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Affiliation(s)
| | - Hal S. Alper
- McKetta Department of Chemical Engineering and
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712;
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52
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Synthetic biology advances for pharmaceutical production. Curr Opin Biotechnol 2015; 35:46-51. [PMID: 25744872 PMCID: PMC4617476 DOI: 10.1016/j.copbio.2015.02.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 01/12/2023]
Abstract
Synthetic biology is quickly moving from proof of concept to industrial application. Pharmaceuticals are a promising target for advanced genetic engineering. Genome sequence data indicate vast underexploited biosynthetic capacity. Synthetic biology can create libraries of novel chemicals enriched for bioactivity. Synthetic biology expands the range of available chassis organisms for industry.
Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems.
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53
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Li M, Borodina I. Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae. FEMS Yeast Res 2015; 15:1-12. [PMID: 25238571 DOI: 10.1111/1567-1364.12213] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/13/2014] [Accepted: 09/15/2014] [Indexed: 11/29/2022] Open
Abstract
Synthetic biology and metabolic engineering enable generation of novel cell factories that efficiently convert renewable feedstocks into biofuels, bulk, and fine chemicals, thus creating the basis for biosustainable economy independent on fossil resources. While over a hundred proof-of-concept chemicals have been made in yeast, only a very small fraction of those has reached commercial-scale production so far. The limiting factor is the high research cost associated with the development of a robust cell factory that can produce the desired chemical at high titer, rate, and yield. Synthetic biology has the potential to bring down this cost by improving our ability to predictably engineer biological systems. This review highlights synthetic biology applications for design, assembly, and optimization of non-native biochemical pathways in baker's yeast Saccharomyces cerevisiae We describe computational tools for the prediction of biochemical pathways, molecular biology methods for assembly of DNA parts into pathways, and for introducing the pathways into the host, and finally approaches for optimizing performance of the introduced pathways.
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Affiliation(s)
- Mingji Li
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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54
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Muschiol J, Peters C, Oberleitner N, Mihovilovic MD, Bornscheuer UT, Rudroff F. Cascade catalysis – strategies and challenges en route to preparative synthetic biology. Chem Commun (Camb) 2015; 51:5798-811. [DOI: 10.1039/c4cc08752f] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this feature article recent progress and future perspectives of cascade catalysis combining bio/bio or bio/chemo catalysts are presented.
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Affiliation(s)
- Jan Muschiol
- Institute of Biochemistry
- Dept. of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17489 Greifswald
- Germany
| | - Christin Peters
- Institute of Biochemistry
- Dept. of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17489 Greifswald
- Germany
| | - Nikolin Oberleitner
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- 1060 Vienna
- Austria
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- 1060 Vienna
- Austria
| | - Uwe T. Bornscheuer
- Institute of Biochemistry
- Dept. of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17489 Greifswald
- Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- 1060 Vienna
- Austria
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55
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Dudley QM, Karim AS, Jewett MC. Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnol J 2015; 10:69-82. [PMID: 25319678 PMCID: PMC4314355 DOI: 10.1002/biot.201400330] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/24/2014] [Accepted: 08/22/2014] [Indexed: 12/20/2022]
Abstract
Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility.
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Affiliation(s)
| | | | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- Member, Institute for Bionanotechnology in Medicine, Northwestern University, Chicago, IL, USA
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56
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Fehér T, Planson AG, Carbonell P, Fernández-Castané A, Grigoras I, Dariy E, Perret A, Faulon JL. Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering. Biotechnol J 2014; 9:1446-57. [PMID: 25224453 DOI: 10.1002/biot.201400055] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 07/28/2014] [Accepted: 09/15/2014] [Indexed: 01/29/2023]
Abstract
Metabolic engineering has succeeded in biosynthesis of numerous commodity or high value compounds. However, the choice of pathways and enzymes used for production was many times made ad hoc, or required expert knowledge of the specific biochemical reactions. In order to rationalize the process of engineering producer strains, we developed the computer-aided design (CAD) tool RetroPath that explores and enumerates metabolic pathways connecting the endogenous metabolites of a chassis cell to the target compound. To experimentally validate our tool, we constructed 12 top-ranked enzyme combinations producing the flavonoid pinocembrin, four of which displayed significant yields. Namely, our tool queried the enzymes found in metabolic databases based on their annotated and predicted activities. Next, it ranked pathways based on the predicted efficiency of the available enzymes, the toxicity of the intermediate metabolites and the calculated maximum product flux. To implement the top-ranking pathway, our procedure narrowed down a list of nine million possible enzyme combinations to 12, a number easily assembled and tested. One round of metabolic network optimization based on RetroPath output further increased pinocembrin titers 17-fold. In total, 12 out of the 13 enzymes tested in this work displayed a relative performance that was in accordance with its predicted score. These results validate the ranking function of our CAD tool, and open the way to its utilization in the biosynthesis of novel compounds.
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Affiliation(s)
- Tamás Fehér
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Evry Cedex, France
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57
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Brophy JAN, Voigt CA. Principles of genetic circuit design. Nat Methods 2014; 11:508-20. [PMID: 24781324 DOI: 10.1038/nmeth.2926] [Citation(s) in RCA: 568] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/18/2014] [Indexed: 12/17/2022]
Abstract
Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.
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Affiliation(s)
- Jennifer A N Brophy
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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58
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Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon JL. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res 2014; 42:W389-94. [PMID: 24792156 PMCID: PMC4086079 DOI: 10.1093/nar/gku362] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As metabolic engineering and synthetic biology progress toward reaching the goal of a more sustainable use of biological resources, the need of increasing the number of value-added chemicals that can be produced in industrial organisms becomes more imperative. Exploring, however, the vast possibility of pathways amenable to engineering through heterologous genes expression in a chassis organism is complex and unattainable manually. Here, we present XTMS, a web-based pathway analysis platform available at http://xtms.issb.genopole.fr, which provides full access to the set of pathways that can be imported into a chassis organism such as Escherichia coli through the application of an Extended Metabolic Space modeling framework. The XTMS approach consists on determining the set of biochemical transformations that can potentially be processed in vivo as modeled by molecular signatures, a specific coding system for derivation of reaction rules for metabolic reactions and enumeration of all the corresponding substrates and products. Most promising routes are described in terms of metabolite exchange, maximum allowable pathway yield, toxicity and enzyme efficiency. By answering such critical design points, XTMS not only paves the road toward the rationalization of metabolic engineering, but also opens new processing possibilities for non-natural metabolites and novel enzymatic transformations.
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Affiliation(s)
- Pablo Carbonell
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | - Pierre Parutto
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | - Joan Herisson
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
| | | | - Jean-Loup Faulon
- University of Evry, iSSB, F-91000 Evry, France CNRS, iSSB, F-91000 Evry, France
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