1
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Alfaro-Palma J, Johnston WA, Behrendorff J, Cui Z, Moradi SV, Alexandrov K. Development of Lyophilized Eukaryotic Cell-Free Protein Expression System Based on Leishmania tarentolae. ACS Synth Biol 2024; 13:449-456. [PMID: 38268082 DOI: 10.1021/acssynbio.3c00428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Eukaryotic cell-free protein expression systems enable rapid production of recombinant multidomain proteins in their functional form. A cell-free system based on the rapidly growing protozoan Leishmania tarentolae (LTE) has been extensively used for protein engineering and analysis of protein interaction networks. However, like other eukaryotic cell-free systems, LTE deteriorates at ambient temperatures and requires deep freezing for transport and storage. In this study, we report the development of a lyophilized version of LTE. Use of lyoprotectants such as poly(ethylene glycol) and trehalose during the drying process allows retention of 76% of protein expression activity versus nonlyophilized controls. Lyophilized LTE is capable of withstanding storage at room temperature for over 2 weeks. We demonstrated that upon reconstitution the lyophilized LTE could be used for in vitro expression of active enzymes, analysis of protein-protein interactions by AlphaLISA assay, and functional analysis of protein biosensors. Development of lyophilized LTE lowers the barriers to its distribution and opens the door to its application in remote areas.
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Affiliation(s)
- Juan Alfaro-Palma
- ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Wayne A Johnston
- ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - James Behrendorff
- ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT 2601, Australia
| | - Zhenling Cui
- ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Shayli Varasteh Moradi
- Protein Expression Facility, AIBN Building, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kirill Alexandrov
- ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
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2
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Brookwell AW, Gonzalez JL, Martinez AW, Oza JP. Development of Solid-State Storage for Cell-Free Expression Systems. ACS Synth Biol 2023; 12:2561-2577. [PMID: 37490644 DOI: 10.1021/acssynbio.3c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The fragility of biological systems during storage, transport, and utilization necessitates reliable cold-chain infrastructure and limits the potential of biotechnological applications. In order to unlock the broad applications of existing and emerging biological technologies, we report the development of a novel solid-state storage platform for complex biologics. The resulting solid-state biologics (SSB) platform meets four key requirements: facile rehydration of solid materials, activation of biochemical activity, ability to support complex downstream applications and functionalities, and compatibility for deployment in a variety of reaction formats and environments. As a model system of biochemical complexity, we utilized crudeEscherichia colicell extracts that retain active cellular metabolism and support robust levels of in vitro transcription and translation. We demonstrate broad versatility and utility of SSB through proof-of-concepts for on-demand in vitro biomanufacturing of proteins at a milliliter scale, the activation of downstream CRISPR activity, as well as deployment on paper-based devices. SSBs unlock a breadth of applications in biomanufacturing, discovery, diagnostics, and education in resource-limited environments on Earth and in space.
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Affiliation(s)
- August W Brookwell
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Jorge L Gonzalez
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Andres W Martinez
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Javin P Oza
- Chemistry & Biochemistry Department, California Polytechnic State University, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California 93407, United States
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3
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Willett E, Banta S. Synthetic NAD(P)(H) Cycle for ATP Regeneration. ACS Synth Biol 2023. [PMID: 37369039 DOI: 10.1021/acssynbio.3c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
ATP is the energy currency of the cell and new methods for ATP regeneration will benefit a range of emerging biotechnology applications including synthetic cells. We designed and assembled a membraneless ATP-regenerating enzymatic cascade by exploiting the substrate specificities of selected NAD(P)(H)-dependent oxidoreductases combined with substrate-specific kinases. The enzymes in the NAD(P)(H) cycle were selected to avoid cross-reactions, and the cascade was driven by irreversible fuel oxidation. As a proof-of-concept, formate oxidation was chosen as the fueling reaction. ATP regeneration was accomplished via the phosphorylation of NADH to NADPH and the subsequent transfer of the phosphate to ADP by a reversible NAD+ kinase. The cascade was able to regenerate ATP at a high rate (up to 0.74 mmol/L/h) for hours, and >90% conversion of ADP to ATP using monophosphate was also demonstrated. The cascade was used to regenerate ATP for use in cell free protein synthesis reactions, and the ATP production rate was further enhanced when powered by the multistep oxidation of methanol. The NAD(P)(H) cycle provides a simple cascade for the in vitro regeneration of ATP without the need for a pH-gradient or costly phosphate donors.
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Affiliation(s)
- Emma Willett
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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4
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De Capitani J, Mutschler H. The Long Road to a Synthetic Self-Replicating Central Dogma. Biochemistry 2023; 62:1221-1232. [PMID: 36944355 PMCID: PMC10077596 DOI: 10.1021/acs.biochem.3c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.
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Affiliation(s)
- Jacopo De Capitani
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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5
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Qin Y, Li Q, Fan L, Ning X, Wei X, You C. Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:1-27. [PMID: 37455283 DOI: 10.1007/10_2023_231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
In vitro biotransformation (ivBT) refers to the use of an artificial biological reaction system that employs purified enzymes for the one-pot conversion of low-cost materials into biocommodities such as ethanol, organic acids, and amino acids. Unshackled from cell growth and metabolism, ivBT exhibits distinct advantages compared with metabolic engineering, including but not limited to high engineering flexibility, ease of operation, fast reaction rate, high product yields, and good scalability. These characteristics position ivBT as a promising next-generation biomanufacturing platform. Nevertheless, challenges persist in the enhancement of bulk enzyme preparation methods, the acquisition of enzymes with superior catalytic properties, and the development of sophisticated approaches for pathway design and system optimization. In alignment with the workflow of ivBT development, this chapter presents a systematic introduction to pathway design, enzyme mining and engineering, system construction, and system optimization. The chapter also proffers perspectives on ivBT development.
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Affiliation(s)
- Yanmei Qin
- University of Chinese Academy of Sciences, Beijing, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qiangzi Li
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Lin Fan
- University of Chinese Academy of Sciences, Beijing, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences Sino-Danish College, Beijing, China
| | - Xiao Ning
- University of Chinese Academy of Sciences, Beijing, China
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xinlei Wei
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Chun You
- In Vitro Synthetic Biology Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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6
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Suryatin Alim G, Suzuki T, Honda K. Cell-Free Production and Regeneration of Cofactors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:29-49. [PMID: 37306696 DOI: 10.1007/10_2023_222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cofactors, such as adenosine triphosphate, nicotinamide adenine dinucleotide, and coenzyme A, are involved in nearly 50% of enzymatic reactions and widely used in biocatalytic production of useful chemicals. Although commercial production of cofactors has been mostly dependent on extraction from microbial cells, this approach has a theoretical limitation to achieve a high-titer, high-yield production of cofactors owing to the tight regulation of cofactor biosynthesis in living cells. Besides the cofactor production, their regeneration is also a key challenge to enable continuous use of costly cofactors and improve the feasibility of enzymatic chemical manufacturing. Construction and implementation of enzyme cascades for cofactor biosynthesis and regeneration in a cell-free environment can be a promising approach to these challenges. In this chapter, we present the available tools for cell-free cofactor production and regeneration, the pros and cons, and how they can contribute to promote the industrial application of enzymes.
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Affiliation(s)
- Gladwin Suryatin Alim
- Department of Chemistry, University of Basel, Basel, Switzerland
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Takuma Suzuki
- International Center for Biotechnology, Osaka University, Osaka, Japan
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, Osaka, Japan.
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan.
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7
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Patterson AT, Styczynski MP. Rapid and Finely-Tuned Expression for Deployable Sensing Applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:141-161. [PMID: 37316621 DOI: 10.1007/10_2023_223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Organisms from across the tree of life have evolved highly efficient mechanisms for sensing molecules of interest using biomolecular machinery that can in turn be quite valuable for the development of biosensors. However, purification of such machinery for use in in vitro biosensors is costly, while the use of whole cells as in vivo biosensors often leads to long sensor response times and unacceptable sensitivity to the chemical makeup of the sample. Cell-free expression systems overcome these weaknesses by removing the requirements associated with maintaining living sensor cells, allowing for increased function in toxic environments and rapid sensor readout at a production cost that is often more reasonable than purification. Here, we focus on the challenge of implementing cell-free protein expression systems that meet the stringent criteria required for them to serve as the basis for field-deployable biosensors. Fine-tuning expression to meet these requirements can be achieved through careful selection of the sensing and output elements, as well as through optimization of reaction conditions via tuning of DNA/RNA concentrations, lysate preparation methods, and buffer conditions. Through careful sensor engineering, cell-free systems can continue to be successfully used for the production of tightly regulated, rapidly expressing genetic circuits for biosensors.
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Affiliation(s)
- Alexandra T Patterson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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8
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Warfel K, Williams A, Wong DA, Sobol SE, Desai P, Li J, Chang YF, DeLisa MP, Karim AS, Jewett MC. A Low-Cost, Thermostable, Cell-Free Protein Synthesis Platform for On-Demand Production of Conjugate Vaccines. ACS Synth Biol 2022; 12:95-107. [PMID: 36548479 PMCID: PMC9872175 DOI: 10.1021/acssynbio.2c00392] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cell-free protein synthesis systems that can be lyophilized for long-term, non-refrigerated storage and transportation have the potential to enable decentralized biomanufacturing. However, increased thermostability and decreased reaction cost are necessary for further technology adoption. Here, we identify maltodextrin as an additive to cell-free reactions that can act as both a lyoprotectant to increase thermostability and a low-cost energy substrate. As a model, we apply optimized formulations to produce conjugate vaccines for ∼$0.50 per dose after storage at room temperature (∼22 °C) or 37 °C for up to 4 weeks, and ∼$1.00 per dose after storage at 50 °C for up to 4 weeks, with costs based on raw materials purchased at the laboratory scale. We show that these conjugate vaccines generate bactericidal antibodies against enterotoxigenic Escherichia coli (ETEC) O78 O-polysaccharide, a pathogen responsible for diarrheal disease, in immunized mice. We anticipate that our low-cost, thermostable cell-free glycoprotein synthesis system will enable new models of medicine biosynthesis and distribution that bypass cold-chain requirements.
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Affiliation(s)
- Katherine
F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States
| | - Asher Williams
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853 United States
| | - Derek A. Wong
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States
| | - Sarah E. Sobol
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States
| | - Primit Desai
- Biochemistry,
Molecular & Cell Biology, Cornell University, Ithaca, New York 14853 United States
| | - Jie Li
- Department
of Population Medicine and Diagnostic Sciences, College of Veterinary
Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Yung-Fu Chang
- Department
of Population Medicine and Diagnostic Sciences, College of Veterinary
Medicine, Cornell University, Ithaca, New York 14853, United States
| | - Matthew P. DeLisa
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853 United States,Biochemistry,
Molecular & Cell Biology, Cornell University, Ithaca, New York 14853 United States,Cornell
Institute of Biotechnology, Cornell University, Ithaca, New York 14853 United States
| | - Ashty S. Karim
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208, United States,Chemistry
of Life Processes Institute, Northwestern
University, 2170 Campus
Drive, Evanston, Illinois 60208, United States,Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Technological
Institute E136, Evanston, Illinois 60208, United States,Robert
H. Lurie Comprehensive Cancer Center, Northwestern
University, 676 North
Saint Clair Street, Suite 1200, Chicago, Illinois 60611, United States,Simpson
Querrey Institute, Northwestern University, 303 East Superior Street, Suite
11-131, Chicago, Illinois 60611, United States,. Phone: 1-847-497-5007
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9
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Nagappa LK, Sato W, Alam F, Chengan K, Smales CM, Von Der Haar T, Polizzi KM, Adamala KP, Moore SJ. A ubiquitous amino acid source for prokaryotic and eukaryotic cell-free transcription-translation systems. Front Bioeng Biotechnol 2022; 10:992708. [PMID: 36185432 PMCID: PMC9524191 DOI: 10.3389/fbioe.2022.992708] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022] Open
Abstract
Cell-free gene expression (CFE) systems are an attractive tool for engineering within synthetic biology and for industrial production of high-value recombinant proteins. CFE reactions require a cell extract, energy system, amino acids, and DNA, to catalyse mRNA transcription and protein synthesis. To provide an amino acid source, CFE systems typically use a commercial standard, which is often proprietary. Herein we show that a range of common microbiology rich media (i.e., tryptone, peptone, yeast extract and casamino acids) unexpectedly provide an effective and low-cost amino acid source. We show that this approach is generalisable, by comparing batch variability and protein production in the following range of CFE systems: Escherichia coli (Rosetta™ 2 (DE3), BL21(DE3)), Streptomyces venezuelae and Pichia pastoris. In all CFE systems, we show equivalent or increased protein synthesis capacity upon replacement of the commercial amino acid source. In conclusion, we suggest rich microbiology media provides a new amino acid source for CFE systems with potential broad use in synthetic biology and industrial biotechnology applications.
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Affiliation(s)
| | - Wakana Sato
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Farzana Alam
- Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | | | | | | | - Karen M Polizzi
- Centre for Synthetic Biology, Imperial College London, London, United Kingdom
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Simon J Moore
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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10
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Bordewick S, Berger RG, Ersoy F. Co-Immobilization of RizA Variants with Acetate Kinase for the Production of Bioactive Arginyl Dipeptides. Molecules 2022; 27:molecules27144352. [PMID: 35889224 PMCID: PMC9321006 DOI: 10.3390/molecules27144352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
The biocatalytic system comprised of RizA and acetate kinase (AckA) combines the specific synthesis of bioactive arginyl dipeptides with efficient ATP regeneration. Immobilization of this coupled enzyme system was performed and characterized in terms of activity, specificity and reusability of the immobilisates. Co-immobilization of RizA and AckA into a single immobilisate conferred no disadvantage in comparison to immobilization of only RizA, and a small addition of AckA (20:1) was sufficient for ATP regeneration. New variants of RizA were constructed by combining mutations to yield variants with increased biocatalytic activity and specificity. A selection of RizA variants were co-immobilized with AckA and used for the production of the salt-taste enhancers Arg-Ser and Arg-Ala and the antihypertensive Arg-Phe. The best variants yielded final dipeptide concentrations of 11.3 mM Arg-Ser (T81F_A158S) and 11.8 mM Arg-Phe (K83F_S156A), the latter of which represents a five-fold increase in comparison to the wild-type enzyme. T81F_A158S retained more than 50% activity for over 96 h and K83F_S156A for over 72 h. This study provides the first example of the successful co-immobilization of an l-amino acid ligase with an ATP-regenerating enzyme and paves the way towards a bioprocess for the production of bioactive dipeptides.
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11
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Guzman-Chavez F, Arce A, Adhikari A, Vadhin S, Pedroza-Garcia JA, Gandini C, Ajioka JW, Molloy J, Sanchez-Nieto S, Varner JD, Federici F, Haseloff J. Constructing Cell-Free Expression Systems for Low-Cost Access. ACS Synth Biol 2022; 11:1114-1128. [PMID: 35259873 PMCID: PMC9098194 DOI: 10.1021/acssynbio.1c00342] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Indexed: 11/29/2022]
Abstract
Cell-free systems for gene expression have gained attention as platforms for the facile study of genetic circuits and as highly effective tools for teaching. Despite recent progress, the technology remains inaccessible for many in low- and middle-income countries due to the expensive reagents required for its manufacturing, as well as specialized equipment required for distribution and storage. To address these challenges, we deconstructed processes required for cell-free mixture preparation and developed a set of alternative low-cost strategies for easy production and sharing of extracts. First, we explored the stability of cell-free reactions dried through a low-cost device based on silica beads, as an alternative to commercial automated freeze dryers. Second, we report the positive effect of lactose as an additive for increasing protein synthesis in maltodextrin-based cell-free reactions using either circular or linear DNA templates. The modifications were used to produce active amounts of two high-value reagents: the isothermal polymerase Bst and the restriction enzyme BsaI. Third, we demonstrated the endogenous regeneration of nucleoside triphosphates and synthesis of pyruvate in cell-free systems (CFSs) based on phosphoenol pyruvate (PEP) and maltodextrin (MDX). We exploited this novel finding to demonstrate the use of a cell-free mixture completely free of any exogenous nucleotide triphosphates (NTPs) to generate high yields of sfGFP expression. Together, these modifications can produce desiccated extracts that are 203-424-fold cheaper than commercial versions. These improvements will facilitate wider use of CFS for research and education purposes.
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Affiliation(s)
| | - Anibal Arce
- ANID
− Millennium Institute for Integrative Biology (iBio), FONDAP
Center for Genome Regulation, Institute for Biological and Medical
Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
| | - Abhinav Adhikari
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Sandra Vadhin
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jose Antonio Pedroza-Garcia
- Department
of Biochemistry, Faculty of Chemistry, National
Autonomous University of Mexico (UNAM), 04510 Mexico City, Mexico
| | - Chiara Gandini
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0FD Cambridge, U.K.
| | - Jim W. Ajioka
- Department
of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP Cambridge, U.K.
| | - Jenny Molloy
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0FD Cambridge, U.K.
| | - Sobeida Sanchez-Nieto
- Department
of Biochemistry, Faculty of Chemistry, National
Autonomous University of Mexico (UNAM), 04510 Mexico City, Mexico
| | - Jeffrey D. Varner
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Fernan Federici
- ANID
− Millennium Institute for Integrative Biology (iBio), FONDAP
Center for Genome Regulation, Institute for Biological and Medical
Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
| | - Jim Haseloff
- Department
of Plant Sciences, University of Cambridge, CB2 3EA Cambridge, U.K.
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12
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An ATP-free in vitro synthetic enzymatic biosystem facilitating one-pot stoichiometric conversion of starch to mannitol. Appl Microbiol Biotechnol 2021; 105:1913-1924. [PMID: 33544214 DOI: 10.1007/s00253-021-11154-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/16/2021] [Accepted: 01/28/2021] [Indexed: 01/05/2023]
Abstract
D-Mannitol (hereinafter as mannitol) is a six-carbon sugar alcohol with diverse applications in food and pharmaceutical industries. To overcome the drawbacks of the chemical hydrogenation method commonly used for mannitol production at present, there is a need to search for novel prospective mannitol production strategies that are of high yield and low cost. In this study, we present a novel approach for the stoichiometric synthesis of mannitol via an in vitro synthetic enzymatic biosystem using the low-cost starch as substrate. By dividing the overall reaction pathway into three modules which could be executed sequentially in one pot, our design aimed at the stoichiometric conversion of starch-based materials into mannitol in an ATP-independent and cofactor-balanced manner. At optimized conditions, high product yields of around 95-98% were achieved using both 10 g/L and 50 g/L maltodextrin as substrate, indicating the potential of our designed system for industrial applications. This study not only provides a high-efficient strategy for the synthesis of mannitol but also expands the product scope of sugar alcohols by the in vitro synthetic enzymatic biosystems using low-cost starch-based materials as the input. KEY POINTS : • We described a design-build-test-learn pipeline to construct in vitro biosystems. • The designed system comprised six key enzymes and another three enzymes. • The system converted maltodextrin stoichiometrically to mannitol in one pot.
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13
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Chen H, Zhang YHPJ. Enzymatic regeneration and conservation of ATP: challenges and opportunities. Crit Rev Biotechnol 2020; 41:16-33. [PMID: 33012193 DOI: 10.1080/07388551.2020.1826403] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Adenosine triphosphate (ATP), the universal energy currency of life, has a central role in numerous biochemical reactions with potential for the synthesis of numerous high-value products. ATP can be regenerated by three types of mechanisms: substrate level phosphorylation, oxidative phosphorylation, and photophosphorylation. Current ATP regeneration methods are mainly based on substrate level phosphorylation catalyzed by one enzyme, several cascade enzymes, or in vitro synthetic enzymatic pathways. Among them, polyphosphate kinases and acetate kinase, along with their respective phosphate donors, are the most popular approaches for in vitro ATP regeneration. For in vitro artificial pathways, either ATP-free or ATP-balancing strategies can be implemented via smart pathway design by choosing ATP-independent enzymes. Also, we discuss some remaining challenges and suggest perspectives, especially for industrial biomanufacturing. Development of ATP regeneration systems featuring low cost, high volumetric productivity, long lifetime, flexible compatibility, and great robustness could be one of the bottom-up strategies for cascade biocatalysis and in vitro synthetic biology.
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Affiliation(s)
- Hongge Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin Airport Economic Area, Tianjin, China
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14
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Liu S, Wang J, Zhu Z, Shi T, Zhang YHPJ. Efficient secretory production of large-size heterologous enzymes in Bacillus subtilis: A secretory partner and directed evolution. Biotechnol Bioeng 2020; 117:2957-2968. [PMID: 32589796 DOI: 10.1002/bit.27478] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 06/25/2020] [Indexed: 12/20/2022]
Abstract
Secretory production of recombinant proteins provides a simple approach to the production and purification of target proteins in the enzyme industry. We developed a combined strategy for the secretory production of three large-size heterologous enzymes with a special focus on 83-kDa isoamylase (IA) from an archaeon Sulfolobus tokodaii in a bacterium Bacillus subtilis. First, a secretory protein of the B. subtilis family 5 glycoside hydrolase endoglucanase (Cel5) was used as a fusion partner, along with the NprB signal peptide, to facilitate secretory production of IA. This secretory partner strategy was effective for the secretion of two other large enzymes: family 9 glycoside hydrolase from Clostridium phytofermentas and cellodextrin phosphorylase from Clostridium thermocellum. Second, the secretion of Cel5-IA was improved by directed evolution with two novel double-layer Petri-dish-based high-throughput screening (HTS) methods. The high-sensitivity HTS relied on the detection of high-activity Cel5 on the carboxymethylcellulose/Congo-red assay. The second modest-sensitivity HTS focused on the detection of low-activity IA on the amylodextrin-I2 assay. After six rounds of HTS, a secretory Cel5-IA level was increased to 234 mg/L, 155 times the wild-type IA with the NprB signal peptide only. This combinatory strategy could be useful to enhance the secretory production of large-size heterologous proteins in B. subtilis.
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Affiliation(s)
- Shan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Juan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ting Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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15
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Kay JE, Jewett MC. A cell-free system for production of 2,3-butanediol is robust to growth-toxic compounds. Metab Eng Commun 2020; 10:e00114. [PMID: 31934547 PMCID: PMC6951449 DOI: 10.1016/j.mec.2019.e00114] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 11/23/2022] Open
Abstract
The need for sustainable, low-cost production of bioenergy and commodity chemicals is increasing. Unfortunately, the engineering potential of whole-cell catalysts to address this need can be hampered by cellular toxicity. When such bottlenecks limit the commercial feasibility of whole-cell fermentation, cell-free, or in vitro, based approaches may offer an alternative. Here, we assess the impact of three classes of growth toxic compounds on crude extract-based, cell-free chemical conversions. As a model system, we test a metabolic pathway for conversion of glucose to 2,3-butanediol (2,3-BDO) in lysates of Escherichia coli. First, we characterized 2,3-BDO production with different classes of antibiotics and found, as expected, that the system is uninhibited by compounds that prevent cell growth by means of cell wall replication and DNA, RNA, and protein synthesis. Second, we considered the impact of polar solvent addition (e.g., methanol, n-butanol). We observed that volumetric productivities (g/L/h) were slowed with increasing hydrophobicity of added alcohols. Finally, we investigated the effects of using pretreated biomass hydrolysate as a feed stock, observing a 25% reduction in 2,3-BDO production as a result of coumaroyl and feruloyl amides. Overall, we find the cell-free system to be robust to working concentrations of antibiotics and other compounds that are toxic to cell growth, but do not denature or inhibit relevant enzymes.
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Affiliation(s)
- Jennifer E. Kay
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center and Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
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16
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Escherichia coli Extract-Based Cell-Free Expression System as an Alternative for Difficult-to-Obtain Protein Biosynthesis. Int J Mol Sci 2020; 21:ijms21030928. [PMID: 32023820 PMCID: PMC7037961 DOI: 10.3390/ijms21030928] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/15/2020] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
Before utilization in biomedical diagnosis, therapeutic treatment, and biotechnology, the diverse variety of peptides and proteins must be preliminarily purified and thoroughly characterized. The recombinant DNA technology and heterologous protein expression have helped simplify the isolation of targeted polypeptides at high purity and their structure-function examinations. Recombinant protein expression in Escherichia coli, the most-established heterologous host organism, has been widely used to produce proteins of commercial and fundamental research interests. Nonetheless, many peptides/proteins are still difficult to express due to their ability to slow down cell growth or disrupt cellular metabolism. Besides, special modifications are often required for proper folding and activity of targeted proteins. The cell-free (CF) or in vitro recombinant protein synthesis system enables the production of such difficult-to-obtain molecules since it is possible to adjust reaction medium and there is no need to support cellular metabolism and viability. Here, we describe E. coli-based CF systems, the optimization steps done toward the development of highly productive and cost-effective CF methodology, and the modification of an in vitro approach required for difficult-to-obtain protein production.
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17
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Lee KH, Kim DM. Recent advances in development of cell-free protein synthesis systems for fast and efficient production of recombinant proteins. FEMS Microbiol Lett 2019; 365:5062788. [PMID: 30084930 DOI: 10.1093/femsle/fny174] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Cell-free protein synthesis has emerged in recent years as a powerful tool that can potentially transform the production of recombinant proteins. Cell-free protein synthesis harnesses the synthetic power of living cells while eliminating many of the constraints of traditional cell-based gene expression methods. Due to the lack of physical barriers separating the protein synthesis machinery from the surrounding environment, a cell-free protein synthesis reaction mixture can be directly programmed using diverse genetic material for the instant production of recombinant proteins without complicated cloning procedures. However, a number of issues must be addressed for this technology to be widely accepted as an alternative platform for protein production, including quality-control of translation machinery preparations, and high reagent cost. This review describes recent efforts to make cell-free protein synthesis more affordable and more easily accessible for generic applications.
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Affiliation(s)
- Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
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18
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Ward VC, Chatzivasileiou AO, Stephanopoulos G. Cell free biosynthesis of isoprenoids from isopentenol. Biotechnol Bioeng 2019; 116:3269-3281. [DOI: 10.1002/bit.27146] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/01/2019] [Accepted: 08/11/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Valerie C.A. Ward
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts
- Department of Chemical Engineering University of Waterloo Waterloo Ontario Canada
| | | | - Gregory Stephanopoulos
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts
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19
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Lim HJ, Kim DM. Cell-Free Metabolic Engineering: Recent Developments and Future Prospects. Methods Protoc 2019; 2:mps2020033. [PMID: 31164613 PMCID: PMC6632161 DOI: 10.3390/mps2020033] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/21/2019] [Accepted: 04/24/2019] [Indexed: 02/03/2023] Open
Abstract
Due to the ongoing crises of fossil fuel depletion, climate change, and environmental pollution, microbial processes are increasingly considered as a potential alternative for cleaner and more efficient production of the diverse chemicals required for modern civilization. However, many issues, including low efficiency of raw material conversion and unintended release of genetically modified microorganisms into the environment, have limited the use of bioprocesses that rely on recombinant microorganisms. Cell-free metabolic engineering is emerging as a new approach that overcomes the limitations of existing cell-based systems. Instead of relying on metabolic processes carried out by living cells, cell-free metabolic engineering harnesses the metabolic activities of cell lysates in vitro. Such approaches offer several potential benefits, including operational simplicity, high conversion yield and productivity, and prevention of environmental release of microorganisms. In this article, we review the recent progress in this field and discuss the prospects of this technique as a next-generation bioconversion platform for the chemical industry.
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Affiliation(s)
- Hye Jin Lim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea.
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea.
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20
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Abstract
Cell-free protein synthesis (CFPS) has become an established tool for rapid protein synthesis in order to accelerate the discovery of new enzymes and the development of proteins with improved characteristics. Over the past years, progress in CFPS system preparation has been made towards simplification, and many applications have been developed with regard to tailor-made solutions for specific purposes. In this review, various preparation methods of CFPS systems are compared and the significance of individual supplements is assessed. The recent applications of CFPS are summarized and the potential for biocatalyst development discussed. One of the central features is the high-throughput synthesis of protein variants, which enables sophisticated approaches for rapid prototyping of enzymes. These applications demonstrate the contribution of CFPS to enhance enzyme functionalities and the complementation to in vivo protein synthesis. However, there are different issues to be addressed, such as the low predictability of CFPS performance and transferability to in vivo protein synthesis. Nevertheless, the usage of CFPS for high-throughput enzyme screening has been proven to be an efficient method to discover novel biocatalysts and improved enzyme variants.
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21
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Caschera F, Karim AS, Gazzola G, d’Aquino AE, Packard NH, Jewett MC. High-Throughput Optimization Cycle of a Cell-Free Ribosome Assembly and Protein Synthesis System. ACS Synth Biol 2018; 7:2841-2853. [PMID: 30354075 DOI: 10.1021/acssynbio.8b00276] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Building variant ribosomes offers opportunities to reveal fundamental principles underlying ribosome biogenesis and to make ribosomes with altered properties. However, cell viability limits mutations that can be made to the ribosome. To address this limitation, the in vitro integrated synthesis, assembly and translation (iSAT) method for ribosome construction from the bottom up was recently developed. Unfortunately, iSAT is complex, costly, and laborious to researchers, partially due to the high cost of reaction buffer containing over 20 components. In this study, we develop iSAT in Escherichia coli BL21Rosetta2 cell lysates, a commonly used bacterial strain, with a cost-effective poly sugar and nucleotide monophosphate-based metabolic scheme. We achieved a 10-fold increase in protein yield over our base case with an evolutionary design of experiments approach, screening 490 reaction conditions to optimize the reaction buffer. The computationally guided, cell-free, high-throughput technology presented here augments the way we approach multicomponent synthetic biology projects and efforts to repurpose ribosomes.
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Affiliation(s)
| | | | - Gianluca Gazzola
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
| | | | - Norman H. Packard
- ProtoLife, Inc., 57 Post Street Suite 908, San Francisco, California 94104, United States
| | - Michael C. Jewett
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
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22
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Wei X, Xie L, Job Zhang YHP, You C. Stoichiometric Regeneration of ATP by A NAD(P)/CoA-free and Phosphate-balanced In Vitro
Synthetic Enzymatic Biosystem. ChemCatChem 2018. [DOI: 10.1002/cctc.201801562] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Xinlei Wei
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Leipeng Xie
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 P. R. China
- College of Life Sciences; Henan Agricultural University; 95 Wenhua Road Zhengzhou 450002 P. R. China
| | - Yi-Heng P. Job Zhang
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 P. R. China
| | - Chun You
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 West 7th Avenue Tianjin Airport Economic Area Tianjin 300308 P. R. China
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23
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Hunter DJB, Bhumkar A, Giles N, Sierecki E, Gambin Y. Unexpected instabilities explain batch-to-batch variability in cell-free protein expression systems. Biotechnol Bioeng 2018; 115:1904-1914. [PMID: 29603735 DOI: 10.1002/bit.26604] [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] [Received: 11/06/2017] [Revised: 02/22/2018] [Accepted: 03/26/2018] [Indexed: 01/09/2023]
Abstract
Cell-free methods of protein synthesis offer rapid access to expressed proteins. Though the amounts produced are generally only at a small scale, these are sufficient to perform protein-protein interaction assays and tests of enzymatic activity. As such they are valuable tools for the biochemistry and bioengineering community. However the most complex, eukaryotic cell-free systems are difficult to manufacture in house and can be prohibitively expensive to obtain from commercial sources. The Leishmania tarentolae system offers a relatively cheap alternative which is capable of producing difficult to express proteins, but which is simpler to produce in large scale. However, this system suffers from batch-to-batch variability, which has been accepted as a consequence of the complexity of the extracts. Here we show an unexpected origin for the variability observed and demonstrate that small variations in a single parameter can dramatically affect expression, such that minor pipetting errors can have major effects on yields. L. tarentolae cell-free lysate activity is shown to be more stable to changes in Mg2+ concentration at a lower ratio of feed solution to lysate in the reaction than typically used, and a higher Mg2+ optimum. These changes essentially eliminate batch-to-batch variability of L. tarentolae lysate activity and permit their full potential to be realized.
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Affiliation(s)
- Dominic J B Hunter
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Akshay Bhumkar
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Nichole Giles
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Emma Sierecki
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Yann Gambin
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
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24
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Jiang L, Zhao J, Lian J, Xu Z. Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology. Synth Syst Biotechnol 2018; 3:90-96. [PMID: 29900421 PMCID: PMC5995451 DOI: 10.1016/j.synbio.2018.02.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/11/2018] [Accepted: 02/14/2018] [Indexed: 11/15/2022] Open
Abstract
Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS) has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors) to speed up design-build-test (DBT) cycles of metabolic engineering and synthetic biology.
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Affiliation(s)
- Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiarun Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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25
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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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26
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Karim AS, Heggestad JT, Crowe SA, Jewett MC. Controlling cell-free metabolism through physiochemical perturbations. Metab Eng 2017; 45:86-94. [PMID: 29155060 DOI: 10.1016/j.ymben.2017.11.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/03/2017] [Accepted: 11/11/2017] [Indexed: 10/18/2022]
Abstract
Building biosynthetic pathways and engineering metabolic reactions in cells can be time-consuming due to complexities in cellular metabolism. These complexities often convolute the combinatorial testing of biosynthetic pathway designs needed to define an optimal biosynthetic system. To simplify the optimization of biosynthetic systems, we recently reported a new cell-free framework for pathway construction and testing. In this framework, multiple crude-cell extracts are selectively enriched with individual pathway enzymes, which are then mixed to construct full biosynthetic pathways on the time scale of a day. This rapid approach to building pathways aids in the study of metabolic pathway performance by providing a unique freedom of design to modify and control biological systems for both fundamental and applied biotechnology. The goal of this work was to demonstrate the ability to probe biosynthetic pathway performance in our cell-free framework by perturbing physiochemical conditions, using n-butanol synthesis as a model. We carried out three unique case studies. First, we demonstrated the power of our cell-free approach to maximize biosynthesis yields by mapping physiochemical landscapes using a robotic liquid-handler. This allowed us to determine that NAD and CoA are the most important factors that govern cell-free n-butanol metabolism. Second, we compared metabolic profile differences between two different approaches for building pathways from enriched lysates, heterologous expression and cell-free protein synthesis. We discover that phosphate from PEP utilization, along with other physiochemical reagents, during cell-free protein synthesis-coupled, crude-lysate metabolic system operation inhibits optimal cell-free n-butanol metabolism. Third, we show that non-phosphorylated secondary energy substrates can be used to fuel cell-free protein synthesis and n-butanol biosynthesis. Taken together, our work highlights the ease of using cell-free systems to explore physiochemical perturbations and suggests the need for a more controllable, multi-step, separated cell-free framework for future pathway prototyping and enzyme discovery efforts.
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Affiliation(s)
- Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Jacob T Heggestad
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Samantha A Crowe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA.
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27
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Cell-free protein synthesis in micro compartments: building a minimal cell from biobricks. N Biotechnol 2017; 39:199-205. [DOI: 10.1016/j.nbt.2017.06.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 12/16/2022]
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28
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Caschera F. Bacterial cell-free expression technology to in vitro systems engineering and optimization. Synth Syst Biotechnol 2017; 2:97-104. [PMID: 29062966 PMCID: PMC5637228 DOI: 10.1016/j.synbio.2017.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 12/26/2022] Open
Abstract
Cell-free expression system is a technology for the synthesis of proteins in vitro. The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.
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29
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Zhang YHP, Sun J, Ma Y. Biomanufacturing: history and perspective. ACTA ACUST UNITED AC 2017; 44:773-784. [PMID: 27837351 DOI: 10.1007/s10295-016-1863-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/30/2016] [Indexed: 01/09/2023]
Abstract
Abstract
Biomanufacturing is a type of manufacturing that utilizes biological systems (e.g., living microorganisms, resting cells, animal cells, plant cells, tissues, enzymes, or in vitro synthetic (enzymatic) systems) to produce commercially important biomolecules for use in the agricultural, food, material, energy, and pharmaceutical industries. History of biomanufacturing could be classified into the three revolutions in terms of respective product types (mainly), production platforms, and research technologies. Biomanufacturing 1.0 focuses on the production of primary metabolites (e.g., butanol, acetone, ethanol, citric acid) by using mono-culture fermentation; biomanufacturing 2.0 focuses on the production of secondary metabolites (e.g., penicillin, streptomycin) by using a dedicated mutant and aerobic submerged liquid fermentation; and biomanufacturing 3.0 focuses on the production of large-size biomolecules—proteins and enzymes (e.g., erythropoietin, insulin, growth hormone, amylase, DNA polymerase) by using recombinant DNA technology and advanced cell culture. Biomanufacturing 4.0 could focus on new products, for example, human tissues or cells made by regenerative medicine, artificial starch made by in vitro synthetic biosystems, isobutanol fermented by metabolic engineering, and synthetic biology-driven microorganisms, as well as exiting products produced by far better approaches. Biomanufacturing 4.0 would help address some of the most important challenges of humankind, such as food security, energy security and sustainability, water crisis, climate change, health issues, and conflict related to the energy, food, and water nexus.
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Affiliation(s)
- Yi-Heng Percival Zhang
- 0000000119573309 grid.9227.e Tianjin Institute of Industrial Biotechnology Chinese Academy of Science 32 West 7th Avenue, Tianjin Airport Economic Area 300308 Tianjin China
- 0000 0001 0694 4940 grid.438526.e Biological Systems Engineering Department Virginia Tech 304 Seitz Hall 24061 Blacksburg VA USA
| | - Jibin Sun
- 0000000119573309 grid.9227.e Tianjin Institute of Industrial Biotechnology Chinese Academy of Science 32 West 7th Avenue, Tianjin Airport Economic Area 300308 Tianjin China
| | - Yanhe Ma
- 0000000119573309 grid.9227.e Tianjin Institute of Industrial Biotechnology Chinese Academy of Science 32 West 7th Avenue, Tianjin Airport Economic Area 300308 Tianjin China
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Peñalber-Johnstone C, Ge X, Tran K, Selock N, Sardesai N, Gurramkonda C, Pilli M, Tolosa M, Tolosa L, Kostov Y, Frey DD, Rao G. Optimizing cell-free protein expression in CHO: Assessing small molecule mass transfer effects in various reactor configurations. Biotechnol Bioeng 2017; 114:1478-1486. [PMID: 28266026 DOI: 10.1002/bit.26282] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/11/2017] [Accepted: 03/01/2017] [Indexed: 01/12/2023]
Abstract
Cell-free protein synthesis (CFPS) is an ideal platform for rapid and convenient protein production. However, bioreactor design remains a critical consideration in optimizing protein expression. Using turbo green fluorescent protein (tGFP) as a model, we tracked small molecule components in a Chinese Hamster Ovary (CHO) CFPS system to optimize protein production. Here, three bioreactors in continuous-exchange cell-free (CECF) format were characterized. A GFP optical sensor was built to monitor the product in real-time. Mass transfer of important substrate and by-product components such as nucleoside triphosphates (NTPs), creatine, and inorganic phosphate (Pi) across a 10-kDa MWCO cellulose membrane was calculated. The highest efficiency measured by tGFP yields were found in a microdialysis device configuration; while a negative effect on yield was observed due to limited mass transfer of NTPs in a dialysis cup configuration. In 24-well plate high-throughput CECF format, addition of up to 40 mM creatine phosphate in the system increased yields by up to ∼60% relative to controls. Direct ATP addition, as opposed to creatine phosphate addition, negatively affected the expression. Pi addition of up to 30 mM to the expression significantly reduced yields by over ∼40% relative to controls. Overall, data presented in this report serves as a valuable reference to optimize the CHO CFPS system for next-generation bioprocessing. Biotechnol. Bioeng. 2017;114: 1478-1486. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Chariz Peñalber-Johnstone
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | | | - Kevin Tran
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Nicholas Selock
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Neha Sardesai
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Chandrasekhar Gurramkonda
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Manohar Pilli
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Michael Tolosa
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Leah Tolosa
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Yordan Kostov
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Douglas D Frey
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
| | - Govind Rao
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore County, 1000 Hilltop Circle, TRC 252, Baltimore, Maryland 21250
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Expression, Purification, and Characterization of a Sucrose Nonfermenting 1-Related Protein Kinases 2 of Arabidopsis thaliana in E. coli-Based Cell-Free System. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9469356. [PMID: 27999818 PMCID: PMC5143698 DOI: 10.1155/2016/9469356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/23/2016] [Indexed: 11/17/2022]
Abstract
The plant-specific sucrose nonfermenting 1-related protein kinase 2 (SnRK2) family is considered an important regulator of plant responses to abiotic stresses such as drought, cold, salinity, and nutrition deficiency. However, little information is available on how SnRK2s regulate sulfur deprivation responses in Arabidopsis. Large-scale production of SnRK2 kinases in vitro can help to elucidate the biochemical properties and physiological functions of this protein family. However, heterogenous expression of SnRK2s usually leads to inactive proteins. In this study, we expressed a recombinant Arabidopsis SnRK2.1 in a modified E. coli cell-free system, which combined two kinds of extracts allowing for a convenient and affordable protein preparation. The recombinant SnRK2.1 was produced in large-scale and the autophosphorylation activity of purified SnRK2.1 was characterized, allowing for further biochemical and substrate binding analysis in sulfur signaling. The application of this improved E. coli cell-free system provides us a promising and convenient platform to enhance expression of the target proteins economically.
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Failmezger J, Nitschel R, Sánchez-Kopper A, Kraml M, Siemann-Herzberg M. Site-Specific Cleavage of Ribosomal RNA in Escherichia coli-Based Cell-Free Protein Synthesis Systems. PLoS One 2016; 11:e0168764. [PMID: 27992588 PMCID: PMC5167549 DOI: 10.1371/journal.pone.0168764] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/06/2016] [Indexed: 01/12/2023] Open
Abstract
Cell-free protein synthesis, which mimics the biological protein production system, allows rapid expression of proteins without the need to maintain a viable cell. Nevertheless, cell-free protein expression relies on active in vivo translation machinery including ribosomes and translation factors. Here, we examined the integrity of the protein synthesis machinery, namely the functionality of ribosomes, during (i) the cell-free extract preparation and (ii) the performance of in vitro protein synthesis by analyzing crucial components involved in translation. Monitoring the 16S rRNA, 23S rRNA, elongation factors and ribosomal protein S1, we show that processing of a cell-free extract results in no substantial alteration of the translation machinery. Moreover, we reveal that the 16S rRNA is specifically cleaved at helix 44 during in vitro translation reactions, resulting in the removal of the anti-Shine-Dalgarno sequence. These defective ribosomes accumulate in the cell-free system. We demonstrate that the specific cleavage of the 16S rRNA is triggered by the decreased concentrations of Mg2+. In addition, we provide evidence that helix 44 of the 30S ribosomal subunit serves as a point-of-entry for ribosome degradation in Escherichia coli. Our results suggest that Mg2+ homeostasis is fundamental to preserving functional ribosomes in cell-free protein synthesis systems, which is of major importance for cell-free protein synthesis at preparative scale, in order to create highly efficient technical in vitro systems.
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MESH Headings
- Cell-Free System/chemistry
- Cell-Free System/metabolism
- Escherichia coli/chemistry
- Escherichia coli/metabolism
- Magnesium/chemistry
- Magnesium/metabolism
- Protein Biosynthesis
- RNA Processing, Post-Transcriptional
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- Ribosome Subunits, Small, Bacterial/chemistry
- Ribosome Subunits, Small, Bacterial/metabolism
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Affiliation(s)
- Jurek Failmezger
- 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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Branduardi P, Porro D. n-butanol: challenges and solutions for shifting natural metabolic pathways into a viable microbial production. FEMS Microbiol Lett 2016; 363:fnw070. [DOI: 10.1093/femsle/fnw070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2016] [Indexed: 12/13/2022] Open
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Ullah MW, Khattak WA, Ul-Islam M, Khan S, Park JK. Metabolic engineering of synthetic cell-free systems: Strategies and applications. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.10.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Zhang YHP. Production of biofuels and biochemicals by in vitro synthetic biosystems: Opportunities and challenges. Biotechnol Adv 2015; 33:1467-83. [DOI: 10.1016/j.biotechadv.2014.10.009] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 10/09/2014] [Accepted: 10/19/2014] [Indexed: 12/20/2022]
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37
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Takahashi MK, Hayes CA, Chappell J, Sun ZZ, Murray RM, Noireaux V, Lucks JB. Characterizing and prototyping genetic networks with cell-free transcription–translation reactions. Methods 2015; 86:60-72. [DOI: 10.1016/j.ymeth.2015.05.020] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 02/07/2023] Open
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38
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Cheng K, Zhang F, Sun F, Chen H, Percival Zhang YH. Doubling Power Output of Starch Biobattery Treated by the Most Thermostable Isoamylase from an Archaeon Sulfolobus tokodaii. Sci Rep 2015; 5:13184. [PMID: 26289411 PMCID: PMC4542469 DOI: 10.1038/srep13184] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/17/2015] [Indexed: 01/07/2023] Open
Abstract
Biobattery, a kind of enzymatic fuel cells, can convert organic compounds (e.g., glucose, starch) to electricity in a closed system without moving parts. Inspired by natural starch metabolism catalyzed by starch phosphorylase, isoamylase is essential to debranch alpha-1,6-glycosidic bonds of starch, yielding linear amylodextrin – the best fuel for sugar-powered biobattery. However, there is no thermostable isoamylase stable enough for simultaneous starch gelatinization and enzymatic hydrolysis, different from the case of thermostable alpha-amylase. A putative isoamylase gene was mined from megagenomic database. The open reading frame ST0928 from a hyperthermophilic archaeron Sulfolobus tokodaii was cloned and expressed in E. coli. The recombinant protein was easily purified by heat precipitation at 80 oC for 30 min. This enzyme was characterized and required Mg2+ as an activator. This enzyme was the most stable isoamylase reported with a half lifetime of 200 min at 90 oC in the presence of 0.5 mM MgCl2, suitable for simultaneous starch gelatinization and isoamylase hydrolysis. The cuvett-based air-breathing biobattery powered by isoamylase-treated starch exhibited nearly doubled power outputs than that powered by the same concentration starch solution, suggesting more glucose 1-phosphate generated.
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Affiliation(s)
- Kun Cheng
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.,Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, USA
| | - Fei Zhang
- Cell Free Bioinnovations Inc. 1800 Kraft Drive, Suite 222, Blacksburg, Virginia 24060, USA
| | - Fangfang Sun
- Cell Free Bioinnovations Inc. 1800 Kraft Drive, Suite 222, Blacksburg, Virginia 24060, USA
| | - Hongge Chen
- College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, USA.,Cell Free Bioinnovations Inc. 1800 Kraft Drive, Suite 222, Blacksburg, Virginia 24060, USA.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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Jackson K, Jin S, Fan ZH. Optimization of a miniaturized fluid array device for cell-free protein synthesis. Biotechnol Bioeng 2015; 112:2459-67. [PMID: 26037852 DOI: 10.1002/bit.25668] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/18/2015] [Accepted: 05/28/2015] [Indexed: 11/06/2022]
Abstract
Cell-free protein synthesis (CFPS), which entails synthesizing proteins outside of intact cells, is conducted in several formats with the continuous-exchange cell-free (CECF) format generally having the greatest protein expression yields. With this format, continuous chemical exchange occurs through a dialysis membrane separating a reaction solution from a feeding solution containing supplemental nutrient/energy molecules. Here, we describe the optimization of the miniaturized fluid array device (µFAD) by studying the effects of structural and experimental parameters responsible for the heightened chemical exchange across the dialysis membranes and enhanced protein expression capabilities of the high-throughput device. The interface area and number between the reaction and feeding solutions have a direct impact on protein expression, with a 1.6% enhancement in protein expression yield with each square millimeter increase in area and a 20% decrease with each additional interface. For nutrient/energy availability, an increasing solution volume ratio and height difference increase protein expression yield until the expression yield plateaus at a volume ratio of 20 to 1 (feeding to reaction solution) and a solution height difference of 2 mm. This yield can be further increased by 7% every 30 min with feeding solution replacement. Of the studied experimental factors (feeding solution stirring, device shaking, and temperature increase), feeding solution stirring has a significant effect on protein expression in this device. In the optimized system, green fluorescent protein (GFP), ß-glucuronidase (GUS), ß-galactosidase (LacZ), luciferase, and tissue plasminogen activator (tPA) expression increased 77.8-, 212-, 3.66-, 463-, and 5.43-fold, respectively, compared to the conventional batch format in a standard microplate. These results highlight the significance of structural/experimental conditions on the productive expression of proteins in the CECF format.
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Affiliation(s)
- Kirsten Jackson
- J.Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, 32611, Florida
| | - Shouguang Jin
- Department of Molecular Genetics and Microbiology, University of Florida, P.O. Box 100266, Gainesville, 32610, Florida
| | - Z Hugh Fan
- J.Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, 32611, Florida. .,Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, 32611, Florida. .,Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, 32611, Florida.
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40
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Anderson MJ, Stark JC, Hodgman CE, Jewett MC. Energizing eukaryotic cell-free protein synthesis with glucose metabolism. FEBS Lett 2015; 589:1723-1727. [PMID: 26054976 DOI: 10.1016/j.febslet.2015.05.045] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 05/14/2015] [Accepted: 05/16/2015] [Indexed: 11/18/2022]
Abstract
Eukaryotic cell-free protein synthesis (CFPS) is limited by the dependence on costly high-energy phosphate compounds and exogenous enzymes to power protein synthesis (e.g., creatine phosphate and creatine kinase, CrP/CrK). Here, we report the ability to use glucose as a secondary energy substrate to regenerate ATP in a Saccharomyces cerevisiae crude extract CFPS platform. We observed synthesis of 3.64±0.35 μg mL(-1) active luciferase in batch reactions with 16 mM glucose and 25 mM phosphate, resulting in a 16% increase in relative protein yield (μg protein/$ reagents) compared to the CrP/CrK system. Our demonstration provides the foundation for development of cost-effective eukaryotic CFPS platforms.
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Affiliation(s)
- Mark J Anderson
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - C Eric Hodgman
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL USA, 60208-3120
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL USA, 60208-3120
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL, USA, 60611-3068
- Simpson Querrey Institute, 303 E. Superior St, Suite 11-131 Chicago, IL USA, 60611-2875
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41
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Dudley QM, Karim AS, Jewett MC. Cell-free metabolic engineering: biomanufacturing beyond the cell. Biotechnol J 2015; 10:69-82. [PMID: 25319678 PMCID: PMC4314355 DOI: 10.1002/biot.201400330] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/24/2014] [Accepted: 08/22/2014] [Indexed: 12/20/2022]
Abstract
Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility.
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Affiliation(s)
| | | | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- Member, Institute for Bionanotechnology in Medicine, Northwestern University, Chicago, IL, USA
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42
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Kelwick R, MacDonald JT, Webb AJ, Freemont P. Developments in the tools and methodologies of synthetic biology. Front Bioeng Biotechnol 2014; 2:60. [PMID: 25505788 PMCID: PMC4244866 DOI: 10.3389/fbioe.2014.00060] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/12/2014] [Indexed: 11/27/2022] Open
Abstract
Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community.
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Affiliation(s)
- Richard Kelwick
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - James T MacDonald
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - Alexander J Webb
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
| | - Paul Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London , London , UK ; Department of Medicine, Imperial College London , London , UK
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43
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A cost-effective polyphosphate-based metabolism fuels an all E. coli cell-free expression system. Metab Eng 2014; 27:29-37. [PMID: 25446973 DOI: 10.1016/j.ymben.2014.10.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/20/2022]
Abstract
A new cost-effective metabolism providing an ATP-regeneration system for cell-free protein synthesis is presented. Hexametaphosphate, a polyphosphate molecule, is used as phosphate donor together with maltodextrin, a polysaccharide used as carbon source to stimulate glycolysis. Remarkably, addition of enzymes is not required for this metabolism, which is carried out by endogenous catalysts present in the Escherichia coli crude extract. This new ATP regeneration system allows efficient recycling of inorganic phosphate, a strong inhibitor of protein synthesis. We show that up to 1.34-1.65mg/mL of active reporter protein is synthesized in batch-mode reaction after 5h of incubation. Unlike typical hybrid in vitro protein synthesis systems based on bacteriophage transcription, expression is carried out through E. coli promoters using only the endogenous transcription-translation molecular machineries provided by the extract. We demonstrate that traditional expensive energy regeneration systems, such as creatine phosphate, phosphoenolpyruvate or phosphoglycerate, can be replaced by a cost-effective metabolic scheme suitable for cell-free protein synthesis applications. Our work also shows that cell-free systems are useful platforms for metabolic engineering.
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44
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Lian Q, Cao H, Wang F. The Cost-Efficiency Realization in the Escherichia coli-Based Cell-Free Protein Synthesis Systems. Appl Biochem Biotechnol 2014; 174:2351-67. [DOI: 10.1007/s12010-014-1143-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 08/06/2014] [Indexed: 01/08/2023]
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45
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Schoborg JA, Hodgman CE, Anderson MJ, Jewett MC. Substrate replenishment and byproduct removal improve yeast cell-free protein synthesis. Biotechnol J 2014; 9:630-40. [PMID: 24323955 DOI: 10.1002/biot.201300383] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/11/2013] [Accepted: 12/06/2013] [Indexed: 12/21/2022]
Abstract
Cell-free protein synthesis (CFPS) platforms are now considered a powerful tool for synthesizing a variety of proteins at scales from pL to 100 L with accelerated process development pipelines. We previously reported the advancement of a novel yeast-based CFPS platform. Here, we studied factors that cause termination of yeast CFPS batch reactions. Specifically, we characterized the substrate and byproduct concentrations in batch, fed-batch, and semi-continuous reaction formats through high-performance liquid chromatography (HPLC) and chemical assays. We discovered that creatine phosphate, the secondary energy substrate, and nucleoside triphosphates were rapidly degraded during batch CFPS, causing a significant drop in the reaction's energy charge (E.C.) and eventual termination of protein synthesis. As a consequence of consuming creatine phosphate, inorganic phosphate accumulated as a toxic byproduct. Additionally, we measured amino acid concentrations and found that aspartic acid was rapidly consumed. By adopting a semi-continuous reaction format, where passive diffusion enables substrate replenishment and byproduct removal, we achieved over a 70% increase in active superfolder green fluorescent protein (sfGFP) as compared with the batch system. This study identifies targets for the future improvement of the batch yeast CFPS reaction. Moreover, it outlines a detailed, generalized method to characterize and improve other CFPS platforms.
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Affiliation(s)
- Jennifer A Schoborg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
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Caschera F, Noireaux V. Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. Biochimie 2013; 99:162-8. [PMID: 24326247 DOI: 10.1016/j.biochi.2013.11.025] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 11/29/2013] [Indexed: 01/29/2023]
Abstract
Cell-free protein synthesis is becoming a useful technique for synthetic biology. As more applications are developed, the demand for novel and more powerful in vitro expression systems is increasing. In this work, an all Escherichia coli cell-free system, that uses the endogenous transcription and translation molecular machineries, is optimized to synthesize up to 2.3 mg/ml of a reporter protein in batch mode reactions. A new metabolism based on maltose allows recycling of inorganic phosphate through its incorporation into newly available glucose molecules, which are processed through the glycolytic pathway to produce more ATP. As a result, the ATP regeneration is more efficient and cell-free protein synthesis lasts up to 10 h. Using a commercial E. coli strain, we show for the first time that more than 2 mg/ml of protein can be synthesized in run-off cell-free transcription-translation reactions by optimizing the energy regeneration and waste products recycling. This work suggests that endogenous enzymes present in the cytoplasmic extract can be used to implement new metabolic pathways for increasing protein yields. This system is the new basis of a cell-free gene expression platform used to construct and to characterize complex biochemical processes in vitro such as gene circuits.
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Affiliation(s)
- Filippo Caschera
- School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis 55455, Minnesota, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 116 Church Street SE, Minneapolis 55455, Minnesota, United States.
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47
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Catherine C, Lee KH, Oh SJ, Kim DM. Cell-free platforms for flexible expression and screening of enzymes. Biotechnol Adv 2013; 31:797-803. [DOI: 10.1016/j.biotechadv.2013.04.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/06/2013] [Accepted: 04/26/2013] [Indexed: 12/20/2022]
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Shrestha P, Smith MT, Bundy BC. Cell-free unnatural amino acid incorporation with alternative energy systems and linear expression templates. N Biotechnol 2013; 31:28-34. [PMID: 24103470 DOI: 10.1016/j.nbt.2013.09.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/17/2013] [Accepted: 09/27/2013] [Indexed: 01/12/2023]
Abstract
Site-specific incorporation of unnatural amino acids (uAAs) during protein synthesis expands the proteomic code through the addition of unique residue chemistry. This field provides a unique tool to improve pharmacokinetics, cancer treatments, vaccine development, proteomics and protein engineering. The limited ability to predict the characteristics of proteins with uAA-incorporation creates a need for a low-cost system with the potential for rapid screening. Escherichia coli-based cell-free protein synthesis is a compelling platform for uAA incorporation due to the open and accessible nature of the reaction environment. However, typical cell-free systems can be expensive due to the high cost of energizing reagents. By employing alternative energy sources, we reduce the cost of uAA-incorporation in CFPS by 55%. While alternative energy systems reduce cost, the time investment to develop gene libraries can remain cumbersome. Cell-free systems allow the direct use of PCR products known as linear expression templates, thus alleviating tedious plasmid library preparations steps. We report the specific costs of CFPS with uAA incorporation, demonstrate that LETs are suitable expression templates with uAA-incorporation, and consider the substantial reduction in labor intensity using LET-based expression for CFPS uAA incorporation.
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Affiliation(s)
- Prashanta Shrestha
- Department of Chemical Engineering, Brigham Young University, 350 Clyde Building, Provo, UT 84602, USA
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Rupp S. New bioproduction systems: from molecular circuits to novel reactor concepts in cell-free biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:103-23. [PMID: 23873094 DOI: 10.1007/10_2013_227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
: The last decades witnessed a strong growth in several areas of biotechnology, especially in fields related to health, as well as in industrial biotechnology. Advances in molecular engineering now enable biotechnologists to design more efficient pathways in order to convert a larger spectrum of renewable resources into industrially used biofuels and chemicals as well as into new pharmaceuticals and therapeutic proteins. In addition material sciences advanced significantly making it more and more possible to integrate biology and engineering. One of the key questions currently is how to develop new ways of engineering biological systems to cope with the complexity and limitations given by the cell. The options to integrate biology with classical engineering advanced cell free technologies in the recent years significantly. Cell free protein production using cellular extracts is now a well-established universal technology for production of proteins derived from many organisms even at the milligram scale. Among other applications it has the potential to supply the demand for a multitude of enzymes and enzyme variants facilitating in vitro metabolic engineering. This review will briefly address the recent achievements and limitations of cell free conversions. Especially, the requirements for reactor systems in cell free biotechnology, a currently underdeveloped field, are reviewed and some perspectives are given on how material sciences and biotechnology might be able to advance these new developments in the future.
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Affiliation(s)
- Steffen Rupp
- Department of Molecular Biotechnology, Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany,
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Whittaker JW. Cell-free protein synthesis: the state of the art. Biotechnol Lett 2013; 35:143-52. [PMID: 23086573 PMCID: PMC3553302 DOI: 10.1007/s10529-012-1075-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
Abstract
Cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. Like PCR, which uses cellular replication machinery to create a DNA amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. By breaking free from the constraints of cell-based systems, it takes the next step towards synthetic biology. Recent advances in reconstituted cell-free protein synthesis (Protein synthesis Using Recombinant Elements expression systems) are creating new opportunities to tailor the reactions for specialized applications including in vitro protein evolution, printing protein microarrays, isotopic labeling, and incorporating nonnatural amino acids.
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Affiliation(s)
- James W Whittaker
- Division of Environmental and Biomolecular Systems, Institute for Environmental Health, Oregon Health and Science University, 20000 N.W. Walker Road, Beaverton, OR 97006-8921, USA.
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