251
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Nucleic acids for the rational design of reaction circuits. Curr Opin Biotechnol 2013; 24:575-80. [DOI: 10.1016/j.copbio.2012.11.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/08/2012] [Accepted: 11/29/2012] [Indexed: 11/18/2022]
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252
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In Vitro Multienzymatic Reaction Systems for Biosynthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:153-84. [DOI: 10.1007/10_2013_232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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253
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Jewett MC, Fritz BR, Timmerman LE, Church GM. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation. Mol Syst Biol 2013; 9:678. [PMID: 23799452 PMCID: PMC3964315 DOI: 10.1038/msb.2013.31] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 05/12/2013] [Indexed: 01/22/2023] Open
Abstract
This report describes an integrated method for in vitro construction of Escherichia coli ribosomes under near-physiological conditions. This method enables coupling of ribosome synthesis and assembly in a single, integrated system. ![]()
An integrated synthesis, assembly, and translation technology (termed iSAT) was developed to construct ribosomes in vitro. iSAT mimics co-transcription of rRNA and ribosome assembly as it occurs in vivo. iSAT makes possible the in vitro construction of modified ribosomes. iSAT is expected to aid studies of ribosome assembly and open new avenues for making ribosomes with altered capabilities.
Purely in vitro ribosome synthesis could provide a critical step towards unraveling the systems biology of ribosome biogenesis, constructing minimal cells from defined components, and engineering ribosomes with new functions. Here, as an initial step towards this goal, we report a method for constructing Escherichia coli ribosomes in crude S150 E. coli extracts. While conventional methods for E. coli ribosome reconstitution are non-physiological, our approach attempts to mimic chemical conditions in the cytoplasm, thus permitting several biological processes to occur simultaneously. Specifically, our integrated synthesis, assembly, and translation (iSAT) technology enables one-step co-activation of rRNA transcription, assembly of transcribed rRNA with native ribosomal proteins into functional ribosomes, and synthesis of active protein by these ribosomes in the same compartment. We show that iSAT makes possible the in vitro construction of modified ribosomes by introducing a 23S rRNA mutation that mediates resistance against clindamycin. We anticipate that iSAT will aid studies of ribosome assembly and open new avenues for making ribosomes with altered properties.
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Affiliation(s)
- Michael C Jewett
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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254
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Nourian Z, Danelon C. Linking genotype and phenotype in protein synthesizing liposomes with external supply of resources. ACS Synth Biol 2013; 2:186-93. [PMID: 23656477 DOI: 10.1021/sb300125z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reconstituting an elementary gene expression system inside self-assembled lipid vesicles to mimic the cellular synthesis machinery is at the core of the development of a minimal cell following a bottom-up synthetic biology approach. The ability to operate the expression of multiple genes in a controlled manner and to generate the output proteins with predictable dynamics in liposomes relies on the link between genotype and phenotype. Here, we established this link in surface-tethered liposomes producing proteins from a linear DNA template using a reconstituted transcription/translation/aminoacylation apparatus fuelled by external supply of feedstock. The amounts of entrapped DNA molecules and synthesized proteins were visualized by fluorescence confocal microscopy in individual vesicles. We showed that there exists no linear correlation between the amount of encapsulated genes and the level of output proteins, which is a consequence of the compositional heterogeneity between liposomes due to the low-copy number of some constituents, as well as interfacing differences with the nutrient-containing environment. In order to decouple gene activity from those sources of variability and, thus, infer the probabilistic occupancy of transcriptionally active genes in protein synthesizing liposomes, we developed a dual gene expression assay consisting of the production of two fluorescent reporter proteins of distinguishable colors from two different DNA templates. The stochastic color-coding of the vesicles was analyzed and compared to the color pattern expected from a Poisson distribution of encapsulated genes. Unexpectedly, we found that the apparent number of transcriptionally active DNA molecules in liposomes corresponds only to ca. 10% of the bulk concentration. We believe that our study provides new insights about the relationship between the genotype and phenotype in protein synthesizing liposomes, which is of primary importance toward the construction of a programmable artificial cell implemented with regulatory gene networks of predictable dynamics.
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Affiliation(s)
- Zohreh Nourian
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628
CJ, Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628
CJ, Delft, The Netherlands
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255
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Woodley JM. Protein engineering of enzymes for process applications. Curr Opin Chem Biol 2013; 17:310-6. [PMID: 23562542 DOI: 10.1016/j.cbpa.2013.03.017] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 12/14/2022]
Abstract
Scientific progress in the field of enzyme modification today enables the opportunity to tune a given biocatalyst for a specific industrial application. Much work has been focused on extending the substrate repertoire and altering selectivity. Nevertheless, it is clear that many new forthcoming opportunities will be targeted on modification to enable process application. This article discusses the challenges involved in enzyme modification focused on process requirements, such as the need to fulfill reaction thermodynamics, specific activity under the required conditions, kinetics at required concentrations, and stability. Finally, future research directions are discussed, including the integration of biocatalysis with neighboring chemical steps.
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Affiliation(s)
- John M Woodley
- Center for Process Engineering and Technology, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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256
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You C, Zhang YHP. Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling. ACS Synth Biol 2013; 2:102-10. [PMID: 23656373 DOI: 10.1021/sb300068g] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One-step purification of a multi-enzyme complex was developed based on a mixture of cell extracts containing three dockerin-containing enzymes and one family 3 cellulose-binding module (CBM3)-containing scaffoldin through high-affinity adsorption on low-cost solid regenerated amorphous cellulose (RAC). The three-enzyme complex, called synthetic metabolon, was self-assembled through the high-affinity interaction between the dockerin in each enzyme and three cohesins in the synthetic scaffoldin. The metabolons were either immobilized on the external surface of RAC or free when the scaffoldin contained an intein between the CBM3 and three cohesins. The immobilized and free metabolons containing triosephosphate isomerase, aldolase, and fructose 1,6-biphosphatase exhibited initial reaction rates 48 and 38 times, respectively, that of the non-complexed three-enzyme mixture at the same enzyme loading. Such reaction rate enhancements indicated strong substrate channeling among synthetic metabolons due to the close spatial organization among cascade enzymes. These results suggested that the construction of synthetic metabolons by using cohesins, dockerins, and cellulose-binding modules from cellulosomes not only decreased protein purification labor and cost for in vitro synthetic biology projects but also accelerated reaction rates by 1 order of magnitude compared to non-complexed enzymes. Synthetic metabolons would be an important biocatalytic module for in vitro and in vivo synthetic biology projects.
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Affiliation(s)
- Chun You
- Biological Systems Engineering Department, Virginia Tech, Blacksburg, VA 24061, USA
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257
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Whittaker JW. Cell-free protein synthesis: the state of the art. Biotechnol Lett 2013; 35:143-52. [PMID: 23086573 PMCID: PMC3553302 DOI: 10.1007/s10529-012-1075-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
Cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. Like PCR, which uses cellular replication machinery to create a DNA amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. By breaking free from the constraints of cell-based systems, it takes the next step towards synthetic biology. Recent advances in reconstituted cell-free protein synthesis (Protein synthesis Using Recombinant Elements expression systems) are creating new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, printing protein microarrays, isotopic labeling, and incorporating nonnatural amino acids.
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Affiliation(s)
- James W Whittaker
- Division of Environmental and Biomolecular Systems, Institute for Environmental Health, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006-8921, USA.
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258
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Chappell J, Jensen K, Freemont PS. Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology. Nucleic Acids Res 2013; 41:3471-81. [PMID: 23371936 PMCID: PMC3597704 DOI: 10.1093/nar/gkt052] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A bottleneck in our capacity to rationally and predictably engineer biological systems is the limited number of well-characterized genetic elements from which to build. Current characterization methods are tied to measurements in living systems, the transformation and culturing of which are inherently time-consuming. To address this, we have validated a completely in vitro approach for the characterization of DNA regulatory elements using Escherichia coli extract cell-free systems. Importantly, we demonstrate that characterization in cell-free systems correlates and is reflective of performance in vivo for the most frequently used DNA regulatory elements. Moreover, we devise a rapid and completely in vitro method to generate DNA templates for cell-free systems, bypassing the need for DNA template generation and amplification from living cells. This in vitro approach is significantly quicker than current characterization methods and is amenable to high-throughput techniques, providing a valuable tool for rapidly prototyping libraries of DNA regulatory elements for synthetic biology.
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Affiliation(s)
- James Chappell
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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259
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Rupp S. Next-generation bioproduction systems: Cell-free conversion concepts for industrial biotechnology. Eng Life Sci 2013. [DOI: 10.1002/elsc.201100237] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Steffen Rupp
- Department of Molecular Biotechnology; Fraunhofer IGB; Stuttgart; Germany
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260
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Goers L, Kylilis N, Tomazou M, Yan Wen K, Freemont P, Polizzi K. Engineering Microbial Biosensors. METHODS IN MICROBIOLOGY 2013. [DOI: 10.1016/b978-0-12-417029-2.00005-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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261
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Cell-free Biosystems in the Production of Electricity and Bioenergy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:125-52. [PMID: 23748347 DOI: 10.1007/10_2013_201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
: Increasing needs of green energy and concerns of climate change are motivating intensive R&D efforts toward the low-cost production of electricity and bioenergy, such as hydrogen, alcohols, and jet fuel, from renewable sugars. Cell-free biosystems for biomanufacturing (CFB2) have been suggested as an emerging platform to replace mainstream microbial fermentation for the cost-effective production of some biocommodities. As compared to whole-cell factories, cell-free biosystems comprised of synthetic enzymatic pathways have numerous advantages, such as high product yield, fast reaction rate, broad reaction condition, easy process control and regulation, tolerance of toxic compound/product, and an unmatched capability of performing unnatural reactions. However, issues pertaining to high costs and low stabilities of enzymes and cofactors as well as compromised optimal conditions for different source enzymes need to be solved before cell-free biosystems are scaled up for biomanufacturing. Here, we review the current status of cell-free technology, update recent advances, and focus on its applications in the production of electricity and bioenergy.
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262
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Affiliation(s)
- Jan-Karl Guterl
- Lehrstuhl für Chemie Biogener Rohstoffe; Technische Universität München; Straubing; Germany
| | - Volker Sieber
- Lehrstuhl für Chemie Biogener Rohstoffe; Technische Universität München; Straubing; Germany
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263
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Shin J, Jardine P, Noireaux V. Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth Biol 2012; 1:408-13. [PMID: 23651338 DOI: 10.1021/sb300049p] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of living entities in the laboratory is a standing challenge that calls for innovative approaches. Using a cell-free transcription-translation system as a molecular programming platform, we show that the bacteriophage T7, encoded by a 40 kbp DNA program composed of about 60 genes, can be entirely synthesized from its genomic DNA in a test tube reaction. More than a billion infectious bacteriophages T7 per milliliter of reaction are produced after a few hours of incubation. The replication of the genomic DNA occurs concurrently with phage gene expression, protein synthesis, and viral assembly. The demonstration that genome-sized viral DNA can be expressed in a test tube, recapitulating the entire chain of information processing including the replication of the DNA instructions, opens new possibilities to program and to study complex biochemical systems in vitro.
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Affiliation(s)
- Jonghyeon Shin
- School
of Physics and Astronomy and ‡Department of Diagnostic and Biological Sciences
and Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Paul Jardine
- School
of Physics and Astronomy and ‡Department of Diagnostic and Biological Sciences
and Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Vincent Noireaux
- School
of Physics and Astronomy and ‡Department of Diagnostic and Biological Sciences
and Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States
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264
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Ye X, Honda K, Sakai T, Okano K, Omasa T, Hirota R, Kuroda A, Ohtake H. Synthetic metabolic engineering-a novel, simple technology for designing a chimeric metabolic pathway. Microb Cell Fact 2012; 11:120. [PMID: 22950411 PMCID: PMC3512521 DOI: 10.1186/1475-2859-11-120] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/31/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The integration of biotechnology into chemical manufacturing has been recognized as a key technology to build a sustainable society. However, the practical applications of biocatalytic chemical conversions are often restricted due to their complexities involving the unpredictability of product yield and the troublesome controls in fermentation processes. One of the possible strategies to overcome these limitations is to eliminate the use of living microorganisms and to use only enzymes involved in the metabolic pathway. Use of recombinant mesophiles producing thermophilic enzymes at high temperature results in denaturation of indigenous proteins and elimination of undesired side reactions; consequently, highly selective and stable biocatalytic modules can be readily prepared. By rationally combining those modules together, artificial synthetic pathways specialized for chemical manufacturing could be designed and constructed. RESULTS A chimeric Embden-Meyerhof (EM) pathway with balanced consumption and regeneration of ATP and ADP was constructed by using nine recombinant E. coli strains overproducing either one of the seven glycolytic enzymes of Thermus thermophilus, the cofactor-independent phosphoglycerate mutase of Pyrococcus horikoshii, or the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase of Thermococcus kodakarensis. By coupling this pathway with the Thermus malate/lactate dehydrogenase, a stoichiometric amount of lactate was produced from glucose with an overall ATP turnover number of 31. CONCLUSIONS In this study, a novel and simple technology for flexible design of a bespoke metabolic pathway was developed. The concept has been testified via a non-ATP-forming chimeric EM pathway. We designated this technology as "synthetic metabolic engineering". Our technology is, in principle, applicable to all thermophilic enzymes as long as they can be functionally expressed in the host, and thus would be potentially applicable to the biocatalytic manufacture of any chemicals or materials on demand.
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Affiliation(s)
- Xiaoting Ye
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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265
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Subsoontorn P, Kim J, Winfree E. Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch. ACS Synth Biol 2012; 1:299-316. [PMID: 23651285 DOI: 10.1021/sb300018h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An overarching goal of synthetic and systems biology is to engineer and understand complex biochemical systems by rationally designing and analyzing their basic component interactions. Practically, the extent to which such reductionist approaches can be applied is unclear especially as the complexity of the system increases. Toward gradually increasing the complexity of systematically engineered systems, programmable synthetic circuits operating in cell-free in vitro environments offer a valuable testing ground for principles for the design, characterization, and analysis of complex biochemical systems. Here we illustrate this approach using in vitro transcriptional circuits ("genelets") while developing an activatable transcriptional switch motif and configuring it as a bistable autoregulatory circuit, using just four synthetic DNA strands and three essential enzymes, bacteriophage T7 RNA polymerase, Escherichia coli ribonuclease H, and ribonuclease R. Fulfilling the promise of predictable system design, the thermodynamic and kinetic constraints prescribed at the sequence level were enough to experimentally demonstrate intended bistable dynamics for the synthetic autoregulatory switch. A simple mathematical model was constructed based on the mechanistic understanding of elementary reactions, and a Monte Carlo Bayesian inference approach was employed to find parameter sets compatible with a training set of experimental results; this ensemble of parameter sets was then used to predict a test set of additional experiments with reasonable agreement and to provide a rigorous basis for confidence in the mechanistic model. Our work demonstrates that programmable in vitro biochemical circuits can serve as a testing ground for evaluating methods for the design and analysis of more complex biochemical systems such as living cells.
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Affiliation(s)
- Pakpoom Subsoontorn
- Departments of †Biology, ‡Computation and Neural Systems, §Computer Science, and ∥Bioengineering, California Institute of Technology,
Pasadena, California, 91125, United States
| | - Jongmin Kim
- Departments of †Biology, ‡Computation and Neural Systems, §Computer Science, and ∥Bioengineering, California Institute of Technology,
Pasadena, California, 91125, United States
| | - Erik Winfree
- Departments of †Biology, ‡Computation and Neural Systems, §Computer Science, and ∥Bioengineering, California Institute of Technology,
Pasadena, California, 91125, United States
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266
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Hockenberry AJ, Jewett MC. Synthetic in vitro circuits. Curr Opin Chem Biol 2012; 16:253-9. [PMID: 22676890 PMCID: PMC3424401 DOI: 10.1016/j.cbpa.2012.05.179] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 04/17/2012] [Accepted: 05/04/2012] [Indexed: 11/19/2022]
Abstract
Inspired by advances in the ability to construct programmable circuits in living organisms, in vitro circuits are emerging as a viable platform for designing, understanding, and exploiting dynamic biochemical circuitry. In vitro systems allow researchers to directly access and manipulate biomolecular parts without the unwieldy complexity and intertwined dependencies that often exist in vivo. Experimental and computational foundations in DNA, DNA/RNA, and DNA/RNA/protein based circuitry have given rise to systems with more than 100 programmed molecular constituents. Functionally, they have diverse capabilities including: complex mathematical calculations, associative memory tasks, and sensing of small molecules. Progress in this field is showing that cell-free synthetic biology is a versatile testing ground for understanding native biological circuits and engineering novel functionality.
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Affiliation(s)
- Adam J. Hockenberry
- Interdepartmental Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
| | - Michael C. Jewett
- Interdepartmental Biological Sciences Graduate Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Feinberg School of Medicine, Northwestern University, 303 E. Superior, Chicago, IL 60611, USA
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267
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Zhang YHP, Huang WD. Constructing the electricity–carbohydrate–hydrogen cycle for a sustainability revolution. Trends Biotechnol 2012; 30:301-6. [DOI: 10.1016/j.tibtech.2012.02.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
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268
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Smolke CD, Tyo KE. Synthetic biology: Emerging methodologies to catalyze the metabolic engineering design cycle. Metab Eng 2012; 14:187-8. [DOI: 10.1016/j.ymben.2012.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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269
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Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry. Curr Opin Biotechnol 2012; 23:672-8. [PMID: 22483202 DOI: 10.1016/j.copbio.2012.02.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 12/12/2022]
Abstract
Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology for synthetic chemistry and using synthetic chemistry to reprogram or mimic biology. In the coming years, the impact of advances inspired by these approaches will make possible the synthesis of nonbiological polymers having new backbone compositions, new chemical properties, new structures, and new functions.
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270
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Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi SP, Forster AC, Jewett MC, Church GM. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synth Biol 2012; 1:43-52. [PMID: 22737598 DOI: 10.1021/sb3000029] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein pathways are dynamic and highly coordinated spatially and temporally, capable of performing a diverse range of complex chemistries and enzymatic reactions with precision and at high efficiency. Biotechnology aims to harvest these natural systems to construct more advanced in vitro reactions, capable of new chemistries and operating at high yield. Here, we present an efficient Multiplex Automated Genome Engineering (MAGE) strategy to simultaneously modify and co-purify large protein complexes and pathways from the model organism Escherichia coli to reconstitute functional synthetic proteomes in vitro. By application of over 110 MAGE cycles, we successfully inserted hexa-histidine sequences into 38 essential genes in vivo that encode for the entire translation machinery. Streamlined co-purification and reconstitution of the translation protein complex enabled protein synthesis in vitro. Our approach can be applied to a growing area of applications in in vitro one-pot multienzyme catalysis (MEC) to manipulate or enhance in vitro pathways such as natural product or carbohydrate biosynthesis.
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Affiliation(s)
| | | | - George Xu
- Program in
Medical Engineering
Medical Physics, Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, United
States
| | | | | | | | | | - Anthony C. Forster
- Department of Cell
and Molecular
Biology, Uppsala University, Uppsala 75124,
Sweden
| | - Michael C. Jewett
- Department of Chemical
and Biological
Engineering and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208,
United States
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271
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Shin J, Noireaux V. An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. ACS Synth Biol 2012; 1:29-41. [PMID: 23651008 DOI: 10.1021/sb200016s] [Citation(s) in RCA: 279] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cell-free protein synthesis is becoming a powerful technique to construct and to study complex informational processes in vitro. Engineering synthetic gene circuits in a test tube, however, is seriously limited by the transcription repertoire of modern cell-free systems, composed of only a few bacteriophage regulatory elements. Here, we report the construction and the phenomenological characterization of synthetic gene circuits engineered with a cell-free expression toolbox that works with the seven E. coli sigma factors. The E. coli endogenous holoenzyme E(70) is used as the primary transcription machinery. Elementary circuit motifs, such as multiple stage cascades, AND gate and negative feedback loops are constructed with the six other sigma factors, two bacteriophage RNA polymerases, and a set of repressors. The circuit dynamics reveal the importance of the global mRNA turnover rate and of passive competition-induced transcriptional regulation. Cell-free reactions can be carried out over long periods of time with a small-scale dialysis reactor or in phospholipid vesicles, an artificial cell system. This toolbox is a unique platform to study complex transcription/translation-based biochemical systems in vitro.
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Affiliation(s)
- Jonghyeon Shin
- School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota
55455, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota
55455, United States
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272
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You C, Zhang YHP. Cell-free biosystems for biomanufacturing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 131:89-119. [PMID: 23111502 DOI: 10.1007/10_2012_159] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although cell-free biosystems have been used as a tool for investigating fundamental aspects of biological systems for more than 100 years, they are becoming an emerging biomanufacturing platform in the production of low-value biocommodities (e.g., H(2), ethanol, and isobutanol), fine chemicals, and high-value protein and carbohydrate drugs and their precursors. Here we would like to define the cell-free biosystems containing more than three catalytic components in a single reaction vessel, which although different from one-, two-, or three-enzyme biocatalysis can be regarded as a straightforward extension of multienzymatic biocatalysis. In this chapter, we compare the advantages and disadvantages of cell-free biosystems versus living organisms, briefly review the history of cell-free biosystems, highlight a few examples, analyze any remaining obstacles to the scale-up of cell-free biosystems, and suggest potential solutions. Cell-free biosystems could become a disruptive technology to microbial fermentation, especially in the production of high-impact low-value biocommodities mainly due to the very high product yields and potentially low production costs.
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Affiliation(s)
- Chun You
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA
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273
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Karig DK, Iyer S, Simpson ML, Doktycz MJ. Expression optimization and synthetic gene networks in cell-free systems. Nucleic Acids Res 2011; 40:3763-74. [PMID: 22180537 PMCID: PMC3333853 DOI: 10.1093/nar/gkr1191] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic biology offers great promise to a variety of applications through the forward engineering of biological function. Most efforts in this field have focused on employing living cells, yet cell-free approaches offer simpler and more flexible contexts. Here, we evaluate cell-free regulatory systems based on T7 promoter-driven expression by characterizing variants of TetR and LacI repressible T7 promoters in a cell-free context and examining sequence elements that determine expression efficiency. Using the resulting constructs, we then explore different approaches for composing regulatory systems, leading to the implementation of inducible negative feedback in Escherichia coli extracts and in the minimal PURE system, which consists of purified proteins necessary for transcription and translation. Despite the fact that negative feedback motifs are common and essential to many natural and engineered systems, this simple building block has not previously been implemented in a cell-free context. As a final step, we then demonstrate that the feedback systems developed using our cell-free approach can be implemented in live E. coli as well, illustrating the potential for using cell-free expression to fast track the development of live cell systems in synthetic biology. Our quantitative cell-free component characterizations and demonstration of negative feedback embody important steps on the path to harnessing biological function in a bottom-up fashion.
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Affiliation(s)
- David K Karig
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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