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Sachs CC, Koepff J, Wiechert W, Grünberger A, Nöh K. mycelyso - high-throughput analysis of Streptomyces mycelium live cell imaging data. BMC Bioinformatics 2019; 20:452. [PMID: 31484491 PMCID: PMC6727546 DOI: 10.1186/s12859-019-3004-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/13/2019] [Indexed: 11/19/2022] Open
Abstract
Background Streptomycetes are filamentous microorganisms of high biotechnological relevance, especially for the production of antibiotics. In submerged cultures, the productivity of these microorganisms is closely linked to their growth morphology. Microfluidic lab-on-a-chip cultivation systems, coupled with automated time-lapse imaging, generate spatio-temporal insights into the mycelium development of streptomycetes, therewith extending the biotechnological toolset by spatio-temporal screening under well-controlled and reproducible conditions. However, the analysis of the complex mycelial structure formation is limited by the extent of manual interventions required during processing of the acquired high-volume image data. These interventions typically lead to high evaluation times and, therewith, limit the analytic throughput and exploitation of microfluidic-based screenings. Results We present the tool mycelyso (MYCElium anaLYsis SOftware), an image analysis system tailored to fully automated hyphae-level processing of image stacks generated by time-lapse microscopy. With mycelyso, the developing hyphal streptomycete network is automatically segmented and tracked over the cultivation period. Versatile key growth parameters such as mycelium network structure, its development over time, and tip growth rates are extracted. Results are presented in the web-based exploration tool mycelyso Inspector, allowing for user friendly quality control and downstream evaluation of the extracted information. In addition, 2D and 3D visualizations show temporal tracking for detailed inspection of morphological growth behaviors. For ease of getting started with mycelyso, bundled Windows packages as well as Docker images along with tutorial videos are available. Conclusion mycelyso is a well-documented, platform-independent open source toolkit for the automated end-to-end analysis of Streptomyces image stacks. The batch-analysis mode facilitates the rapid and reproducible processing of large microfluidic screenings, and easy extraction of morphological parameters. The objective evaluation of image stacks is possible by reproducible evaluation workflows, useful to unravel correlations between morphological, molecular and process parameters at the hyphae- and mycelium-levels with statistical power. Electronic supplementary material The online version of this article (10.1186/s12859-019-3004-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christian Carsten Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Joachim Koepff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, 52074, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany.,Multiscale Bioengineering, Bielefeld University, Universitätsstr. 25, Bielefeld, 33615, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Str., Jülich, 52425, Germany.
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Tsolis KC, Hamed MB, Simoens K, Koepff J, Busche T, Rückert C, Oldiges M, Kalinowski J, Anné J, Kormanec J, Bernaerts K, Karamanou S, Economou A. Secretome Dynamics in a Gram-Positive Bacterial Model. Mol Cell Proteomics 2019; 18:423-436. [PMID: 30498012 PMCID: PMC6398212 DOI: 10.1074/mcp.ra118.000899] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/21/2018] [Indexed: 12/11/2022] Open
Abstract
Protein secretion is a central biological process in all organisms. Most studies dissecting bacterial secretion mechanisms have focused on Gram-negative cell envelopes such as that of Escherichia coli However, proteomics analyses in Gram negatives is hampered by their outer membrane. Here we studied protein secretion in the Gram-positive bacterium Streptomyces lividans TK24, in which most of the secretome is released in the growth medium. We monitored changes of the secretome as a function of growth phase and medium. We determined distinct protein classes of "house-keeping" secreted proteins that do not change their appearance or abundance in the various media and growth phases. These comprise mainly enzymes involved in cell wall maintenance and basic transport. In addition, we detected significant abundance and content changes to a sub-set of the proteome, as a function of growth in the different media. These did not depend on the media being minimal or rich. Transcriptional regulation but not changes in export machinery components can explain some of these changes. However, additional downstream mechanisms must be important for selective secretome funneling. These observations lay the foundations of using S. lividans as a model organism to study how metabolism is linked to optimal secretion and help develop rational optimization of heterologous protein production.
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Affiliation(s)
- Konstantinos C Tsolis
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium
| | - Mohamed Belal Hamed
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium
- ‡‡Molecular Biology Dpt, National Research Centre, Dokki, Giza, Egypt
| | - Kenneth Simoens
- §KU Leuven, Bio- & chemical systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Joachim Koepff
- ¶Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Leo-Brandt-Straβe, 52428, Jülich, Germany
| | - Tobias Busche
- ‖Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- **Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Christian Rückert
- ‖Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Marco Oldiges
- ¶Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Leo-Brandt-Straβe, 52428, Jülich, Germany
| | - Jörn Kalinowski
- ‖Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jozef Anné
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium
| | - Jan Kormanec
- §§Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 84551 Bratislava, Slovakia
| | - Kristel Bernaerts
- §KU Leuven, Bio- & chemical systems Technology, Reactor Engineering and Safety Section, Department of Chemical Engineering, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Spyridoula Karamanou
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium
| | - Anastassios Economou
- From the ‡KU Leuven, Rega Institute, Dpt of Microbiology and Immunology, Herestraat 49, B-3000 Leuven, Belgium;
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Rebets Y, Tsolis KC, Guðmundsdóttir EE, Koepff J, Wawiernia B, Busche T, Bleidt A, Horbal L, Myronovskyi M, Ahmed Y, Wiechert W, Rückert C, Hamed MB, Bilyk B, Anné J, Friðjónsson Ó, Kalinowski J, Oldiges M, Economou A, Luzhetskyy A. Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions. Front Microbiol 2018; 9:3033. [PMID: 30619125 PMCID: PMC6295645 DOI: 10.3389/fmicb.2018.03033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/23/2018] [Indexed: 12/15/2022] Open
Abstract
Alternative sigma factors control numerous aspects of bacterial life, including adaptation to physiological stresses, morphological development, persistence states and virulence. This is especially true for the physiologically complex actinobacteria. Here we report the development of a robust gene deletions system for Streptomyces lividans TK24 based on a BAC library combined with the λ-Red recombination technique. The developed system was validated by systematically deleting the most highly expressed genes encoding alternative sigma factors and several other regulatory genes within the chromosome of S. lividans TK24. To demonstrate the possibility of large scale genomic manipulations, the major part of the undecylprodigiosin gene cluster was deleted as well. The resulting mutant strains were characterized in terms of morphology, growth parameters, secondary metabolites production and response to thiol-oxidation and cell-wall stresses. Deletion of SLIV_12645 gene encoding S. coelicolor SigR1 ortholog has the most prominent phenotypic effect, resulted in overproduction of actinorhodin and coelichelin P1 and increased sensitivity to diamide. The secreted proteome analysis of SLIV_12645 mutant revealed SigR1 influence on trafficking of proteins involved in cell wall biogenesis and refactoring. The reported here gene deletion system will further facilitate work on S. lividans strain improvement as a host for either secondary metabolites or protein production and will contribute to basic research in streptomycetes physiology, morphological development, secondary metabolism. On the other hand, the systematic deletion of sigma factors encoding genes demonstrates the complexity and conservation of regulatory processes conducted by sigma factors in streptomycetes.
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Affiliation(s)
- Yuriy Rebets
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | | | - Joachim Koepff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | | | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Arne Bleidt
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Liliya Horbal
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Yousra Ahmed
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Mohamed B. Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Molecular Biology, National Research Centre, Giza, Egypt
| | - Bohdan Bilyk
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
- Actinobacteria Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
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Hamed MB, Vrancken K, Bilyk B, Koepff J, Novakova R, van Mellaert L, Oldiges M, Luzhetskyy A, Kormanec J, Anné J, Karamanou S, Economou A. Monitoring Protein Secretion in Streptomyces Using Fluorescent Proteins. Front Microbiol 2018; 9:3019. [PMID: 30581427 PMCID: PMC6292873 DOI: 10.3389/fmicb.2018.03019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/22/2018] [Indexed: 01/25/2023] Open
Abstract
Fluorescent proteins are a major cell biology tool to analyze protein sub-cellular topology. Here we have applied this technology to study protein secretion in the Gram-positive bacterium Streptomyces lividans TK24, a widely used host for heterologous protein secretion biotechnology. Green and monomeric red fluorescent proteins were fused behind Sec (SPSec) or Tat (SPTat) signal peptides to direct them through the respective export pathway. Significant secretion of fluorescent eGFP and mRFP was observed exclusively through the Tat and Sec pathways, respectively. Plasmid over-expression was compared to a chromosomally integrated spSec-mRFP gene to allow monitoring secretion under high and low level synthesis in various media. Fluorimetric detection of SPSec-mRFP recorded folded states, while immuno-staining detected even non-folded topological intermediates. Secretion of SPSec-mRFP is unexpectedly complex, is regulated independently of cell growth phase and is influenced by the growth regime. At low level synthesis, highly efficient secretion occurs until it is turned off and secretory preforms accumulate. At high level synthesis, the secretory pathway overflows and proteins are driven to folding and subsequent degradation. High-level synthesis of heterologous secretory proteins, whether secretion competent or not, has a drastic effect on the endogenous secretome, depending on their secretion efficiency. These findings lay the foundations of dissecting how protein targeting and secretion are regulated by the interplay between the metabolome, secretion factors and stress responses in the S. lividans model.
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Affiliation(s)
- Mohamed Belal Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Molecular Biology Department, National Research Centre, Dokki, Egypt
| | - Kristof Vrancken
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Joachim Koepff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Renata Novakova
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lieve van Mellaert
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Zentrum für Infektionsforschung GmbH, Braunschweig, Germany
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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5
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Koepff J, Sachs CC, Wiechert W, Kohlheyer D, Nöh K, Oldiges M, Grünberger A. Germination and Growth Analysis of Streptomyces lividans at the Single-Cell Level Under Varying Medium Compositions. Front Microbiol 2018; 9:2680. [PMID: 30524383 PMCID: PMC6262040 DOI: 10.3389/fmicb.2018.02680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/19/2018] [Indexed: 01/27/2023] Open
Abstract
Quantitative single-cell cultivation has provided fundamental contributions to our understanding of heterogeneity among industrially used microorganisms. Filamentous growing Streptomyces species are emerging platform organisms for industrial production processes, but their exploitation is still limited due to often reported high batch-to-batch variations and unexpected growth and production differences. Population heterogeneity is suspected to be one responsible factor, which is so far not systematically investigated at the single-cell level. Novel microfluidic single-cell cultivation devices offer promising solutions to investigate these phenomena. In this study, we investigated the germination and growth behavior of Streptomyces lividans TK24 under varying medium compositions on different complexity levels (i.e., mycelial growth, hyphal growth and tip elongation) on single-cell level. Our analysis reveals a remarkable stability within growth and germination of spores and early mycelium development when exposed to constant and defined environments. We show that spores undergo long metabolic adaptation processes of up to > 30 h to adjust to new medium conditions, rather than using a "persister" strategy as a possibility to cope with rapidly changing environments. Due to this uniform behavior, we conclude that S. lividans can be cultivated quite robustly under constant environmental conditions as provided by microfluidic cultivation approaches. Failure and non-reproducible cultivations are thus most likely to be found in less controllable larger-scale cultivation workflows and as a result of environmental gradients within large-scale cultivations.
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Affiliation(s)
- Joachim Koepff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christian Carsten Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology, RWTH Aachen University – Aachener Verfahrenstechnik, Aachen, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Microscale Bioengineering, RWTH Aachen University – Aachener Verfahrenstechnik, Aachen, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
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Busche T, Tsolis KC, Koepff J, Rebets Y, Rückert C, Hamed MB, Bleidt A, Wiechert W, Lopatniuk M, Yousra A, Anné J, Karamanou S, Oldiges M, Kalinowski J, Luzhetskyy A, Economou A. Multi-Omics and Targeted Approaches to Determine the Role of Cellular Proteases in Streptomyces Protein Secretion. Front Microbiol 2018; 9:1174. [PMID: 29915569 PMCID: PMC5994538 DOI: 10.3389/fmicb.2018.01174] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/15/2018] [Indexed: 01/29/2023] Open
Abstract
Gram-positive Streptomyces bacteria are profuse secretors of polypeptides using complex, yet unknown mechanisms. Many of their secretory proteins are proteases that play important roles in the acquisition of amino acids from the environment. Other proteases regulate cellular proteostasis. To begin dissecting the possible role of proteases in Streptomyces secretion, we applied a multi-omics approach. We probed the role of the 190 proteases of Streptomyces lividans strain TK24 in protein secretion in defined media at different stages of growth. Transcriptomics analysis revealed transcripts for 93% of these proteases and identified that 41 of them showed high abundance. Proteomics analysis identified 57 membrane-embedded or secreted proteases with variations in their abundance. We focused on 17 of these proteases and putative inhibitors and generated strains deleted of their genes. These were characterized in terms of their fitness, transcriptome and secretome changes. In addition, we performed a targeted analysis in deletion strains that also carried a secretion competent mRFP. One strain, carrying a deletion of the gene for the regulatory protease FtsH, showed significant global changes in overall transcription and enhanced secretome and secreted mRFP levels. These data provide a first multi-omics effort to characterize the complex regulatory mechanisms of protein secretion in Streptomyces lividans and lay the foundations for future rational manipulation of this process.
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Affiliation(s)
- Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - Konstantinos C Tsolis
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Joachim Koepff
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Jülich, Germany
| | - Yuriy Rebets
- Helmholtz-Zentrum für Infektionsforschung GmbH, Braunschweig, Germany.,Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Mohamed B Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.,Department of Molecular Biology, National Research Centre, Giza, Egypt
| | - Arne Bleidt
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Jülich, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Jülich, Germany
| | - Mariia Lopatniuk
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Ahmed Yousra
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marco Oldiges
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz-Zentrum für Infektionsforschung GmbH, Braunschweig, Germany
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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Koepff J, Morschett H, Busche T, Winkler A, Kalinowski J, Wiechert W, Oldiges M. Differential transcriptomic analysis reveals hidden light response in Streptomyces lividans. Biotechnol Prog 2017; 34:287-292. [DOI: 10.1002/btpr.2566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/25/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Joachim Koepff
- Inst. of Bio- and Geosciences, IBG-1: Biotechnology; Jülich Germany
| | - Holger Morschett
- Inst. of Bio- and Geosciences, IBG-1: Biotechnology; Jülich Germany
| | - Tobias Busche
- Bielefeld University, Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld Germany
| | - Anika Winkler
- Bielefeld University, Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld Germany
| | - Jörn Kalinowski
- Bielefeld University, Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld Germany
| | - Wolfgang Wiechert
- Inst. of Bio- and Geosciences, IBG-1: Biotechnology; Jülich Germany
- RWTH Aachen University, Computational Systems Biotechnology, Aachener Verfahrenstechnik; Aachen Germany
| | - Marco Oldiges
- Inst. of Bio- and Geosciences, IBG-1: Biotechnology; Jülich Germany
- RWTH Aachen University, Inst. of Biotechnology; Aachen Germany
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8
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Koepff J, Keller M, Tsolis KC, Busche T, Rückert C, Hamed MB, Anné J, Kalinowski J, Wiechert W, Economou A, Oldiges M. Fast and reliable strain characterization of Streptomyces lividans
through micro-scale cultivation. Biotechnol Bioeng 2017; 114:2011-2022. [DOI: 10.1002/bit.26321] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/15/2017] [Accepted: 04/17/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Joachim Koepff
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Matthias Keller
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Konstantinos C. Tsolis
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Mohamed B. Hamed
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
- Department of Molecular Biology Department; The National Research Centre, Dokki; Giza Egypt
| | - Jozef Anné
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Joern Kalinowski
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
- Institute of Biotechnology; RWTH Aachen University; Worringer Weg 3 52074 Aachen Germany
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9
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Koepff J, Selzer S, Wiechert W, Oldiges M. Filamentous Organisms Catching up: Parallelized, Miniaturized, and Automated Characterization Methods for Streptomyces lividans. CHEM-ING-TECH 2016. [DOI: 10.1002/cite.201650403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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