An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides
ABSTRACT Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs from Pseudomonas in particular, display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity, and stereochemistry (e.g., d- versus...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-08-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01261-22 |
| _version_ | 1818472833907425280 |
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| author | Vic De Roo Yentl Verleysen Benjámin Kovács Matthias De Vleeschouwer Penthip Muangkaew Léa Girard Monica Höfte René De Mot Annemieke Madder Niels Geudens José C. Martins |
| author_facet | Vic De Roo Yentl Verleysen Benjámin Kovács Matthias De Vleeschouwer Penthip Muangkaew Léa Girard Monica Höfte René De Mot Annemieke Madder Niels Geudens José C. Martins |
| author_sort | Vic De Roo |
| collection | DOAJ |
| description | ABSTRACT Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs from Pseudomonas in particular, display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity, and stereochemistry (e.g., d- versus l-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. Increasingly, however, the lack of detailed characterization threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. Using Pseudomonas CLiPs from the Bananamide, Orfamide, and Xantholysin groups as test cases, we demonstrate and validate that the combined 1H and 13C Nuclear Magnetic Resonance (NMR) chemical shifts of CLiPs constitute a spectral fingerprint that is sufficiently sensitive to differentiate between possible diastereomers of a particular sequence even when they only differ in a single d/l configuration. Rapid screening, involving simple matching of the NMR fingerprint of a newly isolated CLiP with that of a reference CLiP of known stereochemistry, can then be applied to resolve dead-ends in configurational characterization and avoid the much more cumbersome chemical characterization protocols. Even when the stereochemistry of a particular reference CLiP remains to be established, its spectral fingerprint allows to quickly verify whether a newly isolated CLiP is novel or already present in the reference collection. We show NMR fingerprinting leads to a simple approach for early on dereplication which should become more effective as more fingerprints are collected. To benefit research involving CLiPs, we have made a publicly available data repository accompanied by a ‘knowledge base’ at https://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures. IMPORTANCE Pseudomonas CLiPs are ubiquitous specialized metabolites, impacting the producer’s lifestyle and interactions with the (a)biotic environment. Consequently, they generate interest for agricultural and clinical applications. Establishing structure-activity relationships as a premise to their development is hindered because full structural characterization including stereochemical information requires labor-intensive analyses, without guarantee for success. Moreover, increasing use of superficial comparison with previously characterized CLiPs introduces or propagates erroneous attributions, clouding further scientific progress. We provide a generally applicable characterization methodology based on matching NMR spectral fingerprints of newly isolated CLiPs to natural and synthetic reference compounds with (un)known stereochemistry. In addition, NMR fingerprinting is shown to provide a suitable basis for structural dereplication. A publicly available reference compound repository promises to facilitate participation of the lipopeptide research community in structural assessment and dereplication of newly isolated CLiPs, which should also support further developments in genome mining for novel CLiPs. |
| first_indexed | 2024-04-14T04:13:53Z |
| format | Article |
| id | doaj.art-245622bbff19407ba87dc418b727cb5f |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-14T04:13:53Z |
| publishDate | 2022-08-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-245622bbff19407ba87dc418b727cb5f2022-12-22T02:13:00ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-08-0110410.1128/spectrum.01261-22An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas LipopeptidesVic De Roo0Yentl Verleysen1Benjámin Kovács2Matthias De Vleeschouwer3Penthip Muangkaew4Léa Girard5Monica Höfte6René De Mot7Annemieke Madder8Niels Geudens9José C. Martins10NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, BelgiumNMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, BelgiumNMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, BelgiumNMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, BelgiumOrganic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, BelgiumCentre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Heverlee-Leuven, BelgiumLaboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent, BelgiumCentre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Heverlee-Leuven, BelgiumOrganic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, BelgiumNMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, BelgiumNMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, BelgiumABSTRACT Cyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs from Pseudomonas in particular, display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity, and stereochemistry (e.g., d- versus l-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. Increasingly, however, the lack of detailed characterization threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. Using Pseudomonas CLiPs from the Bananamide, Orfamide, and Xantholysin groups as test cases, we demonstrate and validate that the combined 1H and 13C Nuclear Magnetic Resonance (NMR) chemical shifts of CLiPs constitute a spectral fingerprint that is sufficiently sensitive to differentiate between possible diastereomers of a particular sequence even when they only differ in a single d/l configuration. Rapid screening, involving simple matching of the NMR fingerprint of a newly isolated CLiP with that of a reference CLiP of known stereochemistry, can then be applied to resolve dead-ends in configurational characterization and avoid the much more cumbersome chemical characterization protocols. Even when the stereochemistry of a particular reference CLiP remains to be established, its spectral fingerprint allows to quickly verify whether a newly isolated CLiP is novel or already present in the reference collection. We show NMR fingerprinting leads to a simple approach for early on dereplication which should become more effective as more fingerprints are collected. To benefit research involving CLiPs, we have made a publicly available data repository accompanied by a ‘knowledge base’ at https://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures. IMPORTANCE Pseudomonas CLiPs are ubiquitous specialized metabolites, impacting the producer’s lifestyle and interactions with the (a)biotic environment. Consequently, they generate interest for agricultural and clinical applications. Establishing structure-activity relationships as a premise to their development is hindered because full structural characterization including stereochemical information requires labor-intensive analyses, without guarantee for success. Moreover, increasing use of superficial comparison with previously characterized CLiPs introduces or propagates erroneous attributions, clouding further scientific progress. We provide a generally applicable characterization methodology based on matching NMR spectral fingerprints of newly isolated CLiPs to natural and synthetic reference compounds with (un)known stereochemistry. In addition, NMR fingerprinting is shown to provide a suitable basis for structural dereplication. A publicly available reference compound repository promises to facilitate participation of the lipopeptide research community in structural assessment and dereplication of newly isolated CLiPs, which should also support further developments in genome mining for novel CLiPs.https://journals.asm.org/doi/10.1128/spectrum.01261-22NMR spectroscopycyclic lipodepsipeptidesPseudomonasstereochemistrydereplication |
| spellingShingle | Vic De Roo Yentl Verleysen Benjámin Kovács Matthias De Vleeschouwer Penthip Muangkaew Léa Girard Monica Höfte René De Mot Annemieke Madder Niels Geudens José C. Martins An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides Microbiology Spectrum NMR spectroscopy cyclic lipodepsipeptides Pseudomonas stereochemistry dereplication |
| title | An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides |
| title_full | An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides |
| title_fullStr | An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides |
| title_full_unstemmed | An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides |
| title_short | An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides |
| title_sort | nuclear magnetic resonance fingerprint matching approach for the identification and structural re evaluation of pseudomonas lipopeptides |
| topic | NMR spectroscopy cyclic lipodepsipeptides Pseudomonas stereochemistry dereplication |
| url | https://journals.asm.org/doi/10.1128/spectrum.01261-22 |
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