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Arpino JAJ, Hancock EJ, Anderson J, Barahona M, Stan GBV, Papachristodoulou A, Polizzi K. Tuning the dials of Synthetic Biology. MICROBIOLOGY-SGM 2013; 159:1236-1253. [PMID: 23704788 PMCID: PMC3749727 DOI: 10.1099/mic.0.067975-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Synthetic Biology is the ‘Engineering of Biology’ – it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components, we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of ‘dials’ that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post-translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others.
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Affiliation(s)
- James A J Arpino
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Edward J Hancock
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - James Anderson
- St John's College, St Giles, Oxford OX1 3JP, UK.,Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Mauricio Barahona
- Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Guy-Bart V Stan
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | - Karen Polizzi
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.,Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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152
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Shong J, Huang YM, Bystroff C, Collins CH. Directed evolution of the quorum-sensing regulator EsaR for increased signal sensitivity. ACS Chem Biol 2013; 8:789-95. [PMID: 23363022 DOI: 10.1021/cb3006402] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of cell-cell communication or "quorum sensing (QS)" elements from Gram-negative Proteobacteria has enabled synthetic biologists to begin engineering systems composed of multiple interacting organisms. However, additional tools are necessary if we are to progress toward synthetic microbial consortia that exhibit more complex, dynamic behaviors. EsaR from Pantoea stewartii subsp. stewartii is a QS regulator that binds to DNA as an apoprotein and releases the DNA when it binds to its cognate signal molecule, 3-oxohexanoyl-homoserine lactone (3OC6HSL). In the absence of 3OC6HSL, EsaR binds to DNA and can act as either an activator or a repressor of transcription. Gene expression from P(esaR), which is repressed by wild-type EsaR, requires 100- to 1000-fold higher concentrations of signal than commonly used QS activators, such as LuxR and LasR. Here we have identified EsaR variants with increased sensitivity to 3OC6HSL using directed evolution and a dual ON/OFF screening strategy. Although we targeted EsaR-dependent derepression of P(esaR), our EsaR variants also showed increased 3OC6HSL sensitivity at a second promoter, P(esaS), which is activated by EsaR in the absence of 3OC6HSL. Here, the increase in AHL sensitivity led to gene expression being turned off at lower concentrations of 3OC6HSL. Overall, we have increased the signal sensitivity of EsaR more than 70-fold and generated a set of EsaR variants that recognize 3OC6HSL concentrations ranging over 4 orders of magnitude. QS-dependent transcriptional regulators that bind to DNA and are active in the absence of a QS signal represent a new set of tools for engineering cell-cell communication-dependent gene expression.
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Affiliation(s)
- Jasmine Shong
- Department
of Chemical and Biological Engineering, ‡Department of Biology, and §Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic
Institute, 110 8th St., Troy, New York 12180, United States
| | - Yao-Ming Huang
- Department
of Chemical and Biological Engineering, ‡Department of Biology, and §Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic
Institute, 110 8th St., Troy, New York 12180, United States
| | - Christopher Bystroff
- Department
of Chemical and Biological Engineering, ‡Department of Biology, and §Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic
Institute, 110 8th St., Troy, New York 12180, United States
| | - Cynthia H. Collins
- Department
of Chemical and Biological Engineering, ‡Department of Biology, and §Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic
Institute, 110 8th St., Troy, New York 12180, United States
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153
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Bacchus W, Fussenegger M. Engineering of synthetic intercellular communication systems. Metab Eng 2013; 16:33-41. [DOI: 10.1016/j.ymben.2012.12.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 12/03/2012] [Accepted: 12/05/2012] [Indexed: 10/27/2022]
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156
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Abstract
Microbial ecosystems play an important role in nature. Engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. Here we provide a review of recent progress in engineering natural and synthetic microbial ecosystems. We highlight important forward engineering design principles, theoretical and quantitative models, new experimental and manipulation tools, and possible applications of microbial ecosystem engineering. We argue that simply engineering individual microbes will lead to fragile homogenous populations that are difficult to sustain, especially in highly heterogeneous and unpredictable environments. Instead, engineered microbial ecosystems are likely to be more robust and able to achieve complex tasks at the spatial and temporal resolution needed for truly programmable biology.
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Affiliation(s)
- Michael T Mee
- Department of Biomedical Engineering, Boston University, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Harris H Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
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157
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Brune KD, Bayer TS. Engineering microbial consortia to enhance biomining and bioremediation. Front Microbiol 2012; 3:203. [PMID: 22679443 PMCID: PMC3367458 DOI: 10.3389/fmicb.2012.00203] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/17/2012] [Indexed: 01/28/2023] Open
Abstract
In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage.
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Affiliation(s)
- Karl D Brune
- Centre for Synthetic Biology and Innovation, Division of Molecular Biosciences, Imperial College London, London, UK
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158
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Abstract
Metabolism is a highly interconnected web of chemical reactions that power life. Though the stoichiometry of metabolism is well understood, the multidimensional aspects of metabolic regulation in time and space remain difficult to define, model and engineer. Complex metabolic conversions can be performed by multiple species working cooperatively and exchanging metabolites via structured networks of organisms and resources. Within cells, metabolism is spatially regulated via sequestration in subcellular compartments and through the assembly of multienzyme complexes. Metabolic engineering and synthetic biology have had success in engineering metabolism in the first and second dimensions, designing linear metabolic pathways and channeling metabolic flux. More recently, engineering of the third dimension has improved output of engineered pathways through isolation and organization of multicell and multienzyme complexes. This review highlights natural and synthetic examples of three-dimensional metabolism both inter- and intracellularly, offering tools and perspectives for biological design.
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