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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Uchiyama C, Fukuda A, Mukaiyama M, Nakazawa Y, Kuramochi Y, Muguruma K, Arimoto M, Ninomiya A, Kako K, Katsuyama Y, Konno S, Taguchi A, Takayama K, Taniguchi A, Nagumo Y, Usui T, Hayashi Y. Structural Revision of Natural Cyclic Depsipeptide MA026 Established by Total Synthesis and Biosynthetic Gene Cluster Analysis. Angew Chem Int Ed Engl 2021; 60:8792-8797. [PMID: 33533101 DOI: 10.1002/anie.202015193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/16/2021] [Indexed: 11/06/2022]
Abstract
A revised structure of natural 14-mer cyclic depsipeptide MA026, isolated from Pseudomonas sp. RtlB026 in 2002 was established by physicochemical analysis with HPLC, MS/MS, and NMR and confirmed by total solid-phase synthesis. The revised structure differs from that previously reported in that two amino acid residues, assigned in error, have been replaced. Synthesized MA026 with the revised structure showed a tight junction (TJ) opening activity like that of the natural one in a cell-based TJ opening assay. Bioinformatic analysis of the putative MA026 biosynthetic gene cluster (BGC) of RtIB026 demonstrated that the stereochemistry of each amino acid residue in the revised structure can be reasonably explained. Phylogenetic analysis with xantholysin BGC indicates an exceptionally high homology (ca. 90 %) between xantholysin and MA026. The TJ opening activity of MA026 when binding to claudin-1 is a key to new avenues for transdermal administration of large hydrophilic biologics.
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Affiliation(s)
- Chihiro Uchiyama
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Akane Fukuda
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Minagi Mukaiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiki Nakazawa
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Yuka Kuramochi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Kyohei Muguruma
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.,Present address: Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, 152-8552, Japan
| | - Mitsue Arimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Akihiro Ninomiya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Koichiro Kako
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Sho Konno
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Yoko Nagumo
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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Uchiyama C, Fukuda A, Mukaiyama M, Nakazawa Y, Kuramochi Y, Muguruma K, Arimoto M, Ninomiya A, Kako K, Katsuyama Y, Konno S, Taguchi A, Takayama K, Taniguchi A, Nagumo Y, Usui T, Hayashi Y. Structural Revision of Natural Cyclic Depsipeptide MA026 Established by Total Synthesis and Biosynthetic Gene Cluster Analysis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chihiro Uchiyama
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Akane Fukuda
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Minagi Mukaiyama
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Yoshiki Nakazawa
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Yuka Kuramochi
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Kyohei Muguruma
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
- Present address: Department of Chemical Science and Engineering School of Materials and Chemical Technology Tokyo Institute of Technology Tokyo 152-8552 Japan
| | - Mitsue Arimoto
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Akihiro Ninomiya
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Koichiro Kako
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Yohei Katsuyama
- Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Bunkyo-ku Tokyo 113-8657 Japan
| | - Sho Konno
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
| | - Yoko Nagumo
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305-8572 Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry School of Pharmacy Tokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi Hachioji Tokyo 192-0392 Japan
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Krzyżanowska DM, Ossowicki A, Rajewska M, Maciąg T, Jabłońska M, Obuchowski M, Heeb S, Jafra S. When Genome-Based Approach Meets the "Old but Good": Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens. Front Microbiol 2016; 7:782. [PMID: 27303376 PMCID: PMC4880745 DOI: 10.3389/fmicb.2016.00782] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
Dickeya solani and Pectobacterium carotovorum subsp. brasiliense are recently established species of bacterial plant pathogens causing black leg and soft rot of many vegetables and ornamental plants. Pseudomonas sp. strain P482 inhibits the growth of these pathogens, a desired trait considering the limited measures to combat these diseases. In this study, we determined the genetic background of the antibacterial activity of P482, and established the phylogenetic position of this strain. Pseudomonas sp. P482 was classified as Pseudomonas donghuensis. Genome mining revealed that the P482 genome does not contain genes determining the synthesis of known antimicrobials. However, the ClusterFinder algorithm, designed to detect atypical or novel classes of secondary metabolite gene clusters, predicted 18 such clusters in the genome. Screening of a Tn5 mutant library yielded an antimicrobial negative transposon mutant. The transposon insertion was located in a gene encoding an HpcH/HpaI aldolase/citrate lyase family protein. This gene is located in a hypothetical cluster predicted by the ClusterFinder, together with the downstream homologs of four nfs genes, that confer production of a non-fluorescent siderophore by P. donghuensis HYST. Site-directed inactivation of the HpcH/HpaI aldolase gene, the adjacent short chain dehydrogenase gene, as well as a homolog of an essential nfs cluster gene, all abolished the antimicrobial activity of the P482, suggesting their involvement in a common biosynthesis pathway. However, none of the mutants showed a decreased siderophore yield, neither was the antimicrobial activity of the wild type P482 compromised by high iron bioavailability. A genomic region comprising the nfs cluster and three upstream genes is involved in the antibacterial activity of P. donghuensis P482 against D. solani and P. carotovorum subsp. brasiliense. The genes studied are unique to the two known P. donghuensis strains. This study illustrates that mining of microbial genomes is a powerful approach for predictingthe presence of novel secondary-metabolite encoding genes especially when coupled with transposon mutagenesis.
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Affiliation(s)
- Dorota M Krzyżanowska
- Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Adam Ossowicki
- Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Magdalena Rajewska
- Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Tomasz Maciąg
- Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Magdalena Jabłońska
- Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Michał Obuchowski
- Laboratory of Molecular Bacteriology, Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Medical University of Gdansk Gdansk, Poland
| | - Stephan Heeb
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham Nottingham, UK
| | - Sylwia Jafra
- Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
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