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McNerney MP, Styczynski MP. Small molecule signaling, regulation, and potential applications in cellular therapeutics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10. [PMID: 28960879 DOI: 10.1002/wsbm.1405] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/20/2017] [Accepted: 08/14/2017] [Indexed: 12/19/2022]
Abstract
Small molecules have many important roles across the tree of life: they regulate processes from metabolism to transcription, they enable signaling within and between species, and they serve as the biochemical building blocks for cells. They also represent valuable phenotypic endpoints that are promising for use as biomarkers of disease states. In the context of engineering cell-based therapeutics, they hold particularly great promise for enabling finer control over the therapeutic cells and allowing them to be responsive to extracellular cues. The natural signaling and regulatory functions of small molecules can be harnessed and rewired to control cell activity and delivery of therapeutic payloads, potentially increasing efficacy while decreasing toxicity. To that end, this review considers small molecule-mediated regulation and signaling in bacteria. We first discuss some of the most prominent applications and aspirations for responsive cell-based therapeutics. We then describe the transport, signaling, and regulation associated with three classes of molecules that may be exploited in the engineering of therapeutic bacteria: amino acids, fatty acids, and quorum-sensing signaling molecules. We also present examples of existing engineering efforts to generate cells that sense and respond to levels of different small molecules. Finally, we discuss future directions for how small molecule-mediated regulation could be harnessed for therapeutic applications, as well as some critical considerations for the ultimate success of such endeavors. WIREs Syst Biol Med 2018, 10:e1405. doi: 10.1002/wsbm.1405 This article is categorized under: Biological Mechanisms > Cell Signaling Biological Mechanisms > Metabolism Translational, Genomic, and Systems Medicine > Therapeutic Methods.
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Affiliation(s)
- Monica P McNerney
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
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Schmitz AC, Hartline CJ, Zhang F. Engineering Microbial Metabolite Dynamics and Heterogeneity. Biotechnol J 2017; 12. [PMID: 28901715 DOI: 10.1002/biot.201700422] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/06/2017] [Indexed: 11/09/2022]
Abstract
As yields for biological chemical production in microorganisms approach their theoretical maximum, metabolic engineering requires new tools, and approaches for improvements beyond what traditional strategies can achieve. Engineering metabolite dynamics and metabolite heterogeneity is necessary to achieve further improvements in product titers, productivities, and yields. Metabolite dynamics, the ensemble change in metabolite concentration over time, arise from the need for microbes to adapt their metabolism in response to the extracellular environment and are important for controlling growth and productivity in industrial fermentations. Metabolite heterogeneity, the cell-to-cell variation in a metabolite concentration in an isoclonal population, has a significant impact on ensemble productivity. Recent advances in single cell analysis enable a more complete understanding of the processes driving metabolite heterogeneity and reveal metabolic engineering targets. The authors present an overview of the mechanistic origins of metabolite dynamics and heterogeneity, why they are important, their potential effects in chemical production processes, and tools and strategies for engineering metabolite dynamics and heterogeneity. The authors emphasize that the ability to control metabolite dynamics and heterogeneity will bring new avenues of engineering to increase productivity of microbial strains.
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Affiliation(s)
- Alexander C Schmitz
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Christopher J Hartline
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, USA.,Division of Biological and Biomedical Sciences, and Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, USA
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53
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Biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass. J Biotechnol 2017; 257:211-221. [DOI: 10.1016/j.jbiotec.2016.11.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 01/17/2023]
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Kadisch M, Willrodt C, Hillen M, Bühler B, Schmid A. Maximizing the stability of metabolic engineering-derived whole-cell biocatalysts. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600170] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/22/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Marvin Kadisch
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Christian Willrodt
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Michael Hillen
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Bruno Bühler
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Andreas Schmid
- Department Solar Materials; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
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Binder D, Drepper T, Jaeger KE, Delvigne F, Wiechert W, Kohlheyer D, Grünberger A. Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity. Metab Eng 2017. [DOI: 10.1016/j.ymben.2017.06.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Delvigne F, Baert J, Sassi H, Fickers P, Grünberger A, Dusny C. Taking control over microbial populations: Current approaches for exploiting biological noise in bioprocesses. Biotechnol J 2017; 12. [PMID: 28544731 DOI: 10.1002/biot.201600549] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 01/19/2023]
Abstract
Phenotypic plasticity of microbial cells has attracted much attention and several research efforts have been dedicated to the description of methods aiming at characterizing phenotypic heterogeneity and its impact on microbial populations. However, different approaches have also been suggested in order to take benefit from noise in a bioprocess perspective, e.g. by increasing the robustness or productivity of a microbial population. This review is dedicated to outline these controlling methods. A common issue, that has still to be addressed, is the experimental identification and the mathematical expression of noise. Indeed, the effective interfacing of microbial physiology with external parameters that can be used for controlling physiology depends on the acquisition of reliable signals. Latest technologies, like single cell microfluidics and advanced flow cytometric approaches, enable linking physiology, noise, heterogeneity in productive microbes with environmental cues and hence allow correctly mapping and predicting biological behavior via mathematical representations. However, like in the field of electronics, signals are perpetually subjected to noise. If appropriately interpreted, this noise can give an additional insight into the behavior of the individual cells within a microbial population of interest. This review focuses on recent progress made at describing, treating and exploiting biological noise in the context of microbial populations used in various bioprocess applications.
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Affiliation(s)
- Frank Delvigne
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Jonathan Baert
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Hosni Sassi
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Patrick Fickers
- University of Liège, TERRA research center, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI lab), Gembloux, Belgium
| | - Alexander Grünberger
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, Jülich, Germany.,Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
| | - Christian Dusny
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
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Westerwalbesloh C, Grünberger A, Wiechert W, Kohlheyer D, von Lieres E. Coarse-graining bacteria colonies for modelling critical solute distributions in picolitre bioreactors for bacterial studies on single-cell level. Microb Biotechnol 2017; 10:845-857. [PMID: 28371389 PMCID: PMC5481542 DOI: 10.1111/1751-7915.12708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 01/18/2023] Open
Abstract
Microfluidic single‐cell bioreactors have found widespread application to investigate growth and gene expression of microbial model organisms, but yet there are few attempts to systematically characterize different design and cultivation concepts. Quantitative measurements of critical solute concentrations, e.g. limiting nutrients, are not yet feasible within the typical volumes in the range of picolitres. A way to gain new insights about the mass transport within those volumes is by simulation, but the complex geometry resulting from the multitude of cells within a colony leads to time and resource consuming computational challenges. In this work, six different concepts for the model representation of cellular microcolonies within microfluidic monolayer growth chamber devices are compared. The Gini coefficient is proposed as new measure for inhomogeneity within cellular colonies. An example cell colony is represented by a single point source, a cylindrical volume with homogeneous reaction rates with and without adjusted diffusion coefficient, as point sources for each single cell and as rod‐shaped, diffusion blocking, three‐dimensional cells with varying shapes. Simulated concentration profiles across the chambers depended strongly on the chosen cell representation. The representation with the lowest degree of abstraction, three‐dimensional cells, leads to complex geometries and high computational effort, but also gives a conservative and therefore preferable estimate for the cultivation conditions within a given cultivation chamber geometry. Interestingly, the cylindrical volume with adjusted diffusion coefficient gives similar results but requires far less computational effort. Therefore, it is proposed to use the three‐dimensional cells for detailed studies and to determine parameters for the cylindrical volume with adjusted diffusion coefficient, which can then be used for experimental design, screening of parameter spaces, and similar applications.
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Affiliation(s)
- Christoph Westerwalbesloh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Eric von Lieres
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
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58
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Genetic biosensors for small-molecule products: Design and applications in high-throughput screening. Front Chem Sci Eng 2017. [DOI: 10.1007/s11705-017-1629-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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59
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Light-Controlled Cell Factories: Employing Photocaged Isopropyl-β-d-Thiogalactopyranoside for Light-Mediated Optimization of lac Promoter-Based Gene Expression and (+)-Valencene Biosynthesis in Corynebacterium glutamicum. Appl Environ Microbiol 2016; 82:6141-6149. [PMID: 27520809 DOI: 10.1128/aem.01457-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 07/28/2016] [Indexed: 11/20/2022] Open
Abstract
Precise control of microbial gene expression resulting in a defined, fast, and homogeneous response is of utmost importance for synthetic bio(techno)logical applications. However, even broadly applied biotechnological workhorses, such as Corynebacterium glutamicum, for which induction of recombinant gene expression commonly relies on the addition of appropriate inducer molecules, perform moderately in this respect. Light offers an alternative to accurately control gene expression, as it allows for simple triggering in a noninvasive fashion with unprecedented spatiotemporal resolution. Thus, optogenetic switches are promising tools to improve the controllability of existing gene expression systems. In this regard, photocaged inducers, whose activities are initially inhibited by light-removable protection groups, represent one of the most valuable photoswitches for microbial gene expression. Here, we report on the evaluation of photocaged isopropyl-β-d-thiogalactopyranoside (IPTG) as a light-responsive control element for the frequently applied tac-based expression module in C. glutamicum In contrast to conventional IPTG, the photocaged inducer mediates a tightly controlled, strong, and homogeneous expression response upon short exposure to UV-A light. To further demonstrate the unique potential of photocaged IPTG for the optimization of production processes in C. glutamicum, the optogenetic switch was finally used to improve biosynthesis of the growth-inhibiting sesquiterpene (+)-valencene, a flavoring agent and aroma compound precursor in food industry. The variation in light intensity as well as the time point of light induction proved crucial for efficient production of this toxic compound. IMPORTANCE Optogenetic tools are light-responsive modules that allow for a simple triggering of cellular functions with unprecedented spatiotemporal resolution and in a noninvasive fashion. Specifically, light-controlled gene expression exhibits an enormous potential for various synthetic bio(techno)logical purposes. Before our study, poor inducibility, together with phenotypic heterogeneity, was reported for the IPTG-mediated induction of lac-based gene expression in Corynebacterium glutamicum By applying photocaged IPTG as a synthetic inducer, however, these drawbacks could be almost completely abolished. Especially for increasing numbers of parallelized expression cultures, noninvasive and spatiotemporal light induction qualifies for a precise, homogeneous, and thus higher-order control to fully automatize or optimize future biotechnological applications.
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60
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Sachs CC, Grünberger A, Helfrich S, Probst C, Wiechert W, Kohlheyer D, Nöh K. Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments. PLoS One 2016; 11:e0163453. [PMID: 27661996 PMCID: PMC5035088 DOI: 10.1371/journal.pone.0163453] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/07/2016] [Indexed: 11/18/2022] Open
Abstract
Background Microfluidic lab-on-chip technology combined with live-cell imaging has enabled the observation of single cells in their spatio-temporal context. The mother machine (MM) cultivation system is particularly attractive for the long-term investigation of rod-shaped bacteria since it facilitates continuous cultivation and observation of individual cells over many generations in a highly parallelized manner. To date, the lack of fully automated image analysis software limits the practical applicability of the MM as a phenotypic screening tool. Results We present an image analysis pipeline for the automated processing of MM time lapse image stacks. The pipeline supports all analysis steps, i.e., image registration, orientation correction, channel/cell detection, cell tracking, and result visualization. Tailored algorithms account for the specialized MM layout to enable a robust automated analysis. Image data generated in a two-day growth study (≈ 90 GB) is analyzed in ≈ 30 min with negligible differences in growth rate between automated and manual evaluation quality. The proposed methods are implemented in the software molyso (MOther machine AnaLYsis SOftware) that provides a new profiling tool to analyze unbiasedly hitherto inaccessible large-scale MM image stacks. Conclusion Presented is the software molyso, a ready-to-use open source software (BSD-licensed) for the unsupervised analysis of MM time-lapse image stacks. molyso source code and user manual are available at https://github.com/modsim/molyso.
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Affiliation(s)
- Christian Carsten Sachs
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Alexander Grünberger
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stefan Helfrich
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christopher Probst
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dietrich Kohlheyer
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Katharina Nöh
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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61
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Binder D, Probst C, Grünberger A, Hilgers F, Loeschcke A, Jaeger KE, Kohlheyer D, Drepper T. Comparative Single-Cell Analysis of Different E. coli Expression Systems during Microfluidic Cultivation. PLoS One 2016; 11:e0160711. [PMID: 27525986 PMCID: PMC4985164 DOI: 10.1371/journal.pone.0160711] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/22/2016] [Indexed: 01/25/2023] Open
Abstract
Recombinant protein production is mostly realized with large-scale cultivations and monitored at the level of the entire population. Detailed knowledge of cell-to-cell variations with respect to cellular growth and product formation is limited, even though phenotypic heterogeneity may distinctly hamper overall production yields, especially for toxic or difficult-to-express proteins. Unraveling phenotypic heterogeneity is thus a key aspect in understanding and optimizing recombinant protein production in biotechnology and synthetic biology. Here, microfluidic single-cell analysis serves as the method of choice to investigate and unmask population heterogeneities in a dynamic and spatiotemporal fashion. In this study, we report on comparative microfluidic single-cell analyses of commonly used E. coli expression systems to uncover system-inherent specifications in the synthetic M9CA growth medium. To this end, the PT7lac/LacI, the PBAD/AraC and the Pm/XylS system were systematically analyzed in order to gain detailed insights into variations of growth behavior and expression phenotypes and thus to uncover individual strengths and deficiencies at the single-cell level. Specifically, we evaluated the impact of different system-specific inducers, inducer concentrations as well as genetic modifications that affect inducer-uptake and regulation of target gene expression on responsiveness and phenotypic heterogeneity. Interestingly, the most frequently applied expression system based on E. coli strain BL21(DE3) clearly fell behind with respect to expression homogeneity and robustness of growth. Moreover, both the choice of inducer and the presence of inducer uptake systems proved crucial for phenotypic heterogeneity. Conclusively, microfluidic evaluation of different inducible E. coli expression systems and setups identified the modified lacY-deficient PT7lac/LacI as well as the Pm/XylS system with conventional m-toluic acid induction as key players for precise and robust triggering of bacterial gene expression in E. coli in a homogeneous fashion.
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Affiliation(s)
- Dennis Binder
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Christopher Probst
- Institute of Bio- and Geosciences (IBG-1), Forschungszentrum Jülich, Jülich, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences (IBG-1), Forschungszentrum Jülich, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-1), Forschungszentrum Jülich, Jülich, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences (IBG-1), Forschungszentrum Jülich, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- * E-mail:
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Mahr R, von Boeselager RF, Wiechert J, Frunzke J. Screening of an Escherichia coli promoter library for a phenylalanine biosensor. Appl Microbiol Biotechnol 2016; 100:6739-6753. [PMID: 27170323 DOI: 10.1007/s00253-016-7575-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/14/2016] [Accepted: 04/21/2016] [Indexed: 02/06/2023]
Abstract
In recent years, the application of transcription factor-based biosensors for the engineering of microbial production strains opened up new opportunities for industrial biotechnology. However, the design of synthetic regulatory circuits depends on the selection of suitable transcription factor-promoter pairs to convert the concentration of effector molecules into a measureable output. Here, we present an efficient strategy to screen promoter libraries for appropriate parts for biosensor design. To this end, we pooled the strains of the Alon library containing about 2000 different Escherichia coli promoter-gfpmut2 fusions, and enriched galactose- and L-phenylalanine-responsive promoters by toggled rounds of positive and negative selection using fluorescence-activated cell sorting (FACS). For both effectors, responsive promoters were isolated and verified by cultivation in microtiter plates. The promoter of mtr, encoding an L-tryptophan-specific transporter, was identified as suitable part for the construction of an L-phenylalanine biosensor. In the following, we performed a comparative analysis of different biosensor constructs based on the mtr promoter. The obtained data revealed a strong influence of the biosensor architecture on the performance characteristics. For proof-of-principle, the mtr sensor was applied in a FACS high-throughput screening of an E. coli MG1655 mutant library for the isolation of L-phenylalanine producers. These results emphasize the developed screening approach as a convenient strategy for the identification of effector-responsive promoters for the design of novel biosensors.
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Affiliation(s)
- Regina Mahr
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | | | - Johanna Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
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Recent advances in amino acid production by microbial cells. Curr Opin Biotechnol 2016; 42:133-146. [PMID: 27151315 DOI: 10.1016/j.copbio.2016.04.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 12/25/2022]
Abstract
Amino acids have been utilized for the production of foods, animal feeds and pharmaceuticals. After the discovery of the glutamic acid-producing bacterium Corynebacterium glutamicum by Japanese researchers, the production of amino acids, which are primary metabolites, has been achieved using various microbial cells as hosts. Recently, metabolic engineering studies on the rational design of amino acid-producing microbial cells have been successfully conducted. Moreover, the technology of systems biology has been applied to metabolic engineering for the creation of amino acid-producing microbial cells. Currently, new technologies including synthetic biology, single-cell analysis, and evolutionary engineering have been utilized to create amino acid-producing microbial cells. In addition, useful compounds from amino acids have been produced by microbial cells. Here, current researches into the metabolic engineering of microbial cells toward production of amino acids and amino acid-related compounds are reviewed.
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64
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Updates on industrial production of amino acids using Corynebacterium glutamicum. World J Microbiol Biotechnol 2016; 32:105. [DOI: 10.1007/s11274-016-2060-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/27/2016] [Indexed: 12/14/2022]
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Abstract
The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.
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Affiliation(s)
- Songzi Kou
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Danhui Cheng
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fei Sun
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - I-Ming Hsing
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong. and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Intermediate-sensor assisted push–pull strategy and its application in heterologous deoxyviolacein production in Escherichia coli. Metab Eng 2016; 33:41-51. [DOI: 10.1016/j.ymben.2015.10.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 09/22/2015] [Accepted: 10/15/2015] [Indexed: 01/29/2023]
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Ma CW, Zhou LB, Zeng AP. Engineering Biomolecular Switches for Dynamic Metabolic Control. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:45-76. [DOI: 10.1007/10_2016_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Tian X, Zhang N, Yang Y, Wang Y, Chu J, Zhuang Y, Zhang S. The effect of redox environment on l -lactic acid production by Lactobacillus paracasei —A proof by genetically encoded in vivo NADH biosensor. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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69
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Westerwalbesloh C, Grünberger A, Stute B, Weber S, Wiechert W, Kohlheyer D, von Lieres E. Modeling and CFD simulation of nutrient distribution in picoliter bioreactors for bacterial growth studies on single-cell level. LAB ON A CHIP 2015; 15:4177-4186. [PMID: 26345659 DOI: 10.1039/c5lc00646e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A microfluidic device for microbial single-cell cultivation of bacteria was modeled and simulated using COMSOL Multiphysics. The liquid velocity field and the mass transfer within the supply channels and cultivation chambers were calculated to gain insight in the distribution of supplied nutrients and metabolic products secreted by the cultivated bacteria. The goal was to identify potential substrate limitations or product accumulations within the cultivation device. The metabolic uptake and production rates, colony size, and growth medium composition were varied covering a wide range of operating conditions. Simulations with glucose as substrate did not show limitations within the typically used concentration range, but for alternative substrates limitations could not be ruled out. This lays the foundation for further studies and the optimization of existing picoliter bioreactor systems.
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Mahr R, Gätgens C, Gätgens J, Polen T, Kalinowski J, Frunzke J. Biosensor-driven adaptive laboratory evolution of l-valine production in Corynebacterium glutamicum. Metab Eng 2015; 32:184-194. [DOI: 10.1016/j.ymben.2015.09.017] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/01/2015] [Accepted: 09/21/2015] [Indexed: 11/25/2022]
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Mahr R, Frunzke J. Transcription factor-based biosensors in biotechnology: current state and future prospects. Appl Microbiol Biotechnol 2015; 100:79-90. [PMID: 26521244 PMCID: PMC4700088 DOI: 10.1007/s00253-015-7090-3] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 01/01/2023]
Abstract
Living organisms have evolved a plethora of sensing systems for the intra- and extracellular detection of small molecules, ions or physical parameters. Several recent studies have demonstrated that these principles can be exploited to devise synthetic regulatory circuits for metabolic engineering strategies. In this context, transcription factors (TFs) controlling microbial physiology at the level of transcription play a major role in biosensor design, since they can be implemented in synthetic circuits controlling gene expression in dependency of, for example, small molecule production. Here, we review recent progress on the utilization of TF-based biosensors in microbial biotechnology highlighting different areas of application. Recent advances in metabolic engineering reveal TF-based sensors to be versatile tools for strain and enzyme development using high-throughput (HT) screening strategies and adaptive laboratory evolution, the optimization of heterologous pathways via the implementation of dynamic control circuits and for the monitoring of single-cell productivity in live cell imaging studies. These examples underline the immense potential of TF-based biosensor circuits but also identify limitations and room for further optimization.
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Affiliation(s)
- Regina Mahr
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Ladner T, Flitsch D, Schlepütz T, Büchs J. Online monitoring of dissolved oxygen tension in microtiter plates based on infrared fluorescent oxygen-sensitive nanoparticles. Microb Cell Fact 2015; 14:161. [PMID: 26452344 PMCID: PMC4600283 DOI: 10.1186/s12934-015-0347-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/25/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND During the past years, new high-throughput screening systems with capabilities of online monitoring turned out to be powerful tools for the characterization of microbial cell cultures. These systems are often easy to use, offer economic advantages compared to larger systems and allow to determine many important process parameters within short time. Fluorescent protein tags tremendously simplified the tracking and observation of cellular activity in vivo. Unfortunately, interferences between established fluorescence based dissolved oxygen tension (DOT) measurement techniques and fluorescence-based protein tags appeared. Therefore, the applicability of new oxygen-sensitive nanoparticles operated within the more suitable infrared wavelength region are introduced and validated for DOT measurement. RESULTS The biocompatibility of the used dispersed oxygen-sensitive nanoparticles was proven via RAMOS cultivations for Hansenula polymorpha, Gluconobacter oxydans, and Escherichia coli. The applicability of the introduced DOT measurement technique for online monitoring of cultivations was demonstrated and successfully validated. The nanoparticles showed no disturbing effect on the online measurement of the fluorescence intensities of the proteins GFP, mCherry and YFP measured by a BioLector prototype. Additionally, the DOT measurement was not influenced by changing concentrations of these proteins. The kLa values for the applied cultivation conditions were successfully determined based on the measured DOT. CONCLUSIONS The introduced technique appeared to be practically as well as economically advantageous for DOT online measuring in microtiter plates. The disadvantage of limited availability of microtiter plates with immobilized sensor spots (optodes) does not apply for this introduced technique. Due to the infrared wavelength range, used for the DOT measurement, no interferences with biogenic fluorescence or with expressed fluorescent proteins (e.g. YFP, GFP or mCherry) occur.
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Affiliation(s)
- Tobias Ladner
- AVT, Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - David Flitsch
- AVT, Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Tino Schlepütz
- AVT, Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Jochen Büchs
- AVT, Aachener Verfahrenstechnik, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
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Grünberger A, Probst C, Helfrich S, Nanda A, Stute B, Wiechert W, von Lieres E, Nöh K, Frunzke J, Kohlheyer D. Spatiotemporal microbial single-cell analysis using a high-throughput microfluidics cultivation platform. Cytometry A 2015; 87:1101-15. [DOI: 10.1002/cyto.a.22779] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/26/2015] [Accepted: 08/19/2015] [Indexed: 12/18/2022]
Affiliation(s)
| | - Christopher Probst
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
| | - Stefan Helfrich
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
| | - Arun Nanda
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
| | - Birgit Stute
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
| | - Eric von Lieres
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
| | - Katharina Nöh
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
| | - Julia Frunzke
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
| | - Dietrich Kohlheyer
- Forschungszentrum Jülich GmbH, IBG-1: Biotechnology; Jülich 52425 Germany
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Helfrich S, Azzouzi CE, Probst C, Seiffarth J, Grünberger A, Wiechert W, Kohlheyer D, Nöh K. Vizardous: interactive analysis of microbial populations with single cell resolution. Bioinformatics 2015; 31:3875-7. [PMID: 26261223 DOI: 10.1093/bioinformatics/btv468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/05/2015] [Indexed: 01/28/2023] Open
Abstract
MOTIVATION Single cell time-lapse microscopy is a powerful method for investigating heterogeneous cell behavior. Advances in microfluidic lab-on-a-chip technologies and live-cell imaging render the parallel observation of the development of individual cells in hundreds of populations possible. While image analysis tools are available for cell detection and tracking, biologists are still confronted with the challenge of exploring and evaluating this data. RESULTS We present the software tool Vizardous that assists scientists with explorative analysis and interpretation tasks of single cell data in an interactive, configurable and visual way. With Vizardous, lineage tree drawings can be augmented with various, time-resolved cellular characteristics. Associated statistical moments bridge the gap between single cell and the population-average level. AVAILABILITY AND IMPLEMENTATION The software, including documentation and examples, is available as executable Java archive as well as in source form at https://github.com/modsim/vizardous. CONTACT k.noeh@fz-juelich.de. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefan Helfrich
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany
| | - Charaf E Azzouzi
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany
| | - Christopher Probst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany
| | - Johannes Seiffarth
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Germany
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Dusny C, Grünberger A, Probst C, Wiechert W, Kohlheyer D, Schmid A. Technical bias of microcultivation environments on single-cell physiology. LAB ON A CHIP 2015; 15:1822-1834. [PMID: 25710324 DOI: 10.1039/c4lc01270d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Microscale cultivation systems are important tools to elucidate cellular dynamics beyond the population average and understand the functional architecture of single cells. However, there is scant knowledge about the bias of different microcultivation technologies on cellular functions. We therefore performed a systematic cross-platform comparison of three different microscale cultivation systems commonly harnessed in single-cell analysis: microfluidic non-contact cell traps driven by negative dielectrophoresis, microfluidic monolayer growth chambers, and semi-solid agarose pads. We assessed the specific single-cell growth rates, division rates and morphological characteristics of single Corynebacterium glutamicum cells and microcolonies as a bacterial model organism with medical and biotechnological relevance under standardized growth conditions. Strikingly, the specific single-cell and microcolony growth rates, μmax, were robust and conserved for several cell generations with all three microcultivation technologies, whereas the division rates of cells grown on agarose pads deviated by up to 50% from those of cells cultivated in negative dielectrophoresis traps and monolayer growth chambers. Furthermore, morphological characteristics like cell lengths and division symmetries of individual cells were affected when the cells were grown on agarose pads. This indicated a significant impact of solid cultivation supports on cellular traits. The results demonstrate the impact of microcultivation technology on microbial physiology for the first time and show the need for a careful selection and design of the microcultivation technology in order to allow unbiased analysis of cellular behavior.
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Affiliation(s)
- Christian Dusny
- Laboratory of Chemical Biotechnology, Department of Biochemical & Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 66, 44227 Dortmund, Germany.
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Vasdekis AE, Stephanopoulos G. Review of methods to probe single cell metabolism and bioenergetics. Metab Eng 2015; 27:115-135. [PMID: 25448400 PMCID: PMC4399830 DOI: 10.1016/j.ymben.2014.09.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 11/26/2022]
Abstract
Single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. Herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. Firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. We also highlight specific advances in microbiology for its implications in metabolic engineering. Methods for probing single cell physiology and metabolism are subsequently reviewed. The primary focus therein is on dynamic and high-content profiling strategies based on label-free and fluorescence microspectroscopy and microscopy. Non-dynamic approaches, such as mass spectrometry and nuclear magnetic resonance, are also briefly discussed.
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Affiliation(s)
- Andreas E Vasdekis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99354, USA.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, MA 02139, USA.
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Delvigne F, Zune Q, Lara AR, Al-Soud W, Sørensen SJ. Metabolic variability in bioprocessing: implications of microbial phenotypic heterogeneity. Trends Biotechnol 2014; 32:608-16. [DOI: 10.1016/j.tibtech.2014.10.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 09/24/2014] [Accepted: 10/01/2014] [Indexed: 12/19/2022]
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79
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Grünberger A, Wiechert W, Kohlheyer D. Single-cell microfluidics: opportunity for bioprocess development. Curr Opin Biotechnol 2014; 29:15-23. [DOI: 10.1016/j.copbio.2014.02.008] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/29/2014] [Accepted: 02/13/2014] [Indexed: 10/25/2022]
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80
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Application of metabolic engineering for the biotechnological production of l-valine. Appl Microbiol Biotechnol 2014; 98:5859-70. [DOI: 10.1007/s00253-014-5782-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/17/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
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81
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Binder D, Grünberger A, Loeschcke A, Probst C, Bier C, Pietruszka J, Wiechert W, Kohlheyer D, Jaeger KE, Drepper T. Light-responsive control of bacterial gene expression: precise triggering of thelacpromoter activity using photocaged IPTG. Integr Biol (Camb) 2014; 6:755-65. [DOI: 10.1039/c4ib00027g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An optogenetic tool was established allowing for precise, gradual and homogeneous light-triggering oflac-based gene expression in a non-invasive fashion.
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