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Halle L, Hollmann N, Tenhaef N, Mbengi L, Glitz C, Wiechert W, Polen T, Baumgart M, Bott M, Noack S. Robotic workflows for automated long-term adaptive laboratory evolution: improving ethanol utilization by Corynebacterium glutamicum. Microb Cell Fact 2023; 22:175. [PMID: 37679814 PMCID: PMC10483779 DOI: 10.1186/s12934-023-02180-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/15/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Adaptive laboratory evolution (ALE) is known as a powerful tool for untargeted engineering of microbial strains and genomics research. It is particularly well suited for the adaptation of microorganisms to new environmental conditions, such as alternative substrate sources. Since the probability of generating beneficial mutations increases with the frequency of DNA replication, ALE experiments are ideally free of constraints on the required duration of cell proliferation. RESULTS Here, we present an extended robotic workflow for performing long-term evolution experiments based on fully automated repetitive batch cultures (rbALE) in a well-controlled microbioreactor environment. Using a microtiter plate recycling approach, the number of batches and thus cell generations is technically unlimited. By applying the validated workflow in three parallel rbALE runs, ethanol utilization by Corynebacterium glutamicum ATCC 13032 (WT) was significantly improved. The evolved mutant strain WT_EtOH-Evo showed a specific ethanol uptake rate of 8.45 ± 0.12 mmolEtOH gCDW-1 h-1 and a growth rate of 0.15 ± 0.01 h-1 in lab-scale bioreactors. Genome sequencing of this strain revealed a striking single nucleotide variation (SNV) upstream of the ald gene (NCgl2698, cg3096) encoding acetaldehyde dehydrogenase (ALDH). The mutated basepair was previously predicted to be part of the binding site for the global transcriptional regulator GlxR, and re-engineering demonstrated that the identified SNV is key for enhanced ethanol assimilation. Decreased binding of GlxR leads to increased synthesis of the rate-limiting enzyme ALDH, which was confirmed by proteomics measurements. CONCLUSIONS The established rbALE technology is generally applicable to any microbial strain and selection pressure that fits the small-scale cultivation format. In addition, our specific results will enable improved production processes with C. glutamicum from ethanol, which is of particular interest for acetyl-CoA-derived products.
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Affiliation(s)
- Lars Halle
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Niels Hollmann
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Lea Mbengi
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Christiane Glitz
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany.
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Baumann PT, Dal Molin M, Aring H, Krumbach K, Müller MF, Vroling B, van Summeren-Wesenhagen PV, Noack S, Marienhagen J. Beyond rational-biosensor-guided isolation of 100 independently evolved bacterial strain variants and comparative analysis of their genomes. BMC Biol 2023; 21:183. [PMID: 37667306 PMCID: PMC10478468 DOI: 10.1186/s12915-023-01688-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND In contrast to modern rational metabolic engineering, classical strain development strongly relies on random mutagenesis and screening for the desired production phenotype. Nowadays, with the availability of biosensor-based FACS screening strategies, these random approaches are coming back into fashion. In this study, we employ this technology in combination with comparative genome analyses to identify novel mutations contributing to product formation in the genome of a Corynebacterium glutamicum L-histidine producer. Since all known genetic targets contributing to L-histidine production have been already rationally engineered in this strain, identification of novel beneficial mutations can be regarded as challenging, as they might not be intuitively linkable to L-histidine biosynthesis. RESULTS In order to identify 100 improved strain variants that had each arisen independently, we performed > 600 chemical mutagenesis experiments, > 200 biosensor-based FACS screenings, isolated > 50,000 variants with increased fluorescence, and characterized > 4500 variants with regard to biomass formation and L-histidine production. Based on comparative genome analyses of these 100 variants accumulating 10-80% more L-histidine, we discovered several beneficial mutations. Combination of selected genetic modifications allowed for the construction of a strain variant characterized by a doubled L-histidine titer (29 mM) and product yield (0.13 C-mol C-mol-1) in comparison to the starting variant. CONCLUSIONS This study may serve as a blueprint for the identification of novel beneficial mutations in microbial producers in a more systematic manner. This way, also previously unexplored genes or genes with previously unknown contribution to the respective production phenotype can be identified. We believe that this technology has a great potential to push industrial production strains towards maximum performance.
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Affiliation(s)
- Philipp T Baumann
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Michael Dal Molin
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
- Department I of Internal Medicine, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Hannah Aring
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Karin Krumbach
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Moritz-Fabian Müller
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Bas Vroling
- Bioprodict GmbH, Nieuwe Marktstraat 54E, 6511AA, Nijmegen, The Netherlands
| | | | - Stephan Noack
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
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Zuchowski R, Schito S, Neuheuser F, Menke P, Berger D, Hollmann N, Gujar S, Sundermeyer L, Mack C, Wirtz A, Weiergräber OH, Polen T, Bott M, Noack S, Baumgart M. Discovery of novel amino acid production traits by evolution of synthetic co-cultures. Microb Cell Fact 2023; 22:71. [PMID: 37061714 PMCID: PMC10105947 DOI: 10.1186/s12934-023-02078-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/02/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Amino acid production features of Corynebacterium glutamicum were extensively studied in the last two decades. Many metabolic pathways, regulatory and transport principles are known, but purely rational approaches often provide only limited progress in production optimization. We recently generated stable synthetic co-cultures, termed Communities of Niche-optimized Strains (CoNoS), that rely on cross-feeding of amino acids for growth. This setup has the potential to evolve strains with improved production by selection of faster growing communities. RESULTS Here we performed adaptive laboratory evolution (ALE) with a CoNoS to identify mutations that are relevant for amino acid production both in mono- and co-cultures. During ALE with the CoNoS composed of strains auxotrophic for either L-leucine or L-arginine, we obtained a 23% growth rate increase. Via whole-genome sequencing and reverse engineering, we identified several mutations involved in amino acid transport that are beneficial for CoNoS growth. The L-leucine auxotrophic strain carried an expression-promoting mutation in the promoter region of brnQ (cg2537), encoding a branched-chain amino acid transporter in combination with mutations in the genes for the Na+/H+-antiporter Mrp1 (cg0326-cg0321). This suggested an unexpected link of Mrp1 to L-leucine transport. The L-arginine auxotrophic partner evolved expression-promoting mutations near the transcriptional start site of the yet uncharacterized operon argTUV (cg1504-02). By mutation studies and ITC, we characterized ArgTUV as the only L-arginine uptake system of C. glutamicum with an affinity of KD = 30 nM. Finally, deletion of argTUV in an L-arginine producer strain resulted in a faster and 24% higher L-arginine production in comparison to the parental strain. CONCLUSION Our work demonstrates the power of the CoNoS-approach for evolution-guided identification of non-obvious production traits, which can also advance amino acid production in monocultures. Further rounds of evolution with import-optimized strains can potentially reveal beneficial mutations also in metabolic pathway enzymes. The approach can easily be extended to all kinds of metabolite cross-feeding pairings of different organisms or different strains of the same organism, thereby enabling the identification of relevant transport systems and other favorable mutations.
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Affiliation(s)
- Rico Zuchowski
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Simone Schito
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Friederike Neuheuser
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Philipp Menke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Berger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niels Hollmann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Srushti Gujar
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Lea Sundermeyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christina Mack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Astrid Wirtz
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Oliver H Weiergräber
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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Metabolomics and modelling approaches for systems metabolic engineering. Metab Eng Commun 2022; 15:e00209. [PMID: 36281261 PMCID: PMC9587336 DOI: 10.1016/j.mec.2022.e00209] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/21/2022] Open
Abstract
Metabolic engineering involves the manipulation of microbes to produce desirable compounds through genetic engineering or synthetic biology approaches. Metabolomics involves the quantitation of intracellular and extracellular metabolites, where mass spectrometry and nuclear magnetic resonance based analytical instrumentation are often used. Here, the experimental designs, sample preparations, metabolite quenching and extraction are essential to the quantitative metabolomics workflow. The resultant metabolomics data can then be used with computational modelling approaches, such as kinetic and constraint-based modelling, to better understand underlying mechanisms and bottlenecks in the synthesis of desired compounds, thereby accelerating research through systems metabolic engineering. Constraint-based models, such as genome scale models, have been used successfully to enhance the yield of desired compounds from engineered microbes, however, unlike kinetic or dynamic models, constraint-based models do not incorporate regulatory effects. Nevertheless, the lack of time-series metabolomic data generation has hindered the usefulness of dynamic models till today. In this review, we show that improvements in automation, dynamic real-time analysis and high throughput workflows can drive the generation of more quality data for dynamic models through time-series metabolomics data generation. Spatial metabolomics also has the potential to be used as a complementary approach to conventional metabolomics, as it provides information on the localization of metabolites. However, more effort must be undertaken to identify metabolites from spatial metabolomics data derived through imaging mass spectrometry, where machine learning approaches could prove useful. On the other hand, single-cell metabolomics has also seen rapid growth, where understanding cell-cell heterogeneity can provide more insights into efficient metabolic engineering of microbes. Moving forward, with potential improvements in automation, dynamic real-time analysis, high throughput workflows, and spatial metabolomics, more data can be produced and studied using machine learning algorithms, in conjunction with dynamic models, to generate qualitative and quantitative predictions to advance metabolic engineering efforts.
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Bleisch R, Freitag L, Ihadjadene Y, Sprenger U, Steingröwer J, Walther T, Krujatz F. Strain Development in Microalgal Biotechnology-Random Mutagenesis Techniques. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070961. [PMID: 35888051 PMCID: PMC9315690 DOI: 10.3390/life12070961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022]
Abstract
Microalgal biomass and metabolites can be used as a renewable source of nutrition, pharmaceuticals and energy to maintain or improve the quality of human life. Microalgae’s high volumetric productivity and low impact on the environment make them a promising raw material in terms of both ecology and economics. To optimize biotechnological processes with microalgae, improving the productivity and robustness of the cell factories is a major step towards economically viable bioprocesses. This review provides an overview of random mutagenesis techniques that are applied to microalgal cell factories, with a particular focus on physical and chemical mutagens, mutagenesis conditions and mutant characteristics.
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Affiliation(s)
- Richard Bleisch
- Institute of Natural Materials Technology, Technische Universität Dresden, 01069 Dresden, Germany; (R.B.); (L.F.); (Y.I.); (U.S.); (J.S.); (T.W.)
| | - Leander Freitag
- Institute of Natural Materials Technology, Technische Universität Dresden, 01069 Dresden, Germany; (R.B.); (L.F.); (Y.I.); (U.S.); (J.S.); (T.W.)
| | - Yob Ihadjadene
- Institute of Natural Materials Technology, Technische Universität Dresden, 01069 Dresden, Germany; (R.B.); (L.F.); (Y.I.); (U.S.); (J.S.); (T.W.)
| | - Una Sprenger
- Institute of Natural Materials Technology, Technische Universität Dresden, 01069 Dresden, Germany; (R.B.); (L.F.); (Y.I.); (U.S.); (J.S.); (T.W.)
| | - Juliane Steingröwer
- Institute of Natural Materials Technology, Technische Universität Dresden, 01069 Dresden, Germany; (R.B.); (L.F.); (Y.I.); (U.S.); (J.S.); (T.W.)
| | - Thomas Walther
- Institute of Natural Materials Technology, Technische Universität Dresden, 01069 Dresden, Germany; (R.B.); (L.F.); (Y.I.); (U.S.); (J.S.); (T.W.)
| | - Felix Krujatz
- Institute of Natural Materials Technology, Technische Universität Dresden, 01069 Dresden, Germany; (R.B.); (L.F.); (Y.I.); (U.S.); (J.S.); (T.W.)
- Biotopa gGmbH—Center for Applied Aquaculture & Bioeconomy, 01454 Radeberg, Germany
- Faculty of Natural and Environmental Sciences, University of Applied Sciences Zittau/Görlitz, 02763 Zittau, Germany
- Correspondence:
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Helleckes LM, Osthege M, Wiechert W, von Lieres E, Oldiges M. Bayesian calibration, process modeling and uncertainty quantification in biotechnology. PLoS Comput Biol 2022; 18:e1009223. [PMID: 35255090 PMCID: PMC8939798 DOI: 10.1371/journal.pcbi.1009223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 03/22/2022] [Accepted: 01/16/2022] [Indexed: 12/23/2022] Open
Abstract
High-throughput experimentation has revolutionized data-driven experimental sciences and opened the door to the application of machine learning techniques. Nevertheless, the quality of any data analysis strongly depends on the quality of the data and specifically the degree to which random effects in the experimental data-generating process are quantified and accounted for. Accordingly calibration, i.e. the quantitative association between observed quantities and measurement responses, is a core element of many workflows in experimental sciences. Particularly in life sciences, univariate calibration, often involving non-linear saturation effects, must be performed to extract quantitative information from measured data. At the same time, the estimation of uncertainty is inseparably connected to quantitative experimentation. Adequate calibration models that describe not only the input/output relationship in a measurement system but also its inherent measurement noise are required. Due to its mathematical nature, statistically robust calibration modeling remains a challenge for many practitioners, at the same time being extremely beneficial for machine learning applications. In this work, we present a bottom-up conceptual and computational approach that solves many problems of understanding and implementing non-linear, empirical calibration modeling for quantification of analytes and process modeling. The methodology is first applied to the optical measurement of biomass concentrations in a high-throughput cultivation system, then to the quantification of glucose by an automated enzymatic assay. We implemented the conceptual framework in two Python packages, calibr8 and murefi, with which we demonstrate how to make uncertainty quantification for various calibration tasks more accessible. Our software packages enable more reproducible and automatable data analysis routines compared to commonly observed workflows in life sciences. Subsequently, we combine the previously established calibration models with a hierarchical Monod-like ordinary differential equation model of microbial growth to describe multiple replicates of Corynebacterium glutamicum batch cultures. Key process model parameters are learned by both maximum likelihood estimation and Bayesian inference, highlighting the flexibility of the statistical and computational framework. In experimental fields like biotechnology, scientists need to quantify process parameters such as concentrations and state the uncertainty around them. However, measurements rarely yield the desired quantity directly; for example, the measurement of scattered light is just an indirect measure for the number of cells in a suspension. For reliable interpretation, scientists must determine the uncertainty around the underlying quantities of interest using statistical methods. A key step in these workflows is the establishment of calibration models to describe the relation between the quantities of interest and measurement outcomes. This is typically done using measurements of reference samples for which the true quantities are known. However, implementing and applying these statistical models often requires skills that are not commonly taught. We therefore developed two software packages, calibr8 and murefi, to simplify such calibration and modeling procedures. To showcase our work, we performed an experiment commonly seen in microbiology: the acquisition of a microbial growth curve, in this case of Corynebacterium glutamicum, in an online measurement device. Using our software, we built a mathematical model of the overall process to quantify relevant parameters with uncertainty, e.g. the growth rate or the yield of biomass per amount of glucose.
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Affiliation(s)
- Laura Marie Helleckes
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Michael Osthege
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany
| | - Eric von Lieres
- 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
- * E-mail:
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7
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Raj K, Venayak N, Diep P, Golla SA, Yakunin AF, Mahadevan R. Automation assisted anaerobic phenotyping for metabolic engineering. Microb Cell Fact 2021; 20:184. [PMID: 34556155 PMCID: PMC8461876 DOI: 10.1186/s12934-021-01675-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microorganisms can be metabolically engineered to produce a wide range of commercially important chemicals. Advancements in computational strategies for strain design and synthetic biological techniques to construct the designed strains have facilitated the generation of large libraries of potential candidates for chemical production. Consequently, there is a need for high-throughput laboratory scale techniques to characterize and screen these candidates to select strains for further investigation in large scale fermentation processes. Several small-scale fermentation techniques, in conjunction with laboratory automation have enhanced the throughput of enzyme and strain phenotyping experiments. However, such high throughput experimentation typically entails large operational costs and generate massive amounts of laboratory plastic waste. RESULTS In this work, we develop an eco-friendly automation workflow that effectively calibrates and decontaminates fixed-tip liquid handling systems to reduce tip waste. We also investigate inexpensive methods to establish anaerobic conditions in microplates for high-throughput anaerobic phenotyping. To validate our phenotyping platform, we perform two case studies-an anaerobic enzyme screen, and a microbial phenotypic screen. We used our automation platform to investigate conditions under which several strains of E. coli exhibit the same phenotypes in 0.5 L bioreactors and in our scaled-down fermentation platform. We also propose the use of dimensionality reduction through t-distributed stochastic neighbours embedding (t-SNE) in conjunction with our phenotyping platform to effectively cluster similarly performing strains at the bioreactor scale. CONCLUSIONS Fixed-tip liquid handling systems can significantly reduce the amount of plastic waste generated in biological laboratories and our decontamination and calibration protocols could facilitate the widespread adoption of such systems. Further, the use of t-SNE in conjunction with our automation platform could serve as an effective scale-down model for bioreactor fermentations. Finally, by integrating an in-house data-analysis pipeline, we were able to accelerate the 'test' phase of the design-build-test-learn cycle of metabolic engineering.
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Affiliation(s)
- Kaushik Raj
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Sai Akhil Golla
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
- School of Natural Sciences, Bangor University, Bangor, LL57 2DG UK
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, M5S 3G9 Canada
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Reiter A, Herbst L, Wiechert W, Oldiges M. Need for speed: evaluation of dilute and shoot-mass spectrometry for accelerated metabolic phenotyping in bioprocess development. Anal Bioanal Chem 2021; 413:3253-3268. [PMID: 33791825 PMCID: PMC8079306 DOI: 10.1007/s00216-021-03261-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/18/2021] [Accepted: 03/01/2021] [Indexed: 01/29/2023]
Abstract
With the utilization of small-scale and highly parallelized cultivation platforms embedded in laboratory robotics, microbial phenotyping and bioprocess development have been substantially accelerated, thus generating a bottleneck in bioanalytical bioprocess sample analytics. While microscale cultivation platforms allow the monitoring of typical process parameters, only limited information about product and by-product formation is provided without comprehensive analytics. The use of liquid chromatography mass spectrometry can provide such a comprehensive and quantitative insight, but is often limited by analysis runtime and throughput. In this study, we developed and evaluated six methods for amino acid quantification based on two strong cation exchanger columns and a dilute and shoot approach in hyphenation with either a triple-quadrupole or a quadrupole time-of-flight mass spectrometer. Isotope dilution mass spectrometry with 13C15N labeled amino acids was used to correct for matrix effects. The versatility of the methods for metabolite profiling studies of microbial cultivation supernatants is confirmed by a detailed method validation study. The methods using chromatography columns showed a linear range of approx. 4 orders of magnitude, sufficient response factors, and low quantification limits (7-443 nM) for single analytes. Overall, relative standard deviation was comparable for all analytes, with < 8% and < 11% for unbuffered and buffered media, respectively. The dilute and shoot methods with an analysis time of 1 min provided similar performance but showed a factor of up to 35 times higher throughput. The performance and applicability of the dilute and shoot method are demonstrated using a library of Corynebacterium glutamicum strains producing L-histidine, obtained from random mutagenesis, which were cultivated in a microscale cultivation platform.
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Affiliation(s)
- Alexander Reiter
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Laura Herbst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Computational Systems Biotechnology, RWTH Aachen University, 52062, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, 52062, Aachen, Germany.
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9
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Jansen R, Küsters K, Morschett H, Wiechert W, Oldiges M. A fully automated pipeline for the dynamic at-line morphology analysis of microscale Aspergillus cultivation. Fungal Biol Biotechnol 2021; 8:2. [PMID: 33676585 PMCID: PMC7937226 DOI: 10.1186/s40694-021-00109-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/16/2021] [Indexed: 11/27/2022] Open
Abstract
Background Morphology, being one of the key factors influencing productivity of filamentous fungi, is of great interest during bioprocess development. With increasing demand of high-throughput phenotyping technologies for fungi due to the emergence of novel time-efficient genetic engineering technologies, workflows for automated liquid handling combined with high-throughput morphology analysis have to be developed. Results In this study, a protocol allowing for 48 parallel microbioreactor cultivations of Aspergillus carbonarius with non-invasive online signals of backscatter and dissolved oxygen was established. To handle the increased cultivation throughput, the utilized microbioreactor is integrated into a liquid handling platform. During cultivation of filamentous fungi, cell suspensions result in either viscous broths or form pellets with varying size throughout the process. Therefore, tailor-made liquid handling parameters such as aspiration/dispense height, velocity and mixing steps were optimized and validated. Development and utilization of a novel injection station enabled a workflow, where biomass samples are automatically transferred into a flow through chamber fixed under a light microscope. In combination with an automated image analysis concept, this enabled an automated morphology analysis pipeline. The workflow was tested in a first application study, where the projected biomass area was determined at two different cultivation temperatures and compared to the microbioreactor online signals. Conclusions A novel and robust workflow starting from microbioreactor cultivation, automated sample harvest and processing via liquid handling robots up to automated morphology analysis was developed. This protocol enables the determination of projected biomass areas for filamentous fungi in an automated and high-throughput manner. This measurement of morphology can be applied to describe overall pellet size distribution and heterogeneity.
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Affiliation(s)
- Roman Jansen
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Kira Küsters
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Holger Morschett
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Computational Systems Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.
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10
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Potential of Integrating Model-Based Design of Experiments Approaches and Process Analytical Technologies for Bioprocess Scale-Down. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021. [PMID: 33381857 DOI: 10.1007/10_2020_154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Typically, bioprocesses on an industrial scale are dynamic systems with a certain degree of variability, system inhomogeneities, and even population heterogeneities. Therefore, the scaling of such processes from laboratory to industrial scale and vice versa is not a trivial task. Traditional scale-down methodologies consider several technical parameters, so that systems on the laboratory scale tend to qualitatively reflect large-scale effects, but not the dynamic situation in an industrial bioreactor over the entire process, from the perspective of a cell. Supported by the enormous increase in computing power, the latest scientific focus is on the application of dynamic models, in combination with computational fluid dynamics to quantitatively describe cell behavior. These models allow the description of possible cellular lifelines which in turn can be used to derive a regime analysis for scale-down experiments. However, the approaches described so far, which were for a very few process examples, are very labor- and time-intensive and cannot be validated easily. In parallel, alternatives have been developed based on the description of the industrial process with hybrid process models, which describe a process mechanistically as far as possible in order to determine the essential process parameters with their respective variances. On-line analytical methods allow the characterization of population heterogeneity directly in the process. This detailed information from the industrial process can be used in laboratory screening systems to select relevant conditions in which the cell and process related parameters reflect the situation in the industrial scale. In our opinion, these technologies, which are available in research for modeling biological systems, in combination with process analytical techniques are so far developed that they can be implemented in industrial routines for faster development of new processes and optimization of existing ones.
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11
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Hemmerich J, Labib M, Steffens C, Reich SJ, Weiske M, Baumgart M, Rückert C, Ruwe M, Siebert D, Wendisch VF, Kalinowski J, Wiechert W, Oldiges M. Screening of a genome-reduced Corynebacterium glutamicum strain library for improved heterologous cutinase secretion. Microb Biotechnol 2020; 13:2020-2031. [PMID: 32893457 PMCID: PMC7533341 DOI: 10.1111/1751-7915.13660] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
The construction of microbial platform organisms by means of genome reduction is an ongoing topic in biotechnology. In this study, we investigated whether the deletion of single or multiple gene clusters has a positive effect on the secretion of cutinase from Fusarium solani pisi in the industrial workhorse Corynebacterium glutamicum. A total of 22 genome-reduced strain variants were compared applying two Sec signal peptides from Bacillus subtilis. High-throughput phenotyping using robotics-integrated microbioreactor technology with automated harvesting revealed distinct cutinase secretion performance for a specific combination of signal peptide and genomic deletions. The biomass-specific cutinase yield for strain GRS41_51_NprE was increased by ~ 200%, although the growth rate was reduced by ~ 60%. Importantly, the causative deletions of genomic clusters cg2801-cg2828 and rrnC-cg3298 could not have been inferred a priori. Strikingly, bioreactor fed-batch cultivations at controlled growth rates resulted in a complete reversal of the screening results, with the cutinase yield for strain GRS41_51_NprE dropping by ~ 25% compared to the reference strain. Thus, the choice of bioprocess conditions may turn a 'high-performance' strain from batch screening into a 'low-performance' strain in fed-batch cultivation. In conclusion, future studies are needed in order to understand metabolic adaptations of C. glutamicum to both genomic deletions and different bioprocess conditions.
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Affiliation(s)
- Johannes Hemmerich
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
- Bioeconomy Science Center (BioSC)Forschungszentrum JülichJülich52425Germany
| | - Mohamed Labib
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
| | - Carmen Steffens
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
| | - Sebastian J. Reich
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
- Present address:
Institute of Microbiology and BiotechnologyUlm UniversityUlm89081Germany
| | - Marc Weiske
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
| | - Meike Baumgart
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
| | - Christian Rückert
- Microbial Genomics and BiotechnologyCenter for BiotechnologyBielefeld UniversityBielefeld33615Germany
| | - Matthias Ruwe
- Microbial Genomics and BiotechnologyCenter for BiotechnologyBielefeld UniversityBielefeld33615Germany
| | - Daniel Siebert
- Faculty of Biology, Chair of Genetics of ProkaryotesBielefeld UniversityBielefeld33615Germany
- Present address:
Microbial BiotechnologyCampus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubing94315Germany
| | - Volker F. Wendisch
- Faculty of Biology, Chair of Genetics of ProkaryotesBielefeld UniversityBielefeld33615Germany
| | - Jörn Kalinowski
- Microbial Genomics and BiotechnologyCenter for BiotechnologyBielefeld UniversityBielefeld33615Germany
| | - Wolfgang Wiechert
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
- Bioeconomy Science Center (BioSC)Forschungszentrum JülichJülich52425Germany
- Computational Systems Biotechnology (AVT.CSB)RWTH Aachen UniversityAachen52074Germany
| | - Marco Oldiges
- Institute of Bio‐ and Geosciences – Biotechnology (IBG‐1)Forschungszentrum Jülich, Institute of Bio‐ and Geosciences ‐ Biotechnology (IBG‐1)Jülich52425Germany
- Bioeconomy Science Center (BioSC)Forschungszentrum JülichJülich52425Germany
- Institute of BiotechnologyRWTH Aachen UniversityAachen52074Germany
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12
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Radivojević T, Costello Z, Workman K, Garcia Martin H. A machine learning Automated Recommendation Tool for synthetic biology. Nat Commun 2020; 11:4879. [PMID: 32978379 PMCID: PMC7519645 DOI: 10.1038/s41467-020-18008-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/27/2020] [Indexed: 01/07/2023] Open
Abstract
Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. Here, we present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. Using sampling-based optimization, ART provides a set of recommended strains to be built in the next engineering cycle, alongside probabilistic predictions of their production levels. We demonstrate the capabilities of ART on simulated data sets, as well as experimental data from real metabolic engineering projects producing renewable biofuels, hoppy flavored beer without hops, fatty acids, and tryptophan. Finally, we discuss the limitations of this approach, and the practical consequences of the underlying assumptions failing.
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Affiliation(s)
- Tijana Radivojević
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Zak Costello
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kenneth Workman
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Hector Garcia Martin
- DOE Agile BioFoundry, Emeryville, CA, 94608, USA.
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- BCAM, Basque Center for Applied Mathematics, Bilbao, 48009, Spain.
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13
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Jansen RP, Müller MF, Schröter SE, Kappelmann J, Klein B, Oldiges M, Noack S. Parallelized disruption of prokaryotic and eukaryotic cells via miniaturized and automated bead mill. Eng Life Sci 2020; 20:350-356. [PMID: 32774207 PMCID: PMC7401235 DOI: 10.1002/elsc.202000002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/17/2020] [Indexed: 11/07/2022] Open
Abstract
The application of integrated microbioreactor systems is rapidly becoming of more interest to accelerate strain characterization and bioprocess development. However, available high-throughput screening capabilities are often limited to target extracellular compounds only. Consequently, there is a great demand for automated technologies allowing for miniaturized and parallel cell disruption providing access to intracellular measurements. In this study, a fully automated bead mill workflow was developed and validated for four different industrial platform organisms: Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Aspergillus niger. The workflow enables up to 48 parallel cell disruptions in microtiter plates and is applicable at-line to running lab-scale cultivations. The resulting cell extracts form the basis for quantitative omics studies where no rapid metabolic quenching is required (e.g., genomics and proteomics).
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Affiliation(s)
- Roman P. Jansen
- IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
| | | | | | | | - Bianca Klein
- IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
| | - Marco Oldiges
- IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
- Institute of BiotechnologyRWTH Aachen UniversityAachenGermany
- Bioeconomy Science Center (BioSC)Forschungszentrum Jülich GmbHJülichGermany
| | - Stephan Noack
- IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
- Bioeconomy Science Center (BioSC)Forschungszentrum Jülich GmbHJülichGermany
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14
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Andriiash GS, Sekan OS, Tigunova OO, Blume YB, Shulga SM. Metabolic Engineering of Lysine Producing Corynebacterium glutamicum Strains. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Venayak N, Raj K, Mahadevan R. Impact framework: A python package for writing data analysis workflows to interpret microbial physiology. Metab Eng Commun 2019; 9:e00089. [PMID: 31011536 PMCID: PMC6462781 DOI: 10.1016/j.mec.2019.e00089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/26/2022] Open
Abstract
Microorganisms can be genetically engineered to solve a range of challenges in diverse including health, environmental protection and sustainability. The natural complexity of biological systems makes this an iterative cycle, perturbing metabolism and making stepwise progress toward a desired phenotype through four major stages: design, build, test, and data interpretation. This cycle has been accelerated by advances in molecular biology (e.g. robust DNA synthesis and assembly techniques), liquid handling automation and scale-down characterization platforms, generating large heterogeneous data sets. Here, we present an extensible Python package for scientists and engineers working with large biological data sets to interpret, model, and visualize data: the IMPACT (Integrated Microbial Physiology: Analysis, Characterization and Translation) framework. Impact aims to ease the development of Python-based data analysis workflows for a range of stakeholders in the bioengineering process, offering open-source tools for data analysis, physiology characterization and translation to visualization. Using this framework, biologists and engineers can opt for reproducible and extensible programmatic data analysis workflows, mediating a bottleneck limiting the throughput of microbial engineering. The Impact framework is available at https://github.com/lmse/impact.
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Affiliation(s)
- Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Kaushik Raj
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
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16
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Ravindran S, Singh P, Nene S, Rale V, Mhetras N, Vaidya A. Microbioreactors and Perfusion Bioreactors for Microbial and Mammalian Cell Culture. Biotechnol Bioeng 2019. [DOI: 10.5772/intechopen.83825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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Otten J, Tenhaef N, Jansen RP, Döbber J, Jungbluth L, Noack S, Oldiges M, Wiechert W, Pohl M. A FRET-based biosensor for the quantification of glucose in culture supernatants of mL scale microbial cultivations. Microb Cell Fact 2019; 18:143. [PMID: 31434564 PMCID: PMC6704555 DOI: 10.1186/s12934-019-1193-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/14/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND In most microbial cultivations D-glucose is the main carbon and energy source. However, quantification of D-glucose especially in small scale is still challenging. Therefore, we developed a FRET-based glucose biosensor, which can be applied in microbioreactor-based cultivations. This sensor consists of a glucose binding protein sandwiched between two fluorescent proteins, constituting a FRET pair. Upon D-glucose binding the sensor undergoes a conformational change which is translated into a FRET-ratio change. RESULTS The selected sensor shows an apparent Kd below 1.5 mM D-glucose and a very high sensitivity of up to 70% FRET-ratio change between the unbound and the glucose-saturated state. The soluble sensor was successfully applied online to monitor the glucose concentration in an Escherichia coli culture. Additionally, this sensor was utilized in an at-line process for a Corynebacterium glutamicum culture as an example for a process with cell-specific background (e.g. autofluorescence) and medium-induced quenching. Immobilization of the sensor via HaloTag® enabled purification and covalent immobilization in one step and increased the stability during application, significantly. CONCLUSION A FRET-based glucose sensor was used to quantify D-glucose consumption in microtiter plate based cultivations. To the best of our knowledge, this is the first method reported for online quantification of D-glucose in microtiter plate based cultivations. In comparison to D-glucose analysis via an enzymatic assay and HPLC, the sensor performed equally well, but enabled much faster measurements, which allowed to speed up microbial strain development significantly.
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Affiliation(s)
- Julia Otten
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Niklas Tenhaef
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Roman P. Jansen
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Johannes Döbber
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Lisa Jungbluth
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Noack
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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18
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Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering. Trends Biotechnol 2019; 37:817-837. [DOI: 10.1016/j.tibtech.2019.01.003] [Citation(s) in RCA: 226] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/12/2022]
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19
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Morschett H, Loomba V, Huber G, Wiechert W, von Lieres E, Oldiges M. Laboratory-scale photobiotechnology-current trends and future perspectives. FEMS Microbiol Lett 2019; 365:4604817. [PMID: 29126108 DOI: 10.1093/femsle/fnx238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/07/2017] [Indexed: 11/13/2022] Open
Abstract
Phototrophic bioprocesses are a promising puzzle piece in future bioeconomy concepts but yet mostly fail for economic reasons. Besides other aspects, this is mainly attributed to the omnipresent issue of optimal light supply impeding scale-up and -down of phototrophic processes according to classic established concepts. This MiniReview examines two current trends in photobiotechnology, namely microscale cultivation and modeling and simulation. Microphotobioreactors are a valuable and promising trend with microfluidic chips and microtiter plates as predominant design concepts. Providing idealized conditions, chip systems are preferably to be used for acquiring physiological data of microalgae while microtiter plate systems are more appropriate for process parameter and medium screenings. However, these systems are far from series technology and significant improvements especially regarding flexible light supply remain crucial. Whereas microscale is less addressed by modeling and simulation so far, benchtop photobioreactor design and operation have successfully been studied using such tools. This particularly includes quantitative model-assisted understanding of mixing, mass transfer, light dispersion and particle tracing as well as their relevance for microalgal performance. The ultimate goal will be to combine physiological data from microphotobioreactors with hybrid models to integrate metabolism and reactor simulation in order to facilitate knowledge-based scale transfer of phototrophic bioprocesses.
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Affiliation(s)
- Holger Morschett
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Varun Loomba
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.,IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Gregor Huber
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Eric von Lieres
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.,Institute of Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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20
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Haby B, Hans S, Anane E, Sawatzki A, Krausch N, Neubauer P, Cruz Bournazou MN. Integrated Robotic Mini Bioreactor Platform for Automated, Parallel Microbial Cultivation With Online Data Handling and Process Control. SLAS Technol 2019; 24:569-582. [PMID: 31288593 DOI: 10.1177/2472630319860775] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During process development, the experimental search space is defined by the number of experiments that can be performed in specific time frames but also by its sophistication (e.g., inputs, sensors, sampling frequency, analytics). High-throughput liquid-handling stations can perform a large number of automated experiments in parallel. Nevertheless, the experimental data sets that are obtained are not always relevant for development of industrial bioprocesses, leading to a high rate of failure during scale-up. We present an automated mini bioreactor platform that enables parallel cultivations in the milliliter scale with online monitoring and control, well-controlled conditions, and advanced feeding strategies similar to industrial processes. The combination of two liquid handlers allows both automated mini bioreactor operation and at-line analysis in parallel. A central database enables end-to-end data exchange and fully integrated device and process control. A model-based operation algorithm allows for the accurate performance of complex cultivations for scale-down studies and strain characterization via optimal experimental redesign, significantly increasing the reliability and transferability of data throughout process development. The platform meets the tradeoff between experimental throughput and process control and monitoring comparable to laboratory-scale bioreactors.
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Affiliation(s)
- Benjamin Haby
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Sebastian Hans
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Emmanuel Anane
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Annina Sawatzki
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Niels Krausch
- Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Peter Neubauer
- Institute of Biotechnology, Technische Universität, Berlin, Germany
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21
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Stella RG, Wiechert J, Noack S, Frunzke J. Evolutionary engineering of
Corynebacterium glutamicum. Biotechnol J 2019; 14:e1800444. [DOI: 10.1002/biot.201800444] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/23/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Roberto G. Stella
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Johanna Wiechert
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Stephan Noack
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
| | - Julia Frunzke
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology, Forschungszentrum Jülich Wilhelm‐Johnen‐Straße 52428 Jülich Germany
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22
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Wendisch VF. Metabolic engineering advances and prospects for amino acid production. Metab Eng 2019; 58:17-34. [PMID: 30940506 DOI: 10.1016/j.ymben.2019.03.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/18/2022]
Abstract
Amino acid fermentation is one of the major pillars of industrial biotechnology. The multi-billion USD amino acid market is rising steadily and is diversifying. Metabolic engineering is no longer focused solely on strain development for the bulk amino acids L-glutamate and L-lysine that are produced at the million-ton scale, but targets specialty amino acids. These demands are met by the development and application of new metabolic engineering tools including CRISPR and biosensor technologies as well as production processes by enabling a flexible feedstock concept, co-production and co-cultivation schemes. Metabolic engineering advances are exemplified for specialty proteinogenic amino acids, cyclic amino acids, omega-amino acids, and amino acids functionalized by hydroxylation, halogenation and N-methylation.
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Affiliation(s)
- Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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Tajsoleiman T, Mears L, Krühne U, Gernaey KV, Cornelissen S. An Industrial Perspective on Scale-Down Challenges Using Miniaturized Bioreactors. Trends Biotechnol 2019; 37:697-706. [PMID: 30737008 DOI: 10.1016/j.tibtech.2019.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/25/2022]
Abstract
Miniaturized stirred bioreactors (MSBRs) are gaining popularity as a cost-effective approach to scale-down experimentation. However, realizing conditions that reflect the large-scale process accurately can be challenging. This article highlights common challenges of using MSBRs for scale-down. The fundamental difference between oxygen mass transfer coefficient (kLa) and oxygen transfer rate scaling is addressed and the difficulty of achieving turbulent flow and industrially relevant tip speeds is described. More practical challenges of using MSBR systems for scale-down are also discussed, including the risk of vortex formation, changed volume dynamics, and wall growth. By highlighting these challenges, the article aims to create more awareness of these difficulties and to contribute to improved design of scale-down experiments.
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Affiliation(s)
- Tannaz Tajsoleiman
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Lisa Mears
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Ulrich Krühne
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Krist V Gernaey
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark. https://twitter.com/@KristGernaey
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Noack S, Baumgart M. Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction. Trends Biotechnol 2019; 37:126-139. [DOI: 10.1016/j.tibtech.2018.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022]
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25
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Demling P, Westerwalbesloh C, Noack S, Wiechert W, Kohlheyer D. Quantitative measurements in single-cell analysis: towards scalability in microbial bioprocess development. Curr Opin Biotechnol 2018; 54:121-127. [DOI: 10.1016/j.copbio.2018.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/02/2018] [Accepted: 01/22/2018] [Indexed: 10/17/2022]
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26
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Hemmerich J, Tenhaef N, Steffens C, Kappelmann J, Weiske M, Reich SJ, Wiechert W, Oldiges M, Noack S. Less Sacrifice, More Insight: Repeated Low-Volume Sampling of Microbioreactor Cultivations Enables Accelerated Deep Phenotyping of Microbial Strain Libraries. Biotechnol J 2018; 14:e1800428. [PMID: 30318833 DOI: 10.1002/biot.201800428] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/26/2018] [Indexed: 12/18/2022]
Abstract
With modern genetic engineering tools, high number of potentially improved production strains can be created in a short time. This results in a bottleneck in the succeeding step of bioprocess development, which can be handled by accelerating quantitative microbial phenotyping. Miniaturization and automation are key technologies to achieve this goal. In this study, a novel workflow for repeated low-volume sampling of BioLector-based cultivation setups is presented. Six samples of 20 μL each can be taken automatically from shaken 48-well microtiter plates without disturbing cell population growth. The volume is sufficient for quantification of substrate and product concentrations by spectrophotometric-based enzyme assays. From transient concentration data and replicate cultures, valid performance indicators (titers, rates, yields) are determined through process modeling and random error propagation analysis. Practical relevance of the workflow is demonstrated with a set of five genome-reduced Corynebacterium glutamicum strains that are engineered for Sec-mediated heterologous cutinase secretion. Quantitative phenotyping of this strain library led to the identification of a strain with a 1.6-fold increase in cutinase yield. The prophage-free strain carries combinatorial deletions of three gene clusters (Δ3102-3111, Δ3263-3301, and Δ3324-3345) of which the last two likely contain novel target genes to foster rational engineering of heterologous cutinase secretion in C. glutamicum.
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Affiliation(s)
- Johannes Hemmerich
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Carmen Steffens
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Jannick Kappelmann
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Marc Weiske
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sebastian J Reich
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen, 52062 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Marco Oldiges
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Biotechnology, RWTH Aachen, 52062 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Noack
- Institute of Bio-und Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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27
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Improved microscale cultivation of Pichia pastoris for clonal screening. Fungal Biol Biotechnol 2018; 5:8. [PMID: 29750118 PMCID: PMC5932850 DOI: 10.1186/s40694-018-0053-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/10/2022] Open
Abstract
Background Expanding the application of technical enzymes, e.g., in industry and agriculture, commands the acceleration and cost-reduction of bioprocess development. Microplates and shake flasks are massively employed during screenings and early phases of bioprocess development, although major drawbacks such as low oxygen transfer rates are well documented. In recent years, miniaturization and parallelization of stirred and shaken bioreactor concepts have led to the development of novel microbioreactor concepts. They combine high cultivation throughput with reproducibility and scalability, and represent promising tools for bioprocess development. Results Parallelized microplate cultivation of the eukaryotic protein production host Pichia pastoris was applied effectively to support miniaturized phenotyping of clonal libraries in batch as well as fed-batch mode. By tailoring a chemically defined growth medium, we show that growth conditions are scalable from microliter to 0.8 L lab-scale bioreactor batch cultivation with different carbon sources. Thus, the set-up allows for a rapid physiological comparison and preselection of promising clones based on online data and simple offline analytics. This is exemplified by screening a clonal library of P. pastoris constitutively expressing AppA phytase from Escherichia coli. The protocol was further modified to establish carbon-limited conditions by employing enzymatic substrate-release to achieve screening conditions relevant for later protein production processes in fed-batch mode. Conclusion The comparison of clonal rankings under batch and fed-batch-like conditions emphasizes the necessity to perform screenings under process-relevant conditions. Increased biomass and product concentrations achieved after fed-batch microscale cultivation facilitates the selection of top producers. By reducing the demand to conduct laborious and cost-intensive lab-scale bioreactor cultivations during process development, this study will contribute to an accelerated development of protein production processes. Electronic supplementary material The online version of this article (10.1186/s40694-018-0053-6) contains supplementary material, which is available to authorized users.
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28
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Hemmerich J, Noack S, Wiechert W, Oldiges M. Microbioreactor Systems for Accelerated Bioprocess Development. Biotechnol J 2018; 13:e1700141. [PMID: 29283217 DOI: 10.1002/biot.201700141] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/15/2017] [Indexed: 12/14/2022]
Abstract
In recent years, microbioreactor (MBR) systems have evolved towards versatile bioprocess engineering tools. They provide a unique solution to combine higher experimental throughput with extensive bioprocess monitoring and control, which is indispensable to develop economically and ecologically competitive bioproduction processes. MBR systems are based either on down-scaled stirred tank reactors or on advanced shaken microtiter plate cultivation devices. Importantly, MBR systems make use of optical measurements for non-invasive, online monitoring of important process variables like biomass concentration, dissolved oxygen, pH, and fluorescence. The application range of MBR systems can be further increased by integration into liquid handling robots, enabling automatization and, thus standardization, of various handling and operation procedures. Finally, the tight integration of quantitative strain phenotyping with bioprocess development under industrially relevant conditions greatly increases the probability of finding the right combination of producer strain and bioprocess control strategy. This review will discuss the current state of the art in the field of MBR systems and we can readily conclude that their importance for industrial biotechnology will further increase in the near future.
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Affiliation(s)
- Johannes Hemmerich
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- RWTH Aachen University, Computational Systems Biotechnology (AVT.CSB), Forckenbeckstraße 51, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,RWTH Aachen University, Institute of Biotechnology, Worringer Weg 3, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
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29
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Baumgart M, Unthan S, Kloß R, Radek A, Polen T, Tenhaef N, Müller MF, Küberl A, Siebert D, Brühl N, Marin K, Hans S, Krämer R, Bott M, Kalinowski J, Wiechert W, Seibold G, Frunzke J, Rückert C, Wendisch VF, Noack S. Corynebacterium glutamicum Chassis C1*: Building and Testing a Novel Platform Host for Synthetic Biology and Industrial Biotechnology. ACS Synth Biol 2018; 7:132-144. [PMID: 28803482 DOI: 10.1021/acssynbio.7b00261] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Targeted top-down strategies for genome reduction are considered to have a high potential for providing robust basic strains for synthetic biology and industrial biotechnology. Recently, we created a library of 26 genome-reduced strains of Corynebacterium glutamicum carrying broad deletions in single gene clusters and showing wild-type-like biological fitness. Here, we proceeded with combinatorial deletions of these irrelevant gene clusters in two parallel orders, and the resulting library of 28 strains was characterized under various environmental conditions. The final chassis strain C1* carries a genome reduction of 13.4% (412 deleted genes) and shows wild-type-like growth behavior in defined medium with d-glucose as carbon and energy source. Moreover, C1* proves to be robust against several stresses (including oxygen limitation) and shows long-term growth stability under defined and complex medium conditions. In addition to providing a novel prokaryotic chassis strain, our results comprise a large strain library and a revised genome annotation list, which will be valuable sources for future systemic studies of C. glutamicum.
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Affiliation(s)
- Meike Baumgart
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Simon Unthan
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ramona Kloß
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Andreas Radek
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Tino Polen
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Niklas Tenhaef
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Moritz Fabian Müller
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Andreas Küberl
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Daniel Siebert
- Institute
for Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Natalie Brühl
- Institute
of Biochemistry, University of Cologne, 50923 Cologne, Germany
| | - Kay Marin
- Evonik Nutrition & Care GmbH, 45128 Essen, Germany
| | - Stephan Hans
- Evonik Nutrition & Care GmbH, 45128 Essen, Germany
| | - Reinhard Krämer
- Institute
of Biochemistry, University of Cologne, 50923 Cologne, Germany
| | - Michael Bott
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jörn Kalinowski
- Microbial
Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Wiechert
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational
Systems Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Gerd Seibold
- Institute
for Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Julia Frunzke
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Christian Rückert
- Microbial
Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Volker F. Wendisch
- Chair
of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Stephan Noack
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
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Barz T, Sommer A, Wilms T, Neubauer P, Cruz Bournazou MN. Adaptive optimal operation of a parallel robotic liquid handling station ⁎ ⁎T.B. and A.S. acknowledge partial funding of this project by the Austrian Research Funding Association (FFG) within the programme Bridge in the project modELTES (project No. 851262). M.N.C.B. acknowledge financial support by the German Federal Ministry of Education and Research (BMBF) within the Framework Concept ‘Research for Tomorrow’s Production’ (AUTOBIO). ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ifacol.2018.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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31
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Radek A, Tenhaef N, Müller MF, Brüsseler C, Wiechert W, Marienhagen J, Polen T, Noack S. Miniaturized and automated adaptive laboratory evolution: Evolving Corynebacterium glutamicum towards an improved d-xylose utilization. BIORESOURCE TECHNOLOGY 2017; 245:1377-1385. [PMID: 28552568 DOI: 10.1016/j.biortech.2017.05.055] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 05/22/2023]
Abstract
Adaptive Laboratory Evolution (ALE) is increasingly being used as a technique for untargeted strain optimization. This work aimed at developing an automated and miniaturized ALE approach based on repetitive batch cultivations in microtiter plates. The new method is applied to the recently published strain Corynebacterium glutamicum pEKEx3-xylXABCDCc, which is capable of utilizing d-xylose via the Weimberg (WMB) pathway. As a result, the significantly improved strain WMB2evo was obtained, showing a specific growth rate of 0.26h-1 on d-xylose as sole carbon and energy source. WMB2evo grows stable during lab-scale bioreactor operation, demonstrating the high potential of this strain for future biorefinery applications. Genome sequencing of cell samples from two different ALE processes revealed potential key mutations, e.g. in the gene cg0196 (encoding for the transcriptional regulator IolR of the myo-inositol metabolism). These findings open up new perspectives for the rational engineering of C. glutamicum towards improved d-xylose utilization.
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Affiliation(s)
- Andreas Radek
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Moritz Fabian Müller
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Christian Brüsseler
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany.
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Hemmerich J, Wiechert W, Oldiges M. Automated growth rate determination in high-throughput microbioreactor systems. BMC Res Notes 2017; 10:617. [PMID: 29178966 PMCID: PMC5702135 DOI: 10.1186/s13104-017-2945-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/17/2017] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE The calculation of growth rates provides basic metric for biological fitness and is standard task when using microbioreactors (MBRs) in microbial phenotyping. MBRs easily produce huge data at high frequency from parallelized high-throughput cultivations with online monitoring of biomass formation at high temporal resolution. Resulting high-density data need to be processed efficiently to accelerate experimental throughput. RESULTS A MATLAB code is presented that detects the exponential growth phase from multiple microbial cultivations in an iterative procedure based on several criteria, according to the model of exponential growth. These were obtained with Corynebacterium glutamicum showing single exponential growth phase and Escherichia coli exhibiting diauxic growth with exponential phase followed by retarded growth. The procedure reproducibly detects the correct biomass data subset for growth rate calculation. The procedure was applied on data set detached from growth phenotyping of library of genome reduced C. glutamicum strains and results agree with previously reported results where manual effort was needed to pre-process the data. Thus, the automated and standardized method enables a fair comparison of strain mutants for biological fitness evaluation. The code is easily parallelized and greatly facilitates experimental throughout in biological fitness testing from strain screenings conducted with MBR systems.
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Affiliation(s)
- Johannes Hemmerich
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
- Computational Systems Biotechnology (AVT.CSB), RWTH Aachen, Aachen, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences-IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biotechnology, RWTH Aachen, Aachen, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, Germany
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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] [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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Glauche F, Glazyrina J, Cruz Bournazou MN, Kiesewetter G, Cuda F, Goelling D, Raab A, Lang C, Neubauer P. Detection of growth rate-dependent product formation in miniaturized parallel fed-batch cultivations. Eng Life Sci 2017; 17:1215-1220. [PMID: 32624749 PMCID: PMC6999230 DOI: 10.1002/elsc.201600029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 04/28/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022] Open
Abstract
Saccharomyces cerevisiae is a popular expression system for recombinant proteins. In most cases, production processes are performed as carbon-limited fed-batch cultures to avoid aerobic ethanol formation. Especially for constitutive expression systems, the specific product formation rate depends on the specific growth rate. The development of optimal feeding strategies strongly depends on laboratory-scale cultivations, which are time and resource consuming, especially when continuous experiments are carried out. It is therefore beneficial for accelerated process development to look at alternatives. In this study, S. cerevisiae AH22 secreting a heterologous endo-polygalacturonase (EPG) was characterized in microwell plates with an enzyme-based fed-batch medium. Through variation of the glucose release rate, different growth profiles were established and the impact on EPG secretion was analyzed. Product formation rates of 200-400 U (gx h)-1 were determined. As a reference, bioreactor experiments using the change-stat cultivation technique were performed. The growth-dependent product formation was analyzed over dilution rates of D = 0.01-0.35 with smooth change of D at a rate of 0.003 h-2. EPG production was found to be comparable with a qp of 400 U (gx h)-1 at D = 0.27 h-1. The presented results indicate that parallel miniaturized fed-batch cultures can be applied to determine product formation profiles of putative production strains. With further automation and parallelization of the concept, strain characterization can be performed in shorter time.
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Affiliation(s)
- Florian Glauche
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | - Julia Glazyrina
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | - Fabian Cuda
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | | | - Peter Neubauer
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
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35
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Wilms T, Rischawy DF, Barz T, Esche E, Repke JU, Wagner A, Neubauer P, Cruz Bournazou MN. Dynamic Optimization of the PyNP/PNP Phosphorolytic Enzymatic Process Using MOSAICmodeling. CHEM-ING-TECH 2017. [DOI: 10.1002/cite.201700065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Terrance Wilms
- TU Berlin; Bioprocess Engineering; Ackerstraße 76 13355 Berlin Germany
| | | | - Tilman Barz
- AIT Austrian Institute of Technology GmbH; Donau-City-Straße 1 1220 Vienna Austria
| | - Erik Esche
- TU Berlin; Process Dynamics and Operations Group; Straße des 17. Juni 135 10623 Berlin Germany
| | - Jens-Uwe Repke
- TU Berlin; Process Dynamics and Operations Group; Straße des 17. Juni 135 10623 Berlin Germany
| | - Anke Wagner
- TU Berlin; Bioprocess Engineering; Ackerstraße 76 13355 Berlin Germany
- BioNukleo GmbH; Ackerstraße 76 13355 Berlin Germany
| | - Peter Neubauer
- TU Berlin; Bioprocess Engineering; Ackerstraße 76 13355 Berlin Germany
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Limberg MH, Joachim M, Klein B, Wiechert W, Oldiges M. pH fluctuations imperil the robustness of C. glutamicum to short term oxygen limitation. J Biotechnol 2017; 259:248-260. [DOI: 10.1016/j.jbiotec.2017.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 11/16/2022]
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Protein Secretion in Gram-Positive Bacteria: From Multiple Pathways to Biotechnology. Curr Top Microbiol Immunol 2017; 404:267-308. [PMID: 27885530 DOI: 10.1007/82_2016_49] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A number of Gram-positive bacteria are important players in industry as producers of a diverse array of economically interesting metabolites and proteins. As discussed in this overview, several Gram-positive bacteria are valuable hosts for the production of heterologous proteins. In contrast to Gram-negative bacteria, proteins secreted by Gram-positive bacteria are released into the culture medium where conditions for correct folding are more appropriate, thus facilitating the isolation and purification of active proteins. Although seven different protein secretion pathways have been identified in Gram-positive bacteria, the majority of heterologous proteins are produced via the general secretion or Sec pathway. Not all proteins are equally well secreted, because heterologous protein production often faces bottlenecks including hampered secretion, susceptibility to proteases, secretion stress, and metabolic burden. These bottlenecks are associated with reduced yields leading to non-marketable products. In this chapter, besides a general overview of the different protein secretion pathways, possible hurdles that may hinder efficient protein secretion are described and attempts to improve yield are discussed including modification of components of the Sec pathway. Attention is also paid to omics-based approaches that may offer a more rational approach to optimize production of heterologous proteins.
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Development of a single-cell GlxR-based cAMP biosensor for Corynebacterium glutamicum. J Biotechnol 2017; 258:33-40. [PMID: 28698098 DOI: 10.1016/j.jbiotec.2017.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/03/2017] [Accepted: 07/03/2017] [Indexed: 11/23/2022]
Abstract
Cyclic adenosine monophosphate (cAMP) plays a regulatory role as second messenger in many species. In the industrial model organism Corynebacterium glutamicum, cAMP acts as effector of the global transcriptional regulator GlxR, a homolog of enterobacterial Crp. The cAMP-GlxR complex activates or represses the expression of about 200 target genes. CyaB, a membrane-bound class III adenylate cyclase, synthesizes cAMP from ATP, but another yet unknown cAMP-forming enzyme is likely present in C. glutamicum. Recently, we identified the cAMP phosphodiesterase CpdA, which catalyzes the conversion of cAMP to AMP. As a tool to search for additional cAMP-forming and degrading enzymes, we constructed a plasmid-based cAMP biosensor by fusing the promoter of cg3195, a gene strongly repressed by GlxR, to the eyfp reporter gene. In control experiments, the biosensor showed the predicted responses to increased levels of cAMP or GlxR. The biosensor was able to distinguish between C. glutamicum wild type and mutants with defects in cAMP biosynthesis or degradation. Most importantly, the sensor allowed successful sorting of mixtures of wild type and mutant strains by fluorescence activated cell sorting (FACS), thus meeting the requirements for high-throughput screening of libraries for single mutant cells with an altered cAMP level.
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Ladner T, Mühlmann M, Schulte A, Wandrey G, Büchs J. Prediction of Escherichia coli expression performance in microtiter plates by analyzing only the temporal development of scattered light during culture. J Biol Eng 2017; 11:20. [PMID: 28680476 PMCID: PMC5494857 DOI: 10.1186/s13036-017-0064-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/26/2017] [Indexed: 01/21/2023] Open
Abstract
Background Escherichia coli is often used for recombinant protein production. The expression of recombinant proteins negatively affects the microbial growth, thus, a balance between protein expression and biomass formation is preferable to reach high product- and space-time-yield. Already in screening experiments, suboptimal conditions causing too weak or too strong induction must be avoided. High-throughput screening devices such as the BioLector are often applied for screening experiments. The BioLector allows optical online monitoring of each well in a continuously orbitally shaken microtiter plate via scattered light and fluorescence measurements. This technique enables a fast identification of promising clones. However, to determine the expression performance of non-fluorescent products elaborated offline analysis is often required. Methods A mathematical method is developed to distinguish between cultures, which are insufficiently, optimally or too strongly induced. Therefore, just the temporal development of the scattered light intensity signal is investigated. It is found that discrimination between the different intensities of induction is possible via principal component analysis. By fitting an extended sigmoidal function to the trajectory of the scattered light over time, two characteristic parameters are found. These are used in an empirical model to predict the expression performance. Results The method was established for a wide range of culture conditions based on 625 E. coli cultures. Three E. coli host strains (Tuner(DE3), BL21(DE3), and BL21-Gold(DE3)) expressing either flavin-mononucleotide-based fluorescent protein (FbFP) or Cellulase celA2 were investigated. Cultures were conducted in two different types of microtiter plates (48- and 96-wells), in two online measurement devices at four temperatures (28 °C, 30 °C, 34 °C, and 37 °C). More than 95% of the predicted values are in agreement with the offline measured expression performances with a satisfying accuracy of ±30%. Conclusions The properties of cultures studied can be represented by only two characteristic parameters (slope at and time of the inflection point) received from fitting an extended sigmoidal function to the respective scattered light trajectory. Based on these two characteristic parameters, predictions of the standardized expression performance are possible and for a first screen elaborated offline analysis can be avoided. To the best of our knowledge, this is the first work presenting a method for the general prediction of expression performance of E. coli based solely on the temporal development of scattered light signals. Electronic supplementary material The online version of this article (doi:10.1186/s13036-017-0064-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Ladner
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Martina Mühlmann
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Andreas Schulte
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Georg Wandrey
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Jochen Büchs
- AVT - Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
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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] [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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Morschett H, Freier L, Rohde J, Wiechert W, von Lieres E, Oldiges M. A framework for accelerated phototrophic bioprocess development: integration of parallelized microscale cultivation, laboratory automation and Kriging-assisted experimental design. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:26. [PMID: 28163783 PMCID: PMC5282810 DOI: 10.1186/s13068-017-0711-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/13/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND Even though microalgae-derived biodiesel has regained interest within the last decade, industrial production is still challenging for economic reasons. Besides reactor design, as well as value chain and strain engineering, laborious and slow early-stage parameter optimization represents a major drawback. RESULTS The present study introduces a framework for the accelerated development of phototrophic bioprocesses. A state-of-the-art micro-photobioreactor supported by a liquid-handling robot for automated medium preparation and product quantification was used. To take full advantage of the technology's experimental capacity, Kriging-assisted experimental design was integrated to enable highly efficient execution of screening applications. The resulting platform was used for medium optimization of a lipid production process using Chlorella vulgaris toward maximum volumetric productivity. Within only four experimental rounds, lipid production was increased approximately threefold to 212 ± 11 mg L-1 d-1. Besides nitrogen availability as a key parameter, magnesium, calcium and various trace elements were shown to be of crucial importance. Here, synergistic multi-parameter interactions as revealed by the experimental design introduced significant further optimization potential. CONCLUSIONS The integration of parallelized microscale cultivation, laboratory automation and Kriging-assisted experimental design proved to be a fruitful tool for the accelerated development of phototrophic bioprocesses. By means of the proposed technology, the targeted optimization task was conducted in a very timely and material-efficient manner.
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Affiliation(s)
- Holger Morschett
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Lars Freier
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Jannis Rohde
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Eric von Lieres
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-1: Biotechnology, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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Mühlmann M, Kunze M, Ribeiro J, Geinitz B, Lehmann C, Schwaneberg U, Commandeur U, Büchs J. Cellulolytic RoboLector - towards an automated high-throughput screening platform for recombinant cellulase expression. J Biol Eng 2017; 11:1. [PMID: 28074108 PMCID: PMC5219752 DOI: 10.1186/s13036-016-0043-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/14/2016] [Indexed: 11/20/2022] Open
Abstract
Background Cellulases are key player in the hydrolyzation of cellulose. Unfortunately, this reaction is slow and a bottleneck in the process chain from biomass to intermediates and biofuels due to low activities of the enzymes. To overcome this draw back, a lot of effort is put into the area of protein engineering, to modify these enzymes by directed evolution or rational design. Huge clone libraries are constructed and have to be screened for improved variants. High-throughput screening is the method of choice to tackle this experimental effort, but up to now only a few process steps are adapted to automated platforms and little attention has been turned to the reproducibility of clone rankings. Results In this study, an extended robotic platform is presented to conduct automated high-throughput screenings of clone libraries including preculture synchronization and biomass specific induction. Automated upstream, downstream and analytical process steps are described and evaluated using E. coli and K. lactis as model organisms. Conventional protocols for media preparation, cell lysis, Azo-CMC assay and PAHBAH assay are successfully adapted to automatable high-throughput protocols. Finally, a recombinant E. coli celA2 clone library was screened and a reliable clone ranking could be realized. Conclusion The RoboLector device is a suitable platform to perform all process steps of an automated high-throughput clone library screening for improved cellulases. On-line biomass growth measurement controlling liquid handling actions enables fair comparison of clone variants. Electronic supplementary material The online version of this article (doi:10.1186/s13036-016-0043-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martina Mühlmann
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Martin Kunze
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Joaquim Ribeiro
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Bertram Geinitz
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Christian Lehmann
- Chair for Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Chair for Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ulrich Commandeur
- Chair for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Jochen Büchs
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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Hemmerich J, Rohe P, Kleine B, Jurischka S, Wiechert W, Freudl R, Oldiges M. Use of a Sec signal peptide library from Bacillus subtilis for the optimization of cutinase secretion in Corynebacterium glutamicum. Microb Cell Fact 2016; 15:208. [PMID: 27927208 PMCID: PMC5142396 DOI: 10.1186/s12934-016-0604-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/24/2016] [Indexed: 12/17/2022] Open
Abstract
Background Technical bulk enzymes represent a huge market, and the extracellular production of such enzymes is favorable due to lowered cost for product recovery. Protein secretion can be achieved via general secretion (Sec) pathway. Specific sequences, signal peptides (SPs), are necessary to direct the target protein into the translocation machinery. For example, >150 Sec-specific SPs have been identified for Bacillus subtilis alone. As the best SP for a target protein of choice cannot be predicted a priori, screening of homologous SPs has been shown to be a powerful tool for different expression organisms. While SP libraries between closely related species were successfully applied to optimize recombinant protein secretion, this was not investigated for distantly related species. Therefore, in this study a Sec SP library from low-GC firmicutes B. subtilis is investigated to optimize protein secretion in high-GC actinobacterium Corynebacterium glutamicum using cutinase from Fusarium solani pisi as model protein. Results A homologous SP library (~150 SP) for recombinant cutinase secretion in B. subtilis was successfully transferred to C. glutamicum as alternative secretion host. Cutinase secretion in C. glutamicum was quantified using an automated micro scale cultivation system for online growth monitoring, cell separation and cutinase activity determination. Secretion phenotyping results were correlated to those from a previous study, in which the same SP library was used to optimize secretion of the same cutinase but using B. subtilis as host. Strikingly, behavior of specific SP-cutinase combinations was changed dramatically between B. subtilis and C. glutamicum. Some SPs showed comparable cutinase secretion performances in both hosts, whereas other SPs caused diametrical extracellular cutinase activities. Conclusion The optimal production strain for a specific target protein of choice still cannot be designed in silico. Not only the best SP for a target protein has to be evaluated each time from scratch, the expression host also affects which SP is best. Thus, (heterologous) SP library screening using high-throughput methods is considered to be crucial to construct an optimal production strain for a target protein. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0604-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johannes Hemmerich
- Institute of Bio- and Geosciences-Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
| | - Peter Rohe
- Institute of Bio- and Geosciences-Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany.,Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach, Germany
| | - Britta Kleine
- Institute of Bio- and Geosciences-Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany.,Thermo Fisher Scientific GENEART GmbH, Regensburg, Germany
| | - Sarah Jurischka
- Institute of Bio- and Geosciences-Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences-Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
| | - Roland Freudl
- Institute of Bio- and Geosciences-Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences-Biotechnology (IBG-1), Forschungszentrum Jülich, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany. .,Bioeconomy Science Center (BioSC), Jülich, Germany.
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Affiliation(s)
- Volker F. Wendisch
- Bielefeld University; Genetics of Prokaryotes, Faculty of Biology and CeBiTec; Postfach 100131 33501 Bielefeld Germany
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45
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Bott M, Eggeling L. Novel Technologies for Optimal Strain Breeding. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:227-254. [PMID: 27872965 DOI: 10.1007/10_2016_33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The implementation of a knowledge-based bioeconomy requires the rapid development of highly efficient microbial production strains that are able to convert renewable carbon sources to value-added products, such as bulk and fine chemicals, pharmaceuticals, or proteins at industrial scale. Starting from classical strain breeding by random mutagenesis and screening in the 1950s via rational design by metabolic engineering initiated in the 1970s, a range of powerful new technologies have been developed in the past two decades that can revolutionize future strain engineering. In particular, next-generation sequencing technologies combined with new methods of genome engineering and high-throughput screening based on genetically encoded biosensors have allowed for new concepts. In this chapter, selected new technologies relevant for breeding microbial production strains with a special emphasis on amino acid producers will be summarized.
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Affiliation(s)
- Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany.
| | - Lothar Eggeling
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany
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Recent advances in high-throughput 13C-fluxomics. Curr Opin Biotechnol 2016; 43:104-109. [PMID: 27838571 DOI: 10.1016/j.copbio.2016.10.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
The rise of high throughput (HT) strain engineering tools accompanying the area of synthetic biology is supporting the generation of a large number of microbial cell factories. A current bottleneck in process development is our limited capacity to rapidly analyze the metabolic state of the engineered strains, and in particular their intracellular fluxes. HT 13C-fluxomics workflows have not yet become commonplace, despite the existence of several HT tools at each of the required stages. This includes cultivation and sampling systems, analytics for isotopic analysis, and software for data processing and flux calculation. Here, we review recent advances in the field and highlight bottlenecks that must be overcome to allow the emergence of true HT 13C-fluxomics workflows.
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Limberg MH, Schulte J, Aryani T, Mahr R, Baumgart M, Bott M, Wiechert W, Oldiges M. Metabolic profile of 1,5-diaminopentane producing Corynebacterium glutamicum
under scale-down conditions: Blueprint for robustness to bioreactor inhomogeneities. Biotechnol Bioeng 2016; 114:560-575. [DOI: 10.1002/bit.26184] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/08/2016] [Accepted: 09/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Michael H. Limberg
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Julia Schulte
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Tita Aryani
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Regina Mahr
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Meike Baumgart
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Michael Bott
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
- Institute of Biotechnology; RWTH Aachen University; Aachen Germany
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A Toolbox of Genetically Encoded FRET-Based Biosensors for Rapid l-Lysine Analysis. SENSORS 2016; 16:s16101604. [PMID: 27690044 PMCID: PMC5087393 DOI: 10.3390/s16101604] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/15/2016] [Accepted: 09/20/2016] [Indexed: 12/12/2022]
Abstract
Background: The fast development of microbial production strains for basic and fine chemicals is increasingly carried out in small scale cultivation systems to allow for higher throughput. Such parallelized systems create a need for new rapid online detection systems to quantify the respective target compound. In this regard, biosensors, especially genetically encoded Förster resonance energy transfer (FRET)-based biosensors, offer tremendous opportunities. As a proof-of-concept, we have created a toolbox of FRET-based biosensors for the ratiometric determination of l-lysine in fermentation broth. Methods: The sensor toolbox was constructed based on a sensor that consists of an optimized central lysine-/arginine-/ornithine-binding protein (LAO-BP) flanked by two fluorescent proteins (enhanced cyan fluorescent protein (ECFP), Citrine). Further sensor variants with altered affinity and sensitivity were obtained by circular permutation of the binding protein as well as the introduction of flexible and rigid linkers between the fluorescent proteins and the LAO-BP, respectively. Results: The sensor prototype was applied to monitor the extracellular l-lysine concentration of the l-lysine producing Corynebacterium glutamicum (C. glutamicum) strain DM1933 in a BioLector® microscale cultivation device. The results matched well with data obtained by HPLC analysis and the Ninhydrin assay, demonstrating the high potential of FRET-based biosensors for high-throughput microbial bioprocess optimization.
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Morschett H, Schiprowski D, Müller C, Mertens K, Felden P, Meyer J, Wiechert W, Oldiges M. Design and validation of a parallelized micro-photobioreactor enabling phototrophic bioprocess development at elevated throughput. Biotechnol Bioeng 2016; 114:122-131. [DOI: 10.1002/bit.26051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/05/2016] [Accepted: 07/15/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Holger Morschett
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology Jülich Germany
| | - Danny Schiprowski
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology Jülich Germany
| | | | | | | | | | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology Jülich Germany
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology Jülich Germany
- Institute of Biotechnology; RWTH Aachen University; Aachen Germany
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Radek A, Müller MF, Gätgens J, Eggeling L, Krumbach K, Marienhagen J, Noack S. Formation of xylitol and xylitol-5-phosphate and its impact on growth of d-xylose-utilizing Corynebacterium glutamicum strains. J Biotechnol 2016; 231:160-166. [PMID: 27297548 DOI: 10.1016/j.jbiotec.2016.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
Abstract
Wild-type Corynebacterium glutamicum has no endogenous metabolic activity for utilizing the lignocellulosic pentose d-xylose for cell growth. Therefore, two different engineering approaches have been pursued resulting in platform strains harbouring a functional version of either the Isomerase (ISO) or the Weimberg (WMB) pathway for d-xylose assimilation. In a previous study we found for C. glutamicum WMB by-product formation of xylitol during growth on d-xylose and speculated that the observed lower growth rates are due to the growth inhibiting effect of this compound. Based on a detailed phenotyping of the ISO, WMB and the wild-type strain of C. glutamicum, we here show that this organism has a natural capability to synthesize xylitol from d-xylose under aerobic cultivation conditions. We furthermore observed the intracellular accumulation of xylitol-5-phosphate as a result of the intracellular phosphorylation of xylitol, which was particularly pronounced in the C. glutamicum ISO strain. Interestingly, low amounts of supplemented xylitol strongly inhibit growth of this strain on d-xylose, d-glucose and d-arabitol. These findings demonstrate that xylitol is a suitable substrate of the endogenous xylulokinase (XK, encoded by xylB) and its overexpression in the ISO strain leads to a significant phosphorylation of xylitol in C. glutamicum. Therefore, in order to circumvent cytotoxicity by xylitol-5-phosphate, the WMB pathway represents an interesting alternative route for engineering C. glutamicum towards efficient d-xylose utilization.
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Affiliation(s)
- Andreas Radek
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Moritz-Fabian Müller
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Jochem Gätgens
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Lothar Eggeling
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Karin Krumbach
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany.
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