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Ravikumar S, David Y, Park SJ, Choi JI. A Chimeric Two-Component Regulatory System-Based Escherichia coli Biosensor Engineered to Detect Glutamate. Appl Biochem Biotechnol 2018; 186:335-349. [DOI: 10.1007/s12010-018-2746-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/21/2018] [Indexed: 12/13/2022]
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Lehning CE, Heidelberger JB, Reinhard J, Nørholm MHH, Draheim RR. A Modular High-Throughput In Vivo Screening Platform Based on Chimeric Bacterial Receptors. ACS Synth Biol 2017; 6:1315-1326. [PMID: 28372360 DOI: 10.1021/acssynbio.6b00288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Multidrug resistance (MDR) is a globally relevant problem that requires novel approaches. Two-component systems are a promising, yet untapped target for novel antibacterials. They are prevalent in bacteria and absent in mammals, and their activity can be modulated upon perception of various stimuli. Screening pre-existing compound libraries could reveal small molecules that inhibit stimulus-perception by virulence-modulating receptors, reduce signal output from essential receptors or identify artificial stimulatory ligands for novel SHKs that are involved in virulence. Those small molecules could possess desirable therapeutic properties to combat MDR. We propose that a modular screening platform in which the periplasmic domain of the targeted receptors are fused to the cytoplasmic domain of a well-characterized receptor that governs fluorescence reporter genes could be employed to rapidly screen currently existing small molecule libraries. Here, we have examined two previously created Tar-EnvZ chimeras and a novel NarX-EnvZ chimera. We demonstrate that it is possible to couple periplasmic stimulus-perceiving domains to an invariable cytoplasmic domain that governs transcription of a dynamic fluorescent reporter system. Furthermore, we show that aromatic tuning, or repositioning the aromatic residues at the end of the second transmembrane helix (TM2), modulates baseline signal output from the tested chimeras and even restores output from a nonfunctional NarX-EnvZ chimera. Finally, we observe an inverse correlation between baseline signal output and the degree of response to cognate stimuli. In summary, we propose that the platform described here, a fluorescent Escherichia coli reporter strain with plasmid-based expression of the aromatically tuned chimeric receptors, represents a synthetic biology approach to rapidly screen pre-existing compound libraries for receptor-modulating activities.
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Affiliation(s)
- Christina E. Lehning
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark
| | | | - John Reinhard
- Buchmann
Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, D-60438, Frankfurt, Germany
| | - Morten H. H. Nørholm
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark
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Chang YC, Armitage JP, Papachristodoulou A, Wadhams GH. A single phosphatase can convert a robust step response into a graded, tunable or adaptive response. MICROBIOLOGY-SGM 2013; 159:1276-1285. [PMID: 23704783 DOI: 10.1099/mic.0.066324-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many biological signalling pathways have evolved to produce responses to environmental signals that are robust to fluctuations in protein copy number and noise. Whilst beneficial for biology, this robustness can be problematic for synthetic biologists wishing to re-engineer and subsequently tune the response of a given system. Here we show that the well-characterized EnvZ/OmpR two-component signalling system from Escherichia coli possesses one such robust step response. However, the synthetic addition of just a single component into the system, an extra independently controllable phosphatase, can change this behaviour to become graded and tunable, and even show adaptation. Our approach introduces a new design principle which can be implemented simply in engineering and redesigning fast signal transduction pathways for synthetic biology.
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Affiliation(s)
- Yo-Cheng Chang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan, ROC.,Oxford Centre for Integrative Systems Biology, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Judith P Armitage
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Oxford Centre for Integrative Systems Biology, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK
| | - Antonis Papachristodoulou
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK.,Oxford Centre for Integrative Systems Biology, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK
| | - George H Wadhams
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Oxford Centre for Integrative Systems Biology, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, UK
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Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression. Curr Opin Biotechnol 2012; 23:689-94. [DOI: 10.1016/j.copbio.2011.12.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 12/14/2011] [Accepted: 12/15/2011] [Indexed: 01/06/2023]
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Lynch JB, Sonnenburg JL. Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system. Mol Microbiol 2012; 85:478-91. [PMID: 22686399 PMCID: PMC3404733 DOI: 10.1111/j.1365-2958.2012.08123.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteroides is a dominant genus within the intestinal microbiota of healthy humans. Key adaptations of the Bacteroides to the dynamic intestinal ecosystem include a diverse repertoire of genes involved in sensing and processing numerous diet- and host-derived polysaccharides. One such adaptation is the carbohydrate-sensing hybrid two-component system (HTCS) family of signalling sensors, which has been widely expanded within the Bacteroides. Using Bacteroides thetaiotaomicron as a model, we have created a chimeric HTCS consisting of the well-characterized sensing domain of one HTCS, BT1754, and the regulatory domain of another HTCS, BT0366, to explore the regulatory capabilities of these molecules. We found that the BT0366 regulatory region directly binds to and mediates induction of the adjacent polysaccharide utilization locus (PUL) using whole-genome transcriptional profiling after inducing signalling through our chimeric protein. We also found that BT0366 activation simultaneously leads to repression of distal PULs involved in mucus carbohydrate consumption. These results suggest a novel mechanism by which an HTCS enforces a nutrient hierarchy within the Bacteroides via induction and repression of multiple PULs. Thus, hybrid two-component systems provide a mechanism for prioritizing consumption of carbohydrates through simultaneous binding and regulation of multiple polysaccharide utilization loci.
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Affiliation(s)
- Jonathan B Lynch
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Ferris HU, Dunin-Horkawicz S, Hornig N, Hulko M, Martin J, Schultz JE, Zeth K, Lupas AN, Coles M. Mechanism of regulation of receptor histidine kinases. Structure 2012; 20:56-66. [PMID: 22244755 DOI: 10.1016/j.str.2011.11.014] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 11/16/2011] [Accepted: 11/17/2011] [Indexed: 02/02/2023]
Abstract
Bacterial transmembrane receptors regulate an intracellular catalytic output in response to extracellular sensory input. To investigate the conformational changes that relay the regulatory signal, we have studied the HAMP domain, a ubiquitous intracellular module connecting input to output domains. HAMP forms a parallel, dimeric, four-helical coiled coil, and rational substitutions in our model domain (Af1503 HAMP) induce a transition in its interhelical packing, characterized by axial rotation of all four helices (the gearbox signaling model). We now illustrate how these conformational changes are propagated to a downstream domain by fusing Af1503 HAMP variants to the DHp domain of EnvZ, a bacterial histidine kinase. Structures of wild-type and mutant constructs are correlated with ligand response in vivo, clearly associating them with distinct signaling states. We propose that altered recognition of the catalytic domain by DHp, rather than a shift in position of the phospho-accepting histidine, forms the basis for regulation of kinase activity.
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Affiliation(s)
- Hedda U Ferris
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
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Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol 2010; 406:215-27. [PMID: 21185306 DOI: 10.1016/j.jmb.2010.12.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Revised: 12/05/2010] [Accepted: 12/08/2010] [Indexed: 11/20/2022]
Abstract
Many applications require cells to switch between discrete phenotypic states. Here, we harness the FimBE inversion switch to flip a promoter, allowing expression to be toggled between two genes oriented in opposite directions. The response characteristics of the switch are characterized using two-color cytometry. This switch is used to toggle between orthogonal chemosensory pathways by controlling the expression of CheW and CheW*, which interact with the Tar (aspartate) and Tsr* (serine) chemoreceptors, respectively. CheW* and Tsr* each contain a mutation at their protein-protein interface such that they interact with each other. The complete genetic program containing an arabinose-inducible FimE controlling CheW/CheW* (and constitutively expressed tar/tsr*) is transformed into an Escherichia coli strain lacking all native chemoreceptors. This program enables bacteria to swim toward serine or aspartate in the absence or in the presence of arabinose, respectively. Thus, the program functions as a multiplexer with arabinose as the selector. This demonstrates the ability of synthetic genetic circuits to connect to a natural signaling network to switch between phenotypes.
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Nistala GJ, Wu K, Rao CV, Bhalerao KD. A modular positive feedback-based gene amplifier. J Biol Eng 2010; 4:4. [PMID: 20187959 PMCID: PMC2845093 DOI: 10.1186/1754-1611-4-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 02/26/2010] [Indexed: 11/13/2022] Open
Abstract
Background Positive feedback is a common mechanism used in the regulation of many gene circuits as it can amplify the response to inducers and also generate binary outputs and hysteresis. In the context of electrical circuit design, positive feedback is often considered in the design of amplifiers. Similar approaches, therefore, may be used for the design of amplifiers in synthetic gene circuits with applications, for example, in cell-based sensors. Results We developed a modular positive feedback circuit that can function as a genetic signal amplifier, heightening the sensitivity to inducer signals as well as increasing maximum expression levels without the need for an external cofactor. The design utilizes a constitutively active, autoinducer-independent variant of the quorum-sensing regulator LuxR. We experimentally tested the ability of the positive feedback module to separately amplify the output of a one-component tetracycline sensor and a two-component aspartate sensor. In each case, the positive feedback module amplified the response to the respective inducers, both with regards to the dynamic range and sensitivity. Conclusions The advantage of our design is that the actual feedback mechanism depends only on a single gene and does not require any other modulation. Furthermore, this circuit can amplify any transcriptional signal, not just one encoded within the circuit or tuned by an external inducer. As our design is modular, it can potentially be used as a component in the design of more complex synthetic gene circuits.
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Affiliation(s)
- Goutam J Nistala
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, 1304 W Pennsylvania Ave, Urbana, IL, 61801, USA
| | - Kang Wu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, 61801, USA
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, 61801, USA
| | - Kaustubh D Bhalerao
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, 1304 W Pennsylvania Ave, Urbana, IL, 61801, USA
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Synthetic gene networks: the next wave in biotechnology? Trends Biotechnol 2009; 27:368-74. [PMID: 19409633 DOI: 10.1016/j.tibtech.2009.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 02/24/2009] [Accepted: 03/02/2009] [Indexed: 11/22/2022]
Abstract
Engineering novel, reusable gene networks to provide greater control over cellular processes is one of the goals of the emerging discipline of synthetic biology. This article reviews the landmark literature pertaining to the development of synthetic gene networks, the engineering framework used to design and characterize them and the technological developments on the horizon that could potentially advance the field in new directions. As gene network engineering enters its second decade, an attempt is also made to outline the challenges in advancing this nascent field, especially with regard to the practical limitations of component reusability and reliability and the opportunities that present themselves in the development of novel gene expression controllers and single-cell biosensors.
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Voigt CA. Genetic parts to program bacteria. Curr Opin Biotechnol 2006; 17:548-57. [PMID: 16978856 DOI: 10.1016/j.copbio.2006.09.001] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 07/21/2006] [Accepted: 09/01/2006] [Indexed: 12/27/2022]
Abstract
Genetic engineering is entering a new era, where microorganisms can be programmed using synthetic constructs of DNA encoding logic and operational commands. A toolbox of modular genetic parts is being developed, comprised of cell-based environmental sensors and genetic circuits. Systems have already been designed to be interconnected with each other and interfaced with the control of cellular processes. Engineering theory will provide a predictive framework to design operational multicomponent systems. On the basis of these developments, increasingly complex cellular machines are being constructed to build specialty chemicals, weave biomaterials, and to deliver therapeutics.
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Affiliation(s)
- Christopher A Voigt
- Biophysics and Chemistry & Chemical Biology, Department of Pharmaceutical Chemistry, University of California San Francisco, QB3 Box 2540, 1700 4th Street, San Francisco, CA 94158, USA.
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