Combining Stable Isotope Labeling and Molecular Networking for Biosynthetic Pathway Characterization
Abstract
Filamentous fungi are a rich source of bioactive compounds, ranging from statins over immunosuppressants to antibiotics. The coupling of genes to metabolites is of large commercial interest for production of the bioactives of the future. To this end, we have investigated the use of stable isotope labeled amino acids (SILAAs). SILAAs were added to the cultivation media of the filamentous fungus Aspergillus nidulans for the study of the cyclic tetrapeptide nidulanin A. Analysis by UHPLC-TOFMS confirmed that the SILAAs were incorporated into produced nidulanin A, and the change in observed m/z could be used to determine whether a compound (known or unknown) incorporated any of the added amino acids. Samples were then analyzed using MS/MS and the data used to perform molecular networking. The molecular network revealed several known and unknown compounds that were also labeled. Assisted by the isotope labeling, it was possible to determine the sequence of several of the compounds, one of which was the known metabolite fungisporin, not previously described in A. nidulans. Several novel analogues of nidulanin A and fungisporin were detected and tentatively identified, and it was determined that these metabolites were all produced by the same nonribosomal peptide synthase. The combination of stable isotope labeling and molecular network generation was shown to very effective for the automated detection of structurally related nonribosomal peptides, while the labeling was effective for determination of the peptide sequence, which could be used to provide information on biosynthesis of bioactive compounds.
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Stable-isotope precursor feeding has been used to identify natural products with specific biosynthetic precursors such as colibactin and xanthomonic acid, and to investigate the biosynthesis of fungisporin and related analogues.
“several studies have made use of stable-isotope precursor feeding to identify natural products with specific biosynthetic precursors such as colibactin,68 xanthomonic acid69 and to investigate the biosynthesis of fungisporin and the discovery of related analogues.70”
From Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products (2024) · cites this paper as [70]
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- Authors
- Klitgaard, A., Nielsen, J. B., Frandsen, R. J. N., Andersen, M. R., & Nielsen, K. F.
- Affiliations
- Technical University of Denmark (DK)
- Corresponding author
- Nielsen, Kristian F.
- ORCID
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-06-09
- Volume
- 87
- Issue
- 13
- Pages
- 6520-6526
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2294110806
- Cited by
- 54
- References
- 33
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 3 · 2023: 3 · 2022: 2 · 2021: 2 · 2020: 4 · 2019: 5 · 2018: 13 · 2017: 6 · 2016: 8 · 2015: 3
- FWCI
- 7.24
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion)
- Funders
- Teknologi og Produktion, Det Frie Forskningsråd (09-064967)
- Topics
- Health Sciences › Medicine › Pharmacology › Microbial Natural Products and Biosynthesis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- molecular networking, nonribosomal peptide synthetase, Aspergillus nidulans, filamentous fungi, cyclic tetrapeptides, peptide identification, bioactive compounds
- MeSH terms
- Aspergillus nidulans, Chromatography, High Pressure Liquid, Isotope Labeling, Mass Spectrometry
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Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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