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Kossmann DF, Huang M, Weihmann R, Xiao X, Gätgens F, Weber TM, Brass HUC, Bitzenhofer NL, Ibrahim S, Bangert K, Rehling L, Mueller C, Tiso T, Blank LM, Drepper T, Jaeger KE, Grundler FMW, Pietruszka J, Schleker ASS, Loeschcke A. Production of tailored hydroxylated prodiginine showing combinatorial activity with rhamnolipids against plant-parasitic nematodes. Front Microbiol 2023; 14:1151882. [PMID: 37200918 PMCID: PMC10187637 DOI: 10.3389/fmicb.2023.1151882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/03/2023] [Indexed: 05/20/2023] Open
Abstract
Bacterial secondary metabolites exhibit diverse remarkable bioactivities and are thus the subject of study for different applications. Recently, the individual effectiveness of tripyrrolic prodiginines and rhamnolipids against the plant-parasitic nematode Heterodera schachtii, which causes tremendous losses in crop plants, was described. Notably, rhamnolipid production in engineered Pseudomonas putida strains has already reached industrial implementation. However, the non-natural hydroxyl-decorated prodiginines, which are of particular interest in this study due to a previously described particularly good plant compatibility and low toxicity, are not as readily accessible. In the present study, a new effective hybrid synthetic route was established. This included the engineering of a novel P. putida strain to provide enhanced levels of a bipyrrole precursor and an optimization of mutasynthesis, i.e., the conversion of chemically synthesized and supplemented monopyrroles to tripyrrolic compounds. Subsequent semisynthesis provided the hydroxylated prodiginine. The prodiginines caused reduced infectiousness of H. schachtii for Arabidopsis thaliana plants resulting from impaired motility and stylet thrusting, providing the first insights on the mode of action in this context. Furthermore, the combined application with rhamnolipids was assessed for the first time and found to be more effective against nematode parasitism than the individual compounds. To obtain, for instance, 50% nematode control, it was sufficient to apply 7.8 μM hydroxylated prodiginine together with 0.7 μg/ml (~ 1.1 μM) di-rhamnolipids, which corresponded to ca. ¼ of the individual EC50 values. In summary, a hybrid synthetic route toward a hydroxylated prodiginine was established and its effects and combinatorial activity with rhamnolipids on plant-parasitic nematode H. schachtii are presented, demonstrating potential application as antinematodal agents. Graphical Abstract.
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Affiliation(s)
- D. F. Kossmann
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bioorganic Chemistry, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - M. Huang
- INRES, Molecular Phytomedicine, University of Bonn, Bonn, Germany
| | - R. Weihmann
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - X. Xiao
- INRES, Molecular Phytomedicine, University of Bonn, Bonn, Germany
| | - F. Gätgens
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - T. M. Weber
- Institute of Bioorganic Chemistry, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - H. U. C. Brass
- Institute of Bioorganic Chemistry, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - N. L. Bitzenhofer
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - S. Ibrahim
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - K. Bangert
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - L. Rehling
- INRES, Molecular Phytomedicine, University of Bonn, Bonn, Germany
| | - C. Mueller
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - T. Tiso
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - L. M. Blank
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - T. Drepper
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | - K.-E. Jaeger
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
| | | | - J. Pietruszka
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bioorganic Chemistry, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
- *Correspondence: J. Pietruszka,
| | - A. S. S. Schleker
- INRES, Molecular Phytomedicine, University of Bonn, Bonn, Germany
- A. S. S. Schleker,
| | - A. Loeschcke
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
- A. Loeschcke,
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Couturier M, Bhalara HD, Monson RE, Salmond GPC, Leeper FJ. Revision in the first steps of the biosynthesis of the red antibiotic prodigiosin: use of a synthetic thioester to validate a new intermediate. RSC Chem Biol 2021; 2:551-555. [PMID: 34458798 PMCID: PMC8341465 DOI: 10.1039/d0cb00173b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/05/2021] [Indexed: 01/14/2023] Open
Abstract
A biosynthetic pathway for the red-antibiotic, prodigiosin, was proposed over a decade ago but not all the suggested intermediates could be detected experimentally. Here we show that a thioester that was not originally included in the pathway is an intermediate. In addition, the enzyme PigE was originally described as a transaminase but we present evidence that it also catalyses the reduction of the thioester intermediate to its aldehyde substrate. A revision is proposed to the biosynthetic pathway to the well-known red pigment prodigiosin via a new thioester intermediate.![]()
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Affiliation(s)
- Maxime Couturier
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Hiral D Bhalara
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Rita E Monson
- Dept. of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1QW UK
| | - George P C Salmond
- Dept. of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1QW UK
| | - Finian J Leeper
- Yusuf Hamied Dept. of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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Abstract
Inflammatory processes occur as a generic response of the immune system and can be triggered by various factors, such as infection with pathogenic microorganisms or damaged tissue. Due to the complexity of the inflammation process and its role in common diseases like asthma, cancer, skin disorders or Alzheimer's disease, anti-inflammatory drugs are of high pharmaceutical interest. Nature is a rich source for compounds with anti-inflammatory properties. Several studies have focused on the structural optimization of natural products to improve their pharmacological properties. As derivatization through total synthesis is often laborious with low yields and limited stereoselectivity, the use of biosynthetic, enzyme-driven reactions is an attractive alternative for synthesizing and modifying complex bioactive molecules. In this minireview, we present an outline of the biotechnological methods used to derivatize anti-inflammatory natural products, including precursor-directed biosynthesis, mutasynthesis, combinatorial biosynthesis, as well as whole-cell and in vitro biotransformation.
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Affiliation(s)
- Lea Winand
- Department of Biochemical and Chemical EngineeringLaboratory of Technical BiologyTU Dortmund UniversityEmil-Figge-Strasse 6644227DortmundGermany
| | - Angela Sester
- Department of Biochemical and Chemical EngineeringLaboratory of Technical BiologyTU Dortmund UniversityEmil-Figge-Strasse 6644227DortmundGermany
- Current address: Chair of Technical BiochemistryTechnical University of DresdenBergstrasse 6601069DresdenGermany
| | - Markus Nett
- Department of Biochemical and Chemical EngineeringLaboratory of Technical BiologyTU Dortmund UniversityEmil-Figge-Strasse 6644227DortmundGermany
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Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059. Mar Drugs 2021; 19:md19020108. [PMID: 33673118 PMCID: PMC7917724 DOI: 10.3390/md19020108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Genome mining of pigmented Pseudoalteromonas has revealed a large potential for the production of bioactive compounds and hydrolytic enzymes. The purpose of the present study was to explore this bioactivity potential in a potent antibiotic and enzyme producer, Pseudoalteromonas rubra strain S4059. Proteomic analyses (data are available via ProteomeXchange with identifier PXD023249) indicated that a highly efficient chitin degradation machinery was present in the red-pigmented P. rubra S4059 when grown on chitin. Four GH18 chitinases and two GH20 hexosaminidases were significantly upregulated under these conditions. GH19 chitinases, which are not common in bacteria, are consistently found in pigmented Pseudoalteromonas, and in S4059, GH19 was only detected when the bacterium was grown on chitin. To explore the possible role of GH19 in pigmented Pseudoalteromonas, we developed a protocol for genetic manipulation of S4059 and deleted the GH19 chitinase, and compared phenotypes of the mutant and wild type. However, none of the chitin degrading ability, secondary metabolite profile, or biofilm-forming capacity was affected by GH19 deletion. In conclusion, we developed a genetic manipulation protocol that can be used to unravel the bioactive potential of pigmented pseudoalteromonads. An efficient chitinolytic enzyme cocktail was identified in S4059, suggesting that this strain could be a candidate with industrial potential.
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Brands S, Sikkens JG, Davari MD, Brass HUC, Klein AS, Pietruszka J, Ruff AJ, Schwaneberg U. Understanding substrate binding and the role of gatekeeping residues in PigC access tunnels. Chem Commun (Camb) 2021; 57:2681-2684. [DOI: 10.1039/d0cc08226k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prodigiosin ligase PigC has been engineered by semi-rational design to accept short chain-pyrroles, providing molecular understanding of access tunnels and the substrate-binding pocket.
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Affiliation(s)
- Stefanie Brands
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- Bioeconomy Science Center (BioSC)
- Worringerweg 3
- Aachen 52074
| | - Jarno G. Sikkens
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- Bioeconomy Science Center (BioSC)
- Worringerweg 3
- Aachen 52074
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- Bioeconomy Science Center (BioSC)
- Worringerweg 3
- Aachen 52074
| | - Hannah U. C. Brass
- Institute of Bioorganic Chemistry
- Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich
- Stetternicher Forst
- Bioeconomy Science Center (BioSC)
- Building 15.8
| | - Andreas S. Klein
- Institute of Bioorganic Chemistry
- Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich
- Stetternicher Forst
- Bioeconomy Science Center (BioSC)
- Building 15.8
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry
- Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich
- Stetternicher Forst
- Bioeconomy Science Center (BioSC)
- Building 15.8
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- Bioeconomy Science Center (BioSC)
- Worringerweg 3
- Aachen 52074
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- Bioeconomy Science Center (BioSC)
- Worringerweg 3
- Aachen 52074
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Grenade NL, Howe GW, Ross AC. The convergence of bacterial natural products from evolutionarily distinct pathways. Curr Opin Biotechnol 2020; 69:17-25. [PMID: 33296737 DOI: 10.1016/j.copbio.2020.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/21/2020] [Accepted: 10/05/2020] [Indexed: 10/22/2022]
Abstract
As bacteria readily convert simple starting materials into a diverse array of complex molecules with useful bioactivities, these microorganisms and their biosynthetic machinery represent attractive alternatives to traditional chemical syntheses. While the well-documented divergent evolution of biosynthesis has allowed bacteria to explore wide swaths of natural product chemical space, the convergent evolution of these pathways remains a comparably rare phenomenon. The emergence of similar phenotypes within disparate genetic contexts provides a unique opportunity to probe the limitations of natural selection and the predictability and reproducibility of evolution under different constraints. Here, we report several recent examples of functional and structural convergence of bacterial natural products, as well as intra- and inter-domain convergence of bacterial biosynthetic machinery. While the genetic underpinnings of biosynthetic pathway evolution are of fundamental interest, the evolutionary constraints exemplified by phenotypic convergence also have immediate implications for efforts to engineer microorganisms for therapeutic small molecule production.
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Affiliation(s)
- Neil L Grenade
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Graeme W Howe
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada.
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Chilczuk T, Monson R, Schmieder P, Christov V, Enke H, Salmond G, Niedermeyer THJ. Ambigols from the Cyanobacterium Fischerella ambigua Increase Prodigiosin Production in Serratia spp. ACS Chem Biol 2020; 15:2929-2936. [PMID: 33143417 DOI: 10.1021/acschembio.0c00554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
When a library of 573 cyanobacteria extracts was screened for inhibition of the quorum sensing regulated prodigiosin production of Serratia marcescens, an extract of the cyanobacterium Fischerella ambigua (Näg.) Gomont 108b was found to drastically increase prodigiosin production. Bioactivity-guided isolation of the active compounds resulted in the two new natural products ambigol D and E along with the known ambigols A and C. Ambigol C treatment increased prodiginine production of Serratia sp. ATCC 39006 (S39006) by a factor of 10, while ambigols A and D were found to have antibiotic activity against this strain. The RNA-Seq of S39006 treated with ambigol C and subsequent differential gene expression and functional enrichment analyses indicated a significant downregulation of genes associated with the translation machinery and fatty acid biosynthesis in Serratia, as well as increased expression of genes related to the uptake of l-proline. These results suggest that the ambigols increase prodiginine production in S39006 not by activating the SmaIR quorum sensing system but possibly by increasing the precursor supply of l-proline and malonyl-CoA.
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Affiliation(s)
- Tomasz Chilczuk
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, University of Halle-Wittenberg, Halle, Germany
| | - Rita Monson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, United Kingdom
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Department of NMR-Supported Structural Biology, Berlin, Germany
| | - Vesselin Christov
- Zentrum für medizinische Grundlagenforschung, University of Halle-Wittenberg, Halle, Germany
| | | | - George Salmond
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Cambridge, CB2 1QW, United Kingdom
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Wang SL, Nguyen VB, Doan CT, Tran TN, Nguyen MT, Nguyen AD. Production and Potential Applications of Bioconversion of Chitin and Protein-Containing Fishery Byproducts into Prodigiosin: A Review. Molecules 2020; 25:E2744. [PMID: 32545769 PMCID: PMC7356639 DOI: 10.3390/molecules25122744] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
The technology of microbial conversion provides a potential way to exploit compounds of biotechnological potential. The red pigment prodigiosin (PG) and other PG-like pigments from bacteria, majorly from Serratia marcescens, have been reported as bioactive secondary metabolites that can be used in the broad fields of agriculture, fine chemicals, and pharmacy. Increasing PG productivity by investigating the culture conditions especially the inexpensive carbon and nitrogen (C/N) sources has become an important factor for large-scale production. Investigations into the bioactivities and applications of PG and its related compounds have also been given increased attention. To save production cost, chitin and protein-containing fishery byproducts have recently been investigated as the sole C/N source for the production of PG and chitinolytic/proteolytic enzymes. This strategy provides an environmentally-friendly selection using inexpensive C/N sources to produce a high yield of PG together with chitinolytic and proteolytic enzymes by S. marcescens. The review article will provide effective references for production, bioactivity, and application of S. marcescens PG in various fields such as biocontrol agents and potential pharmaceutical drugs.
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Affiliation(s)
- San-Lang Wang
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Life Science Development Center, Tamkang University, New Taipei City 25137, Taiwan
| | - Van Bon Nguyen
- Institute of Research and Development, Duy Tan University, Danang 550000, Vietnam
| | - Chien Thang Doan
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam;
| | - Thi Ngoc Tran
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan; (C.T.D.); (T.N.T.)
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam;
| | - Minh Trung Nguyen
- Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam;
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam;
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