101
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Ichihashi N. What can we learn from the construction of in vitro replication systems? Ann N Y Acad Sci 2019; 1447:144-156. [PMID: 30957237 DOI: 10.1111/nyas.14042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 01/08/2023]
Abstract
Replication is a central function of living organisms. Several types of replication systems have been constructed in vitro from various molecules, including peptides, DNA, RNA, and proteins. In this review, I summarize the progress in the construction of replication systems over the past few decades and discuss what we can learn from their construction. I introduce various types of replication systems, supporting the feasibility of the spontaneous appearance of replication early in Earth's history. In the latter part of the review, I focus on parasitic replicators, one of the largest obstacles for sustainable replication. Compartmentalization is discussed as a possible solution.
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Affiliation(s)
- Norikazu Ichihashi
- Graduate School of Arts and Sciences and Komaba Institute for Science, The University of Tokyo, Tokyo, Japan
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102
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Silverman AD, Kelley-Loughnane N, Lucks JB, Jewett MC. Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry. ACS Synth Biol 2019; 8:403-414. [PMID: 30596483 PMCID: PMC6584022 DOI: 10.1021/acssynbio.8b00430] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent advances in cell-free gene expression (CFE) systems have enabled their use for a host of synthetic biology applications, particularly for rapid prototyping of genetic circuits and biosensors. Despite the proliferation of cell-free protein synthesis platforms, the large number of currently existing protocols for making CFE extracts muddles the collective understanding of how the extract preparation method affects its functionality. A key aspect of extract performance relevant to many applications is the activity of the native host transcriptional machinery that can mediate protein synthesis. However, protein yields from genes transcribed in vitro by the native Escherichia coli RNA polymerase are variable for different extract preparation techniques, and specifically low in some conventional crude extracts originally optimized for expression by the bacteriophage transcriptional machinery. Here, we show that cell-free expression of genes under bacterial σ70 promoters is constrained by the rate of transcription in crude extracts, and that processing the extract with a ribosomal runoff reaction and subsequent dialysis alleviates this constraint. Surprisingly, these processing steps only enhance protein synthesis in genes under native regulation, indicating that the translation rate is unaffected. We further investigate the role of other common extract preparation process variants on extract performance and demonstrate that bacterial transcription is inhibited by including glucose in the growth culture but is unaffected by flash-freezing the cell pellet prior to lysis. Our final streamlined and detailed protocol for preparing extract by sonication generates extract that facilitates expression from a diverse set of sensing modalities including protein and RNA regulators. We anticipate that this work will clarify the methodology for generating CFE extracts that are active for biosensing using native transcriptional machinery and will encourage the further proliferation of cell-free gene expression technology for new applications.
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Affiliation(s)
- Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Nancy Kelley-Loughnane
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert H. Lurie Comprehensive Cancer Center, and Member, Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert H. Lurie Comprehensive Cancer Center, and Member, Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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103
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Kai L, Schwille P. Cell-Free Protein Synthesis and Its Perspectives for Assembling Cells from the Bottom-Up. ACTA ACUST UNITED AC 2019; 3:e1800322. [PMID: 32648712 DOI: 10.1002/adbi.201800322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/14/2019] [Indexed: 12/20/2022]
Abstract
The underlying idea of synthetic biology is that biological reactions/modules/systems can be precisely engineered and controlled toward desired products. Numerous efforts in the past decades in deciphering the complexity of biological systems in vivo have led to a variety of tools for synthetic biology, especially based on recombinant DNA. However, one generic limitation of all living systems is that the vast majority of energy input is dedicated to maintain the system as a whole, rather than the small part of interest. Cell-free synthetic biology is aiming at exactly this fundamental limitation, providing the next level of flexibility for engineering and designing biological systems in vitro. New technology has continuously inspired cell-free biology and extended its applications, including gene circuits, spatiotemporally controlled pathways, coactivated catalysts systems, and rationally designed multienzyme pathways, in particular, minimal cell construction. In the context of this special issue, discussing work being carried out in the "MaxSynBio" consortium, the advances in characterizing stochasticity and dynamics of cell-free protein synthesis within cell-sized compartments, as well as the molecular crowding effect, are discussed. The organization of spatial heterogeneity is the key prerequisite for achieving hierarchy and stepwise assembly of minimal cells from the bottom-up.
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Affiliation(s)
- Lei Kai
- School of Life Sciences, Jiangsu Normal University, Shanghai Road 101, 221116, Xuzhou, P. R. China.,Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, D-82152, Martinsried, Germany
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104
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Self-assembly of bio-cellulose nanofibrils through intermediate phase in a cell-free enzyme system. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.11.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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105
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Dudley QM, Nash CJ, Jewett MC. Cell-free biosynthesis of limonene using enzyme-enriched Escherichia coli lysates. Synth Biol (Oxf) 2019; 4:ysz003. [PMID: 30873438 PMCID: PMC6407499 DOI: 10.1093/synbio/ysz003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 11/25/2022] Open
Abstract
Isoprenoids are an attractive class of metabolites for enzymatic synthesis from renewable substrates. However, metabolic engineering of microorganisms for monoterpenoid production is limited by the need for time-consuming, and often non-intuitive, combinatorial tuning of biosynthetic pathway variations to meet design criteria. Towards alleviating this limitation, the goal of this work was to build a modular, cell-free platform for construction and testing of monoterpenoid pathways, using the fragrance and flavoring molecule limonene as a model. In this platform, multiple Escherichia coli lysates, each enriched with a single overexpressed pathway enzyme, are mixed to construct the full biosynthetic pathway. First, we show the ability to synthesize limonene from six enriched lysates with mevalonate substrate, an adenosine triphosphate (ATP) source, and cofactors. Next, we extend the pathway to use glucose as a substrate, which relies on native metabolism in the extract to convert glucose to acetyl-CoA along with three additional enzymes to convert acetyl-CoA to mevalonate. We find that the native E. coli farnesyl diphosphate synthase (IspA) is active in the lysate and diverts flux from the pathway intermediate geranyl pyrophospahte to farnesyl pyrophsophate and the byproduct farnesol. By adjusting the relative levels of cofactors NAD+, ATP and CoA, the system can synthesize 0.66 mM (90.2 mg l-1) limonene over 24 h, a productivity of 3.8 mg l-1 h-1. Our results highlight the flexibility of crude lysates to sustain complex metabolism and, by activating a glucose-to-limonene pathway with 9 heterologous enzymes encompassing 20 biosynthetic steps, expands an approach of using enzyme-enriched lysates for constructing, characterizing and prototyping enzymatic pathways.
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Affiliation(s)
- Quentin M Dudley
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Connor J Nash
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute Northwestern University, Chicago, IL, USA
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106
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Meng D, Wu R, Wang J, Zhu Z, You C. Acceleration of cellodextrin phosphorolysis for bioelectricity generation from cellulosic biomass by integrating a synthetic two-enzyme complex into an in vitro synthetic enzymatic biosystem. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:267. [PMID: 31737096 PMCID: PMC6849236 DOI: 10.1186/s13068-019-1607-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/01/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Cellulosic biomass, the earth's most abundant renewable resource, can be used as substrates for biomanufacturing biofuels or biochemicals via in vitro synthetic enzymatic biosystems in which the first step is the enzymatic phosphorolysis of cellodextrin to glucose 1-phosphate (G1P) by cellodextrin phosphorylase (CDP). However, almost all the CDPs prefer cellodextrin synthesis to phosphorolysis, resulting in the low reaction rate of cellodextrin phosphorolysis for biomanufacturing. RESULTS To increase the reaction rate of cellodextrin phosphorolysis, synthetic enzyme complexes containing CDP and phosphoglucomutase (PGM) were constructed to convert G1P to glucose 6-phosphate (G6P) rapidly, which is an important intermediate for biomanufacturing. Four self-assembled synthetic enzyme complexes were constructed with different spatial organizations based on the high-affinity and high-specific interaction between cohesins and dockerins from natural cellulosomes. Thus, the CDP-PGM enzyme complex with the highest enhancement of initial reaction rate was integrated into an in vitro synthetic enzymatic biosystem for generating bioelectricity from cellodextrin. The in vitro biosystem containing the best CDP-PGM enzyme complex exhibited a much higher current density (3.35-fold) and power density (2.14-fold) than its counterpart biosystem containing free CDP and PGM mixture. CONCLUSIONS Hereby, we first reported bioelectricity generation from cellulosic biomass via in vitro synthetic enzymatic biosystems. This work provided a strategy of how to link non-energetically favorable reaction (cellodextrin phosphorolysis) and energetically favorable reaction (G1P to G6P) together to circumvent unfavorable reaction equilibrium and shed light on improving the reaction efficiency of in vitro synthetic enzymatic biosystems through the construction of synthetic enzyme complexes.
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Affiliation(s)
- Dongdong Meng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308 People’s Republic of China
| | - Ranran Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308 People’s Republic of China
| | - Juan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308 People’s Republic of China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308 People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049 People’s Republic of China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308 People’s Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049 People’s Republic of China
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107
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Liu WQ, Zhang L, Chen M, Li J. Cell-free protein synthesis: Recent advances in bacterial extract sources and expanded applications. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.10.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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108
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Huang WE, Nikel PI. The Synthetic Microbiology Caucus: from abstract ideas to turning microbes into cellular machines and back. Microb Biotechnol 2019; 12:5-7. [PMID: 30461208 PMCID: PMC6302714 DOI: 10.1111/1751-7915.13337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
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109
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Koch M, Faulon JL, Borkowski O. Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster. Front Bioeng Biotechnol 2018; 6:182. [PMID: 30555825 PMCID: PMC6281764 DOI: 10.3389/fbioe.2018.00182] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Cell-free TX-TL is an increasingly mature and useful platform for prototyping, testing, and engineering biological parts and systems. However, to fully accomplish the promises of synthetic biology, mathematical models are required to facilitate the design and predict the behavior of biological components in cell-free extracts. We review here the latest models accounting for transcription, translation, competition, and depletion of resources as well as genome scale models for lysate-based cell-free TX-TL systems, including their current limitations. These models will have to find ways to account for batch-to-batch variability before being quantitatively predictive in cell-free lysate-based platforms.
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Affiliation(s)
- Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, University of Paris-Saclay, Jouy-en-Josas, France
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, University of Paris-Saclay, Jouy-en-Josas, France
- Systems and Synthetic Biology Lab, CEA, CNRS, UMR 8030, Genomics Metabolics, University Paris-Saclay, Évry, France
- SYNBIOCHEM Center, School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Olivier Borkowski
- Micalis Institute, INRA, AgroParisTech, University of Paris-Saclay, Jouy-en-Josas, France
- Systems and Synthetic Biology Lab, CEA, CNRS, UMR 8030, Genomics Metabolics, University Paris-Saclay, Évry, France
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110
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Zhu Z, You C, Ma Y, Zhang YHPJ. In vitro synthetic enzymatic biosystems at the interface of the food-energy-water nexus: A conceptual framework and recent advances. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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111
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Expanding biological applications using cell-free metabolic engineering: An overview. Metab Eng 2018; 50:156-172. [PMID: 30367967 DOI: 10.1016/j.ymben.2018.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/21/2022]
Abstract
Expanding the concept of cell-free biology, implemented both with purified components and crude extracts, is continuing to deepen our appreciation of biological fundamentals while enlarging the range of applications. We are no longer intimidated by the complexity of crude extracts and complicated reaction systems with hundreds of active components, and, instead, coordinately activate and inactivate metabolic processes to focus and expand the capabilities of natural biological processes. This, in turn, dramatically increases the range of benefits offered by new products, both natural and supernatural, that were previously infeasible and/or unimaginable. This overview of cell-free metabolic engineering provides a broad range of examples and insights to guide and motivate continued research that will further expand fundamental understanding and beneficial applications. However, this survey also reveals how far we are from fully unlocking the potential offered by natural and engineered biological components and systems. This is an exciting conclusion, but metabolic engineering by itself is not sufficient. Going forward, innovative metabolic engineering must be intimately combined with creative process engineering to fully realize potential contributions toward a sustainable global civilization.
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112
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Pardatscher G, Schwarz-Schilling M, Sagredo S, Simmel FC. Functional Surface-immobilization of Genes Using Multistep Strand Displacement Lithography. J Vis Exp 2018. [PMID: 30417873 DOI: 10.3791/58634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Immobilization of genes on lithographically structured surfaces allows the study of compartmentalized gene expression processes in an open microfluidic bioreactor system. In contrast to other approaches towards artificial cellular systems, such a setup allows for a continuous supply with gene expression reagents and simultaneous draining of waste products. This facilitates the implementation of cell-free gene expression processes over extended periods of time, which is important for the realization of dynamic gene regulatory feedback systems. Here we provide a detailed protocol for the fabrication of genetic biochips using a simple-to-use lithographic technique based on DNA strand displacement reactions, which exclusively uses commercially available components. We also provide a protocol on the integration of compartmentalized genes with a polydimethylsiloxane (PDMS)-based microfluidic system. Furthermore, we show that the system is compatible with total internal reflection fluorescence (TIRF) microscopy, which can be used for the direct observation of molecular interactions between DNA and molecules contained in the expression mix.
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113
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Loan TD, Easton CJ, Alissandratos A. Recombinant cell-lysate-catalysed synthesis of uridine-5'-triphosphate from nucleobase and ribose, and without addition of ATP. N Biotechnol 2018; 49:104-111. [PMID: 30347258 DOI: 10.1016/j.nbt.2018.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 11/16/2022]
Abstract
Nucleoside triphosphates (NTPs) are important synthetic targets with diverse applications in therapeutics and diagnostics. Enzymatic routes to NTPs from simple building blocks are attractive, however the cost and complexity of assembling the requisite mixtures of multiple enzymes hinders application. Here, we describe the use of an engineered E. coli cell-free lysate as an efficient readily-prepared multi-enzyme biocatalyst for the production of uridine triphosphate (UTP) from free ribose and nucleobase. Endogenous lysate enzymes are able to support the nucleobase ribosylation and nucleotide phosphorylation steps, while uridine phosphorylation and the production of ribose phosphates (ribose 1-phosphate, ribose 5-phosphate and phosphoribosyl pyrophosphate) require recombinant enrichment of endogenous activities. Co-expression vectors encoding all required recombinant enzymes were employed for host cell transformation, such that a cell-free lysate with all necessary activities was obtained from a single bacterial culture. ATP required as phosphorylation cofactor was recycled by endogenous lysate enzymes using cheap, readily-prepared acetyl phosphate. Surprisingly, acetyl phosphate initiated spontaneous generation of ATP in the lysate, most likely from the breakdown of endogenous pools of adenosine-containing starting materials (e.g. adenosine cofactors, ribonucleic acids). The sub-stoichiometric amount of ATP produced and recycled in this way was enough to support all ATP-dependent steps without addition of any exogenous cofactor or auxiliary enzyme. Using this approach, equimolar solutions of orotic acid and ribose are transformed near quantitatively into 1.4 g L-1 UTP within 2.5 h, using a low-cost, readily-generated biocatalytic preparation.
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Affiliation(s)
- Thomas D Loan
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christopher J Easton
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Apostolos Alissandratos
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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114
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Zhang Y, Huang Q, Deng Z, Xu Y, Liu T. Enhancing the efficiency of cell-free protein synthesis system by systematic titration of transcription and translation components. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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115
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Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
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Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
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116
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Jiao Y, Liu Y, Luo D, Huck WTS, Yang D. Microfluidic-Assisted Fabrication of Clay Microgels for Cell-Free Protein Synthesis. ACS APPLIED MATERIALS & INTERFACES 2018; 10:29308-29313. [PMID: 30102514 DOI: 10.1021/acsami.8b09324] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cell-free protein synthesis (CFPS) is a robust platform for the simple, rapid, and cost-effective in vitro production of proteins, as well as an important tool for cell-free synthetic biology research. Here, a microfluidic clay microgel system is reported, which creates compartmentalized microenvironments for CFPS capable of high-yield and repeated protein synthesis, as well as an artificial cell-like structure. As an advantageous platform for CFPS, a modular manner to prepare clay microgels with rationally designed functions is demonstrated: (i) gene/clay microgels enhance protein expression, (ii) gene/clay/magnetic nanoparticle microgels enable a repeated protein production system, and (iii) gene/clay microgels in microfluidic droplets serve as a cell-like structure. Beyond CFPS, considering the compatibility of clay microgels with hydrophilic functional materials, our clay microgels will provide a more general platform for preparing a variety of functional materials such as encapsulating drugs and cells, enabling more biomedical applications.
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Affiliation(s)
- Yi Jiao
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin University , Tianjin 300072 , China
| | - Yang Liu
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin University , Tianjin 300072 , China
| | - Dan Luo
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
- Suzhou Institute of Nano-Tech and Nano-Bionics , Chinese Academy of Sciences , Suzhou 215123 , China
| | - Wilhelm T S Huck
- Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
| | - Dayong Yang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin University , Tianjin 300072 , China
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117
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Kelwick R, Ricci L, Chee SM, Bell D, Webb AJ, Freemont PS. Cell-free prototyping strategies for enhancing the sustainable production of polyhydroxyalkanoates bioplastics. Synth Biol (Oxf) 2018; 3:ysy016. [PMID: 32995523 PMCID: PMC7445755 DOI: 10.1093/synbio/ysy016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 07/29/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
The polyhydroxyalkanoates (PHAs) are microbially-produced biopolymers that could potentially be used as sustainable alternatives to oil-derived plastics. However, PHAs are currently more expensive to produce than oil-derived plastics. Therefore, more efficient production processes would be desirable. Cell-free metabolic engineering strategies have already been used to optimize several biosynthetic pathways and we envisioned that cell-free strategies could be used for optimizing PHAs biosynthetic pathways. To this end, we developed several Escherichia coli cell-free systems for in vitro prototyping PHAs biosynthetic operons, and also for screening relevant metabolite recycling enzymes. Furthermore, we customized our cell-free reactions through the addition of whey permeate, an industrial waste that has been previously used to optimize in vivo PHAs production. We found that the inclusion of an optimal concentration of whey permeate enhanced relative cell-free GFPmut3b production by approximately 50%. In cell-free transcription-translation prototyping reactions, gas chromatography-mass spectrometry quantification of cell-free 3-hydroxybutyrate (3HB) production revealed differences between the activities of the Native ΔPhaC_C319A (1.18 ± 0.39 µM), C104 ΔPhaC_C319A (4.62 ± 1.31 µM) and C101 ΔPhaC_C319A (2.65 ± 1.27 µM) phaCAB operons that were tested. Interestingly, the most active operon, C104 produced higher levels of PHAs (or PHAs monomers) than the Native phaCAB operon in both in vitro and in vivo assays. Coupled cell-free biotransformation/transcription-translation reactions produced greater yields of 3HB (32.87 ± 6.58 µM), and these reactions were also used to characterize a Clostridium propionicum Acetyl-CoA recycling enzyme. Together, these data demonstrate that cell-free approaches complement in vivo workflows for identifying additional strategies for optimizing PHAs production.
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Affiliation(s)
- Richard Kelwick
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
| | - Luca Ricci
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Soo Mei Chee
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
| | - David Bell
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
| | - Alexander J Webb
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
| | - Paul S Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London, UK
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK
- The London DNA Foundry, Imperial College London, London, UK
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Vilkhovoy M, Horvath N, Shih CH, Wayman JA, Calhoun K, Swartz J, Varner JD. Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis. ACS Synth Biol 2018; 7:1844-1857. [PMID: 29944340 DOI: 10.1021/acssynbio.7b00465] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cell-free protein synthesis (CFPS) is a widely used research tool in systems and synthetic biology. However, if CFPS is to become a mainstream technology for applications such as point of care manufacturing, we must understand the performance limits and costs of these systems. Toward this question, we used sequence specific constraint based modeling to evaluate the performance of E. coli cell-free protein synthesis. A core E. coli metabolic network, describing glycolysis, the pentose phosphate pathway, energy metabolism, amino acid biosynthesis, and degradation was augmented with sequence specific descriptions of transcription and translation and effective models of promoter function. Model parameters were largely taken from literature; thus the constraint based approach coupled the transcription and translation of the protein product, and the regulation of gene expression, with the availability of metabolic resources using only a limited number of adjustable model parameters. We tested this approach by simulating the expression of two model proteins: chloramphenicol acetyltransferase and dual emission green fluorescent protein, for which we have data sets; we then expanded the simulations to a range of additional proteins. Protein expression simulations were consistent with measurements for a variety of cases. The constraint based simulations confirmed that oxidative phosphorylation was active in the CAT cell-free extract, as without it there was no feasible solution within the experimental constraints of the system. We then compared the metabolism of theoretically optimal and experimentally constrained CFPS reactions, and developed parameter free correlations which could be used to estimate productivity as a function of carbon number and promoter type. Lastly, global sensitivity analysis identified the key metabolic processes that controlled CFPS productivity and energy efficiency. In summary, sequence specific constraint based modeling of CFPS offered a novel means to a priori estimate the performance of a cell-free system, using only a limited number of adjustable parameters. While we modeled the production of a single protein in this study, the approach could easily be extended to multiprotein synthetic circuits, RNA circuits, or the cell-free production of small molecule products.
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Affiliation(s)
- Michael Vilkhovoy
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Nicholas Horvath
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Che-Hsiao Shih
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Joseph A. Wayman
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Kara Calhoun
- School of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - James Swartz
- School of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Jeffrey D. Varner
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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Bhadra S, Pothukuchy A, Shroff R, Cole AW, Byrom M, Ellefson JW, Gollihar JD, Ellington AD. Cellular reagents for diagnostics and synthetic biology. PLoS One 2018; 13:e0201681. [PMID: 30110361 PMCID: PMC6093680 DOI: 10.1371/journal.pone.0201681] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/19/2018] [Indexed: 11/18/2022] Open
Abstract
We have found that the overproduction of enzymes in bacteria followed by their lyophilization leads to 'cellular reagents' that can be directly used to carry out numerous molecular biology reactions. We demonstrate the use of cellular reagents in a variety of molecular diagnostics, such as TaqMan qPCR with no diminution in sensitivity, and in synthetic biology cornerstones such as the Gibson assembly of DNA fragments, where new plasmids can be constructed solely based on adding cellular reagents. Cellular reagents have significantly reduced complexity and cost of production, storage and implementation, features that should facilitate accessibility and use in resource-poor conditions.
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Affiliation(s)
- Sanchita Bhadra
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Arti Pothukuchy
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Raghav Shroff
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Austin W. Cole
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Michelle Byrom
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Jared W. Ellefson
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Jimmy D. Gollihar
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States of America
- * E-mail:
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Whitford CM, Dymek S, Kerkhoff D, März C, Schmidt O, Edich M, Droste J, Pucker B, Rückert C, Kalinowski J. Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. J Biol Eng 2018; 12:13. [PMID: 30123321 PMCID: PMC6090650 DOI: 10.1186/s13036-018-0105-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer. MAIN BODY Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system. CONCLUSION Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.
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Affiliation(s)
| | - Saskia Dymek
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Denise Kerkhoff
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Camilla März
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Olga Schmidt
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Maximilian Edich
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Julian Droste
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Boas Pucker
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Present address: Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Christian Rückert
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
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121
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Mahour R, Klapproth J, Rexer TFT, Schildbach A, Klamt S, Pietzsch M, Rapp E, Reichl U. Establishment of a five-enzyme cell-free cascade for the synthesis of uridine diphosphate N-acetylglucosamine. J Biotechnol 2018; 283:120-129. [PMID: 30044949 DOI: 10.1016/j.jbiotec.2018.07.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/17/2018] [Accepted: 07/21/2018] [Indexed: 12/17/2022]
Abstract
In spite of huge endeavors in cell line engineering to produce glycoproteins with desired and uniform glycoforms, it is still not possible in vivo. Alternatively, in vitro glycoengineering can be used for the modification of glycans. However, in vitro glycoengineering relies on expensive nucleotide sugars, such as uridine 5'-diphospho-N-acetylglucosamine (UDP-GlcNAc) which serves as GlcNAc donor for the synthesis of various glycans. In this work, we present a systematic study for the cell-free de novo synthesis and regeneration of UDP-GlcNAc from polyphosphate, UMP and GlcNAc by a cascade of five enzymes (N-acetylhexosamine kinase (NahK), Glc-1P uridyltransferase (GalU), uridine monophosphate kinase (URA6), polyphosphate kinase (PPK3), and inorganic diphosphatase (PmPpA). All enzymes were expressed in E. coli BL21 Gold (DE3) and purified using immobilized metal affinity chromatography (IMAC). Results from one-pot experiments demonstrate the successful production of UDP-GlcNAc with a yield approaching 100%. The highest volumetric productivity of the cascade was about 0.81 g L-1 h-1 of UDP-GlcNAc. A simple model based on mass action kinetics was sufficient to capture the dynamic behavior of the multienzyme pathway. Moreover, a design equation based on metabolic control analysis was established to investigate the effect of enzyme concentration on the UDP-GlcNAc flux and to demonstrate that the flux of UDP-GlcNAc can be controlled by means of the enzyme concentrations. The effect of temperature on the UDP-GlcNAc flux followed an Arrhenius equation and the optimal co-factor concentration (Mg2+) for high UDP-GlcNAc synthesis rates depended on the working temperature. In conclusion, the study covers the entire engineering process of a multienzyme cascade, i.e. pathway design, enzyme expression, enzyme purification, reaction kinetics and investigation of the influence of basic parameters (temperature, co-factor concentration, enzyme concentration) on the synthesis rate. Thus, the study lays the foundation for future cascade optimization, preparative scale UDP-GlcNAc synthesis and for in situ coupling of the network with UDP-GlcNAc transferases to efficiently regenerate UDP-GlcNAc. Hence, this study provides a further step towards cost-effective in vitro glycoengineering of antibodies and other glycosylated proteins.
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Affiliation(s)
- Reza Mahour
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Jan Klapproth
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Thomas F T Rexer
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Anna Schildbach
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany.
| | - Markus Pietzsch
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Department of Downstream Processing, Halle (Saale), Germany.
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany; Otto-von-Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany.
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122
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Abstract
Engineering biological systems for the production of biofuels and bioproducts holds great potential to transform the bioeconomy, but often requires laborious, time-consuming design-build-test cycles. For decades cell-free systems have offered quick and facile approaches to study enzymes with hopes of informing cellular processes, mainly in the form of purified single-enzyme activity assays. Over the past 20 years, cell-free systems have grown to include multienzymatic systems, both purified and crude. By decoupling cellular growth objectives from enzyme pathway engineering objectives, cell-free systems provide a controllable environment to direct substrates toward a single, desired product. Cell-free approaches are being developed for prototyping and for biomanufacturing. In prototyping applications, the idea is to use cell-free systems to test and optimize biosynthetic pathways before implementation in live cells and scale-up. We present a detailed method for the generation of crude lysates for cell-free pathway prototyping, mix-and-match cell-free metabolic engineering using preenriched lysates, and cell-free protein synthesis driven cell-free metabolic engineering. The cell-free synthetic biology methods described herein are generalizable to any biosynthetic pathway of interest and provide a powerful approach to building pathways in crude lysates for the purpose of prototyping. The foundational principle of the presented approach is that we can construct discrete metabolic pathways through modular assembly of cell-free lysates containing enzyme components produced by overexpression in the lysate chassis strain or by cell-free protein synthesis (in vitro production). Overall, the modular and cell-free nature of our pathway prototyping framework is poised to facilitate multiplexed, automated study of biosynthetic pathways to inform systems-level cellular design.
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Affiliation(s)
- Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States; Center for Synthetic Biology, Northwestern University, Evanston, IL, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States; Center for Synthetic Biology, Northwestern University, Evanston, IL, United States; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, United States; Simpson Querrey Institute, Northwestern University, Chicago, IL, United States.
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123
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Ogawa A, Murashige Y, Takahashi H. Canonical translation-modulating OFF-riboswitches with a single aptamer binding to a small molecule that function in a higher eukaryotic cell-free expression system. Bioorg Med Chem Lett 2018; 28:2353-2357. [PMID: 29941191 DOI: 10.1016/j.bmcl.2018.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 12/30/2022]
Abstract
We have found that OFF-riboswitches that ligand-dependently downregulate the canonical translation in a higher eukaryotic expression system (wheat germ extract) can be easily created by inserting a single aptamer into the 5' untranslated region (UTR) of mRNA, even if its ligand is as small as theophylline. The key is the position of the inserted aptamer: the 5' end (+0 position) is much better than other positions for inhibiting canonical translation with the aptamer-ligand complex. The data showed that ribosome loading is suppressed by a rigid structure in the 5' end, and this suppression is dependent on the structure's stability but not on its size. Although this preference of aptamer insertion point contradicts the results in a lower eukaryote, it accords with the fact that the 5'-end structural hindrance is more effective for blocking the ribosome in higher eukaryotes. Therefore, the present type of OFF-riboswitch would function in various higher eukaryotic expression systems.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
| | - Yuta Murashige
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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124
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Conversion of d-glucose to l-lactate via pyruvate by an optimized cell-free enzymatic biosystem containing minimized reactions. Synth Syst Biotechnol 2018; 3:204-210. [PMID: 30345406 PMCID: PMC6190511 DOI: 10.1016/j.synbio.2018.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 11/22/2022] Open
Abstract
Cell-free synthetic enzymatic biosystem is emerging to expand the traditional biotechnological mode by utilizing a number of purified/partially purified enzymes and coenzymes in a single reaction vessel for the production of desired products from low-cost substrates. Here, a cell-free synthetic biosystem containing minimized number of reactions was designed for the conversion of d-glucose to l-lactate via pyruvate. This NADH-balanced biosystem was comprised of only 5 thermophilic enzymes without ATP supplementation. After optimization of enzyme loading amounts, buffer concentration and cofactor concentration, d-glucose was converted to l-lactate with a product yield of ∼90%. Our study has provided an emerging platform with potentials in producing pyruvate-derived chemicals, and may promote the development of cell-free synthetic enzymatic biosystems for biomanufacturing.
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125
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Jin X, Kightlinger W, Kwon YC, Hong SH. Rapid production and characterization of antimicrobial colicins using Escherichia coli-based cell-free protein synthesis. Synth Biol (Oxf) 2018; 3:ysy004. [PMID: 32995513 PMCID: PMC7445778 DOI: 10.1093/synbio/ysy004] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022] Open
Abstract
Colicins are antimicrobial proteins produced by Escherichia coli, which, upon secretion from the host, kill non-host E. coli strains by forming pores in the inner membrane and degrading internal cellular components such as DNA and RNA. Due to their unique cell-killing activities, colicins are considered viable alternatives to conventional antibiotics. Recombinant production of colicins requires co-production of immunity proteins to protect host cells; otherwise, the colicins are lethal to the host. In this study, we used cell-free protein synthesis (CFPS) to produce active colicins without the need for protein purification and co-production of immunity proteins. Cell-free synthesized colicins were active in killing model E. coli cells with different modes of cytotoxicity. Pore-forming colicins E1 and nuclease colicin E2 killed actively growing cells in a nutrient-rich medium, but the cytotoxicity of colicin Ia was low compared to E1 and E2. Moreover, colicin E1 effectively killed cells in a nutrient-free solution, while the activity of E2 was decreased compared to nutrient-rich conditions. Both colicins E1 and E2 decreased the level of persister cells (metabolically dormant cell populations that are insensitive to antibiotics) by up to six orders of magnitude compared to that of the rifampin pretreated persister cells. This study finds that colicins can eradicate non-growing cells including persisters, and that CFPS is a promising platform for rapid production and characterization of toxic proteins.
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Affiliation(s)
- Xing Jin
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Yong-Chan Kwon
- Department of Biological and Agricultural Engineering, LSU Agricultural Center, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, 60616, USA
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126
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Wang S, Majumder S, Emery NJ, Liu AP. Simultaneous monitoring of transcription and translation in mammalian cell-free expression in bulk and in cell-sized droplets. Synth Biol (Oxf) 2018; 3:ysy005. [PMID: 30003145 PMCID: PMC6034425 DOI: 10.1093/synbio/ysy005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/24/2018] [Accepted: 04/17/2018] [Indexed: 12/17/2022] Open
Abstract
Transcription and translation are two critical processes during eukaryotic gene expression that regulate cellular activities. The development of mammalian cell-free expression (CFE) systems provides a platform for studying these two critical processes in vitro for bottom-up synthetic biology applications such as construction of an artificial cell. Moreover, real-time monitoring of the dynamics of synthesized mRNA and protein is key to characterize and optimize gene circuits before implementing in living cells or in artificial cells. However, there are few tools for measurement of mRNA and protein dynamics in mammalian CFE systems. Here, we developed a locked nucleic acid (LNA) probe for monitoring transcription in a HeLa-based CFE system in real-time. By using this LNA probe in conjunction with a fluorescent reporter protein, we were able to simultaneously monitor mRNA and protein dynamics in bulk reactions and cell-sized single-emulsion droplets. We found rapid production of mRNA transcripts that decreased over time as protein production ensued in bulk reactions. Our results also showed that transcription in cell-sized droplets has different dynamics compared to the transcription in bulk reactions. The use of this LNA probe in conjunction with fluorescent proteins in HeLa-based mammalian CFE system provides a versatile in vitro platform for studying mRNA dynamics for bottom-up synthetic biology applications.
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Affiliation(s)
- Shue Wang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sagardip Majumder
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas J Emery
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA.,Biophysics Program, University of Michigan, Ann Arbor, MI, USA
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127
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Wohlgemuth R. Horizons of Systems Biocatalysis and Renaissance of Metabolite Synthesis. Biotechnol J 2018; 13:e1700620. [DOI: 10.1002/biot.201700620] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Roland Wohlgemuth
- European Federation of Biotechnology; Section on Applied Biocatalysis (ESAB); Theodor-Heuss-Allee 25,Frankfurt am Main 60486 Germany
- Sigma-Aldrich; Member of Merck Group; Industriestrasse 25,Buchs 9470 Switzerland
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128
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Li P, Chen Q, Wang TC, Vermeulen NA, Mehdi BL, Dohnalkova A, Browning ND, Shen D, Anderson R, Gómez-Gualdrón DA, Cetin FM, Jagiello J, Asiri AM, Stoddart JF, Farha OK. Hierarchically Engineered Mesoporous Metal-Organic Frameworks toward Cell-free Immobilized Enzyme Systems. Chem 2018. [DOI: 10.1016/j.chempr.2018.03.001] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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129
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Jayaraman P, Yeoh JW, Jayaraman S, Teh AY, Zhang J, Poh CL. Cell-Free Optogenetic Gene Expression System. ACS Synth Biol 2018; 7:986-994. [PMID: 29596741 DOI: 10.1021/acssynbio.7b00422] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Optogenetic tools provide a new and efficient way to dynamically program gene expression with unmatched spatiotemporal precision. To date, their vast potential remains untapped in the field of cell-free synthetic biology, largely due to the lack of simple and efficient light-switchable systems. Here, to bridge the gap between cell-free systems and optogenetics, we studied our previously engineered one component-based blue light-inducible Escherichia coli promoter in a cell-free environment through experimental characterization and mathematical modeling. We achieved >10-fold dynamic expression and demonstrated rapid and reversible activation of the target gene to generate oscillatory response. The deterministic model developed was able to recapitulate the system behavior and helped to provide quantitative insights to optimize dynamic response. This in vitro optogenetic approach could be a powerful new high-throughput screening technology for rapid prototyping of complex biological networks in both space and time without the need for chemical induction.
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130
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Damiati S, Mhanna R, Kodzius R, Ehmoser EK. Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics. Genes (Basel) 2018; 9:E144. [PMID: 29509709 PMCID: PMC5867865 DOI: 10.3390/genes9030144] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 11/16/2022] Open
Abstract
Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Rami Mhanna
- Biomedical Engineering Program, The American University of Beirut (AUB), Beirut 1107-2020, Lebanon.
| | - Rimantas Kodzius
- Mathematics and Natural Sciences Department, The American University of Iraq, Sulaimani, Sulaymaniyah 46001, Iraq.
- Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 80539 Munich, Germany.
- Faculty of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany.
| | - Eva-Kathrin Ehmoser
- Department of Nanobiotechnology, Institute for Synthetic Bioarchitecture, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
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131
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Cell-free synthetic biology for in vitro biosynthesis of pharmaceutical natural products. Synth Syst Biotechnol 2018; 3:83-89. [PMID: 29900420 PMCID: PMC5995452 DOI: 10.1016/j.synbio.2018.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/29/2018] [Accepted: 02/08/2018] [Indexed: 01/26/2023] Open
Abstract
Natural products with significant biological activities continuously act as rich sources for drug discovery and development. To harness the potential of these valuable compounds, robust methods need to be developed for their rapid and sustainable production. Cell-free biosynthesis of pharmaceutical natural products by in vitro reconstruction of the entire biosynthetic pathways represents one such solution. In this review, we focus on in vitro biosynthesis of two important classes of natural products, polyketides (PKs) and nonribosomal peptides (NRPs). First, we summarize purified enzyme-based systems for the biosynthesis of PKs, NRPs, and PK/NRP hybrids. Then, we introduce the cell-free protein synthesis (CFPS)-based technology for natural product production. With that, we discuss challenges and opportunities of cell-free synthetic biology for in vitro biosynthesis of natural products.
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132
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Synthetic Biology with an All E. coli TXTL System: Quantitative Characterization of Regulatory Elements and Gene Circuits. Methods Mol Biol 2018; 1772:61-93. [PMID: 29754223 DOI: 10.1007/978-1-4939-7795-6_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the past decade, a new generation of cell-free transcription-translation (TXTL) systems has been devised for emerging multidisciplinary applications. The DNA-dependent in vitro protein synthesis technology has been developed to tackle applications in synthetic biology, biological and chemical engineering, as well as quantitative disciplines such as biophysics. In addition to being convenient at the biosafety level, the new TXTL platforms are user-friendly; more affordable; more versatile at the level of transcription, with a TX repertoire covering hundreds of parts; and more powerful, with protein production reaching a few mg/mL in batch and continuous modes. As a consequence, TXTL is rising up as a popular research tool and is used by a growing research community. While TXTL is proving reliable for an increasing number of applications, it is important to gain appropriate TXTL skills, especially for quantitative applications. TXTL has become particularly useful to rapidly prototype genetic devices , from single regulatory elements to elementary circuit motifs . In this chapter, we describe the basic procedures to develop appropriate TXTL practices for the characterization of such genetic parts. We use an all E. coli TXTL system developed in our lab, now commercialized by Arbor Biosciences under the name myTXTL.
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133
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Katano Y, Li T, Baba M, Nakamura M, Ito M, Kojima K, Takita T, Yasukawa K. Generation of thermostable Moloney murine leukemia virus reverse transcriptase variants using site saturation mutagenesis library and cell-free protein expression system. Biosci Biotechnol Biochem 2017; 81:2339-2345. [DOI: 10.1080/09168451.2017.1394790] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract
We attempted to increase the thermostability of Moloney murine leukemia virus (MMLV) reverse transcriptase (RT). The eight-site saturation mutagenesis libraries corresponding to Ala70−Arg469 in the whole MMLV RT (Thr24−Leu671), in each of which 1 out of 50 amino acid residues was replaced with other amino acid residue, were constructed. Seven-hundred and sixty eight MMLV RT clones were expressed using a cell-free protein expression system, and their thermostabilities were assessed by the temperature of thermal treatment at which they retained cDNA synthesis activity. One clone D200C was selected as the most thermostable variant. The highest temperature of thermal treatment at which D200C exhibited cDNA synthesis activity was 57ºC, which was higher than for WT (53ºC). Our results suggest that a combination of site saturation mutagenesis library and cell-free protein expression system might be useful for generation of thermostable MMLV RT in a short period of time for expression and selection.
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Affiliation(s)
- Yuta Katano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tongyang Li
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Miyo Nakamura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masaaki Ito
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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134
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Hohagen H, Schwarz D, Schenk G, Guddat LW, Schieder D, Carsten J, Sieber V. Deacidification of grass silage press juice by continuous production of acetoin from its lactate via an immobilized enzymatic reaction cascade. BIORESOURCE TECHNOLOGY 2017; 245:1084-1092. [PMID: 28946391 DOI: 10.1016/j.biortech.2017.08.203] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 05/27/2023]
Abstract
An immobilized enzymatic reaction cascade was designed and optimized for the deacidification of grass silage press juice (SPJ), thus facilitating the production of bio-based chemicals. The cascade involves a three-step process using four enzymes immobilized in a Ca-alginate gel and uses lactic acid to form acetoin, a value-added product. The reaction is performed with a continuous, pH-dependent substrate feed under oxygenation. With titrated lactic acid yields of up to 91% and reaction times of ca. 6h was achieved. Using SPJ as titrant yields of 49% were obtained within 6h. In this deacidification process, with acetoin one value-added bio-based chemical is produced while simultaneously the remaining press juice can be used in applications that require a higher pH. Such, this system can be applied in a multi-product biorefinery concept to take full advantage of nutrient-rich SPJ, which is a widely available and easily storable renewable resource.
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Affiliation(s)
- Hendrik Hohagen
- Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315 Straubing, Germany
| | - Dominik Schwarz
- Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315 Straubing, Germany
| | - Gerhard Schenk
- The University of Queensland, School of Chemistry and Molecular Biosciences, 68 Cooper Road, St. Lucia 4072, Australia
| | - Luke W Guddat
- The University of Queensland, School of Chemistry and Molecular Biosciences, 68 Cooper Road, St. Lucia 4072, Australia
| | - Doris Schieder
- Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315 Straubing, Germany
| | - Jörg Carsten
- Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315 Straubing, Germany; Catalysis Research Center, Technical University of Munich, 85748 Garching, Germany
| | - Volker Sieber
- Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315 Straubing, Germany; The University of Queensland, School of Chemistry and Molecular Biosciences, 68 Cooper Road, St. Lucia 4072, Australia; Catalysis Research Center, Technical University of Munich, 85748 Garching, Germany; Fraunhofer IGB, Straubing Branch Bio, Electro, and Chemocatalysis BioCat, 94315 Straubing, Germany.
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135
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Failmezger J, Rauter M, Nitschel R, Kraml M, Siemann-Herzberg M. Cell-free protein synthesis from non-growing, stressed Escherichia coli. Sci Rep 2017; 7:16524. [PMID: 29184159 PMCID: PMC5705671 DOI: 10.1038/s41598-017-16767-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/16/2017] [Indexed: 01/01/2023] Open
Abstract
Cell-free protein synthesis is a versatile protein production system. Performance of the protein synthesis depends on highly active cytoplasmic extracts. Extracts from E. coli are believed to work best; they are routinely obtained from exponential growing cells, aiming to capture the most active translation system. Here, we report an active cell-free protein synthesis system derived from cells harvested at non-growth, stressed conditions. We found a downshift of ribosomes and proteins. However, a characterization revealed that the stoichiometry of ribosomes and key translation factors was conserved, pointing to a fully intact translation system. This was emphasized by synthesis rates, which were comparable to those of systems obtained from fast-growing cells. Our approach is less laborious than traditional extract preparation methods and multiplies the yield of extract per cultivation. This simplified growth protocol has the potential to attract new entrants to cell-free protein synthesis and to broaden the pool of applications. In this respect, a translation system originating from heat stressed, non-growing E. coli enabled an extension of endogenous transcription units. This was demonstrated by the sigma factor depending activation of parallel transcription. Our cell-free expression platform adds to the existing versatility of cell-free translation systems and presents a tool for cell-free biology.
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Affiliation(s)
- Jurek Failmezger
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Michael Rauter
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Robert Nitschel
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Michael Kraml
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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136
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Fields C, Levin M. Multiscale memory and bioelectric error correction in the cytoplasm-cytoskeleton-membrane system. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10. [DOI: 10.1002/wsbm.1410] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/19/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Chris Fields
- 21 Rue des Lavandiéres, 11160 Caunes Minervois; France
| | - Michael Levin
- Allen Discovery Center at Tufts University; Medford MA USA
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137
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Kim JE, Kim EJ, Chen H, Wu CH, Adams MW, Zhang YHP. Advanced water splitting for green hydrogen gas production through complete oxidation of starch by in vitro metabolic engineering. Metab Eng 2017; 44:246-252. [DOI: 10.1016/j.ymben.2017.09.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/24/2017] [Accepted: 09/21/2017] [Indexed: 01/11/2023]
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138
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Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
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139
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Oesterle S, Roberts TM, Widmer LA, Mustafa H, Panke S, Billerbeck S. Sequence-based prediction of permissive stretches for internal protein tagging and knockdown. BMC Biol 2017; 15:100. [PMID: 29084520 PMCID: PMC5661948 DOI: 10.1186/s12915-017-0440-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool. METHODS We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins. RESULTS We verify that a protein's primary structure information alone is sufficient to identify PSs. Identified PSs are predicted to be predominantly surface accessible; hence, the position of inserted peptides is likely suitable for diverse applications. We demonstrate the viability of this approach by inserting a Tobacco etch virus protease recognition site (TEV-tag) into several PSs in a wide range of proteins, from small monomeric enzymes (adenylate kinase) to large multi-subunit molecular machines (ATP synthase) and verify their functionality after insertion. We apply this method to engineer conditional protein knockdowns directly in the Escherichia coli chromosome and generate a cell-free platform with enhanced nucleotide stability. CONCLUSIONS Functional internally tagged proteins can be rationally designed and directly chromosomally implemented. Critical for the successful design of protein knockdowns was the incorporation of surface accessibility and secondary structure predictions, as well as the design of an improved TEV-tag that enables efficient hydrolysis when inserted into the middle of a protein. This versatile and portable approach can likely be adapted for other applications, and broadly adopted. We provide guidelines for the design of internally tagged proteins in order to empower scientists with little or no protein engineering expertise to internally tag their target proteins.
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Affiliation(s)
- Sabine Oesterle
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Tania Michelle Roberts
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Lukas Andreas Widmer
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
- Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland
- Life Science Zürich Graduate School in Systems Biology, Zürich, Switzerland
| | - Harun Mustafa
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sonja Billerbeck
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
- Present address: Chemistry Department, Columbia University, 550 West 120th Street, New York, NY, 10027, USA.
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140
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Hurst GB, Asano KG, Doktycz CJ, Consoli EJ, Doktycz WL, Foster CM, Morrell-Falvey JL, Standaert RF, Doktycz MJ. Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis. Anal Chem 2017; 89:11443-11451. [DOI: 10.1021/acs.analchem.7b02555] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Robert F. Standaert
- University of Tennessee, Department of Biochemistry & Cellular and Molecular Biology, Knoxville, Tennessee 37996, United States
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141
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Kang Z, Ding W, Gong X, Liu Q, Du G, Chen J. Recent advances in production of 5-aminolevulinic acid using biological strategies. World J Microbiol Biotechnol 2017; 33:200. [PMID: 29038905 DOI: 10.1007/s11274-017-2366-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/11/2017] [Indexed: 01/26/2023]
Abstract
5-Aminolevulinic acid (5-ALA) is the precursor for the biosynthesis of tetrapyrrole compounds and has broad applications in the medical and agricultural fields. Because of the disadvantages of chemical synthesis methods, microbial production of 5-ALA has drawn intensive attention and has been regarded as an alternative in the last years, especially with the rapid development of metabolic engineering and synthetic biology. In this mini-review, recent advances on the application and microbial production of 5-ALA using novel biological approaches (such as whole-cell enzymatic-transformation, metabolic pathway engineering and cell-free process) are described and discussed in detail. In addition, the challenges and prospects of synthetic biology are discussed.
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Affiliation(s)
- Zhen Kang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Wenwen Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xu Gong
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Qingtao Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Synergetic Innovation Center of Food Safety and Nutrition, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
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142
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You C, Huang R, Wei X, Zhu Z, Zhang YHP. Protein engineering of oxidoreductases utilizing nicotinamide-based coenzymes, with applications in synthetic biology. Synth Syst Biotechnol 2017; 2:208-218. [PMID: 29318201 PMCID: PMC5655348 DOI: 10.1016/j.synbio.2017.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 09/08/2017] [Accepted: 09/22/2017] [Indexed: 01/01/2023] Open
Abstract
Two natural nicotinamide-based coenzymes (NAD and NADP) are indispensably required by the vast majority of oxidoreductases for catabolism and anabolism, respectively. Most NAD(P)-dependent oxidoreductases prefer one coenzyme as an electron acceptor or donor to the other depending on their different metabolic roles. This coenzyme preference associated with coenzyme imbalance presents some challenges for the construction of high-efficiency in vivo and in vitro synthetic biology pathways. Changing the coenzyme preference of NAD(P)-dependent oxidoreductases is an important area of protein engineering, which is closely related to product-oriented synthetic biology projects. This review focuses on the methodology of nicotinamide-based coenzyme engineering, with its application in improving product yields and decreasing production costs. Biomimetic nicotinamide-containing coenzymes have been proposed to replace natural coenzymes because they are more stable and less costly than natural coenzymes. Recent advances in the switching of coenzyme preference from natural to biomimetic coenzymes are also covered in this review. Engineering coenzyme preferences from natural to biomimetic coenzymes has become an important direction for coenzyme engineering, especially for in vitro synthetic pathways and in vivo bioorthogonal redox pathways.
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Affiliation(s)
- Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
| | - Xinlei Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China
| | - Yi-Heng Percival Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA 24061, USA
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143
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Ogawa A, Masuoka H, Ota T. Artificial OFF-Riboswitches That Downregulate Internal Ribosome Entry without Hybridization Switches in a Eukaryotic Cell-Free Translation System. ACS Synth Biol 2017; 6:1656-1662. [PMID: 28613837 DOI: 10.1021/acssynbio.7b00124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We constructed novel artificial riboswitches that function in a eukaryotic translation system (wheat germ extract), by rationally implanting an in vitro-selected aptamer into the intergenic internal ribosome entry site (IRES) of Plautia stali intestine virus. These eukaryotic OFF-riboswitches (OFF-eRSs) ligand-dose-dependently downregulate IRES-mediated translation without hybridization switches, which typical riboswitches utilize for gene regulation. The hybridization-switch-free mechanism not only allows for easy design but also requires less energy for regulation, resulting in a higher switching efficiency than hybridization-switch-based OFF-eRSs provide. In addition, even a small ligand such as theophylline can induce satisfactory repression, in contrast to other types of OFF-eRSs that modulate the 5' cap-dependent canonical translation. Because our proposed hybridization-switch-free OFF-eRSs are based on a versatile IRES that functions well in many types of eukaryotic translation systems, they would be widely usable elements for synthetic gene circuits in both cell-free and cell-based synthetic biology.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Hiroki Masuoka
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Tsubasa Ota
- Proteo-Science Center, Ehime University, 3
Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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144
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Chen X, Zhang C, Zou R, Stephanopoulos G, Too HP. In Vitro Metabolic Engineering of Amorpha-4,11-diene Biosynthesis at Enhanced Rate and Specific Yield of Production. ACS Synth Biol 2017; 6:1691-1700. [PMID: 28520394 DOI: 10.1021/acssynbio.6b00377] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In vitro metabolic engineering is an alternative approach to cell-based biosynthesis. It offers unprecedented flexibility for the study of biochemical pathways, thus providing useful information for the rational design and assembly of reaction modules. Herein, we took the advantage of in vitro metabolic engineering to initially gain insight into the regulatory network of a reconstituted amorpha-4,11-diene (AD) synthetic pathway. Guided by lin-log approximation, we rapidly identified the hitherto unrecognized inhibition of adenosine triphosphate (ATP) on both farnesyl pyrophosphate synthase (FPPS) and amorpha-4,11-diene synthase (ADS). Furthermore, the byproduct, pyrophosphate (PPi), potently inhibits ADS, but not FPPS. To lower the inhibition, an ATP recycling system and pyrophosphatase were used and resulted in a significant (∼3-fold) enhancement in the rate of AD production (∼5.7 μmol L-1 min-1). A coimmobilized multienzyme reaction system was then developed to recycle the enzymes. When inhibitory metabolites concentrations were reduced, the specific enzymatic yield of AD was further enhanced (>6-fold). This study demonstrated that mitigating the accumulation of inhibitory metabolites can result in higher yields of AD production by in vitro multienzymatic reactions.
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Affiliation(s)
- Xixian Chen
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
- Biotransformation
Innovation Platform, Agency for Science Technology and Research, Singapore 138632
| | - Congqiang Zhang
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
- Biotransformation
Innovation Platform, Agency for Science Technology and Research, Singapore 138632
| | - Ruiyang Zou
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
| | - Gregory Stephanopoulos
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Heng-Phon Too
- Chemical
and Pharmaceutical Engineering, Singapore-MIT Alliance, Singapore 138602
- Department
of Biochemistry, National University of Singapore, Singapore 119077
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145
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Hong EY, Lee SG, Park BJ, Lee JM, Yun H, Kim BG. Simultaneously Enhancing the Stability and Catalytic Activity of Multimeric Lysine Decarboxylase CadA by Engineering Interface Regions for Enzymatic Production of Cadaverine at High Concentration of Lysine. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700278] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/08/2017] [Indexed: 01/25/2023]
Affiliation(s)
- Eun Young Hong
- School of Chemical and Biological Engineering; Seoul National University; Seoul South Korea
| | - Sun-Gu Lee
- Department of Chemical Engineering; Pusan National University; Busan 609-735 South Korea
| | - Byung Jun Park
- School of Chemical and Biological Engineering; Seoul National University; Seoul South Korea
| | - Jong Min Lee
- School of Chemical and Biological Engineering; Seoul National University; Seoul South Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology; Konkuk University; Seoul South Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering; Seoul National University; Seoul South Korea
- Institute of Bioengineering; Seoul National University; Seoul South Korea
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146
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Rustad M, Eastlund A, Marshall R, Jardine P, Noireaux V. Synthesis of Infectious Bacteriophages in an E. coli-based Cell-free Expression System. J Vis Exp 2017. [PMID: 28872145 DOI: 10.3791/56144] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel capabilities to perform basic and applied sciences in test tube reactions. Over the past decade, cell-free TXTL has become a powerful technique for a broad range of novel multidisciplinary research areas related to quantitative and synthetic biology. The new TXTL platforms are particularly useful to construct and interrogate biochemical systems through the execution of synthetic or natural gene circuits. In vitro TXTL has proven convenient to rapidly prototype regulatory elements and biological networks as well as to recapitulate molecular self-assembly mechanisms found in living systems. In this article, we describe how infectious bacteriophages, such as MS2 (RNA), ΦΧ174 (ssDNA), and T7 (dsDNA), are entirely synthesized from their genome in one-pot reactions using an all Escherichia coli, cell-free TXTL system. Synthesis of the three coliphages is quantified using the plaque assay. We show how the yield of synthesized phage depends on the biochemical settings of the reactions. Molecular crowding, emulated through a controlled concentration of PEG 8000, affects the amount of synthesized phages by orders of magnitudes. We also describe how to amplify the phages and how to purify their genomes. The set of protocols and results presented in this work should be of interest to multidisciplinary researchers involved in cell-free synthetic biology and bioengineering.
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Affiliation(s)
- Mark Rustad
- School of Physics and Astronomy, University of Minnesota
| | - Allen Eastlund
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota
| | - Ryan Marshall
- School of Physics and Astronomy, University of Minnesota
| | - Paul Jardine
- Department of Diagnostic and Biological Sciences and Institute for Molecular Virology, University of Minnesota
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147
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Rampley CPN, Davison PA, Qian P, Preston GM, Hunter CN, Thompson IP, Wu LJ, Huang WE. Development of SimCells as a novel chassis for functional biosensors. Sci Rep 2017; 7:7261. [PMID: 28775370 PMCID: PMC5543166 DOI: 10.1038/s41598-017-07391-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/28/2017] [Indexed: 01/31/2023] Open
Abstract
This work serves as a proof-of-concept for bacterially derived SimCells (Simple Cells), which contain the cell machinery from bacteria and designed DNA (or potentially a simplified genome) to instruct the cell to carry out novel, specific tasks. SimCells represent a reprogrammable chassis without a native chromosome, which can host designed DNA to perform defined functions. In this paper, the use of Escherichia coli MC1000 ∆minD minicells as a non-reproducing chassis for SimCells was explored, as demonstrated by their ability to act as sensitive biosensors for small molecules. Highly purified minicells derived from E. coli strains containing gene circuits for biosensing were able to transduce the input signals from several small molecules (glucarate, acrylate and arabinose) into the production of green fluorescent protein (GFP). A mathematical model was developed to fit the experimental data for induction of gene expression in SimCells. The intracellular ATP level was shown to be important for SimCell function. A purification and storage protocol was developed to prepare SimCells which could retain their functions for an extended period of time. This study demonstrates that SimCells are able to perform as ‘smart bioparticles’ controlled by designed gene circuits.
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Affiliation(s)
- Cordelia P N Rampley
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, Oxford, United Kingdom
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Ling Juan Wu
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom.
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148
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An In Vitro Enzyme System for the Production of myo-Inositol from Starch. Appl Environ Microbiol 2017; 83:AEM.00550-17. [PMID: 28600316 DOI: 10.1128/aem.00550-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/29/2017] [Indexed: 02/02/2023] Open
Abstract
We developed an in vitro enzyme system to produce myo-inositol from starch. Four enzymes were used, maltodextrin phosphorylase (MalP), phosphoglucomutase (PGM), myo-inositol-3-phosphate synthase (MIPS), and inositol monophosphatase (IMPase). The enzymes were thermostable: MalP and PGM from the hyperthermophilic archaeon Thermococcus kodakarensis, MIPS from the hyperthermophilic archaeon Archaeoglobus fulgidus, and IMPase from the hyperthermophilic bacterium Thermotoga maritima The enzymes were individually produced in Escherichia coli and partially purified by subjecting cell extracts to heat treatment and removing denatured proteins. The four enzyme samples were incubated at 90°C with amylose, phosphate, and NAD+, resulting in the production of myo-inositol with a yield of over 90% at 2 h. The effects of varying the concentrations of reaction components were examined. When the system volume was increased and NAD+ was added every 2 h, we observed the production of 2.9 g myo-inositol from 2.9 g amylose after 7 h, achieving gram-scale production with a molar conversion of approximately 96%. We further integrated the pullulanase from T. maritima into the system and observed myo-inositol production from soluble starch and raw potato with yields of 73% and 57 to 61%, respectively.IMPORTANCEmyo-Inositol is an important nutrient for human health and provides a wide variety of benefits as a dietary supplement. This study demonstrates an alternative method to produce myo-inositol from starch with an in vitro enzyme system using thermostable maltodextrin phosphorylase (MalP), phosphoglucomutase (PGM), myo-inositol-3-phosphate synthase, and myo-inositol monophosphatase. By utilizing MalP and PGM to generate glucose 6-phosphate, we can avoid the addition of phosphate donors such as ATP, the use of which would not be practical for scaled-up production of myo-inositol. myo-Inositol was produced from amylose on the gram scale with yields exceeding 90%. Conversion rates were also high, producing over 2 g of myo-inositol within 4 h in a 200-ml reaction mixture. By adding a thermostable pullulanase, we produced myo-inositol from raw potato with yields of 57 to 61% (wt/wt). The system developed here should provide an attractive alternative to conventional methods that rely on extraction or microbial production of myo-inositol.
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149
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Wang P, Chang AY, Novosad V, Chupin VV, Schaller RD, Rozhkova EA. Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion. ACS NANO 2017; 11:6739-6745. [PMID: 28602073 DOI: 10.1021/acsnano.7b01142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report on an entirely man-made nano-bio architecture fabricated through noncovalent assembly of a cell-free expressed transmembrane proton pump and TiO2 semiconductor nanoparticles as an efficient nanophotocatalyst for H2 evolution. The system produces hydrogen at a turnover of about 240 μmol of H2 (μmol protein)-1 h-1 and 17.74 mmol of H2 (μmol protein)-1 h-1 under monochromatic green and white light, respectively, at ambient conditions, in water at neutral pH and room temperature, with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allow for systemic manipulation at the nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.
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Affiliation(s)
- Peng Wang
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
- State Key Laboratory of Crystal Materials, Shandong University , Jinan, Shandong 250100, People's Republic of China
| | - Angela Y Chang
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Valentyn Novosad
- Materials Science Division, Argonne National Laboratory , Argonne, Illinois 60439-4855, United States
| | - Vladimir V Chupin
- Laboratory Chemistry and Physics of Lipids, Department of General and Applied Physics, Moscow Institute of Physics and Technology , Dolgoprudny, Moscow Region 141701, Russia
| | - Richard D Schaller
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Elena A Rozhkova
- Center for Nanoscale Materials, Argonne National Laboratory , 9700 South Cass Avenue, Argonne, Illinois 60439-4855, United States
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150
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Satagopan S, Sun Y, Parquette JR, Tabita FR. Synthetic CO 2-fixation enzyme cascades immobilized on self-assembled nanostructures that enhance CO 2/O 2 selectivity of RubisCO. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:175. [PMID: 28694846 PMCID: PMC5501267 DOI: 10.1186/s13068-017-0861-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND With increasing concerns over global warming and depletion of fossil-fuel reserves, it is attractive to develop innovative strategies to assimilate CO2, a greenhouse gas, into usable organic carbon. Cell-free systems can be designed to operate as catalytic platforms with enzymes that offer exceptional selectivity and efficiency, without the need to support ancillary reactions of metabolic pathways operating in intact cells. Such systems are yet to be exploited for applications involving CO2 utilization and subsequent conversion to valuable products, including biofuels. The Calvin-Benson-Bassham (CBB) cycle and the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) play a pivotal role in global CO2 fixation. RESULTS We hereby demonstrate the co-assembly of two RubisCO-associated multienzyme cascades with self-assembled synthetic amphiphilic peptide nanostructures. The immobilized enzyme cascades sequentially convert either ribose-5-phosphate (R-5-P) or glucose, a simpler substrate, to ribulose 1,5-bisphosphate (RuBP), the acceptor for incoming CO2 in the carboxylation reaction catalyzed by RubisCO. Protection from proteolytic degradation was observed in nanostructures associated with the small dimeric form of RubisCO and ancillary enzymes. Furthermore, nanostructures associated with a larger variant of RubisCO resulted in a significant enhancement of the enzyme's selectivity towards CO2, without adversely affecting the catalytic activity. CONCLUSIONS The ability to assemble a cascade of enzymes for CO2 capture using self-assembling nanostructure scaffolds with functional enhancements show promise for potentially engineering entire pathways (with RubisCO or other CO2-fixing enzymes) to redirect carbon from industrial effluents into useful bioproducts.
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Affiliation(s)
- Sriram Satagopan
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292 USA
| | - Yuan Sun
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210-1185 USA
| | - Jon R. Parquette
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210-1185 USA
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292 USA
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