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Calderón Celis F, González-Álvarez I, Fabjanowicz M, Godin S, Ouerdane L, Lauga B, Łobiński R. Unveiling the Pool of Metallophores in Native Environments and Correlation with Their Potential Producers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17302-17311. [PMID: 37921623 DOI: 10.1021/acs.est.3c04582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
For many organisms, metallophores are essential biogenic ligands that ensure metal scavenging and acquisition from their environment. Their identification is challenging in highly organic matter rich environments like peatlands due to low solubilization and metal scarcity and high matrix complexity. In contrast to common approaches based on sample modification by spiking of metal isotope tags, we have developed a two-dimensional (2D) Solid-phase extraction-Liquid chromatography-mass spectrometry (SPE-LC-MS) approach for the highly sensitive (LOD 40 fmol per g of soil), high-resolution direct detection and identification of metallophores in both their noncomplexed (apo) and metal-complexed forms in native environments. The characterization of peat collected in the Bernadouze (France) peatland resulted in the identification of 53 metallophores by a database mass-based search, 36 among which are bacterial. Furthermore, the detection of the characteristic (natural) metal isotope patterns in MS resulted in the detection of both Fe and Cu potential complexes. A taxonomic-based inference method was implemented based on literature and public database (antiSMASH database version 3.0) searches, enabling to associate over 40% of the identified bacterial metallophores with potential producers. In some cases, low completeness with the MIBiG reference BCG might be indicative of alternative producers in the ecosystem. Thus, coupling of metallophore detection and producers' inference could pave a new way to investigate poorly documented environment searching for new metallophores and their producers yet unknown.
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Affiliation(s)
| | | | - Magdalena Fabjanowicz
- Faculty of Chemistry, Department of Analytical Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Simon Godin
- E2S UPPA, CNRS, IPREM, Universite de Pau et des Pays de l'Adour, 64000 Pau, France
| | - Laurent Ouerdane
- E2S UPPA, CNRS, IPREM, Universite de Pau et des Pays de l'Adour, 64000 Pau, France
| | - Béatrice Lauga
- E2S UPPA, CNRS, IPREM, Universite de Pau et des Pays de l'Adour, 64000 Pau, France
| | - Ryszard Łobiński
- E2S UPPA, CNRS, IPREM, Universite de Pau et des Pays de l'Adour, 64000 Pau, France
- Chair of Analytical Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
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2
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Iminova L, Delegan Y, Frantsuzova E, Bogun A, Zvonarev A, Suzina N, Anbumani S, Solyanikova I. Physiological and biochemical characterization and genome analysis of Rhodococcus qingshengii strain 7B capable of crude oil degradation and plant stimulation. BIOTECHNOLOGY REPORTS 2022; 35:e00741. [PMID: 35665370 PMCID: PMC9157199 DOI: 10.1016/j.btre.2022.e00741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/12/2022] [Accepted: 05/20/2022] [Indexed: 11/24/2022]
Abstract
Strain 7B grows in the presence of up to 10% sodium chloride and degrades crude oil, oil sludge and individual hydrocarbons. Over 15 days of the experiment, the strain utilized 51% of oil at 28°C and 24% at 45°C. When colonizing the wheat root, the strain forms biofilms in the calyptrogen sheath and at the base of the root hairs.
Rhodococci are typical soil inhabitants which take part in remediation of soil polluted with hydrocarbons. In this paper, we describe a new strain, Rhodococcus qingshengii 7B, which is capable of growth and hydrocarbon degradation at 45°C and in the presence of up to 10% NaCl in the medium. The genome of the 7B strain consists of a 6,278,280 bp chromosome and two plasmids. The circular plasmid is 103,992 bp in length. The linear plasmid is 416,450 bp in length. Genome analysis revealed the genes of degradation of various hydrocarbons, resistance to salt stress and plant growth promoting activity. This strain is promising for use in remediation of oil-contaminated soils, because it has a pronounced ability to utilize crude oil, oil sludge and individual hydrocarbons in a wide temperature range. Over 15 days of the experiment, the strain utilized 51% of crude oil at 28°C and 24% at 45 °С.
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3
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An isotopic labeling approach linking natural products with biosynthetic gene clusters. Nat Chem Biol 2022; 18:295-304. [PMID: 34969972 PMCID: PMC8891042 DOI: 10.1038/s41589-021-00949-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/29/2021] [Indexed: 12/31/2022]
Abstract
Major advances in genome sequencing and large-scale biosynthetic gene cluster (BGC) analysis have prompted an age of natural product discovery driven by genome mining. Still, connecting molecules to their cognate BGCs is a substantial bottleneck for this approach. We have developed a mass-spectrometry-based parallel stable isotope labeling platform, termed IsoAnalyst, which assists in associating metabolite stable isotope labeling patterns with BGC structure prediction to connect natural products to their corresponding BGCs. Here we show that IsoAnalyst can quickly associate both known metabolites and unknown analytes with BGCs to elucidate the complex chemical phenotypes of these biosynthetic systems. We validate this approach for a range of compound classes, using both the type strain Saccharopolyspora erythraea and an environmentally isolated Micromonospora sp. We further demonstrate the utility of this tool with the discovery of lobosamide D, a new and structurally unique member of the family of lobosamide macrolactams.
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Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
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Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
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5
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Hydroxamate siderophores: Natural occurrence, chemical synthesis, iron binding affinity and use as Trojan horses against pathogens. Eur J Med Chem 2020; 208:112791. [DOI: 10.1016/j.ejmech.2020.112791] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022]
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6
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Thompson D, Cognat V, Goodfellow M, Koechler S, Heintz D, Carapito C, Van Dorsselaer A, Mahmoud H, Sangal V, Ismail W. Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8. Front Microbiol 2020; 11:1417. [PMID: 32733398 PMCID: PMC7358434 DOI: 10.3389/fmicb.2020.01417] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/02/2020] [Indexed: 01/02/2023] Open
Abstract
Rhodococcus strain IGTS8 is the most extensively studied model bacterium for biodesulfurization of fossil fuels via the non–destructive sulfur–specific 4S pathway. This strain was initially assigned to Rhodococcus rhodochrous and later to Rhodococcus erythropolis thus making its taxonomic status debatable and reflecting the limited resolution of methods available at the time. In this study, phylogenomic analyses of the whole genome sequences of strain IGTS8 and closely related rhodococci showed that R. erythropolis and Rhodococcus qingshengii are very closely related species, that Rhodococcus strain IGTS8 is a R. qingshengii strain and that several strains identified as R. erythropolis should be re-classified as R. qingshengii. The genomes of strains assigned to these species contain potentially novel biosynthetic gene clusters showing that members of these taxa should be given greater importance in the search for new antimicrobials and other industrially important biomolecules. The plasmid-borne dsz operon encoding fossil fuel desulfurization enzymes was present in R. qingshengii IGTS8 and R. erythropolis XP suggesting that it might be transferable between members of these species.
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Affiliation(s)
- Dean Thompson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Valérie Cognat
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes, Centre National de Recherche Scientifique (CNRS), Université de Strasbourg, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS, Université de Strasbourg, Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-organique, Institut Pluridisciplinaire Hubert Curien, UMR 7178 CNRS, Université de Strasbourg, Strasbourg, France
| | - Huda Mahmoud
- Department of Biological Sciences, College of Science, Kuwait University, Safat, Kuwait
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wael Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Bahrain
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Guerrero-Garzón JF, Zehl M, Schneider O, Rückert C, Busche T, Kalinowski J, Bredholt H, Zotchev SB. Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products. Front Microbiol 2020; 11:437. [PMID: 32256483 PMCID: PMC7093587 DOI: 10.3389/fmicb.2020.00437] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/02/2020] [Indexed: 01/25/2023] Open
Abstract
Actinomycete bacteria from marine environments represent a potential source for new antibiotics and anti-tumor drugs. Ten strains belonging to the genus Streptomyces isolated from the marine sponge Antho dichotoma collected at the bottom of the Trondheim fjord (Norway) were screened for antibiotic activity. Since only few isolates proved to be bioactive in the conditions tested, we decided to gain an insight into their biosynthetic potential using genome sequencing and analysis. Draft genomes were analyzed for the presence of secondary metabolite biosynthesis gene clusters (BGCs) using antiSMASH software. BGCs specifying both known and potentially novel secondary metabolites were identified, suggesting that these isolates might be sources for new bioactive compounds. The results of this analysis also implied horizontal transfer of several gene clusters between the studied isolates, which was especially evident for the lantibiotic- and thiopeptide-encoding BGCs. The latter implies the significance of particular secondary metabolites for the adaptation of Streptomyces to the spatially enclosed marine environments such as marine sponges. Two bioactive isolates, one showing activity against both yeast and Bacillus subtilis, and one only against yeast were analyzed in details, leading to the identification of cycloheximide, linearmycins, and echinomycins that are presumably responsible for the observed bioactivities.
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Affiliation(s)
| | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Olha Schneider
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | | | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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8
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Rego A, Sousa AGG, Santos JP, Pascoal F, Canário J, Leão PN, Magalhães C. Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica. Microorganisms 2020; 8:microorganisms8020279. [PMID: 32085500 PMCID: PMC7074882 DOI: 10.3390/microorganisms8020279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial natural products (NPs) are still a major source of new drug leads. Polyketides (PKs) and non-ribosomal peptides (NRP) are two pharmaceutically important families of NPs and recent studies have revealed Antarctica to harbor endemic polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, likely to be involved in the production of novel metabolites. Despite this, the diversity of secondary metabolites genes in Antarctica is still poorly explored. In this study, a computational bioprospection approach was employed to study the diversity and identity of PKS and NRPS genes to one of the most biodiverse areas in maritime Antarctica—Maxwell Bay. Amplicon sequencing of soil samples targeting ketosynthase (KS) and adenylation (AD) domains of PKS and NRPS genes, respectively, revealed abundant and unexplored chemical diversity in this peninsula. About 20% of AD domain sequences were only distantly related to characterized biosynthetic genes. Several PKS and NRPS genes were found to be closely associated to recently described metabolites including those from uncultured and candidate phyla. The combination of new approaches in computational biology and new culture-dependent and -independent strategies is thus critical for the recovery of the potential novel chemistry encoded in Antarctica microorganisms.
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Affiliation(s)
- Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - António G. G. Sousa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
| | - João P. Santos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Institute F.-A. Forel, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva, 66, Boulevard Carl-Vogt, 1211 Genève 4, Switzerland
| | - Francisco Pascoal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
| | - João Canário
- Centro de Química Estrutural at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal;
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Correspondence: (P.N.L); (C.M.)
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4450-208 Matosinhos, Portugal; (A.R.); (A.G.G.S.); (J.P.S.); (F.P.)
- Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
- School of Science, University of Waikato, Hamilton 3216, New Zealand
- Correspondence: (P.N.L); (C.M.)
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9
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Sano S, Nakao M, Adachi A, Kitaike S. Synthesis of Three Stereoisomers of Erythrochelin, a Hydroxamate-Type Tetrapeptide Siderophore from Saccharopolyspora erythraea. HETEROCYCLES 2020. [DOI: 10.3987/com-19-s(f)27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Baldeweg F, Warncke P, Fischer D, Gressler M. Fungal Biosurfactants from Mortierella alpina. Org Lett 2019; 21:1444-1448. [PMID: 30789272 DOI: 10.1021/acs.orglett.9b00193] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The zygomycete Mortierella alpina is a well-known producer of polyunsaturated fatty acids in the food industry. Two series of its secondary metabolites are reported: Malpinins, a family of amphiphilic acetylated hexapeptides, were chemically characterized and serve as natural emulsifiers during lipid secretion. Additionally, hydrophobic cyclopentapeptides, malpibaldins, were structurally elucidated by NMR experiments, and their absolute stereochemistry was elucidated through chemical derivatization and synthesis. This work highlights lower fungi as a novel reservoir for natural products.
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Affiliation(s)
- Florian Baldeweg
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute , Friedrich-Schiller-University Jena , Winzerlaer Strasse 2 , 07745 Jena , Germany
| | - Paul Warncke
- Pharmaceutical Technology and Biopharmacy , Friedrich-Schiller-University Jena , Lessingstrasse 8 , 07743 Jena , Germany
| | - Dagmar Fischer
- Pharmaceutical Technology and Biopharmacy , Friedrich-Schiller-University Jena , Lessingstrasse 8 , 07743 Jena , Germany
| | - Markus Gressler
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute , Friedrich-Schiller-University Jena , Winzerlaer Strasse 2 , 07745 Jena , Germany
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11
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Li Z, Zhu D, Shen Y. Discovery of novel bioactive natural products driven by genome mining. Drug Discov Ther 2018; 12:318-328. [DOI: 10.5582/ddt.2018.01066] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhongyue Li
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University
| | - Deyu Zhu
- School of Basic Medical Sciences, Shandong University
| | - Yuemao Shen
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University
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12
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Niehs SP, Dose B, Scherlach K, Roth M, Hertweck C. Genomics-Driven Discovery of a Symbiont-Specific Cyclopeptide from Bacteria Residing in the Rice Seedling Blight Fungus. Chembiochem 2018; 19:2167-2172. [PMID: 30113119 DOI: 10.1002/cbic.201800400] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 12/24/2022]
Abstract
The rice seedling blight fungus Rhizopus microsporus harbors endosymbiotic bacteria (Burkholderia rhizoxinica) that produce the virulence factor rhizoxin and control host development. Genome mining indicated a massive inventory of cryptic nonribosomal peptide synthetase (NRPS) genes, which have not yet been linked to any natural products. The discovery and full characterization of a novel cyclopeptide from endofungal bacteria is reported. In silico analysis of an orphan, symbiont-specific NRPS predicted the structure of a nonribosomal peptide, which was targeted by LC-MS/MS profiling of wild-type and engineered null mutants. NMR spectroscopy and chemical derivatization elucidated the structure of the bacterial cyclopeptide. Phylogenetic analyses revealed the relationship of starter C domains for rare N-acetyl-capped peptides. Heptarhizin is produced under symbiotic conditions in geographically constrained strains from the Pacific clade; this indicates a potential ecological role of the peptide.
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Affiliation(s)
- Sarah P Niehs
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Martin Roth
- BioPilotPlant, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Friedrich Schiller University Jena, 07743, Jena, Germany
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13
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Nakao M. Development of Novel Functional Molecules Based on the Molecular Structure Characteristics of Diketopiperazines. YAKUGAKU ZASSHI 2017; 137:1505-1516. [DOI: 10.1248/yakushi.17-00176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Michiyasu Nakao
- Graduate School of Pharmaceutical Sciences, Tokushima University
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14
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Abstract
Covering: 2006 to 2017Actinomycetes have been, for decades, one of the most important sources for the discovery of new antibiotics with an important number of drugs and analogs successfully introduced in the market and still used today in clinical practice. The intensive antibacterial discovery effort that generated the large number of highly potent broad-spectrum antibiotics, has seen a dramatic decline in the large pharma industry in the last two decades resulting in a lack of new classes of antibiotics with novel mechanisms of action reaching the clinic. Whereas the decline in the number of new chemical scaffolds and the rediscovery problem of old known molecules has become a hurdle for industrial natural products discovery programs, new actinomycetes compounds and leads have continued to be discovered and developed to the preclinical stages. Actinomycetes are still one of the most important sources of chemical diversity and a reservoir to mine for novel structures that is requiring the integration of diverse disciplines. These can range from novel strategies to isolate species previously not cultivated, innovative whole cell screening approaches and on-site analytical detection and dereplication tools for novel compounds, to in silico biosynthetic predictions from whole gene sequences and novel engineered heterologous expression, that have inspired the isolation of new NPs and shown their potential application in the discovery of novel antibiotics. This review will address the discovery of antibiotics from actinomycetes from two different perspectives including: (1) an update of the most important antibiotics that have only reached the clinical development in the recent years despite their early discovery, and (2) an overview of the most recent classes of antibiotics described from 2006 to 2017 in the framework of the different strategies employed to untap novel compounds previously overlooked with traditional approaches.
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Affiliation(s)
- Olga Genilloud
- Fundación MEDINA, Avda Conocimiento 34, 18016 Granada, Spain.
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15
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Christoff RM, Murray GL, Kostoulias XP, Peleg AY, Abbott BM. Synthesis of novel 1,2,5-oxadiazoles and evaluation of action against Acinetobacter baumannii. Bioorg Med Chem 2017; 25:6267-6272. [PMID: 29032931 DOI: 10.1016/j.bmc.2017.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 07/31/2017] [Accepted: 08/08/2017] [Indexed: 11/27/2022]
Abstract
With multidrug resistant bacteria on the rise, novel antibiotics are becoming highly sought after. In 2008, eleven compounds were identified by high throughput screening as inhibitors of BasE, a key enzyme of the non-ribosomal peptide synthetase pathway found in Acinetobacter baumannii. Herein, we describe the preparation of four structurally similar heterocyclic lead compounds from that study, including one 1,2,5-oxadiazole. A further library of 30 analogues containing the oxadiazole moiety was then generated. All compounds were screened against Acinetobacter baumannii and their minimum inhibitory concentration data is reported, with (E)-3-(2-hydroxyphenyl)-N-(4-methyl-1,2,5-oxadiazol-3-yl)acrylamide 32 found to have an MIC of 0.5mM. This work provides the foundation for further investigation of 1,2,5-oxadizoles as novel inhibitors of A. baumannii.
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Affiliation(s)
- Rebecca M Christoff
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Gerald L Murray
- Murdoch Childrens Research Institute, Melbourne, Victoria 3052, Australia; Royal Women's Hospital, Melbourne, Victoria 3052, Australia; Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Xenia P Kostoulias
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Anton Y Peleg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia; Department of Infectious Diseases, The Alfred Hospital and Monash University, Melbourne, Victoria 3004, Australia
| | - Belinda M Abbott
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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16
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Holmes NA, Innocent TM, Heine D, Bassam MA, Worsley SF, Trottmann F, Patrick EH, Yu DW, Murrell JC, Schiøtt M, Wilkinson B, Boomsma JJ, Hutchings MI. Genome Analysis of Two Pseudonocardia Phylotypes Associated with Acromyrmex Leafcutter Ants Reveals Their Biosynthetic Potential. Front Microbiol 2016; 7:2073. [PMID: 28082956 PMCID: PMC5183585 DOI: 10.3389/fmicb.2016.02073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 12/08/2016] [Indexed: 11/13/2022] Open
Abstract
The attine ants of South and Central America are ancient farmers, having evolved a symbiosis with a fungal food crop >50 million years ago. The most evolutionarily derived attines are the Atta and Acromyrmex leafcutter ants, which harvest fresh leaves to feed their fungus. Acromyrmex and many other attines vertically transmit a mutualistic strain of Pseudonocardia and use antifungal compounds made by these bacteria to protect their fungal partner against co-evolved fungal pathogens of the genus Escovopsis. Pseudonocardia mutualists associated with the attines Apterostigma dentigerum and Trachymyrmex cornetzi make novel cyclic depsipeptide compounds called gerumycins, while a mutualist strain isolated from derived Acromyrmex octospinosus makes an unusual polyene antifungal called nystatin P1. The novelty of these antimicrobials suggests there is merit in exploring secondary metabolites of Pseudonocardia on a genome-wide scale. Here, we report a genomic analysis of the Pseudonocardia phylotypes Ps1 and Ps2 that are consistently associated with Acromyrmex ants collected in Gamboa, Panama. These were previously distinguished solely on the basis of 16S rRNA gene sequencing but genome sequencing of five Ps1 and five Ps2 strains revealed that the phylotypes are distinct species and each encodes between 11 and 15 secondary metabolite biosynthetic gene clusters (BGCs). There are signature BGCs for Ps1 and Ps2 strains and some that are conserved in both. Ps1 strains all contain BGCs encoding nystatin P1-like antifungals, while the Ps2 strains encode novel nystatin-like molecules. Strains show variations in the arrangement of these BGCs that resemble those seen in gerumycin gene clusters. Genome analyses and invasion assays support our hypothesis that vertically transmitted Ps1 and Ps2 strains have antibacterial activity that could help shape the cuticular microbiome. Thus, our work defines the Pseudonocardia species associated with Acromyrmex ants and supports the hypothesis that Pseudonocardia species could provide a valuable source of new antimicrobials.
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Affiliation(s)
- Neil A Holmes
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Tabitha M Innocent
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Mahmoud Al Bassam
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Felix Trottmann
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Elaine H Patrick
- School of Biological Sciences, University of East Anglia (UEA) Norwich, UK
| | - Douglas W Yu
- School of Biological Sciences, University of East Anglia (UEA)Norwich, UK; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyKunming, China
| | - J C Murrell
- School of Environmental Sciences, University of East Anglia (UEA) Norwich, UK
| | - Morten Schiøtt
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre Norwich, UK
| | - Jacobus J Boomsma
- Centre for Social Evolution, University of Copenhagen Copenhagen, Denmark
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17
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Fazary AE, Ju YH, Al-Shihri AS, Alfaifi MY, Alshehri MA. Biodegradable siderophores: survey on their production, chelating and complexing properties. REV INORG CHEM 2016. [DOI: 10.1515/revic-2016-0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe academic and industrial research on the interactions of complexing agents with the environment has received more attention for more than half a century ago and has always been concerned with the applications of chelating agents in the environment. In contrast, in recent years, an increasing scholarly interest has been demonstrated in the chemical and biological degradation of chelating agents. This is reflected by the increasing number of chelating agents-related publications between 1950 and middle of 2016. Consequently, the discovery of new green biodegradable chelating agents is of great importance and has an impact in the non-biodegradable chelating agent’s replacement with their green chemistry analogs. To acquire iron, many bacteria growing aerobically, including marine species, produce siderophores, which are low-molecular-weight compounds produced to facilitate acquisition of iron. To date and to the best of our knowledge, this is a concise and complete review article of the current and previous relevant studies conducted in the field of production, purification of siderophore compounds and their metal complexes, and their roles in biology and medicine.
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18
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Giessen TW, Marahiel MA. Rational and combinatorial tailoring of bioactive cyclic dipeptides. Front Microbiol 2015; 6:785. [PMID: 26284060 PMCID: PMC4519757 DOI: 10.3389/fmicb.2015.00785] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/17/2015] [Indexed: 01/17/2023] Open
Abstract
Modified cyclic dipeptides represent a diverse family of microbial secondary metabolites. They display a broad variety of biological and pharmacological activities and have long been recognized as privileged structures with the ability to bind to a wide range of receptors. This is due to their conformationally constrained 2, 5-diketopiperazine (DKP) scaffold and the diverse set of DKP tailoring enzymes present in nature. After initial DKP assembly through different biosynthetic systems modifying enzymes are responsible for installing functional groups crucial for the biological activities of the resulting modified DKPs. They represent a vast and largely untapped enzyme repository very useful for synthetic biology approaches aiming at introducing structural variations into DKP scaffolds. In this review we focus on these DKP modification enzymes found in various microbial secondary metabolite gene clusters. We will give a brief overview of their distribution and highlight a select number of characterized DKP tailoring enzymes before turning to their application potential in combinatorial biosynthesis with the aim of producing molecules with improved or entirely new biological and medicinally relevant properties.
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Affiliation(s)
- Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston MA, USA ; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston MA, USA
| | - Mohamed A Marahiel
- Department of Chemistry, Philipps-University Marburg Marburg, Germany ; LOEWE Center for Synthetic Microbiology, Philipps-University Marburg Marburg, Germany
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19
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Structure determination of a siderophore peucechelin from Streptomyces peucetius. Biometals 2015; 28:791-801. [DOI: 10.1007/s10534-015-9866-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 06/08/2015] [Indexed: 01/24/2023]
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20
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Isolation and structure determination of new siderophore albachelin from Amycolatopsis alba. Biometals 2015; 28:381-9. [PMID: 25749409 DOI: 10.1007/s10534-015-9842-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 02/23/2015] [Indexed: 10/23/2022]
Abstract
A new siderophore named albachelin was isolated from iron deficient culture of Amycolatopsis alba. The planar structure of albachelin was elucidated by the combination of ESI-MS/MS experiment and NMR spectroscopic analyses of the gallium (III) complex. The structure of albachelin was determined to be a linear peptide consisting of 6 mol of amino acids including 3 mol of serine, one mol each of N-α-acethyl-N-δ-hydroxy-N-δ-formylornithine, N-α-methyl-N-δ-hydroxyornithine, and cyclic N-hydroxyornithine. The stereochemistries of amino acids constituting albachelin were analyzed by applying modified Marfey method to the hydrolysate of albachelin. Based on bioinformatics, we deduced and discussed the possible biosynthetic gene cluster involved in albachelin biosynthesis from the genome sequence of A. alba. By prediction of substrates for adenylation domains, a non-ribosomal peptide biosynthetase gene (AMYAL_RS0130210) was proposed to be the main biosynthetic gene for albachelin biosynthesis. The related genes including transporter for siderophore were found near the NRPS gene as a gene cluster.
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21
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Milshteyn A, Schneider JS, Brady SF. Mining the metabiome: identifying novel natural products from microbial communities. CHEMISTRY & BIOLOGY 2014; 21:1211-23. [PMID: 25237864 PMCID: PMC4171686 DOI: 10.1016/j.chembiol.2014.08.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 12/21/2022]
Abstract
Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review, we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of reinvigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities.
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Affiliation(s)
- Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jessica S Schneider
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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22
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Bosello M, Zeyadi M, Kraas FI, Linne U, Xie X, Marahiel MA. Structural characterization of the heterobactin siderophores from Rhodococcus erythropolis PR4 and elucidation of their biosynthetic machinery. JOURNAL OF NATURAL PRODUCTS 2013; 76:2282-2290. [PMID: 24274668 DOI: 10.1021/np4006579] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In this study, the isolation, the structural characterization, and the elucidation of the biosynthetic origin of heterobactins, catecholate-hydroxamate mixed-type siderophores from Rhodococcus erythropolis PR4, are reported. The structure elucidation of heterobactin A was accomplished via MS(n) analysis and NMR spectroscopy and revealed the noteworthy presence of a peptide bond between the guanidine group of an arginine residue and a 2,3-dihydroxybenzoate moiety. The two heterobactin S1 and S2 variants are derivatives of heterobactin A that have sulfonation modifications on the aromatic rings. The bioinformatic analysis of the R. erythropolis PR4 genome and the subsequent genetic and biochemical characterization of the putative biosynthetic machinery identified the gene cluster responsible for the biosynthesis of the heterobactins. Interestingly, the HtbG NRPS presents an unprecedented C-PCP-A domain organization within the second module of the synthetase that may help the correct elongation of the peptide intermediate. Finally, the present work revises the structure of heterobactin A that was described by Carrano et al. in 2001.
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Affiliation(s)
- Mattia Bosello
- Biochemistry, Department of Chemistry, Philipps-University Marburg , Hans-Meerwein-Strasse D-35043 Marburg, Germany
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23
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Deane CD, Mitchell DA. Lessons learned from the transformation of natural product discovery to a genome-driven endeavor. J Ind Microbiol Biotechnol 2013; 41:315-31. [PMID: 24142337 DOI: 10.1007/s10295-013-1361-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 09/30/2013] [Indexed: 12/24/2022]
Abstract
Natural product discovery is currently undergoing a transformation from a phenotype-driven field to a genotype-driven one. The increasing availability of genome sequences, coupled with improved techniques for identifying biosynthetic gene clusters, has revealed that secondary metabolomes are strikingly vaster than previously thought. New approaches to correlate biosynthetic gene clusters with the compounds they produce have facilitated the production and isolation of a rapidly growing collection of what we refer to as "reverse-discovered" natural products, in analogy to reverse genetics. In this review, we present an extensive list of reverse-discovered natural products and discuss seven important lessons for natural product discovery by genome-guided methods: structure prediction, accurate annotation, continued study of model organisms, avoiding genome-size bias, genetic manipulation, heterologous expression, and potential engineering of natural product analogs.
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Affiliation(s)
- Caitlin D Deane
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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24
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Giessen TW, von Tesmar AM, Marahiel MA. A tRNA-Dependent Two-Enzyme Pathway for the Generation of Singly and Doubly Methylated Ditryptophan 2,5-Diketopiperazines. Biochemistry 2013; 52:4274-83. [DOI: 10.1021/bi4004827] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tobias W. Giessen
- Department of Chemistry
and LOEWE-Center for Synthetic
Microbiology, Philipps-University, Hans-Meerwein-Strasse-4,
35032 Marburg, Germany
| | - Alexander M. von Tesmar
- Department of Chemistry
and LOEWE-Center for Synthetic
Microbiology, Philipps-University, Hans-Meerwein-Strasse-4,
35032 Marburg, Germany
| | - Mohamed A. Marahiel
- Department of Chemistry
and LOEWE-Center for Synthetic
Microbiology, Philipps-University, Hans-Meerwein-Strasse-4,
35032 Marburg, Germany
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25
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Reconstruction of the Saccharopolyspora erythraea genome-scale model and its use for enhancing erythromycin production. Antonie van Leeuwenhoek 2012; 102:493-502. [DOI: 10.1007/s10482-012-9783-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 07/21/2012] [Indexed: 10/28/2022]
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26
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Genome-based cryptic gene discovery and functional identification of NRPS siderophore peptide in Streptomyces peucetius. Appl Microbiol Biotechnol 2012; 97:1213-22. [DOI: 10.1007/s00253-012-4268-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 06/21/2012] [Accepted: 06/25/2012] [Indexed: 10/28/2022]
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27
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Giessen TW, Franke KB, Knappe TA, Kraas FI, Bosello M, Xie X, Linne U, Marahiel MA. Isolation, structure elucidation, and biosynthesis of an unusual hydroxamic acid ester-containing siderophore from Actinosynnema mirum. JOURNAL OF NATURAL PRODUCTS 2012; 75:905-914. [PMID: 22578145 DOI: 10.1021/np300046k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this study we report the isolation, structure elucidation, and biosynthesis of mirubactin (1), a siderophore containing an unprecedented chemical functionality in natural products, namely, an O-acyl hydroxamic acid ester. Mirubactin represents the first siderophore isolated from the genus Actinosynnema and the first natural product produced by Actinosynnema mirum whose biosynthetic gene cluster could be identified. Structure elucidation was accomplished through a combination of spectroscopic (NMR, IR, and UV/vis) and mass spectrometric methods and revealed the presence of an unusual ester bond between the δ-N-hydroxyl group of δ-N-formyl-δ-N-hydroxyornithine and a 2,3-dihydroxybenzoate moiety. Bioinformatic analysis of the A. mirum genome and subsequent biochemical characterization of the putative biosynthetic machinery identified the gene cluster responsible for mirubactin assembly. The proposed biosynthesis of mirubactin comprises the iterative use of a stand-alone carrier-protein-bound substrate, as well as an ester-bond-forming step catalyzed by a C-terminal condensation domain, thus revealing an interesting system for further biochemical studies to gain a deeper understanding of nonribosomal peptide synthetase-catalyzed siderophore biosynthesis.
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Affiliation(s)
- Tobias W Giessen
- Department of Chemistry/Biochemistry, Philipps-University , Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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28
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Kreutzer MF, Kage H, Nett M. Structure and Biosynthetic Assembly of Cupriachelin, a Photoreactive Siderophore from the Bioplastic Producer Cupriavidus necator H16. J Am Chem Soc 2012; 134:5415-22. [DOI: 10.1021/ja300620z] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin F. Kreutzer
- Junior Research Group “Secondary Metabolism
of Predatory Bacteria”, Leibniz Institute for Natural Product
Research and Infection Biology e.V., Hans-Knöll-Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Hirokazu Kage
- Junior Research Group “Secondary Metabolism
of Predatory Bacteria”, Leibniz Institute for Natural Product
Research and Infection Biology e.V., Hans-Knöll-Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Markus Nett
- Junior Research Group “Secondary Metabolism
of Predatory Bacteria”, Leibniz Institute for Natural Product
Research and Infection Biology e.V., Hans-Knöll-Institute, Beutenbergstrasse 11a, 07745 Jena, Germany
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29
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Kreutzer MF, Nett M. Genomics-driven discovery of taiwachelin, a lipopeptide siderophore from Cupriavidus taiwanensis. Org Biomol Chem 2012; 10:9338-43. [DOI: 10.1039/c2ob26296g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Dimise EJ, Condurso HL, Stoker GE, Bruner SD. Synthesis and structure confirmation of fuscachelins A and B, structurally unique natural product siderophores from Thermobifida fusca. Org Biomol Chem 2012; 10:5353-6. [DOI: 10.1039/c2ob26010g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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Gomez-Escribano JP, Song L, Fox DJ, Yeo V, Bibb MJ, Challis GL. Structure and biosynthesis of the unusual polyketide alkaloid coelimycin P1, a metabolic product of the cpk gene cluster of Streptomyces coelicolor M145. Chem Sci 2012. [DOI: 10.1039/c2sc20410j] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Wen Y, Wu X, Teng Y, Qian C, Zhan Z, Zhao Y, Li O. Identification and analysis of the gene cluster involved in biosynthesis of paenibactin, a catecholate siderophore produced by Paenibacillus elgii B69. Environ Microbiol 2011; 13:2726-37. [DOI: 10.1111/j.1462-2920.2011.02542.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Seyedsayamdost MR, Traxler MF, Zheng SL, Kolter R, Clardy J. Structure and biosynthesis of amychelin, an unusual mixed-ligand siderophore from Amycolatopsis sp. AA4. J Am Chem Soc 2011; 133:11434-7. [PMID: 21699219 PMCID: PMC3144690 DOI: 10.1021/ja203577e] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Actinobacteria generate a large number of structurally diverse small molecules with potential therapeutic value. Genomic analyses of this productive group of bacteria show that their genetic potential to manufacture small molecules exceeds their observed ability by roughly an order of magnitude, and this revelation has prompted a number of studies to identify members of the unknown majority. As a potential window into this cryptic secondary metabolome, pairwise assays for developmental interactions within a set of 20 sequenced actinomycetes were carried out. These assays revealed that Amycolatopsis sp. AA4, a so-called “rare” actinomycete, produces a novel siderophore, amychelin, which alters the developmental processes of several neighboring streptomycetes. Using this phenotype as an assay, we isolated amychelin and solved its structure by NMR and MS methods coupled with an X-ray crystallographic analysis of its Fe-complex. The iron binding affinity of amychelin was determined using EDTA competition assays, and a biosynthetic cluster was identified and annotated to provide a tentative biosynthetic scheme for amychelin.
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Affiliation(s)
- Mohammad R Seyedsayamdost
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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34
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Robbel L, Helmetag V, Knappe TA, Marahiel MA. Consecutive enzymatic modification of ornithine generates the hydroxamate moieties of the siderophore erythrochelin. Biochemistry 2011; 50:6073-80. [PMID: 21650455 DOI: 10.1021/bi200699x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biosynthesis of the hydroxamate-type siderophore erythrochelin requires the generation of δ-N-acetyl-δ-N-hydroxy-L-ornithine (L-haOrn), which is incorporated into the tetrapeptide at positions 1 and 4. Bioinformatic analysis revealed the FAD-dependent monooxygenase EtcB and the bifunctional malonyl-CoA decarboxylase/acetyltransferase Mcd to be putatively involved in the generation of L-haOrn. To investigate if EtcB and Mcd constitute a two-enzyme pathway for the biosynthesis of L-haOrn, they were produced in a recombinant manner and subjected to biochemical studies in vitro. Hydroxylation assays employing recombinant EtcB gave rise to δ-N-hydroxy-L-ornithine (L-hOrn) and confirmed the enzyme to be involved in building block assembly. Acetylation assays were carried out by incubating L-hOrn with recombinant Mcd and malonyl-CoA as the acetyl group donor. Substrate turnover was increased by substituting malonyl-CoA with acetyl-CoA, bypassing the decarboxylation reaction which represents the rate-limiting step. Consecutive enzymatic synthesis of L-haOrn was accomplished in coupled assays employing both the L-ornithine hydroxylase and Mcd. In summary, a biosynthetic route for the generation of δ-N-acetyl-δ-N-hydroxy-L-ornithine starting from L-ornithine has been established in vitro by tandem action of the FAD-dependent monooxygenase EtcB and the bifunctional malonyl-CoA decarboxylase/acetyltransferase Mcd.
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Affiliation(s)
- Lars Robbel
- Department of Chemistry/Biochemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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35
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Bosello M, Robbel L, Linne U, Xie X, Marahiel MA. Biosynthesis of the siderophore rhodochelin requires the coordinated expression of three independent gene clusters in Rhodococcus jostii RHA1. J Am Chem Soc 2011; 133:4587-95. [PMID: 21381663 DOI: 10.1021/ja1109453] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work we report the isolation, structural characterization, and the genetic analysis of the biosynthetic origin of rhodochelin, a unique mixed-type catecholate-hydroxamate siderophore isolated from Rhodococcus jostii RHA1. Rhodochelin structural elucidation was accomplished via MS(n)- and NMR-analysis and revealed the tetrapeptide to contain an unusual ester bond between an L-δ-N-formyl-δ-N-hydroxyornithine moiety and the side chain of a threonine residue. Gene deletions within three putative biosynthetic gene clusters abolish rhodochelin production, proving that the ORFs responsible for rhodochelin biosynthesis are located in different chromosomal loci. These results demonstrate the efficient cross-talk between distantly located secondary metabolite gene clusters and outline new insights into the comprehension of natural product biosynthesis.
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Affiliation(s)
- Mattia Bosello
- Biochemistry, Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse D-35043 Marburg, Germany
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36
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Winter JM, Behnken S, Hertweck C. Genomics-inspired discovery of natural products. Curr Opin Chem Biol 2010; 15:22-31. [PMID: 21111667 DOI: 10.1016/j.cbpa.2010.10.020] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 10/15/2010] [Indexed: 12/30/2022]
Abstract
The massive surge in genome sequencing projects has opened our eyes to the overlooked biosynthetic potential and metabolic diversity of microorganisms. While traditional approaches have been successful at identifying many useful therapeutic agents from these organisms, new tactics are needed in order to exploit their true biosynthetic potential. Several genomics-inspired strategies have been successful in unveiling new metabolites that were overlooked under standard fermentation and detection conditions. In addition, genome sequences have given us valuable insight for genetically engineering biosynthesis gene clusters that remain silent or are poorly expressed in the absence of a specific trigger. As more genome sequences are becoming available, we are noticing the emergence of underexplored or neglected organisms as alternative resources for new therapeutic agents.
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Affiliation(s)
- Jaclyn M Winter
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena D-07745, Germany
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37
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Davies J. How to discover new antibiotics: harvesting the parvome. Curr Opin Chem Biol 2010; 15:5-10. [PMID: 21111668 DOI: 10.1016/j.cbpa.2010.11.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 10/29/2010] [Accepted: 11/01/2010] [Indexed: 10/18/2022]
Abstract
There is a dire need for new antibiotics; commercial discovery programs have essentially dried up and there is talk of 'a return to the pre-antibiotic era'. Natural products are an inexhaustible source of bioactive compounds (antibiotics among them), and recent technical advances such as DNA sequencing and bioinformatics offer new approaches to small molecule discovery. Given that nucleotide sequence studies of actinomycetes genomes reveal the presence of 20 or more pathways for the synthesis of bioactive compounds, 'mining' these sequences offers the potential of expanding the repertoire of antibiotics and other drugs. Combined with advanced chemical separation and characterization techniques, the construction of large chemically diverse libraries of bioactive compounds for therapeutic applications is a realistic near-term goal.
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Affiliation(s)
- Julian Davies
- Department of Microbiology and Immunology, Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver BC V6T 1Z3, Canada.
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38
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Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica. J Bacteriol 2010; 193:441-8. [PMID: 21097631 DOI: 10.1128/jb.00897-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified the biosynthetic gene clusters of the siderophore nocobactin NA. The nbt clusters, which were discovered as genes highly homologous to the mycobactin biosynthesis genes by the genomic sequencing of Nocardia farcinica IFM 10152, consist of 10 genes separately located at two genomic regions. The gene organization of the nbt clusters and the predicted functions of the nbt genes, particularly the cyclization and epimerization domains, were in good agreement with the chemical structure of nocobactin NA. Disruptions of the nbtA and nbtE genes, respectively, reduced and abolished the productivity of nocobactin NA. The heterologous expression of the nbtS gene revealed that this gene encoded a salicylate synthase. These results indicate that the nbt clusters are responsible for the biosynthesis of nocobactin NA. We also found putative IdeR-binding sequences upstream of the nbtA, -G, -H, -S, and -T genes, whose expression was more than 10-fold higher in the low-iron condition than in the high-iron condition. These results suggest that nbt genes are regulated coordinately by IdeR protein in an iron-dependent manner. The ΔnbtE mutant was found to be impaired in cytotoxicity against J774A.1 cells, suggesting that nocobactin NA production is required for virulence of N. farcinica.
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