An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides

Roo, Vic De; Verleysen, Yentl; Kovács, Benjámin; Vleeschouwer, Matthias De; Muangkaew, Penthip; Girard, Léa; Höfte, Monica; Mot, René De; Madder, Annemieke; Geudens, Niels; Martins, José

doi:10.1128/spectrum.01261-22

Cited by 11 publications

(13 citation statements)

References 82 publications

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“…This tree is further populated with additional producers identified in this study, either of known or novel LPs. In most cases, stereochemistry could be assessed by NMR spectral matching ( 24 ). However, in cases where no reference NMR spectrum was available, the stereochemical make-up currently remains elusive.…”

Section: Resultsmentioning

confidence: 99%

“…S11F), revealing distinct clusters for the CLPs produced by Pseudomonas bananamidigenes BW11P2 T ( 31 ), Pseudomonas botevensis COW3 T ( 32 ), and Pseudomonas granadensis LMG 27940 T ( 33 ), all affiliated with the Koreensis SG. MDN-0066 is also synthesized by a member of the Fluorescens SG, Pseudomonas azadiae SWRI103 T ( 24 ) ( Fig. 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…The NRPS enzymes of Pseudomonas sessilinigenes CMR12a T ( 11 ), Pseudomonas aestus CMR5c ( 40 ), and Pseudomonas sp. PH1b ( 24 ), an isolate from the same carnivorous plant niche as nepenthesin producer H1h ( 30 ), have diverged substantially from the prototypical P. protegens producers, apparently reflecting speciation (Fig. S11G).…”

Section: Resultsmentioning

confidence: 99%

“…Restriction to A domains for our comprehensive comparative analyses alleviated the need to account for the three different types of C domains and their relative positions in the NRPSs. Phylogenetic differentiation of C and C/E domains is straightforward but has limitations for stereochemical predictions, as the expected epimerization activity of a C/E domain is regularly lacking ( 8 , 24 ). Therefore, predictions of AA stereochemistry were not attempted in this study.…”

Section: Methodsmentioning

confidence: 99%

“…Moreover, the occurrence of epimerization-inactive C/E domains complicates this process further. In both respects, NMR fingerprint matching can provide a fast and unambiguous tool for the dereplication and/or elucidation of LP structures ( https://www.rhizoclip.be ; 24 ) and was applied here. Limiting the need for elaborate chemical analyses, NMR fingerprint matching only requires the comparison of the NMR spectrum of a newly isolated compound with that of available, previously described, reference compounds.…”

Section: Introductionmentioning

confidence: 99%

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Charting the Lipopeptidome of Nonpathogenic Pseudomonas

et al. 2023

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Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Charting the Lipopeptidome of Nonpathogenic Pseudomonas

et al. 2023

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Total Synthesis and Structure Correction of the Cyclic Lipodepsipeptide Orfamide A

Bando

Hou

Seyfarth

et al. 2022

Chemistry A European J

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A total synthesis of the cyclic lipodepsipeptide natural product orfamide A was achieved. By developing a synthesis format using an aminoacid ester building block and SPPS protocol adaptation, a focused library of target compounds was obtained, in high yield and purity. Spectral and LC-HRMS data of all library members with the isolated natural product identified the 5 Leu residue to be d-and the 3'-OH group to be R-configured. The structural correction of orfamide A by chemical synthesis and analysis was confirmed by biological activity comparison in Chlamydomonas reinhardtii, which indicated compound configuration to be important for bioactivity. Acute toxicity was also found against Trypanosoma brucei, the parasite causing African sleeping sickness.

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Breaking Cycles: Saponification‐Enhanced NMR Fingerprint Matching for the Identification and Stereochemical Evaluation of Cyclic Lipodepsipeptides from Natural Sources

Muangkaew,

Prasad,

De Roo

et al. 2024

Chemistry A European J

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We previously described NMR based fingerprint matching with peptide backbone resonances as a fast and reliable structural dereplication approach for Pseudomonas cyclic lipodepsipeptides (CLiPs). In combination with total synthesis of a small library of configurational CLiP congeners this also allows unambiguous determination of stereochemistry, facilitating structure‐activity relationship studies and enabling three‐dimensional structure determination. However, the on‐resin macrocycle formation in the synthetic workflow brings considerable burden and limits universal applicability. This drawback is here removed altogether by also transforming the native CLiP into a linearized analogue by controlled saponification of the ester bond. This eliminates the need for macrocycle formation, limiting the synthesis effort to linear peptide analogues. NMR fingerprints of such linear peptide analogues display a sufficiently distinctive chemical shift fingerprint to act as effective discriminators. The approach is developed using viscosin group CLiPs and subsequently demonstrated on putisolvin, leading to a structural revision, and tanniamide from Pseudomonas ekonensis COR58, a newly isolated lipododecapeptide that defines a new group characterized by a ten‐residue large macrocycle, the largest to date in the Pseudomonas CLiP portfolio. These examples demonstrate the effectiveness of the saponification‐ enhanced approach that broadens applicability of NMR fingerprint matching for the determination of the stereochemistry of CLiPs.

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An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides

Abstract: 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.

Cited by 11 publications

References 82 publications

Charting the Lipopeptidome of Nonpathogenic Pseudomonas

Charting the Lipopeptidome of Nonpathogenic Pseudomonas

Total Synthesis and Structure Correction of the Cyclic Lipodepsipeptide Orfamide A

Breaking Cycles: Saponification‐Enhanced NMR Fingerprint Matching for the Identification and Stereochemical Evaluation of Cyclic Lipodepsipeptides from Natural Sources

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