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Cells
Special Issues
Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods
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Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Plant, Algae and Fungi Cell Biology".

Deadline for manuscript submissions: closed (25 September 2022) | Viewed by 27196

Special Issue Editors

Dr. Franz Hadacek

E-Mail Website
Guest Editor
Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-Universität-Göttingen, 37073 Göttingen, Germany
Interests: plant metabolites; GC–MS; LC–MS; MS-based identification
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Petr Karlovsky

E-Mail Website
Guest Editor
Molecular Phytopathology and Mycotoxin Research, Georg-August-Universität Göttingen, Göttingen, Germany
Interests: secondary metabolites; mycotoxins, fungal pathogens in grain crops; chemical ecology of fungal secondary metabolites; rhizosphere biology

Special Issue Information

Dear Colleagues,

Nearly all organisms except birds and mammals produce secondary, or as they are recently called, specialized metabolites. They comprise terpenoids (non-aromatic compounds formed from C5 isoprene units), aromatic and non-aromatic polyketides (formed from acetic acid units), phenols (usually formed from the aromatic amino acids phenylalanine and tyrosine that arise from the shikimic acid pathway), and alkaloids that combine amino acids with precursors from the previously mentioned pathways. Last but not least, non-ribosomal peptides are also classified as secondary metabolites. Plants accumulate notably large amounts in specialized tissues and, thus, many of them have gained a reputation as drug sources in traditional medicine. Furthermore, many prokaryotic and eukaryotic microbes are also efficient producers of secondary metabolites, some of which have gained importance as antibiotics in the treatment of bacterial human diseases. The general view is that secondary metabolites help the producing organism to control its predators and competitors due to their antifeedant, antimicrobial, and generally toxic properties. However, some studies point out that, besides biotic stress, secondary metabolites can help also to survive abiotic stress or to assist in the uptake of the required amounts of trace minerals, such as iron or copper. The antioxidant properties of some secondary metabolites have directed attention to them as beneficial food additives. By contrast, fungal metabolites are regarded as highly toxic mycotoxins when fungi produce them on foodstuffs or crops. Pro-oxidative activity can serve as signal in low dosages, whereas higher dosages are generally considered as toxic. Small-structured secondary metabolites are volatile. They have evolved as important signals that, for examples, can attract pollinators to flowers, but also parasites to their prey. In attempts to explore their often-controversial biological function and their effects as drugs, beneficial nutritional compounds, or toxic food constituents, efficient qualitative and quantitative analytical methods are required for analysis. Linking gas- and liquid chromatography to mass spectrometry has developed into the method of choice for state-of-the-art profiling for secondary metabolites.

The aim of this Special Issue is to provide an overview on the analysis of secondary metabolites in the age of metabolomics with mass spectrometry-based methods. Ideally, it should not only contain success stories of case studies but also point out inherent pitfalls and constraints. Comments on useful statistical methods, available databases for structure elucidation, and progress in methodology are welcome. We hope that the insights presented from expert laboratories will be a valuable guide for the community of researchers investigating secondary metabolites besides of primary metabolites (sugars, organic- and amino acids amongst others) that usually represent the focus in metabolomic studies.

Dr. Franz Hadacek
Prof. Dr. Petr Karlovsky
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • secondary metabolites
  • specialized metabolites
  • all organisms
  • mass spectrometry
  • gas chromatography
  • liquid chromatography

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Published Papers (8 papers)

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Research

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14 pages, 3035 KiB  
Article
Volatile Compounds in Actinomycete Communities: A New Tool for Biosynthetic Gene Cluster Activation, Cooperative Growth Promotion, and Drug Discovery
by Lorena Cuervo, Carmen Méndez, José A. Salas, Carlos Olano and Mónica G. Malmierca
Cells 2022, 11(21), 3510; https://doi.org/10.3390/cells11213510 - 5 Nov 2022
Cited by 10 | Viewed by 3179
Abstract
The increasing appearance of multiresistant pathogens, as well as emerging diseases, has highlighted the need for new strategies to discover natural compounds that can be used as therapeutic alternatives, especially in the genus Streptomyces, which is one of the largest producers of [...] Read more.
The increasing appearance of multiresistant pathogens, as well as emerging diseases, has highlighted the need for new strategies to discover natural compounds that can be used as therapeutic alternatives, especially in the genus Streptomyces, which is one of the largest producers of bioactive metabolites. In recent years, the study of volatile compounds (VOCs) has raised interest because of the variety of their biological properties in addition to their involvement in cell communication. In this work, we analyze the implications of VOCs as mediating molecules capable of inducing the activation of biosynthetic pathways of bioactive compounds in surrounding Actinomycetes. For this purpose, several strains of Streptomyces were co-cultured in chamber devices that allowed VOC exchange while avoiding physical contact. In several of those strains, secondary metabolism was activated by VOCs emitted by companion strains, resulting in increased antibiotic production and synthesis of new VOCs. This study shows a novel strategy to exploit the metabolic potential of Actinomycetes as well as emphasizes the importance of studying the interactions between different microorganisms sharing the same ecological niche. Full article
(This article belongs to the Special Issue Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods)
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15 pages, 364 KiB  
Article
LC-DAD–ESI-MS/MS and NMR Analysis of Conifer Wood Specialized Metabolites
by Andrzej Patyra, Marta Katarzyna Dudek and Anna Karolina Kiss
Cells 2022, 11(20), 3332; https://doi.org/10.3390/cells11203332 - 21 Oct 2022
Cited by 11 | Viewed by 3692
Abstract
Many species from the Pinaceae family have been recognized as a rich source of lignans, flavonoids, and other polyphenolics. The great common occurrence of conifers in Europe, as well as their use in the wood industry, makes both plant material and industrial waste [...] Read more.
Many species from the Pinaceae family have been recognized as a rich source of lignans, flavonoids, and other polyphenolics. The great common occurrence of conifers in Europe, as well as their use in the wood industry, makes both plant material and industrial waste material easily accessible and inexpensive. This is a promising prognosis for both discovery of new active compounds as well as for finding new applications for wood and its industry waste products. This study aimed to analyze and phytochemically profile 13 wood extracts of the Pinaceae family species, endemic or introduced in Polish flora, using the LC-DAD–ESI-MS/MS method and compare their respective metabolite profiles. Branch wood methanolic extracts were phytochemically profiled. Lignans, stilbenes, flavonoids, diterpenes, procyanidins, and other compounds were detected, with a considerable variety of chemical content among distinct species. Norway spruce (Picea abies (L.) H.Karst.) branch wood was the most abundant source of stilbenes, European larch (Larix decidua Mill.) mostly contained flavonoids, while silver fir (Abies alba Mill.) was rich in lignans. Furthermore, 10 lignans were isolated from the studied material. Our findings confirm that wood industry waste materials, such as conifer branches, can be a potent source of different phytochemicals, with the plant matrix being relatively simple, facilitating future isolation of target compounds. Full article
(This article belongs to the Special Issue Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods)
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27 pages, 6194 KiB  
Article
Metabolomic Aspects of Conservative and Resistance-Related Elements of Response to Fusarium culmorum in the Grass Family
by Anna Piasecka, Aneta Sawikowska, Natalia Witaszak, Agnieszka Waśkiewicz, Marta Kańczurzewska, Joanna Kaczmarek and Justyna Lalak-Kańczugowska
Cells 2022, 11(20), 3213; https://doi.org/10.3390/cells11203213 - 13 Oct 2022
Cited by 5 | Viewed by 3183
Abstract
Background: Fusarium head blight (FHB) is a serious fungal disease affecting crop plants, causing substantial yield reductions and the production of mycotoxins in the infected grains. Achieving progress in the breeding of crops with increased resistance and maintaining a high yield is not [...] Read more.
Background: Fusarium head blight (FHB) is a serious fungal disease affecting crop plants, causing substantial yield reductions and the production of mycotoxins in the infected grains. Achieving progress in the breeding of crops with increased resistance and maintaining a high yield is not possible without a thorough examination of the molecular basis of plant immunity responses. Methods: LC-MS-based metabolomics approaches powered by three-way ANOVA and the selec-tion of differentially accumulated metabolites (DAMs) were used for studying plant immunity. A correlation network and functional enrichment analysis were conducted on grains of barley and wheat genotypes that were resistant or susceptible to FHB, as well as on the model grass Brachypodium distachyon (Bd), as this is still poorly understood at the metabolomic level. Results: We selected common and genotype-specific DAMs in response to F. culmorum inoculation. The immunological reaction at the metabolomic level was strongly diversified between resistant and susceptible genotypes. DAMs that were common to all tested species from the porphyrin, flavonoid, and phenylpropanoid metabolic pathways were highly correlated, reflecting con-servativeness in the FHB response in the Poaceae family. Resistance-related DAMs belonged to different structural classes, including tryptophan-derived metabolites, pyrimidines, the amino acids proline and serine, as well as phenylpropanoids and flavonoids. The physiological re-sponse to F. culmorum of Bd was close to that of barley and wheat genotypes; however, metabo-lomic changes were strongly diversified. Conclusions: Combined targeted and untargeted metabolomics provides comprehensive knowledge about significant elements of plant immuni-ty that have the potential to be molecular biomarkers of enhanced resistance to FHB in the grass family. Thorough examination of the Bd metabolome in juxtaposition with diversified geno-types of barley and wheat facilitated its use as a model grass for plant–microbe interaction. Full article
(This article belongs to the Special Issue Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods)
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21 pages, 5713 KiB  
Article
Secondary or Specialized Metabolites, or Natural Products: A Case Study of Untargeted LC–QTOF Auto-MS/MS Analysis
by Franz Hadacek
Cells 2022, 11(6), 1025; https://doi.org/10.3390/cells11061025 - 17 Mar 2022
Cited by 1 | Viewed by 2757
Abstract
The large structural diversity of specialized metabolites represents a substantial challenge in untargeted metabolomics. Modern LC–QTOF instruments can provide three- to four-digit numbers of auto-MS/MS spectra from sample sets. This case study utilizes twelve structurally closely related flavonol glycosides, characteristic specialized metabolites of [...] Read more.
The large structural diversity of specialized metabolites represents a substantial challenge in untargeted metabolomics. Modern LC–QTOF instruments can provide three- to four-digit numbers of auto-MS/MS spectra from sample sets. This case study utilizes twelve structurally closely related flavonol glycosides, characteristic specialized metabolites of plant tissues, some of them isomeric and isobaric, to illustrate the possibilities and limitations of their identification. This process requires specific software tools that perform peak picking and feature alignment after spectral deconvolution and facilitate molecular structure base searching with subsequent in silico fragmentation to obtain initial ideas about possible structures. The final assignment of a putative identification, so long as spectral databases are not complete enough, requires structure searches in a chemical reference database, such as SciFindern, in attempts to obtain additional information about specific product ions of a metabolite candidate or check its feasibility. The highlighted problems in this process not only apply to specialized metabolites in plants but to those occurring in other organisms as well. This case study is aimed at providing guidelines for all researchers who obtain data from such analyses but are interested in deeper information than just Venn diagrams of the feature distribution in their sample groups. Full article
(This article belongs to the Special Issue Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods)
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16 pages, 2372 KiB  
Article
(±)-Catechin—A Mass-Spectrometry-Based Exploration Coordination Complex Formation with FeII and FeIII
by Lenka Kubicova, Gert Bachmann, Wolfram Weckwerth and Vladimir Chobot
Cells 2022, 11(6), 958; https://doi.org/10.3390/cells11060958 - 11 Mar 2022
Cited by 2 | Viewed by 3212
Abstract
Catechin is an extensively investigated plant flavan-3-ol with a beneficial impact on human health that is often associated with antioxidant activities and iron coordination complex formation. The aim of this study was to explore these properties with FeII and FeIII using [...] Read more.
Catechin is an extensively investigated plant flavan-3-ol with a beneficial impact on human health that is often associated with antioxidant activities and iron coordination complex formation. The aim of this study was to explore these properties with FeII and FeIII using a combination of nanoelectrospray-mass spectrometry, differential pulse voltammetry, site-specific deoxyribose degradation assay, FeII autoxidation assay, and brine shrimp mortality assay. Catechin primarily favored coordination complex formation with Fe ions of the stoichiometry catechin:Fe in the ratio of 1:1 or 2:1. In the detected Fe–catechin coordination complexes, FeII prevailed. Differential pulse voltammetry, the site-specific deoxyribose degradation, and FeII autoxidation assays proved that coordination complex formation affected catechin’s antioxidant effects. In situ formed Fe–catechin coordination complexes showed no toxic activities in the brine shrimp mortality assay. In summary, catechin has properties for the possible treatment of pathological processes associated with ageing and degeneration, such as Alzheimer’s and Parkinson’s diseases. Full article
(This article belongs to the Special Issue Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods)
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16 pages, 40845 KiB  
Article
Computational Workflow to Study the Diversity of Secondary Metabolites in Fourteen Different Isatis Species
by Doudou Huang, Chen Zhang, Junfeng Chen, Ying Xiao, Mingming Li, Lianna Sun, Shi Qiu and Wansheng Chen
Cells 2022, 11(5), 907; https://doi.org/10.3390/cells11050907 - 6 Mar 2022
Cited by 1 | Viewed by 2495
Abstract
The screening of real features among thousands of ions remains a great challenge in the study of metabolomics. In this research, a workflow designed based on the MetaboFR tool and “feature-rating” rule was developed to screen the real features in large-scale data analyses. [...] Read more.
The screening of real features among thousands of ions remains a great challenge in the study of metabolomics. In this research, a workflow designed based on the MetaboFR tool and “feature-rating” rule was developed to screen the real features in large-scale data analyses. Seventy-four reference standards were used to test the feasibility, with 83.21% of real features being obtained after MetaboFR processing. Moreover, the full workflow was applied for systematic characterization of 14 species of the genus Isatis, with the result that 87.72% of real features were retained and 69.19% of the in-source fragments were removed. To gain insights into metabolite diversity within this plant family, 1697 real features were tentatively identified, including lipids, phenylpropanoids, organic acids, indole derivatives, etc. Indole derivatives were demonstrated to be the best chemical markers with which to differentiate different species. The rare existence of indole derivatives in Isatis cappadocica (cap) and Isatis cappadocica subsp. Steveniana (capS) indicates that the biosynthesis of indole derivatives could play a key role in driving the chemical diversity and evolution of genus Isatis. Our workflow provides the foundations for the exploration of real features in metabolomics, and has the potential to reveal the chemical composition and marker metabolites of secondary metabolites in plant fields. Full article
(This article belongs to the Special Issue Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods)
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13 pages, 1485 KiB  
Article
A Molecular Networking Strategy: High-Throughput Screening and Chemical Analysis of Brazilian Cerrado Plant Extracts against Cancer Cells
by Patrícia C. Cortelo, Daniel P. Demarque, Renata G. Dusi, Lorena C. Albernaz, Raimundo Braz-Filho, Ekaterina I. Goncharova, Heidi R. Bokesch, Kirk R. Gustafson, John A. Beutler and Laila S. Espindola
Cells 2021, 10(3), 691; https://doi.org/10.3390/cells10030691 - 20 Mar 2021
Cited by 17 | Viewed by 4064
Abstract
Plants have historically been a rich source of successful anticancer drugs and chemotherapeutic agents, with research indicating that this trend will continue. In this contribution, we performed high-throughput cytotoxicity screening of 702 extracts from 95 plant species, representing 40 families of the Brazilian [...] Read more.
Plants have historically been a rich source of successful anticancer drugs and chemotherapeutic agents, with research indicating that this trend will continue. In this contribution, we performed high-throughput cytotoxicity screening of 702 extracts from 95 plant species, representing 40 families of the Brazilian Cerrado biome. Activity was investigated against the following cancer cell lines: colon (Colo205 and Km12), renal (A498 and U031), liver (HEP3B and SKHEP), and osteosarcoma (MG63 and MG63.3). Dose-response tests were conducted with 44 of the most active extracts, with 22 demonstrating IC50 values ranging from <1.3 to 20 µg/mL. A molecular networking strategy was formulated using the Global Natural Product Social Molecular Networking (GNPS) platform to visualize, analyze, and annotate the compounds present in 17 extracts active against NCI-60 cell lines. Significant cytotoxic activity was found for Salacia crassifolia, Salacia elliptica, Simarouba versicolor, Diospyros hispida, Schinus terebinthifolia, Casearia sylvestris var. lingua, Magonia pubescens, and Rapanea guianensis. Molecular networking resulted in the annotation of 27 compounds. This strategy provided an initial overview of a complex and diverse natural product data set, yielded a large amount of chemical information, identified patterns and known compounds, and assisted in defining priorities for further studies. Full article
(This article belongs to the Special Issue Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods)
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Review

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22 pages, 1696 KiB  
Review
NMR-Based Chromatography Readouts: Indispensable Tools to “Translate” Analytical Features into Molecular Structures
by Christoph Seger and Sonja Sturm
Cells 2022, 11(21), 3526; https://doi.org/10.3390/cells11213526 - 7 Nov 2022
Cited by 3 | Viewed by 2969
Abstract
Gaining structural information is a must to allow the unequivocal structural characterization of analytes from natural sources. In liquid state, NMR spectroscopy is almost the only possible alternative to HPLC-MS and hyphenating the effluent of an analyte separation device to the probe head [...] Read more.
Gaining structural information is a must to allow the unequivocal structural characterization of analytes from natural sources. In liquid state, NMR spectroscopy is almost the only possible alternative to HPLC-MS and hyphenating the effluent of an analyte separation device to the probe head of an NMR spectrometer has therefore been pursued for more than three decades. The purpose of this review article was to demonstrate that, while it is possible to use mass spectrometry and similar methods to differentiate, group, and often assign the differentiating variables to entities that can be recognized as single molecules, the structural characterization of these putative biomarkers usually requires the use of NMR spectroscopy. Full article
(This article belongs to the Special Issue Profiling of Secondary Metabolites with Mass Spectroscopy-Based Methods)
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