1
|
Muangkaew P, Prasad D, De Roo V, Verleysen Y, Zhou L, De Mot R, Höfte M, Madder A, Geudens N, Martins JC. Breaking Cycles: Saponification-Enhanced NMR Fingerprint Matching for the Identification and Stereochemical Evaluation of Cyclic Lipodepsipeptides from Natural Sources. Chemistry 2024; 30:e202400667. [PMID: 38647356 DOI: 10.1002/chem.202400667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 04/25/2024]
Abstract
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.
Collapse
Affiliation(s)
- Penthip Muangkaew
- Organic Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Durga Prasad
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Vic De Roo
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Yentl Verleysen
- Organic Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - René De Mot
- Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Kasteelpark Arenberg 20, 3001, Leuven, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Annemieke Madder
- Organic Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4bis, 9000, Ghent, Belgium
| |
Collapse
|
2
|
Zhou L, Höfte M, Hennessy RC. Does regulation hold the key to optimizing lipopeptide production in Pseudomonas for biotechnology? Front Bioeng Biotechnol 2024; 12:1363183. [PMID: 38476965 PMCID: PMC10928948 DOI: 10.3389/fbioe.2024.1363183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Lipopeptides (LPs) produced by Pseudomonas spp. are specialized metabolites with diverse structures and functions, including powerful biosurfactant and antimicrobial properties. Despite their enormous potential in environmental and industrial biotechnology, low yield and high production cost limit their practical use. While genome mining and functional genomics have identified a multitude of LP biosynthetic gene clusters, the regulatory mechanisms underlying their biosynthesis remain poorly understood. We propose that regulation holds the key to unlocking LP production in Pseudomonas for biotechnology. In this review, we summarize the structure and function of Pseudomonas-derived LPs and describe the molecular basis for their biosynthesis and regulation. We examine the global and specific regulator-driven mechanisms controlling LP synthesis including the influence of environmental signals. Understanding LP regulation is key to modulating production of these valuable compounds, both quantitatively and qualitatively, for industrial and environmental biotechnology.
Collapse
Affiliation(s)
- Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Rosanna C. Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
3
|
Paquette AR, Boddy CN. Macrocyclization strategies for the total synthesis of cyclic depsipeptides. Org Biomol Chem 2023; 21:8043-8053. [PMID: 37750186 DOI: 10.1039/d3ob01229h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Cyclic depsipeptides are an important class of peptide natural products that are defined by the presence of ester and amide bonds within the macrocycle. The structural diversity of depsipeptides has required the development of a broad range of synthetic strategies to access these biologically active compounds. Solid phase peptide synthesis (SPPS) strategies have been an invaluable tool in their synthesis. The key aspect of their synthesis is the macrocyclization strategy. Three main strategies are used, solution phase macrolactamization of acyclic ester containing peptide, on-resin macrolactamization of a sidechain-anchored peptide, and the solution phase macrolactonization of a linear peptide. Additionally, biocatalysts have been used to produce these compounds in a regio- and chemo-selective manner. Each compound offers unique challenges, requiring careful synthetic design to avoid undesirable side reactivity or unwanted epimerization during the esterification and macrocyclizing steps. This focused review analyzes these three strategies for cyclic depsipeptide natural product total synthesis with selected examples from the literature between 2001-2023.
Collapse
Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| |
Collapse
|
4
|
De Roo V, Verleysen Y, Kovács B, De Vleeschouwer M, Muangkaew P, Girard L, Höfte M, De Mot R, Madder A, Geudens N, Martins JC. An Nuclear Magnetic Resonance Fingerprint Matching Approach for the Identification and Structural Re-Evaluation of Pseudomonas Lipopeptides. Microbiol Spectr 2022; 10:e0126122. [PMID: 35876524 PMCID: PMC9431178 DOI: 10.1128/spectrum.01261-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/26/2022] [Indexed: 01/21/2023] Open
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.
Collapse
Affiliation(s)
- Vic De Roo
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Yentl Verleysen
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Benjámin Kovács
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Matthias De Vleeschouwer
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Penthip Muangkaew
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Léa Girard
- Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Heverlee-Leuven, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent, Belgium
| | - René De Mot
- Centre for Microbial and Plant Genetics, Faculty of Bioscience Engineering, KULeuven, Heverlee-Leuven, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - Niels Geudens
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| | - José C. Martins
- NMR and Structure Analysis Unit, Ghent University, Department of Organic and Macromolecular Chemistry, Ghent, Belgium
| |
Collapse
|
5
|
Bando Y, Hou Y, Seyfarth L, Probst J, Götze S, Bogacz M, Hellmich UA, Stallforth P, Mittag M, Arndt H. Total Synthesis and Structure Correction of the Cyclic Lipodepsipeptide Orfamide A. Chemistry 2022; 28:e202104417. [PMID: 35199896 PMCID: PMC9311703 DOI: 10.1002/chem.202104417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Indexed: 11/15/2022]
Abstract
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.
Collapse
Affiliation(s)
- Yuko Bando
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Yu Hou
- Friedrich Schiller University Jena Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular BotanyAm Planetarium 107743JenaGermany
| | - Lydia Seyfarth
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Jannik Probst
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Sebastian Götze
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll InstituteDepartment of PaleobiotechnologyBeutenbergstraße 11a07745JenaGermany
| | - Marta Bogacz
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Ute A. Hellmich
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| | - Pierre Stallforth
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll InstituteDepartment of PaleobiotechnologyBeutenbergstraße 11a07745JenaGermany
| | - Maria Mittag
- Friedrich Schiller University Jena Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular BotanyAm Planetarium 107743JenaGermany
| | - Hans‐Dieter Arndt
- Friedrich Schiller University JenaInstitute for Organic Chemistry and Macromolecular ChemistryHumboldtstr. 1007743JenaGermany
| |
Collapse
|
6
|
Dagher F, Nickzad A, Zheng J, Hoffmann M, Déziel E. Characterization of the biocontrol activity of three bacterial isolates against the phytopathogen Erwinia amylovora. Microbiologyopen 2021; 10:e1202. [PMID: 34180603 PMCID: PMC8182272 DOI: 10.1002/mbo3.1202] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 01/21/2023] Open
Abstract
Antibiotics are sprayed on apple and pear orchards to control, among other pathogens, the bacterium Erwinia amylovora, the causative agent of fire blight. As with many other pathogens, we observe the emergence of antibiotic-resistant strains of E. amylovora. Consequently, growers are looking for alternative solutions to combat fire blight. To find alternatives to antibiotics against this pathogen, we have previously isolated three bacterial strains with antagonistic and extracellular activity against E. amylovora, both in vitro and in planta, corresponding to three different bacterial genera: Here, we identified the inhibitory mode of action of each of the three isolates against E. amylovora. Isolate Bacillus amyloliquefaciens subsp. plantarum (now B. velezensis) FL50S produces several secondary metabolites including surfactins, iturins, and fengycins. Specifically, we identified oxydifficidin as the most active against E. amylovora S435. Pseudomonas poae FL10F produces an active extracellular compound against E. amylovora S435 that can be attributed to white-line-inducing principle (WLIP), a cyclic lipopeptide belonging to the viscosin subfamily (massetolide E, F, L, or viscosin). Pantoea agglomerans NY60 has a direct cell-to-cell antagonistic effect against E. amylovora S435. By screening mutants of this strain generated by random transposon insertion with decreased antagonist activity against strain S435, we identified several defective transposants. Of particular interest was a mutant in a gene coding for a Major Facilitator Superfamily (MFS) transporter corresponding to a transmembrane protein predicted to be involved in the extracytoplasmic localization of griseoluteic acid, an intermediate in the biosynthesis of the broad-spectrum phenazine antibiotic D-alanylgriseoluteic acid.
Collapse
Affiliation(s)
- Fadi Dagher
- Centre Armand‐Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS)LavalQuébecH7V 1B7Canada
| | - Arvin Nickzad
- Centre Armand‐Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS)LavalQuébecH7V 1B7Canada
| | - Jie Zheng
- US Food and Drug Administration Regulatory Science Center for Food Safety and Applied NutritionCollege ParkMarylandUSA
| | - Maria Hoffmann
- US Food and Drug Administration Regulatory Science Center for Food Safety and Applied NutritionCollege ParkMarylandUSA
| | - Eric Déziel
- Centre Armand‐Frappier Santé Biotechnologie, Institut national de la recherche scientifique (INRS)LavalQuébecH7V 1B7Canada
| |
Collapse
|
7
|
De Vleeschouwer M, Van Kersavond T, Verleysen Y, Sinnaeve D, Coenye T, Martins JC, Madder A. Identification of the Molecular Determinants Involved in Antimicrobial Activity of Pseudodesmin A, a Cyclic Lipopeptide From the Viscosin Group. Front Microbiol 2020; 11:646. [PMID: 32373092 PMCID: PMC7187754 DOI: 10.3389/fmicb.2020.00646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/20/2020] [Indexed: 12/24/2022] Open
Abstract
Cyclic lipo(depsi)peptides (CLiPs) from Pseudomonas constitute a class of natural products involved in a broad range of biological functions for their producers. They also display interesting antimicrobial potential including activity against Gram-positive bacteria. Literature has indicated that these compounds can induce membrane permeabilization, possibly through pore-formation, leading to the general view that the cellular membrane constitutes the primary target in their mode of action. In support of this view, we previously demonstrated that the enantiomer of pseudodesmin A, a member of the viscosin group of CLiPs, shows identical activity against a test panel of six Gram-positive bacterial strains. Here, a previously developed total organic synthesis route is used and partly adapted to generate 20 novel pseudodesmin A analogs in an effort to derive links between molecular constitution, structure and activity. From these, the importance of a macrocycle closed by an ester bond as well as a critical length of β-OH fatty acid chain capping the N-terminus is conclusively demonstrated, providing further evidence for the importance of peptide-membrane interactions in the mode of action. Moreover, an alanine scan is used to unearth the contribution of specific amino acid residues to biological activity. Subsequent interpretation in terms of a structural model describing the location and orientation of pseudodesmin A in a membrane environment, allows first insight in the peptide-membrane interactions involved. The biological screening also identified residue positions that appear less sensitive to conservative modifications, allowing the introduction of a non-perturbing tryptophan residue which will pave the way toward biophysical studies using fluorescence spectroscopy.
Collapse
Affiliation(s)
- Matthias De Vleeschouwer
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium.,NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Tim Van Kersavond
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium.,NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Yentl Verleysen
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium.,NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Davy Sinnaeve
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Department of Pharmaceutical Analysis, Ghent University, Ghent, Belgium
| | - José C Martins
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| |
Collapse
|
8
|
Shahid I, Malik KA, Mehnaz S. A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s42398-018-0006-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|