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Lammens EM, Volke DC, Schroven K, Voet M, Kerremans A, Lavigne R, Hendrix H. A SEVA-based, CRISPR-Cas3-assisted genome engineering approach for Pseudomonas with efficient vector curing. Microbiol Spectr 2023; 11:e0270723. [PMID: 37975669 PMCID: PMC10715078 DOI: 10.1128/spectrum.02707-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The CRISPR-Cas3 editing system as presented here facilitates the creation of genomic alterations in Pseudomonas putida and Pseudomonas aeruginosa in a straightforward manner. By providing the Cas3 system as a vector set with Golden Gate compatibility and different antibiotic markers, as well as by employing the established Standard European Vector Architecture (SEVA) vector set to provide the homology repair template, this system is flexible and can readily be ported to a multitude of Gram-negative hosts. Besides genome editing, the Cas3 system can also be used as an effective and universal tool for vector curing. This is achieved by introducing a spacer that targets the origin-of-transfer, present on the majority of established (SEVA) vectors. Based on this, the Cas3 system efficiently removes up to three vectors in only a few days. As such, this curing approach may also benefit other genomic engineering methods or remove naturally occurring plasmids from bacteria.
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Affiliation(s)
| | - Daniel Christophe Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kaat Schroven
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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Xia L, Wen J. Available strategies for improving the biosynthesis of surfactin: a review. Crit Rev Biotechnol 2023; 43:1111-1128. [PMID: 36001039 DOI: 10.1080/07388551.2022.2095252] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022]
Abstract
Surfactin is an excellent biosurfactant with a wide range of application prospects in many industrial fields. However, its low productivity and high cost have largely limited its commercial applications. In this review, the pathways for surfactin synthesis in Bacillus strains are summarized and discussed. Further, the latest strategies for improving surfactin production, including: medium optimization, genome engineering methods (rational genetic engineering, genome reduction, and genome shuffling), heterologous synthesis, and the use of synthetic biology combined with metabolic engineering approaches to construct high-quality artificial cells for surfactin production using xylose, are described. Finally, the prospects for improving surfactin synthesis are discussed in detail.
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Affiliation(s)
- Li Xia
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
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3
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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
| | | | - A. Loeschcke
- Institute of Molecular Enzyme Technology, Forschungszentrum Jülich, Heinrich Heine University Düsseldorf, Jülich, Germany
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Lammens EM, Feyaerts N, Kerremans A, Boon M, Lavigne R. Assessing the Orthogonality of Phage-Encoded RNA Polymerases for Tailored Synthetic Biology Applications in Pseudomonas Species. Int J Mol Sci 2023; 24:ijms24087175. [PMID: 37108338 PMCID: PMC10138996 DOI: 10.3390/ijms24087175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
The phage T7 RNA polymerase (RNAP) and lysozyme form the basis of the widely used pET expression system for recombinant expression in the biotechnology field and as a tool in microbial synthetic biology. Attempts to transfer this genetic circuitry from Escherichia coli to non-model bacterial organisms with high potential have been restricted by the cytotoxicity of the T7 RNAP in the receiving hosts. We here explore the diversity of T7-like RNAPs mined directly from Pseudomonas phages for implementation in Pseudomonas species, thus relying on the co-evolution and natural adaptation of the system towards its host. By screening and characterizing different viral transcription machinery using a vector-based system in P. putida., we identified a set of four non-toxic phage RNAPs from phages phi15, PPPL-1, Pf-10, and 67PfluR64PP, showing a broad activity range and orthogonality to each other and the T7 RNAP. In addition, we confirmed the transcription start sites of their predicted promoters and improved the stringency of the phage RNAP expression systems by introducing and optimizing phage lysozymes for RNAP inhibition. This set of viral RNAPs expands the adaption of T7-inspired circuitry towards Pseudomonas species and highlights the potential of mining tailored genetic parts and tools from phages for their non-model host.
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Affiliation(s)
- Eveline-Marie Lammens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Nathalie Feyaerts
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
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5
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Weihmann R, Kubicki S, Bitzenhofer NL, Domröse A, Bator I, Kirschen LM, Kofler F, Funk A, Tiso T, Blank LM, Jaeger KE, Drepper T, Thies S, Loeschcke A. The modular pYT vector series employed for chromosomal gene integration and expression to produce carbazoles and glycolipids in P. putida. FEMS MICROBES 2022; 4:xtac030. [PMID: 37333445 PMCID: PMC10117823 DOI: 10.1093/femsmc/xtac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 10/22/2023] Open
Abstract
The expression of biosynthetic genes in bacterial hosts can enable access to high-value compounds, for which appropriate molecular genetic tools are essential. Therefore, we developed a toolbox of modular vectors, which facilitate chromosomal gene integration and expression in Pseudomonas putida KT2440. To this end, we designed an integrative sequence, allowing customisation regarding the modes of integration (random, at attTn7, or into the 16S rRNA gene), promoters, antibiotic resistance markers as well as fluorescent proteins and enzymes as transcription reporters. We thus established a toolbox of vectors carrying integrative sequences, designated as pYT series, of which we present 27 ready-to-use variants along with a set of strains equipped with unique 'landing pads' for directing a pYT interposon into one specific copy of the 16S rRNA gene. We used genes of the well-described violacein biosynthesis as reporter to showcase random Tn5-based chromosomal integration leading to constitutive expression and production of violacein and deoxyviolacein. Deoxyviolacein was likewise produced after gene integration into the 16S rRNA gene of rrn operons. Integration in the attTn7 site was used to characterise the suitability of different inducible promoters and successive strain development for the metabolically challenging production of mono-rhamnolipids. Finally, to establish arcyriaflavin A production in P. putida for the first time, we compared different integration and expression modes, revealing integration at attTn7 and expression with NagR/PnagAa to be most suitable. In summary, the new toolbox can be utilised for the rapid generation of various types of P. putida expression and production strains.
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Affiliation(s)
- Robin Weihmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sonja Kubicki
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Andreas Domröse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Isabel Bator
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lisa-Marie Kirschen
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Franziska Kofler
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Aileen Funk
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Till Tiso
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lars M Blank
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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6
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Lammens EM, Boon M, Grimon D, Briers Y, Lavigne R. SEVAtile: a standardised DNA assembly method optimised for Pseudomonas. Microb Biotechnol 2021; 15:370-386. [PMID: 34651450 PMCID: PMC8719830 DOI: 10.1111/1751-7915.13922] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/29/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022] Open
Abstract
To meet the needs of synthetic biologists, DNA assembly methods have transformed from simple 'cut-and-paste' procedures to highly advanced, standardised assembly techniques. Implementing these standardised DNA assembly methods in biotechnological research conducted in non-model hosts, including Pseudomonas putida and Pseudomonas aeruginosa, could greatly benefit reproducibility and predictability of experimental results. SEVAtile is a Type IIs-based assembly approach, which enables the rapid and standardised assembly of genetic parts - or tiles - to create genetic circuits in the established SEVA-vector backbone. Contrary to existing DNA assembly methods, SEVAtile is an easy and straightforward method, which is compatible with any vector, both SEVA- and non-SEVA. To prove the efficiency of the SEVAtile method, a three-vector system was successfully generated to independently co-express three different proteins in P. putida and P. aeruginosa. More specifically, one of the vectors, pBGDes, enables genomic integration of assembled circuits in the Tn7 landing site, while self-replicatory vectors pSTDesX and pSTDesR enable inducible expression from the XylS/Pm and RhaRS/PrhaB expression systems, respectively. Together, we hope these vector systems will support research in both the microbial SynBio and Pseudomonas field.
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Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
| | - Dennis Grimon
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, Gent, 9000, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, Gent, 9000, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
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8
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Tiso T, Ihling N, Kubicki S, Biselli A, Schonhoff A, Bator I, Thies S, Karmainski T, Kruth S, Willenbrink AL, Loeschcke A, Zapp P, Jupke A, Jaeger KE, Büchs J, Blank LM. Integration of Genetic and Process Engineering for Optimized Rhamnolipid Production Using Pseudomonas putida. Front Bioeng Biotechnol 2020; 8:976. [PMID: 32974309 PMCID: PMC7468518 DOI: 10.3389/fbioe.2020.00976] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
Rhamnolipids are biosurfactants produced by microorganisms with the potential to replace synthetic compounds with petrochemical origin. To promote industrial use of rhamnolipids, recombinant rhamnolipid production from sugars needs to be intensified. Since this remains challenging, the aim of the presented research is to utilize a multidisciplinary approach to take a step toward developing a sustainable rhamnolipid production process. Here, we developed expression cassettes for stable integration of the rhamnolipid biosynthesis genes into the genome outperformed plasmid-based expression systems. Furthermore, the genetic stability of the production strain was improved by using an inducible promoter. To enhance rhamnolipid synthesis, energy- and/or carbon-consuming traits were removed: mutants negative for the synthesis of the flagellar machinery or the storage polymer PHA showed increased production by 50%. Variation of time of induction resulted in an 18% increase in titers. A scale-up from shake flasks was carried out using a 1-L bioreactor. By recycling of the foam, biomass loss could be minimized and a rhamnolipid titer of up to 1.5 g/L was achieved without using mechanical foam destroyers or antifoaming agents. Subsequent liquid-liquid extraction was optimized by using a suitable minimal medium during fermentation to reduce undesired interphase formation. A technical-scale production process was designed and evaluated by a life-cycle assessment (LCA). Different process chains and their specific environmental impact were examined. It was found that next to biomass supply, the fermentation had the biggest environmental impact. The present work underlines the need for multidisciplinary approaches to address the challenges associated with achieving sustainable production of microbial secondary metabolites. The results are discussed in the context of the challenges of microbial biosurfactant production using hydrophilic substrates on an industrial scale.
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Affiliation(s)
- Till Tiso
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Nina Ihling
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | - Sonja Kubicki
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Andreas Biselli
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Aachen, Germany
| | - Andreas Schonhoff
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Energy and Climate Research – Systems Analysis and Technology Evaluation (IEK-STE), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Isabel Bator
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stephan Thies
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Tobias Karmainski
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Sebastian Kruth
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anna-Lena Willenbrink
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Aachen, Germany
| | - Anita Loeschcke
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Petra Zapp
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Energy and Climate Research – Systems Analysis and Technology Evaluation (IEK-STE), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Andreas Jupke
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Aachen, Germany
| | - Karl-Erich Jaeger
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- Institute of Bio- and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jochen Büchs
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | - Lars M. Blank
- iAMB – Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, Jülich, Germany
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Loeschcke A, Thies S. Engineering of natural product biosynthesis in Pseudomonas putida. Curr Opin Biotechnol 2020; 65:213-224. [PMID: 32498036 DOI: 10.1016/j.copbio.2020.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/01/2020] [Accepted: 03/30/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Germany.
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Germany.
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Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications. Mar Drugs 2019; 17:md17070408. [PMID: 31323998 PMCID: PMC6669457 DOI: 10.3390/md17070408] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022] Open
Abstract
Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.
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Weihmann R, Domröse A, Drepper T, Jaeger KE, Loeschcke A. Protocols for yTREX/Tn5-based gene cluster expression in Pseudomonas putida. Microb Biotechnol 2019; 13:250-262. [PMID: 31162833 PMCID: PMC6922528 DOI: 10.1111/1751-7915.13402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/25/2019] [Accepted: 03/08/2019] [Indexed: 11/30/2022] Open
Abstract
Bacterial gene clusters, which represent a genetic treasure trove for secondary metabolite pathways, often need to be activated in a heterologous host to access the valuable biosynthetic products. We provide here a detailed protocol for the application of the yTREX ‘gene cluster transplantation tool’: Via yeast recombinational cloning, a gene cluster of interest can be cloned in the yTREX vector, which enables the robust conjugational transfer of the gene cluster to bacteria like Pseudomonas putida, and their subsequent transposon Tn5‐based insertion into the host chromosome. Depending on the gene cluster architecture and chromosomal insertion site, the respective pathway genes can be transcribed effectively from a chromosomal promoter, thereby enabling the biosynthesis of a natural product. We describe workflows for the design of a gene cluster expression cassette, cloning of the cassette in the yTREX vector by yeast recombineering, and subsequent transfer and expression in P. putida. As an example for yTREX‐based transplantation of a natural product biosynthesis, we provide details on the cloning and activation of the phenazine‐1‐carboxylic acid biosynthetic genes from Pseudomonas aeruginosa in P. putidaKT2440 as well as the use of β‐galactosidase‐encoding lacZ as a reporter of production levels.
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Affiliation(s)
- Robin Weihmann
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Andreas Domröse
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University, Düsseldorf, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
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