101
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Abstract
There is a growing need to enhance our capabilities in medical and environmental diagnostics. Synthetic biologists have begun to focus their biomolecular engineering approaches toward this goal, offering promising results that could lead to the development of new classes of inexpensive, rapidly deployable diagnostics. Many conventional diagnostics rely on antibody-based platforms that, although exquisitely sensitive, are slow and costly to generate and cannot readily confront rapidly emerging pathogens or be applied to orphan diseases. Synthetic biology, with its rational and short design-to-production cycles, has the potential to overcome many of these limitations. Synthetic biology devices, such as engineered gene circuits, bring new capabilities to molecular diagnostics, expanding the molecular detection palette, creating dynamic sensors, and untethering reactions from laboratory equipment. The field is also beginning to move toward in vivo diagnostics, which could provide near real-time surveillance of multiple pathological conditions. Here, we describe current efforts in synthetic biology, focusing on the translation of promising technologies into pragmatic diagnostic tools and platforms.
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102
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Schwarz-Schilling M, Aufinger L, Mückl A, Simmel FC. Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets. Integr Biol (Camb) 2016; 8:564-70. [PMID: 26778746 DOI: 10.1039/c5ib00301f] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Position-dependent gene expression in gradients of morphogens is one of the key processes involved in cellular differentiation during development. Here, we study a simple artificial differentiation process, which is based on the diffusion of genetic inducers within one-dimensional arrangements of 50 μm large water-in-oil droplets. The droplets are filled with either bacteria or cell-free gene expression systems, both equipped with genetic constructs that produce inducers or respond to them via expression of a fluorescent protein. We quantitatively study the coupled diffusion-gene expression process and demonstrate that gene expression can be made position-dependent both within bacteria-containing and cell-free droplets. By generating diffusing quorum sensing signals in situ, we also establish communication between artificial cell-free sender cells and bacterial receivers, and vice versa.
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Affiliation(s)
- M Schwarz-Schilling
- Technical University of Munich, Physics Department E14 and ZNN/WSI, Am Coulombwall 4a, 85748 Garching, Germany.
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103
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Rodrigo G, Prakash S, Cordero T, Kushwaha M, Jaramillo A. Functionalization of an Antisense Small RNA. J Mol Biol 2016; 428:889-92. [PMID: 26756967 PMCID: PMC4819895 DOI: 10.1016/j.jmb.2015.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 12/24/2022]
Abstract
In order to explore the possibility of adding new functions to preexisting genes, we considered a framework of riboregulation. We created a new riboregulator consisting of the reverse complement of a known riboregulator. Using computational design, we engineered a cis-repressing 5′ untranslated region that can be activated by this new riboregulator. As a result, both RNAs can orthogonally trans-activate translation of their cognate, independent targets. The two riboregulators can also repress each other by antisense interaction, although not symmetrically. Our work highlights that antisense small RNAs can work as regulatory agents beyond the antisense paradigm and that, hence, they could be interfaced with other circuits used in synthetic biology. We have engineered a riboregulator as the negative-sense strand of another riboregulator. This new RNA molecule performs the cellular function of titration of a functional molecule or trans-activation of gene expression. We have followed a computational design approach with energetic and structural criteria to obtain the nucleotide sequence of a 5′ untranslated region responding to the new riboregulator. We have engineered different regulatory circuits with trans-activating and anti-trans-activating small RNAs and characterized them at the population and single-cell levels.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Satya Prakash
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Teresa Cordero
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Manish Kushwaha
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alfonso Jaramillo
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom; Institute of Systems and Synthetic Biology, Centre National de la Recherche Scientifique, Université d'Evry val d'Essonne, 91000 Évry, France.
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104
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Glasscock C, Lucks J, DeLisa M. Engineered Protein Machines: Emergent Tools for Synthetic Biology. Cell Chem Biol 2016; 23:45-56. [DOI: 10.1016/j.chembiol.2015.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022]
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105
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Niederholtmeyer H, Sun ZZ, Hori Y, Yeung E, Verpoorte A, Murray RM, Maerkl SJ. Rapid cell-free forward engineering of novel genetic ring oscillators. eLife 2015; 4:e09771. [PMID: 26430766 PMCID: PMC4714972 DOI: 10.7554/elife.09771] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/01/2015] [Indexed: 12/17/2022] Open
Abstract
While complex dynamic biological networks control gene expression in all living organisms, the forward engineering of comparable synthetic networks remains challenging. The current paradigm of characterizing synthetic networks in cells results in lengthy design-build-test cycles, minimal data collection, and poor quantitative characterization. Cell-free systems are appealing alternative environments, but it remains questionable whether biological networks behave similarly in cell-free systems and in cells. We characterized in a cell-free system the ‘repressilator’, a three-node synthetic oscillator. We then engineered novel three, four, and five-gene ring architectures, from characterization of circuit components to rapid analysis of complete networks. When implemented in cells, our novel 3-node networks produced population-wide oscillations and 95% of 5-node oscillator cells oscillated for up to 72 hr. Oscillation periods in cells matched the cell-free system results for all networks tested. An alternate forward engineering paradigm using cell-free systems can thus accurately capture cellular behavior. DOI:http://dx.doi.org/10.7554/eLife.09771.001 Engineers often use simplified models to test their ideas. For example, engineers test small-scale models of new airplane designs in wind tunnels to see how easily air flows by them. This saves the engineers the time and expense of building a full-sized aircraft only to learn it has serious design flaws. The interactions of genes and proteins within living cells can be incredibly complex, and working out how a particular network works can take months or years in living cells. To try to speed up and simplify the process, scientists are developing models that do not involve cells. These models replicate the chemistry inside of the cells and allow scientists to observe complex interactions between genes, proteins and other cellular components. Some scientists have recreated complex patterns of gene expression in these cell-free models, but these systems still take a long time to make. It is also not yet clear whether these models accurately depict what happens in living cells. Now, Niederholtmeyer, Sun et al. have created a cell-free system that allows the interactions of a large network of genes to be examined in a single day – a process that would previously have taken weeks or months. To test the model, Niederholtmeyer, Sun et al. recreated how networks of genes in the bacterium Escherichia coli interact to form “oscillations”, which produce a regular rhythm of gene expression. When the cell-free oscillator networks were inserted into live E. coli cells, the oscillators continued to produce the same patterns of gene expression as they did outside the cells. Overall, the experiments show that cell-free models can accurately reproduce, or emulate, the behavior of cellular networks. This work now opens the door for engineering ever more complex genetic networks in a cell-free system, which in turn will enable rapid prototyping and detailed characterization of complex biological reaction networks. DOI:http://dx.doi.org/10.7554/eLife.09771.002
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Affiliation(s)
- Henrike Niederholtmeyer
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zachary Z Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Yutaka Hori
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, United States
| | - Enoch Yeung
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, United States
| | - Amanda Verpoorte
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Division of Engineering and Applied Science, California Institute of Technology, Pasadena, United States
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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106
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Meyer S, Chappell J, Sankar S, Chew R, Lucks JB. Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies. Biotechnol Bioeng 2015; 113:216-25. [PMID: 26134708 DOI: 10.1002/bit.25693] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/04/2015] [Accepted: 06/23/2015] [Indexed: 01/16/2023]
Abstract
Regulatory RNAs have become integral components of the synthetic biology and bioengineering toolbox for controlling gene expression. We recently expanded this toolbox by creating small transcription activating RNAs (STARs) that act by disrupting the formation of a target transcriptional terminator hairpin placed upstream of a gene. While STARs are a promising addition to the repertoire of RNA regulators, much work remains to be done to optimize the fold activation of these systems. Here we apply rational RNA engineering strategies to improve the fold activation of two STAR regulators. We demonstrate that a combination of promoter strength tuning and multiple RNA engineering strategies can improve fold activation from 5.4-fold to 13.4-fold for a STAR regulator derived from the pbuE riboswitch terminator. We then validate the generality of our approach and show that these same strategies improve fold activation from 2.1-fold to 14.6-fold for an unrelated STAR regulator, opening the door to creating a range of additional STARs to use in a broad array of biotechnologies. We also establish that the optimizations preserve the orthogonality of these STARs between themselves and a set of RNA transcriptional repressors, enabling these optimized STARs to be used in sophisticated circuits.
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Affiliation(s)
- Sarai Meyer
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853
| | - James Chappell
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853
| | - Sitara Sankar
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853
| | - Rebecca Chew
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853
| | - Julius B Lucks
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853.
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107
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Takahashi MK, Hayes CA, Chappell J, Sun ZZ, Murray RM, Noireaux V, Lucks JB. Characterizing and prototyping genetic networks with cell-free transcription–translation reactions. Methods 2015; 86:60-72. [DOI: 10.1016/j.ymeth.2015.05.020] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 02/07/2023] Open
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108
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Hu CY, Varner JD, Lucks JB. Generating Effective Models and Parameters for RNA Genetic Circuits. ACS Synth Biol 2015; 4:914-26. [PMID: 26046393 DOI: 10.1021/acssynbio.5b00077] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA genetic circuitry is emerging as a powerful tool to control gene expression. However, little work has been done to create a theoretical foundation for RNA circuit design. A prerequisite to this is a quantitative modeling framework that accurately describes the dynamics of RNA circuits. In this work, we develop an ordinary differential equation model of transcriptional RNA genetic circuitry, using an RNA cascade as a test case. We show that parameter sensitivity analysis can be used to design a set of four simple experiments that can be performed in parallel using rapid cell-free transcription-translation (TX-TL) reactions to determine the 13 parameters of the model. The resulting model accurately recapitulates the dynamic behavior of the cascade, and can be easily extended to predict the function of new cascade variants that utilize new elements with limited additional characterization experiments. Interestingly, we show that inconsistencies between model predictions and experiments led to the model-guided discovery of a previously unknown maturation step required for RNA regulator function. We also determine circuit parameters in two different batches of TX-TL, and show that batch-to-batch variation can be attributed to differences in parameters that are directly related to the concentrations of core gene expression machinery. We anticipate the RNA circuit models developed here will inform the creation of computer aided genetic circuit design tools that can incorporate the growing number of RNA regulators, and that the parametrization method will find use in determining functional parameters of a broad array of natural and synthetic regulatory systems.
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Affiliation(s)
- Chelsea Y. Hu
- School
of Chemical and Biomolecular
Engineering, Cornell University, Ithaca New York 14850, United States
| | - Jeffrey D. Varner
- School
of Chemical and Biomolecular
Engineering, Cornell University, Ithaca New York 14850, United States
| | - Julius B. Lucks
- School
of Chemical and Biomolecular
Engineering, Cornell University, Ithaca New York 14850, United States
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109
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Chappell J, Watters KE, Takahashi MK, Lucks JB. A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future. Curr Opin Chem Biol 2015; 28:47-56. [PMID: 26093826 DOI: 10.1016/j.cbpa.2015.05.018] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 01/01/2023]
Abstract
Since our ability to engineer biological systems is directly related to our ability to control gene expression, a central focus of synthetic biology has been to develop programmable genetic regulatory systems. Researchers are increasingly turning to RNA regulators for this task because of their versatility, and the emergence of new powerful RNA design principles. Here we review advances that are transforming the way we use RNAs to engineer biological systems. First, we examine new designable RNA mechanisms that are enabling large libraries of regulators with protein-like dynamic ranges. Next, we review emerging applications, from RNA genetic circuits to molecular diagnostics. Finally, we describe new experimental and computational tools that promise to accelerate our understanding of RNA folding, function and design.
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Affiliation(s)
- James Chappell
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Kyle E Watters
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Melissa K Takahashi
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Julius B Lucks
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States.
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110
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Anderson MJ, Stark JC, Hodgman CE, Jewett MC. Energizing eukaryotic cell-free protein synthesis with glucose metabolism. FEBS Lett 2015; 589:1723-1727. [PMID: 26054976 DOI: 10.1016/j.febslet.2015.05.045] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 05/14/2015] [Accepted: 05/16/2015] [Indexed: 11/18/2022]
Abstract
Eukaryotic cell-free protein synthesis (CFPS) is limited by the dependence on costly high-energy phosphate compounds and exogenous enzymes to power protein synthesis (e.g., creatine phosphate and creatine kinase, CrP/CrK). Here, we report the ability to use glucose as a secondary energy substrate to regenerate ATP in a Saccharomyces cerevisiae crude extract CFPS platform. We observed synthesis of 3.64±0.35 μg mL(-1) active luciferase in batch reactions with 16 mM glucose and 25 mM phosphate, resulting in a 16% increase in relative protein yield (μg protein/$ reagents) compared to the CrP/CrK system. Our demonstration provides the foundation for development of cost-effective eukaryotic CFPS platforms.
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Affiliation(s)
- Mark J Anderson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - C Eric Hodgman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL, USA, 60611-3068
- Simpson Querrey Institute, 303 E. Superior St, Suite 11-131 Chicago, IL USA, 60611-2875
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111
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Hoynes-O'Connor A, Hinman K, Kirchner L, Moon TS. De novo design of heat-repressible RNA thermosensors in E. coli. Nucleic Acids Res 2015; 43:6166-79. [PMID: 25979263 PMCID: PMC4499127 DOI: 10.1093/nar/gkv499] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/04/2015] [Indexed: 11/15/2022] Open
Abstract
RNA-based temperature sensing is common in bacteria that live in fluctuating environments. Most naturally-occurring RNA thermosensors are heat-inducible, have long sequences, and function by sequestering the ribosome binding site in a hairpin structure at lower temperatures. Here, we demonstrate the de novo design of short, heat-repressible RNA thermosensors. These thermosensors contain a cleavage site for RNase E, an enzyme native to Escherichia coli and many other organisms, in the 5′ untranslated region of the target gene. At low temperatures, the cleavage site is sequestered in a stem–loop, and gene expression is unobstructed. At high temperatures, the stem–loop unfolds, allowing for mRNA degradation and turning off expression. We demonstrated that these thermosensors respond specifically to temperature and provided experimental support for the central role of RNase E in the mechanism. We also demonstrated the modularity of these RNA thermosensors by constructing a three-input composite circuit that utilizes transcriptional, post-transcriptional, and post-translational regulation. A thorough analysis of the 24 thermosensors allowed for the development of design guidelines for systematic construction of similar thermosensors in future applications. These short, modular RNA thermosensors can be applied to the construction of complex genetic circuits, facilitating rational reprogramming of cellular processes for synthetic biology applications.
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Affiliation(s)
- Allison Hoynes-O'Connor
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kristina Hinman
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lukas Kirchner
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tae Seok Moon
- Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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112
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Abstract
The natural versatility of RNA makes it an ideal substrate for bioengineering. Its structural properties and predictable base-pairing permit its use as molecular scaffold, and its ability to interact with nucleic acids, proteins and small molecules confers a regulatory potential that can be harvested to design RNA regulators in diverse contexts.
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113
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Kwon YC, Jewett MC. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep 2015; 5:8663. [PMID: 25727242 PMCID: PMC4345344 DOI: 10.1038/srep08663] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/15/2015] [Indexed: 12/24/2022] Open
Abstract
Crude extract based cell-free protein synthesis (CFPS) has emerged as a powerful technology platform for high-throughput protein production and genetic part characterization. Unfortunately, robust preparation of highly active extracts generally requires specialized and costly equipment and can be labor and time intensive. Moreover, cell lysis procedures can be hard to standardize, leading to different extract performance across laboratories. These challenges limit new entrants to the field and new applications, such as comprehensive genome engineering programs to improve extract performance. To address these challenges, we developed a generalizable and easily accessible high-throughput crude extract preparation method for CFPS based on sonication. To validate our approach, we investigated two Escherichia coli strains: BL21 Star™ (DE3) and a K12 MG1655 variant, achieving similar productivity (defined as CFPS yield in g/L) by varying only a few parameters. In addition, we observed identical productivity of cell extracts generated from culture volumes spanning three orders of magnitude (10 mL culture tubes to 10 L fermentation). We anticipate that our rapid and robust extract preparation method will speed-up screening of genomically engineered strains for CFPS applications, make possible highly active extracts from non-model organisms, and promote a more general use of CFPS in synthetic biology and biotechnology.
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Affiliation(s)
- Yong-Chan Kwon
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- 1] Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA [2] Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA [3] Robert H. Lurie Comprehensive Cancer Center, Medicine Northwestern University, Chicago, IL 60611, USA [4] Institute of Bionanotechnology in Medicine Northwestern University, Chicago, IL 60611, USA
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114
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Creating small transcription activating RNAs. Nat Chem Biol 2015; 11:214-20. [PMID: 25643173 DOI: 10.1038/nchembio.1737] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 11/25/2014] [Indexed: 12/28/2022]
Abstract
We expanded the mechanistic capability of small RNAs by creating an entirely synthetic mode of regulation: small transcription activating RNAs (STARs). Using two strategies, we engineered synthetic STAR regulators to disrupt the formation of an intrinsic transcription terminator placed upstream of a gene in Escherichia coli. This resulted in a group of four highly orthogonal STARs that had up to 94-fold activation. By systematically modifying sequence features of this group, we derived design principles for STAR function, which we then used to forward engineer a STAR that targets a terminator found in the Escherichia coli genome. Finally, we showed that STARs could be combined in tandem to create previously unattainable RNA-only transcriptional logic gates. STARs provide a new mechanism of regulation that will expand our ability to use small RNAs to construct synthetic gene networks that precisely control gene expression.
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115
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Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. Paper-based synthetic gene networks. Cell 2014; 159:940-54. [PMID: 25417167 PMCID: PMC4243060 DOI: 10.1016/j.cell.2014.10.004] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 09/29/2014] [Accepted: 10/03/2014] [Indexed: 01/21/2023]
Abstract
Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides an alternate, versatile venue for synthetic biologists to operate and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze dried onto paper, enabling the inexpensive, sterile, and abiotic distribution of synthetic-biology-based technologies for the clinic, global health, industry, research, and education. For field use, we create circuits with colorimetric outputs for detection by eye and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small-molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors.
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Affiliation(s)
- Keith Pardee
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA
| | - Alexander A Green
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA
| | - Tom Ferrante
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - D Ewen Cameron
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ajay DaleyKeyser
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Peng Yin
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - James J Collins
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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