1
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Wynands B, Kofler F, Sieberichs A, da Silva N, Wierckx N. Engineering a Pseudomonas taiwanensis 4-coumarate platform for production of para-hydroxy aromatics with high yield and specificity. Metab Eng 2023; 78:115-127. [PMID: 37209862 PMCID: PMC10360455 DOI: 10.1016/j.ymben.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/26/2023] [Accepted: 05/16/2023] [Indexed: 05/22/2023]
Abstract
Aromatics are valuable bulk or fine chemicals with a myriad of important applications. Currently, their vast majority is produced from petroleum associated with many negative aspects. The bio-based synthesis of aromatics contributes to the much-required shift towards a sustainable economy. To this end, microbial whole-cell catalysis is a promising strategy allowing the valorization of abundant feedstocks derived from biomass to yield de novo-synthesized aromatics. Here, we engineered tyrosine-overproducing derivatives of the streamlined chassis strain Pseudomonas taiwanensis GRC3 for efficient and specific production of 4-coumarate and derived aromatics. This required pathway optimization to avoid the accumulation of tyrosine or trans-cinnamate as byproducts. Although application of tyrosine-specific ammonia-lyases prevented the formation of trans-cinnamate, they did not completely convert tyrosine to 4-coumarate, thereby displaying a significant bottleneck. The use of a fast but unspecific phenylalanine/tyrosine ammonia-lyase from Rhodosporidium toruloides (RtPAL) alleviated this bottleneck, but caused phenylalanine conversion to trans-cinnamate. This byproduct formation was greatly reduced through the reverse engineering of a point mutation in prephenate dehydratase domain-encoding pheA. This upstream pathway engineering enabled efficient 4-coumarate production with a specificity of >95% despite using an unspecific ammonia-lyase, without creating an auxotrophy. In shake flask batch cultivations, 4-coumarate yields of up to 21.5% (Cmol/Cmol) from glucose and 32.4% (Cmol/Cmol) from glycerol were achieved. Additionally, the product spectrum was diversified by extending the 4-coumarate biosynthetic pathway to enable the production of 4-vinylphenol, 4-hydroxyphenylacetate, and 4-hydroxybenzoate with yields of 32.0, 23.0, and 34.8% (Cmol/Cmol) from glycerol, respectively.
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Affiliation(s)
- Benedikt Wynands
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Franziska Kofler
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Anka Sieberichs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Nadine da Silva
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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2
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Hechard T, Wang H. Determination of Growth Rate and Virulence Plasmid Copy Number During Yersinia pseudotuberculosis Infection Using Droplet Digital PCR. Methods Mol Biol 2023; 2674:101-115. [PMID: 37258963 DOI: 10.1007/978-1-0716-3243-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pathogenic bacteria have evolved the ability to evade their host defenses and cause diseases. Virulence factors encompass a wide range of adaptations that allow pathogens to survive and proliferate in the hostile host environment during successful infection. In human pathogenic Yersinia species, the potent type III secretion system (T3SS) and other essential virulence factors are encoded on a virulence plasmid. Here, we investigated the bacterial growth rate and plasmid copy number following a Yersinia infection using droplet digital PCR (ddPCR). ddPCR is an exceptionally sensitive, highly precise, and cost-efficient method. It enables precise quantification even from very small amounts of target DNA. This method also enables analysis of complex samples with large amounts of interfering DNA, such as infected tissues or microbiome studies.
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Affiliation(s)
- Tifaine Hechard
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Helen Wang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
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3
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Enabling Ethanologenesis in Moorella thermoacetica through Construction of a Replicating Shuttle Vector. FERMENTATION 2022. [DOI: 10.3390/fermentation8110585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Replicating plasmid shuttle vectors are key tools for efficient genetic and metabolic engineering applications, allowing the development of sustainable bioprocesses using non-model organisms with unique metabolic capabilities. To date, very limited genetic manipulation has been achieved in the thermophilic acetogen, Moorella thermoacetica, partly due to the lack of suitable shuttle vectors. However, M. thermoacetica has considerable potential as an industrial chassis organism, which can only be unlocked if reliable and effective genetic tools are in place. This study reports the construction of a replicating shuttle vector for M. thermoacetica through the identification and implementation of a compatible Gram-positive replicon to allow plasmid maintenance within the host. Although characterisation of plasmid behaviour proved difficult, the designed shuttle vector was subsequently applied for ethanologenesis, i.e., ethanol production in this organism. The non-native ethanologenesis in M. thermoacetica was achieved via plasmid-borne overexpression of the native aldh gene and heterologous expression of Clostridium autoethanogenum adhE1 gene. This result demonstrates the importance of the developed replicating plasmid vector for genetic and metabolic engineering efforts in industrially important M. thermoacetica.
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4
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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5
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Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways. Essays Biochem 2021; 65:319-336. [PMID: 34223620 PMCID: PMC8314020 DOI: 10.1042/ebc20200173] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/01/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Biotechnological production in bacteria enables access to numerous valuable chemical compounds. Nowadays, advanced molecular genetic toolsets, enzyme engineering as well as the combinatorial use of biocatalysts, pathways, and circuits even bring new-to-nature compounds within reach. However, the associated substrates and biosynthetic products often cause severe chemical stress to the bacterial hosts. Species of the Pseudomonas clade thus represent especially valuable chassis as they are endowed with multiple stress response mechanisms, which allow them to cope with a variety of harmful chemicals. A built-in cell envelope stress response enables fast adaptations that sustain membrane integrity under adverse conditions. Further, effective export machineries can prevent intracellular accumulation of diverse harmful compounds. Finally, toxic chemicals such as reactive aldehydes can be eliminated by oxidation and stress-induced damage can be recovered. Exploiting and engineering these features will be essential to support an effective production of natural compounds and new chemicals. In this article, we therefore discuss major resistance strategies of Pseudomonads along with approaches pursued for their targeted exploitation and engineering in a biotechnological context. We further highlight strategies for the identification of yet unknown tolerance-associated genes and their utilisation for engineering next-generation chassis and finally discuss effective measures for pathway fine-tuning to establish stable cell factories for the effective production of natural compounds and novel biochemicals.
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6
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Köbbing S, Blank LM, Wierckx N. Characterization of Context-Dependent Effects on Synthetic Promoters. Front Bioeng Biotechnol 2020; 8:551. [PMID: 32596224 PMCID: PMC7303508 DOI: 10.3389/fbioe.2020.00551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/07/2020] [Indexed: 11/13/2022] Open
Abstract
Understanding the composability of genetic elements is central to synthetic biology. Even for seemingly well-known elements such as a sigma 70 promoter the genetic context-dependent variability of promoter activity remains poorly understood. The lack of understanding of sequence to function results in highly limited de novo design of novel genetic element combinations. To address this issue, we characterized in detail concatenated "stacked" synthetic promoters including varying spacer sequence lengths and compared the transcription strength to the output of the individual promoters. The proxy for promoter activity, the msfGFP synthesis from stacked promoters was consistently lower than expected from the sum of the activities of the single promoters. While the spacer sequence itself had no activity, it drastically affected promoter activities when placed up- or downstream of a promoter. Single promoter-spacer combinations revealed a bivalent effect on msfGFP synthesis. By systematic analysis of promoter and spacer combinations, a semi-empirical correlation was developed to determine the combined activity of stacked promoters.
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Affiliation(s)
- Sebastian Köbbing
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, Jülich, Germany
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7
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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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8
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Neves D, Vos S, Blank LM, Ebert BE. Pseudomonas mRNA 2.0: Boosting Gene Expression Through Enhanced mRNA Stability and Translational Efficiency. Front Bioeng Biotechnol 2020; 7:458. [PMID: 32039175 PMCID: PMC6993053 DOI: 10.3389/fbioe.2019.00458] [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: 09/29/2019] [Accepted: 12/19/2019] [Indexed: 11/14/2022] Open
Abstract
High gene expression of enzymes partaking in recombinant production pathways is a desirable trait among cell factories belonging to all different kingdoms of life. High enzyme abundance is generally aimed for by utilizing strong promoters, which ramp up gene transcription and mRNA levels. Increased protein abundance can alternatively be achieved by optimizing the expression on the post-transcriptional level. Here, we evaluated protein synthesis with a previously proposed optimized gene expression architecture, in which mRNA stability and translation initiation are modulated by genetic parts such as self-cleaving ribozymes and a bicistronic design, which have initially been described to support the standardization of gene expression. The optimized gene expression architecture was tested in Pseudomonas taiwanensis VLB120, a promising, novel microbial cell factory. The expression cassette was employed on a plasmid basis and after single genomic integration. We used three constitutive and two inducible promoters to drive the expression of two fluorescent reporter proteins and a short acetoin biosynthesis pathway. The performance was confronted with that of a traditional expression cassette harboring the same promoter and gene of interest but lacking the genetic parts for increased expression efficiency. The optimized expression cassette granted higher protein abundance independently of the expression basis or promoter used proving its value for applications requiring high protein abundance.
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Affiliation(s)
- Dário Neves
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Stefan Vos
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Birgitta E Ebert
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, QLD, Australia
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9
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Akkaya Ö, Arslan E. Biotransformation of 2,4-dinitrotoluene by the beneficial association of engineered Pseudomonas putida with Arabidopsis thaliana. 3 Biotech 2019; 9:408. [PMID: 31692640 DOI: 10.1007/s13205-019-1933-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/09/2019] [Indexed: 11/29/2022] Open
Abstract
2,4-dinitrotoluene (2,4-DNT) is a priority environmental xenobiotic pollutant which has toxic, mutagenic, and carcinogenic properties. Thus, its biodegradation by applying recent approaches such as taking advantage of plant-bacteria interactions is crucial. In this work, the genes from Burkholderia sp. R34, necessary for 2,4-DNT degradation, were integrated into wild-type Pseudomonas putida (P. putida) KT2440 genome, and this strain, named KT.DNT, was inoculated to soil in in vitro conditions. To estimate the disappearance of 2,4-DNT in contaminated soil, samples were taken from different time intervals, extracted and analyzed using high-performance liquid chromatography (HPLC). Biotransformation of 2,4-DNT increased gradually and the degradation in soil after 14-days of treatment with the bacterium was found to be the 97.1%, indicating that the engineered strain could be a remarkable candidate for in situ bioremediation of 2,4-DNT-contaminated sites. In addition, in vitro interaction of this bacterium with a model plant, Arabidopsis thaliana (A. thaliana), enhanced lateral root and root hair formation together with dry root weight. Moreover, the initial 2,4-DNT concentration was decreased to 68% within 2 h with the plant-associated KT.DNT in liquid culture. Hence, the usage of this bacterium with plants could also be a promising application for the 2,4-DNT biotransformation.
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Affiliation(s)
- Özlem Akkaya
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Ebru Arslan
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400 Kocaeli, Turkey
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10
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Otto M, Wynands B, Drepper T, Jaeger KE, Thies S, Loeschcke A, Blank LM, Wierckx N. Targeting 16S rDNA for Stable Recombinant Gene Expression in Pseudomonas. ACS Synth Biol 2019; 8:1901-1912. [PMID: 31298831 DOI: 10.1021/acssynbio.9b00195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ribosomal RNA (rRNA) operons have recently been identified as promising sites for chromosomal integration of genetic elements in Pseudomonas putida, a bacterium that has gained considerable popularity as a microbial cell factory. We have developed a tool for targeted integration of recombinant genes into the rRNA operons of various Pseudomonas strains, where the native context of the rRNA clusters enables effective transcription of heterologous genes. However, a sufficient translation of foreign mRNA transcriptionally fused to rRNA required optimization of RNA secondary structures, which was achieved utilizing synthetic ribozymes and a bicistronic design. The generated tool further enabled the characterization of the six rRNA promoter units of P. putida S12 under different growth conditions. The presence of multiple, almost identical rRNA operons in Pseudomonas also allowed the integration of multiple copies of heterologous genetic elements. The integration of two expression cassettes and the resulting disruption of rRNA units only moderately affects growth rates, and the constructs were highly stable over more than 160 generations.
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Affiliation(s)
- Maike Otto
- Institute of Applied Microbiology, RWTH Aachen University, 52074 Aachen, Germany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Benedikt Wynands
- Institute of Applied Microbiology, RWTH Aachen University, 52074 Aachen, Germany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology, RWTH Aachen University, 52074 Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology, RWTH Aachen University, 52074 Aachen, Germany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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11
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Lenzen C, Wynands B, Otto M, Bolzenius J, Mennicken P, Blank LM, Wierckx N. High-Yield Production of 4-Hydroxybenzoate From Glucose or Glycerol by an Engineered Pseudomonas taiwanensis VLB120. Front Bioeng Biotechnol 2019; 7:130. [PMID: 31245364 PMCID: PMC6581684 DOI: 10.3389/fbioe.2019.00130] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 05/14/2019] [Indexed: 12/19/2022] Open
Abstract
Aromatic compounds such as 4-hydroxybenzoic acid are broadly applied in industry for a myriad of applications used in everyday life. However, their industrial production currently relies heavily on fossil resources and involves environmentally unfriendly production conditions, thus creating the need for more sustainable biotechnological alternatives. In this study, synthetic biology was applied to metabolically engineer Pseudomonas taiwanensis VLB120 to produce 4-hydroxybenzoate from glucose, xylose, or glycerol as sole carbon sources. Genes encoding a 4-hydroxybenzoate production pathway were integrated into the host genome and the flux toward the central precursor tyrosine was enhanced by overexpressing genes encoding key enzymes of the shikimate pathway. The flux toward tryptophan biosynthesis was decreased by introducing a P290S point mutation in the trpE gene, and degradation pathways for 4-hydroxybenzoate, 4-hydroxyphenylpyruvate and 3-dehydroshikimate were knocked out. The resulting production strains were tailored for the utilization of glucose and glycerol through the rational modification of central carbon metabolism. In batch cultivations with a completely mineral medium, the best strain produced 1.37 mM 4-hydroxybenzoate from xylose with a C-mol yield of 8% and 3.3 mM from glucose with a C-mol yield of 19.0%. Using glycerol as a sole carbon source, the C-mol yield increased to 29.6%. To our knowledge, this is the highest yield achieved by any species in a fully mineral medium. In all, the efficient conversion of bio-based substrates into 4-hydroxybenzoate by these deeply engineered P. taiwanensis strains brings the renewable production of aromatics one step closer.
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Affiliation(s)
- Christoph Lenzen
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany
| | - Benedikt Wynands
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany.,Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
| | - Maike Otto
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany.,Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
| | - Johanna Bolzenius
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany
| | - Philip Mennicken
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology iAMB, RWTH Aachen University, Aachen, Germany.,Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
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12
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Volmer J, Lindmeyer M, Seipp J, Schmid A, Bühler B. Constitutively solvent‐tolerantPseudomonas taiwanensisVLB120∆C∆ttgVsupports particularly high‐styrene epoxidation activities when grown under glucose excess conditions. Biotechnol Bioeng 2019; 116:1089-1101. [DOI: 10.1002/bit.26924] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/17/2018] [Accepted: 01/06/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Jan Volmer
- Department of Biochemical and Chemical EngineeringTU Dortmund UniversityDortmund Germany
| | - Martin Lindmeyer
- Department of Biochemical and Chemical EngineeringTU Dortmund UniversityDortmund Germany
- Department of Solar MaterialsHelmholtz Centre for Environmental Research GmbH–UFZLeipzig Germany
| | - Julia Seipp
- Department of Biochemical and Chemical EngineeringTU Dortmund UniversityDortmund Germany
| | - Andreas Schmid
- Department of Solar MaterialsHelmholtz Centre for Environmental Research GmbH–UFZLeipzig Germany
| | - Bruno Bühler
- Department of Solar MaterialsHelmholtz Centre for Environmental Research GmbH–UFZLeipzig Germany
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13
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Haringa C, Mudde RF, Noorman HJ. From industrial fermentor to CFD-guided downscaling: what have we learned? Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Vaghchhipawala Z, Radke S, Nagy E, Russell ML, Johnson S, Gelvin SB, Gilbertson LA, Ye X. RepB C-terminus mutation of a pRi-repABC binary vector affects plasmid copy number in Agrobacterium and transgene copy number in plants. PLoS One 2018; 13:e0200972. [PMID: 30412579 PMCID: PMC6226153 DOI: 10.1371/journal.pone.0200972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/26/2018] [Indexed: 12/23/2022] Open
Abstract
A native repABC replication origin from pRiA4b was previously reported as a single copy plasmid in Agrobacterium tumefaciens and can improve the production of transgenic plants with a single copy insertion of transgenes when it is used in binary vectors for Agrobacterium-mediated transformation. A high copy pRi-repABC variant plasmid, pTF::Ri, which does not improve the frequency of single copy transgenic plants, has been reported in the literature. Sequencing the high copy pTF::Ri repABC operon revealed the presence of two mutations: one silent mutation and one missense mutation that changes a tyrosine to a histidine (Y299H) in a highly conserved area of the C-terminus of the RepB protein (RepBY299H). Reproducing these mutations in the wild-type pRi-repABC binary vector showed that Agrobacterium cells with the RepBY299H mutation grow faster on both solidified and in liquid medium, and have higher plasmid copy number as determined by ddPCR. In order to investigate the impact of the RepBY299H mutation on transformation and quality plant production, the RepBY299H mutated pRi-repABC binary vector was compared with the original wild-type pRi-repABC binary vector and a multi-copy oriV binary vector in canola transformation. Molecular analyses of the canola transgenic plants demonstrated that the multi-copy pRi-repABC with the RepBY299H mutation provides no advantage in generating high frequency single copy, backbone-free transgenic plants in comparison with the single copy wild-type pRi-repABC binary vector.
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Affiliation(s)
| | - Sharon Radke
- Woodland Campus, Monsanto Company, Woodland, CA, United States of America
| | - Ervin Nagy
- Monsanto Company, St. Louis, MO, United States of America
| | - Mary L. Russell
- Woodland Campus, Monsanto Company, Woodland, CA, United States of America
| | - Susan Johnson
- Monsanto Company, St. Louis, MO, United States of America
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
| | - Stanton B. Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
| | | | - Xudong Ye
- Monsanto Company, St. Louis, MO, United States of America
- * E-mail:
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15
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Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142-155. [DOI: 10.1016/j.ymben.2018.05.005] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
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16
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Lambrecht J, Schattenberg F, Harms H, Mueller S. Characterizing Microbiome Dynamics - Flow Cytometry Based Workflows from Pure Cultures to Natural Communities. J Vis Exp 2018. [PMID: 30059034 DOI: 10.3791/58033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The investigation of pure cultures and monitoring of microbial community dynamics is vital to understand and control natural ecosystems and technical applications driven by microorganisms. Next generation sequencing methods are widely utilized to resolve microbiomes, but they are generally resource and time intensive and deliver mostly qualitative information. Flow cytometric microbiome analysis does not suffer from those disadvantages and can provide relative subcommunity abundances and absolute cell numbers at-line. Although it does not deliver direct phylogenetic information, it can enhance the analysis depth and resolution of sequencing approaches. In sharp contrast to medical applications in both research and routine settings, flow cytometry is still not widely used for microbiome analysis. Missing information on sample preparation and data analysis pipelines may create an entry barrier for the researchers facing microbiome analysis challenges that would often be textbook flow cytometry applications. Here, we present three comprehensive workflows for pure cultures, complex communities in clear medium and complex communities in challenging matrices, respectively. We describe individual sampling and fixation procedures and optimized staining protocols for the respective sample sets. We elaborate the cytometric analysis with a complex research centered and an application focused bench top device, describe the cell sorting procedure and suggest data analysis packages. We furthermore propose important experimental controls and apply the presented workflows to the respective sample sets.
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Affiliation(s)
- Johannes Lambrecht
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ
| | - Florian Schattenberg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ
| | - Susann Mueller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ;
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17
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Rouzeau C, Dagkesamanskaya A, Langer K, Bibette J, Baudry J, Pompon D, Anton-Leberre V. Adaptive response of yeast cells to triggered toxicity of phosphoribulokinase. Res Microbiol 2018; 169:335-342. [PMID: 29964131 DOI: 10.1016/j.resmic.2018.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 11/26/2022]
Abstract
Adjustment of plasmid copy number resulting from the balance between positive and negative impacts of borne synthetic genes, plays a critical role in the global efficiency of multistep metabolic engineering. Differential expression of co-expressed engineered genes is frequently observed depending on growth phases, metabolic status and triggered adjustments of plasmid copy numbers, constituting a dynamic process contributing to minimize global engineering burden. A yeast model involving plasmid based expression of phosphoribulokinase (PRKp), a key enzyme for the reconstruction of synthetic Calvin cycle, was designed to gain further insights into such a mechanism. A conditional PRK expression cassette was cloned either onto a low (ARS-CEN based) or a high (2-micron origin based) copy number plasmid using complementation of a trp1 genomic mutation as constant positive selection. Evolution of plasmid copy numbers, PRKp expressions, and cell growth rates were dynamically monitored following gene de-repression through external doxycycline concentration shifts. In the absence of RubisCO encoding gene permitting metabolic recycling, PRKp expression that led to depletion of ribulose phosphate, a critical metabolite for aromatic amino-acids biosynthesis, and accumulation of the dead-end diphosphate product contribute to toxicity. Triggered copy number adjustment was found to be a dynamic process depending both on plasmid types and levels of PRK induction. With the ARS-CEN plasmid, cell growth was abruptly affected only when level PRKp expression exceeded a threshold value. In contrast, a proportional relationship was observed with the 2-micron plasmid consistent with large copy number adjustments. Micro-compartment partitioning of bulk cultures by embedding individual cells into inverse culture medium/oil droplets, revealed the presence of slow and fast growing subpopulations that differ in relative proportions for low and high copy number plasmids.
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Affiliation(s)
| | | | - Krzysztof Langer
- Laboratoire Colloïdes et Matériaux Divisés, From the Institute of Chemistry, Biology and Innovation (CBI), ESPCI ParisTech, CNRS, UMR 8231, PSL Research University, 10 rue Vauquelin, 75005, Paris, France
| | - Jérôme Bibette
- Laboratoire Colloïdes et Matériaux Divisés, From the Institute of Chemistry, Biology and Innovation (CBI), ESPCI ParisTech, CNRS, UMR 8231, PSL Research University, 10 rue Vauquelin, 75005, Paris, France
| | - Jean Baudry
- Laboratoire Colloïdes et Matériaux Divisés, From the Institute of Chemistry, Biology and Innovation (CBI), ESPCI ParisTech, CNRS, UMR 8231, PSL Research University, 10 rue Vauquelin, 75005, Paris, France
| | - Denis Pompon
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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18
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Abundances of Clinically Relevant Antibiotic Resistance Genes and Bacterial Community Diversity in the Weihe River, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040708. [PMID: 29642605 PMCID: PMC5923750 DOI: 10.3390/ijerph15040708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/30/2018] [Accepted: 04/07/2018] [Indexed: 12/17/2022]
Abstract
The spread of antibiotic resistance genes in river systems is an emerging environmental issue due to their potential threat to aquatic ecosystems and public health. In this study, we used droplet digital polymerase chain reaction (ddPCR) to evaluate pollution with clinically relevant antibiotic resistance genes (ARGs) at 13 monitoring sites along the main stream of the Weihe River in China. Six clinically relevant ARGs and a class I integron-integrase (intI1) gene were analyzed using ddPCR, and the bacterial community was evaluated based on the bacterial 16S rRNA V3–V4 regions using MiSeq sequencing. The results indicated Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes as the dominant phyla in the water samples from the Weihe River. Higher abundances of blaTEM, strB, aadA, and intI1 genes (103 to 105 copies/mL) were detected in the surface water samples compared with the relatively low abundances of strA, mecA, and vanA genes (0–1.94 copies/mL). Eight bacterial genera were identified as possible hosts of the intI1 gene and three ARGs (strA, strB, and aadA) based on network analysis. The results suggested that the bacterial community structure and horizontal gene transfer were associated with the variations in ARGs.
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19
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Characterization of Four Novel Plasmids from Lactobacillus plantarum BM4. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.12894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Binder D, Drepper T, Jaeger KE, Delvigne F, Wiechert W, Kohlheyer D, Grünberger A. Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity. Metab Eng 2017. [DOI: 10.1016/j.ymben.2017.06.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Delvigne F, Baert J, Sassi H, Fickers P, Grünberger A, Dusny C. Taking control over microbial populations: Current approaches for exploiting biological noise in bioprocesses. Biotechnol J 2017; 12. [PMID: 28544731 DOI: 10.1002/biot.201600549] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 01/19/2023]
Abstract
Phenotypic plasticity of microbial cells has attracted much attention and several research efforts have been dedicated to the description of methods aiming at characterizing phenotypic heterogeneity and its impact on microbial populations. However, different approaches have also been suggested in order to take benefit from noise in a bioprocess perspective, e.g. by increasing the robustness or productivity of a microbial population. This review is dedicated to outline these controlling methods. A common issue, that has still to be addressed, is the experimental identification and the mathematical expression of noise. Indeed, the effective interfacing of microbial physiology with external parameters that can be used for controlling physiology depends on the acquisition of reliable signals. Latest technologies, like single cell microfluidics and advanced flow cytometric approaches, enable linking physiology, noise, heterogeneity in productive microbes with environmental cues and hence allow correctly mapping and predicting biological behavior via mathematical representations. However, like in the field of electronics, signals are perpetually subjected to noise. If appropriately interpreted, this noise can give an additional insight into the behavior of the individual cells within a microbial population of interest. This review focuses on recent progress made at describing, treating and exploiting biological noise in the context of microbial populations used in various bioprocess applications.
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Affiliation(s)
- Frank Delvigne
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Jonathan Baert
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Hosni Sassi
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Patrick Fickers
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Alexander Grünberger
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
| | - Christian Dusny
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
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22
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Quantification of Plasmid Copy Number with Single Colour Droplet Digital PCR. PLoS One 2017; 12:e0169846. [PMID: 28085908 PMCID: PMC5234771 DOI: 10.1371/journal.pone.0169846] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/23/2016] [Indexed: 11/19/2022] Open
Abstract
Bacteria can be considered as biological nanofactories that manufacture a cornucopia of bioproducts most notably recombinant proteins. As such, they must perfectly match with appropriate plasmid vectors to ensure successful overexpression of target genes. Among many parameters that correlate positively with protein productivity plasmid copy number plays pivotal role. Therefore, development of new and more accurate methods to assess this critical parameter will result in optimization of expression of plasmid-encoded genes. In this study, we present a simple and highly accurate method for quantifying plasmid copy number utilizing an EvaGreen single colour, droplet digital PCR. We demonstrate the effectiveness of this method by examining the copy number of the pBR322 vector within Escherichia coli DH5α cells. The obtained results were successfully validated by real-time PCR. However, we observed a strong dependency of the plasmid copy number on the method chosen for isolation of the total DNA. We found that application of silica-membrane-based columns for DNA purification or DNA isolation with use of bead-beating, a mechanical cell disruption lead to determination of an average of 20.5 or 7.3 plasmid copies per chromosome, respectively. We found that recovery of the chromosomal DNA from purification columns was less efficient than plasmid DNA (46.5 ± 1.9% and 87.4 ± 5.5%, respectively) which may lead to observed differences in plasmid copy number. Besides, the plasmid copy number variations dependent on DNA template isolation method, we found that droplet digital PCR is a very convenient method for measuring bacterial plasmid content. Careful determination of plasmid copy number is essential for better understanding and optimization of recombinant proteins production process. Droplet digital PCR is a very precise method that allows performing thousands of individual PCR reactions in a single tube. The ddPCR does not depend on running standard curves and is a straightforward and reliable method to quantify the plasmid copy number. Therefore we believe that the ddPCR designed in this study will be widely used for any plasmid copy number calculation in the future.
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23
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Jahn M, Vorpahl C, Hübschmann T, Harms H, Müller S. Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR. Microb Cell Fact 2016; 15:211. [PMID: 27993152 PMCID: PMC5168713 DOI: 10.1186/s12934-016-0610-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/02/2016] [Indexed: 12/31/2022] Open
Abstract
Background Plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. Constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (PCN) and stability are rarely known. The crucial factor determining the PCN is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the Standard European Vector Architecture (SEVA). Results In this study, the PCN was determined in a set of seven SEVA-based expression plasmids only differing in the replication system. The average PCN for all constructs was determined by Droplet Digital PCR and ranged between 2 and 40 per chromosome in the host organism Escherichia coli. Furthermore, a plasmid-encoded EGFP reporter protein served as a means to assess variability in reporter gene expression on the single cell level. Only cells with one type of plasmid (RSF1010 replication system) showed a high degree of heterogeneity with a clear bimodal distribution of EGFP intensity while the others showed a normal distribution. The heterogeneous RSF1010-carrying cell population and one normally distributed population (ColE1 replication system) were further analyzed by sorting cells of sub-populations selected according to EGFP intensity. For both plasmids, low and highly fluorescent sub-populations showed a remarkable difference in PCN, ranging from 9.2 to 123.4 for ColE1 and from 0.5 to 11.8 for RSF1010, respectively. Conclusions The average PCN determined here for a set of standardized plasmids was generally at the lower end of previously reported ranges and not related to the degree of heterogeneity. Further characterization of a heterogeneous and a homogeneous population demonstrated considerable differences in the PCN of sub-populations. We therefore present direct molecular evidence that the average PCN does not represent the true number of plasmid molecules in individual cells. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0610-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Jahn
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.,School of Biotechnology, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Carsten Vorpahl
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Susann Müller
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
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24
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Tian H, Sun Y, Liu C, Duan X, Tang W, Li Z. Precise Quantitation of MicroRNA in a Single Cell with Droplet Digital PCR Based on Ligation Reaction. Anal Chem 2016; 88:11384-11389. [DOI: 10.1021/acs.analchem.6b01225] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hui Tian
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Yuanyuan Sun
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Chenghui Liu
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Xinrui Duan
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Wei Tang
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
| | - Zhengping Li
- Key laboratory of Analytical
Chemistry for Life Science of Shaanxi Province, School of Chemistry
and Chemical Engineering, Shaanxi Normal University, 620 Xi Chang’an
Street, Xi’an, Shaanxi 710119, P. R. China
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25
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Nakashoji Y, Tanaka H, Tsukagoshi K, Hashimoto M. A poly(dimethylsiloxane) microfluidic sheet reversibly adhered on a glass plate for creation of emulsion droplets for droplet digital PCR. Electrophoresis 2016; 38:296-304. [DOI: 10.1002/elps.201600309] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/21/2016] [Accepted: 08/21/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Yuta Nakashoji
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Hironari Tanaka
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Kazuhiko Tsukagoshi
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering; Doshisha University; Kyotanabe Kyoto Japan
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26
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Bydlinski N, Harreither E, Baumann M. The 6th International Conference on Analysis of Microbial Cells at the Single Cell Level, Retz, Austria, 19-22 July 2015. N Biotechnol 2016; 34:S1871-6784(15)00277-0. [PMID: 26772727 DOI: 10.1016/j.nbt.2015.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 12/01/2022]
Abstract
The 6th International Conference on Analysis of Microbial Cells at the Single Cell Level, held in Retz, Austria from 19 to 22 July 2015, brought together experts from different areas working with bacterial, yeast and mammalian cell systems. The conference highlighted the importance of dissecting cell behaviour down to the single cell level, as analysis of mixed populations can obscure crucial cell-to-cell variations. The sessions covered advances in the fields of image analysis and microscopy, flow cytometry and cell sorting as well as bioinformatics, including recent developments and new applications of existing tools. In addition, a high speed poster slam session contributed to the lively discussions and exchange of expertise among academic and industrial researchers.
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Affiliation(s)
- Nina Bydlinski
- University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, Vienna 1190, Austria
| | - Eva Harreither
- University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, Vienna 1190, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, Vienna 1190, Austria.
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27
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Arnfinnsdottir NB, Bjørkøy AV, Lale R, Sletmoen M. Heterogeneity in GFP expression in isogenic populations of P. putida KT2440 investigated using flow cytometry and bacterial microarrays. RSC Adv 2016. [DOI: 10.1039/c5ra23757b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fluorescence intensities were determined using both flow cytometry and bacterial microarrays for Pseudomonas putida expressing GFP upon addition of an inducer. Fluorescence micrographs revealed static inter-cell differences in fluorescence emission.
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Affiliation(s)
- N. B. Arnfinnsdottir
- Biophysics and Medical Technology
- Department of Physics
- Norwegian University of Science and Technology
- NO-7491 Trondheim
- Norway
| | - A. V. Bjørkøy
- Biophysics and Medical Technology
- Department of Physics
- Norwegian University of Science and Technology
- NO-7491 Trondheim
- Norway
| | - R. Lale
- Department of Biotechnology
- Norwegian University of Science and Technology
- NO-7491 Trondheim
- Norway
| | - M. Sletmoen
- Department of Biotechnology
- Norwegian University of Science and Technology
- NO-7491 Trondheim
- Norway
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28
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Zobel S, Benedetti I, Eisenbach L, de Lorenzo V, Wierckx N, Blank LM. Tn7-Based Device for Calibrated Heterologous Gene Expression in Pseudomonas putida. ACS Synth Biol 2015; 4:1341-51. [PMID: 26133359 DOI: 10.1021/acssynbio.5b00058] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The soil bacterium Pseudomonas putida is increasingly attracting considerable interest as a platform for advanced metabolic engineering through synthetic biology approaches. However, genomic context, gene copy number, and transcription/translation interplay often introduce considerable uncertainty to the design of reliable genetic constructs. In this work, we have established a standardized heterologous expression device in which the promoter strength is the only variable; the remaining parameters of the flow have stable default values. To this end, we tailored a mini-Tn7 delivery transposon vector that inserts the constructs in a single genomic locus of P. putida's chromosome. This was then merged with a promoter insertion site, an unvarying translational coupler, and a downstream location for placing the gene(s) of interest under fixed assembly rules. This arrangement was exploited to benchmark a collection of synthetic promoters with low transcriptional noise in this bacterial host. Growth experiments and flow cytometry with single-copy promoter-GFP constructs revealed a robust, constitutive behavior of these promoters, whose strengths and properties could be faithfully compared. This standardized expression device significantly extends the repertoire of tools available for reliable metabolic engineering and other genetic enhancements of P. putida.
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Affiliation(s)
- Sebastian Zobel
- Institute
of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ilaria Benedetti
- Systems
Biology Program, Centro Nacional de Biotecnologia, CSIC, C/Darwin, 3 (Campus
de Cantoblanco), Madrid 28049, Spain
| | - Lara Eisenbach
- Institute
of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Victor de Lorenzo
- Systems
Biology Program, Centro Nacional de Biotecnologia, CSIC, C/Darwin, 3 (Campus
de Cantoblanco), Madrid 28049, Spain
| | - Nick Wierckx
- Institute
of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lars M. Blank
- Institute
of Applied Microbiology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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29
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A microfluidic droplet digital PCR for simultaneous detection of pathogenic Escherichia coli O157 and Listeria monocytogenes. Biosens Bioelectron 2015; 74:770-7. [DOI: 10.1016/j.bios.2015.07.016] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 06/30/2015] [Accepted: 07/08/2015] [Indexed: 01/08/2023]
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30
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Lieder S, Jahn M, Koepff J, Müller S, Takors R. Environmental stress speeds up DNA replication inPseudomonas putidain chemostat cultivations. Biotechnol J 2015; 11:155-63. [DOI: 10.1002/biot.201500059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 06/10/2015] [Accepted: 08/04/2015] [Indexed: 01/31/2023]
Affiliation(s)
- Sarah Lieder
- Institute for Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Michael Jahn
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Joachim Koepff
- Institute for Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Susann Müller
- Department of Environmental Microbiology; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Ralf Takors
- Institute for Biochemical Engineering; University of Stuttgart; Stuttgart Germany
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31
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Lindmeyer M, Jahn M, Vorpahl C, Müller S, Schmid A, Bühler B. Variability in subpopulation formation propagates into biocatalytic variability of engineered Pseudomonas putida strains. Front Microbiol 2015; 6:1042. [PMID: 26483771 PMCID: PMC4589675 DOI: 10.3389/fmicb.2015.01042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/14/2015] [Indexed: 01/01/2023] Open
Abstract
Pivotal challenges in industrial biotechnology are the identification and overcoming of cell-to-cell heterogeneity in microbial processes. While the development of subpopulations of isogenic cells in bioprocesses is well described (intra-population variability), a possible variability between genetically identical cultures growing under macroscopically identical conditions (clonal variability) is not. A high such clonal variability has been found for the recombinant expression of the styrene monooxygenase genes styAB from Pseudomonas taiwanensis VLB120 in solvent-tolerant Pseudomonas putida DOT-T1E using the alk-regulatory system from P. putida GPo1. In this study, the oxygenase subunit StyA fused to eGFP was used as readout tool to characterize the population structure in P. putida DOT-T1E regarding recombinant protein content. Flow cytometric analyses revealed that in individual cultures, at least two subpopulations with highly differing recombinant StyA-eGFP protein contents appeared (intra-population variability). Interestingly, subpopulation sizes varied from culture-to-culture correlating with the specific styrene epoxidation activity of cells derived from respective cultures (clonal variability). In addition, flow cytometric cell sorting coupled to plasmid copy number (PCN) determination revealed that detected clonal variations cannot be correlated to the PCN, but depend on the combination of the regulatory system and the host strain employed. This is, to the best of our knowledge, the first work reporting that intra-population variability (with differing protein contents in the presented case study) causes clonal variability of genetically identical cultures. Respective impacts on bioprocess reliability and performance and strategies to overcome respective reliability issues are discussed.
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Affiliation(s)
- Martin Lindmeyer
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University Dortmund, Germany
| | - Michael Jahn
- Helmholtz Centre for Environmental Research - UFZ, Department for Environmental Microbiology Leipzig, Germany
| | - Carsten Vorpahl
- Helmholtz Centre for Environmental Research - UFZ, Department for Environmental Microbiology Leipzig, Germany
| | - Susann Müller
- Helmholtz Centre for Environmental Research - UFZ, Department for Environmental Microbiology Leipzig, Germany
| | - Andreas Schmid
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University Dortmund, Germany ; Helmholtz Centre for Environmental Research - UFZ, Department of Solar Materials Leipzig, Germany
| | - Bruno Bühler
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University Dortmund, Germany ; Helmholtz Centre for Environmental Research - UFZ, Department of Solar Materials Leipzig, Germany
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32
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The dynamic influence of cells on the formation of stable emulsions in organic–aqueous biotransformations. ACTA ACUST UNITED AC 2015; 42:1011-26. [DOI: 10.1007/s10295-015-1621-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/10/2015] [Indexed: 10/23/2022]
Abstract
Abstract
Emulsion stability plays a crucial role for mass transfer and downstream processing in organic–aqueous bioprocesses based on whole microbial cells. In this study, emulsion stability dynamics and the factors determining them during two-liquid phase biotransformation were investigated for stereoselective styrene epoxidation catalyzed by recombinant Escherichia coli. Upon organic phase addition, emulsion stability rapidly increased correlating with a loss of solubilized protein from the aqueous cultivation broth and the emergence of a hydrophobic cell fraction associated with the organic–aqueous interface. A novel phase inversion-based method was developed to isolate and analyze cellular material from the interface. In cell-free experiments, a similar loss of aqueous protein did not correlate with high emulsion stability, indicating that the observed particle-based emulsions arise from a convergence of factors related to cell density, protein adsorption, and bioreactor conditions. During styrene epoxidation, emulsion destabilization occurred correlating with product-induced cell toxification. For biphasic whole-cell biotransformations, this study indicates that control of aqueous protein concentrations and selective toxification of cells enables emulsion destabilization and emphasizes that biological factors and related dynamics must be considered in the design and modeling of respective upstream and especially downstream processes.
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Jahn M, Günther S, Müller S. Non-random distribution of macromolecules as driving forces for phenotypic variation. Curr Opin Microbiol 2015; 25:49-55. [DOI: 10.1016/j.mib.2015.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/04/2015] [Accepted: 04/21/2015] [Indexed: 12/19/2022]
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Volmer J, Schmid A, Bühler B. Guiding bioprocess design by microbial ecology. Curr Opin Microbiol 2015; 25:25-32. [DOI: 10.1016/j.mib.2015.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/26/2015] [Accepted: 02/26/2015] [Indexed: 12/20/2022]
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Lindmeyer M, Meyer D, Kuhn D, Bühler B, Schmid A. Making variability less variable: matching expression system and host for oxygenase-based biotransformations. ACTA ACUST UNITED AC 2015; 42:851-66. [DOI: 10.1007/s10295-015-1615-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/26/2015] [Indexed: 01/11/2023]
Abstract
Abstract
Variability in whole-cell biocatalyst performance represents a critical aspect for stable and productive bioprocessing. In order to investigate whether and how oxygenase-catalyzed reactions are affected by such variability issues in solvent-tolerant Pseudomonas, different inducers, expression systems, and host strains were tested for the reproducibility of xylene and styrene monooxygenase catalyzed hydroxylation and epoxidation reactions, respectively. Significantly higher activity variations were found for biocatalysts based on solvent-tolerant Pseudomonas putida DOT-TIE and S12 compared with solvent-sensitive P. putida KT2440, Escherichia coli JM101, and solvent-tolerant Pseudomonas taiwanensis VLB120. Specific styrene epoxidation rates corresponded to cellular styrene monooxygenase contents. Detected variations in activity strictly depended on the type of regulatory system employed, being high with the alk- and low with the lac-system. These results show that the occurrence of clonal variability in recombinant gene expression in Pseudomonas depends on the combination of regulatory system and host strain, does not correlate with a general phenotype such as solvent tolerance, and must be evaluated case by case.
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Affiliation(s)
- Martin Lindmeyer
- grid.5675.1 0000000104169637 Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering TU Dortmund University Emil-Figge-Strasse 66 44227 Dortmund Germany
| | - Daniel Meyer
- grid.5675.1 0000000104169637 Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering TU Dortmund University Emil-Figge-Strasse 66 44227 Dortmund Germany
- grid.5801.c 0000000121562780 Department of Biosystems Science and Engineering ETH Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Daniel Kuhn
- grid.5675.1 0000000104169637 Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering TU Dortmund University Emil-Figge-Strasse 66 44227 Dortmund Germany
- grid.419481.1 0000 0001 1515 9979 ESBATech, a Novartis company Wagistrasse 12 8952 Zürich-Schlieren Switzerland
| | - Bruno Bühler
- grid.5675.1 0000000104169637 Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering TU Dortmund University Emil-Figge-Strasse 66 44227 Dortmund Germany
- grid.7492.8 0000000404923830 Department Solar Materials Center for Environmental Research - UFZ GmbH Permoser Strasse 15 04318 Leipzig Germany
| | - Andreas Schmid
- grid.5675.1 0000000104169637 Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering TU Dortmund University Emil-Figge-Strasse 66 44227 Dortmund Germany
- grid.7492.8 0000000404923830 Department Solar Materials Center for Environmental Research - UFZ GmbH Permoser Strasse 15 04318 Leipzig Germany
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