatic amino acids (NA-ArAAs). The NA-ArAAs are not broadly recognized, even by those interested in the endocannabinoids and endocannabinoid-related lipids. Herein, the NA-ArAAs that have been identified from a biological source will be highlighted and pathways for their biosynthesis, degradation, enzymatic modification, and transport will be presented. Also, information about the cellular functions of the NA-ArAAs will be placed in context with the data regarding the identification and metabolism of these N-acylated amino acids. A review of the current state-of-knowledge about the NA-ArAAs is to stimulate future research about this underappreciated sub-class of the fatty acid amide family.

Identification and Quantitation of Taste-Active Compounds in Dried Scallops by Combined Application of the Sensomics and a Quantitative NMR Approach

Application of the sensomics concept on dried scallops, a Japanese specialty produced from the adductor muscle of scallops, revealed after activity-guided fractionation with subsequent (comparative) taste dilution analyses besides nucleotides, amino acids, organic acids, and inorganic ions, the presence of taste-modulating quaternary ammonium compounds and opines in highly taste-active fractions. In order to recreate the taste of dried scallops, two independent quantitation approaches were applied and compared. The first approach used multiple targeted UHPLC-MS/MS and high-performance ion chromatography methods. Besides already established quantitation methods for basic taste compounds, a new HILIC-UHPLC-MS/MS_MRM method for the quantitation of chromatographically challenging opines, using synthesized stable isotope-labeled standards, was developed. Furthermore, a qHNMR approach was applied, enabling a direct identification and quantitation of organic taste compounds in a food extract without prior fractionation using a reference ¹H NMR database. Both methods yielded similar quantitative results of taste-active compounds in dried scallop extracts and subsequent taste recombination experiments based on these data were able to recreate the taste of dried scallops.

Quantitative Proton NMR Spectroscopy for Basic Taste Recombinant Reconstitution Using the Taste Recombinant Database

The quantitative determination of putative taste active metabolites, the ranking of these compounds in their sensory impact based on dose-overthreshold (DoT) factors, followed by confirmation of their relevance by reconstitution and omission experiments enables the decoding of the non-volatile sensometabolome of certain foods. The identification and quantitation of target taste compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS), high-performance liquid chromatography-ultraviolet/visible (HPLC-UV/Vis) spectroscopy, or high-performance ion chromatography (HPIC) is often laborious and time-consuming. In this work, we present a novel quantitative ¹H NMR approach for reconstituting basic taste recombinants of different foods, including apple juice, balsamic vinegar, golden chanterelles, process flavor, and shrimp. Compound identification using the taste recombinant database, followed by absolute quantitation via quantitative ¹H NMR (qHNMR), enables a fast and direct reconstitution of basic taste recombinants. The taste profile analysis of basic taste recombinants was generated via qHNMR in less than 15 min and compared with literature data acquired by LC-MS/MS and/or HPLC-UV/Vis and revealed identical results for all taste qualities. A determination of limit of detection (LoD) values for S/N = 50 of various proton signals with different integrals and multiplicities demonstrated that taste recognition thresholds of all basic tastants are far above those of LoD concentrations under the chosen conditions. Therefore, our experimental setup is able to detect basic taste-active compounds well below their taste recognition thresholds.

Untargeted Metabolite Profiling of Antimicrobial Compounds in the Brown Film of Lentinula edodes Mycelium via LC-MS/MS Analysis

The brown film (BF) of Lentinula edodes mycelium has been reported to exert biological activities during mushroom cultivation; however, to date, there is limited information on its chemical composition. In this study, untargeted metabolomics analysis was performed via liquid chromatography-mass spectrometry (LC-MS), and the results were used to screen the antimicrobial compounds. A total of 236 differential metabolites were found among the BF stages compared with the white hyphal stage. Among them, five important antimicrobial metabolites related to antimicrobial activities, namely, 6-deoxyerythronolide B, tanikolide, hydroxyanthraquinone, benzylideneacetone, and 9-OxooTrE, were present at high levels in the BF samples. The score plots of the principal component analysis indicated that the samples from four time points could be classified into two groups. This study provided a comprehensive profile of the antimicrobial compounds produced during BF formation and partly clarified the antibacterial and antifungal mechanism of the BF of L. edodes mycelium.

NMR-based Structural Classification, Identification, and Quantification of Triterpenoids from Edible Mushroom Ganoderma resinaceum

Ganoderma mushrooms have been widely used as functional food in China, Japan, and Korea. Ganoderma triterpenoids are deemed to be the main functional constituents. The structures of Ganoderma triterpenoids are complex but quite similar, which makes their analyses markedly limited. In this study, we developed a general 2D NMR method to differentiate Ganoderma triterpenoids, which classifies them into six types (A-F). Then, by the NMR-based isolation of A-F type triterpenoids from the fruiting bodies of G. resinaceum, four new compounds (1-4) and eight known compounds (5-12) were obtained. Moreover, combined with spiking experiments in 1D and 2D NMR spectra, compounds 5, 7, and 8, which belong to triterpenoids of A and B types, were identified. At the end, to achieve a more extensive application for this NMR method, a qNMR method for the absolute quantification of 5, 7, and 8 in the gross triterpenoids from G. resinaceum was set up. The results showed that this NMR method is reliable for the NMR-guided isolation and quantification of triterpenoids in G. resinaceum.

Novel Taste-Enhancing 4-Amino-2-methyl-5-heteroalkypyrimidines Formed from Thiamine by Maillard-Type Reactions

Increasing the thiamine concentration in a respective process flavor yields a product with a significant higher kokumi activity. S-plot analysis of the mass spectrometric data revealed beside thiamine itself, 4-methyl-5-thiazoleethanol, (S)-((4-amino-2-methylpyrimidin-5-yl)methyl)-l-cysteine, N-((4-amino-2-methylpyrimidin-5-yl)methyl)formamide, 3-(((4-amino-2-methylpyrimidin-5-yl)methyl)thio)-5-hydroxypentan-2-one, and 2-methyl-5-(((2-methylfuran-3-yl)thio)methyl)pyrimidin-4-amine as marker molecules for a process flavor with higher thiamine concentration. Sensory-based targeted isolation revealed that (S)-((4-amino-2-methylpyrimidin-5-yl)methyl)-l-cysteine, 3-(((4-amino-2-methylpyrimidin-5-yl)methyl)thio)-5-hydroxypentan-2-one, and 2-methyl-5-(((2-methylfuran-3-yl)thio)methyl)pyrimidin-4-amine showed an influence on the kokumi taste activity with taste threshold concentrations between 35 and 120 μmol/L. An adapted mass spectrometric-based carbon module labeling experiment as well as quantitative studies clearly demonstrated thiamine as the only precursor and an intermolecular formation pathway for the compounds (S)-(((4-amino-2-methylpyrimidin-5-yl)methyl)thio)-5-hydroxypentan-2-one and 2-methyl-5-(((2-methylfuran-3-yl)thio)methyl)pyrimidin-4-amine. On the basis of the knowledge that several thiamine derivatives showed taste-modulating activity, selected thiamine-based binary model reactions and synthesis were carried out. This resulted in the isolation of further thiamine-derived taste modulators like (S)-((4-amino-2-methylpyrimidin-5-yl)methyl)-l-cysteinylglycine, (S)-3-((((4-amino-2-methylpyrimidin-5-yl)methyl)thio)methyl)piperazine-2,5-dione, 3-(((4-amino-2-methylpyrimidin-5-yl)methyl)thio)pentan-2-one, 5-(((furan-2-ylmethyl)thio)methyl)-2-methylpyrimidin-4-amine, and (4-amino-2-methylpyrimidin-5-yl)methanethiol, 2-methyl-5-((methylthio)methyl)pyrimidin-4-amine with taste thresholds ranging from 35 to 880 μmol/L.

Tyrosine Induced Metabolome Alterations of Penicillium roqueforti and Quantitation of Secondary Key Metabolites in Blue-Mold Cheese

To map qualitative and quantitative metabolome alterations when Penicillium roqueforti is grown in an environment where l-tyrosine levels are perturbed, the recently established differential off-line LC-NMR (DOLC-NMR) approach was successfully applied in connection with an absolute metabolite quantitation using a quantitative ¹H NMR protocol following the ERETIC 2 (Electronic REference To access In vivo Concentrations) methodology. Among the 23 influenced metabolites, amino acid degradation products like 2-(4-hydroxyphenyl)acetic acid and 2-(3,4-dihydroxyphenyl)acetic acid underwent a tremendous upregulation in the amino acid perturbed approach. Moreover, the output of secondary metabolites like andrastin A, eremofortin B, and the tetrapeptide d-Phe-l-Val-d-Val-l-Tyr was affected in the case of the presence or absence of the added aromatic amino acid. Furthermore, the isolated secondary metabolites of P. roqueforti have been quantified for the first time in five divergent Penicillium isolates by means of a validated LC-ECHO-MS/MS method. This technique is used to compensate the effect of co-extracted matrix compounds during the analysis and to utilize quasi-internal standards to quantify all metabolites of interest accurately. This screening outlined the great variety between the different fungi of the same species. The metabolite spectra of wild-type fungi included more toxic intermediates compared to a selected fungi used as a starter culture for blue-mold cheese production. In addition, these secondary metabolites were quantified in commercially available white- and blue-mold cheese samples. The main differences between the analyte profiles of white and blue cheeses were linked to the impact of the used starter culture. Specific metabolites detected from P. roqueforti like andrastin A and B or roquefortine C could not be detected in white cheese. Among the blue cheese samples, different metabolite pattern could be observed regarding various P. roqueforti starter cultures.

Functional Metabolome Analysis of Penicillium roqueforti by Means of Differential Off-Line LC-NMR

UPLC-TOF/MS profiling, followed by the recently reported differential off-line LC-NMR (DOLC-NMR) and quantitative ¹H NMR spectroscopy (qHNMR), led to the differential qualitative analysis and accurate quantitation of l-tryptophan-induced metabolome alterations of Penicillium roqueforti, which is typically used in making blue-mold cheese. Among the 24 metabolites identified, two tetrapeptides, namely, d-Phe-l-Val-d-Val-l-Tyr and d-Phe-l-Val-d-Val-l-Phe, as well as cis-bis(methylthio)silvatin, are reported for the first time as metabolites of P. roqueforti. Antimicrobial activity tests showed strong effects of the catabolic l-tryptophan metabolites 3-hydroxyanthranilic acid, anthranilic acid, and 3-indolacetic acid against Saccharomyces cerevisiae, with IC₅₀ values between 15.6 and 24.0 μg/mL, while roquefortine C and cis-bis(methylthio)silvatin inhibited the growth of Gram-negative Escherichia coli and Gram-positive Bacillus subtilis with IC₅₀ values between 30.0 and 62.5 μg/mL.

Functional Metabolomics—A Useful Tool to Characterize Stress-Induced Metabolome Alterations Opening New Avenues towards Tailoring Food Crop Quality

The breeding of stress-tolerant cultivated plants that would allow for a reduction in harvest losses and undesirable decrease in quality attributes requires a new quality of knowledge on molecular markers associated with relevant agronomic traits, on quantitative metabolic responses of plants to stress challenges, and on the mechanisms controlling the biosynthesis of these molecules. By combining metabolomics with genomics, transcriptomics and proteomics datasets a more comprehensive knowledge of the composition of crop plants used for food or animal feed is possible. In order to optimize crop trait developments, to enhance crop yields and quality, as well as to guarantee nutritional and health factors that provide the possibility to create functional food or feedstuffs, knowledge about the plants’ metabolome is crucial. Next to classical metabolomics studies, this review focuses on several metabolomics-based working techniques, such as sensomics, lipidomics, hormonomics and phytometabolomics, which were used to characterize metabolome alterations during abiotic and biotic stress in order to find resistant food crops with a preferred quality or at least to produce functional food crops.

Metabolomics Investigation of an Association of Induced Features and Corresponding Fungus during the Co-culture of Trametes versicolor and Ganoderma applanatum

The co-culture of Trametes versicolor and Ganoderma applanatum is a model of intense basidiomycete interaction, which induces many newly synthesized or highly produced features. Currently, one of the major challenges is an identification of the origin of induced features during the co-culture. Herein, we report a ¹³C-dynamic labeling analysis used to determine an association of induced features and corresponding fungus even if the identities of metabolites were not available or almost nothing was known of biochemical aspects. After the co-culture of T. versicolor and G. applanatum for 10 days, the mycelium pellets of T. versicolor and G. applanatum were sterilely harvested and then mono-cultured in the liquid medium containing half fresh medium with ¹³C-labeled glucose as carbon source and half co-cultured supernatants collected on day 10. ¹³C-labeled metabolome analyzed by LC-MS revealed that 31 induced features including 3-phenyllactic acid and orsellinic acid were isotopically labeled in the mono-culture after the co-culture stimulation. Twenty features were derived from T. versicolor, 6 from G. applanatum, and 5 features were synthesized by both T. versicolor and G. applanatum. ¹³C-labeling further suggested that 12 features such as previously identified novel xyloside [N-(4-methoxyphenyl)formamide 2-O-beta-D-xyloside] were likely induced through the direct physical interaction of mycelia. Use of molecular network analysis combined with ¹³C-labeling provided an insight into the link between the generation of structural analogs and producing fungus. Compound 1 with m/z 309.0757, increased 15.4-fold in the co-culture and observed ¹³C incorporation in the mono-culture of both T. versicolor and G. applanatum, was purified and identified as a phenyl polyketide, 2,5,6-trihydroxy-4, 6-diphenylcyclohex-4-ene-1,3-dione. The biological activity study indicated that this compound has a potential to inhibit cell viability of leukemic cell line U937. The current work sets an important basis for further investigations including novel metabolites discovery and biosynthetic capacity improvement.